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QuoteGenomes
Ancient DNA Links Native Americans With Europe

    Michael Balter
    Podcasts Science Podcast: 25 October Show
    Science 25 October 2013: 485.

SANTA FE—Where did the first Americans come from? Most researchers agree that Paleoamericans moved across the Bering Land Bridge from Asia sometime before 15,000 years ago, suggesting roots in East Asia. But just where the source populations arose has long been a mystery.

Now comes a surprising twist, from the complete nuclear genome of a Siberian boy who died 24,000 years ago—the oldest complete genome of a modern human sequenced to date. His DNA shows close ties to those of today's Native Americans. Yet he apparently descended not from East Asians, but from people who had lived in Europe or western Asia. The finding suggests that about a third of the ancestry of today's Native Americans can be traced to "western Eurasia," with the other two-thirds coming from eastern Asia, according to a talk at a meeting* here by ancient DNA expert Eske Willerslev of the University of Copenhagen. It also implies that traces of European ancestry previously detected in modern Native Americans do not come solely from mixing with European colonists, as most scientists had assumed, but have much deeper roots.
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Headed east.

The Mal'ta boy was related to people who later migrated across Beringia to the Americas.
"CREDIT: G. GRULLÓN/SCIENCE"

"I'm still processing that Native Americans are one-third European," says geneticist Connie Mulligan of the University of Florida in Gainesville. "It's jaw-dropping." At the very least, says geneticist Dennis O'Rourke of the University of Utah in Salt Lake City, "this is going to stimulate a lot of discussion."

Researchers have been trying to parse the origins of the first Americans for decades. Most agree that people moved across Beringia, via a vast ice age land bridge (see map p. 410), and began spreading through the Americas, reaching Chile by 14,500 years ago. But the origins of the source populations are not clear, and some archaeologists have even suggested that ancient Europeans crossing the Atlantic were part of the mix (Science, 16 March 2012, p. 1289). Others have contended that early skeletons found in the Americas, such as the 9000-year-old Kennewick Man, show some European features (Science, 10 April 1998, p. 190). In his talk, Willerslev argued that the ancient genome "can actually explain a lot of these inconsistencies," by offering glimpses of prehistoric populations before more recent migrations and other demographic events blurred the picture.

The genome comes from the right upper arm bone of a boy aged about 4 years, who lived by Siberia's Belaya River. Those who buried him adorned his grave with flint tools, pendants, a bead necklace, and a sprinkling of ochre. In the 1920s, Russian archaeologists discovered the burial and other artifacts near a village called Mal'ta, which gave the celebrated site its name. Willerslev and co-author Kelly Graf of Texas A&M University in College Station, traveled to the State Hermitage Museum in St. Petersburg, Russia, where the boy's remains are housed, and took a bone sample.

Willerslev reported that the team was able to sequence the boy's genome, and also to radiocarbon date the bone. The team then used a variety of statistical methods to compare the genome with that of living populations. They found that a portion of the boy's genome is shared only by today's Native Americans and no other groups, showing a close relationship. Yet the child's Y chromosome belongs to a genetic group called Y haplogroup R, and its mitochondrial DNA to a haplogroup U. Today, those haplogroups are found almost exclusively in people living in Europe and regions of Asia west of the Altai Mountains, which are near the borders of Russia, China, and Mongolia.

One expected relationship was missing from the picture: The boy's genome showed no connection to modern East Asians. DNA studies of living people strongly suggest that East Asians—perhaps Siberians, Chinese, or Japanese—make up the major part of Native American ancestors. So how could the boy be related to living Native Americans, but not to East Asians? "This was kind of puzzling at first," Willerslev told the meeting. But there seemed little doubt that the finding was correct, he said, because nearly all Native Americans from North and South America were equally related to the Mal'ta child, indicating that he represented very deep Native American roots.

The team proposes a relatively simple scenario: Before 24,000 years ago, the ancestors of Native Americans and the ancestors of today's East Asians split into distinct groups. The Mal'ta child represents a population of Native American ancestors who moved into Siberia, probably from Europe or west Asia. Then, sometime after the Mal'ta boy died, this population mixed with East Asians. The new, admixed population eventually made its way to the Americas. Exactly when and where the admixture happened is not clear, Willerslev said. But the deep roots in Europe or west Asia could help explain features of some Paleoamerican skeletons and of Native American DNA today. "The west Eurasian [genetic] signatures that we very often find in today's Native Americans don't all come from postcolonial admixture," Willerslev said in his talk. "Some of them are ancient."

The talk sparked lively exchange, and not everyone was ready to buy the team's scenario, at least until they can read the full paper, which is in press at Nature. "This is a lot to hang on one skeleton," Mulligan says. Willerslev said during the discussion that his group is now trying to sequence the genomes of skeletons "further west."

The new findings are consistent with a report published in Genetics last year (and almost entirely ignored at the time) that used modern DNA to conclude that Native Americans have significant—and ancient—ties to Europeans. "Our group is very excited to see this," says Alexander Kim, who works with geneticist David Reich at Harvard Medical School in Boston and represented the group at the meeting. Reich's team found that populations they identified as Native American ancestors in Asia apparently also contributed genes to populations in northern Europe. Thus, both studies suggest a source population in Asia whose genes made their way east all the way to the Americas, and west, all the way to Europe.

"Mal'ta might be a missing link, a representative of the Asian population that admixed both into Europeans and Native Americans," Reich says. If so, he adds, it shows "the value of ancient DNA in peeling back history and resolving mysteries that are difficult to solve using only present day samples."

Quote from: Siege on November 03, 2013, 08:58:54 PM
Come on, this is Eurocentrism.
Appearanly is not enough that Europe got the Renainssance Event because of their savage political fragmentation while quite civilized civilizations got fucked.

Quote from: Siege on November 03, 2013, 08:58:54 PM
Come on, this is Eurocentrism.
Appearanly is not enough that Europe got the Renainssance Event because of their savage political fragmentation while quite civilized civilizations got fucked.

Quote from: Razgovory on November 03, 2013, 11:06:31 PM
What the fuck is Twerking?  And No, don't give me a link.  I don't want to look it up, that's why I'm asking here.

Quote from: Razgovory on November 03, 2013, 09:34:47 PM
Is it just me, or is he getting loopier?

Quote from: Siege on November 03, 2013, 08:58:54 PM
Come on, this is Eurocentrism.
Appearanly is not enough that Europe got the Renainssance Event because of their savage political fragmentation while quite civilized civilizations got fucked.

Quote from: MadImmortalMan on November 04, 2013, 05:53:45 AM
Come on. There's always been a difference between Siege posting and Siege posting drunk. I think most of us can tell the difference now.  :P

Quote from: MadImmortalMan on November 04, 2013, 05:53:45 AM
Come on. There's always been a difference between Siege posting and Siege posting drunk. I think most of us can tell the difference now.  :P

Quote from: Siege on November 03, 2013, 09:45:26 PM
Still, it is racism and Eurocentrism.

Take for example, Twerking.

That shit been around for 20 years. 1993 New Orleans first recorded event. Since then, in thousands of hip-hop videos by African-americans.

Yet it took a white trash girl, Miley Cyrus, to do it in the MTV Video Awards, for the word to be added to the Oxford Dictionary.

If this is not racism, I don't know what it is.

Quote from: Siege on November 03, 2013, 08:58:54 PM
quite civilized civilizations got fucked.

Quote from: Siege on November 03, 2013, 09:45:26 PM
Still, it is racism and Eurocentrism.

Take for example, Twerking.

That shit been around for 20 years. 1993 New Orleans first recorded event. Since then, in thousands of hip-hop videos by African-americans.

Yet it took a white trash girl, Miley Cyrus, to do it in the MTV Video Awards, for the word to be added to the Oxford Dictionary.

If this is not racism, I don't know what it is.

Quote from: viper37 on November 04, 2013, 10:43:07 AM

Quote from: Siege on November 03, 2013, 08:58:54 PM
quite civilized civilizations got fucked.

Like the Arab civilization?

Quote from: Siege on November 03, 2013, 09:45:26 PM
That shit been around for 20 years. 1993 New Orleans first recorded event. Since then, in thousands of hip-hop videos by African-americans.

Quote from: crazy canuck on November 04, 2013, 12:30:25 PM

Quote from: Siege on November 03, 2013, 09:45:26 PM
That shit been around for 20 years. 1993 New Orleans first recorded event. Since then, in thousands of hip-hop videos by African-americans.

I saw it in clubs in the 80s.  Unfortunately I did not recorded it.  We do not know whether the first inhabitants of North America twerked.

We do know that it took a white girl doing it go convince some school boards to ban twerking at school dances.

Quote from: Razgovory on November 03, 2013, 09:34:47 PM
Is it just me, or is he getting loopier?

Quote from: Peter Wiggin on November 04, 2013, 11:20:04 PM

Quote from: Razgovory on November 03, 2013, 09:34:47 PM
Is it just me, or is he getting loopier?

Nah, it's both of you.  :P

Quote

Selection happens; but where, when, and why?
By Razib Khan | November 8, 2013 3:49 am

One of the secondary issues which cropped up with Nina Davuluri winning Miss America is that it seems implausible that someone with her complexion would be able to win any Indian beauty contest. A quick skim of Google images "Miss India" will make clear the reality that I'm alluding to. The Indian beauty ideal, especially for females, is skewed to the lighter end of the complexion distribution of native South Asians. Nina Davuluri herself is not particularly dark skinned if you compared her to the average South Asian; in fact she is likely at the median. But it would be surprising to see a woman who looks like her held up as conventionally beautiful in the mainstream Indian media. When I've pointed this peculiar aspect out to Indians* some of them of will submit that there are dark skinned female celebrities, but when I look up the actresses in question they are invariably not very dark skinned, though perhaps by comparison to what is the norm in that industry they may be. But whatever the cultural reality is, the fraught relationship of color variation to aesthetic variation prompts us to ask, why are South Asians so diverse in their complexions in the first place? A new paper in PLoS Genetics, The Light Skin Allele of SLC24A5 in South Asians and Europeans Shares Identity by Descent, explores this genetic question in depth.

Much of the low hanging fruit in this area was picked years ago. A few large effect genetic variants which are known to be polymorphic across many populations in Western Eurasia segregate within South Asian populations. What this means in plainer language is that a few genes which cause major changes in phenotype are floating around in alternative flavors even within families among people of Indian subcontinental origin. Ergo, you can see huge differences between full siblings in complexion (African Americans, as an admixed population, are analogous). While loss of pigmentation in eastern and western Eurasia seems to be a case of convergent evolution (different mutations in overlapping sets of genes), the H. sapiens sapiens ancestral condition of darker skin is well conserved from Melanesia to Africa.


So what's the angle on this paper you may ask? Two things. The first is that it has excellent coverage of South Asian populations. This matters because to understand variation in complexion you should probably look at populations which vary a great deal. Much of the previous work has focused on populations at the extremes of the human distribution, Africans and Europeans. There are obvious limitations using this approach. If you are looking at variant traits, then focusing on populations where the full range of variation is expressed can be useful. Second, this paper digs deeply into the subtle evolutionary and phylogenomic questions which are posed by the diversification of human pigmentation. It is often said that race is often skin deep, as if to dismiss the importance of human biological variation. But skin is a rather big deal. It's our biggest organ, and the pigmentation loci do seem to be rather peculiar.

You probably know that on the order of ~20% of genetic variation is partitioned between continent populations (races). But this is not the case at all genes. And pigmentation ones tend to be particular notable exceptions to the rule. In late 2005 a paper was published which arguably ushered in the era of modern pigmentation genomics, SLC24A5, a putative cation exchanger, affects pigmentation in zebrafish and humans. The authors found that one nonsynonomous mutation was responsible for on the order of 25 to 33% of the variation in skin color difference between Africans and Europeans. And, the allele frequency was nearly disjoint across the two populations, and between Europeans and East Asians. When comparing Europeans to Africans and East Asians almost all the variation was partitioned across the populations, with very little within them. The derived SNP, which differs from the ancestral state, is found at ~100% frequency in Europeans, and ~0% in Africans and East Asians. It is often stated (you can Google it!) that this variant is the second most ancestrally informative allele in the human genome in relation to Europeans vs. Africans.

SLC24A5 was just the beginning. SLC45A2, TYR, OCA2, and KITLG are just some of the numerous alphabet soup of loci which has come to be understood to affect normal human variation in pigmentation. Despite the relatively large roll call of pigmentation genes one can safely say that between any two reasonably distinct geographic populations ~90 percent of the between population variation in the trait is going to be due to ~10 genes. Often there is a power law distribution as well. The first few genes of large effect are over 50% of the variance, while subsequent loci are progressively less important.

So how does this work to push the overall results forward?

- With their population coverage the authors confirm that SLC24A5 seems to be polymorphic in all Indo-European and Dravidian speaking populations in the subcontinent. The frequency of the derived variant ranges from ~90% in the Northwest, and ~80% in Brahmin populations all over the subcontinent, to ~10-20% in some tribal groups.

- Though there is a north-south gradient, it is modest, with a correlation of ~0.25. There is a much stronger correlation with longtitude, but I'm rather sure that this is an artifact of their low sampling of Indo-European populations in the eastern Gangetic plain. As hinted in the piece the correlation with longitude has to do with the fact that Tibetan and Burman populations in these fringe regions tend to lack the West Eurasian allele.

- Using haplotype based tests of natural selection the authors infer that the frequency of this allele has been driven up positively in north, but not south, India. It could be that the authors lack power to detect selection in the south because of lower frequency of the derived allele. And, I did wonder if selection in the north was simply an echo of what occurred in West Eurasia. But if you look at the frequency of the A allele in the north most of the populations seem to have a higher frequency of the derived variant than they do of inferred "Ancestral North Indian".

What's perhaps more interesting is the bigger picture of human evolutionary dynamics and phylogenetics that these results illuminate. Resequencing the region around SLC24A5 these researchers confirmed it does look like the derived variant is identical by descent in all populations across Western Eurasia and into South Asia. What this means is that this mutation arose in someone at some point around the Last Glacial Maximum, after West Eurasians separated from East Eurasians. The authors gives some numbers using some standard phylogenetic techniques, but admit that it is ancient DNA that will give true clarity on the deeper questions. When I see something written like that my hunch, and hope, is that more papers are coming soon.

When I first read The Light Skin Allele of SLC24A5 in South Asians and Europeans Shares Identity by Descent, I thought that it was essential to read Ancient DNA Links Native Americans With Europe and Efficient moment-based inference of admixture parameters and sources of gene flow. The reason goes back to the plot which I generated at the top of this post: notice that Native Americans do not carry the West Eurasian variant of SLC24A5. What the find of the ~24,000 Siberian boy, and his ancient DNA, suggest is that there was a population with affinities closer to West Eurasians than East Eurasians that contributed to the ancestry of Native Americans. The lack of the European variant of SLC24A5 in Native Americans suggests to me that the sweep had not begun, or, that the European variant was disfavored. What the other paper reports is that on the order of 20-40% of the ancestry of Europeans may be derived from an ancient North Eurasian population, unrelated to West Eurasians (or at least not closely related). It is likely that this population has something to do with the Siberian boy. Since Europeans are fixed for the derived variant of SLC24A5, that implies to me that sweep must have occurred after 24,000 years ago.

journal.pgen.1003912.g002At this point I have to admit that I believe need to be careful calling this a "European variant." Just because it is nearly fixed in Europe, does not imply that the variant arose in Europe. If you look at the frequency of the derived variant you see it is rather high in the northern Middle East. Looking at some of the populations in the Middle Eastern panel the ancestral variant might be all explained by admixture in historical time from Africa. If the sweep began during the last Ice Age, then most of Europe would have been uninhabited. The modern distribution is informative, but it surely does not tell the whole story.

Where we are is that SLC24A5 , and pigmentation as a whole, is coming to be genomically characterized fully. We don't know the whole story of why light skin was selected so strongly. And we don't quite know where the selection began, and when it began. But through gradually filling in pieces of the puzzle we may come to grips with this adaptively significant trait in the nearly future.

Citation: Basu Mallick C, Iliescu FM, Möls M, Hill S, Tamang R, et al. (2013) The Light Skin Allele of SLC24A5 in South Asians and Europeans Shares Identity by Descent. PLoS Genet 9(11): e1003912. doi:10.1371/journal.pgen.1003912

* From my personal experience American born Indians often do not share the same prejudices and biases, partly because subtle shades of brown which are relevant in the Indian context seem ludicrous in the United States.

Quote
By CARL ZIMMER
Published: November 14, 2013

Where did dogs come from? That simple question is the subject of a scientific debate right now. In May, a team of scientists published a study pointing to East Asia as the place where dogs evolved from wolves. Now, another group of researchers has announced that dogs evolved several thousand miles to the west, in Europe.

This controversy is intriguing even if you're not a dog lover. It illuminates the challenges scientists face as they excavate the history of any species from its DNA.

Scientists have long agreed that the closest living relatives of dogs are wolves, their link confirmed by both anatomy and DNA. Somewhere, at some point, some wolves became domesticated. They evolved not only a different body shape, but also a different behavior. Instead of traveling in a pack to hunt down prey, dogs began lingering around humans. Eventually, those humans bred them into their many forms, from shar-peis to Newfoundlands.

A few fossils supply some tantalizing clues to that transformation. Dating back as far as 36,000 years, they look like wolfish dogs or doggish wolves. The oldest of these fossils have mostly turned up in Europe.

In the 1990s, scientists started using new techniques to explore the origin of dogs. They sequenced bits of DNA from living dog breeds and wolves from various parts of the world to see how they were related. And the DNA told a different story than the bones. In fact, it told different stories.

In a 2002 study, for example, Peter Savolainen, now at the Royal Institute of Technology in Sweden, and his colleagues concluded that dogs evolved in East Asia. Eight years later, however, Robert Wayne, a geneticist at the University of California, Los Angeles, and his colleagues analyzed some new dog breeds and concluded that the Middle East was where dogs got their start. (All such studies suggest that a few breeds may have been independently domesticated, although they differ on which ones and where.)

Dr. Savolainen and his colleagues continued to sequence DNA from more dogs, and they published more evidence for an East Asian origin of dogs — narrowing it down to South China.

While early studies of canine origins were limited to fragments of DNA, scientists are now starting to sequence entire genomes of dogs and wolves. In May, for example, Dr. Salovainen and Chinese colleagues reported that Chinese native dogs had the most wolflike genomes. By tallying up the mutations in the different dog and wolf genomes, they estimated that the ancestors of Chinese village dogs and wolves split about 32,000 years ago.

If this were true, then the first dogs would have become domesticated not by farmers, but by Chinese hunter-gatherers more than 20,000 years before the dawn of agriculture.

Dr. Wayne and his colleagues think that is wrong.

A dog may have wolflike DNA because it is a dog-wolf hybrid. In a paper that is not yet published, they analyze wolf and dog genomes to look for signs of ancient interbreeding. They cite evidence that, indeed, some of the DNA in dogs in East Asia comes from wolf interbreeding.

"That's going to pump up the resemblance," Dr. Wayne said.

Now Dr. Wayne and his colleagues are introducing a new line of evidence to the dog debate: ancient DNA. Over the past two decades, scientists have developed increasingly powerful tools to rescue fragments of DNA from fossils, producing "an explosion in the samples," said Beth Shapiro of the University of California, Santa Cruz, a collaborator with Dr. Wayne.

On Thursday in the journal Science, Dr. Wayne, Dr. Shapiro and their colleagues report on the first large-scale comparison of DNA from both living and fossil dogs and wolves. They managed to extract DNA from 18 fossils found in Europe, Russia and the New World. They compared their genes to those from 49 wolves, 77 dogs and 4 coyotes.

The scientists examined a special kind of DNA found in a structure in the cell called the mitochondrion. Mitochondrial DNA comes only from mothers. Because each cell may have thousands of mitochondria, it is easier to gather enough genetic fragments to reconstruct its DNA.

The scientists did not find that living dogs were closely related to wolves from the Middle East or China. Instead, their closest relatives were ancient dogs and wolves from Europe.

"It's a simple story, and the story is they were domesticated in Europe," Dr. Shapiro said.

Dr. Shapiro and Dr. Wayne and their colleagues estimate that dogs split off from European wolves sometime between 18,000 and 30,000 years ago. At the time, Northern Europe was covered in glaciers and the southern portion was a grassland steppe where humans hunted for mammoths, horses and other big game.

"Humans couldn't take everything, and that was a great treasure trove," Dr. Wayne said. Some wolves began to follow the European hunters to scavenge on the carcasses they left behind. As they migrated along with people, they became isolated from other wolves.

Dog evolution experts praised the scientists for gathering so much new data. "I think it's terrific," said Adam Boyko, a Cornell biologist. Dr. Savolainen agreed. "I think it's a fantastic sample," he said.

But Dr. Savolainen said the analysis was flawed. "It's not a correct scientific study, because it's geographically biased," he said.

The study lacks ancient DNA from fossils from East Asia or the Middle East, and so it's not possible to tell whether the roots of dog evolution are anchored in those regions. "You just need to have samples from everywhere," Dr. Savolainen said.

He also rejects Dr. Wayne's argument that interbreeding in East Asia creates an illusion that dogs originated there. Dr. Savolainen points out that the study suggesting interbreeding was based on a wolf from northern China. "What they need to have is samples from south China," he said.

There's just one catch. South China is now so densely settled by people that no wolves live there. A similar problem applies to the fossil record.

"It may be impossible to go this way," Dr. Savolainen said.

Dr. Wayne is not quite so pessimistic. He and his colleagues are hoping to widen their scope and find more DNA from fossils of dogs outside of Europe, while also looking at the genes of living dogs that might hold important clues. Yet he thinks it unlikely that the new evidence will change the basic conclusion of his latest study.

"But there have been so many surprises in the history of this research on dog domestication that I'm holding my breath till we get more information," Dr. Wayne said.

QuoteSteamy gene pool: Extinct human relatives had sex with mystery ancestor
Nidhi Subbaraman NBC News

5 hours ago

Ancient hominids were a frisky bunch that freely interbred with genetically distant human-ish relatives, as well as with closely related members of their own groups, according to new research.

A close read of the genomes of our ancient cousins the Neanderthals and a more distantly related hominid group, the Denisovans, throws up incriminatory evidence that the two "archaic" lines mated with each other, and with humans, much more than scientists had previously understood, Nature News reports. They've also found evidence that a third mystery ancestor interbred with the Denisovan group at some point in their history.

No one knows what the Denisovans looked like, and only a few fossils including a stub of a young girl's pinkie bone have been found at a single cave in the Altai region in Russia. From this ancient genome researchers say they've found genetic evidence of an even older human ancestor, from Asia, that has not been documented.

David Reich, of Harvard Medical School, presented the early results of the new findings this week at a conference hosted by the Royal Society in London.

At a different meeting in Cold Spring Harbor Labs in New York this year, Svante Pääbo, a member of the research team and a professor of genetics at the Max Planck Institute for Evolutionary Anthropology, said that they'd found a section of DNA in the Denisovan sample that came from an even older ancestor, "something unknown," that made up 4 percent of the group's genetic material, according to a news report published in May.

The group also analyzed a toe bone found in the same cave, and identified that it belonged to an inbred local group of Neanderthals, "about what would be expected from a mating of half siblings," they explain.

Reich, Pääbo and colleagues developed a method to sequence ancient DNA in spectacular detail, which they documented in a Science paper in August 2012. Results of the Denisovan sequencing are filling out a picture of a group of archaic humans that vanished from the planet leaving behind almost no trace.

Traces of Neanderthal DNA are still found in many of us today, making up 2.5 percent of the DNA of all modern humans not from Africa. In comparison, in the Denisovan sample, 17 percent of the genome was Neanderthal in origin.

Because the new results are yet to be published, Reich and Pääbo said they were unable to comment for this story.

QuoteMystery humans spiced up ancients' rampant sex lives

Genome analysis suggests interbreeding between modern humans, Neanderthals, Denisovans and a mysterious archaic population.

Ewen Callaway
19 November 2013

An excavation in Denisova cave in Siberia, Russia, where remains of Denisovan hominins were first discovered.

RIA NOVOSTI/SPL

New genome sequences from two extinct human relatives suggest that these 'archaic' groups bred with humans and with each other more extensively than was previously known.

The ancient genomes, one from a Neanderthal and one from a different archaic human group, the Denisovans, were presented on 18 November at a meeting at the Royal Society in London. They suggest that interbreeding went on between the members of several ancient human-like groups living in Europe and Asia more than 30,000 years ago, including an as-yet unknown human ancestor from Asia.

"What it begins to suggest is that we're looking at a 'Lord of the Rings'-type world — that there were many hominid populations," says Mark Thomas, an evolutionary geneticist at University College London who was at the meeting but was not involved in the work.

The first Neanderthal1 and the Denisovan2 genome sequences revolutionized the study of ancient human history, not least because they showed that these groups interbred with anatomically modern humans, contributing to the genetic diversity of many people alive today.

All humans whose ancestry originates outside of Africa owe about 2% of their genome to Neanderthals; and certain populations living in Oceania, such as Papua New Guineans and Australian Aboriginals, got about 4% of their DNA from interbreeding between their ancestors and Denisovans, who are named after the cave in Siberia's Altai Mountains where they were discovered. The cave contains remains deposited there between 30,000 and 50,000 years ago.

Those conclusions however were based on low-quality genome sequences, riddled with errors and full of gaps, David Reich, an evolutionary geneticist at Harvard Medical School in Boston, Massachusetts said at the meeting. His team, in collaboration with Svante Pääbo at the Max Planck Institute for Evolutionary Anthropology in Leipzig, Germany, have now produced much more complete versions of the Denisovan and Neanderthal genomes — matching the quality of contemporary human genomes. The high-quality Denisovan genome data and new Neanderthal genome both come from bones recovered from Denisova Cave.

The new Denisovan genome indicates that this enigmatic population got around: Reich said at the meeting that they interbred with Neanderthals and with the ancestors of human populations that now live in China and other parts of East Asia, in addition to Oceanic populations, as his team previously reported. Most surprisingly, Reich said, the new genomes indicate that Denisovans interbred with another extinct population of archaic humans that lived in Asia more than 30,000 years ago, which is neither human nor Neanderthal.

The meeting was abuzz with conjecture about the identity of this potentially new population of humans. "We don't have the faintest idea," says Chris Stringer, a paleoanthropologist at the London Natural History Museum, who was not involved in the work. He speculates that the population could be related to Homo heidelbergensis, a species that left Africa around half a million years ago and later gave rise to Neanderthals in Europe. "Perhaps it lived on in Asia as well," Stringer says.

QuoteEarliest Human DNA Shows Unforeseen Mixing with Mystery Population

Analysis of oldest sequence from a human ancestor reveals close link with Denisovans

By Ewen Callaway and Nature magazine

Another ancient genome, another mystery. DNA gleaned from a 400,000-year-old femur from Spain has revealed an unexpected link between Europe's hominin inhabitants of the time and a cryptic population, the Denisovans, who are known to have lived much more recently in southwestern Siberia.

The DNA, which represents the oldest hominin sequence yet published, has left researchers baffled because most of them believed that the bones would be more closely linked to Neanderthals than to Denisovans. "That's not what I would have expected; that's not what anyone would have expected," says Chris Stringer, a paleoanthropologist at London's Natural History Museum who was not involved in sequencing the femur DNA.

The fossil was excavated in the 1990s from a deep cave in a well-studied site in northern Spain called Sima de los Huesos ('pit of bones'). This femur and the remains of more than two dozen other hominins found at the site have previously been attributed either to early forms of Neanderthals, who lived in Europe until about 30,000 years ago, or to Homo heidelbergensis, a loosely defined hominin population that gave rise to Neanderthals in Europe and possibly humans in Africa.

But a closer link to Neanderthals than to Denisovans was not what was discovered by the team led by Svante Pääbo, a molecular geneticist at the Max Planck Institute for Evolutionary Anthropology in Leipzig, Germany.

The team sequenced most of the femur's mitochondrial genome, which is made up of DNA from the cell's energy-producing structures and passed down the maternal line. The resulting phylogenetic analysis ­— which shows branches in evolutionary history — placed the DNA closer to that of Denisovans than to Neanderthals or modern humans. "This really raises more questions than it answers," Pääbo says.

The team's finding, published online in Nature this week (M. Meyer et al. Nature http://dx.doi.org/10.1038/nature12788; (http://dx.doi.org/10.1038/nature12788;) 2013), does not necessarily mean that the Sima de los Huesos hominins are more closely related to the Denisovans, a population that lived thousands of kilometres away and hundreds of thousands of years later, than to nearby Neanderthals. This is because the mitochondrial genome tells the history of just an individual's mother, and her mother, and so on.



Nuclear DNA, by contrast, contains material from both parents (and all of their ancestors) and typically provides a more accurate overview of a population's history. But this was not available from the femur.

With that caveat in mind, researchers interested in human evolution are scrambling to explain the surprising link, and everyone seems to have their own ideas.

Pääbo notes that previously published full nuclear genomes of Neanderthals and Denisovans suggest that the two had a common ancestor that lived up to 700,000 years ago. He suggests that the Sima de los Huesos hominins could represent a founder population that once lived all over Eurasia and gave rise to the two groups. Both may have then carried the mitochondrial sequence seen in the caves. But these mitochondrial lineages go extinct whenever a female does not give birth to a daughter, so the Neanderthals could have simply lost that sequence while it lived on in Denisovan women.

"I've got my own twist on it," says Stringer, who has previously argued that the Sima de los Huesos hominins are indeed early Neanderthals (C. Stringer Evol. Anthropol. 21, 101–107; 2012). He thinks that the newly decoded mitochondrial genome may have come from another distinct group of hominins. Not far from the caves, researchers have discovered hominin bones from about 800,000 years ago that have been attributed to an archaic hominin called Homo antecessor, thought to be a European descendant of Homo erectus. Stringer proposes that this species interbred with a population that was ancestral to both Denisovans and Sima de los Huesos hominins, introducing the newly decoded mitochondrial lineage to both populations (see 'Family mystery').

This scenario, Stringer says, explains another oddity thrown up by the sequencing of ancient hominin DNA. As part of a widely discussed and soon-to-be-released analysis of high-quality Denisovan and Neanderthal nuclear genomes, Pääbo's team suggests that Denisovans seem to have interbred with a mysterious hominin group (see Nature http://doi.org/p9t; (http://doi.org/p9t;) 2013).

The situation will become clearer if Pääbo's team can eke nuclear DNA out of the bones from the Sima de los Huesos hominins, which his team hopes to achieve within a year or so.

Obtaining such sequences will not be simple, because nuclear DNA is present in bone at much lower levels than mitochondrial DNA. And even obtaining the partial mitochondrial genome was not easy: the team had to grind up almost two grams of bone and relied on various technical and computational methods to sequence the contaminated and damaged DNA and to arrange it into a genome. To make sure that they had identified genuine ancient sequences, they analyzed only very short DNA strands that contained chemical modifications characteristic of ancient DNA.

Clive Finlayson, an archaeologist at the Gibraltar Museum, calls the latest paper "sobering and refreshing", and says that too many ideas about human evolution have been derived from limited samples and preconceived ideas. "The genetics, to me, don't lie," he adds.

Even Pääbo admits that he was befuddled by his team's latest discovery. "My hope is, of course, eventually we will not bring turmoil but clarity to this world," he says.

This article is reproduced with permission from the magazine Nature. The article was first published on December 4, 2013.

QuoteIt will come to no surprise to people who noticed an earlier paper on cave bear mtDNA from Atapuerca that the folks at the Max Planck Institute would try to do the same for the plentiful human remains found in the Pit of Bones.

A new paper in Nature reports their success, and overnight increases by an order of magnitude the time depth for which we now have human mtDNA from what is commonly designated as Homo heidelbergensis, from right in the middle of the Middle Pleistocene. Obviously, this opens new vistas for archaeogenetic research, making it possible to directly look at early pre-sapiens forms of humans, and not only on their final forms prior to their replacement, the Neandertals and Denisovans.

The most impressive aspect of the new paper is most likely the technical challenges that the researchers must've overcome to achieve this result. The cave bear DNA showed that this was possible, but human DNA adds an additional complication in the form of contamination by a closely related species, us.

But, the new evolutionary result which will interest those of us not interested in the minutiae of biomolecules will no doubt be the fact that the Sima hominin's mtDNA formed a clade with the much more recent Denisova girl.

Until now, we knew that Neandertal mtDNA grouped together and so did modern human mtDNA. The two groups shared a Middle Pleistocene common ancestor and a much more distant common ancestor (~1 million years) with the mtDNA found in Denisova. The new Sima specimen shares descent from Denisova. This is important because it shows that whatever archaic human population the Denisovan mtDNA belonged to also extended to western Europe. And, surprisingly, the Sima specimen did not group with Neandertals, as might be expected because of the incipient Neanderthaloid morphology of the Sima hominins which has been a matter of controversy as it pushes back the evolutionary lineage of H. neandertalensis deeper into the Middle Pleistocene that some researchers accept.

Before this paper, it was believed that H. heidelbergensis evolved somewhere (perhaps Near East or Africa), a subset of it evolved to H. sapiens in Africa, and a different subset evolved in Eurasia, leading up to H. neandertalensis in the west, and unknown forms in the east, of which the Denisova girl was a matrilineal descendant. The next question is: when did Neandertals and Neandertal mtDNA appear in Europe?

It can now be hoped that such questions will be answered directly. The Sima individual studied in this paper is not some frozen specimen from the Arctic, preserved by a freak accident in pristine form for hundreds of thousands of years, but a person who lived in Southwestern Europe. I am fairly sure that this won't be the last really old human we see a paper about in the coming years. Human mtDNA used to present a simple picture at the time of the discovery of African mitochondrial Eve: the deepest splits were in Africa and Eurasians belonged to a subset of African variation. But, as more and more archaic Eurasian mtDNA is sampled, it now appears that modern human mtDNA is a subset of world human mtDNA whose deepest splits are in Eurasia, and the next deepest splits are in Africa. Obviously, this may be a consequence of the fact that archaic human mtDNA has only been sampled from Eurasia, for factors relating to DNA preservation. But, it is nonetheless interesting to wonder where on the tree the mtDNA of archaic Africans would fall.

Nature (2013) doi:10.1038/nature12788

A mitochondrial genome sequence of a hominin from Sima de los Huesos

Matthias Meyer et al.

Excavations of a complex of caves in the Sierra de Atapuerca in northern Spain have unearthed hominin fossils that range in age from the early Pleistocene to the Holocene1. One of these sites, the 'Sima de los Huesos' ('pit of bones'), has yielded the world's largest assemblage of Middle Pleistocene hominin fossils2, 3, consisting of at least 28 individuals4 dated to over 300,000 years ago5. The skeletal remains share a number of morphological features with fossils classified as Homo heidelbergensis and also display distinct Neanderthal-derived traits6, 7, 8. Here we determine an almost complete mitochondrial genome sequence of a hominin from Sima de los Huesos and show that it is closely related to the lineage leading to mitochondrial genomes of Denisovans9, 10, an eastern Eurasian sister group to Neanderthals. Our results pave the way for DNA research on hominins from the Middle Pleistocene.

Quote from: Malthus on December 05, 2013, 08:25:43 AM
If ancient humans would screw anything even remotely human-looking, I wonder how the populations ever came to drift in the first place.  :lol:

Quote from: Malthus on December 05, 2013, 08:25:43 AM
If ancient humans would screw anything even remotely human-looking,

Quote from: Malthus on December 05, 2013, 08:25:43 AM
If ancient humans would screw anything even remotely human-looking, I wonder how the populations ever came to drift in the first place.  :lol:

QuoteThe Denisova-Sima de los Huesos connection
Wed, 2013-12-04 23:27 -- John Hawks

I direct your attention to a new paper by Mattias Meyer and colleagues describing a mitochondrial DNA sequence from Sima de los Huesos, Spain (Meyer et al. 2013). It is super awesomely cool work, and I can't wait for the further development as they attempt to get more DNA sequence data from the Sima sample. The recovery of cave bear DNA earlier this year from Sima presaged the current paper, and it seems we are now in a time where we can expect more results from Middle Pleistocene human remains. Very, very good.

Still, there seems to be a widespread confusion about the current result, which shows the Sima mtDNA sequence to be on the same clade as the mtDNA sequences from Denisova, Russia.

I mean, take a look at the quotes from these news articles:

In the New York Times story by Carl Zimmer ("At 400,000 Years, Oldest Human DNA Yet Found Raises New Mysteries"):

    Dr. Meyer is hopeful that he and his colleagues will be able to get more DNA from the Spanish fossil, as well as other fossils from the site, to help solve the puzzle they have now stumbled across. "It's extremely hard to make sense of," Dr. Meyer said. "We still are a bit lost here."

From Ewen Callaway's Nature news article ("Hominin DNA baffles experts"):

    Even Pääbo admits that he was befuddled by his team's latest discovery. "My hope is, of course, eventually we will not bring turmoil but clarity to this world," he says.

I sort of understand the confusion.

For more than a hundred years, scientists have been drawing straight lines connecting different fossils, to try to understand the human family tree. Those straight lines always diverged over time, leading toward increasing specialization and extinction of fossil groups. And for more than twenty-five years, geneticists have been assuming that the lines connecting the genealogy of mtDNA should be the same as the lines connecting the fossils. When those lines were different, geneticists have been happy to toss the fossils out of the human family tree, content to accept the story that the fossil people had become too specialized, too peripheral to be ancestors of today's people.

But the last five years have made clear that both groups -- the fossil scientists drawing straight lines of diverging fossil populations, and the geneticists drawing straight lines of diverging -- were wrong.

Just look at the evidence. Humans today descend in part from Neandertals, even though Neandertal mtDNA is gone. Europeans today are largely different from the Europeans of 10,000 years ago, with a massive mtDNA replacement along with the introduction of Neolithic culture, and at least a second later large-scale replacement of genetic diversity. Earlier Neandertals in Europe have different mtDNA diversity than later Neandertals in Europe. Denisova cave was home to an earlier population of hominins with different mtDNA than the later Neandertals who lived there. Mitochondrial DNA has never been a straight line linking earlier and later populations within a single location. Whenever we look at ancient DNA in hominins, the earlier populations have different mtDNA diversity than the later ones. Moreover, wherever we have ancient mtDNA from other species -- bison, mammoths, cave bears, and others -- we find that later mtDNA sequences do not represent the earlier diversity. The Sima cave bear mtDNA is a direct example of this, but the same phenomenon has happened again and again.

The fossil evidence, we now know, is no different. Paleoanthropologists have widely assumed that the Sima de los Huesos hominins are ancestors of Neandertals. That's a straight line.

There are essentially two reasons for this assumption. One is that Neandertals need ancestors, and the Sima sample seems to be in the right place at the right time -- 300,000 years ago or more, in western Europe.

The other reason is a bit more substantial: the Sima sample exhibits a number of features that are shared with Neandertals but not African fossil humans, and are rare in recent humans. So the sample is not only at the right place and the right time, it sort of looks the part of incipient Neandertals. Jean-Jacques Hublin and others have described this idea as an "accretion" of Neandertal features in European populations over time. Go back far enough in Europe -- say, to the Gran Dolina sample -- and you don't see fossils with Neandertal features. As you proceed forward through the Middle Pleistocene, you start seeing more similarity to Neandertals. Scientists fitted this data to a straight line, projecting a gradual divergence of the European population away from other human populations, eventually becoming Neandertals.

However, over the last few years, neither of these straight-line reasons has been looking especially good. First, the mtDNA landscape of Neandertals has shifted our knowledge of their population dynamics. Dalen and colleagues (2012) showed that later Neandertals do not have the same diversity as earlier Neandertals in western Europe, and that central Asian Neandertals have more diversity than European ones. From this perspective, the evolution of Neandertals looks less and less like a European phenomenon. Instead, Europe may have been invaded repeatedly by Neandertal populations that were much more numerous elsewhere, such as western or central Asia. I developed that idea last year (Hawks 2012), but in fact it is an old idea going back to the 1950s or earlier.

Now that we know that the last 100,000 years of Neandertal evolution was complex and not centered in western Europe, I don't see why we should assume a straight line between Sima de los Huesos at more than 300,000 years ago and later Neandertals.

Second, the Denisova discoveries have made it clear that other populations existed outside the current visibility of our fossil and archaeological evidence. Why should we assume that these populations looked different from Neandertals? The reality is that we know essentially nothing about the morphology of West or Central Asian hominins of 300,000 years ago. South Asia and Southeast Asia were likewise inhabited throughout this period but we have only the barest hints about the morphology of their inhabitants. These peoples existed just inside the range of archaeological visibility but we lack any but the most rudimentary fossil evidence of them.

To be sure, many people have been assuming that the Denisovans were some kind of East Asian population, for example in China or Southeast Asia. In the process, they have projected the characteristics of the Asian fossil record upon them. That idea has been supported by the existence of Neandertals to the west, and also the sharing of some Denisovan similarity in the genomes of living Australians and Melanesians.

But that's a big assumption. Let's explore an alternative: that the Denisovans we know are in part descendants of an earlier stratum of the western Eurasian population. Although they are on the same mtDNA clade, the difference between Sima and Denisova sequences is about as large as the difference between Neandertal and living human sequences. It would not be fair to say that Denisova and Sima represent a single population, any more than that Neandertals and living people do. But they could share a heritage within the Middle Pleistocene of western Eurasia, deriving their mtDNA from this earlier population.

We know that the Denisovan nuclear genome is much closer to Neandertals than the Denisovan mtDNA. We are still waiting for the long-rumored publication of the idea that Denisovan genomes have a "mystery hominin" element in their ancestry. They could be a mixture of any number of earlier populations. None of these have to be East Asian, and as yet we have no suggestion that this "earlier" element of Denisovan ancestry could be as ancient as the first known habitation of Eurasia, as much as 1.8 million years ago. Maybe the Sima hominins represent this "mystery hominin" population.

Maybe the Denisovans were west Asian Neandertals. It does seem like known genetics of Neandertals may represent something like an earlier iteration of the origin of modern humans -- more African than earlier hominins like the Sima sample, less influenced by Eurasian mixture than the Denisova genome, only a subset of the diversity of surrounding contemporaries. But we have no idea what the Neandertals of the Levant or southwest Asia may have been like genetically -- maybe they were more like Denisovans. This is all basically speculation, which indicates how little we still understand about the dynamics of these populations.

They were complicated. Their relationships cannot be described by drawing straight lines between fossil samples. There were multiple lines of influence among them, small degrees of mixture and large-scale migrations. Europe was far from a slowly evolving population "accreting" Neandertal features over time. The Neandertals we know did not lumber into their doom; they expanded rapidly, multiple times, from non-European origins. They were as dynamic as the Middle Stone Age Africans who would later mix with them and expand across the world.

So I don't find the Sima mtDNA to be the least bit surprising. It's refreshing!

Quote from: Siege on November 03, 2013, 09:45:26 PM
If this is not racism, I don't know what it is.

QuoteHorse Fossil Yields Astonishingly Old Genome—Are Similarly Ancient Human Genomes Next?

By Kate Wong | June 26, 2013 |  Comments2

Researchers have recovered DNA from a nearly 700,000-year-old horse fossil and assembled a draft of the animal's genome from it. It is the oldest complete genome to date by a long shot–hundreds of thousands of years older than the previous record holder, which came from an archaic human that lived around 80,000 years ago. The genome elucidates the evolution of modern horses and their relatives, and raises the question of whether scientists might someday be able to obtain similarly ancient genomes of human ancestors.

Ludovic Orlando of the University of Copenhagen and his colleagues extracted the DNA from a foot bone found at the site of Thistle Creek in Canada's Yukon Territory in permafrost dating to between 560,000 and 780,000 years ago, which falls within the so-called early Middle Pleistocene time period. They then mapped the fragments of DNA they obtained against the genome of a modern horse to piece together a draft of the ancient horse's genome.

Comparing that sequence to the genomes of a 43,000-year-old horse, a donkey, five modern domestic horses and a modern Przewalski's horse (a type of wild horse native to Mongolia), the researchers were able to gain insights into some key aspects of horse evolution. Their findings indicate that the last common ancestor of the members of the genus Equus—which includes modern horses, donkeys, asses and zebras, along with their extinct relatives–lived some 4 million to 4.5 million years ago, double the estimate suggested by the oldest unequivocal Equus fossils. The results also allowed the team to chart the demographic history of horses over the past two million years, revealing how the population waxed and waned as climate shifted and grasslands expanded and contracted. In addition, the researchers identified several genome regions in modern horses that seem to have been targeted by natural selection acting to promote advantageous gene variants related to immunity and olfaction, as well as a number of genome regions that may have undergone selection related to domestication. A report detailing the study will be published in the June 27 Nature. (Scientific American is part of Nature Publishing Group.)

This is a pretty exciting development (so exciting, in fact, that I'm interrupting my vacation to write about it). And I can't help but think back, as I do whenever a new ancient DNA story breaks, to the first time I ever reported on DNA from deep time. The year was 1997. Researchers had just announced that they had sequenced DNA from a 40,000-year-old Neandertal fossil. Specifically they had sequenced DNA from mitochondria—the cell's energy-producing organelles, which contain their own DNA that is passed on along the maternal line.

The Neandertal mitochondrial genome was a huge breakthrough—and it seemed to settle a long-running debate over Neandertals and the origin of anatomically modern Homo sapiens. But mitochondrial DNA represents only a tiny fraction of an individual's genetic information; the real action is in the DNA that resides in the cell's nucleus—the nuclear genome. The scientists I spoke to back then—geneticists and paleontologists—longed for a nuclear genome from a Neandertal. But they were quite certain that they would never ever get one. Mitochondrial DNA is far more abundant than nuclear DNA, because a cell can contain hundreds of mitochondria, whereas it has just one nucleus. Thus the chances of finding nuclear DNA that has survived the ravages of time is far, far lower than those of obtaining mitochondrial DNA—itself a rarity.

And yet. Fast forward to 2010 and the impossible dream was realized: a draft sequence of a nuclear genome of a Neandertal. More recently the sequencing of nuclear DNA retrieved from an enigmatic finger bone from Denisova Cave in Siberia has revealed a previously unknown kind of human. And scientists have obtained an astonishingly complete Neandertal genome from the same cave site. These ancient nuclear genomes paint a rather different picture of archaic-modern human relations than the early mitochondrial DNA work did, and are providing a wealth of fascinating insights into our own evolution and that of our relatively recently extinct cousins.

This fantastically old horse genome got me thinking about the possibility of recovering DNA from comparably ancient human relatives—ones who roamed the earth long before the Neandertals and the Denisovans. If scientists had such data, what would they try to learn from it? When I asked paleoanthropologist John Hawks of the University of Wisconsin this question, he had this to say:

"Right now the Denisovan and Neandertal genomes have raised a new scenario of population structure for Middle Pleistocene people. They show us that earlier hominins in Eurasia were largely supplanted, possibly with some mixture, by a dispersal of Neandertal and Denisovan ancestors. What was that pre-Neandertal population like? Did it have its own unique events shaping its evolution? How many times did large-scale dispersals of human populations sweep across the Old World? And what happened to African ancestors during this key Middle Pleistocene time period?"

Now, lest we get ahead of ourselves, it must be noted that the horse fossil was found in permafrost, which no doubt contributed to the preservation of the DNA. So will scientists have to find a Middle Pleistocene human on ice (or ice-cold soil) to have any hope of getting a genome out of it? Not necessarily. The Denisova specimens weren't preserved in permafrost and their ancient DNA is first class. Still, they are far younger than the horse fossil. But according to ancient DNA expert Hendrik Poinar of McMaster University in Canada, the key to DNA preservation is dry conditions. "While cold and dry is best, warm and dry will still work," he explains.

Poinar additionally noted that he is certain that researchers will eventually recover genomes even older than this 700,000-year-old (give or take) one. Which brings me to my final thought. When I learned of the horse genome, the first thing I thought was: what does this mean for Australopithecus sediba, the two million-year-old fossil species unearthed in at the site of Malapa in South Africa a few years ago. It has been held up as a candidate for the long-sought ancestor of our genus, Homo. These fossils are exquisitely preserved and may even contain organic material. Some of the remains are completely encased in rock, visible only with computed tomography and other imaging techniques. Might scientist be able to extract DNA from these fossils—and might that DNA be sufficiently well preserved to yield a genome? "I think DNA from Malapa is very possible and an exciting prospect," Poinar says.

In fact, efforts are already under way to recover DNA from the A. sediba fossils, "We are in the process of looking and there are specimens presently being investigated," says paleoanthropologist Lee Berger of the University of the Witwatersrand, who is leading the recovery and analysis of the fossils from Malapa. "It is of course unlikely in a [two million-year-old] fossil," he notes, "nevertheless, Malapa has as good a chance as anywhere if the impossible is going to prove possible."

I'm going to resume my vacation now. But I'll be daydreaming about genomes from our long-vanished cousins. The future of ancient DNA research has never looked brighter.

Quotea 700,000 year old horse

QuoteToe Fossil Provides Complete Neanderthal Genome
Published: December 18, 2013

By CARL ZIMMER
Published: December 18, 2013

Scientists have extracted the entire genome of a 130,000-year-old Neanderthal from a single toe bone in a Siberian cave, an accomplishment that far outstrips any previous work on Neanderthal genes.

The accuracy of the new genome is of similar quality to what scientists would achieve if they were sequencing the DNA of a living person.

"It's an amazing technical accomplishment," said Sarah A. Tishkoff, an expert on human evolution at the University of Pennsylvania, who was not involved in the research. "Twenty years ago, I would have thought this would never be possible."

The new Neanderthal genome, which is described in the current issue of Nature, is part of an extraordinary flurry of advances in studying ancient human DNA. Earlier this month, for example, scientists reconstructed a small segment of genes from a 400,000-year-old fossil in Spain, setting a record for the oldest human DNA ever found.

While the Spanish DNA only provided faint, tantalizing clues about human evolution, the new Neanderthal genome is more like a genetic encyclopedia, rich with new insights. The Neanderthal to whom the bone belonged was highly inbred, for example, offering a glimpse into the social lives of Neanderthals.

The new Neanderthal genome also contains evidence of more interbreeding between ancient human populations than previously known.

The authors of the new study also compared the Neanderthal genome to modern human DNA to better understand what makes our own lineage unique. They have come up with a list of mutations that evolved in modern humans after their ancestors branched off from Neanderthals some 600,000 years ago.

"The list of modern human things is quite short," said John Hawks, a paleoanthropologist at the University of Wisconsin who was not involved in the study.

Neanderthals have intrigued scientists ever since their first fossils were found in 1856. Experts argued whether they were part of our own species or a separate one. Since the initial discovery, researchers have found remains of these heavy-browed, solidly built humans from Spain to Central Asia. Their fossil record now stretches from about 200,000 years ago to about 30,000 years ago.

Some of these fossils still hold fragments of Neanderthal DNA. In 1997, Svante Paabo of the Max Planck Institute for Evolutionary Anthropology and his colleagues extracted a snippet from a 40,000-year-old Neanderthal fossil. In 2010, after gathering more DNA from fossils, Dr. Paabo's team published a rough draft of the entire Neanderthal genome.

Using improved methods, the scientists were able to reconstruct the genome from another trove of DNA from an 80,000-year-old finger bone retrieved by a team of Russian explorers from a cave called Denisova.

Much to their surprise, the genome belonged to a separate lineage of humans that had not been known from the fossil record before. The scientists called these mysterious people the Denisovans.

By comparing the rough drafts of the Denisovan and Neanderthal genomes to modern human DNA, Dr. Paabo and his colleagues found clues to how we're all related. Modern humans, Neanderthals and Denisovans all descended from a common ancestor that lived several hundred thousand years ago. The ancestors of modern humans then branched away on their own lineage. It wasn't until later that Neanderthals and Denisovans split apart from each other.

The researchers also discovered some Neanderthal and Denisovan DNA in the genomes of living humans.

Dr. Paabo and his colleagues concluded that modern humans interbred with both Neanderthals and Denisovans before those two lineages became extinct.

The scientists then developed better methods for reconstructing ancient DNA. They were able to create a new version of the Denisovan genome that was extremely accurate and complete.

There was just one catch: the latest reconstruction methods demanded a lot of ancient DNA, which is a rare thing to find in fossils. But when Dr. Paabo and his colleagues studied more bones from Denisova, they hit the jackpot again, discovering an abundance of DNA in a toe bone.

"We thought it would be a Denisovan toe," said Dr. Paabo, "but it very clearly was a Neanderthal."

The scientists were able to reconstruct the new Neanderthal genome even more accurately than the Denisovan one.
(Page 2 of 2)

The crisp focus of the new genome is yielding new discoveries about Neanderthals. For example, Dr. Paabo and his colleagues can distinguish the origin of each piece of DNA — whether it came from the Neanderthal's mother or father. With an X chromosome from each parent, the toe belonged to a female.

A closer look at these two sets of DNA revealed that the Neanderthal female was extremely inbred. Her two parental sets of genes were identical for long stretches. Such similarity can only come about when close relatives have children.

"We don't know if this is typical of all Neanderthals, or just this population in Siberia," said Dr. Paabo. It will take more high-caliber Neanderthal genomes to settle that question.

The new genome reveals not just inbreeding but interbreeding. The accompanying diagram summarizes the flow of DNA between human lineages over the past half million years, based on a comparison of the new Neanderthal genome with other Neanderthal DNA sequences, the Denisovan genome and the genomes of

Dr. Paabo and his colleagues were able to detect not one, but two injections of Denisovan DNA into the modern human gene pool.

Intriguingly, the Denisovan genome also contains hints of even more exotic interbreeding. A few percent of their DNA appears to have originated from a more distant branch of our evolutionary tree.

Dr. Paabo said it was possible that the branch was a species known as Homo erectus, which lived across much of the Old World from 1.8 million to about 50,000 years ago.

Dr. Tishkoff thinks this is a possible explanation of the data, but not the only one. She thinks it is possible that the same pattern could have emerged if the ancestors of humans, Neanderthals and Denisovans in Africa became separated from each other early on, evolving different DNA sequences.

Despite all the flowing DNA, Neanderthals, Denisovans and modern humans did not become one big genetic blur. After Denisovan and Neanderthal DNA made its way into the modern human gene pool, most of it gradually disappeared. And modern humans took their own evolutionary path.

By comparing their high-quality ancient genomes to human genomes, Dr. Paabo and his colleagues are drawing up a list of mutations that are unique to our own lineage. "I would say it is a definitive list," said Dr. Paabo.

Dr. Paabo is intrigued by some mutations that affect genes involved in the development of the brain. But he sees the list as only a starting point for research.

"What lies ahead is to understand which of these is important," said Dr. Paabo. "That's totally up in the air."

QuoteThe Altai Neandertal
December 18, 2013

It is notable that we now have evidence for interbreeding among every kind of hominin we have DNA from, and some we don't.

Neandertals and humans. Denisovans and humans. Neandertals and Denisovans. Some living sub-Saharan Africans and one or more unknown ancient populations. Denisovans and one or more unknown, even more ancient populations. They were all mixing.

The picture of Pleistocene human evolution has come rapidly into focus during the last two years. Before the last 30,000 years, the world was full of human populations that were around twice as different from each other as the most diverse recent human groups. Some of these ancient groups grew at the expense of others, but the "losers" over the long term still survived within the genomes of the "winners".

The process of selection on human genes spanned these different human populations, as genes of adaptive value were exchanged between them, long surviving their progenitor populations. Each of the groups shared genetic variation from their common ancestors, but some local populations were markedly restricted in variation by inbreeding. All in all, humans of the past had a population structure rather like today's chimpanzees, although ancient humans were slightly more alike across a much larger geographic range.

Last spring we heard that the Max Planck Institute for Evolutionary Anthropology had successfully sequenced a high-coverage genome from a hominin toe bone found at Denisova Cave, Russia. In the announcement they made clear that this genome was substantially different from the existing high-coverage genome from Denisova. That first genome, from the bone of a pinky finger, represented a previously-unknown human population, quite different from Neandertals. This new genome, from the Denisova toe bone, is much more similar to the genomes of other Neandertals already known from Vindija, El Sidrón, Feldhofer and Mezmaiskaya. That seems like enough to call the toe a Neandertal.

Yet this week's paper makes clear that this genome is not just another Neandertal. Kay Prüfer and colleagues (2013) describe several kinds of analyses on the high-coverage data. The most important of these analyses establish the pattern of similarities and differences between this genome and others, allowing us to test some hypotheses about the relationships of Neandertals, Denisovans and modern humans.

At the moment, I am just going to present and explain a few of the major conclusions of the study. The paper itself is only 7 pages long, but the supplementary data stretch across 248 dense pages of text and figures. It's much more than a dissertation's worth of information, and it is going to take some time for me to completely digest. There will be much more to discuss over the next few weeks. Further papers that use these data are in the pipeline, with some interesting additional results. This is good work and I am excited by it, but I am going to present some notes of caution as well. I think some interpretations are likely to shift as we learn more.

Here are the major insights of the present study:

    The new genome appears to represent an individual that has fewer new derived mutations than the Denisovan high-coverage genome. The research suggests this as a means of "molecular dating" of the specimens, proposing that the Denisovans lived in Denisova cave after this Neandertal population.

    The Denisovan high-coverage genome includes portions that reflect ancestry from Neandertals.

    The new genome groups with previously known Neandertals in a genome-wide cluster analysis, but represents a more divergent population of Neandertals than those yet described. Under a model where genetic differences reflect a branching population history, the "Altai Neandertal" population seems to have diverged from other Neandertals sometime between 77,000 and 114,000 years ago.

    The high-coverage Neandertal genome shares many derived mutations with sub-Saharan Africans, while the high-coverage Denisova genome shares fewer. If these archaic populations were equally related to Africans, they would have the same number of shared derived mutations with Africans. Prüfer and colleagues infer that the Denisovan genome had ancestors who belonged to a yet more ancient hominin population. They suggest this population represents around 4 percent of the ancestry of Denisovans, and that it diverged from the common ancestors of Neandertals and sub-Saharan Africans sometime around a million years ago. The confidence intervals on both estimates are large.

    The new genome has many extended runs of homozygosity, consistent with inbreeding. The study concludes that the parents of this individual were likely 1/4 degree relatives -- such as uncle/niece or half-sibling mating.

    A comparison of the archaic human genomes with the 1000 Genomes Project samples shows only 96 amino-acid-coding changes shared by nearly all of the 1094 recent humans but absent from Denisovan and Neandertal genomes. A larger number (over 3000) of mutations that "possibly affect gene regulation" are also near fixed in recent humans. These are potentially interesting because they may be related to recent behavioral or anatomical evolution of modern humans.

    The paper reports on new sequencing of the Mezmaiskaya Neandertal to 0.5x coverage. This genome is substantially closer to recent humans than are the other Neandertal genomes. Presumably the population of Neandertals that accounts for present-day Neandertal genes in living people was closer to the Mezmaiskaya Neandertal than others.

    The high-coverage Neandertal and Denisova sequences allow a new estimate of the amount of Neandertal and Denisovan ancestry in human populations. Neandertal ancestry of living non-Africans is now estimated between 1.5 and 2.1 percent. This is lower than previous estimates, a discrepancy that the paper does not explain.

    The paper finds significant evidence for Denisovan ancestry of mainland Asian and Native American populations. The Denisovan fraction in these populations is small, only around two tenths of a percent on average, but the ancestry is spread throughout these populations into the New World.

    The Denisovan ancestry of living populations of New Guinea represents a substantially different genetic background than the Denisova high-coverage genome. The divergence between the Siberian Denisovan high-coverage genome and the Denisovan intermixture with humans is greater than the divergence between any living groups of humans with each other.

We can now see that the original description of the Denisovan genome in 2010 and follow-up analyses in 2011 were based on a number of inaccurate assumptions. The current high-coverage data have added a lot of precision to some analyses, but several of the changes in this new research have actually come from the adoption of new assumptions and more refined models.

Some of the conclusions in this paper will not last long as more ancient genomes are sequenced. We have recently seen with the publication of the Sima de los Huesos mtDNA that many assumptions about the Denisova population are questionable ("The Denisova-Sima de los Huesos connection").

Some examples:

    Why should we assume that the Denisovan ancestry includes only a single "mystery population"? The Sima de los Huesos result shows that several populations may have been in a position to mix with the ancestors of Denisovans.

    Why should we assume that the Denisovans were a single population? The genetic differences among "Denisovan" groups by our current definition were greater than those between any two human groups today.

    This current paper is noncommittal about the rate of mutations that should be applied to the ancient genomes, which leads to an uncertainty of more than a factor of two in the date estimates presented. This is unfortunate because the uncertainty prevents the DNA from shedding light on the relationships of pre-Neandertal, Neandertal and modern human fossil remains. But the uncertainty is real, as the relevant mutation rates remain a matter of debate ("A longer timescale for human evolution", "What is the human mutation rate?").

At any rate, the new genome has tremendous value for the further study of how we evolved. As I continue to study the supplements of the paper, I will be updating on several areas of interest.

Quote from: Queequeg on December 19, 2013, 11:09:44 PM
IDK how people ever doubted that Neanderthals and Humans mixed while Madds Mikkelsen exists.

QuoteBones Give Peek Into the Lives of Neanderthals
El Cidrón Research

REMAINS The bone fragments of the family were retrieved at El Cidrón.
By CARL ZIMMER
Published: December 20, 2010

Deep in a cave in the forests of northern Spain are the remains of a gruesome massacre. The first clues came to light in 1994, when explorers came across a pair of what they thought were human jawbones in the cave, called El Sidrón. At first, the bones were believed to date to the Spanish Civil War. Back then, Republican fighters used the cave as a hide-out. The police discovered more bone fragments in El Sidrón, which they sent to forensic scientists, who determined that the bones did not belong to soldiers, or even to modern humans. They were the remains of Neanderthals who died 50,000 years ago.

Today, El Sidrón is one of the most important sites on Earth for learning about Neanderthals, who thrived across Europe and Asia from about 240,000 to 30,000 years ago. Scientists have found 1,800 more Neanderthal bone fragments in the cave, some of which have yielded snippets of DNA.

But the mystery has lingered on for 16 years. What happened to the El Sidrón victims? In a paper this week in The Proceedings of the National Academy of Sciences, Spanish scientists who analyzed the bones and DNA report the gruesome answer. The victims were a dozen members of an extended family, slaughtered by cannibals.

"It's an amazing find," said Todd Disotell, an anthropologist at New York University. Chris Stringer of the Natural History Museum of London said the report "gives us the first glimpse of Neanderthal social structures."

All of the bones were located in a room-size space the scientists dubbed the Tunnel of Bones. They were mixed into a jumble of gravel and mud, which suggests that the Neanderthals did not die in the chamber. Instead, they died on the surface above the cave.

Their remains couldn't have stayed there for long. "The bones haven't been scavenged or worn out by erosion," said Carles Lalueza-Fox of Pompeu Fabra University in Barcelona, a co-author of the new paper. Part of the ceiling in the Tunnel of Bones most likely collapsed during a storm, and the bones fell into the cave.

No animal bones washed into the Tunnel of Bones along with the Neanderthals'. In fact, the only other things scientists have found there are fragments of Neanderthal stone blades. And when the scientists closely examined the Neanderthal bones, they found cut marks — signs that the blades had been used to slice muscle from bone. The long bones had been snapped open. From these clues, the scientists concluded that the Neanderthals were victims of cannibalism. Scientists have found hints of cannibalism among Neanderthals at other sites, but El Sidrón is exceptional for the scale of evidence.

As the researchers examined bone fragments, they tried to match them to each other. Some loose teeth fit neatly into jawbones, for example. "The whole thing was quite complicated. In fact, it was a mess," said Dr. Lalueza-Fox.

After spending years on these anatomical jigsaw puzzles, Dr. Lalueza-Fox and his colleagues could identify 12 individuals. The shape of the bones allowed the scientists to estimate their age and sex. The bones belonged to three men, three women, three teenage boys and three children, including one infant.

Once the scientists knew who they were dealing with, they looked for DNA in the bones. The cold, damp darkness of El Sidrón has made it an excellent storehouse for ancient DNA. Dr. Lalueza-Fox and his colleagues have published a string of intriguing reports on their DNA. In two individuals, for example, they found a gene variant that may have given them red hair. They launched an ambitious project to find DNA in the teeth of all 12 individuals. In one test, they were able to identify a Y chromosome in four. The scientists had already identified all four of them as males — the three men and one teenage boy — based on their bones.

The scientists then hunted for mitochondrial DNA, which is passed from mothers to their children. They looked for two short stretches in particular, called HVR1 and HVR2, that are especially prone to mutate from generation to generation. All 12 Neanderthals yielded HVR1 and HVR2. The scientists found that seven of them belonged to the same mitochondrial lineage, four to a second, and one to a third.

Dr. Lalueza-Fox argues that the Neanderthals must have been closely related. "If you go to the street and sample 12 individuals at random, there's no way you're going to find seven out of 12 with the same mitochondrial lineage," he said. "But if you go to the birthday party for a grandmother, chances are you'll find brothers and sisters and first cousins. You'd easily find seven with the same mitochondrial lineage."

All three men had the same mitochondrial DNA, which could mean they were brothers, cousins, or uncles. The females, however, all came from different lineages. Dr. Lalueza-Fox suggests that Neanderthals lived in small bands of close relatives. When two bands met, they sometimes exchanged daughters.

"I cannot help but suppose that Neanderthal girls wept as bitterly as modern girls faced by the prospect of leaving closest family behind on their 'wedding' day," said Mary Stiner, an anthropologist at the University of Arizona.

Linda Vigilant, an anthropologist at the Max Planck Institute for Evolutionary Anthropology in Germany, considers the research "a nice start." But she challenges Dr. Lalueza-Fox's claim that the Neanderthals must be immediate family because they belong to the same mitochondrial lineage. In her own work on wild chimpanzees, she finds that some chimpanzees with identical HVR1 and HVR2 are not closely related.

The best way to settle the debate, said Dr. Vigilant, is to find more Neanderthal DNA to which the El Sidrón genes can be compared. "It is exciting to think that we might actually be able to tackle the question in the near future," said Dr. Vigilant.

Dr. Lalueza-Fox thinks it may be possible to draw a detailed genealogy of the El Sidrón Neanderthals in the next few years. He also hopes to get a better idea of how they died. The stone blades may provide a clue. They were made from rocks located just a few miles away from the cave. The victims might have wandered into the territory of another band of Neanderthals. For their act of trespass, they paid the ultimate price.

Quote from: Razgovory on December 21, 2013, 04:59:37 AM
Actually since the claims are being rewritten every year it seems it's extremely unclear what exactly is going on.

Quote from: jimmy olsen on December 21, 2013, 05:21:25 AM

Quote from: Razgovory on December 21, 2013, 04:59:37 AM
Actually since the claims are being rewritten every year it seems it's extremely unclear what exactly is going on.

Which claims?

Quote from: Razgovory on December 21, 2013, 05:23:13 AM

Quote from: jimmy olsen on December 21, 2013, 05:21:25 AM

Quote from: Razgovory on December 21, 2013, 04:59:37 AM
Actually since the claims are being rewritten every year it seems it's extremely unclear what exactly is going on.

Which claims?

For instance a study showing that humans and Neanderthals did not interbreed with humans and one that showed they did interbreed with humans was released in one year.

Quote from: Razgovory on December 21, 2013, 05:23:13 AM

Quote from: jimmy olsen on December 21, 2013, 05:21:25 AM

Quote from: Razgovory on December 21, 2013, 04:59:37 AM
Actually since the claims are being rewritten every year it seems it's extremely unclear what exactly is going on.

Which claims?

For instance a study showing that humans and Neanderthals did not interbreed with humans and one that showed they did interbreed with humans was released in one year.

Quote from: Razgovory on December 21, 2013, 06:43:54 AM
And what are the limits to these tests?

Quote from: jimmy olsen on December 21, 2013, 12:07:36 PM

Quote from: Razgovory on December 21, 2013, 06:43:54 AM
And what are the limits to these tests?

That's the best thing about it, the technology is getting better and better at an enormous rate. 10 years ago you could only manage to recover and analyze mtDNA and now they can sequence the entire nuclear genome of a Neanderthal as well as they could that of a living person.

Quote from: Razgovory on December 21, 2013, 04:13:09 PM

Quote from: jimmy olsen on December 21, 2013, 12:07:36 PM

Quote from: Razgovory on December 21, 2013, 06:43:54 AM
And what are the limits to these tests?

That's the best thing about it, the technology is getting better and better at an enormous rate. 10 years ago you could only manage to recover and analyze mtDNA and now they can sequence the entire nuclear genome of a Neanderthal as well as they could that of a living person.

You didn't answer my question, what are the limits with this test?

Quote from: jimmy olsen on December 21, 2013, 10:26:28 PM

Quote from: Razgovory on December 21, 2013, 04:13:09 PM

Quote from: jimmy olsen on December 21, 2013, 12:07:36 PM

Quote from: Razgovory on December 21, 2013, 06:43:54 AM
And what are the limits to these tests?

That's the best thing about it, the technology is getting better and better at an enormous rate. 10 years ago you could only manage to recover and analyze mtDNA and now they can sequence the entire nuclear genome of a Neanderthal as well as they could that of a living person.

You didn't answer my question, what are the limits with this test?

I'm not sure what you mean.

Do you mean how far they can go back and successfully sequence something?  The record so far is 700,000 years (done on a horse).

QuoteTibetan altitude gene inherited 'from extinct species'
By Paul Rincon Science editor, BBC News website
Tibetans

A gene that allows present-day people to cope with life at high altitude was inherited from an extinct species of human, Nature journal has reported.

The variant of the EPAS-1 gene, which affects blood oxygen, is common in Tibetans - many of whom live at altitudes of 4,000m all year round.

But the DNA sequence matches one found in the extinct Denisovan people.

Many of us carry DNA from extinct humans who interbred with our ancestors as the latter expanded out of Africa.

Both the Neanderthals - who emerged around 400,000 years ago and lived in Europe and western Asia until 35,000 years ago - and the enigmatic Denisovans contributed DNA to present-day people.

The Denisovans are known only from DNA extracted from the finger bone of a girl unearthed at a cave in central Siberia. This 40,000-50,000-year-old bone fragment, as well as a rather large tooth from another individual, are all that is known of this species.

The tiny "pinky" bone yielded an entire genome sequence, allowing scientists to compare it to the DNA of modern people in order to better understand the legacy of ancient interbreeding.

Now, researchers have linked an unusual variant of the EPAS1 gene, which is involved in regulating the body's production of haemoglobin - the molecule that carries oxygen in the blood - to the Denisovans. When the body is exposed to the low oxygen levels encountered at high elevations, EPAS1 tells other genes in the body to become active, stimulating a response that includes the production of extra red blood cells.

The unusual variant common among Tibetans probably spread through natural selection after their ancestors moved onto the high-altitude plateau in Asia several thousand years ago.

"We have very clear evidence that this version of the gene came from Denisovans," said principal author co-author Rasmus Nielsen, from the University of California, Berkeley.

He told BBC News: "If you and I go up to high altitude, we'll immediately have various negative physiological effects. We'll be out of breath, we might suffer from altitude sickness.

"After a little while, we'll try to compensate for this by producing more red blood cells. But because we're not adapted to the high altitude environment, our response would be maladaptive - we would produce too many red blood cells.

"The blood becomes too thick and raises our blood pressure, placing us at risk of stroke and pre-eclampsia (in pregnant women)."

But Tibetans are protected against these risks by producing fewer red blood cells at high altitude. This keeps their blood from thickening.

The Tibetan variant of EPAS1 was discovered by Prof Nielsen's team in 2010. But the researchers couldn't explain why it was so different from the DNA sequences found in all other humans today, so they looked to more ancient genome sequences for an answer.

"We compared it to Neanderthals, but we couldn't find a match. Then we compared it to Denisovans and to our surprise there was an almost exact match," he explained.

He says the interbreeding event with Denisovans probably happened very long ago.

"After the Denisovan DNA came into modern humans, it lingered in different Asian populations at low frequencies for a long time," Prof Nielsen said.

"Then, when the ancestors of Tibetans moved to high altitudes, it favoured this genetic variant which then spread to the point where most Tibetans carry it today."

He says it remains unclear whether the Denisovans were also adapted to life at high altitudes. Denisova Cave lies at an elevation of 760m - not particularly high. But it is close to the Altai Mountains which rise above 3,000m.

Prof Nielsen said it was a "clear and direct" example of humans adapting to new environments through genes acquired via interbreeding with other human species.

Previous research has shown that ancient humans introduced genes that may help us cope with viruses outside Africa.

And a study of Eurasian populations showed that Neanderthal DNA is over-represented in parts of the genome involved in making skin, hair and nails - hinting, perhaps, at something advantageous that allowed Homo sapiens to adapt to conditions in Eurasia.

Quote from: jimmy olsen on July 04, 2014, 10:30:52 AM
There's highlights

QuoteHow Europeans evolved white skin
By Ann Gibbons  2 April 2015 5:00 pm 14 Comments

ST. LOUIS, MISSOURI—Most of us think of Europe as the ancestral home of white people. But a new study shows that pale skin, as well as other traits such as tallness and the ability to digest milk as adults, arrived in most of the continent relatively recently. The work, presented here last week at the 84th annual meeting of the American Association of Physical Anthropologists, offers dramatic evidence of recent evolution in Europe and shows that most modern Europeans don't look much like those of 8000 years ago.

The origins of Europeans have come into sharp focus in the past year as researchers have sequenced the genomes of ancient populations, rather than only a few individuals. By comparing key parts of the DNA across the genomes of 83 ancient individuals from archaeological sites throughout Europe, the international team of researchers reported earlier this year that Europeans today are a mix of the blending of at least three ancient populations of hunter-gatherers and farmers who moved into Europe in separate migrations over the past 8000 years. The study revealed that a massive migration of Yamnaya herders from the steppes north of the Black Sea may have brought Indo-European languages to Europe about 4500 years ago.

Now, a new study from the same team drills down further into that remarkable data to search for genes that were under strong natural selection—including traits so favorable that they spread rapidly throughout Europe in the past 8000 years. By comparing the ancient European genomes with those of recent ones from the 1000 Genomes Project, population geneticist Iain Mathieson, a postdoc in the Harvard University lab of population geneticist David Reich, found five genes associated with changes in diet and skin pigmentation that underwent strong natural selection.

First, the scientists confirmed an earlier report that the hunter-gatherers in Europe could not digest the sugars in milk 8000 years ago, according to a poster. They also noted an interesting twist: The first farmers also couldn't digest milk. The farmers who came from the Near East about 7800 years ago and the Yamnaya pastoralists who came from the steppes 4800 years ago lacked the version of the LCT gene that allows adults to digest sugars in milk. It wasn't until about 4300 years ago that lactose tolerance swept through Europe.

When it comes to skin color, the team found a patchwork of evolution in different places, and three separate genes that produce light skin, telling a complex story for how European's skin evolved to be much lighter during the past 8000 years. The modern humans who came out of Africa to originally settle Europe about 40,000 years are presumed to have had dark skin, which is advantageous in sunny latitudes. And the new data confirm that about 8500 years ago, early hunter-gatherers in Spain, Luxembourg, and Hungary also had darker skin: They lacked versions of two genes—SLC24A5 and SLC45A2—that lead to depigmentation and, therefore, pale skin in Europeans today.

But in the far north—where low light levels would favor pale skin—the team found a different picture in hunter-gatherers: Seven people from the 7700-year-old Motala archaeological site in southern Sweden had both light skin gene variants, SLC24A5 and SLC45A2. They also had a third gene, HERC2/OCA2, which causes blue eyes and may also contribute to light skin and blond hair. Thus ancient hunter-gatherers of the far north were already pale and blue-eyed, but those of central and southern Europe had darker skin.

Then, the first farmers from the Near East arrived in Europe; they carried both genes for light skin. As they interbred with the indigenous hunter-gatherers, one of their light-skin genes swept through Europe, so that central and southern Europeans also began to have lighter skin. The other gene variant, SLC45A2, was at low levels until about 5800 years ago when it swept up to high frequency.

The team also tracked complex traits, such as height, which are the result of the interaction of many genes. They found that selection strongly favored several gene variants for tallness in northern and central Europeans, starting 8000 years ago, with a boost coming from the Yamnaya migration, starting 4800 years ago. The Yamnaya have the greatest genetic potential for being tall of any of the populations, which is consistent with measurements of their ancient skeletons. In contrast, selection favored shorter people in Italy and Spain starting 8000 years ago, according to the paper now posted on the bioRxiv preprint server. Spaniards, in particular, shrank in stature 6000 years ago, perhaps as a result of adapting to colder temperatures and a poor diet.

Surprisingly, the team found no immune genes under intense selection, which is counter to hypotheses that diseases would have increased after the development of agriculture.

The paper doesn't specify why these genes might have been under such strong selection. But the likely explanation for the pigmentation genes is to maximize vitamin D synthesis, said paleoanthropologist Nina Jablonski of Pennsylvania State University (Penn State), University Park, as she looked at the poster's results at the meeting. People living in northern latitudes often don't get enough UV to synthesize vitamin D in their skin so natural selection has favored two genetic solutions to that problem—evolving pale skin that absorbs UV more efficiently or favoring lactose tolerance to be able to digest the sugars and vitamin D naturally found in milk. "What we thought was a fairly simple picture of the emergence of depigmented skin in Europe is an exciting patchwork of selection as populations disperse into northern latitudes," Jablonski says. "This data is fun because it shows how much recent evolution has taken place."

Anthropological geneticist George Perry, also of Penn State, notes that the work reveals how an individual's genetic potential is shaped by their diet and adaptation to their habitat. "We're getting a much more detailed picture now of how selection works."

Quote

Team Characterizing DNA from Ancient Human with Recent Neanderthal Ancestry

May 08, 2015   | Andrea Anderson   
COLD SPRING HARBOR, NY (GenomeWeb) – An international team has discovered recent Neanderthal ancestry in an ancient jaw sample from a modern human who lived in present-day Romania roughly 37,000 to 42,000 years ago, attendees heard at the Biology of Genomes meeting.

The finding clashes with the notion that most mixing between modern humans and Neanderthals occurred in the Middle East shortly after humans migrated out of Africa, explained Qiaomei Fu, a researcher affiliated with the Max Planck Institute for Evolutionary Anthropology, the Chinese Academy of Sciences, and Harvard Medical School. Fu presented the work during a session on evolutionary and non-human genomics here today.

Instead, genetic patterns in the ancient human hint at the potential of admixture between modern humans and Neanderthals in Europe that may have persisted until not long before Neanderthals disappeared from the continent some 40,000 years ago.

Past studies have uncovered gene flow from Neanderthals into all tested modern human populations outside of Africa, with non-African individuals carrying between 1 percent and 4 percent Neanderthal sequences in their genomes, on average. The details of this modern human-Neanderthal mixing remain somewhat murky, though it's believed that the archaic and modern human groups first encountered each other not long after humans migrated out of Africa.

To flesh out the details of these interactions, researchers are tapping into fossils samples found outside of Africa after this time, between about 100,000 years ago and 30,000 years ago, Fu noted.

In this case, she and her colleagues focused on DNA from a mandible found at the Pestera cu Oase site in Romania, which contained relatively low levels of endogenous DNA, pronounced DNA degradation, and a large proportion of microbial contaminants that interfered with attempts to directly shotgun sequence the ancient human.

To get around such complications, the team turned to in-solution capture, isolating ancient DNA from more than 2 million sites in the genome.

Though the individual — known as Oase 1 — was clearly human, Fu explained, the resulting sequences indicated that some 5 to 11 percent of his genome originated from Neanderthals.

To look at this in more detail, the researchers used another capture step to scrutinize more than 78,000 sites in the genome that typically differ between modern humans and Neanderthals.

From those variants, the team detected long stretches of Neanderthal DNA that had not been interrupted by admixture, suggesting the individual's Neanderthal ancestry was more recent than that of any modern human tested previously.

In particular, Fu said, roughly half of the Oase 1 individual's chromosome 12 sequence coincided with Neanderthals rather than modern humans. Based on the SNP patterns detected in the sample, the researchers estimated that the individual had a Neanderthal ancestor within the past four to six generations, pointing to later-than-anticipated admixture between Neanderthals and the modern human population to which Oase 1 belonged.

Meanwhile, comparisons between genetic variants in Oase 1 and those in present-day populations or previously sequenced ancient samples suggested that the ancient individual from Romania belonged to a population that was becoming somewhat European.

But while this group resembled both European and Asian populations, Fu noted, it appears to have been far removed from agricultural populations in Europe and does not appear to have contributed much genetically to present-day human populations.

The team is continuing to tease apart patterns from genetic profiles in the sample, including genotyping analyses of the Oase 1 individual's Y chromosome, she said.

QuoteNeandertals Turned Eagle Talons into Jewelry 130,000 Years Ago
By Kate Wong | March 12, 2015  |


As longtime readers may have noticed, I have an abiding interest in Neandertals. To help me keep up with the latest scientific insights into these mysterious relatives of ours, I have a Google alert set for "Neandertal" (and the alternate spelling, "Neanderthal"). I'm always excited to see the email notification that a new story about our closest relative is available for my reading pleasure. There's just one problem: nearly half the time, the story isn't about Neandertals at all. Rather the word appears as an invective hurled at whichever politician or other despised figure has attracted the writer's ire.

Neandertals are the Rodney Dangerfields of the human family—they don't get no respect. Despite mounting evidence that our prehistoric cousins hunted with great skill, made beautiful stone tools, showed compassion toward one another and buried their dead, among other advanced behaviors, the word Neandertal remains a widely used pejorative. Disdain toward Neandertals lingers even after the revelation several years ago that most people today carry their DNA, thanks to long-ago hook-ups between Neandertals and anatomically modern Homo sapiens.

Now a stunning new discovery underscores that it is time to welcome Neandertals in from the cold. Researchers have found markings on eagle talons from a well-known Neandertal site in Croatia that indicate Neandertals harvested the claws and wore them as jewelry. Such evidence attests to a capacity for symbolic thought, long considered a hallmark of modern humans. Davorka Radovčić of the Croatian Natural History Museum in Zagreb, David Frayer of the University of Kansas and their colleagues describe the find in a paper published March 11 in PLOS ONE.

This find is not the first to show Neandertals used raptor claws. Researchers have previously described isolated talons from several Neandertal sites in Europe. But the new discovery, from the site of Krapina in northern Croatia, includes eight talons from at least three white-tailed eagles. The cut marks and polished facets on the talons suggest human modification rather than, say, trampling by animals. The researchers suggest that the talons were part of a single piece of jewelry, possibly a necklace, tied together with string or sinew.

What makes this discovery additionally important is that it predates by a long shot the arrival of anatomically modern Homo sapiens in Europe some 45,000 years ago. Many previous finds suggestive of Neandertal symbolism date to the interval during which Neandertals and moderns overlapped in Europe, leaving open the possibility that Neandertals simply copied the newcomers or that modern items got mixed in with Neandertal remains. But the Krapina assemblage dates to around 130,000 years ago—tens of thousands of years before moderns reached Europe. If the Neandertals there were making jewelry, their endeavor cannot be chalked up to modern influence. They must have conceived of this form of symbolic expression on their own.

Ultimately, such adornments feed into the million-dollar question of whether Neandertals had language, because both art and language stem from the ability to think symbolically. Archaeologists used to hold that symbolic thinking and other elements of so-called behavioral modernity emerged only within the past 50,000 years or so and in anatomically modern humans alone. But traces of symbolic behavior far older than that have emerged at early modern human sites in Africa. The fact that Neandertals decorated their bodies (and their cave homes) suggests that both Neandertals and moderns inherited this capacity for symbolic thinking—and, by extension, language—from an even older common ancestor.

For more on Neandertal cognition, check out my feature article in the February 2015 Scientific American.

Quote from: jimmy olsen on November 03, 2013, 11:08:23 PM

Quote from: Razgovory on November 03, 2013, 11:06:31 PM
What the fuck is Twerking?  And No, don't give me a link.  I don't want to look it up, that's why I'm asking here.

Woman bends over and grinds her ass into your crotch on the dance floor.

QuoteScientists 'Resurrect' Woolly Mammoth Gene in Human Cell

By Carl Engelking | July 2, 2015 3:33 pm

We all know that woolly mammoths are modern-day elephants' distant shaggier cousins, but why, exactly, were mammoths so different?

That's a tough question, but scientists believe they have some answers after performing the first comprehensive analysis of the woolly mammoth genome. Not only did scientists uncover the genetic changes that allowed mammoths to thrive in the Arctic, they also resurrected a mammoth gene by transplanting it into a human cell.

If the Genes Fit

To home in on what makes woolly mammoths so unique, scientists played a highly complex game of compare and contrast. Geneticist Vincent Lynch and his team first sequenced the genomes of three modern-day Asian elephants — the closest living relatives to mammoths — and two woolly mammoths that died roughly 20,000 to 60,000 years ago. Then, they compared genomes from the two species to find genetic variations that were unique to mammoths.

Scientists identified roughly 1.4 million genetic variants that were unique to woolly mammoths, and these variants caused changes to the proteins produced by roughly 1,600 different genes — different proteins means different physical and biochemical features.

Not surprisingly, most of these variations in mammoths had something to do with thriving in cold weather. They included genes known to be involved in circadian rhythms, lipid metabolism, skin and hair development, temperature sensation and fat tissue formation — all which would help a creature survive in cold weather. Scientists published their findings Thursday in the journal Cell Reports.

Thermostat Gene

Here's where things got really cool: To make sure they were on the right track, scientists actually "resurrected" a mammoth gene by transplanting it into a human kidney cell in the lab. The gene, called TRPV3, is known to affect temperature sensation and hair growth regulation. When they added the mammoth TRPV3 gene to a human cell, the gene produced a protein that was less responsive to heat than modern elephants. In other words, mammoths' unique TRPV3 gene may have contributed to their cold tolerance.

Lynch says their genome-wide analysis can't say with absolute certainty how each of these mammoth genes affected them physically, but effects can be inferred through lab tests. In order to truly understand the interplay of mammoth genes, we'd have to fully resurrect one of the beasts.

If you read Discover, you know bringing back the woolly mammoth is probably feasible. And with these results it's become clearer than ever how it could be done.

QuoteAncient genomes link early farmers from Atapuerca in Spain to modern-day Basques

...

The consequences of the Neolithic transition in Europe—one of the most important cultural changes in human prehistory—is a subject of great interest. However, its effect on prehistoric and modernday people in Iberia, the westernmost frontier of the European continent, remains unresolved. We present, to our knowledge, thefirst genome-wide sequence data from eight human remains, dated to between 5,500 and 3,500 years before present, excavated in the El Portalón cave at Sierra de Atapuerca, Spain. We show that these individuals emerged from the same ancestral gene pool as early farmers in other parts of Europe, suggesting that migration was the dominant mode of transferring farming practices throughout western Eurasia. In contrast to central and northern early European farmers, the Chalcolithic El Portalón individuals additionally mixed with local southwestern hunter–gatherers. The proportion of hunter–gatherer-related admixture into early farmers also increased over the course of two millennia. The Chalcolithic El Portalón individuals showed greatest genetic affinity to modern-day Basques, who have long been considered linguistic and genetic isolates linked to the Mesolithic whereas all other European early farmers show greater genetic similarity to modern-day Sardinians. These genetic links suggest that Basques and their language may be linked with the spread of agriculture during the Neolithic. Furthermore, all modern-day Iberian groups except the Basques display distinct admixture with Caucasus/Central Asian and North African groups, possibly related to historical migration events. The El Portalón genomes uncover important pieces of the demographic history
of Iberia and Europe and reveal how prehistoric groups relate to modern-day people.

QuoteBy Ann Gibbons
11 September 2015 10:15 am
78 Comments

LONDON—In a remarkable technical feat, researchers have sequenced DNA from fossils in Spain that are about 300,000 to 400,000 years old and have found an ancestor—or close relative—of Neandertals. The nuclear DNA, which is the oldest ever sequenced from a member of the human family, may push back the date for the origins of the distinct ancestors of Neandertals and modern humans, according to a presentation here yesterday at the fifth annual meeting of the European Society for the study of human evolution.

Ever since researchers first discovered thousands of bones and teeth from 28 individuals in the mid-1990s from Sima de los Huesos ("pit of bones"), a cave in the Atapuerca Mountains of Spain, they had noted that the fossils looked a lot like primitive Neandertals. The Sima people, who lived before Neandertals, were thought to have emerged in Europe. Yet their teeth, jaws, and large nasal cavities were among the traits that closely resembled those of Neandertals, according to a team led by paleontologist Juan-Luis Arsuaga of the Complutense University of Madrid. As a result, his team classified the fossils as members of Homo heidelbergensis, a species that lived about 600,000 to 250,000 years ago in Europe, Africa, and Asia. Many researchers have thought H. heidelbergensis gave rise to Neandertals and perhaps also to our species, H. sapiens, in the past 400,000 years or so.

But in 2013, the Sima fossils' identity suddenly became complicated when a study of the maternally inherited mitochondrial DNA (mtDNA) from one of the bones revealed that it did not resemble that of a Neandertal. Instead, it more closely matched the mtDNA of a Denisovan, an elusive type of extinct human discovered when its DNA was sequenced from a finger bone from Denisova Cave in Siberia. That finding was puzzling, prompting researchers to speculate that perhaps the Sima fossils had interbred with very early Denisovans or that the "Denisovan" mtDNA was the signature of an even more ancient hominin lineage, such as H. erectus. At the time, researchers at the Max Planck Institute for Evolutionary Anthropology in Leipzig, Germany, who had obtained the mtDNA announced that they would try to sequence the nuclear DNA of the fossils to solve the mystery.

After 2 years of intense effort, paleogeneticist Matthias Meyer of the Max Planck Institute for Evolutionary Anthropology has finally sequenced enough nuclear DNA from fossils of a tooth and a leg bone from the pit to solve the mystery. The task was especially challenging because the ancient DNA was degraded to short fragments, made up of as few as 25 to 40 single nucleotides. (Nucleotides—also known as base pairs—are the building blocks of DNA.) Although he and his colleagues did not sequence the entire genomes of the fossils, Meyer reported at the meeting that they did get 1 million to 2 million base pairs of ancient nuclear DNA.

They scanned this DNA for unique markers found only in Neandertals or Denisovans or modern humans, and found that the two Sima fossils shared far more alleles—different nucleotides at the same address in the genome—with Neandertals than Denisovans or modern humans. "Indeed, the Sima de los Huesos specimens are early Neandertals or related to early Neandertals," suggesting that the split of Denisovans and Neandertals should be moved back in time, Meyer reported at the meeting.

Researchers at the meeting were impressed by this new breakthrough in ancient DNA research. "This has been the next frontier with ancient DNA," says evolutionary biologist Greger Larson of the University of Oxford in the United Kingdom.

The close affinity with Neandertals, but not with Denisovans or modern humans, suggests that the lineage leading to Neandertals was separate from other archaic humans earlier than most researchers have thought. That means that the ancestors of modern humans also had to split earlier than expected from the population that gave rise to Neandertals and Denisovans, who were more closely related to each other than they were to modern humans. (Although all three groups interbred at low levels after their evolutionary paths diverged—and such interbreeding may have been the source of the Denisovan mtDNA in the first Sima fossil whose DNA was sequenced.) Indeed, Meyer suggested in his talk that the ancestors of H. sapiens may have diverged from the branch leading to Neandertals and Denisovans as early as 550,000 to 765,000 years ago, although those results depend on different mutation rates in humans and are still unpublished.

That would mean that the ancestors of humans were already wandering down a solitary path apart from the other kinds of archaic humans on the planet 100,000 to 400,000 years earlier than expected. "It resolves one controversy—that they're in the Neandertal clade," says paleoanthropologist Chris Stringer of the Natural History Museum in London. "But it's not all good news: From my point of view, it pushes back the origin of H. sapiens from the Neandertals and Denisovans." The possibility that humans were a distinct group so early shakes up the human family tree, promising to lead to new debate about when and where the branches belong.

Quote from: crazy canuck on September 19, 2015, 11:28:46 PM
Very interesting.  Thanks for posting.

Quote

In Ancient DNA, Evidence of Plague Much Earlier Than Previously Known

October 22, 2015
Carl Zimmer

Bacteria can change history.

In the 14th century, a microbe called Yersinia pestis caused an epidemic of plague known as the Black Death that killed off a third or more of the population of Europe. The long-term shortage of workers that followed helped bring about the end of feudalism.

Historians and microbiologists alike have searched for decades for the origins of plague. Until now, the first clear evidence of Yersinia pestis infection was the Plague of Justinian in the 6th century, which severely weakened the Byzantine Empire.

But in a new study, published on Thursday in the journal Cell, researchers report that the bacterium was infecting people as long as 5,000 years ago.

Exactly what those early outbreaks were like is impossible to know. But the authors of the new study suggest that plague epidemics in the Bronze Age may have opened the doors to waves of migrants in regions decimated by disease.

"To my mind, this leaves little doubt that this has played a major role in those population replacements," said Eske Willerslev, a co-author of the new study and the director of the Center for GeoGenetics at the University of Copenhagen.

David M. Wagner, a microbial geneticist at Northern Arizona University who was not involved in the study, said that the new research should prompt other scientists to look at mysterious outbreaks in early history, such as the epidemic that devastated Athens during the Peloponnesian War. "It opens up whole new areas of research," he said.

The new study arose from previous research by Dr. Willerslev and his colleagues. They were able to extract human DNA from101 bones found in Europe and Asia, ranging in age from about 3,000 to 5,000 years old.

As they reported in June, the genetic profiles of people during that 2,000-year period changed with surprising abruptness. About 4,500 years ago, for example, the DNA of Europe's inhabitants suddenly took on a strong resemblance to that of the Yamnaya, a nomadic people from western Russia.

Wondering what could have triggered such a shift, Dr. Willerslev and his colleagues realized they could test one hypothesis: that epidemics had decimated some populations, allowing new groups to establish themselves.

When researchers search for ancient human genetic material in a piece of bone, they begin by retrieving all the DNA in the sample. Most of it is not human, belonging instead to bacteria and other microbes that colonize bones after death.

Once scientists have gathered all the DNA, they assemble the genetic fragments into larger pieces and try to match them to sequences already identified in earlier research. Normally they set aside microbial DNA to focus on the human material.

Dr. Willerslev and his colleagues wondered if some of the nonhuman DNA they had collected from Bronze Age remains might belong to pathogens. They decided to look for traces of Yersinia pestis, even though the earliest evidence of the infection dates to thousands of years later.

"Plague was just a long shot," said Dr. Willerslev.

But sometimes long shots pay off. Of 101 Bronze Age individuals, the researchers found Yersinia pestis DNA in seven. Plague DNA was present in teeth recovered from sites stretching from Poland to Siberia.

By comparing the ancient Yersinia to more recent strains, the scientists also were able to reconstruct its evolutionary history.

Plague can take several different forms. In bubonic plague, the most common, the bacteria invade the lymphatic system. Left untreated, it can kill a victim within days.

The infection is spread by fleas hopping between rats and humans. But 5,000 years ago, Dr. Willerslev and his colleagues found, Yersinia pestis didn't yet have a gene known to be essential for survival in fleas.

The bacterium did have many of the genes that make it deadly to humans. Dr. Wagner suggested that people may have become infected with plague in ancient times not by fleas, but bybreathing in the microbes or by hunting infected rodents for food.

After acquiring the ability to infect fleas, Yersinia pestis may have begun to spread more readily from one rodent to another, eventually causing widespread epidemics. "It really says something about the rapid evolution of pathogens," said Dr. Wagner.

Hendrik N. Poinar, a geneticist at McMaster University who was not involved in the study, found this evolutionary scenario persuasive — "a slam dunk," he said. But he isn't convinced that huge outbreaks of primitive plague rocked ancient societies and questioned whether the bacteria could have spread quickly without infecting fleas.

"It is speculation as to whether these strains were responsible for high mortality rates in the Bronze Age," he said.

Dr. Willerslev and his colleagues are now looking for more clues to how the plague affected the Bronze Age world — as well as other pathogens that may have left behind genetic traces. He is now grateful that he and his colleagues didn't simply throw out all their nonhuman DNA.

"It was just annoying waste lying there that we had to bully our way through," said Dr. Willerslev. "Now it's not waste anymore. It's a potential gold mine."

Quote from: crazy canuck on October 23, 2015, 12:08:15 PM
Very interesting if they can trace this to the Bronze Age collapse.

QuoteDNA of Ancient Children Offers Clues on How People Settled the Americas


OCT. 26, 2015
Carl Zimmer

Researchers have long wondered how people settled the Americas, particularly the path they took to the new territory and the timing of their expansion. Until recently, archaeologists studying these questions were limited mostly to digging up skeletons and artifacts.

But now scientists have begun extracting DNA from human bones, and the findings are providing new glimpses at the history of the first Americans. On Monday, researchers at the University of Alaska and elsewhere published an important addition to the growing genetic archive.

In the Proceedings of the National Academy of Sciences, the researchers reported that they had  recovered DNA from two skeletons of children who lived in Alaska 11,500 years ago. The genetic material is not only among the oldest ever found in the Americas, but also the first ancient DNA discovered in Beringia, the region around the Bering Strait where many researchers believe Asians first settled before spreading through North and South America.

The archaeological site, near Upward Sun River, was discovered in 2010. Excavations there have revealed that between 13,200 and 8,000 years ago, people visited during the summer, catching salmon and hares. They built tentlike structures where they made fires and slept.

In 2011, archaeologists discovered cremated bones on a hearth at the site. Research revealed that the bones belonged to a 3-year-old child. Below the hearth, the team discovered a burial pit containing the skeletons of two other children.

One of the buried children was an infant who died a few months after birth; the other was likely a late-term fetus. After the baby and the fetus died, their bodies were carefully laid atop a bed of red ocher, surrounded by antlers fashioned into hunting darts.

"These things we hardly ever find — it's a very rare window into the worldview of these people," said Ben A. Potter, an archaeologist at the University of Alaska Fairbanks who has led the research at Upward Sun River.

Clearly, the children had been ceremonially buried. But why the two bodies ended up in the same grave is impossible to know. With the consent of Native American tribes that live around the site, Dr. Potter and his colleagues drilled small pieces of bone from the two skeletons and sent them to geneticists at the University of Utah.

The vast majority of our DNA lies in the nucleus of the cell. But the cell's energy factories, called mitochondria, also carry small bits of their own DNA inherited solely from our mothers.

Because each cell can contain hundreds of mitochondria, it is easier to reconstruct their DNA than that of the cellular nuclei. The Utah geneticists focused their search on mitochondrial DNA in the Upward Sun River bones.

They succeeded in recovering mitochondrial DNA from both bone samples. But to their surprise, the genes were markedly different. The infant and the fetus did not share the same mother or even maternal grandmother.

The researchers can only speculate how an infant and a fetus from different mothers ended up in the same grave. They might have had the same father, or they might have belonged to different families who suffered terrible losses at the same time.

But the significance of the DNA found at Upward Sun River extends far beyond the story of two children. It sheds light on how people first moved into the Americas.

In 2007, Ripan Malhi of the University of Illinois and his colleagues proposed a model for this migration, known as the Beringian Standstill. Early Siberians expanded east into Beringia about 25,000 years ago, they proposed, and stayed there for about 10,000 years.

Humans were able to thrive in Beringia because even at the height of the last ice age, the region was not covered by glaciers. It was mainly tundra and shrub land, with scattered stands of trees.

Humans could not expand eastward into the rest of the Americas because they were blocked by glaciers. About 15,000 years ago, as the glaciers retreated, the standstill came to an end.

"It opened up new ecological zones that were being colonized by plants and animals," said Dennis O'Rourke of the University of Utah, a co-author of the new study.

According to the standstill hypothesis, the ancestors of Native Americans would have built up a large degree of genetic diversity in the thousands of years they were confined to Beringia — more so than if these populations had migrated directly from Siberia to the Americas.

The fact that two children who died at roughly the same time in the same community shared so few genes is consistent with the idea that the population was prevented from moving into the Americas for thousands of years, Dr. O'Rourke said.

But the two children died after the glaciers melted, he noted, and their settlement "may well be a remnant of that original Beringian group. It may give us a snapshot of that earlier time."

Dr. Malhi, who was not involved in the new study, thought the new DNA was too recent to provide proof of the idea that humans were trapped in Beringia for thousands of years. "It's valuable information, but it's a little bit late to be extremely informative to let us know if the Beringian Standstill hypothesis holds," he said.

More conclusive findings would be possible if scientists found older DNA from people who lived during the Beringian Standstill. Archaeologists are now looking for skeletons from that age, but Dr. Malhi is not holding his breath.

Many of the sites where people lived may now be impossible to reach, because sea levels rose at the end of the ice age.

"There are archaeologists up there looking for such sites," Dr. Malhi said. "But I think it's probably unlikely, largely because a lot of Beringia is now under water."

Quote from: jimmy olsen on October 27, 2015, 12:10:15 AM

Quote from: crazy canuck on October 23, 2015, 12:08:15 PM
Very interesting if they can trace this to the Bronze Age collapse.

I read 1177 B.C., The Year Civilization Collapsed relatively recently and I don't remember an epidemic being high up on the list of possible causes. It was combination of climate change leading to famine and migration/invasion.

Quote from: jimmy olsen on October 27, 2015, 12:10:15 AM1177 B.C., The Year Civilization Collapsed

Quote from: MadImmortalMan on October 27, 2015, 03:12:16 PM

Quote from: jimmy olsen on October 27, 2015, 12:10:15 AM1177 B.C., The Year Civilization Collapsed

Any good?

Quote from: MadImmortalMan on October 27, 2015, 03:12:16 PM

Quote from: jimmy olsen on October 27, 2015, 12:10:15 AM1177 B.C., The Year Civilization Collapsed

Any good?

Quote
Another Denisovan from Denisova Cave
18 Nov 2015

Denisova Cave is one of the most fascinating places in the story of human origins. The cave is in the northern wall of the Anuy River valley, within the Altai Krai region of Russia but very near the border with the Altai Republic.

The cave's East Gallery, where excavators still work through part of the Altai summer, feels like a walk-in refrigerator. Archaeologists work inside wearing rugged jackets as they work slowly down through sediments at five degrees Celsius. In the winter, the temperature inside the cave is below freezing. The exceptional cold has made this cave into a time capsule for ancient genetic sequences.

The fossil hominins from the cave are mere scraps, some of them possibly leftovers from hyena meals. But before now three of the bones and teeth have produced genetic sequences, including two from a previously-unknown population that we now call the "Denisovans".

Today there's something new. Another hominin tooth, Denisova 8, has now yielded a partial low-coverage genome, and we can welcome it as a new member of the Denisovan population. Its DNA sequence shows that this tooth is older than the other Denisovan specimens, maybe 60,000 years older. And its DNA increases the diversity of the known sample of Denisovan specimens.

What's important about this? And how does it fit into the already-complicated Denisova family?

The Denisova cast of characters

The story of the hominins from this cave has been fast-moving for the last five years. If you haven't been following closely, it probably seems like a telenovella. Many characters jump out for attention, each with a special, distinctive story.

The first and most famous of the specimens is the distal phalanx from a fifth finger, Denisova 3. When ancient mitochondrial DNA from Denisova 3 was first reported in 2010 by Johannes Krause and colleagues, they found it was very different from any known human or Neandertal—so different that they called this hominin the "X-Woman".

That name didn't last long. Later in 2010, David Reich and colleagues followed up on the mtDNA by sequencing a low-coverage nuclear genome from the specimen. They showed that even though the mtDNA of Denisova 3 last shared an ancestor with us more than a million years ago, the nuclear genome is much less divergent. The "Denisovan" really did belong to a previously unknown population, very different from living humans. But it shared an ancestry with Neandertals within the last half million years.

At the same time, Reich and colleagues sampled the mtDNA from a second hominin specimen. This one, Denisova 4, is a third molar, or "wisdom tooth" representing a different individual from the finger bone. The mtDNA of this tooth is not identical to the finger, but it does belong to the same highly divergent lineage.

In 2012, Mattias Meyer and colleagues did more work on the Denisova 3 sample, ultimately yielding a very high coverage genome. From this genome it was possible to show that Denisova 3 came from a very endogamous population, one that had been small for a very long time.

Then, in 2014, Kay Prüfer and colleagues sequenced the DNA from another Denisova Cave specimen. This one, a toe bone, came from a similar archaeological level as the original Denisova 3 sequence, although it lay a bit lower in the sequence and therefore is probably a bit older. This toe bone produced another high-coverage genome, the second from the site. And unlike the other two Denisova specimens, this toe belonged to a Neandertal.

That's quite a trick, telling Neandertals from previously unknown populations based on fingers and toes. Anthropologists would never attempt such a thing from the bones themselves. Or, maybe more accurately, some anthropologists would make extravagant claims from the finger and toe bones, and they would be fools.

But a whole genome gives millions of bits of evidence about relationships. The two Denisova mtDNA sequences stand apart from any known Neandertal or modern human. The nuclear genome of Denisova 3 differs from any known Neandertal or modern human at millions of base pairs. Still, that Denisova 3 genome has large stretches of DNA shared with the Neandertal toe bone, indicating that the Neandertal population interbred with the ancestors of the Denisovan individuals at some point.

And the Neandertal toe bone itself was highly inbred—as homozygous across its whole genome as people whose parents are half-siblings.

It's a Paleolithic telenovella.
Denisova 8

Now, Susanna Sawyer and colleagues report this week in Proceedings of the National Academy of Sciences on the genetic data from a third Denisovan individual, Denisova 8. And they add nuclear genetic sequence, at low coverage, from the Denisova 4 tooth.

Denisova 8 is another tooth, again, likely a third molar. The two teeth are morphologically different from each other, with little indication that they reflect a single gene pool, except that the teeth are both quite large relative to most later Pleistocene humans.

One of the main genetic results is that the two molars (Denisova 4 and 8) clearly group with the original pinky (Denisova 3) genome in their nuclear and mitochondrial DNA. However, Denisova 8 is an outlier to the other two, more different from them in mtDNA sequence than any Neandertals are from each other, and somewhat more different in the nuclear genome than would be typical for Neandertals.

Part of that difference is due to the age of Denisova 8. Its mtDNA branch is shorter than the other two specimens. It is missing evolutionary history that is present in Denisova 3 and Denisova 4, enough to suggest that Denisova 8 lived some 60,000 years earlier in time than those other two. The nuclear genome is consistent with such an age estimate, although the low-coverage sequence is not really sufficient to give an any accuracy on its own. So one reason why Denisova 8 increases the diversity of the Denisova sample is that it lacks tens of thousands of years of genetic drift that was shared in the ancestry of the later specimens.

Still, when we look at the variation in the two low-coverage genomes from Denisova 4 and 8 in comparison with the high-coverage Denisova 3 genome, all the Denisovans together seem to have been just a bit less inbred than Neandertals. Sawyer and colleagues provide a measure of genetic difference between genomes that is scaled to the difference between humans and chimpanzees. To accomplish this measurement, they take the preserved sequence that overlaps between two low-coverage genomes (or high-coverage genomes), examine every site within the overlapping sequence where either of the two hominin sequences differs from the chimpanzee genome, and examine the fraction of times that the two hominin sequences are discrepant from each other. This gives a measure of difference between the two genomes relative to their difference from chimpanzees.

For the Denisovan genomes, this difference averages 2.9 percent. For Neandertal genomes compared to each other, the difference averages 2.5 percent. So Denisovans are a bit more diverse than Neandertals by this measure.

For human populations, the differences range between 4.2 and 9.5 percent. The least diverse pair of individuals are Karitiana people from South America. This highly endogamous human group is still half again as diverse as Denisovans.

Both the Denisovans and Neandertals were very endogamous relative to today's people, even just comparing to Europeans today. That endogamy must reflect something about the ancient population structure of these archaic people. One consequence of the endogamy — as two preprints by Graham Coop's lab and Rasmus Nielsen's lab show — is that Neandertals may have carried a load of slightly deleterious genetic variants. When the Neandertals and Denisovans mated with the more diverse population that dispersed from Africa in the Late Pleistocene, some of these deleterious genetic variants may have been slowly weeded out of the modern human population by purifying selection.

How big were the Denisovans' teeth?

We don't know very much about what Denisovans may have looked like, with only a fingertip and two wisdom teeth to go on. So it's tempting to take these slim data and make something more out of them than we probably should.

With two teeth, we at least can measure their sizes. They're big. Bigger than most living humans, bigger than any Neandertals, as big as some third molars of Australopithecus.

We can't make too much out of the large size of these third molars, because similarly large teeth do occasionally occur among Upper Paleolithic people. The supplementary material to Sawyer and colleagues' paper gives a brief review, noting that the Oase 2 skull has such a large third molar, as does a tooth from a partial juvenile dentition of a probable Neandertal from Obi-Rakhmat, Uzbekistan.

    Two Late Pleistocene specimens are comparably large in size, the M3s of the early Upper Paleolithic modern human Oase 2 and the M2/3 of Obi-Rakhmat 1 (14, 15). Oase 2 does not show large extra cusps, but instead strong crenulation (16). Obi-Rakhmat shows a large extra cusp, but mesially, not distally (Main text, Figure 1), and a large number of accessory cusps possibly due to gemination (17).

The Oase 2 specimen is the earliest modern human known from Europe. This is not the same individual as the Oase 1 mandible, but it may be relevant that the Oase 1 specimen had more Neandertal ancestry than any known living person, and that Neandertal ancestry was quite recent, possibly within four generations.

Is it odd that we have large third molars in some individuals in Eastern Europe and Central Asia, including the Denisovans? I think to answer this we will need a larger sample of fossil humans from other places. There is at least one Chinese third molar specimen from Xujiayao that approaches the size of these large teeth. Perhaps the Chinese specimen is a Denisovan, or maybe this is one morphological extreme that is distributed among Late Pleistocene populations.

The thing is, if there was one piece of morphological evidence I would throw away and pay no attention to above all others, it's the morphology of the third molar. It is just enormously variable among living humans and living primates. I wouldn't trust it to tell us about relationships of hominin groups.

OK, so maybe I would trust the third molar above the pinky finger.

UPDATE (2015-11-18): I've known about these results for a long time, as the authors kindly shared them with me. But I forgot that the results were also previously a part of the documentary "Sex in the Stone Age", until I found a letter from a reader in my archives:

   

Quote from: Me! I just watched the National Geographic documentary "Sex in the Stone Age" and was surprised by the reference to the discovery of a 2nd Denisovan tooth, one whose mitochondrial DNA was distinct enough from that of the mtDNA in the finger and original tooth to indicate that the Denisovan population had as much genetic diversity as H. Sapiens currently has today. This is interesting, since if I recall correctly, Neanderthals had low levels of genetic diversity, with evidence of replacement of their western European population by an Eastern population. This perhaps indicates that the Denisoans had a larger population than that of the Neanderthals. I don't recall reading about this find on your website or anywhere else.

At the time I gave some context to that report from the documentary but had little more to say.

What's interesting about this week's publication is that the nuclear genome and mtDNA have contrasting patterns. The genetic variation within Denisovans is best assessed across the nuclear genome, and they are low in a similar way as Neandertals.

Still, the Neandertal sample covers a very large geographic area, from Spain to the Altai. Our intuition might lead us to expect that extensive range to encompass more variation than three Denisovan individuals from a single site. But the Denisovan genomes cover a longer time than the low-coverage Neandertal genomes, and across such a time they may actually sample very different populations. If we had a Neandertal low-coverage genome as early as Denisova 8, their variation might look different.

To me, the core observation is that both these populations were highly endogamous compared to any living human groups. I'll have a bit more to say about the mtDNA discrepancy shortly...
Reference

Sawyer S, Renaud G, Viola B, Hublin J-J, Gansauge M-T, Shunkov MV, Derevianko AP, Prüfer K, Kelso J, Pääbo S. 2015. Nuclear and mitochondrial DNA sequences from two Denisovan individuals. Proceedings of the National Academy of Sciences, USA (early edition) doi:10.1073/pnas.1519905112

QuoteNeolithic farmers from Greece and Anatolia

A couple of new papers appeared this week. First, an article in Nature on natural selection in ancient Europe includes a sample of Anatolian Neolithic farmers and concludes that the European Neolithic farmers were descended from them with a bit of extra European hunter-gatherer admixture. Second, a new preprint on the bioRxiv includes Neolithic samples from northern Greece and finds that they too resemble the Anatolian and European farmers. I think it is time to declare the problem of "Neolithization of Europe" done. It took less than 4 years to solve it with ancient DNA. Here is a (non-exhaustive) list of papers in historical review:

Keller et al. (2012): Iceman (5kya) looks Sardinian! Was this a fluke? (http://www.nature.com/ncomms/journal/v3/n2/full/ncomms1701.html)
Skoglund et al. (2012): No, because... Swedish farmer (5kya) looked Sardinian too! When did these "Sardinians" come to Europe? (https://www.sciencemag.org/content/336/6080/466)
Lazaridis et al. (2014): No later than an LBK farmer from Germany (7kya) but what about western Europe? (http://www.nature.com/nature/journal/v513/n7518/full/nature13673.html)
Haak, Lazaridis et al. (2015): Spanish early farmers from northern Spain looked Sardinian too  (http://www.nature.com/nature/journal/v522/n7555/abs/nature14317.html)
Olalde, Schroeder et al. (2015): Ditto for Mediterranean Spain! So where did they all come from? (http://mbe.oxfordjournals.org/content/early/2015/09/02/molbev.msv181)
Mathieson et al. (2015): Anatolia! (http://www.nature.com/nature/journal/vaop/ncurrent/full/nature16152.html)
Hofmanová, Kreutzer et al. (2015): via Greece! (http://biorxiv.org/content/early/2015/11/25/032763)

Quote
Iain Mathieson et al.

Ancient DNA makes it possible to observe natural selection directly by analysing samples from populations before, during and after adaptation events. Here we report a genome-wide scan for selection using ancient DNA, capitalizing on the largest ancient DNA data set yet assembled: 230 West Eurasians who lived between 6500 and 300 BC, including 163 with newly reported data. The new samples include, to our knowledge, the first genome-wide ancient DNA from Anatolian Neolithic farmers, whose genetic material we obtained by extracting from petrous bones, and who we show were members of the population that was the source of Europe's first farmers. We also report a transect of the steppe region in Samara between 5600 and 300 BC, which allows us to identify admixture into the steppe from at least two external sources. We detect selection at loci associated with diet, pigmentation and immunity, and two independent episodes of selection on height.

QuoteEarly farmers from across Europe directly descended from Neolithic Aegeans

Zuzana Hofmanová, Susanne Kreutzer et al.

Farming and sedentism first appear in southwest Asia during the early Holocene and later spread to neighboring regions, including Europe, along multiple dispersal routes. Conspicuous uncertainties remain about the relative roles of migration, cultural diffusion and admixture with local foragers in the early Neolithisation of Europe. Here we present paleogenomic data for five Neolithic individuals from northwestern Turkey and northern Greece, spanning the time and region of the earliest spread of farming into Europe. We observe striking genetic similarity both among Aegean early farmers and with those from across Europe. Our study demonstrates a direct genetic link between Mediterranean and Central European early farmers and those of Greece and Anatolia, extending the European Neolithic migratory chain all the way back to southwestern Asia.

Quote from: Queequeg on November 27, 2015, 03:42:37 AM
The Anatolian hypothesis is primarily linguistic.  And it's rubbish.

Quote from: Razgovory on November 27, 2015, 02:56:32 PM
Tim, I don't think you understand what the Anatolian Hypothesis is.  It has to do with the homeland of Proto-Indo Europeans not where farming came from.

QuoteThe Anatolian hypothesis proposes that the dispersal of Proto-Indo-Europeans originated in Neolithic Anatolia. The hypothesis suggests that the speakers of the Proto-Indo-European language (PIE) lived in Anatolia during the Neolithic era, and associates the distribution of historical Indo-European languages with the expansion during the Neolithic revolution of the seventh and sixth millennia BC. An alternative (and academically more favored view) is the Kurgan hypothesis.

The main proponent of the Anatolian hypothesis, Colin Renfrew, suggested in 1987 a peaceful Indo-Europeanization of Europe from Anatolia from around 7000 BC, with the advance of farming by demic diffusion ("wave of advance"). Accordingly, most of the inhabitants of Neolithic Europe would have spoken Indo-European languages, and later migrations would at best have replaced these Indo-European varieties with other Indo-European varieties.[1]

Quote from: Jaron on November 27, 2015, 03:02:03 AM
Tim, you are famous!

Quote from: jimmy olsen on November 27, 2015, 09:22:58 PM

Quote from: Razgovory on November 27, 2015, 02:56:32 PM
Tim, I don't think you understand what the Anatolian Hypothesis is.  It has to do with the homeland of Proto-Indo Europeans not where farming came from.

I know, I'm saying these farmers are the Proto-Indo Europeans.

https://en.wikipedia.org/wiki/Anatolian_hypothesis

QuoteThe Anatolian hypothesis proposes that the dispersal of Proto-Indo-Europeans originated in Neolithic Anatolia. The hypothesis suggests that the speakers of the Proto-Indo-European language (PIE) lived in Anatolia during the Neolithic era, and associates the distribution of historical Indo-European languages with the expansion during the Neolithic revolution of the seventh and sixth millennia BC. An alternative (and academically more favored view) is the Kurgan hypothesis.

The main proponent of the Anatolian hypothesis, Colin Renfrew, suggested in 1987 a peaceful Indo-Europeanization of Europe from Anatolia from around 7000 BC, with the advance of farming by demic diffusion ("wave of advance"). Accordingly, most of the inhabitants of Neolithic Europe would have spoken Indo-European languages, and later migrations would at best have replaced these Indo-European varieties with other Indo-European varieties.[1]

Quote from: Queequeg on November 29, 2015, 05:16:38 AM

Quote from: jimmy olsen on November 27, 2015, 09:22:58 PM

Quote from: Razgovory on November 27, 2015, 02:56:32 PM
Tim, I don't think you understand what the Anatolian Hypothesis is.  It has to do with the homeland of Proto-Indo Europeans not where farming came from.

I know, I'm saying these farmers are the Proto-Indo Europeans.

https://en.wikipedia.org/wiki/Anatolian_hypothesis

QuoteThe Anatolian hypothesis proposes that the dispersal of Proto-Indo-Europeans originated in Neolithic Anatolia. The hypothesis suggests that the speakers of the Proto-Indo-European language (PIE) lived in Anatolia during the Neolithic era, and associates the distribution of historical Indo-European languages with the expansion during the Neolithic revolution of the seventh and sixth millennia BC. An alternative (and academically more favored view) is the Kurgan hypothesis.

The main proponent of the Anatolian hypothesis, Colin Renfrew, suggested in 1987 a peaceful Indo-Europeanization of Europe from Anatolia from around 7000 BC, with the advance of farming by demic diffusion ("wave of advance"). Accordingly, most of the inhabitants of Neolithic Europe would have spoken Indo-European languages, and later migrations would at best have replaced these Indo-European varieties with other Indo-European varieties.[1]

yes language is genetics
that's why african americans are indistinguishable from villagers in rural east anglia and natives of edirne look like koreans

Quote from: Queequeg on November 29, 2015, 09:00:39 AM
People UNDERSTOOD that Sanskirt, Latin and Greek were related going back to the first Portuguese missions to India

Quote from: Grinning_Colossus on November 29, 2015, 10:19:54 AM

Quote from: Queequeg on November 29, 2015, 09:00:39 AM
People UNDERSTOOD that Sanskirt, Latin and Greek were related going back to the first Portuguese missions to India

Really? It was my understanding that, until the advent of modern linguistics, people didn't understand that, e.g., French and Spanish were descended from Latin; they thought that all contemporary languages were created by God when he destroyed the Tower of Babel.

Quote from: dps on November 29, 2015, 10:29:36 AM

Quote from: Grinning_Colossus on November 29, 2015, 10:19:54 AM

Quote from: Queequeg on November 29, 2015, 09:00:39 AM
People UNDERSTOOD that Sanskirt, Latin and Greek were related going back to the first Portuguese missions to India

Really? It was my understanding that, until the advent of modern linguistics, people didn't understand that, e.g., French and Spanish were descended from Latin; they thought that all contemporary languages were created by God when he destroyed the Tower of Babel.

My understanding was more along the lines of that studying the comparisons of Sanskrit to Greek and Latin was essentially the foundation of modern linguistics.

QuoteThe Sanscrit language, whatever be its antiquity, is of a wonderful structure; more perfect than the Greek, more copious than the Latin, and more exquisitely refined than either, yet bearing to both of them a stronger affinity, both in the roots of verbs and the forms of grammar, than could possibly have been produced by accident; so strong indeed, that no philologer could examine them all three, without believing them to have sprung from some common source, which, perhaps, no longer exists; there is a similar reason, though not quite so forcible, for supposing that both the Gothic and the Celtic, though blended with a very different idiom, had the same origin with the Sanscrit; and the old Persian might be added to the same family.

Quote

Credit: Casey Staff


BINGHAMTON, NY - Research into human fossils dating back to approximately two million years ago reveals that the hearing pattern resembles chimpanzees, but with some slight differences in the direction of humans.

Rolf Quam, assistant professor of anthropology at Binghamton University, led an international research team in reconstructing an aspect of sensory perception in several fossil hominin individuals from the sites of Sterkfontein and Swartkrans in South Africa. The study relied on the use of CT scans and virtual computer reconstructions to study the internal anatomy of the ear. The results suggest that the early hominin species Australopithecus africanus and Paranthropus robustus, both of which lived around 2 million years ago, had hearing abilities similar to a chimpanzee, but with some slight differences in the direction of humans.

Humans are distinct from most other primates, including chimpanzees, in having better hearing across a wider range of frequencies, generally between 1.0-6.0 kHz. Within this same frequency range, which encompasses many of the sounds emitted during spoken language, chimpanzees and most other primates lose sensitivity compared to humans.

"We know that the hearing patterns, or audiograms, in chimpanzees and humans are distinct because their hearing abilities have been measured in the laboratory in living subjects," said Quam. "So we were interested in finding out when this human-like hearing pattern first emerged during our evolutionary history."

Previously, Quam and colleagues studied the hearing abilities in several fossil hominin individuals from the site of the Sima de los Huesos (Pit of the Bones) in northern Spain. These fossils are about 430,000 years old and are considered to represent ancestors of the later Neandertals. The hearing abilities in the Sima hominins were nearly identical to living humans. In contrast, the much earlier South African specimens had a hearing pattern that was much more similar to a chimpanzee.

In the South African fossils, the region of maximum hearing sensitivity was shifted towards slightly higher frequencies compared with chimpanzees, and the early hominins showed better hearing than either chimpanzees or humans from about 1.0-3.0 kHz. It turns out that this auditory pattern may have been particularly favorable for living on the savanna. In more open environments, sound waves don't travel as far as in the rainforest canopy, so short range communication is favored on the savanna.

"We know these species regularly occupied the savanna since their diet included up to 50 percent of resources found in open environments" said Quam. The researchers argue that this combination of auditory features may have favored short-range communication in open environments.

That sounds a lot like language. Does this mean these early hominins had language? "No," said Quam. "We're not arguing that. They certainly could communicate vocally. All primates do, but we're not saying they had fully developed human language, which implies a symbolic content."

The emergence of language is one of the most hotly debated questions in paleoanthropology, the branch of anthropology that studies human origins, since the capacity for spoken language is often held to be a defining human feature. There is a general consensus among anthropologists that the small brain size and ape-like cranial anatomy and vocal tract in these early hominins indicates they likely did not have the capacity for language.

"We feel our research line does have considerable potential to provide new insights into when the human hearing pattern emerged and, by extension, when we developed language," said Quam.

Ignacio Martinez, a collaborator on the study, said, "We're pretty confident about our results and our interpretation. In particular, it's very gratifying when several independent lines of evidence converge on a consistent interpretation."

How do these results compare with the discovery of a new hominin species, Homo naledi, announced just two weeks ago from a different site in South Africa?

"It would be really interesting to study the hearing pattern in this new species," said Quam. "Stay tuned."

The study was published on Sept. 25 in the journal Science Advances.

QuoteThe Neolithic and Bronze Age transitions were profound cultural shifts catalyzed in parts of Europe by migrations, first of early farmers from the Near East and then Bronze Age herders from the Pontic Steppe. However, a decades-long, unresolved controversy is whether population change or cultural adoption occurred at the Atlantic edge, within the British Isles. We address this issue by using the first whole genome data from prehistoric Irish individuals. A Neolithic woman (3343–3020 cal BC) from a megalithic burial (10.3× coverage) possessed a genome of predominantly Near Eastern origin. She had some hunter–gatherer ancestry but belonged to a population of large effective size, suggesting a substantial influx of early farmers to the island. Three Bronze Age individuals from Rathlin Island (2026–1534 cal BC), including one high coverage (10.5×) genome, showed substantial Steppe genetic heritage indicating that the European population upheavals of the third millennium manifested all of the way from southern Siberia to the western ocean. This turnover invites the possibility of accompanying introduction of Indo-European, perhaps early Celtic, language. Irish Bronze Age haplotypic similarity is strongest within modern Irish, Scottish, and Welsh populations, and several important genetic variants that today show maximal or very high frequencies in Ireland appear at this horizon. These include those coding for lactase persistence, blue eye color, Y chromosome R1b haplotypes, and the hemochromatosis C282Y allele; to our knowledge, the first detection of a known Mendelian disease variant in prehistory. These findings together suggest the establishment of central attributes of the Irish genome 4,000 y ago

Quote from: Caliga on January 05, 2016, 10:04:20 AM
I shall let you people know what percent Neanderthal I am. :)

Quote from: jimmy olsen on January 05, 2016, 11:08:45 AM
Unless you're from Sub-Saharan Africa 0.0% is not going to happen Cal

Quote from: Caliga on January 05, 2016, 11:14:33 AM

Quote from: jimmy olsen on January 05, 2016, 11:08:45 AM
Unless you're from Sub-Saharan Africa 0.0% is not going to happen Cal

What makes you think I'm not?

Quote from: Caliga on January 05, 2016, 10:04:20 AM
On a related note, I am having my DNA sequenced.  I shall let you people know what percent Neanderthal and Denisovan I am. :)

Quote from: jimmy olsen on November 29, 2015, 07:12:25 AM
"Pots, not people" has been thoroughly discredited. The history of Eurasia, in both historical,  prehistoric and even pre-anatomically modern times is one of migration and population replacement. Languages, like all other artifacts of culture were spread primarily by such demographic change, rather than through the simple exchange of ideas. Such did not become a dominant means of exchange until the development of extensive trade routes during the iron age.

Quote from: Caliga on January 05, 2016, 11:14:33 AM

Quote from: jimmy olsen on January 05, 2016, 11:08:45 AM
Unless you're from Sub-Saharan Africa 0.0% is not going to happen Cal

What makes you think I'm not?

Quote from: The Minsky Moment on January 05, 2016, 11:57:53 AM

Quote from: jimmy olsen on November 29, 2015, 07:12:25 AM
"Pots, not people" has been thoroughly discredited. The history of Eurasia, in both historical,  prehistoric and even pre-anatomically modern times is one of migration and population replacement. Languages, like all other artifacts of culture were spread primarily by such demographic change, rather than through the simple exchange of ideas. Such did not become a dominant means of exchange until the development of extensive trade routes during the iron age.

That's ipse dixit, not argument.

"pots, not people" can't be discredited, much less thoroughly, because it is a truism.  Pots are not people.  Physical material and ideas, and yes even language can be transmitted across space without mass migration.  So some other *facts* are needed to establish mass "migration and population replacement" in any given instance where it is hypothesized.

Quote from: jimmy olsen on January 05, 2016, 11:18:48 PM
DNA sequencing of ancient populations has provided massive, direct evidence for mass migration and population replacement.

Quote from: jimmy olsen on January 05, 2016, 11:16:37 PM
Because we've met in person?  :huh:

Quote from: The Minsky Moment on January 06, 2016, 11:01:24 AM

Quote from: jimmy olsen on January 05, 2016, 11:18:48 PM
DNA sequencing of ancient populations has provided massive, direct evidence for mass migration and population replacement.

No it hasn't, certainly not as a general matter.  It has confirmed that people move over time, which is not an enormous surprise.  But outright population replacement is not common, other than in "ancient" cases where the indigenous population was so small or ephemeral that even small numbers of migrants could have disproportionate genetic impact.  To take but one example, the DNA evidence does not support the hypothesis of mass population replacement via the Anglo-Saxon and Nordic invasion of British isles, which would have been one of the most promising historical episodes for a replacement scenario.  Sykes' book in fact indicated the genetic heritage of the British Isles did not significantly change since the Neolithic, and with a very substantial contribution still existing from the Mesolithic populations.

Quote from: jimmy olsen on January 06, 2016, 06:04:23 PM
We were not talking about the modern period, though I note that the Anglo-Saxon invasion of North America and the following waves of European immigration seems to have been rather successful, we were talking about the Neolirhic period in which there were massive waves of migration from the Near East and the Steppe into Europe by early farmers and pastoralists.

Quote from: The Minsky Moment on January 06, 2016, 06:22:13 PM

Quote from: jimmy olsen on January 06, 2016, 06:04:23 PM
We were not talking about the modern period, though I note that the Anglo-Saxon invasion of North America and the following waves of European immigration seems to have been rather successful, we were talking about the Neolirhic period in which there were massive waves of migration from the Near East and the Steppe into Europe by early farmers and pastoralists.

The reference to "massive waves of migration" is question begging. 
The DNA evidence is ambiguous, and there remains a very lively academic debate between the demic diffusion and cultural diffusion hypotheses (as well as many positions in between).  And even if widespread "Near Eastern" genetic markers could be established beyond any doubt - as yet far from the case - it doesn't necessarily imply "massive waves" if one assumed that Mesolithic population levels in Europe were not enormous to begin with.

Quote from: Queequeg on January 06, 2016, 11:23:09 AM
This is reflected in some sense in my own heritage.  My mom's family is, if you go back far enough, from NE/NC England, the old Danelaw, and that's probably the reason I'm tall and blonde. 

Quote from: jimmy olsen on January 05, 2016, 11:16:37 PM
Because we've met in person?  :huh:

Also, you're not shy about your German heritage.

Quote from: The Minsky Moment on January 06, 2016, 06:38:02 PM
Scale is relative to a point.

Imagine a scenario where small groups of cultivators are gradually drifting west, towards "virgin lands." If you also assume these people have a technological advantage that permits higher reproduction rates, then over the course of a couple thousand years there can be a significant infusion of new genetic types.  But it's hard to call such a scenario "waves of mass migration" with a straight face.

Quote from: Malthus on January 07, 2016, 04:23:48 PM

Quote from: The Minsky Moment on January 06, 2016, 06:38:02 PM
Scale is relative to a point.

Imagine a scenario where small groups of cultivators are gradually drifting west, towards "virgin lands." If you also assume these people have a technological advantage that permits higher reproduction rates, then over the course of a couple thousand years there can be a significant infusion of new genetic types.  But it's hard to call such a scenario "waves of mass migration" with a straight face.

No one ever theorizes from the DNA evidence that some folks were just hotter than others.  :D Mesolithic rock stars, if you will.  ;)

Quote from: Razgovory on January 07, 2016, 07:27:42 PM
Really?  Try and think harder.

Quote from: jimmy olsen on January 07, 2016, 07:31:31 PM

Quote from: Razgovory on January 07, 2016, 07:27:42 PM
Really?  Try and think harder.

There's no benifit to having blue eyes over brown.

QuoteÖtzi the Iceman's Stomach Bacteria Offers Clues on Human Migration

An insight into the peopling of Europe has emerged from an unlikely source — the stomach contents of a 5,300-year-old body pulled from a thawing glacier in the eastern Italian Alps.

Since his discovery in 1991, Ötzi the Iceman, as he was named, has provided a trove of information about the life of Europeans at that time. His long-frozen tissues have now yielded another surprise: Scientists have been able to recover from his stomach samples of Helicobacter pylori, a bacterium that infects about half the human population and can occasionally cause stomach ulcers.

The bacterium is transmitted only through intimate contact, and its distribution around the world matches almost perfectly the distribution of human populations. The bacterium's genetic variations are therefore used by researchers as a supplement to human genetics in tracking ancient human migrations.

Researchers led by Frank Maixner and Albert Zink of the Institute for Mummies and the Iceman, at the European Research Academy in Bolzano, Italy, reported on Thursday in Science that they had been able to reconstruct the entire DNA sequence of the ulcer bacterium from samples taken from the iceman's stomach.

Modern-day Europeans carry a type of H. pylori that is a hybrid of two ancient strains, one of which originated somewhere in Eurasia and the other in Africa, after modern humans first left that continent about 50,000 years ago.

One theory is that this hybridization occurred in the Middle East before or during the Last Glacial Maximum, a catastrophically cold period during the last ice age when glaciers swept south and made much of Europe uninhabitable.

After the glaciers began to retreat, about 20,000 years ago, people from the Middle East and other southern refuges moved north to recolonize Europe. It could have been these migrants who brought the hybridized ulcer bacterium to Europe.

Yet the ulcer bacterium from Ötzi is related only to the Eurasian strain, the researchers found, implying that hybridization with the African strain must have occurred much later, within the last 5,000 years.

The finding suggests that it may have been the first farmers, who brought the agricultural revolution to Europe from the Middle East starting about 8,000 years ago, who were the carriers of the African strain, said Yoshan Moodley of the University of Venda in South Africa, a co-author of the new report.

Reconstructing the history of human pathogens, a new science made possible by the ability to decode DNA molecules many thousands of years old, can yield deep insights into both medicine and history. Last October a team led by Eske Willerslev of the University of Copenhagen extracted Yersinia pestis, the plague bacterium, from human teeth up to 5,000 years old.

The plague bacterium, spread by fleas and rats, caused three devastating pandemics — the Justinian plague of the sixth century, the Black Death in 14th-century Europe and the global pandemic that erupted in the 1890s.

Mark Achtman, a leading expert on ancient pathogens at the University of Warwick in England, said that the authors of the Ötzi paper had done well to extract the ulcer bacterium from the iceman, but that it was difficult to infer from a single sample anything about the bacterium's distribution in Europe 5,000 years ago.

Besides looking at the DNA of the ulcer bacterium, the authors also found proteins in the iceman's stomach that are involved in inflammation, but the stomach is too poorly preserved to confirm that he suffered from gastric disease.

QuoteAfter the glaciers began to retreat, about 20,000 years ago, people from the Middle East and other southern refuges moved North

Quote from: The Brain on January 08, 2016, 06:12:13 AM

QuoteAfter the glaciers began to retreat, about 20,000 years ago, people from the Middle East and other southern refuges moved North

We can only imagine what this must have looked like.

Quote from: The Brain on January 08, 2016, 06:12:13 AM

QuoteAfter the glaciers began to retreat, about 20,000 years ago, people from the Middle East and other southern refuges moved North

We can only imagine what this must have looked like.

Quote from: Caliga on January 08, 2016, 03:28:36 PM
vaguely related: I found a death certificate for one of my distant great uncles and he died from anthrax.  Next I expect to find an ancestor who died in the iron maiden. :punk:

Quote from: Caliga on January 18, 2016, 06:22:55 PM
So I have my DNA analysis results and have been attention whoring about them on Facebook all day. :)

Quote from: Caliga on January 18, 2016, 06:22:55 PM
So I have my DNA analysis results and have been attention whoring about them on Facebook all day. :)

Quote from: katmai on January 18, 2016, 06:42:38 PM

Quote from: Caliga on January 18, 2016, 06:22:55 PM
So I have my DNA analysis results and have been attention whoring about them on Facebook all day. :)

If i find out we are closely related i'm be so pissed.

Quote from: Caliga on January 18, 2016, 06:43:24 PM

Quote from: katmai on January 18, 2016, 06:42:38 PM

Quote from: Caliga on January 18, 2016, 06:22:55 PM
So I have my DNA analysis results and have been attention whoring about them on Facebook all day. :)

If i find out we are closely related i'm be so pissed.

You'd need to take a DNA test too for us to find that out dawg.

Quote from: Caliga on January 18, 2016, 06:42:55 PM
@Tim We're friended on Facebook. :sleep:

Quote from: crazy canuck on January 18, 2016, 07:04:10 PM

Quote from: Caliga on January 18, 2016, 06:42:55 PM
@Tim We're friended on Facebook. :sleep:

And for those of us who don't use facebook?

Quote from: katmai on January 18, 2016, 06:44:53 PM
Um i have, hence my last comment. I'm only 8% from Iberian peninsula.

Quote from: crazy canuck on January 18, 2016, 07:04:10 PM
And for those of us who don't use facebook?

Quote from: Caliga on January 18, 2016, 08:06:47 PM

Quote from: crazy canuck on January 18, 2016, 07:04:10 PM
And for those of us who don't use facebook?

I'll make a followup post in TBR. :)

Quote from: Caliga on January 18, 2016, 08:06:23 PM

Quote from: katmai on January 18, 2016, 06:44:53 PM
Um i have, hence my last comment. I'm only 8% from Iberian peninsula.

:huh: Do you have an Ancestry account?

Quote
Phylogenetic analyses suggests fairy tales are much older than thought
January 20, 2016 by Bob Yirka

(Phys.org)—A pair of researchers has conducted a phylogenetic analysis on common fairy tales and has found that many of them appear to be much older than has been thought. In their paper published in Royal Society Open Science, Sara Graça da Silva, a social scientist/folklorist with New University of Lisbon and Jamshid Tehrani, an anthropologist with Durham University describe the linguistic study they carried out and why they believe at least one fairy tale had its origins in the Bronze Age.

Fairy tales are popular the world over, some so much that they have crossed over into multiple societies—Beauty and the Beast for example, has been told in one form or another across the globe. Modern linguists and anthropologists have set the origin of most such fairy tales to just prior to the time they were written down, which would make them several hundred years old. But this new research suggests they are much older than that, with some going back thousands of years.

To come to these conclusions, the researchers applied a technique normally used in biology—building phylogenetic trees to trace linguistic attributes back to their origin. They started with 275 fairy tales, each rooted in magic, and whittled them down to 76 basic stories. Trees were then built based on Indo-European languages, some of which have gone extinct. In so doing, the researchers found evidence that some fairy tales, such as Jack and the Beanstalk, were rooted in other stories, and could be traced back to a time when Western and Eastern Indo-European languages split, which was approximately 5,000 years ago, which means of course that they predate the Bible, for example, or even Greek myths.

The researchers placed confidence factors on different results, depending on how strong the trees were that could be built—some were obviously less clear than others, but one fairy tale in particular, they note, was very clear—called The Smith and The Devil, they traced it back approximately 6,000 years, to the Bronze Age.

Notably, Wilhelm Grimm, of the famous Grimm brothers who published many fairy tales back in 1812, wrote that he believed the tales were many thousands of years old—that notion was discredited not long after, but now, the researchers suggest, they believe he was right all along.

Quote from: jimmy olsen on January 21, 2016, 05:42:03 PM
:huh: Six thousand years ago predates the bronze age.

Quote
The researchers placed confidence factors on different results, depending on how strong the trees were that could be built—some were obviously less clear than others, but one fairy tale in particular, they note, was very clear—called The Smith and The Devil, they traced it back approximately 6,000 years, to the Bronze Age.

Quote from: PRC on January 21, 2016, 05:52:57 PM

Quote from: jimmy olsen on January 21, 2016, 05:42:03 PM
:huh: Six thousand years ago predates the bronze age.

The article doesn't say anything about 6,000 years predating the bronze age.

Quote
The researchers placed confidence factors on different results, depending on how strong the trees were that could be built—some were obviously less clear than others, but one fairy tale in particular, they note, was very clear—called The Smith and The Devil, they traced it back approximately 6,000 years, to the Bronze Age.

Quote from: jimmy olsen on January 21, 2016, 05:59:49 PM
I'm saying it.

It doesn't make sense for there have to been a myth about magic smiths at the time if bronze working hadn't been invented yet.

Quote from: The Minsky Moment on January 21, 2016, 06:07:00 PM

Quote from: jimmy olsen on January 21, 2016, 05:59:49 PM
I'm saying it.

It doesn't make sense for there have to been a myth about magic smiths at the time if bronze working hadn't been invented yet.

There I have to disagree, as copper smelting probably existed at that time.

Quote

In some cases, it may also be possible to evaluate inferences about ancestral tale corpora in relation to other sources of information about past societies, such as historical, archaeological, linguistic and genetic data. Our findings regarding the origins of ATU 330 'The Smith and the Devil' are a case in point. The basic plot of this tale—which is stable throughout the Indo-European speaking world, from India to Scandinavia—concerns a blacksmith who strikes a deal with a malevolent supernatural being (e.g. the Devil, Death, a jinn, etc.). The smith exchanges his soul for the power to weld any materials together, which he then uses to stick the villain to an immovable object (e.g. a tree) to renege on his side of the bargain [26]. The likely presence of this tale in the last common ancestor of Indo-European-speaking cultures resonates strongly with wider debates in Indo-European prehistory, since it implies the existence of metallurgy in Proto-Indo-European society. This inference is consistent with the so-called 'Kurgan hypothesis', which links the origins of the Indo-European language family to archaeological and genetic evidence of massive territorial expansions made by nomadic pastoralist tribes from the Pontic steppe 5000–6000 years ago [3,46–48]. The association of these peoples with a Bronze Age technological complex, as reconstructed from material culture data [49] and palaeo-linguistic inferences of PIE vocabulary (which include a putative word for metal, a⌢ios) [50], suggests a plausible context for the cultural evolution of a tale about a cunning smith who attains a superhuman level of mastery over his craft.  By contrast, the presence of this story in PIE society appears to be incompatible with the alternative 'Anatolian hypothesis' of Indo-European origins. The latter proposes a much earlier and more gradual process of demic diffusion associated with the spread of agriculture from Neolithic Anatolia 8000–9000 years ago [51]—prior to the invention of metallurgy. However, it should be noted that according to some variants of the model [2,52], the lineage leading to all surviving Indo-European languages may have diverged from the now extinct Anatolian languages as recently as 7000–5500 B.C.E, a range which overlaps with the earliest archaeological evidence for smelting at numerous sites in Eurasia [53]. Consequently, a Bronze Age origin for ATU 330 seems plausible under both major models of Indo-European prehistory.

Quote from: jimmy olsen on November 27, 2015, 03:48:04 AM

Quote from: Queequeg on November 27, 2015, 03:42:37 AM
The Anatolian hypothesis is primarily linguistic.  And it's rubbish.

Who do you think speaks a language? Who spreads it?

It's people of course.

The farmers of Anatolia colonized Europe, overwhelming the natives with the numbers and assimilating them. They doubtlessly brought their language with them.

Quote from: Siege on February 24, 2016, 08:22:56 AM
I was under the impression that farming spread through the adoption of the technology by imitation, not through migration.

Quote from: The Minsky Moment on February 24, 2016, 10:45:38 AM

Quote from: Siege on February 24, 2016, 08:22:56 AM
I was under the impression that farming spread through the adoption of the technology by imitation, not through migration.

Both happen.
Migration is a significant phenomenon historically, always has been.

Where the debate centers around is Jimmy-like claims of "masses" of migrants overwhelming indigenous populations demographically.  My 2c is that can happen but it isn't the common pattern.  There are plenty of historical examples where linguistic and cultural change is driven by relatively small numbers of migrants.
E.g. the spread of English to the US and Australia are examples of linguistic change through mass migration and demographic overpowering.
But the spread of English to the British Isles or to India is an example of minority migration and cultural influence. That is more typical in the pre-modern world because of the logistical challenges involved in mass population movements.

Quote from: Caliga on March 23, 2016, 09:45:29 PM
I had my mother do a DNA test also and the results just came back.  She is nearly 50% Scandinavian. :hmm:

QuoteNuclear DNA sequences from the Middle Pleistocene Sima de los Huesos hominins

A unique assemblage of 28 hominin individuals, found in Sima de los Huesos in the Sierra de Atapuerca in Spain, has recently been dated to approximately 430,000 years ago1. An interesting question is how these Middle Pleistocene hominins were related to those who lived in the Late Pleistocene epoch, in particular to Neanderthals in western Eurasia and to Denisovans, a sister group of Neanderthals so far known only from southern Siberia. While the Sima de los Huesos hominins share some derived morphological features with Neanderthals, the mitochondrial genome retrieved from one individual from Sima de los Huesos is more closely related to the mitochondrial DNA of Denisovans than to that of Neanderthals2. However, since the mitochondrial DNA does not reveal the full picture of relationships among populations, we have investigated DNA preservation in several individuals found at Sima de los Huesos. Here we recover nuclear DNA sequences from two specimens, which show that the Sima de los Huesos hominins were related to Neanderthals rather than to Denisovans, indicating that the population divergence between Neanderthals and Denisovans predates 430,000 years ago. A mitochondrial DNA recovered from one of the specimens shares the previously described relationship to Denisovan mitochondrial DNAs, suggesting, among other possibilities, that the mitochondrial DNA gene pool of Neanderthals turned over later in their history.

Quote from: Tamas on March 24, 2016, 05:57:10 AM
How do you guys know this whole thing isn't just a scam where they just have a random generator tell you something about your "ancestry"?

Quote from: Caliga on March 25, 2016, 06:09:10 AM
to distinguish someone from Lesotho from someone from Switzerland.

Quote
Neandertal sex acts are beyond counting 

21 Mar 2016

I've given a lot of thought over the years to the genetic ties between today's people and ancient populations. Just last month, I wrote a lot about the relationships of Neandertal and modern human populations ("Earlier mixture from modern humans into Neandertal populations"). Last week, three new papers came out that bear heavily on this topic, and I've been writing quite a lot more.

I've seen a widespread misconception about Neandertal sex. I follow many professional colleagues on Facebook, some of whom are highly respected for their work but maybe not so up-to-date on genetic methods. I have seen a few of them taking up this misconception and spreading it through their professional networks. I won't point to those social media posts here, because their authors did not intend them for widespread distribution, but I do want to address the misconception.

Their idea is that geneticists are trying to count the number of sexual encounters between modern humans and Neandertals. Not the number of contacts between populations, but an actual coital count. Like they are reading the credits of a porno movie.

Neandertal sex scene
Image by Elisabeth Daynes, via Illustreret Videnskab

Where did they get such a kooky idea?

Unfortunately, when writers have discussed Neandertal and Denisovan introgression, it is common to see them refer to a "distinct number of matings" or some similar phrasing. For example, in Science last week, the excellent Ann Gibbons wrote:

By developing powerful new statistical methods, an international team has identified how often and on which continents modern humans, Neandertals, and a second kind of archaic human called Denisovans met and mated. The researchers conclude that if you're an East Asian, you have three Neandertals in your family tree; Europeans and South Asians have two, and Melanesians only one.

"Three Neandertals in your family tree" makes it sound as if only three Neandertal individuals were part of the ancestry of any human populations today. The message is unfortunately reinforced by the headline (and I know writers do not usually choose their headlines):

Five matings for moderns, Neandertals

Again, that emphasizes the idea that somebody is counting marriages, or couplings, or some discrete number of coital episodes.

This is a misconception. Nobody is counting the "matings" between Neandertals and modern human populations.

Gibbons elsewhere refers to a "rich sexual history" of humans and Neandertals, which is a phrase I like quite a lot. But some anthropologists, confused by the misconception about counting the matings, noted that five matings is hardly a rich history!

In fact, we do not know how many sex acts are represented by the Neandertal ancestry within human genomes. The question itself reflects a kind of biblical, pre-evolutionary thinking. The underlying assumption is that races spring from individuals, like Ham, Shem and Japheth, and so the sex acts of a few individuals can explain the phylogenetic patterns of later populations. This is false, three episodes of Neandertal coitus cannot account for the present distribution of Neandertal genes in living populations.

Meeting between Esau and Jacob
Meeting between Esau and Jacob, by Raffaellino Bottalla. Esau chose his wives from among the Hittites.

We have a fairly clear idea of what fraction of the ancestry of today's people came from Neandertals; this fraction was around about 2% for most people worldwide, a bit more for many of the populations of East Asia, and very little for most populations of sub-Saharan Africa today. Vernot and colleagues' new paper (Science 10.1126/science.aad9416) helps to confirm that the elevation of Neandertal genetic similarity among East Asian populations is the result of additional mixture that does not characterize the ancestry of today's western Eurasian populations. The authors further infer that all of today's Eurasian samples share evidence of Neandertal mixture above and beyond that present in today's Melanesian populations. By showing that there are at least three different levels of Neandertal ancestry in different populations, with partially non-overlapping haplotype distributions, they have demonstrated that admixture must have occurred at a minimum of three places and times, among ancestors of three different subsets of today's people.

How many hybrids?

I'm going to do some napkin calculations about the number of individuals necessary to deliver our Neandertal ancestry. How many hybrids do we need? The exercise is unrealistic because we have to make some assumptions that I find to be unjustifiable. But it's easy to show that the answer is a lot more than three, and probably is more than a few thousand.

Who were hybrids? First, let's assume that Neandertal genes came into the modern population only through the vehicle of Neandertal-modern F1 hybrids who were uniformly 50% Neandertal. This corresponds to the minimum possible amount of interbreeding between the two varieties, and the assumption rules out staged admixture, substantial modern gene flow into Neandertals, and long-term gene flow between African and Neandertal populations as they originated. I'm unwilling to rule out these alternative scenarios. All of these alternatives would tend to increase the amount of interbreeding necessary to account for today's ancestry fraction from Neandertals. I also recognize that many people wouldn't use the term "hybrid" at all for these individuals.

Effective population size. We further have to assume something about the proportion of effective population size to census population size. The effective size of a population is a measure of the rate of genetic drift it experiences; this rate is determined in part by nonrandom mating within the population and in part by its size. The contribution of nonrandom mating means that the effective size is usually different from the number of breeding individuals, it may be quite a lot smaller. I have a great book chapter explaining this concept in more detail on Academia.edu, if you are interested in how we relate genetics to population sizes.

The concept of effective population size allows geneticists to use the "effective" number to talk about drift and loss of variation without needing to know the exact ratio of genetic variation to the true, or census, population size. But in the case of hybridization and introgression, drift may often have a different effect on the hybrids than it does on the population at large. This makes it difficult to estimate the ratio of hybrid to non-hybrid individuals even when we know the genetic effect of the hybrids. For simplicity, I'll again go with an unrealistic assumption: that the ratio of effective to census numbers is the same for the hybrids as it is for the modern population as a whole.

Initial admixture. Let's consider first the population that gave rise to all modern humans outside Africa today. If the mixing with Neandertals had been instantaneous, in a single generation, that generation would have included approximately 4% F1 Neandertal hybrids.

The effective size of the ancestral non-African modern population at the moment of such mixture was small relative to today's populations. Indeed, our best models suggest that the effective size of this population may have been as small as 10,000 effective individuals at one point. This is what is usually termed the "genetic bottleneck" leading to the settlement of areas outside Africa. We do not know that this genetic bottleneck was really a single reduction in numbers, but clearly this ancestral population was separated from sub-Saharan African populations for some time and underwent substantial genetic drift, which may even reflect multiple events over time.

Importantly, there is no sign that the population was ever much smaller than 10,000 effective individuals, and that puts a lower limit on the number of hybrids that must have been introduced into this population to account for the Neandertal ancestry of its descendants.  If these ancestors mixed with Neandertals during the minimum of such a bottleneck, then the effective number of F1 hybrids responsible for this mixture may have been as small as 400. But if mixture happened at some other time than the minimum, or if mixture happened over some longer period of time, then the effective number of F1 hybrids must have been larger, possibly more than an order of magnitude larger.

Later admixture. The same considerations apply to the ancestral populations that led to western Eurasian (south Asian and European) and East Asian population samples, each of which experienced additional admixture from Neandertals. The additional Neandertal ancestry present in today's East Asian populations would have required another 1-2% F1 hybrid representation in their ancestral population.

Interestingly, the number of F1 hybrids underlying the small bump in Neandertal ancestry in East Asians might actually be greater than the number underlying the initial mixture within the common ancestral population of all non-African populations. This is because the effective number of F1 hybrids necessary for this later admixture again depends on the effective sizes of these populations. The genetic data suggest that these ancestral populations experienced a lower level of drift when compared to their common out-of-Africa ancestor. This may mean a larger effective population size for these East Asian and other populations, a population in which 1-2% F1 Neandertal hybrids may have actually been many hundreds or thousands of individuals, not the 100-200 that would correspond to a very small effective size.

But none of these effective numbers are actually known, and I have little confidence that we can estimate them from today's simplistic population models. All of them almost certainly grew over time, so that the timing of mixture makes a large difference to how we estimate the number of hybrids that contributed to it. Early hybrids probably made a much larger relative difference than later ones.

We cannot talk about effective numbers of F1 hybrids without recognizing that the effective sizes of human populations are substantially smaller than their census sizes. If the relation is the same for Neandertal-modern hybrids, then we may be looking at several true individuals for every "effective" individual. For a total effective number of 600-1000 F1 hybrid individuals, which is a bare minimum, this might mean upward of 2000-3000 actual F1 hybrids. But then all of my assumptions to this point have been unrealistic, all minimizing the extent of interbreeding between populations. In reality, many more individuals must have been mating, over a much longer span of time than a single generation.

Some of these hybrids were the products of Neandertal love affairs. Many were the daughters and sons of Neandertal wives or husbands who spent long passionate lives with modern mates. Some were likely the children of captured Neandertal slaves. Some were siblings, so the number of Neandertal mothers or fathers was to some extent smaller than the number of hybrids introduced into modern populations.

So if you ask me how many hybrid individuals may have been direct ancestors of today's populations, I think the number is minimally close to a thousand and likely many thousands. And if you ask me how many Neandertal sex acts took place, I suppose I'll smile and ask, "Who wants to know?"

Quote from: Tamas on March 24, 2016, 05:57:10 AM
How do you guys know this whole thing isn't just a scam where they just have a random generator tell you something about your "ancestry"?

Quote from: Caliga on April 05, 2016, 08:15:07 PM
I exchanged DNA with a chick I work with (not the same one I mentioned earlier).

Quote from: Caliga on April 05, 2016, 08:15:07 PM
I exchanged DNA with a chick I work with

Quote from: Caliga on March 23, 2016, 09:45:29 PM
I had my mother do a DNA test also and the results just came back.  She is nearly 50% Scandinavian. :hmm:

Also, there is this guy in my hometown who is an annoying old curmudgeonly nerd who my parents can't stand.  It turns out he is her third cousin. :lol:  She will not be pleased to find this out.

Quote from: Tyr on April 06, 2016, 03:38:26 PM
I really am curious to get it done. But just can't bring myself to blow 120 on it when it'll be a fraction of that in a few years.
Plus that you are their main product ala Google et al, yet you're paying them for you giving them your data.

Quote
I wonder. Why did you get your mother to do it?
I thought the results were able to show your paternal and maternal line.

Quote from: Caliga on April 06, 2016, 03:42:58 PM

Quote from: Tyr on April 06, 2016, 03:38:26 PM
I really am curious to get it done. But just can't bring myself to blow 120 on it when it'll be a fraction of that in a few years.
Plus that you are their main product ala Google et al, yet you're paying them for you giving them your data.

You make a good point.  The cost of this has been coming down steadily as more services pop up, and will probably drop more still.

Quote
I wonder. Why did you get your mother to do it?
I thought the results were able to show your paternal and maternal line.

No, the results cannot distinguish what portion of your DNA came from your mother vs. your father.

Quote from: Caliga on April 06, 2016, 05:26:05 PM
:hmm:

Quote from: jimmy olsen on April 06, 2016, 07:42:53 PM

Quote from: Caliga on April 06, 2016, 05:26:05 PM
:hmm:

I seem to recall reading scientifc papers of ancient genomes where they can tell which parental line certain genes came from, whether that was more specific outside parental line a and b outside the sex chromosomes, I can't recall.

QuoteThe Ancestry test is notorious for overestimating Scandinavian ancestry.  I guess maybe their test pool for 'Scandinavia' was too generic or something.  I know some of my English ancestry comes from areas settled by Scandinavians, so I was expecting that result (and all of my English ancestry is on my mother's side, so her much higher result than mine also makes sense).

Quote from: Queequeg on April 07, 2016, 10:52:22 AM
Doesn't this make a lot of sense?  Differentiating from Saxons in southern Denmark and Danes from Denmark and Celts from Bavaria must not be incredibly easy.

Quote from: The Brain on April 07, 2016, 12:13:00 PM
They have to make a living. No one wants to be a fucking Saxon or Bavarian.

Quote from: Queequeg on April 07, 2016, 10:52:22 AM

QuoteThe Ancestry test is notorious for overestimating Scandinavian ancestry.  I guess maybe their test pool for 'Scandinavia' was too generic or something.  I know some of my English ancestry comes from areas settled by Scandinavians, so I was expecting that result (and all of my English ancestry is on my mother's side, so her much higher result than mine also makes sense).

Doesn't this make a lot of sense?  Differentiating from Saxons in southern Denmark and Danes from Denmark and Celts from Bavaria must not be incredibly easy.

Quote from: Archy on April 08, 2016, 04:43:48 PM
Not much sense for me doing such a test, 100% west European mutt aka Belgian

Quote from: Ed Anger on April 08, 2016, 08:12:48 PM
I'm 100% asshole.

QuoteFathered by the Mailman? It's Mostly an Urban Legend
MATTER

Five days a week, you can tune into "Paternity Court," a television show featuring couples embroiled in disputes over fatherhood. It's entertainment with a very old theme: Uncertainty over paternity goes back a long way in literature. Even Shakespeare and Chaucer cracked wise about cuckolds, who were often depicted wearing horns.

But in a number of recent studies, researchers have found that our obsession with cuckolded fathers is seriously overblown. A number of recent genetic studies challenge the notion that mistaken paternity is commonplace.

"It's absolutely ridiculous," said Maarten H.D. Larmuseau, a geneticist at the University of Leuven in Belgium who has led much of this new research.

The term cuckold traditionally refers to the husband of an adulteress, but Dr. Larmuseau and other researchers focus on those cases that produce a child, which scientists politely call "extra-pair paternity."

Until the 20th century, it was difficult to prove that a particular man was the biological father of a particular child.

In 1304 a British husband went to court to dispute the paternity of his wife's child, born while he was abroad for three years. Despite the obvious logistical challenges, the court rejected the husband's objection.

"The privity between a man and his wife cannot be known," the judge ruled.

Modern biology lifted the veil from this mystery, albeit slowly. In the early 1900s, researchers discovered that people have distinct blood types inherited from their parents.

In a 1943 lawsuit, Charlie Chaplin relied on blood-type testing to prove that he was not the father of the actress Joan Barry's child. (The court refused to accept the evidence and forced Chaplin to pay child support anyway.)

It wasn't until DNA sequencing emerged in the 1990s that paternity tests earned the legal system's confidence. Labs were able to compare DNA markers in children to those of their purported fathers to see if they matched.

As the lab tests piled up, researchers collated the results and came to a startling conclusion: Ten percent to 30 percent of the tested men were not the biological fathers of their children.

Those figures were spread far and wide, ending up in many science books. But the problem with the lab data, Dr. Larmuseau said, was that it didn't come from a random sample of people. The people who ordered the tests already had reason to doubt paternity.

Dr. Larmuseau and other scientists developed other methods to get an unbiased look at cuckoldry.

In a 2013 study, Dr. Larmuseau and his colleagues used Belgium's detailed birth records to reconstruct large family genealogies reaching back four centuries. Then the scientists tracked down living male descendants and asked to sequence their Y chromosomes.

Y chromosomes are passed down in almost identical form from fathers to sons. Men who are related to the same male ancestor should also share his Y chromosome, providing that some unknown father didn't introduce his own Y somewhere along the way.

Comparing the chromosomes of living related men, Dr. Larmuseau and his colleagues came up with a cuckoldry rate of less than 1 percent. Similar studies have generally produced the same low results in such countries as Spain, Italy and Germany, as well as agricultural villages in Mali.

The scientists got the same results after trying a different tack. They studied men in Flanders, a part of Belgium to which French people emigrated in the late 1500s.

The Y chromosomes in Flemish men with French surnames, the researchers found, had the same genetic markers found in men who live today in the region of France where their ancestors originated. Had there had been a lot of cuckoldry over the centuries, the link between genetics and surnames should have been weaker, or disappeared altogether.

In a commentary in Trends in Ecology and Evolution, Dr. Larmuseau and his colleagues argue that it's long past time to toss out frequent cuckoldry as a myth. Studies relying on different methods in different cultures all point to cuckoldry rates of about 1 percent.

And because many of those studies are based on genealogies that reach back many generations, he argues, these rates must have been low for at least several centuries.

Beverly I. Strassmann, a University of Michigan anthropologist who gathered the data on paternity rates in Mali, agreed that widespread cuckoldry "was an urban legend. It seemed to have a life of its own."

The New York Times
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Science
Fathered by the Mailman? It's Mostly an Urban Legend

    87

Photo illustration by Stephen Webster
April 8, 2016
Carl Zimmer
Carl Zimmer
MATTER

Five days a week, you can tune into "Paternity Court," a television show featuring couples embroiled in disputes over fatherhood. It's entertainment with a very old theme: Uncertainty over paternity goes back a long way in literature. Even Shakespeare and Chaucer cracked wise about cuckolds, who were often depicted wearing horns.

But in a number of recent studies, researchers have found that our obsession with cuckolded fathers is seriously overblown. A number of recent genetic studies challenge the notion that mistaken paternity is commonplace.

"It's absolutely ridiculous," said Maarten H.D. Larmuseau, a geneticist at the University of Leuven in Belgium who has led much of this new research.

The term cuckold traditionally refers to the husband of an adulteress, but Dr. Larmuseau and other researchers focus on those cases that produce a child, which scientists politely call "extra-pair paternity."

Until the 20th century, it was difficult to prove that a particular man was the biological father of a particular child.

In 1304 a British husband went to court to dispute the paternity of his wife's child, born while he was abroad for three years. Despite the obvious logistical challenges, the court rejected the husband's objection.

"The privity between a man and his wife cannot be known," the judge ruled.

Modern biology lifted the veil from this mystery, albeit slowly. In the early 1900s, researchers discovered that people have distinct blood types inherited from their parents.

In a 1943 lawsuit, Charlie Chaplin relied on blood-type testing to prove that he was not the father of the actress Joan Barry's child. (The court refused to accept the evidence and forced Chaplin to pay child support anyway.)

Interactive Feature | A Week of Misconceptions We're using the first week of April as an opportunity to debunk some of the misconceptions about health and science that circulate all year round.

It wasn't until DNA sequencing emerged in the 1990s that paternity tests earned the legal system's confidence. Labs were able to compare DNA markers in children to those of their purported fathers to see if they matched.

As the lab tests piled up, researchers collated the results and came to a startling conclusion: Ten percent to 30 percent of the tested men were not the biological fathers of their children.

Those figures were spread far and wide, ending up in many science books. But the problem with the lab data, Dr. Larmuseau said, was that it didn't come from a random sample of people. The people who ordered the tests already had reason to doubt paternity.

Dr. Larmuseau and other scientists developed other methods to get an unbiased look at cuckoldry.

In a 2013 study, Dr. Larmuseau and his colleagues used Belgium's detailed birth records to reconstruct large family genealogies reaching back four centuries. Then the scientists tracked down living male descendants and asked to sequence their Y chromosomes.

Y chromosomes are passed down in almost identical form from fathers to sons. Men who are related to the same male ancestor should also share his Y chromosome, providing that some unknown father didn't introduce his own Y somewhere along the way.

Comparing the chromosomes of living related men, Dr. Larmuseau and his colleagues came up with a cuckoldry rate of less than 1 percent. Similar studies have generally produced the same low results in such countries as Spain, Italy and Germany, as well as agricultural villages in Mali.

The scientists got the same results after trying a different tack. They studied men in Flanders, a part of Belgium to which French people emigrated in the late 1500s.

The Y chromosomes in Flemish men with French surnames, the researchers found, had the same genetic markers found in men who live today in the region of France where their ancestors originated. Had there had been a lot of cuckoldry over the centuries, the link between genetics and surnames should have been weaker, or disappeared altogether.

In a commentary in Trends in Ecology and Evolution, Dr. Larmuseau and his colleagues argue that it's long past time to toss out frequent cuckoldry as a myth. Studies relying on different methods in different cultures all point to cuckoldry rates of about 1 percent.

And because many of those studies are based on genealogies that reach back many generations, he argues, these rates must have been low for at least several centuries.

Beverly I. Strassmann, a University of Michigan anthropologist who gathered the data on paternity rates in Mali, agreed that widespread cuckoldry "was an urban legend. It seemed to have a life of its own."

The evidence of low rates of cuckoldry comes not just from gene studies, she noted. In species where females mate with many males, the males tend to evolve sperm that are good at competing for fertilization. The males may produce large amounts of sperm, for example, and a high percentage swim well.

Humans, however, don't rate in the sperm department.

"It's of amazingly low quality," Dr. Strassmann said. "Half the sperm can be duds; they can have two heads; they can be defective in all sorts of ways."

The only way for men to have evolved comparatively ineffectual sperm, she added, was for them to have experienced high rates of paternity over time.

It's not that widespread cuckoldry doesn't exist in some cultures, Dr. Larmuseau said. Some South American tribes with high rates share a belief that more than one man can contribute to the formation of a fetus.

But Dr. Larmuseau suspects that these populations are the exception, not the rule. Humans have evolved to avoid cuckoldry, he said, because of our peculiar biology.

Human infants are born quite helpless, compared with the newborns of other animals, and they need a lot of food over a long period to fuel the growth of their calorie-hungry brains. Mothers needed fathers to help find the food.

"Babies really need good investment from the fathers," Dr. Larmuseau said, "and the paternity has to be very sure in order for them to make those investments."

Quote

Everything we know about how wolves became dogs

Ed Yong, The Atlantic

Jun. 4, 2016, 6:55 PM
   

Tens of thousands of years ago, before the internet, before the Industrial Revolution, before literature and mathematics, bronze and iron, before the advent of agriculture, early humans formed an unlikely partnership with another animal—the grey wolf. The fates of our two species became braided together.

The wolves changed in body and temperament. Their skulls, teeth, and paws shrank.

Their ears flopped. They gained a docile disposition, becoming both less frightening and less fearful. They learned to read the complex expressions that ripple across human faces. They turned into dogs.

Today, dogs are such familiar parts of our lives—our reputed best friends and subject of many a meme—that it's easy to take them, and what they represent, for granted.

Dogs were the first domesticated animals, and their barks heralded the Anthropocene. We raised puppies well before we raised kittens or chickens; before we herded cows, goats, pigs, and sheep; before we planted rice, wheat, barley, and corn; before we remade the world.



"Remove domestication from the human species, and there's probably a couple of million of us on the planet, max," says archaeologist and geneticist Greger Larson. "Instead, what do we have? Seven billion people, climate change, travel, innovation and everything. Domestication has influenced the entire earth. And dogs were the first." For most of human history, "we're not dissimilar to any other wild primate.

We're manipulating our environments, but not on a scale bigger than, say, a herd of African elephants. And then, we go into partnership with this group of wolves. They altered our relationship with the natural world."

Larson wants to pin down their origins. He wants to know when, where, and how they were domesticated from wolves. But after decades of dogged effort, he and his fellow scientists are still arguing about the answers. They agree that all dogs, from low-slung corgis to towering mastiffs, are the tame descendants of wild ancestral wolves. But everything else is up for grabs.

Some say wolves were domesticated around 10,000 years ago, while others say 30,000. Some claim it happened in Europe, others in the Middle East, or East Asia. Some think early human hunter-gatherers actively tamed and bred wolves. Others say wolves domesticated themselves, by scavenging the carcasses left by human hunters, or loitering around campfires, growing tamer with each generation until they became permanent companions.

Dogs were domesticated so long ago, and have cross-bred so often with wolves and each other, that their genes are like "a completely homogenous bowl of soup," Larson tells me, in his office at the University of Oxford. "Somebody goes: what ingredients were added, in what proportion and in what order, to make that soup?" He shrugs his shoulders. "The patterns we see could have been created by 17 different narrative scenarios, and we have no way of discriminating between them."



The only way of doing so is to look into the past. Larson, who is fast-talking, eminently likable, and grounded in both archaeology and genetics, has been gathering fossils and collaborators in an attempt to yank the DNA out of as many dog and wolf fossils as he can. Those sequences will show exactly how the ancient canines relate to each other and to modern pooches. They're the field's best hope for getting firm answers to questions that have hounded them for decades.

And already, they have yielded a surprising discovery that could radically reframe the debate around dog domestication, so that the big question is no longer when it happened, or where, but how many times.

On the eastern edge of Ireland lies Newgrange, a 4,800-year-old monument that predates Stonehenge and the pyramids of Giza. Beneath its large circular mound and within its underground chambers lie many fragments of animal bones. And among those fragments, Dan Bradley from Trinity College Dublin found the petrous bone of a dog.

Press your finger behind your ear. That's the petrous. It's a bulbous knob of very dense bone that's exceptionally good at preserving DNA. If you try to pull DNA out of a fossil, most of it will come from contaminating microbes and just a few percent will come from the bone's actual owner. But if you've got a petrous bone, that proportion can be as high as 80 percent. And indeed, Bradley found DNA galore within the bone, enough to sequence the full genome of the long-dead dog.

Larson and his colleague Laurent Frantz then compared the Newgrange sequences with those of almost 700 modern dogs, and built a family tree that revealed the relationships between these individuals. To their surprise, that tree had an obvious fork in its trunk—a deep divide between two doggie dynasties. One includes all the dogs from eastern Eurasia, such as Shar Peis and Tibetan mastiffs. The other includes all the western Eurasian breeds, and the Newgrange dog.

The genomes of the dogs from the western branch suggest that they went through a population bottleneck—a dramatic dwindling of numbers. Larson interprets this as evidence of a long migration. He thinks that the two dog lineages began as a single population in the east, before one branch broke off and headed west. This supports the idea that dogs were domesticated somewhere in China.

But there's a critical twist.

The team calculated that the two dog dynasties split from each other between 6,400 and 14,000 years ago.  But the oldest dog fossils in both western and eastern Eurasia are older than that. Which means that when those eastern dogs migrated west into Europe, there were already dogs there.

To Larson, these details only make sense if dogs were domesticated twice.

Here's the full story, as he sees it. Many thousands of years ago, somewhere in western Eurasia, humans domesticated grey wolves. The same thing happened independently, far away in the east. So, at this time, there were two distinct and geographically separated groups of dogs.

Let's call them Ancient Western and Ancient Eastern. Around the Bronze Age, some of the Ancient Eastern dogs migrated westward alongside their human partners, separating from their homebound peers and creating the deep split in Larson's tree. Along their travels, these migrants encountered the indigenous Ancient Western dogs, mated with them (doggy style, presumably), and effectively replaced them.

Today's eastern dogs are the descendants of the Ancient Eastern ones. But today's western dogs (and the Newgrange one) trace most of their ancestry to the Ancient Eastern migrants. Less than 10 percent comes from the Ancient Western dogs, which have since gone extinct.

This is a bold story for Larson to endorse, not least because he himself has come down hard on other papers suggesting that cows, sheep, or other species were domesticated twice. "Any claims for more than one need to be substantially backed up by a lot of evidence," he says. "Pigs were clearly domesticated in Anatolia and in East Asia. Everything else is once." Well, except maybe dogs.

Other canine genetics experts think that Larson's barking up the wrong tree. "I'm somewhat underwhelmed, since it's based on a single specimen," says Bob Wayne from the University of California, Los Angeles. He buys that there's a deep genetic division between modern dogs. But, it's still possible that dogs were domesticated just once, creating a large, widespread, interbreeding population that only later resolved into two distinct lineages.

In 2013, Wayne's team compared the mitochondrial genomes (small rings of DNA that sit outside the main set) of 126 modern dogs and wolves, and 18 fossils. They concluded that dogs were domesticated somewhere in Europe or western Siberia, between 18,800 and 32,100 years ago. And genes aside, "the density of fossils from Europe tells us something," says Wayne. "There are many things that look like dogs, and nothing quite like that in east Asia."

Peter Savolainen from the KTH Royal Institute of Technology in Stockholm disagrees. By comparing the full genomes of 58 modern wolves and dogs, his team has shown that dogs in southern China are the most genetically diverse in the world. They must have originated there around 33,000 years ago, he says, before a subset of them migrated west 18,000 years later.

That's essentially the same story that Larson is telling. The key difference is that Savolainen doesn't buy the existence of an independently domesticated group of western dogs. "That's stretching the data very much," he says. Those Ancient Western dogs might have just been wolves, he says. Or perhaps they were an even earlier group of migrants from the east. "I think the picture must seem a bit chaotic," he says understatedly. "But for me, it's pretty clear. It must have happened in southern East Asia. You can't interpret it any other way."

Except, you totally can. Wayne does ("I'm certainly less dogmatic than Peter," he says). Adam Boyko from Cornell University does, too: after studying the genes of village dogs—free-ranging mutts that live near human settlements—he argued for a single domestication in Central Asia, somewhere near India or Nepal. And clearly, Larson does as well.

Larson adds that his gene-focused peers are ignoring one crucial line of evidence—bones. If dogs originated just once, there should be a neat gradient of fossils with the oldest ones at the center of domestication and the youngest ones far away from it. That's not what we have. Instead, archaeologists have found 15,000-year-old dog fossils in western Europe, 12,500-year-old ones in east Asia, and nothing older than 8,000 years in between.

"If we're wrong, then how on earth do you explain the archaeological data?" says Larson. "Did dogs jump from East Asia to Western Europe in a week, and then go all the way back 4,000 years later?" No. A dual domestication makes more sense. Mietje Genompré, an archaeologist from the Royal Belgian Institute of Natural Sciences, agrees that the bones support Larson's idea. "For me, it's very convincing," she says.

But even Larson is hedging his bets. When I ask him how strong his evidence is, he says, "Like, put a number on it? If was being bold, I'd say it's a 7 out of 10. We lack the smoking gun."

Why is this so hard? Of all the problems that scientists struggle with, why has the origin of dogs been such a bitch to solve?

For starters, the timing is hard to pin down because no one knows exactly how fast dog genomes change. That pace—the mutation rate—underpins a lot of genetic studies. It allows scientists to compare modern dogs and ask: How long ago must these lineages have diverged in order to build up this many differences in their genes? And since individual teams use mutation rate estimates that are wildly different, it's no wonder they've arrived at conflicting answers.

Regardless of the exact date, it's clear that over thousands of years, dogs have mated with each other, cross-bred with wolves, travelled over the world, and been deliberately bred by humans. The resulting ebb and flow of genes has turned their history into a muddy, turbid mess—the homogeneous soup that Larson envisages.

Wolves provide no clarity. Grey wolves used to live across the entire Northern Hemisphere, so they could have potentially been domesticated anywhere within that vast range (although North America is certainly out). What's more, genetic studies tell us that no living group of wolves is more closely related to dogs than any other, which means that the wolves that originally gave rise to dogs are now extinct. Sequencing living wolves and dogs will never truly reveal their shrouded past; it'd be, as Larson says, like trying to solve a crime when the culprit isn't even on the list of suspects.

"The only way to know for sure is to go back in time," he adds.

The study informally known as the Big Dog Project was born of frustration. Back in 2011, Larson was working hard on the origin of domestic pigs, and became annoyed that scientists studying dogs were getting less rigorous papers in more prestigious journals, simply because their subjects were that much more charismatic and media-friendly. So he called up his longstanding collaborator Keith Dobney. "Through gritted teeth, I said: We're fucking doing dogs. And he said: I'm in."

Right from the start, the duo realized that studying living dogs would never settle the great domestication debate. The only way to do that was to sequence ancient DNA from fossil dogs and wolves, throughout their range and at different points in history. While other scientists were studying the soup of dog genetics by tasting the finished product, Larson would reach back in time to taste it at every step of its creation, allowing him to definitively reconstruct the entire recipe.

In recent decades, scientists have become increasingly successful at extracting and sequencing strands of DNA from fossils. This ancient DNA has done wonders for our understanding of our own evolution. It showed, for example, how Europe was colonized 40,000 years ago by hunter-gatherers moving up from Africa, then 8,000 years ago by Middle Eastern farmers, and 5,000 years ago by horse-riding herders from the Russian steppes. "Everyone in Europe today is a blend of those three populations," says Larson, who hopes to parse the dog genome in the same way, by slicing it into its constituent ingredients.

Larson originally envisaged a small project—just him and Dobney analyzing a few fossils. But he got more funding, collaborators, and samples than he expected. "It just kind of metastasized out of all proportion," he says. He and his colleagues would travel the world, drilling into fossils and carting chips of bone back to Oxford. They went to museums and private collections. ("There was a guy up in York who had a ton of stuff in his garage.") They grabbed bones from archaeological sites.

The pieces of bone come back to a facility in Oxford called the Palaeo-BARN—the Palaeogenomics and Bioarchaeology Research Network. When I toured the facility with Larson, we wore white overalls, surgical masks, oversoles, and purple gloves, to keep our DNA (and that of our skin microbes) away from the precious fossil samples. Larson called them 'spacesuits.' I was thinking 'thrift-store ninja.'

In one room, the team shoves pieces of bone into a machine that pounds it with a small ball bearing, turning solid shards into fine powder. They then send the powder through a gauntlet of chemicals and filters to pull out the DNA and get rid of everything else. The result is a tiny drop of liquid that contains the genetic essence of a long-dead dog or wolf. Larson's freezer contains 1,500 such drops, and many more are on the way. "It's truly fantastic the kind of data that he has gathered," says Savolainen.

True to his roots in archaeology, Larson isn't ignoring the bones. His team photographed the skulls of some 7,000 prehistoric dogs and wolves at 220 angles each, and rebuilt them in virtual space. They can use a technique calledgeometric morphometrics to see how different features on the skulls have evolved over time.

The two lines of evidence—DNA and bones—should either support or refute the double domestication idea. It will also help to clear some confusion over a few peculiar fossils, such as a 36,000 year old skull from Goyet cave in Belgium. Genompré thinks it's a primitive dog. "It falls outside the variability of wolves: it's smaller and the snout is different," she says. Others say it's too dissimilar to modern dogs. Wayne has suggested that it represents an aborted attempt at domestication—a line of dogs that didn't contribute to modern populations and is now extinct.

Maybe the Goyet hound was part of Larson's hypothetical Ancient Western group, domesticated shortly after modern humans arrived in Europe. Maybe it represented yet another separate flirtation with domestication. All of these options are on the table, and Larson thinks he has the data to tell them apart. "We can start putting numbers on the difference between dogs and wolves," he says. "We can say this is what all the wolves at this time period look like; does the Goyet material fall within that realm, or does it look like dogs from later on?"

Larson hopes to have the first big answers within six to twelve months. "I think it'll clearly show that some things can't be right, and will narrow down the number of hypotheses," says Boyko. "It may narrow it down to one but I'm not holding my breath on that." Wayne is more optimistic. "Ancient DNA will provide much more definitive data than we had in the past," he says. "[Larson] convinced everyone of that. He's a great diplomat."

Indeed, beyond accumulating DNA and virtual skulls, Larson's greatest skill is in gathering collaborators. In 2013, he rounded up as many dog researchers as he could and flew them to Aberdeen, so he could get them talking. "I won't say there was no tension," he says. "You go into a room with someone who has written something that sort of implies you aren't doing very good science... there will be tension. But it went away very quickly. And, frankly: alcohol."

"Everyone was like: You know what? If I'm completely wrong and I have to eat crow on this, I don't give a shit. I just want to know."

Quote from: jimmy olsen on May 30, 2016, 10:05:05 AM
First Phonecian sequenced truns out to be from an obscure European lineage. If true, it's not surprising given how mobile people were. However, very few ancient Africans have been sequenced due to the environment being bad for preservation.  This lineage could have originated in Africa long ago and then moved to Europe where we deteced their last descendants. We just can't tell until we get more data.

http://m.csmonitor.com/Science/2016/0529/Ancient-Phoenician-DNA-may-change-the-way-we-see-human-migration

Quote from: The Minsky Moment on June 07, 2016, 09:30:05 AM
Hmm I thought it was pretty much assumed that the Lebanese coast received invaders/migrants/refugees from the Aegean in bronze age collapse, thus wouldn't be totally surprising that European genes would be found in the iron age Phoenician population.

QuoteI'm currently reading John Lane's excellent book, Coyote Settles the South. It is an excellent book, and I will be reviewing it here very soon. The whole time I've been reading it I thinking about my encounter with the male Eastern coyote I called in back in March.

He's not exactly the same coyote that Lane is writing about. He's a coyote of the gray woods, not the subtropical pine forests and river bottoms.

But in some ways, he is the same. He is the same creature that has adjusted to all that Western man can throw at him and thrived.

And he's thrived at the expense of the wolves that once roamed over the Northeastern US and the South. He's just the right size to live on a diet of rodents and rabbits but also has the ability to pack up and hunt deer. He can be an omnivore, enjoying wild apples and pears that fall to the ground, almost as much as he would if he came across a winter-killed deer.

The coyote is a survivor. I've written on this space several times that the reason he has thrived is because he has been here far longer than the wolves that once harried his kind. Until last week, it was assumed that the coyote split from the wolf some 1 million years ago. This million year split has been used for virtually every study that has examined the relationships between different populations or species in the genus Canis. It is used to set the molecular clock so that we can figure out when wolves and dogs split and perhaps give us some idea as to when dogs may have been domesticated.

This assumption has been directly challenged in a new study that was released in Science Advances last week. The paper examined full genome sequences of several different canids, and it can be argued that it pretty much ended the debate as to whether the red wolf and Eastern wolf are species. They aren't. Instead, they are the result of hybridization between wolves and coyotes. Most of the media attention has paid attention to this discovery in the study.

It's the most important practical implications, because the US Fish and Wildlife Service delisted the gray or Holarctic wolf in most of the Eastern, Southern, and Midwestern states in favor of protecting the Eastern and red wolves. Red wolves are called Canis rufus, and  Eastern wolf is Canis lycaon. With them being recognized as hybrids, this greatly complicates the issue of how to conserve them under the Endangered Species Act, which, as its name suggests, is meant to conserve actual species and not hybrids between species.

The authors of the study feel that these hybrid populations are still worth conserving, largely because the red wolf contains the last reservoir of genes belonging to the now extinct wolves of the Southeast.

But in order to make this work, we're probably going to have to rewrite the Endangered Species Act, and that is not going to happen any time soon.

However, the finding in the study that is worth discussing more is that not only showed that red and Eastern wolves were not some relict ancient species of wolf. It is the finding that coyotes and wolves split only 50,000 years ago.

Using a simple isolation model and a summary likelihood approach, we estimated a Eurasian gray wolf–coyote divergence time of T = 0.38 N generations (95% confidence interval, 0.376 to 0.386 N), where N is the effective population size. If we assume a generation time of 3 years, and an effective population size of 45,000 (24, 25), then this corresponds to a divergence time of 50.8 to 52.1 thousand years ago (ka), roughly the same as previous estimates of the divergence time of extant gray wolves.

This finding means that the studies that use that 1 million year divergence time to set the molecular clock for all those dog domestication studies need to be reworked. This is going to have some effect on how we think about dog domestication, and although the domestication dates have been moved back in recent years, the actual split between dogs and wolves is likely to be much later than when we see the first signs of domestication in subfossil canids.

That's one important finding that comes from this discovery that wolves and coyotes are much more closely related.

The other is that yes, it did pretty much end Canis rufus and Canis lycaon as actual species, but it probably also ends the validity of Canis latrans as a valid species. Coyotes could be classified as a subspecies of wolf. Indeed, they are much more closely related to wolves than Old World red foxes are to New World red foxes, which split 4oo,ooo years ago. And there is still some debate as to whether these two foxes are distinct species, because we've traditionally classified them as a single species. Plus, if we start splitting them into two species, we're likely to find the same thing exists with least weasels living in the Old and New World. And the same thing with stoats.

And then it's not long we're fighting over the house mouse species complex.

But if we're going to lump red foxes, it's pretty hard not to lump coyotes and wolves. It is true that wolves normally kill coyotes in their territory, but it also found that wolves in Alsaska and Yellowstone, wolves that were thought to be entirely free of any New World ancestry, also had some coyote genes.

So the coyote, like the extinct Honshu wolf and the current Arabian wolf, could be correctly thought of a small subspecies of wolf. We know from paleontology that in both North America and Eurasia there were various forms of canid that varied from jackal-like to wolf-like, and although we know the jackal-like form is the earliest form, these two types have ebbed and flowed across Eurasia and North America. We've assumed that the jackal-like forms gave became the coyote and the larger wolf-like forms have become the gray, red, and dire wolves.

But what we're looking at now is the coyote isn't the ancient species we thought it was. It's very likely that some ancestral wolf population came into North America, and instead assuming the pack-hunting behavior of Eurasian wolves, it tended toward the behavior of a golden jackal. When this ancient wolf walked into North America, it would have found that the pack-hunting niche was already occupied by dire wolves. There were many other large predators around as well, and evolving to the jackal-like niche would have made a lot more sense in evolutionary terms.

This is what the coyote is.

The pack-hunting modern wolf came into the continent and took it by storm, and the coyote exchanged genes with it. They lived together as sort of species-like populations in the West, but when wolves became rare from persecution following European settlement, the coyote and wolf began to exchange genes much more.

So with one study using complete genomes, the entire taxonomy of North American Canis is truly blown asunder.

And the implications for dog domestication studies and for the practical application of the Endangered Species Act could not be any more consequential.

Very rarely do you get studies like this one.

It changes so much, and the question about what a coyote is has become unusually unsettling but also oddly amazing.

I will never think of a coyote the same way.

The mystery is even more mysterious.

QuoteAbstract

Epidemiological and genetic association studies show that genetics play an important role in the attainment of education. Here, we investigate the effect of this genetic component on the reproductive history of 109,120 Icelanders and the consequent impact on the gene pool over time. We show that an educational attainment polygenic score, POLYEDU, constructed from results of a recent study is associated with delayed reproduction (P < 10−100) and fewer children overall. The effect is stronger for women and remains highly significant after adjusting for educational attainment. Based on 129,808 Icelanders born between 1910 and 1990, we find that the average POLYEDU has been declining at a rate of ∼0.010 standard units per decade, which is substantial on an evolutionary timescale. Most importantly, because POLYEDU only captures a fraction of the overall underlying genetic component the latter could be declining at a rate that is two to three times faster.

    selection educational attainment genes fertility sequence variants

Epidemiological studies have estimated that the genetic component of educational attainment can account for as much as 40% of the trait variance (1). Recent meta-analyses (2, 3) yielded sequence variants contributing to the underlying genetic component. A negative correlation between educational attainment and number of children has been observed in many populations (4⇓⇓–7). A recent study of ∼20,000 genotyped Americans born between 1931 and 1953 provided direct evidence that the genetic propensity for educational attainment is associated with reduced fertility (8, 9), supporting previously postulated notions (10) that the population average of the genetic propensity for educational attainment and related traits must be declining. Here, using a population-wide sample that is both much larger and covers a substantially greater time span, and with additional auxiliary information, we aim to estimate the change of the genetic propensity of educational attainment in the Icelandic population over the last few decades, starting with an in-depth investigation of the relationship between a measurable genetic component of educational attainment and various aspects of reproduction (11⇓⇓–14).

Quote from: jimmy olsen on January 18, 2017, 12:57:32 PM
More proof that intelligence in modern society is being selected against by natural selection

Quote

DNA Offers Clues to Mysterious Crypt in Ancient Pueblo

It's a question that eluded answers for more than a century: Who were the 14 people buried in the tiny tomb known as Room 33?

By Andrew Curry

PUBLISHED February 21, 2017

Using DNA from skeletons excavated in New Mexico more than a century ago, researchers have shown that more than a dozen people buried in a small, hidden chamber were likely members of a powerful Native American dynasty related through their mothers.

New Mexico's Chaco Canyon was once the center of the most influential culture in the American Southwest. Between approximately 800 A.D. and 1100 A.D., the ancient Chacoans built settlements called pueblos with huge, five-story buildings and grand ceremonial plazas. Elaborate road networks connected the pueblos, and at its peak the culture covered most of modern New Mexico, along with parts of Utah, Colorado, and Arizona.

At the center of Chacoan society was Pueblo Bonito, Spanish for "beautiful town." Covering more than four acres, the elaborate pueblo was a honeycomb of nearly 650 rooms. Close to the pueblo's center was a hidden chamber measuring just six feet long by six feet wide and accessible only through a small hatch in the roof.

Archaeologists who excavated Room 33 in 1896 were stunned by the richness of the burial goods, including thousands of turquoise beads, as well as jewelry and instruments made from shells imported from the Pacific.
 
Archaeologists working for New York's American Museum of Natural History (AMNH) excavated Pueblo Bonito in 1896. Inside the tiny innermost chamber they discovered the remains of 14 people buried under the room's sandy floor, with grave stacked on grave in the tight space. The excavators labeled the mysterious chamber Room 33.

The two men buried at the bottom of the room were surrounded by stunning wealth. The first man buried in the chamber, known as Burial 14, was found with more than 12,000 turquoise beads and dozens of turquoise sculptures—more of the precious stone than in all the other Chacoan sites combined. A conch shell trumpet, likely from the Pacific, and other musical instruments rounded out the chamber's grave goods. Scarlet macaws imported from more than 1,000 miles away in Central America were found in a nearby room.

Female Power Line

The artifacts and human remains from Room 33 have been stored at the American Museum of Natural History since they were excavated in the 19th century. Since then the skeletons have remained a mystery: Who were these people, and why were they buried in a walled-off room in the middle of the mighty pueblo?

Recently, new radiocarbon dates and ancient DNA analysis of the millennia-old bones revealed that the burials may represent an early Native American dynasty. In a paper published today in the journal Nature Communications, researchers show that the men and women buried in the chamber are all related through their mothers, a connection known as a matriline. Many Native American groups still pass membership on through the mother's side, as do most of the world's Jewish communities.

"One pair may be a grandmother and her grandson, another two mother and daughter. They may not all have been rulers, but they were related," says University of Virginia archaeologist and study co-author Stephen Plog. "The evidence suggests it's a long matriline, in control for a long, long time."

Most researchers once thought Chacoan cultures were egalitarian, with no real hierarchy. Many modern Native American groups in the region are governed communally today.

But the grave goods show that Burial 14—a man who died around 880 A.D., likely killed by a blow to the head—was a big deal in life. And DNA evidence showing three centuries of relatives buried in the same room suggests that spending eternity with him was a high honor, one restricted to his matrilineal descendants.

Put together, the clues seem to indicate that Burial 14 was the founder of a political dynasty that lasted 300 or more years.

"It's likely Burial 14 is really the first individual to differentiate himself politically from other people in the canyon," Plog says. "I'm confident his matriline was the most powerful in Pueblo Bonito, and probably in Chaco Canyon. It was an elite group, able to control resources and have influence over broad areas of the Southwest."

Source of Status

The results are some of the first to use DNA to tackle a fundamental question in the study of human history: Where does status come from?

Hereditary leadership—power and status based on birth—is a hallmark of complex societies. In societies that use writing, evidence for hereditary leadership is easy to come by: In Europe, written histories hold the answers. In the Americas, Aztec and Maya ruling families have been indentified from carved inscriptions.

But without such records it's difficult to prove that leadership and power in ancient societies without writing was hereditary. "If these results hold up, I think it's a game changer," says American Museum of Natural History archaeologist David Thomas, who was not involved in the research.

Testing Ancestral Remains

For many groups who consider the people of Chaco Canyon their ancestors, the research may be controversial. Tribes including the Navajo, Hopi, Zuni, and Acoma all consider themselves descendants of the Chaco Canyon people, and some have religious objections to invasive, destructive testing on human remains.

Though the bones were excavated more than a century ago, curators at the American Museum of Natural History still weighed such concerns before authorizing the testing. "We can be sensitive and deal with communities in a respectful way and still do the best science we can do," says Thomas. "I think there's a middle ground."

Quote from: The Minsky Moment on June 07, 2016, 09:30:05 AM

Quote from: jimmy olsen on May 30, 2016, 10:05:05 AM
First Phonecian sequenced truns out to be from an obscure European lineage. If true, it's not surprising given how mobile people were. However, very few ancient Africans have been sequenced due to the environment being bad for preservation.  This lineage could have originated in Africa long ago and then moved to Europe where we deteced their last descendants. We just can't tell until we get more data.

http://m.csmonitor.com/Science/2016/0529/Ancient-Phoenician-DNA-may-change-the-way-we-see-human-migration (http://m.csmonitor.com/Science/2016/0529/Ancient-Phoenician-DNA-may-change-the-way-we-see-human-migration)

Hmm I thought it was pretty much assumed that the Lebanese coast received invaders/migrants/refugees from the Aegean in bronze age collapse, thus wouldn't be totally surprising that European genes would be found in the iron age Phoenician population.

Quote from: katmai on April 04, 2017, 03:23:57 PM
Hey Cal, are ancestry and 23and me the only two you've done?

Quote from: Caliga on April 04, 2017, 04:27:08 PM

Quote from: katmai on April 04, 2017, 03:23:57 PM
Hey Cal, are ancestry and 23and me the only two you've done?

I have only done Ancestry in the sense that I spit in a tube and mailed them the tube.

I've also run my results through FTDNA, GEDMatch, and Promethease.

Quote from: Caliga on April 04, 2017, 10:52:56 PM
Interesting, do you know when it will be done or if it's done already?

I just checked and I forget what it said about me before, but now it thinks I am 53% British Isles, 22% West and Central Europe, 16% Iberia, 4% Scandinavia, <2% Eastern Europe, and <2% Southeast Europe.

Quote
British Isles 13%
East Europe 8%
Finland 0%
Scandinavia 0%
Southeast Europe 6%
Iberia 30%
West and Central Europe 13%

North and Central America 18%
South America 0%

Ashkenazi 0%
Sephardic 9%

Quote from: Valmy on April 05, 2017, 07:59:28 AM
Wow. You really are the DNA of Texas Katmai.

QuoteEast Central Africa < 2%
North Africa < 2%
South Central Asia < 2%
Siberia < 2%

Quote from: derspiess on April 05, 2017, 08:41:19 AM
Waiting for Ancestry DNA to process my sample.  I'm interested to see how the Genetic Communities thing plays out.

Quote from: katmai on April 05, 2017, 03:13:19 PM

Quote from: Valmy on April 05, 2017, 07:59:28 AM
Wow. You really are the DNA of Texas Katmai.

I didn't even show you the <2% traces
:) :lol:

QuoteEast Central Africa < 2%
North Africa < 2%
South Central Asia < 2%
Siberia < 2%

Quote from: Ed Anger on April 05, 2017, 07:42:27 PM
Katmai:

40% whale
40% Manatee
20% hot air

Quote from: katmai on April 05, 2017, 07:47:44 PM

Quote from: Ed Anger on April 05, 2017, 07:42:27 PM
Katmai:

40% whale
40% Manatee
20% hot air

:cry:
So mean to me, I'm quitting Languish for twice as long as Ed Anger!

Quote from: katmai on April 05, 2017, 07:47:44 PM

Quote from: Ed Anger on April 05, 2017, 07:42:27 PM
Katmai:

40% whale
40% Manatee
20% hot air

:cry:
So mean to me, I'm quitting Languish for twice as long as Ed Anger!

Quote from: Ed Anger on April 05, 2017, 07:42:27 PM
Katmai:

40% whale
40% Manatee
20% hot air

Quote from: The Minsky Moment on April 06, 2017, 02:47:55 PM
What more can be expected from the moderator of the failing languish.org.

Quote from: derspiess on April 25, 2017, 03:34:58 PM
Still waiting on my Ancestry DNA results :rolleyes: but I was playing around on ancestry.com and traced one of our lines back to a dude that was knighted by Elizabeth I. Switching to a different site, it looks like I can trace back to ca. 1180.  Apparently that family line (Booth/de Bothe) was originally from Normandy and came over during or after the invasion.  At least a couple direct ancestors were baronets of Dunham Massey.

Quote from: Ed Anger on April 25, 2017, 07:35:10 PM
Hey! I claim Normandy for the Hawkins line. Pretenders will be flogged.

Quote from: derspiess on April 26, 2017, 10:48:00 AM

One of the more interesting characters was a hardcore Puritan dude named Hatevil Nutter that came over from England and settled in New Hampshire in the 1600s.  He was a church elder and was most widely known for his hatred of Quakers :lol:

Quote from: derspiess on April 26, 2017, 10:48:00 AM
Every time I got back into the 1700s and saw someone from "Ireland" I got a little spooked,

Quote from: Grinning_Colossus on April 26, 2017, 12:10:22 PM

Quote from: derspiess on April 26, 2017, 10:48:00 AM
Every time I got back into the 1700s and saw someone from "Ireland" I got a little spooked,

:lol:

In any case, I'm glad that your German ancestor was a coward, so that his descendants couldn't turn into Nazis

Quote from: derspiess on April 26, 2017, 12:38:02 PM
Ooh, my 19th great grandfather was the first recorded speaker of the House of Commons.

Quote from: Valmy on April 26, 2017, 12:38:53 PM

Quote from: derspiess on April 26, 2017, 12:38:02 PM
Ooh, my 19th great grandfather was the first recorded speaker of the House of Commons.

I am descended from Charlemagne and so are you!

Quote from: Malthus on April 26, 2017, 11:15:05 AM

Our most interesting ancestor was "half-hanged Mary" - a woman accused of witchcraft and hanged ... who survived.

https://en.wikipedia.org/wiki/Mary_Webster_(alleged_witch)

An account of her witchery: http://quod.lib.umich.edu/e/evans/N00392.0001.001/1:6?rgn=div1;view=fulltext;q1=Witchcraft

Quote from: derspiess on April 25, 2017, 08:12:38 PM

Quote from: Ed Anger on April 25, 2017, 07:35:10 PM
Hey! I claim Normandy for the Hawkins line. Pretenders will be flogged.

I'll relinquish all claims in exchange for Calvados.

Quote from: Valmy on April 26, 2017, 12:38:53 PM

Quote from: derspiess on April 26, 2017, 12:38:02 PM
Ooh, my 19th great grandfather was the first recorded speaker of the House of Commons.

I am descended from Charlemagne and so are you!

Quote from: Valmy on January 18, 2017, 01:20:41 PM

Quote from: jimmy olsen on January 18, 2017, 12:57:32 PM
More proof that intelligence in modern society is being selected against by natural selection

Counter point is the impressive fecundity of BB and I right?

Quote from: jimmy olsen on April 26, 2017, 05:33:21 PM

Quote from: Malthus on April 26, 2017, 11:15:05 AM

Our most interesting ancestor was "half-hanged Mary" - a woman accused of witchcraft and hanged ... who survived.

https://en.wikipedia.org/wiki/Mary_Webster_(alleged_witch)

An account of her witchery: http://quod.lib.umich.edu/e/evans/N00392.0001.001/1:6?rgn=div1;view=fulltext;q1=Witchcraft

What better proof of witchcraft is that? ;)

Quote from: Barrister on April 27, 2017, 10:10:47 AM
My understanding is that if you wanted to trace back my dad's line you hit a huge brick wall as soon as you the generation before they came to Canada - we don't know where precisely in Ukraine (well, Russia or Austria in those days) they came from, and even if we did the records would likely have been demolished in a little tiff called WWII.

SOme day when I have a spare $200 I wouldn't mind seeing what a DNA ancestry check would have to say.

Quote130,000-year-old mastodon bones could rewrite story of how humans first appeared in the Americas

Shattered mastodon bones from a Southern California site bear the scars of human activity from 130,700 years ago, a team of scientists says — pushing back the generally accepted date that humans are thought to have settled North America by a whopping 115,000 or so years.

If verified and corroborated by other scientists, the discovery described in the journal Nature could radically rewrite the timeline of when humans first arrived in the Americas.

"This is the first time there's been a demonstrated archaeological site with all the bells and whistles," said Curtis Runnels, an archaeologist at Boston University who was not involved with the study, referring to the combination of several lines of evidence at the site. "This makes it absolutely first-water importance. This is up there with one of the discoveries of the century, I would say."
[...]

Quote from: viper37 on April 27, 2017, 10:34:24 AM
I know my maternal ancestor who first came here was from Poitou (from my grandfather line), but I have no idea what he was doing for a living. 

Quote from: derspiess on April 27, 2017, 10:51:59 AM
That is where my Huguenot ancestors were from.  Family name was Monnet (or Monnett).  Looks like they fled to London sometime in the 17th century and then one of them ended up in Maryland, where the name was anglicized to Money.  Going back before that, I have at least 4 direct ancestors that were killed in the St. Bartholomew's Day Massacre in 1572.

Quote from: Grinning_Colossus on April 27, 2017, 10:52:44 AM
If Homo sapiens did this, it also pushes the migration out of Africa back by tens of thousands of years. Could it have been Erectus, or a North American descendant?

Quote from: Admiral Yi on April 27, 2017, 10:54:18 AM

Quote from: derspiess on April 27, 2017, 10:51:59 AM
That is where my Huguenot ancestors were from.  Family name was Monnet (or Monnett).  Looks like they fled to London sometime in the 17th century and then one of them ended up in Maryland, where the name was anglicized to Money.  Going back before that, I have at least 4 direct ancestors that were killed in the St. Bartholomew's Day Massacre in 1572.

That's a long time to hold a grudge dude.

Quote from: The Minsky Moment on April 27, 2017, 10:58:58 AM

Quote from: Grinning_Colossus on April 27, 2017, 10:52:44 AM
If Homo sapiens did this, it also pushes the migration out of Africa back by tens of thousands of years. Could it have been Erectus, or a North American descendant?

Is there any evidence of sapiens in Siberia or East Asia 130-140K YA?  It does suggest Erectus or some variant.

Quote from: derspiess on April 27, 2017, 10:51:59 AM
Family name was Monnet (or Monnett).  Looks like they fled to London sometime in the 17th century and then one of them ended up in Maryland, where the name was anglicized to Money. 

Quote from: Grinning_Colossus on April 27, 2017, 10:52:44 AM
If Homo sapiens did this, it also pushes the migration out of Africa back by tens of thousands of years. Could it have been Erectus, or a North American descendant?

Quote"The implications are massive in terms of human migrations, because for a start we don't really know which human was actually in North America 130,000 years ago," Fullagar said. "There are possibilities; it could be Neanderthal or Denisovan or an early anatomically modern human, but there are no human remains in northeastern Siberia of anything like that sort of age. So it's an unknown, and it extends in a way the capacity of these early humans to have made such a journey — especially if it were by boat and involved sea crossings as opposed to a land crossing."

Quote from: viper37 on April 27, 2017, 12:57:53 PM

Quote from: derspiess on April 27, 2017, 10:51:59 AM
Family name was Monnet (or Monnett).  Looks like they fled to London sometime in the 17th century and then one of them ended up in Maryland, where the name was anglicized to Money. 

Do you share a common ancestor with our Count here?   :ph34r:

Quote from: Barrister on April 27, 2017, 10:10:47 AM
My understanding is that if you wanted to trace back my dad's line you hit a huge brick wall as soon as you the generation before they came to Canada - we don't know where precisely in Ukraine (well, Russia or Austria in those days) they came from, and even if we did the records would likely have been demolished in a little tiff called WWII.

SOme day when I have a spare $200 I wouldn't mind seeing what a DNA ancestry check would have to say.

Quote from: viper37 on April 27, 2017, 10:40:42 AM
Given the tangent this thread has taken, I'm hesitant to bring it back to its roots... ;)

But, this is a major discovery, mastodon bones, most likely killed and skinned by humans:
First humans in California dated to 130 000 years ago (http://www.latimes.com/science/sciencenow/la-sci-sn-americas-first-humans-20170426-story.html)

Quote130,000-year-old mastodon bones could rewrite story of how humans first appeared in the Americas

Shattered mastodon bones from a Southern California site bear the scars of human activity from 130,700 years ago, a team of scientists says — pushing back the generally accepted date that humans are thought to have settled North America by a whopping 115,000 or so years.

If verified and corroborated by other scientists, the discovery described in the journal Nature could radically rewrite the timeline of when humans first arrived in the Americas.

"This is the first time there's been a demonstrated archaeological site with all the bells and whistles," said Curtis Runnels, an archaeologist at Boston University who was not involved with the study, referring to the combination of several lines of evidence at the site. "This makes it absolutely first-water importance. This is up there with one of the discoveries of the century, I would say."
[...]

Quote
Humans in California 130,000 Years Ago? Get the Facts

A new study has dropped a bombshell on archaeology, claiming signs of human activity in the Americas far earlier than thought.

By Michael Greshko
PUBLISHED April 26, 2017

In an announcement sure to spark a firestorm of controversy, researchers say they've found signs of ancient humans in California between 120,000 and 140,000 years ago—more than a hundred thousand years before humans were thought to exist anywhere in the Americas.

If the researchers are right, the so-called Cerutti mastodon site could force a rewrite of the story of humankind.

"I realize that 130,000 years is a really old date and makes our site the oldest archaeological site in the Americas," says study leader Tom Deméré, the paleontologist at the San Diego Natural History Museum, whose team describes their analysis today in Nature. "Of course, extraordinary claims like this require extraordinary evidence, and we feel like the Cerutti mastodon site presents this evidence."

To be clear, the team has not found human bones at the site. But as Deméré and their colleagues tell it, their evidence—a mastodon skeleton, bone flakes, and several large stones—shows that the area was a "bone quarry," where an unknown hominin allegedly smashed fresh mastodon bones with stone hammers, perhaps to extract marrow or to mine the skeleton for raw materials.

However, many of the world's leading experts in American archaeology already have expressed some form of skepticism to the paper's claims. Some have rejected it outright.

"The earliest occupation of the Americas is a highly contentious subject," says University of Southampton archaeologist John McNabb. "The date of the find at 130,000 years ago is a really big ask for archaeologists who are used to talking about 12, 13, 14,000 years ago. It's a big, big time difference."

Here's everything you need to know about the discovery and the reactions of other archaeology experts.

Where is the mastodon site, and how was it found?

The site was discovered in 1992, when an excavator dug up large bone fragments as California's State Route 54 was being built through San Diego County.

The California Department of Transportation requires that paleontologists be on call at major excavations, just in case any fossils pop up amid the carnage. Richard Cerutti, the San Diego Natural History Museum field paleontologist who was on call at the time, flagged the site for follow-up.

He and Deméré then blocked off the area and excavated it, digging down to material undisturbed by the heavy machinery overhead. (Deméré received a grant from the National Geographic Society in January 1993 to support emergency excavations of the site.)

The site struck Deméré as unusual from the beginning, given the large rocks associated with the site, apparent concentrations of bone flakes around the largest stones, and the mastodon remains' odd arrangement. One of its tusks, for example, was embedded vertically in the dirt.

Wait, the site was found in 1992 and excavated in 1993 ... why is it only being announced now?

The main delay came from the sheer difficulty in accurately dating the site. It wasn't until 2011 and 2012 that Jim Paces of the U.S. Geological Survey could provide state-of-the-art ages for the mastodon bones, based on the relative amounts of uranium and thorium within them.

Deméré, a paleontologist by training, also had a lot of other projects on his plate. After writing a brief report on the site in 1995 for the California Department of Transportation, he turned his attention to his other research projects, including the evolution of baleen whales.

In the meantime, a small band of online commenters had seized upon his 1995 report as a sign that evidence on the peopling of the Americas was being "suppressed." Deméré appears surprised and confused by the charge. "Nobody ever said, Forget this ever happened," he says. "That's just baloney."

OK. What's the new evidence being presented?

To start, the wear features on the rocks match what one would expect from stone tools, specifically those used for smashing up bones, says research team member Richard Fullagar, an archaeologist at Australia's University of Wollongong.

There's also the matter of the stones' placement. The site was entombed in siltstone, a type of sedimentary rock that forms from fine-grained sediments—the sort that would settle out only in very slow-moving, low-energy water. But the large stones that appear to be rudimentary tools are far heavier than the surrounding particles. One is roughly 30 pounds. If water didn't move the rocks there, then perhaps people carried them to the site.

In addition, fractures on the mastodon bones suggest they were broken while fresh—and the researchers say they couldn't have been smashed by natural processes. The skeleton likely were not trampled by other large creatures, the team argues, since some of the mastodon's more fragile bones—such as its ribs and vertebrae—are less shattered than the sturdy limb bones. Nor could smaller animals have done it, the team argues, because scavenging carnivores can't chew their way through the middle of a fresh mastodon femur.

The team also provided experimental evidence that hammerstones and anvils make similar fracture patterns in fresh elephant bones, suggesting by analogy that such a process could have been at work at the Cerutti site.

Sounds intriguing! Why are other experts so skeptical?

One of the main critiques is that the study doesn't definitively rule out natural causes for the presence of the purported stone tools, the breakage patterns in the mastodon bones, or the patterns of breakage and wear on their surfaces.

For one, the paper doesn't satisfyingly rule out the possibility that natural processes carried the large rocks to the scene, says Vanderbilt University archaeologist Tom Dillehay. Nor does it fully rule out the possibility that the wear patterns on the stones were a result of rocks bumping against one another in a stream, he says.

"When you put the total package together, there's certainly more evidence to reject [the study] than accept it," Dillehay says.

It's not impossible that human history in the Americas is older than currently thought, says Southern Methodist University archaeologist and National Geographic grantee David Meltzer, an expert on early Americans.

"But to prove it, you cannot take broken bones and nondescript stones to make the case, not without demonstrating that nature could not have broken those bones and modified those stones," he says.

Andy Hemmings, the lead archaeologist at a site of ancient human habitation in Florida called Old Vero, agrees. "We just have to accept that the stones were carried in, [but] from where, and by whom? These are things I'd like to see answered before I'd be willing to put much faith in the conclusions."

Are there any other concerns about the tools?

Archaeologists also take issue with the stone tools that aren't there. Usually, hammer-and-anvil sites also come with lithics, flaked stone tools and the debris from their manufacture and use, notes Jim Adovasio, the Florida Atlantic University archaeologist who excavated Meadowcroft Rockshelter, one of North America's oldest archaeological sites.

These types of tools are missing entirely from the Cerutti site, even though it supposedly dates to a time when hominins were perfectly capable of making sophisticated hand axes.

"They make a statement that the [evidence at Cerutti] is consistent with many other sites," says Adovasio. "Well, I'm sorry, it's not—that just isn't simply true."

Steve Holen of the Center for American Paleolithic Research, one of the research team's archaeologists, rebuts the charge, saying that there's evidence for archaeological sites in the Americas that don't have flaked stone tools. For the last 25 years, Holen has studied two sites in Kansas and Nebraska that are about 14,000 to 33,000 years old. He claims these sites are also bone quarries where humans did not use flaked stone tools, much like the Cerutti site.

Hemmings however, isn't convinced that the evidence uniformly supports the idea that humans at Cerutti were trying to use the mastodon bones as tools. In particular, one of the mastodon's teeth is shattered for no obvious reason.

"Everything that's broken was still there, so it wasn't mined for tools, and you're certainly not getting marrow out of the bone of a mastodon tooth," he says. "So what exactly is supposed to have gone on?"

If the stones are tools, though, does that cinch the case for humans?

Not necessarily. The human line doesn't have a monopoly on tool use, after all. For at least 4,000 years, chimpanzees in Côte d'Ivoire have been cracking nuts with stone hammers. And in Brazil, bearded capuchin monkeys have smashed cashews with rocks for at least a hundred generations.

However, the fossil record of the Americas lacks a marrow-munching, non-human primate at 130,000 years ago. One of the site's rocks is also nearly 30 pounds—far heavier than the rocks Brazil's capuchins wield. In addition, "capuchins are too small to generate the kinetic force needed to crack a mastodon bone," says the University of Georgia's Dorothy Fragaszy, a National Geographic Explorer who studies capuchin tool use. "I agree with the authors that, if these are hammer stones, humans used them."

Michael Haslam, an Oxford archaeologist who studies tool use in non-human primates, agrees. "I think that the evidence presented in this paper backs up the authors' claim that a mastodon has been broken apart using stone tools," he says. "Overall, I think that we need to consider humans as the starting hypothesis for this site, and go from there."

Well, that sounds more promising! So if the authors are right, is it possible I'm related to these ancient mastodon miners?

Maybe, although even if the interpretation holds up, it's unlikely that the tool bearers were anatomically modern humans. At present, there's no evidence that Homo sapiens sapiens left Africa earlier than 120,000 years ago. But at least four sister species were living in East Asia around the time, and three would be contenders for crossing into the Americas. (The fourth is Homo floresiensis, the much-ballyhooed "hobbits" of Indonesia's island of Flores—but they're probably not involved.)


Might the tool users have been Homo erectus, our direct ancestors and the earliest known fire-starters? What about Homo neanderthalensis, which had made it to present-day Kazakhstan around the time of the activity at Cerutti? Or could they have been the Denisovans, the enigmatic East Asian group known from DNA samples collected in a single Russian cave?


At present, it's impossible to say.


How would any of these species have made the crossing?


The answers vary, since the span of possible ages for the site—120,000 to 140,000 years ago—cover the beginning of the last interglacial, the warm period before the last ice age.


If the site is 140,000 years old, then it's possible that any tool-wielding hominins could have come to the Americas via Beringia, the land bridge that once connected Siberia and Alaska, says McNabb. But if it's 120,000 years old—well into the last interglacial—then sea levels would have been much higher. Any would-be migrants would be facing a sea crossing at least 50 miles long.


By 130,000 years ago, hominins undoubtedly figured out how to cross open water. A site in Crete called Mochlos bears stone tools that could be about 130,000 years old, but Crete was never connected to the Greek mainland by a land bridge.


But at present, there's no solid evidence that hominins had made it into northeastern Siberia before about 30,000 years ago—much less any evidence that they floated across the Bering Strait a hundred thousand years before that.

"I think a sea crossing to the Americas with a much higher sea level is a much more difficult proposition," says McNabb.

Have claims for sites this early been made before?

For the most part, American archaeology has been caught in a bitter debate over whether humans arrived a couple thousand years earlier than previously thought—not a hundred thousand years before.

"The earliest occupation of the Americas is a highly contentious subject," says McNabb.

"I think a sea crossing to the Americas with a much higher sea level is a much more difficult proposition," says McNabb.

Have claims for sites this early been made before?

For the most part, American archaeology has been caught in a bitter debate over whether humans arrived a couple thousand years earlier than previously thought—not a hundred thousand years before.

"The earliest occupation of the Americas is a highly contentious subject," says McNabb.

Quote from: The Brain on April 27, 2017, 12:27:58 PM

Quote from: The Minsky Moment on April 27, 2017, 10:58:58 AM

Quote from: Grinning_Colossus on April 27, 2017, 10:52:44 AM
If Homo sapiens did this, it also pushes the migration out of Africa back by tens of thousands of years. Could it have been Erectus, or a North American descendant?

Is there any evidence of sapiens in Siberia or East Asia 130-140K YA?  It does suggest Erectus or some variant.

Well it must be one of the major Homos.

Quote from: derspiess on April 27, 2017, 07:10:05 PM
And from what I've seen so far the last foreign immigrant ancestor of mine got here before the end of the War of Independence.

Quote from: derspiess on April 27, 2017, 07:10:05 PM
And from what I've seen so far the last foreign immigrant ancestor of mine got here before the end of the War of Independence.

Quote from: derspiess on April 27, 2017, 10:02:58 PM
None that I found. I'm just 100% 'Merican.

Quote from: derspiess on April 27, 2017, 11:08:55 PM
Okay, you lost me.

Quote from: derspiess on April 27, 2017, 10:02:58 PM
None that I found. I'm just 100% 'Merican.

Quote from: Archy on April 28, 2017, 12:47:08 AM

Quote from: derspiess on April 27, 2017, 10:02:58 PM
None that I found. I'm just 100% 'Merican.

I would call that 100% Wasp and you broke that tradition by Marrying an immigrant :sad:

Quote from: derspiess on April 28, 2017, 08:24:20 AM

Quote from: Archy on April 28, 2017, 12:47:08 AM

Quote from: derspiess on April 27, 2017, 10:02:58 PM
None that I found. I'm just 100% 'Merican.

I would call that 100% Wasp and you broke that tradition by Marrying an immigrant :sad:

Yeah, but she bore me WASP babies :winning:

Quote from: katmai on May 02, 2017, 03:57:32 AM
That's not how it works, how any of this works.

Quote from: Caliga on May 16, 2017, 02:15:34 PM
I've never actually counted mine up but I have a number who fought as well, so many so that I have a whole bunch of well-documented choices if I ever wanted to apply to SAR.

My grandfather mentioned to me once that we had a Hessian ancestor, but I'm not sure who that is.  I know I have a Loyalist ancestor but I don't know that he actually took up arms.  After the war ended a bunch of townies burned his store down or something like that in an act of revenge.

Quote from: derspiess on May 16, 2017, 02:57:26 PM
Oh, I also found some more Pennsylvania Dutch and some Swiss  :swiss:

Quote from: Ed Anger on May 16, 2017, 05:53:43 PM
My ancestors liked to fuck the natives.

Quote from: jimmy olsen on May 16, 2017, 06:45:14 PM

Quote from: Ed Anger on May 16, 2017, 05:53:43 PM
My ancestors liked to fuck the natives.

What a shocker!

Quote from: Ed Anger on May 16, 2017, 05:53:43 PM
My ancestors liked to fuck the natives.

Quote from: Caliga on May 16, 2017, 08:34:52 PM
Shocking.  A native Kentuckian who thinks he is part Cherokee.  Ed has that in common with 99% of the hicks who grew up here. :)

Quote from: derspiess on May 16, 2017, 08:40:15 PM

Quote from: Ed Anger on May 16, 2017, 05:53:43 PM
My ancestors liked to fuck the natives.

Mine didn't seem to.

Quote from: Ed Anger on May 16, 2017, 08:43:27 PM
Did I say I was part Cherokee? No. So shut the fuck up fatty.

Quote from: derspiess on May 16, 2017, 08:40:15 PM

Quote from: Ed Anger on May 16, 2017, 05:53:43 PM
My ancestors liked to fuck the natives.

Mine didn't seem to.

Quote from: Valmy on May 16, 2017, 09:38:24 PM

Quote from: derspiess on May 16, 2017, 08:40:15 PM

Quote from: Ed Anger on May 16, 2017, 05:53:43 PM
My ancestors liked to fuck the natives.

Mine didn't seem to.

I don't think mine came in contact with the natives much.

Quote from: derspiess on May 17, 2017, 08:36:17 AM
I'm pretty sure mine had some "contact".  They got into Virginia and Ohio pretty early. 

Quote from: Caliga on May 17, 2017, 09:06:44 AM
Probably contact in the sense of stealing land, killing, infecting with smallpox, etc. :)

Early colonial settlers didn't spend much time having children with the Cherokee, despite what so many rednecks down here seem to think about their heritage.  Generally I assume people who claim Cherokee heritage really have slave ancestry and their ancestors were ashamed of it, so they lied and the truth was eventually forgotten.

Quote from: Valmy on May 17, 2017, 09:20:30 AM
They might have seen them and had some unfriendly interactions but I meant they do not seem the types to trade and live beside them. The sorts of activities that lead to one having children with them :P

Quote from: Caliga on May 17, 2017, 09:37:27 AM

Quote from: Valmy on May 17, 2017, 09:20:30 AM
They might have seen them and had some unfriendly interactions but I meant they do not seem the types to trade and live beside them. The sorts of activities that lead to one having children with them :P

There were most definitely unions between whites and Native Americans, but my understanding is that most of the time these individuals resided with the native tribes, and their descendants probably either went extinct with the rest of the tribe or moved onto the reservations.

That said, I believe there's a Spanish noble family that is directly descended from Monteczuma. :)

Quote from: Valmy on May 17, 2017, 09:38:20 AM
Spanish and French colonies are a whole different story when it comes to breeding with the locals :lol:

Quote from: Caliga on May 17, 2017, 09:41:45 AM

Quote from: Valmy on May 17, 2017, 09:38:20 AM
Spanish and French colonies are a whole different story when it comes to breeding with the locals :lol:

Well the French tried to maintain friendly trade relations with the Canadian Natives, hence the Metis.  Friendliness leads to pounding as you mentioned earlier. :cool:

In the case of the Spanish, I think they simply had no choice... most of the immigrants from Spain were men so if you wanted to get laid... well...

Quote from: HVC on May 17, 2017, 09:48:03 AM
Keeping separate from the natives was more of a English thing (and I guess protestant. did the dutch mix with Africans and Asians?). Everyone else banged in their colonies

Quote from: Caliga on May 16, 2017, 08:34:52 PM
Shocking.  A native Kentuckian who thinks he is part Cherokee.  Ed has that in common with 99% of the hicks who grew up here. :)

Quote from: Valmy on May 17, 2017, 11:43:05 AM
The Creeks and Chickasaw considered the Cherokee a bunch of sluts.

Quote from: Caliga on May 17, 2017, 11:34:15 AM
I've also heard a few people claim Sioux ancestry.

I do find it interesting that the most commonly-claimed ancestral tribe is also one of the best known.  I wonder if there are cases of people with legit ancestry, but from another tribe, but their ancestors ended up forgetting which one so just said 'Cherokee' because in the south, the Cherokee are thought to be OSSUM.

Quote from: Caliga on May 17, 2017, 11:45:10 AM

Quote from: Valmy on May 17, 2017, 11:43:05 AM
The Creeks and Chickasaw considered the Cherokee a bunch of sluts.

I believe the Creek were originally more numerous than the Cherokee, but you want to know why nobody ever claims Creek ancestry?  Because they're gone.  Lots of hicks vacation in the Smokies where one can find the.... Cherokee Reservation (and Casino!  :cool: )

I guess if hicks enjoyed vacationing in Oklahoma, more of them might claim Creek ancestry? :hmm:

Quote from: Maximus on May 17, 2017, 11:45:57 AM
I suspect it's because that knowledge/rumour is passed orally and many people have only heard of a few tribes so those are the ones they attach to.

Quote from: Caliga on May 16, 2017, 08:34:52 PM
Shocking.  A native Kentuckian who thinks he is part Cherokee.  Ed has that in common with 99% of the hicks who grew up here. :)

Quote from: viper37 on May 17, 2017, 01:06:53 PM
My cousin just discovered his newborn son is part american indian.  They believe it comes from the mother side (and I think so too).

Quote from: Caliga on May 17, 2017, 01:33:14 PM
I think I just determined that 59% of my DNA came from my mom and 41% came from my dad. :)

Quote from: Valmy on May 17, 2017, 11:47:41 AM
I enjoyed reading the account of my wife's greatxsomething grandfather's military experience in the War of 1812 against the Creeks. 'We invaded and were beaten. We ran back to Georgia and re-organized. Then we attacked again. We lost again and ran back to Georgia. Then we re-organized and attacked again. We lost again. Then we heard Andrew Jackson won the war for us. Drinks were served.'

Quote from: Caliga on May 17, 2017, 01:42:40 PM
Hmmmm.... but now that I think about it, I think you're supposed to receive exactly 50% of your DNA from each parent.

It may just be that that 50% contained more than half of the segments she shares with her half-sister.

Quote from: Barrister on May 17, 2017, 01:43:32 PM

Quote from: Caliga on May 17, 2017, 01:33:14 PM
I think I just determined that 59% of my DNA came from my mom and 41% came from my dad. :)

Isn't that, like, impossible?  Aren't you guaranteed to get 50% of your DNA from each parent?

The DNA testing that is done doesn't give you a complete sequencing of your DNA.  It tests for I don't know how many genetic markers, but not literally every gene in your body.  I suspect what you're seeing is an artifact of that more limited sampling of your DNA.

Quote from: Caliga on May 17, 2017, 03:10:03 PM
There are actually tools you can run your DNA through to tell if your parents are related.  Mine are not. :cool:

Quote from: Maximus on May 17, 2017, 03:30:58 PM
Which one isn't human?

Quote from: Maximus on May 17, 2017, 03:30:58 PM

Quote from: Caliga on May 17, 2017, 03:10:03 PM
There are actually tools you can run your DNA through to tell if your parents are related.  Mine are not. :cool:

Which one isn't human?

Quote from: Caliga on May 17, 2017, 01:19:18 PM

Quote from: viper37 on May 17, 2017, 01:06:53 PM
My cousin just discovered his newborn son is part american indian.  They believe it comes from the mother side (and I think so too).

How'd he discover it?

Quote from: Caliga on May 17, 2017, 03:32:31 PM

Quote from: Maximus on May 17, 2017, 03:30:58 PM
Which one isn't human?

The one with all the Mennonite heritage. :sleep:

Quote from: Maximus on May 17, 2017, 11:45:57 AM

Quote from: Caliga on May 17, 2017, 11:34:15 AM
I've also heard a few people claim Sioux ancestry.

I do find it interesting that the most commonly-claimed ancestral tribe is also one of the best known.  I wonder if there are cases of people with legit ancestry, but from another tribe, but their ancestors ended up forgetting which one so just said 'Cherokee' because in the south, the Cherokee are thought to be OSSUM.

I suspect it's because that knowledge/rumour is passed orally and many people have only heard of a few tribes so those are the ones they attach to.

Quote from: Malthus on May 17, 2017, 03:35:14 PM

Quote from: Maximus on May 17, 2017, 03:30:58 PM

Quote from: Caliga on May 17, 2017, 03:10:03 PM
There are actually tools you can run your DNA through to tell if your parents are related.  Mine are not. :cool:

Which one isn't human?

Perhaps Caliga, like Gilgamesh, is two-thirds god, and has three parents.  ;)

Quote from: jimmy olsen on May 21, 2017, 07:34:19 PM
Not so sure about the credibility of the Siberian times

Quote from: jimmy olsen on May 17, 2017, 11:05:37 PM

Quote from: Maximus on May 17, 2017, 11:45:57 AM

Quote from: Caliga on May 17, 2017, 11:34:15 AM
I've also heard a few people claim Sioux ancestry.

I do find it interesting that the most commonly-claimed ancestral tribe is also one of the best known.  I wonder if there are cases of people with legit ancestry, but from another tribe, but their ancestors ended up forgetting which one so just said 'Cherokee' because in the south, the Cherokee are thought to be OSSUM.

I suspect it's because that knowledge/rumour is passed orally and many people have only heard of a few tribes so those are the ones they attach to.

My Mom's dad is from Quebec. IIRC one of his grandmothers was a native. My Mom met her once. What tribes are still around up there Huron?

Quote from: viper37 on May 22, 2017, 10:34:31 AM

Quote from: jimmy olsen on May 17, 2017, 11:05:37 PM

Quote from: Maximus on May 17, 2017, 11:45:57 AM

Quote from: Caliga on May 17, 2017, 11:34:15 AM
I've also heard a few people claim Sioux ancestry.

I do find it interesting that the most commonly-claimed ancestral tribe is also one of the best known.  I wonder if there are cases of people with legit ancestry, but from another tribe, but their ancestors ended up forgetting which one so just said 'Cherokee' because in the south, the Cherokee are thought to be OSSUM.

I suspect it's because that knowledge/rumour is passed orally and many people have only heard of a few tribes so those are the ones they attach to.

My Mom's dad is from Quebec. IIRC one of his grandmothers was a native. My Mom met her once. What tribes are still around up there Huron?

Huron, Abenakis, Montagnais, Mohawk, Innus, Temiskaming, Alguonquins, Crees up North:
http://www.nanations.com/canada/quebec.htm

Quote'First of our kind' found in Morocco

By Pallab Ghosh
Science correspondent, BBC News, Paris
6 hours ago

From the section Science & Environment

The idea that modern people evolved in a single "cradle of humanity" in East Africa some 200,000 years ago is no longer tenable, new research suggests.

Fossils of five early humans have been found in North Africa that show Homo sapiens emerged at least 100,000 years earlier than previously recognised.

It suggests that our species evolved all across the continent, the scientists involved say.

Their work is published in the journal Nature.

Prof Jean-Jacques Hublin, of the Max Planck Institute for Evolutionary Anthropology in Leipzig, Germany, told me that the discovery would "rewrite the text books" about our emergence as a species.

"It is not the story of it happening in a rapid way in a 'Garden of Eden' somewhere in Africa. Our view is that it was a more gradual development and it involved the whole continent. So if there was a Garden of Eden, it was all of Africa."

Prof Hublin was speaking at a news conference at the College de France in Paris, where he proudly showed journalists casts of the fossil remains his team has excavated at a site in Jebel Irhoud in Morocco. The specimens include skulls, teeth, and long bones.

Earlier finds from the same site in the 1960s had been dated to be 40,000 years old and ascribed to an African form of Neanderthal, a close evolutionary cousin of Homo sapiens.

But Prof Hublin was always troubled by that initial interpretation, and when he joined the MPI he began reassessing Jebel Irhoud. And more than 10 years later he is now presenting new evidence that tells a very different story.

The latest material has been dated by hi-tech methods to be between 300,000 and 350,000 years old. And the skull form is almost identical to modern humans.

The few significant differences are seen in a slightly more prominent brow line and smaller brain cavity.

Prof Hublin's excavation has further revealed that these ancient people had employed stone tools and had learned how to make and control fire. So, not only did they look like Homo sapiens, they acted like them as well.

Until now, the earliest fossils of our kind were from Ethiopia (from a site known as Omo Kibish) in eastern Africa and were dated to be approximately 195,000 years old.

"We now have to modify the vision of how the first modern humans emerged," Prof Hublin told me with an impish grin.

Before our species evolved there were many different types of primitive human species, each of which looked different and had its own strengths and weaknesses. And these various species of human, just like other animals, evolved and changed their appearance gradually, with just the occasional spurt. They did this over hundreds of thousands of years.

By contrast, the mainstream view has been that Homo sapiens evolved suddenly from more primitive humans in East Africa around 200,000 years ago; and it is at that point that we assumed, broadly speaking, the features we display now. What is more, only then do we spread throughout Africa and eventually to rest of planet. Prof Hublin's discoveries would appear to shatter this view.

Jebel Irhoud is typical of many archaeological sites across Africa that date back 300,000 years. Many of these locations have similar tools and evidence for the use of fire. What they do not have is any fossil remains.

Because most experts have worked on the assumption that our species did not emerge until 200,000 years ago, it was natural to think therefore that these other sites were occupied by an older, different species of human. But the Jebel Irhoud finds now make it possible that it was actually Homo sapiens that left the tool and fire evidence in these places.

"We are not trying to say that the origin of our species was in Morocco - rather that the Jebel Irhoud discoveries show that we know that [these type of sites] were found all across Africa 300,000 years ago," said MPI team member Dr Shannon McPhearon.

Prof Chris Stringer from the Natural History Museum in London, UK, was not involved in the research. He told BBC News: "This shows that there are multiple places in Africa where Homo sapiens was emerging. We need to get away from this idea that there was a single 'cradle'."

And he raises the possibility that Homo sapiens may even have existed outside of Africa at the same time: "We have fossils from Israel that are probably the same age and they show what could be described as proto-Homo sapiens features."

Prof Stringer says it is not inconceivable that primitive humans who had smaller brains, bigger faces, stronger brow ridges and bigger teeth - but who were nonetheless Homo sapiens - may have existed even earlier in time, possibly as far back as half a million years ago. This is a startling shift in what those who study human origins believed not so long ago.

"I was saying 20 years ago that the only thing we should be calling Homo sapiens are humans that look like us. This was a view that Homo sapiens suddenly appeared in Africa at some point in time and that was the beginning of our species. But it now looks like I was wrong," Prof Stringer told BBC News.

 

Quote from: jimmy olsen on June 07, 2017, 10:48:01 PM
"I was saying 20 years ago that the only thing we should be calling Homo sapiens are humans that look like us. This was a view that Homo sapiens suddenly appeared in Africa at some point in time and that was the beginning of our species. But it now looks like I was wrong," Prof Stringer told BBC News.

Quote from: derspiess on June 08, 2017, 09:04:18 AM
Well at least I don't have any Dayton-Xenia ancestors.

Quote from: derspiess on June 08, 2017, 08:44:56 AM
Valmy will mock me for this (OMG Charlemagne) but I was able to trace a line back to the viking Rollo.  Also through that same branch traced to dukes of Brittany with really weird names.  Supposedly there's a way to trace back to William the Conquerer but I haven't found it yet.

Quote from: Ed Anger on June 08, 2017, 09:31:04 AM
I hope you was talking to spicy. I'd cut you if you said I was a damn Scot.

Quote from: Eddie Teach on June 08, 2017, 09:29:58 AM
Didn't you say you were part Scottish? The Scotti came over from Ireland.

Quote from: The Minsky Moment on June 08, 2017, 09:31:10 AM

Quote from: derspiess on June 08, 2017, 08:44:56 AM
Valmy will mock me for this (OMG Charlemagne) but I was able to trace a line back to the viking Rollo.  Also through that same branch traced to dukes of Brittany with really weird names.  Supposedly there's a way to trace back to William the Conquerer but I haven't found it yet.

Sorry about all that - but don't get too down about it. Just because you are descended from gangs of violent degenerates doesn't mean you are doomed to be bad person yourself.

Quote from: Ed Anger on June 08, 2017, 08:14:21 PM
Secret Ed Anger ancestry fact: There is a Portuguese in the woodpile.

I am so ashamed.

Quote from: The Minsky Moment on June 08, 2017, 09:31:10 AM
doesn't mean you are doomed to be bad person yourself.

Quote from: derspiess on June 08, 2017, 08:44:56 AM
Valmy will mock me for this (OMG Charlemagne) but I was able to trace a line back to the viking Rollo.  Also through that same branch traced to dukes of Brittany with really weird names.  Supposedly there's a way to trace back to William the Conquerer but I haven't found it yet.

Quote from: viper37 on June 09, 2017, 09:13:24 AM

Quote from: derspiess on June 08, 2017, 08:44:56 AM
Valmy will mock me for this (OMG Charlemagne) but I was able to trace a line back to the viking Rollo.  Also through that same branch traced to dukes of Brittany with really weird names.  Supposedly there's a way to trace back to William the Conquerer but I haven't found it yet.

well, William is a descendant of Rollo.  Rollo had a daughter and a son, Gerloc and William Longsword.  Gerloc married to the duc of Aquitaine (and also count of Poitou), and one of their children took the Duchy and the daughter took the French king as husband, so if your ancestors were still in Normandy later, we can exclude that branch.

In turn, William had only one son before being killed, Richard.

And this is where the fun begins, as he was... prollific:
https://en.wikipedia.org/wiki/Richard_I_of_Normandy (https://en.wikipedia.org/wiki/Richard_I_of_Normandy)
13 children to trace.  Have fun! :P

The line goes from: Rollo - William - Richard I - Richard II - Robert I (or II, but not the archbishop) - William the Conqueror.

Since William the Conqueror was an illegitimate son, you have to be related on the paternal side.

Quote from: derspiess on June 09, 2017, 10:29:31 AM
my 15th great grandmother (Catherine de Montfort, 1441-1498)

Quote from: HVC on June 09, 2017, 11:44:13 AM
you're all the kids of a some stable boy or butler who nailed the queen/duchess somewhere along the line. Just like prince Harry :P

Quote from: Valmy on June 09, 2017, 11:49:27 AM

Actually DNA testing indicates this was shockingly rare. Women were more loyal than all you misogynistic pigs presumed.

However since I am descended through royal bastards (as was Henry Tudor himself I think) this is already taken into account :P

Quote from: HVC on June 09, 2017, 11:52:24 AM
:unsure: I just wanted to call derspiess a bastard.

Quote from: Valmy on June 09, 2017, 11:49:27 AM
Actually DNA testing indicates this was shockingly rare. Women were more loyal than all you misogynistic pigs presumed.

Quote from: HVC on June 09, 2017, 11:52:24 AM

Quote from: Valmy on June 09, 2017, 11:49:27 AM

Actually DNA testing indicates this was shockingly rare. Women were more loyal than all you misogynistic pigs presumed.

However since I am descended through royal bastards (as was Henry Tudor himself I think) this is already taken into account :P

:unsure: I just wanted to call derspiess a bastard.

Quote from: derspiess on June 09, 2017, 12:57:32 PM

Quote from: HVC on June 09, 2017, 11:52:24 AM

Quote from: Valmy on June 09, 2017, 11:49:27 AM

Actually DNA testing indicates this was shockingly rare. Women were more loyal than all you misogynistic pigs presumed.

However since I am descended through royal bastards (as was Henry Tudor himself I think) this is already taken into account :P

:unsure: I just wanted to call derspiess a bastard.

That's practically a compliment around here :hug:

Quote from: HVC on June 09, 2017, 01:00:23 PM

:D
Though, think of your poor genes. From proud French and English nobility to mixing with an Argentinian. an Argentinian!

Quote from: viper37 on June 09, 2017, 12:26:48 PM

Quote from: Valmy on June 09, 2017, 11:49:27 AM
Actually DNA testing indicates this was shockingly rare. Women were more loyal than all you misogynistic pigs presumed.

It indicates two possible things, non mutually exclusive:
1) Male infidelity was more common, with unmarried women, rather than the married women kept under lock at home.
2) Women knew of birth control and abortion even if frowned upon.

Quote from: Tonitrus on June 13, 2017, 07:39:11 PM
I am mostly Dutch.  I tell people I stick fingers into dikes.

QuoteWhite nationalists are flocking to genetic ancestry tests — but many don't like their results

It was a strange moment of triumph against racism: The gun-slinging white supremacist Craig Cobb, dressed up for daytime TV in a dark suit and red tie, hearing that his DNA testing revealed his ancestry to be only "86% European, and ... 14% Sub-Saharan African."

The studio audience whooped and laughed and cheered. And Cobb — who was, in 2013, charged with terrorizing people while trying to create an all-white enclave in North Dakota — reacted like a sore loser in the schoolyard.

"Wait a minute, wait a minute, hold on, just wait a minute," he said, trying to put on an all-knowing smile. "This is called statistical noise."

Then, according to the Southern Poverty Law Center, he took to the white nationalist website Stormfront to dispute those results. That's not uncommon: With the rise of spit-in-a-cup genetic testing, there's a trend of white nationalists using these services to prove their racial identity, and then using online forums to discuss the results.

But like Cobb, many are disappointed to find out that their ancestry is not as "white" as they'd hoped. In a new study, sociologists Aaron Panofsky and Joan Donovan examined years' worth of posts on Stormfront to see how members dealt with the news.

It's striking, they say, that white nationalists would post these results online at all. After all, as Panofsky put it, "they will basically say if you want to be a member of Stormfront you have to be 100% white European, not Jewish."

But instead of rejecting members who get contrary results, Donovan said, the conversations are "overwhelmingly" focused on helping the person to rethink the validity of the genetic test. And some of those critiques — while emerging from deep-seated racism — are close to scientists' own qualms about commercial genetic ancestry testing.

Panofsky and Donovan presented their findings at a sociology conference in Montreal on Monday. The timing of the talk — some 48 hours after the violent white nationalist rally in Charlottesville, Va. — was coincidental. But the analysis provides a useful, if frightening, window into how these extremist groups think about their genes.

Reckoning with results

Stormfront was launched in the mid-1990s by Don Black, a former grand wizard of the Ku Klux Klan. His skills in computer programming were directly related to his criminal activities: He learned them while in prison for trying to invade the Caribbean island nation of Dominica in 1981, and then worked as a web developer after he got out. That means this website dates back to the early years of the internet, forming a kind of deep archive of online hate.

To find relevant comments in the 12 million posts written by over 300,000 members, the authors enlisted a team at the University of California, Los Angeles, to search for terms like "DNA test," "haplotype," "23andMe," and "National Geographic." Then the researchers combed through the posts they found, not to mention many others as background. Donovan, who has moved from UCLA to the Data & Society Research Institute, estimated that she spent some four hours a day reading Stormfront in 2016. The team winnowed their results down to 70 discussion threads in which 153 users posted their genetic ancestry test results, with over 3,000 individual posts.

About a third of the people posting their results were pleased with what they found. "Pretty damn pure blood," said a user with the username Sloth. But the majority didn't find themselves in that situation. Instead, the community often helped them reject the test, or argue with its results.

Some rejected the tests entirely, saying that an individual's knowledge about his or her own genealogy is better than whatever a genetic test can reveal. "They will talk about the mirror test," said Panofsky, who is a sociologist of science at UCLA's Institute for Society and Genetics. "They will say things like, 'If you see a Jew in the mirror looking back at you, that's a problem; if you don't, you're fine.'" Others, he said, responded to unwanted genetic results by saying that those kinds of tests don't matter if you are truly committed to being a white nationalist. Yet others tried to discredit the genetic tests as a Jewish conspiracy "that is trying to confuse true white Americans about their ancestry," Panofsky said.

But some took a more scientific angle in their critiques, calling into doubt the method by which these companies determine ancestry — specifically how companies pick those people whose genetic material will be considered the reference for a particular geographical group.

And that criticism, though motivated by very different ideas, is one that some researchers have made as well, even as other scientists have used similar data to better understand how populations move and change.

"There is a mainstream critical literature on genetic ancestry tests — geneticists and anthropologists and sociologists who have said precisely those things: that these tests give an illusion of certainty, but once you know how the sausage is made, you should be much more cautious about these results," said Panofsky.

A community's genetic rules
Companies like Ancestry.com and 23andMe are meticulous in how they analyze your genetic material. As points of comparison, they use both preexisting datasets as well as some reference populations that they have recruited themselves. The protocol includes genetic material from thousands of individuals, and looks at thousands of genetic variations.

"When a 23andMe research participant tells us that they have four grandparents all born in the same country — and the country isn't a colonial nation like the U.S., Canada, or Australia — that person becomes a candidate for inclusion in the reference data," explained Jhulianna Cintron, a product specialist at 23andMe. Then, she went on, the company excludes close relatives, as that could distort the data, and removes outliers whose genetic data don't seem to match with what they wrote on their survey.

But specialists both inside and outside these companies recognize that the geopolitical boundaries we use now are pretty new, and so consumers may be using imprecise categories when thinking about their own genetic ancestry within the sweeping history of human migration. And users' ancestry results can change depending on the dataset to which their genetic material is being compared — a fact which some Stormfront users said they took advantage of, uploading their data to various sites to get a more "white" result.

J. Scott Roberts, an associate professor at the University of Michigan, who has studied consumer use of genetic tests and was not involved with the study, said the companies tend to be reliable at identifying genetic variants. Interpreting them in terms of health risk or ancestry, though, is another story. "The science is often murky in those areas and gives ambiguous information," he said. "They try to give specific percentages from this region, or x percent disease risk, and my sense is that that is an artificially precise estimate."

For the study authors, what was most interesting was to watch this online community negotiating its own boundaries, rethinking who counts as "white." That involved plenty of contradictions. They saw people excluded for their genetic test results, often in very nasty (and unquotable) ways, but that tended to happen for newer members of the anonymous online community, Panofsky said, and not so much for longtime, trusted members. Others were told that they could remain part of white nationalist groups, in spite of the ancestry they revealed, as long as they didn't "mate," or only had children with certain ethnic groups. Still others used these test results to put forth a twisted notion of diversity, one "that allows them to say, 'No, we're really diverse and we don't need non-white people to have a diverse society,'" said Panofsky.

That's a far cry from the message of reconciliation that genetic ancestry testing companies hope to promote.

"Sweetheart, you have a little black in you," the talk show host Trisha Goddard told Craig Cobb on that day in 2013. But that didn't stop him from redoing the test with a different company, trying to alter or parse the data until it matched his racist worldview.

Quote from: Caliga on August 19, 2017, 08:09:39 PM
I don't even have any trace African ancestry.

I do however have trace  :Joos ancestry. :)

Quote from: Caliga on August 19, 2017, 08:09:39 PM
I don't even have any trace African ancestry.

I do however have trace  :Joos ancestry. :)

Quote from: Razgovory on August 23, 2017, 12:15:13 PM
That's a pretty shitty travel company.

Quote from: Caliga on August 23, 2017, 12:16:09 PM

Quote from: Razgovory on August 23, 2017, 12:15:13 PM
That's a pretty shitty travel company.

If you think that's bad, the Ontario brother's descendant now lives in Saskatchewan. :cry:

Quote from: Caliga on August 23, 2017, 12:16:09 PM
If you think that's bad, the Ontario brother's descendant now lives in Saskatchewan. :cry:

Quote from: jimmy olsen on August 24, 2017, 06:30:14 PM
This is not how wolves were domesticated.

Quote from: dps on August 24, 2017, 10:16:54 PM

Quote from: jimmy olsen on August 24, 2017, 06:30:14 PM
This is not how wolves were domesticated.

You know that because grumbler gave you a first-hand account, right?

Quote from: dps on August 24, 2017, 11:24:11 PM
Tim, it was a joke about grumbler's allegedly ancient age, not an invitation for you to go all pedagogue on us.

Quote from: garbon on August 25, 2017, 02:25:49 AM
Alone in your room with any internet capable devices turned off.

QuoteAbsract

Europe has played a major role in dog evolution, harbouring the oldest uncontested Palaeolithic remains and having been the centre of modern dog breed creation. Here we sequence the genomes of an Early and End Neolithic dog from Germany, including a sample associated with an early European farming community. Both dogs demonstrate continuity with each other and predominantly share ancestry with modern European dogs, contradicting a previously suggested Late Neolithic population replacement. We find no genetic evidence to support the recent hypothesis proposing dual origins of dog domestication. By calibrating the mutation rate using our oldest dog, we narrow the timing of dog domestication to 20,000–40,000 years ago.

Interestingly, we do not observe the extreme copy number expansion of the AMY2B gene characteristic of modern dogs that has previously been proposed as an adaptation to a starch-rich diet driven by the widespread adoption of agriculture in the Neolithic.

Quote from: Grinning_Colossus on August 27, 2017, 05:51:04 PM
A migration is confirmed. It may not have taken the form of blond beasts on horseback sacking Harappa to the tune of Wagner.  :P

QuoteScientists carried out a thorough genomic analysis of the Inuit people living in Greenland and discovered two active genes, namely, TBX15 and WARS2, which help them adapt to extreme cold conditions. These genes are responsible for generating body heat by burning fat so that the Inuit people can survive in extreme cold conditions.

Further investigations made by a different team of scientists under Fernando Racimo studied the natural selection of the Inuit people, in order to trace back the origin of these genetic adaptations. They compared the genomic data of 200 Greenlandic Inuit people with the ancient hominid DNA obtained from fossilized Neanderthals and Denisovans. The study revealed that the TBX15 and WARS2 genes were transferred to modern Inuit people from the archaic hominid population. The study was published in the Molecular Biology and Evolution journal.

Fernando Racimo, the lead investigator of the project, said, "The Inuit DNA sequence in this region matches very well with the Denisovan genome, and it is highly differentiated from other present-day human sequences, though we can't discard the possibility that the variant was introduced from another archaic group whose genomes we haven't sampled yet," Phys.org reported.

It was also found that the gene was present in high frequency in the Inuit people and in the Native Americans but is almost absent in the African population. The study also revealed that there were remarkable differences in the methylation patterns of the TBX15 and WARS2 gene region among the Denisovan genome, the Neanderthals and the modern day human beings.

"All this suggests that the introduced variant may have altered the regulation of these genes, thought the exact mechanism by which this occurred remains elusive," Racimo said.

On the basis of these results, the scientists speculated that the presence of this archaic gene variant may have been responsible for the survival of modern men during their expansion to Siberia, Beringia and later into the Americas.

Quote from: Eddie Teach on August 28, 2017, 10:49:22 AM
Best dogs are mongrels, same as always.

Quote from: Valmy on August 28, 2017, 04:53:28 PM

Quote from: Eddie Teach on August 28, 2017, 10:49:22 AM
Best dogs are mongrels, same as always.

Nah they are basically the same thing. The only real difference is that 'pure breeds' are easier to predict in their behaviors.

Quote from: Valmy on August 28, 2017, 04:53:28 PM

Quote from: Eddie Teach on August 28, 2017, 10:49:22 AM
Best dogs are mongrels, same as always.

Nah they are basically the same thing. The only real difference is that 'pure breeds' are easier to predict in their behaviors.

Quote from: jimmy olsen on August 28, 2017, 05:38:26 PM

Quote from: Valmy on August 28, 2017, 04:53:28 PM

Quote from: Eddie Teach on August 28, 2017, 10:49:22 AM
Best dogs are mongrels, same as always.

Nah they are basically the same thing. The only real difference is that 'pure breeds' are easier to predict in their behaviors.

If I was rich, I'd have a new designer breed made for me. Try and replicate the morphology of the early Pleistocene dogs. Start off by crossing Central Asian Shepherds with Alaskan Malmalutes and go from there.

Quote from: The Brain on August 28, 2017, 05:47:00 PM

Quote from: jimmy olsen on August 28, 2017, 05:38:26 PM

Quote from: Valmy on August 28, 2017, 04:53:28 PM

Quote from: Eddie Teach on August 28, 2017, 10:49:22 AM
Best dogs are mongrels, same as always.

Nah they are basically the same thing. The only real difference is that 'pure breeds' are easier to predict in their behaviors.

If I was rich, I'd have a new designer breed made for me. Try and replicate the morphology of the early Pleistocene dogs. Start off by crossing Central Asian Shepherds with Alaskan Malmalutes and go from there.

ikr

Quote from: Grinning_Colossus on August 28, 2017, 05:19:31 PM
The little mongrel village dogs that you see all over the crappier parts of Eurasia and probably make up a majority of the world's dog population are pretty mellow and timid from thousands of years of having rocks thrown at them.

Quote from: Grinning_Colossus on August 28, 2017, 05:19:31 PM
The little mongrel village dogs that you see all over the crappier parts of Eurasia and probably make up a majority of the world's dog population are pretty mellow and timid from thousands of years of having rocks thrown at them.

Quote from: jimmy olsen on August 27, 2017, 05:32:27 PM
Aryan invasion of India circa 2000 BC confirmed by ancient DNA.

http://www.thehindu.com/sci-tech/science/how-genetics-is-settling-the-aryan-migration-debate/article19090301.ece

Quote...ancient DNA suggests that living Greeks are indeed the descendants of Mycenaeans, with only a small proportion of DNA from later migrations to Greece. And the Mycenaeans themselves were closely related to the earlier Minoans...

The ancient Mycenaeans and Minoans were most closely related to each other, and they both got three-quarters of their DNA from early farmers who lived in Greece and southwestern Anatolia, which is now part of Turkey, the team reports today in Nature. Both cultures additionally inherited DNA from people from the eastern Caucasus, near modern-day Iran, suggesting an early migration of people from the east after the early farmers settled there but before Mycenaeans split from Minoans.

The Mycenaeans did have an important difference: They had some DNA—4% to 16%—from northern ancestors who came from Eastern Europe or Siberia. This suggests that a second wave of people from the Eurasian steppe came to mainland Greece by way of Eastern Europe or Armenia, but didn't reach Crete, says Iosif Lazaridis, a population geneticist at Harvard University who co-led the study.

QuoteWas this ancient person from China the offspring of modern humans and Neandertals?

By Ann GibbonsOct. 12, 2017 , 12:00 PM

When scientists excavated a 40,000-year-old skeleton in China in 2003, they thought they had discovered the offspring of a Neandertal and a modern human. But ancient DNA now reveals that the "Tianyuan Man" has only traces of Neandertal DNA and none detectable from another type of extinct human known as a Denisovan. Instead, he was a full-fledged member of our species, Homo sapiens, and a distant relative of people who today live in East Asia and South America. The work could help scientists retrace some of the earliest steps of human migration.

"The paper is very exciting because it is the first genome to fill a really big gap, both geographically and temporally, in East Asia," says paleogeneticist Pontus Skoglund of Harvard Medical School in Boston, who was not involved in the work.

The first modern humans arose in Africa about 300,000 years ago. By 60,000 years ago, a subset swept out of Africa and mated with Neandertals, perhaps in the Middle East. After that, they spread around the world—DNA from ancient humans in Europe, western Asia, and the Americas has revealed the identity of those early migrants and whether they were related to people living today, especially in Europe. But the trail grows cold in eastern Asia, where warmer climates have made it hard to get ancient DNA from fossils.

The new genome sheds some light on those missing years. In the first genome-wide study of an ancient East Asian, researchers led by Qiaomei Fu, a paleogeneticist at the Chinese Academy of Sciences in Beijing, extracted DNA from the thighbone of the Tianyuan Man—so named because he was found in Tianyuan Cave, 56 kilometers southwest of Beijing.

The team calculated that the Tianyuan Man inherited about as much Neandertal DNA—4% to 5%—as ancient Europeans and Asians of similar age. That's a bit higher than the 1.8% to 2.6% of Neandertal DNA in living Europeans and Asians. The Tianyuan Man did not have any detectable DNA from Denisovans, an elusive cousin of Neandertals known only from their DNA extracted from a few teeth and small bones from a Siberian cave and from traces of their DNA that can still be found in people in Melanesia—where they got it is a major mystery. 

A big surprise is that the Tianyuan Man shares DNA with one ancient European—a 35,000-year-old modern human from Goyet Caves in Belgium. But he doesn't share it with other ancient humans who lived at roughly the same time in Romania and Siberia—or with living Europeans. But the Tianyuan Man is most closely related to living people in east Asia—including in China, Japan, and the Koreas—and in Southeast Asia, including Papua New Guinea and Australia.

All of this suggests that the Tianyuan Man was not a direct ancestor, but rather a distant cousin, of a founding population in Asia that gave rise to present-day Asians, Fu's team reports today in Current Biology. It also shows that these ancient "populations moved around a lot and intermixed," says paleoanthropologist Erik Trinkaus of Washington University in St. Louis in Missouri, who is not a co-author.

And some left offspring whereas others did not. "I find it interesting that ... some of the early modern colonizers of Eurasia were successful while others were not," says co-author Svante Pääbo, a paleogeneticist at the Max Planck Institute for Evolutionary Anthropology in Leipzig, Germany.

The Tianyuan Man also was a distant relative of Native Americans living today in the Amazon of South America, such as the Karitiana and Surui peoples of Brazil and the Chane people of northern Argentina and southern Bolivia. They inherited about 9% to 15% of their DNA from an ancestral population in Asia that also gave rise to the Tianyuan Man. But he is not an ancestor to ancient or living Native Americans in North America, which suggests there were two different source populations in Asia for Native Americans.

This is welcome news to Skoglund, who found in a separate study in 2015 that the Karitiana and Surui peoples are closely related to indigenous Australians, New Guineans, and Andaman Islanders. At the time, he predicted that they came from the same "ghost" source population in Asia, which was separate from another Asian population that gave rise to Native Americans in North America. "It's fascinating that a prediction of a 'ghost population' based on modern-day populations alone can be confirmed in this way," he says.

Quote from: crazy canuck on October 18, 2017, 11:11:35 PM
From August, but I think interesting confirmation that the Greeks are directly descended from the Bronze age cultures that inhabited the area.  And little support for the other theories that those peoples were entirely displaced - or that they came from Africa.

Quote from: The Minsky Moment on October 19, 2017, 09:51:23 AM

Quote from: crazy canuck on October 18, 2017, 11:11:35 PM
From August, but I think interesting confirmation that the Greeks are directly descended from the Bronze age cultures that inhabited the area.  And little support for the other theories that those peoples were entirely displaced - or that they came from Africa.

Anything else would be pretty surprising.  Bronze Age Greece would have had a population near or even over 1 million.  Even assuming significant losses in the collapse, it would take very large migrations to make a big dent in the ethnic composition in the area.  The logistical challenges of moving large numbers of people long distances with pre-modern technology can't be overstated.

Quote from: The Minsky Moment on October 19, 2017, 09:51:23 AM

Quote from: crazy canuck on October 18, 2017, 11:11:35 PM
From August, but I think interesting confirmation that the Greeks are directly descended from the Bronze age cultures that inhabited the area.  And little support for the other theories that those peoples were entirely displaced - or that they came from Africa.

Anything else would be pretty surprising.  Bronze Age Greece would have had a population near or even over 1 million.  Even assuming significant losses in the collapse, it would take very large migrations to make a big dent in the ethnic composition in the area.  The logistical challenges of moving large numbers of people long distances with pre-modern technology can't be overstated.

Quote from: grumbler on October 19, 2017, 10:52:02 AM
However, the shift in England away from a primarily Celtic to a primarily Norse and German population shows that such invasions can happen when the technology is there.

Quote from: The Minsky Moment on October 19, 2017, 03:27:43 PM
East Anglia IIRC has the highest concentration of "Germanic" DNA markers so something to the idea of high levels of Angle migration.  It's a patrilineal lineage though.  It doesn't seem to have been a full-scale population movement.

Quote from: Caliga on October 19, 2017, 04:17:30 PM

Quote from: The Minsky Moment on October 19, 2017, 03:27:43 PM
East Anglia IIRC has the highest concentration of "Germanic" DNA markers so something to the idea of high levels of Angle migration.  It's a patrilineal lineage though.  It doesn't seem to have been a full-scale population movement.

Isn't East Anglia where most of the Danes settled under the Danelaw as well?

Quote from: Ed Anger on October 18, 2017, 08:58:28 PM
Spellus got Anatoilan Deluge when was ridden by a Turk bareback.

Quote from: Caliga on October 19, 2017, 04:17:30 PM

Quote from: The Minsky Moment on October 19, 2017, 03:27:43 PM
East Anglia IIRC has the highest concentration of "Germanic" DNA markers so something to the idea of high levels of Angle migration.  It's a patrilineal lineage though.  It doesn't seem to have been a full-scale population movement.

Isn't East Anglia where most of the Danes settled under the Danelaw as well?

Quote from: dps on October 19, 2017, 04:59:26 PM

Quote from: Caliga on October 19, 2017, 04:17:30 PM

Quote from: The Minsky Moment on October 19, 2017, 03:27:43 PM
East Anglia IIRC has the highest concentration of "Germanic" DNA markers so something to the idea of high levels of Angle migration.  It's a patrilineal lineage though.  It doesn't seem to have been a full-scale population movement.

Isn't East Anglia where most of the Danes settled under the Danelaw as well?

I thought it was Northumbria.  But I could easily be mistaken.

Quote from: jimmy olsen on October 19, 2017, 05:28:34 PM
Lots of huge migrations occured within the neolithic and early bronze age. For example the native hunter gatherers of Great Britain were almost complete replaced in the Neolithic by agricultural people from the mainland. The same thing happened in the rest of Europe as well

Quote from: Ed Anger on October 19, 2017, 07:39:27 PM

Quote from: Ed Anger on October 18, 2017, 08:58:28 PM
Spellus got Anatoilan Deluge when was ridden by a Turk bareback.

Totally wasted on you rubes. Assholes.

Quote from: The Minsky Moment on October 19, 2017, 11:38:15 PM

Quote from: jimmy olsen on October 19, 2017, 05:28:34 PM
Lots of huge migrations occured within the neolithic and early bronze age. For example the native hunter gatherers of Great Britain were almost complete replaced in the Neolithic by agricultural people from the mainland. The same thing happened in the rest of Europe as well

See this is what I mean
The H-G population was small and diffuse.  The Neolithic  migrants came to Britain over thousands of years.  This is not a "huge" migration.  A steady trickle over a long period of time does the trick along with natural increase using more reliable food gathering techniques.

Quote...
In contrast to the Corded Ware Complex, which has previously been identified as arriving in central Europe following migration from the east, we observe limited genetic affinity between Iberian and central European Beaker Complex-associated individuals, and thus exclude migration as a significant mechanism of spread between these two regions. However, human migration did have an important role in the further dissemination of the Beaker Complex, which we document most clearly in Britain using data from 80 newly reported individuals dating to 3900-1200 BCE. British Neolithic farmers were genetically similar to contemporary populations in continental Europe and in particular to Neolithic Iberians, suggesting that a portion of the farmer ancestry in Britain came from the Mediterranean rather than the Danubian route of farming expansion.

Beginning with the Beaker period, and continuing through the Bronze Age, all British individuals harboured high proportions of Steppe ancestry and were genetically closely related to Beaker-associated individuals from the Lower Rhine area. We use these observations to show that the spread of the Beaker Complex to Britain was mediated by migration from the continent that replaced >90% of Britain's Neolithic gene pool within a few hundred years, continuing the process that brought Steppe ancestry into central and northern Europe 400 years earlier.
...

QuoteNature
Ancient-genome study finds Bronze Age 'Beaker culture' invaded Britain
Famous bell-shaped pots associated with group of immigrants who may have displaced Neolithic farmers.

• Ewen Callaway (http://'http://www.nature.com/news/ancient-genome-study-finds-bronze-age-beaker-culture-invaded-britain-1.21996#auth-1')
  

17 May 2017

(https://languish.org/forums/proxy.php?request=http%3A%2F%2Fwww.nature.com%2Fpolopoly_fs%2F7.44157.1494947036%21%2Fimage%2FWEB_alamyH7YWKA.jpg_gen%2Fderivatives%2Flandscape_630%2FWEB_alamyH7YWKA.jpg&hash=003256c50460ce71229d9107f3ae507e28e0a284)
Bell-shaped pottery from Segovia, Spain, that is characteristic of the Bronze Age 'Bell Beaker' culture.

Around 4,500 years ago, a mysterious craze for bell-shaped pottery swept across prehistoric Europe. Archaeologists have debated the significance of the pots — artefacts that define the 'Bell Beaker' culture — for more than a century. Some argue that they were the Bronze Age's hottest fashion, shared across different groups of people. But others see them as evidence for an immense migration of 'Beaker folk' across the continent.

Now, one of the biggest ever ancient-genome studies suggests both ideas are true. The study, posted on bioRxiv (http://'http://biorxiv.org/content/early/2017/05/09/135962') on 9 May1 (http://'http://www.nature.com/news/ancient-genome-study-finds-bronze-age-beaker-culture-invaded-britain-1.21996#b1'), analysed the genomes of 170 ancient Europeans and compared them to hundreds of other ancient and modern genomes. In Iberia and central Europe, skeletons found near Bell Beaker artefacts share few genetic ties — suggesting that they were not one migrating population. But in Britain, individuals connected to Beaker pots seem to be a distinct, genetically related group that almost wholly replaced the island's earlier inhabitants (see 'Bell Beaker fashion (http://'http://www.nature.com/news/ancient-genome-study-finds-bronze-age-beaker-culture-invaded-britain-1.21996#map')').

If true, this suggests that Britain's Neolithic farmers (who left behind massive rock relics, including Stonehenge (http://'http://www.nature.com/news/2007/070129/full/news070129-7.html')) were elbowed out by Beaker invaders. "To me, that's definitely surprising," says Pontus Skoglund, a population geneticist at Harvard Medical School in Boston, Massachusetts, who was not involved in the research. "The people who built Stonehenge probably didn't contribute any ancestry to later people, or if they did, it was very little."

Some archaeologists say that the study does not prove the scale of the British Beaker invasion, but agree that it is a major work that typifies how huge ancient-DNA studies are disrupting archaeology. It's "groundbreaking", says Benjamin Roberts, an archaeologist at Durham University, UK.

The Bell Beaker phenomenon
The variety of Beaker artefacts makes it hard to define them as emerging from one distinctive culture: many researchers prefer to call their spread the 'Bell Beaker phenomenon', says Marc Vander Linden, an archaeologist at University College London. The distinctive pots, possibly used as drinking vessels, are nearly ubiquitous; flint arrowheads, copper daggers and stone wrist guards are common, too. But there are regional differences in ceramics and burial style. And the immense, yet discontinuous, geographical range of Beaker sites — from Scandinavia to Morocco, and Ireland to Hungary — has sown more confusion. After a few hundred years, the pots vanish from the record.2 (http://'http://www.nature.com/news/ancient-genome-study-finds-bronze-age-beaker-culture-invaded-britain-1.21996#b2'). Past ancient-DNA studies have also hinted at a huge migration, linking Beaker-associated individuals in central Europe to an influx of 'Steppe' peoples from what is now Russia and Ukraine (http://'http://www.nature.com/news/steppe-migration-rekindles-debate-on-language-origin-1.16935')3 (http://'http://www.nature.com/news/ancient-genome-study-finds-bronze-age-beaker-culture-invaded-britain-1.21996#b3').

The latest work, led by geneticists Iñigo Olalde and David Reich at Harvard Medical School, involved 103 researchers at dozens of institutions, including Bronze Age archaeologists. Reich's team analysed more than 1 million DNA variants across the genomes of individuals who lived in Europe between 4700 and 1200 bc. The team declined to comment because the paper has not yet been published in a peer-reviewed journal.

The analysis seems to dispel the idea of one 'Beaker people' arising from a specific source. Individuals in Iberia (which has been proposed as the wellspring for the culture) shared little ancestry with those in central Europe. Even Beaker-associated people in the same region came from different genetic stock. That pattern contrasts with earlier upheavals in Europe driven by mass migrations (http://'http://www.nature.com/news/ancient-swedish-farmer-came-from-the-mediterranean-1.10541'), says Skoglund. Bell Beaker "is the best example of something that is pots and not people" that are spreading, he says.

But in Britain, the arrival of Bell Beaker pots coincided with a shift in the island's genetics. Reich's team analysed the genomes of 19 Beaker individuals across Britain and found that they shared little similarity with those of 35 Neolithic farmers there. The pot-makers were more closely related to 14 individuals from the Netherlands, and had lighter-coloured skin and eyes than the people they replaced. By 2000 bc, signals of Neolithic ancestry disappear from ancient genomes in Britain, Reich's team find — largely replaced by Beaker-associated DNA. Such turnover is "pretty striking", says Garrett Hellenthal, a statistical geneticist at University College London who has studied the peopling of the island through the genomes of living Brits (http://'http://www.nature.com/news/uk-mapped-out-by-genetic-ancestry-1.17136'). More data could reveal surprises, but the team makes a good case that Beaker folk replaced the region's early farmers, he says.

Reich's team calculates that Britain saw a  greater than 90% shift in its genetic make-up. But Roberts says he doesn't see evidence for such a huge shift in the archaeological record. The rise of cremation in Bronze Age Britain could have biased the finding, he cautions, because it might have eliminated bones that could have been sampled for DNA. Although archaeologists are excited to see ancient DNA yield breakthroughs in problems that have vexed their field for decades (http://'http://www.nature.com/news/source-material-1.19962'), says Linden, he expects some push back against the latest study's conclusions. "It's not at all the end of the story."

Quote from: jimmy olsen on October 20, 2017, 01:32:37 AM
Incorrect

Quote from: Valmy on December 01, 2017, 04:46:46 PM
Awesome!

Wait he was friends with somebody who betrayed God's appointed Queen of Ireland? TRAITOR!

Quote from: Grinning_Colossus on December 22, 2017, 04:10:05 PM
Cool. IIRC, Malthus's aunt is Ursula Le Guin or something. We're all related to sci fi writers. :)

Quote from: Admiral Yi on December 22, 2017, 04:15:35 PM

Quote from: Grinning_Colossus on December 22, 2017, 04:10:05 PM
Cool. IIRC, Malthus's aunt is Ursula Le Guin or something. We're all related to sci fi writers. :)

Margaret Atwood is Malthus' aunt.  Malthus and El Frijole Grande are kin.

Quote from: garbon on December 22, 2017, 04:20:11 PM
I assumed it was a joke. Calling Atwood a science fiction writer would be skipping a lot (most?) of her body of work.

Quote from: mongers on December 22, 2017, 04:55:54 PM
Upward of 1,024 people are ancestors of mine, who cool is that for them.   :cool:

Quote from: Valmy on December 22, 2017, 05:29:04 PM

Quote from: mongers on December 22, 2017, 04:55:54 PM
Upward of 1,024 people are ancestors of mine, who cool is that for them.   :cool:

I find it rather disturbing that if I calculate my mathematical number of ancestors in the year 1400 it is well over twice the estimated population of the world at the time. Which means humanity is: extremely inbred.

Quote from: The Minsky Moment on January 10, 2018, 11:25:17 AM
It's the old joke.  A Jewish sailor is shipwrecked on a desert island a Jewish Robinson Crusoe.  Many years later he is found by a passing ship.  His rescuers notice that the sailor constructed three separate buildings, and inquire why. 

"That's my house, where I live" he says, pointed to the first one.
"What's the one next to that?" the rescuers ask. 
"That's the synaogue where I go to pray to God." 
"And the third?" 
"That's the synagogue I don't go to."

Quote from: The Minsky Moment on January 10, 2018, 11:25:17 AM
It's the old joke.  A Jewish sailor is shipwrecked on a desert island a Jewish Robinson Crusoe.  Many years later he is found by a passing ship.  His rescuers notice that the sailor constructed three separate buildings, and inquire why. 

"That's my house, where I live" he says, pointed to the first one.
"What's the one next to that?" the rescuers ask. 
"That's the synaogue where I go to pray to God." 
"And the third?" 
"That's the synagogue I don't go to."

Quote from: Razgovory on January 10, 2018, 04:17:43 PM
Oh okay.  I was just trying to figure out what it had to do with Neanderthal DNA.

Quote from: The Minsky Moment on January 10, 2018, 03:44:49 PM
The "lesson" is that making artificial divisions is core to human experience.  We just can't help ourselves.  Proximity or family connection often makes it worse, not better.

Quote from: Valmy on December 22, 2017, 05:29:04 PM

Quote from: mongers on December 22, 2017, 04:55:54 PM
Upward of 1,024 people are ancestors of mine, who cool is that for them.   :cool:

I find it rather disturbing that if I calculate my mathematical number of ancestors in the year 1400 it is well over twice the estimated population of the world at the time. Which means I am: extremely inbred.

Quote


You're Descended from Royalty and So Is Everybody Else

Anybody you can name from ancient history is in your family tree.

By Adam Rutherford
January 4, 2018

Charlemagne, Carolingian King of the Franks, Holy Roman Emperor, the great European conciliator; your ancestor. I am making an assumption that you are broadly of European descent, which is not statistically unreasonable but certainly not definitive. If you're not, be patient, and we'll come to your own very regal ancestry soon enough.

Along with Alexander and Alfred, Charlemagne is one of a handful of kings who gets awarded the post-nominal accolade "the Great." His early life remains mysterious and the stories are assembled from various sources, but it seems he was born around 742 A.D., just at the time when the Plague of Justinian was dispatching millions at the eastern edge of the moribund Roman Empire. The precise place of his birth is also unknown, but it's likely to be in a town such as Aachen, now in contemporary Germany, or Liège in Belgium. Even Einhard, his dedicated servant and biographer, wouldn't get drawn into the specifics of Charlemagne's early life in his fawning magnum opus, The Life of Charles the Great. The very fact that this account exists—probably the first biography of a European ruler—is testament to how important he was (or at least was seen to be). In many European languages, the word "king" is itself derived from Charlemagne's name.

He was the son of Pippin the Short, an aggressive ruler of France who expanded the Frankish kingdom until his death during the return journey from a campaign against the persistently rebellious realm of Aquitaine in 768. Charlemagne stepped up as his successor, and continued the expansion with aplomb. He battled the Saxons to the northeast, the Lombards in Italy, and Muslims in Spain. He capitalized on his father's good political relations with the Vatican, and in 800 was crowned the first Holy Roman Emperor by Pope Leo III in St Peter's Basilica, an event so momentous that Charlemagne marked it by giving Leo one of the great medieval relics as a thank you—the Holy Prepuce, better known as Jesus' foreskin.

Rutherford_BR-1

A fecund ruler, Charlemagne sired at least 18 children by motley wives and concubines, including nine by his second wife, Hildegard of Vinzgau. These kin included Charles the Younger, Pippin the Hunchback, Drogo of Metz, Hruodrud, Ruodhaid, Adalheid, Hludowic, and not forgetting Hugh, and he consolidated his reign by installing many of his sons in positions of power across the expanding empire. Royal lineages are historically the only ones to get documented well until the modern era, and Charlemagne's lineage is bountiful. We can trace a path directly from his fruitful loin: It begins with his son Louis the Pious, via Lothar, Bertha, Willa, Rosele, eight men called Baldwin, and so on through the ages until it reaches the 21st century in a Dutch family called the Backer-Dirks, whose family tree all the way back to the king is publicly available online.


This pedigree, by gorgeous chance, also contains Joachim Neumann, a 17th-century German Protestant preacher, who sought peace and meditation away from the political machinations and church hullabaloo of Dusseldorf in a small cave near the river Dussel. He had changed his name from Neumann to a Greek version with the same meaning: new man. He wasn't the only new man in that cave. This was the location of the very first new human to be identified, a century later, in the valley of Joachim Neander—Neanderthal man.


Sometime at the end of the 13th century lived a man or woman from whom all Europeans could trace ancestry.

What a lineage to behold! It comes as no great surprise that in the world of amateur genealogy, being descended from imperial royalty is considered of high cachet. In fact, descent from anyone actually named from history brings prestige, as the vast majority of humans have drifted into and out of existence leaving little or no historical footprint that shows they ever drew breath. To be drawn from the bloodline of a king, and not just any old Holy Roman Emperor, but the very first, must be momentous.


Christopher Lee—the great actor who among his roles counts Dracula; Tolkien's Saruman the White; the Man with the Golden Gun himself, Scaramanga; the fallen Jedi Count Dooku; and The Wicker Man's Lord Summerisle—claimed direct ancestry to King Charlemagne via the ancient house of his mother, Countess Estelle Marie (née Carandini di Sarzano):

The Carandini family is one of the oldest in Europe and traces itself back to the first century A.D. It is believed to have been connected with the Emperor Charlemagne, and as such was granted the right to bear the coat of arms of the Holy Roman Empire by Emperor Frederick Barbarossa.1

Maybe it was to enhance his august yet sinister screen image as having played some of the wickedest characters in film history. Most people don't have a coat of arms, but I can say with absolute confidence that if you're vaguely of European extraction, just like cinema's greatest Prince of Darkness, you are descended from Charlemagne too. Hail to the king!

We are all special, which also means that none of us is. This is merely a numbers game. You have two parents, four grandparents, eight great-grandparents, and so on. Each generation back the number of ancestors you have doubles. But this ancestral expansion is not borne back ceaselessly into the past. If it were, your family tree when Charlemagne was Le Grand Fromage would harbor around 137,438,953,472 individuals on it—more people than were alive then, now, or in total. What this means is that pedigrees begin to fold in on themselves a few generations back, and become less arboreal, and more a mesh or weblike. You can be, and in fact are, descended from the same individual many times over. Your great-great-great-great-great-grandmother might hold that position in your family tree twice, or many times, as her lines of descent branch out from her, but collapse onto you. The further back through time we go, the more these lines will coalesce on fewer individuals. "Pedigree" is a word derived from the middle French phrase "pied de grue"—the crane's foot—as the digits and hallux spread from a single joint at the bottom of the tibia, roughly equivalent to our ankle. This branching describes one or a few generations of a family tree, but it's wholly inaccurate as we climb upward into the past. Rather, each person can act as a node into whom the genetic past flows, and from whom the future spills out, if indeed they left descendants at all.

This I find relatively easy to digest. The simple logic is that there are more living people on Earth now than at any single moment in the past, which means that many fewer people act as multiple ancestors of people alive today. But how can we say with utter confidence that any individual European is, like Christopher Lee, directly descended from the great European conciliator?

The answer came before high-powered DNA sequencing and ancient genetic analysis. Instead it comes from mathematics. Joseph Chang is a statistician from Yale University and wished to analyze our ancestry not with genetics or family trees, but just with numbers. By asking how recently the people of Europe would have a common ancestor, he constructed a mathematical model that incorporated the number of ancestors an individual is presumed to have had (each with two parents), and given the current population size, the point at which all those possible lines of ascent up the family trees would cross. The answer was merely 600 years ago. Sometime at the end of the 13th century lived a man or woman from whom all Europeans could trace ancestry, if records permitted (which they don't). If this sounds unlikely or weird, remember that this individual is one of thousands of lines of descent that you and everyone else has at this moment in time, and whoever this unknown individual was, they represent a tiny proportion of your total familial webbed pedigree. But if we could document the total family tree of everyone alive back through 600 years, among the impenetrable mess, everyone European alive would be able to select a line that would cross everyone else's around the time of Richard II.

Chang's calculations get even weirder if you go back a few more centuries. A thousand years in the past, the numbers say something very clear, and a bit disorienting. One-fifth of people alive a millennium ago in Europe are the ancestors of no one alive today. Their lines of descent petered out at some point, when they or one of their progeny did not leave any of their own. Conversely, the remaining 80 percent are the ancestor of everyone living today. All lines of ancestry coalesce on every individual in the 10th century.

One way to think of it is to accept that everyone of European descent should have billions of ancestors at a time in the 10th century, but there weren't billions of people around then, so try to cram them into the number of people that actually were. The math that falls out of that apparent impasse is that all of the billions of lines of ancestry have coalesced into not just a small number of people, but effectively literally everyone who was alive at that time. So, by inference, if Charlemagne was alive in the ninth century, which we know he was, and he left descendants who are alive today, which we also know is true, then he is the ancestor of everyone of European descent alive in Europe today.

It's not even relevant that he had 18 children, a decent brood for any era. If he'd had one child who lived and whose family propagated through the ages until now, the story would be the same. The fact that he had 18 increases the chances of his being in the 80 percent rather than the 20 percent who left no 21st-century descendants, but most of his contemporaries, to whom you are all also directly related, will have had fewer than 18 kids, and some only one, and yet they are all also in your family tree, unequivocally, definitely, and assuredly.


DNA says exactly the same thing as mathematical ancestry: Our family trees are not trees at all, but entangled meshes.

At least that's the theory. With the advent of easy and cheap DNA sequencing came the possibility of testing this math. DNA is the bearer of biological ancestry, and you get all of your DNA from your two parents, pretty much a 50:50 split. They in turn got all of their DNA from their parents, so one quarter of your DNA is the same as a quarter of each of your grandparents. If you have a cousin, then you share around an eighth of your DNA, as you have a pair of grandparents in common. These shared bits of DNA are not the same sections though. And it doesn't keep halving perfectly as you meander up through your family tree. Remember that DNA gets shuffled when a sperm or egg is made, and every single shuffle is different, but it's quite clumsy shuffling. In the newly shuffled deck, that is, your own personal genome, big chunks of it are the same as your father or mother. The more closely related two people are, the more DNA they will share in big chunks. This is why identical twins are identical (all the chunks are the same), and why siblings and parents look similar (half of their DNA is the same as each other). In genetics, we call these sections of DNA identical by descent, and they are very useful for measuring the relatedness of two individuals.


In 2013, geneticists Peter Ralph and Graham Coop showed that DNA says exactly the same thing as Chang's mathematical ancestry: Our family trees are not trees at all, but entangled meshes. They looked for lengths of identical by descent DNA in 2,257 people from around Europe (to mitigate the influence of recent migration, all the subjects selected had four grandparents from the same region or country). By measuring the lengths of the shared DNA, they could estimate how long ago that deck got shuffled, and therefore how related any two people are. Computing and DNA have empowered this field, and this is shown in their dataset and the number crunching that follows.

Joseph Chang's mathematical calculation didn't account for something very obvious, which is that we don't mate randomly. We typically marry within socioeconomic groups, within small geographical areas, within shared languages. But with Coop and Ralph's genetic analysis, it didn't seem to matter that much. Ancestry is such that genes can spread very quickly over generations. It might seem that a remote tribe would have been isolated from others for centuries in, for example, the Amazon. But no one is isolated indefinitely, and it only takes a very small number of people to breed out with people from beyond their direct gene pool for that DNA to rapidly descend through the generations.

Chang factored that into a further study of common ancestry beyond Europe, and concluded in 2003 that the most recent common ancestor of everyone alive today on Earth lived only around 3,400 years ago.

He used two calculations, one that simply crunched the math of ancestry, and another that incorporated a simplified model of towns and migration and ports and people. In the computer model, a port has a higher rate of immigration, and growth rates are higher. With all these and other factors input, the computer calculates when lines of ancestry cross, and the number comes out at around 1400 B.C. It places that person somewhere in Asia, too, but that is more likely to do with the geographical center point from which the migrations are calculated. If this sounds too recent, or baffling because of remote populations in South America or the islands of the South Pacific, remember that no population is known to have remained isolated over a sustained period of time, even in those remote locations. The influx of the Spanish into South America meant their genes spread rapidly into decimated indigenous tribes, and eventually to the most remote peoples. The inhabitants of the minuscule Pingelap and Mokil atolls in the mid-Pacific have incorporated Europeans into their gene pools after they were discovered in the years of the 19th century. Even religiously isolated groups such as the Samaritans, who number fewer than 800 and are sequestered within Israel, have elected to outbreed in order to expand their limited gene pool.

You are of royal descent, because everyone is. You are of Viking descent, because everyone is.

When Chang factored in new, highly conservative variables, such as reducing the number of migrants across the Bering Straits to one person every 10 generations, the age of the most recent common ancestor of everyone alive went up to 3,600 years ago.

This number may not feel right, and when I talk about it in lectures, it often results in a frown of disbelief. We're not very good at imagining generational time. We see families as discrete units in our lifetimes, which they are. But they're fluid and continuous over longer periods beyond our view, and our family trees sprawl in all directions. The concluding paragraph of Chang's otherwise tricky mathematical and highly technical study is neither of those things. It's beautiful writing, extremely unusual in an academic paper, and it deserves to be shared in full:

Our findings suggest a remarkable proposition: No matter the languages we speak or the color of our skin, we share ancestors who planted rice on the banks of the Yangtze, who first domesticated horses on the steppes of the Ukraine, who hunted giant sloths in the forests of North and South America, and who laboured to build the Great Pyramid of Khufu.

You are of royal descent, because everyone is. You are of Viking descent, because everyone is. You are of Saracen, Roman, Goth, Hun, Jewish descent, because, well, you get the idea. All Europeans are descended from exactly the same people, and not that long ago. Everyone alive in the 10th century who left descendants is the ancestor of every living European today, including Charlemagne, and his children Drogo, Pippin, and, of course, not forgetting Hugh. If you're broadly eastern Asian, you're almost certain to have Genghis Kahn sitting atop your tree somewhere in the same manner, as is often claimed. If you're a human being on Earth, you almost certainly have Nefertiti, Confucius, or anyone we can actually name from ancient history in your tree, if they left children. The further back we go, the more the certainty of ancestry increases, though the knowledge of our ancestors decreases. It is simultaneously wonderful, trivial, meaningless, and fun.

The truth is that we all are a bit of everything, and we come from all over. Even if you live in the most remote parts of the Hebrides, or the edge of the Greek Aegean, we share an ancestor only a few hundred years ago. A thousand years ago, we Europeans share all of our ancestry. Triple that time and we share all our ancestry with everyone on Earth. We are all cousins, of some degree. I find this pleasing, a warm light for all mankind to share. Our DNA threads through all of us.

Ancestry is messy and difficult. Genetics is messy and mathematical, but powerful if deployed in the right way. People are horny. Lives are complex. A secret history is truly hidden in the mosaics of our genomes, but caveat emptor. No scientific test exists that will tell you where the DNA that you would come to inherit was precisely located in the past. Human history is replete with the fluid movement of people, and tribes and countries and cultures and empires are never, ever permanent. Over a long enough timescale, not one of these descriptions of historical people holds steadfast, and only a thousand years ago your DNA began being threaded from millions from every culture, tribe, and country. If you want to spend your cash on someone in a white coat telling you that you're from a tribe of wandering Germanic topless warriors, or descended from Vikings, Saracens, Saxons, or Drogo of Metz, or even the Great Emperor Charlemagne, help yourself. I, or hundreds of geneticists around the world, will shrug and do it for free: You are. And you don't even need to spit in a tube—your majesty.

QuoteThe numbers and the genes say the most recent ancestor for all living people was 3400 years ago.

Quote from: Grinning_Colossus on January 10, 2018, 07:58:11 PM

QuoteThe numbers and the genes say the most recent ancestor for all living people was 3400 years ago.

That seems very unlikely unless there are literally no pure blooded Aboriginals or Native Americans left.

Quote from: Valmy on January 10, 2018, 08:01:32 PM

Quote from: Grinning_Colossus on January 10, 2018, 07:58:11 PM

QuoteThe numbers and the genes say the most recent ancestor for all living people was 3400 years ago.

That seems very unlikely unless there are literally no pure blooded Aboriginals or Native Americans left.

Yeah it is probably more like 20,000 years ago. I just figure if I go back to the Roman Empire I am descended from Pompey Magnus billions of different ways...and you are to!

Quote from: Ed Anger on January 10, 2018, 08:35:40 PM
Ewwwwww. Pompey.  :yucky:

Quote from: Grinning_Colossus on January 10, 2018, 07:58:11 PM

QuoteThe numbers and the genes say the most recent ancestor for all living people was 3400 years ago.

That seems very unlikely unless there are literally no pure blooded Aboriginals or Native Americans left.

Quote from: Barrister on January 10, 2018, 09:04:17 PM

Quote from: Grinning_Colossus on January 10, 2018, 07:58:11 PM

QuoteThe numbers and the genes say the most recent ancestor for all living people was 3400 years ago.

That seems very unlikely unless there are literally no pure blooded Aboriginals or Native Americans left.

There probably aren't any.  There's been substantial intermixing in the last 500 years.

Quote from: Grinning_Colossus on January 10, 2018, 07:58:11 PM

QuoteThe numbers and the genes say the most recent ancestor for all living people was 3400 years ago.

That seems very unlikely unless there are literally no pure blooded Aboriginals or Native Americans left.

QuoteBefore about 1930, European maps showed the highlands as uninhabited forests,  When first flown over by aircraft, numerous settlements with agricultural terraces and stockades were observed. The most startling discovery took place on 4 August 1938, when Richard Archbold discovered the Grand Valley of the Baliem River, which had 50,000 yet-undiscovered Stone Age farmers living in orderly villages. The people, known as the Dani, were the last society of its size to make first contact with the rest of the world

Quote from: Malthus on January 11, 2018, 09:00:23 AM
Seems unlikely - given that (say) Highland New Guinea was only discovered as being densely inhabited in the late 1930s (by aircraft!), and there has been no particular movement to flood the place with immigrants since. It is entirely possible that a child may still be alive from before such contact - they would be 80 or so.

QuoteBefore about 1930, European maps showed the highlands as uninhabited forests,  When first flown over by aircraft, numerous settlements with agricultural terraces and stockades were observed. The most startling discovery took place on 4 August 1938, when Richard Archbold discovered the Grand Valley of the Baliem River, which had 50,000 yet-undiscovered Stone Age farmers living in orderly villages. The people, known as the Dani, were the last society of its size to make first contact with the rest of the world

https://en.wikipedia.org/wiki/New_Guinea#European_contact

A single holdout bloodline there would push that number back by tens of thousands of years.

Quote from: mongers on January 11, 2018, 09:08:15 AM

Quote from: Malthus on January 11, 2018, 09:00:23 AM
Seems unlikely - given that (say) Highland New Guinea was only discovered as being densely inhabited in the late 1930s (by aircraft!), and there has been no particular movement to flood the place with immigrants since. It is entirely possible that a child may still be alive from before such contact - they would be 80 or so.

QuoteBefore about 1930, European maps showed the highlands as uninhabited forests,  When first flown over by aircraft, numerous settlements with agricultural terraces and stockades were observed. The most startling discovery took place on 4 August 1938, when Richard Archbold discovered the Grand Valley of the Baliem River, which had 50,000 yet-undiscovered Stone Age farmers living in orderly villages. The people, known as the Dani, were the last society of its size to make first contact with the rest of the world

https://en.wikipedia.org/wiki/New_Guinea#European_contact

A single holdout bloodline there would push that number back by tens of thousands of years.

But that's recorded contact, are you suggesting for thousands of years an invisible barrier exited between this interior spot and the rest of PNG/the coast, that sealed it off from contact with other humans and the inevitable sexual exchanges that goes with such contact?

QuoteThe indigenous population of Papua New Guinea is one of the most heterogeneous in the world. Papua New Guinea has several thousand separate communities, most with only a few hundred people. Divided by language, customs, and tradition, some of these communities have engaged in endemic warfare with their neighbors for centuries. It is the second most populous nation in Oceania.

The isolation created by the mountainous terrain is so great that some groups, until recently, were unaware of the existence of neighboring groups only a few kilometers away. The diversity, reflected in a folk saying, "For each village, a different culture", is perhaps best shown in the local languages. Spoken mainly on the island of New Guinea, about 650 of these Papuan languages have been identified; of these, only 350-450 are related. The remainder of the Papuan languages seem to be totally unrelated either to each other or to the other major groupings. In addition, many languages belonging to Austronesian language group are used in Papua New Guinea, and in total, more than 800 languages are spoken in Papua New Guinea.[1] Native languages are spoken by a few hundred to a few thousand, although Enga language, used in Enga Province, is spoken by some 130,000 people.

QuoteThe first large-scale genetic study of people in Papua New Guinea has shown that different groups within the country are genetically highly different from each other. Scientists reveal that the people there have remained genetically independent from Europe and Asia for most of the last 50,000 years, and that people from the country's isolated highlands region have been completely independent even until the present day.

QuoteProfessor Stephen J. Oppenheimer, second author of the paper from the Wellcome Trust Centre for Human Genetics, University of Oxford, said: "We found a striking difference between the groups of people who live in the mountainous highlands and those in the lowlands, with genetic separation dating back 10,000-20,000 years between the two. This makes sense culturally, as the highland groups historically have kept to themselves, but such a strong genetic barrier between otherwise geographically close groups is still very unusual and fascinating."