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

[The Brain]

So everyone in Europe and North America is descended from Elagabalus. Makes sense.

[Malthus]

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.

Before 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.

[mongers]

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.

Before 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?

[Caliga]

Also don't forget the Sentineli of North Sentinel Island.

[Grinning_Colossus]

There have been extremely isolated populations, though--e.g., Tasmanians or Sentinelese--and it only takes on lineage.

[Malthus]

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.

Before 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?

As a matter of fact ... the interior of NG had remarkably little contact with the coast, because of it horrific geography (impenetrable mountains and swamps) and because NG was split up into ferocious tribes, who were in the habit of being permanently at war with all of their neighbors (occasionally, to eat them).

This is reflected in the language situation - NG is, by far, the most linguistically diverse place on Earth:

The 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.

[Emphasis added]

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

There is no doubt that modern colonialism mixed that up somewhat - but, as noted, some major communities (50,000 plus inhabitants) weren't even identified until 1938! So it hasn't had long to work.

[Malthus]

This may be of interest:

https://www.sciencedaily.com/releases/2017/09/170914152337.htm

The 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.

[Emphasis added]

Professor 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."

If this is true, it directly contradicts the claim of a common ancestor 3,400 or so years ago.

[The Minsky Moment]

Oh okay.  I was just trying to figure out what it had to do with Neanderthal DNA.

It's purely a Denisovan issue.

[The Minsky Moment]

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.
. . .
A single holdout bloodline there would push that number back by tens of thousands of years.

So amend the claim to:
The most recent ancestor (or ancestor of involuntary dinner guest) of all living people was 3400 years ago.

[Malthus]

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.
. . .
A single holdout bloodline there would push that number back by tens of thousands of years.

So amend the claim to:
The most recent ancestor (or ancestor of involuntary dinner guest) of all living people was 3400 years ago.

I love the gruesomeness of the fact that there is a disease in New Guinea that can only be spread by ... eating human brains.

https://en.wikipedia.org/wiki/Kuru_(disease)

Even more bizarre: it's a prion disease. Those things are freaky.

[jimmy olsen]

This is awesome news for archaeology

http://johnhawks.net/weblog/reviews/genetics/forensic/ancient-enamel-amelogenin-sex-2018.html

Testing the sex of ancient individuals from their enamel proteins

13 Jan 2018

A recent paper by Nicolas Stewart and colleagues presents a way to determine the sex of ancient individuals by examining the composition of their tooth enamel: "Sex determination of human remains from peptides in tooth enamel".

Amelogenin is a protein component of tooth enamel. Humans have two different genes for amelogenin, AMELX on the X chromosome, and AMELY on the Y chromosome. The protein products of these genes have slightly different amino acid sequences. Enamel from males, who have both X and Y chromosomes, has a mix of the two proteins, while females have only the AMELX product.

Stewart and coworkers etch the ancient enamel with an acid, freeing protein fragments, or peptides. They use a mass spectrometer to detect the signatures of the Y chromosome and X chromosome specific peptide variations.

The ability to determine the sex of infant and juvenile remains completely revolutionizes studies of growth, child care, epidemiology, and demography in the past. For the first time, it will allow osteologists to examine sex-specific cultural treatment and differentiate between the health of boys and girls, as well as sex-specific growth trajectories and past developmental milestones, such as age of puberty and subsequent repercussions for fertility. Sites with poor preservation are common in archaeological contexts, and at such sites teeth generally survive better than bone, and thus sex can be established for adults as well as juvenile skeletons in the absence of key skeletal identifiers. In addition, the dimorphic peptide sequence is identical in apes (Fig. S1) and so should be present in all hominins.

This is potentially very important for a number of questions that cannot be answered from archaeological sites without direct evidence of sex. The sex of young children in particular is almost impossible to establish reliably from skeletal indicators. In some recent contexts, sex can be inferred from grave goods or from inscriptions. But for most ancient people–including Neandertals and other Paleolithic populations–the sex of young children is unknown.

Amelogenin has previously been used as a forensic sex determination test in humans and in other mammal species. In humans, this test fails to identify males a small fraction of the time because the Y chromosome sometimes has large deletions that include the Y amelogenin (AMELY) gene. That implies that a small fraction of misidentification (biased toward misidentifying males as females) should result from this test applied to ancient samples.

It's not known whether this difference between males and females has any functional consequences for enamel. Some researchers have been interested in whether the presence of an additional amelogenin variant in males might influence caries. In some populations, females are more likely to have caries than males. The AMELY protein makes up only around 10 percent of the total amelogenin in a tooth, as the Y chromosome version of the gene is not expressed as highly as the X version, but the presence of an alternative form of the protein might make some difference. However, it is very hard to test whether sex-specific life history traits, such as diet differences during development, pregnancy, or other environmental factors, might instead lead to a difference in caries risk.

At any rate, caries incidence was very, very low during most of our evolutionary history compared to the past 20,000 years (and is low in nearly all other mammals). The amelogenin in both sexes did its job pretty well for most of our existence.

Reference

Stewart, N. A., Gerlach, R. F., Gowland, R. L., Gron, K. J., & Montgomery, J. (2017). Sex determination of human remains from peptides in tooth enamel. Proceedings of the National Academy of Sciences, 114(52), 13649-13654.

[Jacob]

That's pretty cool.

[jimmy olsen]

This is a mind blowing achievement. I mean, sure it's only possible because of how anal retentive and weird Icelanders are, but still, wow!

https://futurism.com/dna-man-died-1827-recreated-remains/

DNA of Man Who Died in 1827 Recreated Without His Remains

by  Chelsea Gohd  on January 15, 2018 18876   

Recreating a deceased person or animal's DNA has required that DNA be extracted from the remains of the individual, but a new study has shown that may not be the only way. The DNA of a man who died nearly 200 years ago has been recreated from his living descendants rather than his physical remains — something that has never been done before.

deCODE Genetics a biopharmaceutical company in Iceland, achieved this feat by taking DNA samples from 182 Icelandic descendants of Hans Jonatan, a man who is quite an icon in Iceland, most well known for having freed himself from slavery in a heroic series of seemingly impossible events.

It was the unique circumstances of Hans Jonatan's life that made it possible for his DNA to be recreated after his death. For one, Jonatan was the first Icelandic inhabitant with African heritage. Iceland also boasts an extensive and highly detailed collection of genealogical records. The combination of Jonatan's unique heritage and the country's record-keeping for inhabitants' family trees made this remarkable recreation possible.

deCODE used DNA screened from 182 relatives, first reconstructing 38 percent of Jonatan's mother Emilia's DNA (which accounted for 19 percent of Jonatan's). Published in Nature Genetics, this elaborate study began with a whopping 788 of Jonatan's known descendants, but was able to be narrowed down to 182 through DNA screening against known markers.

While this is truly an amazing feat, according to Robin Allaby of the University of Warwick in the United Kingdom,  it "seems to be the sort of analysis you could only do under particular circumstances when an immigrant genome is of a very rare type." Despite these limitations, deCODE believes the technique could have extensive applications.

Historical Research

Kári Stefánsson of deCODE said that "It's all a question of the amount of data you have. In principle, it could be done anywhere with any ancestors, but what made it easy in Iceland was that there were no other Africans."

Allaby does believe the results of this study could give us additional avenues to explore the DNA of those who have long since passed. "It's the sort of study that could, for instance, be used to recover genomes of explorers who had interbred with isolated native communities."

Theoretically, a technique like this could help researchers create "virtual ancient DNA," which would allow scientists to recreate the DNA of historical figures. Agnar Helgason of deCODE stated that "Any historic figure born after 1500 who has known descendants could be reconstructed."

While it's exciting, there are still major hurdles to overcome in terms of the potential future applications. The quantity, scale, and detail of the DNA from living ancestors required to recreate a person's DNA make it impractical for use within most families. Additionally, with each new generation identifiable DNA fragments get smaller and more difficult to work with.

To that end, more immediate applications might involve repairing and filling in spaces within family trees. But if it's honed, it could become a valuable historical tool, giving us an in-depth look at what life was like for historical figures like Jonatan. Scientists could genetically resurrect anyone, providing us with a more thorough understanding of our species both from our own personal familial perspectives and through the more macrocosmic lens of human history.

[jimmy olsen]

This is not that surprising on the other hand.

https://theconversation.com/ancient-dna-sheds-light-on-the-mysterious-origins-of-the-first-scandinavians-89703

Ancient DNA sheds light on the mysterious origins of the first Scandinavians   
January 10, 2018 9.19pm AEDT .

Author Jan Apel   
Senior Lecturer of Archaeology, Lund University

Tracking the migration of humans isn't easy, but genetics is helping us uncover new information at breathtaking speed. We know that our species originated in Africa and likely reached Europe from the southeast no later than 42,000 years ago. During the last ice age some 33,000-20,000 years ago, when a permanent ice sheet covered northern and parts of central Europe, modern humans in southwest Europe were isolated from groups further to the east.

When the ice sheet retreated, some of these hunter gatherers eventually colonised Scandinavia from the south about 11,700 years ago, making it one of the last areas of Europe to be inhabited. But exactly who these individuals were and how they got there has remained a puzzle for researchers. Now we have sequenced the genomes of seven hunter gatherers, dated to be 9,500-6,000 years old, to find out.

One of the reasons the origins of the first Scandinavians is so enigmatic is a major shift in stone tool technology that appeared soon after they got there. This new technology seemed to have had an origin in eastern Europe and it has been an open question how it reached Scandinavia.

Early migration

Our interdisciplinary research team combined genetic and archaeological data with reconstructions of the ice sheets to investigate the earliest people of the Scandinavian peninsula. We extracted DNA for sequencing from bones and teeth of the seven individuals from the Norwegian Atlantic coast and the Baltic islands of Gotland and Stora Karlsö.

We then compared the genomic data with the genetic variation of contemporary hunter gatherers from other parts of Europe. To our surprise, hunter gatherers from the Norwegian Atlantic coast were genetically more similar to contemporaneous populations from east of the Baltic Sea, while hunter gatherers from what is Sweden today were genetically more similar to those from central and western Europe. One could say that – in Scandinavia at that time – the geographic west was the genetic east and vice versa.

This contradiction between genetics and geography can only be explained by two main migrations into Scandinavia. It would have started with an initial pulse from the south – modern day Denmark and Germany – that took place just after 11,700 years ago. Then there would have been an additional migration from the northeast, following the Atlantic coast in northern Finland and Norway becoming free of ice.


Artist's impression of the last ice age. wikipedia, CC BY-SA
.
These results, published in the PLOS Biology, agree with archaeological observations that the earliest occurrences of the new stone tool technology in Scandinavia were recorded in Finland, northwest Russia and Norway – dating to about 10,300 years ago. This kind of technology only appeared in southern Sweden and Denmark later on.

Blue eyes, blonde hair

Knowing the genomes of these hunter gatherer groups also allowed us to look deeper into the population dynamics in stone age Scandinavia. One consequence of the two groups mixing was a surprisingly large number of genetic variants in Scandinavian hunter gatherers. These groups were genetically more diverse than the groups that lived in central, western and southern Europe at the same time. That is in stark contrast to the pattern we see today where more genetic variation is found in southern Europe and less in the north.


Axe, fish hook and other stone tools from the earliest Scandinavians, found in a cave on Gotland. Jan Apel, Author provided
.
The two groups that came to Scandinavia were originally genetically quite different, and displayed distinct physical appearances. The people from the south had blue eyes and relatively dark skin. The people from the northeast, on the other hand, had a variation of eye colours and pale skin.

Originally, humans are a species from warmer climates closer to the equator and we mainly cope with challenging environments with specific behaviour and technology. This includes making fires, clothes and specialised hunting equipment. However, in the long term there is also potential for adaptation through genetic changes.

For example, we found that genetic variants associated with light skin and eye pigmentation were carried, on average, in greater frequency among Scandinavian hunter gatherers than their ancestors from other parts of Europe. Scientists believe that light skin pigmentation helps people better absorb sunlight and synthesise vitamin D from it.

That suggests that local adaptation to the high-latitude climate associated with low levels of sunlight and low temperatures took place in Scandinavia after these groups arrived. In fact, this is in agreement with the worldwide pattern of pigmentation decreasing with distance to the equator.

Modern people of northern Europe trace relatively little genetic ancestry back to the early Scandinavians studied by us. That's because several later migrations have changed the Scandinavian gene pool over time. We know that migrations during the later stone age, the bronze age and historical times have brought new genetic material as well as novel technologies, cultures and languages.

The picture is similarly complex in other parts of the world. Hopefully it won't be long before genetics helps us work out the detailed picture of exactly how humans have spread across the world since we first emerged.

[derspiess]

Was mapping out one of the lines on my dad's side and found that William Shakespeare is my 1st cousin... 13x removed

edit: I am guessing that is fairly common, since his grandmother, Mary Webb (my 13th great grandmother) was spitting out kids like a Pez dispenser.