Archaic Admixture in Africa, a Final Solution for Cultural Anthropology and the New World Roots of the Oldest Dog: News from Around the Web

I haven’t been blogging for a while because of a new demanding leadership job. It will keep me busy, so I’m shifting to more of a bite-size blog post format. In the meantime, I’ve been active on Gisele Horvat’s Human Migrations forum discussing the various aspects of out-of-America thinking as well as the new interesting proposal by Joseph Wilson to interpret Na-Dene populations as a recent (within the past 1500 years) reflux from Siberia.

A number of interesting articles and notable discussions have come out in the past couple of months.

Genetics doi: 10.1534/genetics.112.148213

Higher Levels of Neanderthal Ancestry in East Asians Than in Europeans

Wall, Jeffrey D., Melinda A. Yang, Flora Jay, Sung K. Kim, Eric Y. Durand, Laurie S. Stevison, Christopher Gignoux, August Woerner, Michael F. Hammer and Montgomery Slatkin.

Neanderthals were a group of archaic hominins that occupied most of Europe and parts of Western Asia from roughly 30-300 thousand years ago (Kya). They coexisted with modern humans during part of this time. Previous genetic analyses that compared a draft sequence of the Neanderthal genome with genomes of several modern humans concluded that Neanderthals made a small (1-4%) contribution to the gene pools of all non-African populations. This observation was consistent with a single episode of admixture from Neanderthals into the ancestors of all non-Africans when the two groups coexisted in the Middle East 50-80 Kya. We examined the relationship between Neanderthals and modern humans in greater detail by applying two complementary methods to the published draft Neanderthal genome and an expanded set of high-coverage modern human genome sequences. We find that, consistent with the recent finding of Meyer et al. (2012), Neanderthals contributed more DNA to modern East Asians than to modern Europeans. Furthermore we find that the Maasai of East Africa have a small but significant fraction of Neanderthal DNA. Because our analysis is of several genomic samples from each modern human population considered, we are able to document the extent of variation in Neanderthal ancestry within and among populations. Our results combined with those previously published show that a more complex model of admixture between Neanderthals and modern humans is necessary to account for the different levels of Neanderthal ancestry among human populations. In particular, at least some Neanderthal-modern human admixture must postdate the separation of the ancestors of modern European and modern East Asian populations.

Link

This paper supports Meyer et al.’s (2012) conclusion that East Asians are closer to Neandertals than Europeans. The difference is estimated on the order of 40%. This makes it unlikely that the 1-4% similarity between non-African human and Neandertal genomes, to the exclusion of African human genomes, is product of admixture between Neandertals and expanding modern humans. If this was the case, Europeans would have been more heavily admixed than East Asians. The asymmetrical connection between an archaic hominin species and a modern human population is further found in the case of Denisovans, whose remains are geographically located in East Asia but who show greater similarity to modern Melanesians than to East Asians. Wall et al. (2013) report that they failed to find any traces of admixture between Denisovans and East Asians (contra Skoglund & Jacobsson 2011) but they sampled only Japanese and Han Chinese, while Skoglund & Jacobsson reported the highest frequencies of Denisova alleles outside of Melanesia, in Southeast Asia and America (see more here). For the archaic admixture hypothesis to hold, one would need to postulate the dilution of Neandertal alleles in Europe and Denisovan alleles in East Asia by the subsequent (e.g., Neolithic) gene flow of populations unadmixed with Neandertals and Denisovans into these regions. The only place where these populations could have originated is Africa, but there’s no evidence for an excess of African alleles in East Asians and Europeans compared with Melanesians. Hence, the genomic pattern of association between Neandertals, Denisovans and non-African humans may be better explained as common descent, with African humans derived from non-African humans. Wall et al. (2013, 21) found evidence that can be interpreted precisely to such an effect:

“Also, we find evidence for a small but significant amount of Neanderthal admixture into the Maasai genomes (p ~ 0.03, Table S4). When compared to the Yoruba, the Maasai have a higher average D than the Luhya (Figure 3b, Table S4). When the Maasai are
compared to all other African samples the average D is positive (Figure 3d). In addition, when East Asians and Europeans are compared to the Maasai, the average D’s are somewhat lower than when they are compared to either the Yoruba or Luhya.”

Table S4 shows that all of Wall et al.’s African samples have a Neandertal component, with Yoruba and Luhya training slightly behind Maasai. The paucity of Neandertal and Denisovan alleles in such “Paleoafricans” as Khoisans is better explained as product of admixture with African archaics that diluted the original Eurasia-derived gene pool of Africans.

American Journal of Human Genetics 10.1016/j.ajhg.2013.02.002

An African American Paternal Lineage Adds an Extremely Ancient Root to the Human Y Chromosome Phylogenetic Tree 

Fernando L. Mendez, Thomas Krahn, Bonnie Schrack, Astrid-Maria Krahn, Krishna R. Veeramah, August E. Woerner, Forka Leypey, Mathew Fomine, Neil Bradman, Mark G. Thomas, Tatiana M. Karafet, Michael F. Hammer.
We report the discovery of an African American Y chromosome that carries the ancestral state of all SNPs that defined the basal portion of the Y chromosome phylogenetic tree. We sequenced ∼240 kb of this chromosome to identify private, derived mutations on this lineage, which we named A00. We then estimated the time to the most recent common ancestor (TMRCA) for the Y tree as 338 thousand years ago (kya) (95% confidence interval = 237–581 kya). Remarkably, this exceeds current estimates of the mtDNA TMRCA, as well as those of the age of the oldest anatomically modern human fossils. The extremely ancient age combined with the rarity of the A00 lineage, which we also find at very low frequency in central Africa, point to the importance of considering more complex models for the origin of Y chromosome diversity. These models include ancient population structure and the possibility of archaic introgression of Y chromosomes into anatomically modern humans. The A00 lineage was discovered in a large database of consumer samples of African Americans and has not been identified in traditional hunter-gatherer populations from sub-Saharan Africa. This underscores how the stochastic nature of the genealogical process can affect inference from a single locus and warrants caution during the interpretation of the geographic location of divergent branches of the Y chromosome phylogenetic tree for the elucidation of human origins.

The hypothesis of archaic admixture in Africa (and, importantly, the lack thereof outside of Africa) is further confirmed by Mendez et al. (2013). Up until now it was assumed that mtDNA and Y-DNA do not show traces of archaic admixture in modern humans. Mendez et al (2013) refute this assumption by detecting a very divergent Y-DNA lineage (A00) among West Africans and West Africa-derived African Americans. The dates obtained for the coalescence of A00 are some 130,000 years older than the earliest paleobiological evidence for anatomically modern humans in Africa. This is another inconvenient fact for the proponents of out-of-Africa. The data at hand increasingly suggests that the out-of-Africa theory mistook signs of archaic admixture in Africa for the antiquity of modern humans in Africa. Y-DNA hgs A and B, which are not found outside of Africa, are the other possible candidates for archaic introgression in Africa. The massive migration of modern humans into Africa manifests itself in African-specific and pan-African hg E, which is nested within the Eurasian CT clade.

In the category of bizarre, a right-wing, pseudo science blogger Razib Khan who writes under the Discover magazine banner, proposed a “final solution” for cultural anthropology (Cultural Anthropology Delenda Est!). He unleashed against cultural anthropology a transnational potpurri of everything that modern brown-shirted punditry can offer – from a mud-slinging spree (“the discipline is properly thought of as an obscure, if vociferous, form of politics”) to a McCarthyian-like witch hunt (“Once he [Jared Diamond]’s taken down, the kommissars may come for us all”) to a radical Islamesque attack on infidels who dare to create caricatures of such sacred objects as the gene (“This is not “Not Even Wrong.” It is “Not Even Aspiring to be Right”) to scientistic stigmatization of dissidents of all kinds as “creationists” (“And though I am more positively disposed toward evolutionary psychology and sociobiology than most, the bracketing of population genetics into the same class as these to me definitely justifies the label of Left Creationist for Michael Scroggins”). Cultural anthropology embodies everything Razib “Mein Kampf” Khan hates – it’s inauthentic, dominating, conniving and lethal to pure-bred scientists – hence, a final solution is in order.

Anthropology is indeed fraught with internal conflicts and contradictions, which I personally experienced during my years at Stanford University (see here). But it’s very easy to see that anthropology is not the only discipline that’s critical of mainstream science. Recently, the application of methods derived from evolutionary biology to the problem of Indo-European origins and world phonemic diversity met with an emphatic rejection by linguists and geographers (see a video here culminating a series of posts by Asya Pereltsvaig and Martin Lewis). (The funny irony of scientific discourse in the blogosphere is that Asya Pereltsvaig, who’s a descriptive linguist far removed from genetics, recently praised Razib Khan’s critique of the Khazarian hypothesis of Azhkenazi Jewish origins from a population genetic perspective as “eminently sensible.” The deaf is leading the blind through the fantasy land?)

Razib Khan’s problem is that he is incapable of interpreting human reality rationally, analytically and objectively. He looks at everything through the prism of his own subjective psychology (“I have deep and long standing personal experience with inter-cultural variation in a visceral and emotional sense”) and petty political frustrations. This comes from the lack of education and work ethic in the areas (such as anthropology, political science, religion, history, etc.) where he seems to have the strongest opinions. His interest in population and behavioral genetics likely satisfies a deep emotional void and adds a veneer of science to his blogging. But notably he hasn’t produced any original contributions to this field. His most original contribution to date is the application of Khitlerite propaganda against Jews in the 1920-1930s to cultural anthropology. Such propaganda won’t lead to the victory of science over obscurantism. It will create rabid scientific fundamentalism to complement and reinforce creationism.

It’s likely that a large number of people will end up looking at the complex intersections of science and anthropology through the prism of opinions of such an eminently “stupid, ignorant and lazy” person as Razib Khan. But, truth be told, it’s all just online chatter, so does it really matter?

PLoS ONE 8(3) 2013: e57754. doi:10.1371/journal.pone.0057754

Ancient DNA Analysis Affirms the Canid from Altai as a Primitive Dog

Druzhkova, Anna S., Olaf Thalmann, Vladimir A. Trifonov, Jennifer A. Leonard,Nadezhda V. Vorobieva, Nikolai D. Ovodov, Alexander S. Graphodatsky, Robert K. Wayne.

The origin of domestic dogs remains controversial, with genetic data indicating a separation between modern dogs and wolves in the Late Pleistocene. However, only a few dog-like fossils are found prior to the Last Glacial Maximum, and it is widely accepted that the dog domestication predates the beginning of agriculture about 10,000 years ago. In order to evaluate the genetic relationship of one of the oldest dogs, we have isolated ancient DNA from the recently described putative 33,000-year old Pleistocene dog from Altai and analysed 413 nucleotides of the mitochondrial control region. Our analyses reveal that the unique haplotype of the Altai dog is more closely related to modern dogs and prehistoric New World canids than it is to contemporary wolves. Further genetic analyses of ancient canids may reveal a more exact date and centre of domestication.

Link

Apparently, God lives in South Siberia and he’s been lately quite busy landing his whip on the backs of arrogant and omniscient scientists. The finding of a 33,000 year-old dog in the Razboinichya Cave in the Altai Mountains ranks next to the discovery of a hominin pinkie in the Denisova Cave and Neandertal remains in the Okladnikova Cave as findings shattering the odd belief of the mainstream science of human origins that it surely has figured out human evolution by the end of 20th century. Not only that the Altai dog doesn’t come from such “priority areas of human evolution” as Europe, West Asia and Africa (see here), but it exceeds the next oldest canine remains by some 20,000 years. What’s especially intriguing is that, outside of the pool of modern dogs from all continents including the New World, it shows greater similarity to pre-Columbian, East Beringian dogs and New World wolves (see below, Fig. 4).

Pending further research and considering that dog DNA contains a lot of noise due to frequent hybridization, a hypothesis should be entertained that pre-Columbian dogs are direct descendants of the earliest domestication event that took place in the New World and the Altai dog is the early Old World offshoot from a New World source of canine domestication.