Anthropology.net

Hans-Peter Uerpmann of the University of Tubingen has lead a team excavating the Jebel Faya site in the United Arab Emirates, right near the Straits of Hormuz. They’ve found 125,000 year old stone tools that look like early modern human tools from East Africa around the same time. They’ve published their findings in today’s Science, under the title, “The Southern Route “Out of Africa”: Evidence for an Early Expansion of Modern Humans into Arabia.”

The current understanding is what we know as anatomically modern humans (AMH) originated in Africa about 250,000 years ago. The oldest Home sapiens, known as H. sapiens idaltu, was found to be 160,000 years old, found at the Middle Awash site in Ethiopia. Then between 80k-100k years ago, modern humans began appearing in the middle east, as remains from sites like the Qafzeh cave in Israel have yielded. Most agree that AMH stayed in Africa and about 140,000 years ago they began migrating out. There was an exception, a colonization remained or failed in Israel about 100,000 years ago.

One of the hand axes from Jebel Faya, UAE (Photograph courtesy Science/AAAS)

These hand axes, pictured above, show a pattern of flaking distinct from that made by Neandertals and also dissimilar to those by ~100,000 year old Israeli tools. They are two sided and very similar to stone tools seen only in early Africa.

What this means is early humans left Africa 20,000 years earlier than thought. Just how did they do it? 130,000 years ago, there was a window of climate change. They figured this out by using luminescence dating to determine the age of sand grains buried with the stone tools. Luminescence dating is a technique that measures naturally occurring radiation stored in the sand. The data showed that 130,000 years ago, the Arabian Peninsula was relatively more warm which caused more rainfall, turning it into a series of lush habitable land. During this period the southern Red Sea’s levels dropped and was only 2.5 miles or 4 km wide. This offered a brief window of time for humans to easily cross the sea and cross the Peninsula to opposing sites like Jebel Faya.

Does this study tell us that modern humans left Africa, into Arabia and out from there? It is most certainly a possibility. However, these axes could be of an abandoned migration like the site in Israel I’ve mentioned. I say that because no genetic clade, be it from mitochondrial, Y-chromosome, or somatic genome, shows an earlier divergence of modern humans from Africa earlier than 60,000 years ago. At the very minimum a find like this tells us humans left Africa a bit sooner than we thought, but does not really tell us that these were the humans that helped seed the Eurasia.

Armitage, S., Jasim, S., Marks, A., Parker, A., Usik, V., & Uerpmann, H. (2011). The Southern Route “Out of Africa”: Evidence for an Early Expansion of Modern Humans into Arabia Science, 331 (6016), 453-456 DOI: 10.1126/science.1199113

The American Journal of Human Genetics has published an article titled, “Correcting for Purifying Selection: An Improved Human Mitochondrial Molecular Clock,” in which a more accurate method of dating ancient human migration, even when no corroborating archaeological evidence exists, is announced.

How does was this done?

The authors started with a sample of 2,000 fully sequenced mtDNA genomes. Not only does this increase the accuracy, but also the precision, ultimately allowing for more narrow temporal ranged. Furthermore, the new method integrates the process of natural selection, which normally skews migration results. In doing so, they authors confirmed that their new methodology works by comparing it against known colonization of Polynesia in the Pacific (approximately 3,000 years ago), and the Canary Islands (approximately 2,500 years ago) extracted from archaeological data.

Aside from confirmation, some more ‘surprising’ results have also been extracted. Last author, Martin B. Richards comments,

“We can settle the debate regarding mankind’s expansion through the Americas. Researchers have been estimating dates from mtDNA that are too old for the archaeological evidence, but our calculations confirm the date to be some 15,000 years ago, around the time of the first unequivocal archaeological remains.

Furthermore, we can say with some confidence that the estimate of humanity’s ‘out of Africa’ migration was around 60-70,000 years ago — some 10-20,000 years earlier than previously thought.”

The press release says that the team has made their  simple calculator freely available on on the University of Leeds website. But I can’t seem to find it, but the supplemental data includes an Excel spreadsheet version of the calculator for you to use and dissect. Anyone got the link to the online calculator?

Pedro Soares, Luca Ermini1, Noel Thomson, Maru Mormina, Teresa Rito, Arne Röhl, Antonio Salas, Stephen Oppenheimer, Vincent Macaulay, & Martin B. Richards (2009). Correcting for Purifying Selection: An Improved Human Mitochondrial Molecular Clock American Journal of Human Genetics

John Hawks shared an interesting news bit the other day. The study basically sampled head lice off of 1,000 year old Peruvian mummies and with some sequence variation comparisons to other lice, the authors were able conclude that lice have been with humans ever since they migrated out of Africa. I’ve tracked down the original paper to investigate their claim.

The paper, “Molecular Identification of Lice from Pre‐Columbian Mummies” is published in an early release of the Journal of Infectious Diseases. The authors amplified the Cytb and Cox1 genes of lice found on three 1,000 year old Peruvian mummies. The mummies are associated with the Chiribaya culture, a post Moche movement, that originated in the Azapa Valley of Northern Chile. I’ve cut and pasted a photo of one of the mummies sampled from the article, in this photo the authors show the lice still present on the head.

They next sequenced these amplified genes, and constructed phylogenetic trees of the genetic similarities these lice have to sequences of lice from other areas of the world. What they found from their cladistic analysis was that the lice associated with the mummies clustered only with sequences in the type A clade. Since type A clade are almost exclusive to Asia and Africa, the authors could confidently claim that the lice were not of European origin, which sports the type B clade of lice.

New World mummies as old has 10,000 years ago have lice, and the genetic evidence from this study now confirms the lice that existed in New World for the last 1,000 years was not of European origin. This work also tells of migration patterns of humans, much like the study on rat genetics did early this week. We can see that founding populations of people from the Old World carried over the type A clade of lice, over the Bering straight and to the Americas.

I really appreciated this article. Had it not been for this one citation to the Bible, about the presence of lice in historical populations, I would say this article is a perfect example of simple, enlightening science. The authors didn’t obfuscate their research and provided a very graceful example of how a host-specific parasites of human brought in an additional line of evidence to understand human migrations. One last thing, I wonder what’s the genotype of the lice found on the mummies in Arizona?

Raoult, D., Reed, D., Dittmar, K., Kirchman, J., Rolain, J., Guillen, S., Light, J. (2008). Molecular Identification of Lice from Pre-Columbian Mummies. The Journal of Infectious Diseases DOI: 10.1086/526520

The web is abuzz over a new publication in PLoS Genetics about a single main migration across Bering Strait. From what I can tell, this new paper, “Genetic Variation and Population Structure,” coincides with a recent publication in PLoS One that sampled mtDNA and figured out people moved in waves, but first they spent some time in Beringia.

Both of these papers use microsattelites or SNPs in genes from native American populations to answer the question, did a small population from Siberia trek across the Bering Strait land bridge some 12,000 years ago and give rise to the native peoples of North and South America? Or did people come from other parts of Asia or Polynesia, arriving in multiple times, at several places on the two continents, by sea as well as by land, in successive migrations that began as early as 30,000 years ago?

To answer this question, the authors picked out 678 markers in the DNA of present-day members of 29 Native American populations across North, Central and South America. They also analyzed data from two Siberian groups. The figure to your right is from the publication, which illustrates who and where the populations sampled are from.

They figured out that a unique genetic variant, which is part of a noncoding region, is widespread in Native Americans across both American continents and it originated in Siberia. This implies that the first populations came into the Americas came from a single migration or multiple waves from a single source. This rules out the possibility that people came in waves of migrations from different sources. The following graph documents this:

Furthermore, the genetic diversity, as well as genetic similarity is very close to the Siberian groups tested. This supplements to existing archaeological and genetic evidence that the ancestors of native North and South Americans came by the northwest route.

Additional findings that are also interesting are that populations in the Andes and Central America are genetically similar. And populations from western South America showed more genetic variation than populations from eastern South America. And to appease the linguists out there, the populations more similar linguistically were also more similar genetically. Pretty cool, huh?

Anyways, please check out Blaine Bettinger, a.k.a, the Genetic Genealogist’s and Yann‘s posts on this, as well as my old post about the waves from Beringia, which collaborates with this finding.

A new study of over 600 mtDNAs from 20 American and 26 Asian populations is shedding some unique insight on how the Americas were peopled. As you may have been taught, it was thought that the Americas were founded by a not so diverse founding population or two. Before this paper, only about 70 left their genetic print in modern descendants, a very small but effective founder population.

But, there are new results, which were published almost two months ago, that show that there was much more genetic diversity in the founder population than was previously thought. I didn’t catch it until I saw both Razib and Science Daily report on it a couple days ago.

The paper, “Beringian Standstill and Spread of Native American Founders,” was published in the freely accessible PLoS One. Beringia is a fancy way of naming the Bering Land Straight that once connected the north east Asia continent to north west America continent.

One of the more interesting lines of evidence they found from their sequence comparison and their revised phylogenetic map is that the ancestral population literally chilled out in Beringia for a long time. The authors estimate about 15,000 years. That’s long enough so that specific mutations accumulated which separated the New World founder lineages from the Asian sister-clades.

The other more interesting thing that was uncovered was that the founding haplotypes are uniformly distributed across North and South America. They do not show a nested structure from north to south. That means that after what the authors are terming the Beringian standstill and what I’m calling the Beringian chillout, the initial North to South migration was very swift. It was not a gradual diffusion.

And as Razib pointed out in his post, during the last 30,000 years, there was a lot more bouncing back and forth from Northeast Asia and North America. The analysis shows that there was a series of back migrations to Northeast Asia as well as forward migrations to the Americas from Beringia, “more recent bi-directional gene flow between Siberia and the North American Arctic.”

Overall, this study tells us a lot on how people were moving about in the northern hemisphere. But what about oceanic travel, and the recent chicken population genetic similarities? They seem to have made some cultural if not genetic contribution to populations here.

Related sidenote, I like how this study one ups an older PLoS paper, which I reffered to above (the 70 people one). If you want, check out that paper, “On the Number of New World Founders: A Population Genetic Portrait of the Peopling of the Americas.”

Thanks to the very helpful readers who have sent me a copy of the latest from Pääbo and crew, “Neanderthals in central Asia and Siberia.” I’ve read it, and it is a pretty good paper with solid methods. This study is important because it compliments paleoanthropology with molecular biology to fill in discrepancies with using morphology to classify remains. As you all know, fossils don’t come out as clean and intact as your grandmother’s china. Almost always hominid fossils are fragmented and incomplete.

That being said, the hominid remains from the Teshik Tash cave in Uzbekistan and the Okladnikov cave in the Altai region of Siberia are so fragmented and hard to classify, that for a long time paleoanthropologists have just put them aside. Lead author Krause et al. decided to dust off these specimens and break off about a fifth of a gram of bone from each to sequence and compare. Specifically, they harvested samples from the femur of the Teshik Tash kid and from three Okladnikov long bones.

Fossils don’t hold much DNA. Upon death, the body begins degrading DNA immediately, and only under certain conditions is DNA preserved enough so that one can extract DNA from a fossil. And once DNA is extracted, it is a really tiny amount which is muddled in a lot of contaminated DNA. So, in order to exponentially increase the amount of starting DNA, a technique called PCR, or polymerase chain reaction, is used. To do so, each segment of DNA needs to be primed, so that the PCR polymerases can bind to them and being duplicating. The DNA from these bones were amplified with three different primer pairs, I guess to test out which primer pair worked best.

Once the PCR reaction was complete the authors next sorted out modern human amplified DNA from Neandertal amplified DNA. They did this because, as I mentioned, there’s a lot of contamination, especially from modern human mtDNA on fossil bone. This is most likely due to handling and excavating the bone. After figuring out the modern human amplified products, it was found that the Teshik Tash kid and a subadult from Okladnikov, both yielded about 2 clones each of 60 Neandertal specific base pairs.

Since paleoanthropologists have spent all their time debating on how to classify the Okladnikov fossils, there seems to not be reliable dates for them. Krause and team dated them, and noted that the subadult from Okladnikov, the one that had Neandertal specific base pairs, was old enough (37,000 years old) to be a Neandertal.

With this date and the two pairs of Neandertal clones, the team narrowed down their scopes. They specifically designed primers that worked on amplifying only the hypervariable region 1 (HVR1) of Neandertal mtDNA. Why the HVR1? For starters the HVR1 is longer section than the 60 or so base pairs they already have. And since the HVR1 is an area where base pairs repeat and are highly polymorphic, it is a more informative section. Having longer sequences to align, compare, and analyze is much more statistically significant than shorter ones.

The authors sent off the Teshik Tash and Okladnikov samples to a DNA lab in France, which exactly matched up to their results, and confirmed they were doing the right stuff. After all the statistics, 300 base pairs from both the Teshik Tash and Okladnikov were compared to the same section of HVR1 from seven other Neandertals. They only differ in about 6 bases from the other Neandertals… that’s about a 98% similarity. Not bad at all.

What this study does is it pushes the geographical range of Neandertals, by 2,000 kilometers to the east. We already had an inkling Neandertals may have made it out to what is now Uzbekistan… hell they’ve been found in Iran. But to see that one of the Okladnikov fossils has Neandertal mtDNA that matches to European Neandertal mtDNA, calls for a big whoa. Neandertals in Siberia, whoa.

Coming up in the September 2007 issue of PLoS Genetics will be a unique study that reports on using a new computer algorithm to help trace the genetic ancestry of thousands of individuals in minutes, without any prior knowledge of their background. I reported on how Ancestry.com will be providing DNA tests for sale last month.

This study does not need an individual’s ancestry and background to narrow down the scope for specific DNA markers known as single nucleotide polymorphisms, or SNPs. The new algorithm needs nothing more than a DNA sample. Previous genetic data collected is used to perform and confirm the research.

Just how accurate is the study? It was 99% accurate in correctly identifying hundreds of people’s ancestry from similar and complex background, such as Chinese, Japanese, and Puerto Ricans. Petros Drineas, one of authors of the paper from the Rensselaer Polytechnic Institute discusses expanding the study,

“Now that we have found that the program works well, we hope to implement it on a much larger scale, using hundreds of thousands of SNPs and thousands of individuals.”

Algorithms are not only useful to help people understand their personal heritage, anthropologists benefit form these large scale screens to help understand where and when different populations originated and how humans evolved into such a diverse, global society.

I’ll report more on this once the paper comes out, in the mean time this was adapted from this press release.