DNA Sequencing Megathread! Neanderthals, Denisovans and other ancient DNA!

[Eddie Teach]

[Lettow77]

But that tea party looked fun 

[Eddie Teach]

Many weak beverages were imbibed.

[Siege]

Nobody commenting on the elections in Virginia?

[Sheilbh]

That's in the Fermi paradox thread

[Siege]

What? Didn't see it.

[Queequeg]

 

[Siege]

Ok, what's so funny?

[jimmy olsen]

Interesting history of the development of light skin in European populations. I'm a bit surprised it is so recent, I would have assumed this is something that would have been picked up via introgression with Neanderthals.

http://blogs.discovermagazine.com/gnxp/2013/11/big-sweeps-happen/#.UoL2uSdjGOs

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.

[Grinning_Colossus]

I recall a theory that European populations started losing melanin with the introduction of agriculture to the Baltic Sea region. Regional climatic effects (Gulf Stream, etc.) created an unique environment in which agriculture could be productive at that latitude. Whereas populations at similar latitudes remained mainly non-agricultural and hunted quite a lot, the Baltic people were able to grow most of their calories and thus had issues with vitamin D deficiency. Selection then favored albinism to enable greater vitamin D synthesis, and boom, white people. Since the move to the Americas was a paleolithic migration it would have preceded the emergence of the gene.

[jimmy olsen]

This would mean dogs are two or three times older than any other domesticated animal and evolved along with us in our original state as hunter gatherers.

http://www.nytimes.com/2013/11/14/science/wolf-to-dog-scientists-agree-on-how-but-not-where.html

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.

[Josquius]

Yeah, that's quite a well known theory about dogs.
We co-evolved into a partnership where civilization could develop.

[jimmy olsen]

It's been one theory among many, and was not the most favored for quite a while.


Now for some new stuff.

As far as I know there have been three Denisovan genomes analyzed. How is that a large enough sample size to figure that 4% of their genome originated in yet another hominin?
http://www.nbcnews.com/science/steamy-gene-pool-extinct-human-relatives-had-sex-mystery-ancestor-2D11623882

Steamy 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.

http://www.nature.com/news/mystery-humans-spiced-up-ancients-rampant-sex-lives-1.14196?WT.mc_id=TWT_NatureNews

Mystery 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.

[jimmy olsen]

Very interesting news on the Denisovans.  Did not expect to find genetic evidence of them in Spain. 

The Max Planck Institute for Evolutionary Anthropology managed to sequence the 400,000 year mtDNA of H. hidelbergenis from the Pit of Bones in Spain. Surprisingly rather than being an ancestor of Neanderthal mtDNA clades, it is most closely related to those of the Denisovans.

I think this has a more simple explanation than many of the scientists quoted seem to favor, simple genetic drift. Given that mtDNA is only inherited through the maternal line and the small effective populations of both the Neanderthals and Denisovans, genetic drift would have been a significant factor over time. If the ancestral population had both the Denisovan and Neanderthal mtDNA sequences in it, it is well within the range of possibility that after the divergence into two separate populations the Denisovans eventually lost what came to be known as the Neanderthal mtDNA sequences and the Neanderthals eventually lost what came to be known as the Denisovan sequences.


http://www.scientificamerican.com/article.cfm?id=earliest-human-dna-shows-unforeseen-mixing-with-mystery-population

Earliest 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; 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; 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.

http://dienekes.blogspot.kr/2013/12/400-thousand-year-old-human-mtdna-from.html

It 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.

[Malthus]

If ancient humans would screw anything even remotely human-looking, I wonder how the populations ever came to drift in the first place.