Oldest Evidence of Siberian Crossing of Native Americans

UPI has a story about evidence from around Lake Baikal that links populations of Siberia to the earliest groups who came over from Siberia to the New World.  Brooks Hays writes:

New genomic analysis of ancient remains in Siberia -- detailed this week in the journal Cell -- have offered scientists fresh insights into the movements of human populations across Eurasia and into the Americas at the end of the Stone Age.

“Previous studies observed the genetic differences between individuals from different time periods, but didn't investigate the differences by dating the admixture events,” lead study author He Yu, postdoctoral researcher at the Max Planck Institute for the Science of Human History in Germany, told UPI in an email. “Our study reports a 14,000-year-old individual, which actually fills in a large blank of ancient genomes in this region, between 23,000 and approximately 8,000 years ago.”

By using the DNA of a tooth from the 14 ky old individual, Yu and his team have established links to the earliest Native Americans.

“The deep connection observed in this study is sharing of the same admixed ancestry between Upper Paleolithic Siberian and First Americans," Yu said. "We are not suggesting interbreeding between Native American and Siberian, or any back flow of Native American ancestry into Siberia. But we are suggesting that, the First American ancestry was formed in Siberia and also existed there, in a large range of time and space, so we can detect it in ancient Siberian individuals.”

There have always been conflicting theories about how and when the migrations to the New World occurred and there has always been evidence for movements from the Lena River, in Siberia and the northern Amur river in northern China.

Interestingly, they also found genetic evidence of the plague in some of the Bronze age populations from the area, which they hypothesized came from Europe, indicating that there was considerable movement between these populations.

The Ancient History of Neanderthals in Europe

The Max Planck Society has a post in PhysOrg, a highly-regarded science site, on the history of Neandertals (they have used the old spelling). 

Researchers at the Max Planck Institute for Evolutionary Anthropology in Leipzig, Germany, have retrieved nuclear genome sequences from the femur of a male Neanderthal discovered in 1937 in Hohlenstein-Stadel Cave, Germany, and from the maxillary bone of a Neanderthal girl found in 1993 in Scladina Cave, Belgium. Both Neanderthals lived around 120,000 years ago, and therefore predate most of the Neanderthals whose genomes have been sequenced to date.

Perhaps the most interesting aspect of the research was how much evolution within Neandertals was revealed:

Intriguingly, unlike the nuclear genome, the mitochondrial genome of the Neanderthal from Hohlenstein-Stadel Cave in Germany is quite different from that of later Neanderthals—a previous report showed that more than 70 mutations distinguish it from the mitochondrial genomes of other Neanderthals. The researchers suggest that early European Neanderthals may have inherited DNA from a yet undescribed population.

As with what is going on in human fossil research in China, it seems as though there is a tangled web of relationships between human populations extending through both time and space.  Whatever complexity we envision for these groups, it is probably far more so.  As I wrote about the Chinese material:

The implications of these skulls are stark: there has been widespread population mixing and regional continuity in Europe and Asia for at least 400 thousand years. Not only did the Neandertals feel enough cultural kinship to mate and have children with these East Asian people, the early modern humans coming out of Africa did, as well.  As Chris Davis of China Daily News put it: “One big happy family.”

It is becoming increasingly clear that our simplistic notions of population replacement and regional continuity are probably wrong. Is evolution occurring in these human groups? It absolutely is. Just how these puzzle pieces relate to each other is the question.

New Homo sapiens Fossil Found in Arabia

A new fossil finger has been unearthed as Arabia that purports to be 87 ky old.  UPI is on it.

The fossil was found buried beneath the sands of the Nefud Desert, which today stretches across the Northern Arabia Peninsula. The site where the fossil was found was once home to a freshwater lake.

Around the time humans showed up, a climatic shift brought monsoons to the region, spawning grasslands. Animal fossils suggest antelope grazed the land and hippos swam in the ancient lake.

Researchers measured ratios of radioactive elements in the finger bone and compared the ratios to those found in animal fossils with confirmed dates. The analysis confirmed the age of the human fossil, the oldest found in Arabia.

"This discovery for the first time conclusively shows that early members of our species colonized an expansive region of southwest Asia and were not just restricted to the Levant," Huw Groucutt, a researcher with the University of Oxford and the Max Planck Institute for the Science of Human History, said in a news release.

How do we know it was from Homo sapiens?

Among these finds was a well preserved and small fossil, just 3.2 cm long, which was immediately recognized as a human finger bone. The bone was scanned in three dimensions and its shape compared to various other finger bones, both of recent Homo sapiens individuals and bones from other species of primates and other forms of early humans, such as Neanderthals. The results conclusively showed that the finger bone, the first ancient human fossil found in Arabia, belonged to our own species.

I do not have access to this article as neither the lab nor UT has a subscription to Nature: Ecology & Evolution. Aside: Given our focus on materials science and computing, I kind of get why ORNL does not have a subscription.  UT, not so much.  This journal should be in their wheelhouse.  According to the abstract, the find is securely dated and:

The palaeoenvironmental context of Al Wusta demonstrates that H. sapiens using Middle Palaeolithic stone tools dispersed into Arabia during a phase of increased precipitation driven by orbital forcing, in association with a primarily African fauna.

Maddenly, there is no information in the abstract about the morphology of the find, especially given that Neandertal and early anatomically modern phalanges are remarkably similar. I am sure they were able to differentiate it, but I would sure like to know how.

The Effect of Neandertal DNA on Modern Humans

After the 2013 sequencing of the Neandertal DNA, Janet Kelso, of the Max Planck Institute undertook a study to see what genes present in Neandertals still had an effect on modern humans.  The study employed the data from a genotyping project done by UK Biobank, which surveyed 500,000 people.  What did they find? 

Kelso and her team first narrowed the sample to include only the 112,338 individuals with white European ancestry (whose genomes contain Neanderthal DNA), and used these data to tease out which traits are influenced by Neanderthal genetic variants. The traits they identified included those that affect hair color, skin color, skin tanning and burning, sleeping patterns, mood, and tobacco use.

For example, being a self-described night owl and being prone to daytime napping were both traits positively influenced by Neanderthal variants, as were loneliness, low mood, and smoking. Genetic loci associated with having red hair were found to be devoid of Neanderthal variants, suggesting red-headed Neanderthals were either rare or non-existent. The new study also supports Capra and colleagues’ previous observations that Neanderthal variants are associated with sun-induced skin lesions, mood disorders, and smoking.

That traits such as skin color, sun-burning, and sleep patterns were identified by the analyses might be explained by the Neanderthals’ adaptations to life at more northern latitudes, suggests Capra. But for other traits, he notes, determining how the effects seen in present-day people might once have affected Neanderthals themselves “is one of our crucial challenges.” For example, he says, “of course, Neanderthals were not smoking.”

Maybe I am behind the times but I did not know there was a “trait” for tobacco use. I figured you either did that or you didn't. Like Robin Williams says in Dead Again: either be a smoker or don't be a smoker. Choose it and be it.

I suspect we will continue to find effects of the Neandertal genome, especially since our understanding of how much interbreeding there was continues to change.  It is also a testament to the stability of the human genome that, even after a separation of some several hundred thousand years, interbreeding was still possible.  

National Geographic Special on Denisova

National Geographic is running a special report on the importance of the Denisova hominin for later human evolution.  The timing is curious since this was big news two years ago, but “The Case of the Missing Human Ancestor” goes into the depths of the discovery, the tests done, the complex stratigraphy of the cave, and the significance of what the Max Planck Institute found.  Further, it is written by Jamie Shreeve, and he is always a good read.  He writes:

In the summer of 2010 a human toe bone had emerged, along with the enormous tooth, from Layer 11. In Leipzig a graduate student named Susanna Sawyer analyzed its DNA. At the symposium in 2011 she presented her results for the first time. To everyone’s shock, the toe bone had turned out to be Neanderthal, deepening the mystery of the place.

The green stone bracelet found earlier in Layer 11 had almost surely been made by modern humans. The toe bone was Neanderthal. And the finger bone was something else entirely. One cave, three kinds of human being. “Denisova is magical,” said Pääbo. “It’s the one spot on Earth that we know of where Neanderthals, Denisovans, and modern humans all lived.” All week, during breaks in the conference, he kept returning alone to the cave. It was as if he thought he might find clues by standing where the little girl may have stood and touching the cool stone walls she too may have touched.

Look for this site to continue to influence models of later human evolution. There seem to have been several locations at which there were both, at various times, Neandertals and modern humans.

Denisovan DNA Sequenced

Science Insider is reporting that the entire genetic sequence of the Denisova Cave individual has been completed and posted on the web site at the Max Planck Institute for Evolutionary Anthropology. Ann Gibbons writes:

A year ago, researchers published the first rough draft of the genome of an archaic girl who lived in Denisova Cave, Siberia, at least 30,000 years ago. In January, Max Planck paleogeneticist Svante Pääbo was at a meeting in Sweden when he realized that researchers in other labs were poring over year-old sequence data that was far less complete than what his colleagues had obtained in the lab in the past year using sensitive, new methods to sequence ancient DNA. "I felt bad knowing that we had this very much better version of the same genome and that it would be a few months before it became available," says Pääbo.

I am curious to see what sorts of ERVs are present and if any are derived from the Neandertal condition. A wealth of studies are just waiting to be done.

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