Denisovans: Homo erectus after all?

Greg Cochran:

The new paper in Science about an Australian genome (An Aboriginal Australian Genome Reveals Separate Human Dispersals into Asia) hints at something new. Comments in the supplement (and by Ann Gibbon) suggest that the Denisovans may stem from Homo erectus, at least in part, rather than being a sister group to Neanderthals as suggested in the paper by Reich and Patterson back in December. In the supplement, the authors suggest that they may be a sister clade to the last common ancestor of Neanderthals and modern humans. Ann Gibbons say the same, concerning the Denisovan girl whose pinky we found: “She was not a modern human, but a descendant of Homo erectus, an ancestral species that left Africa almost 2 million years ago. “

Denisovan mtDNA is deeply diverged from modern human or Neanderthal mtDNA, while the Denisovan teeth found look strangely old-fashioned. Moreover, it now looks as if admixture between hominid subspecies is the norm rather than the exception. So, although Denisovans as an admixture between H. erectus and some branch of Neanderthals was always a possibility, evidence, signs, and portents are starting to make it look likely.

From the supplementary data (pdf) for the Aborigine genome paper:

Denisovans are more elusive. The term refers to a hypothetical population or possible species of archaic hominin, identified on the basis of ancient DNA, and with possible genetic affinities to both H. erectus and H. sapiens/neanderthalensis. They have been proposed as a sister clade to the last common ancestor of Neanderthals and modern humans.

"East Asian" mtDNA in Neolithic Hungary?

I don't have access to the paper at the moment. According to Jean M:

The details have been added to Ancient Western Eurasian DNA. The team actually tested remains from:

• Earliest Neolithic in Hungary, the Körös (N9a, C5, H? and a novel haplogroup 16235G, 16261T, 16291T, 16293G, 16304C)
• Alföld (N1a, N9a, D1/G1a1, H?. The reported M/R24 is a partial result)
• Final Neolithic Lengyel culture (H?)
• 9th-century AD Zalavár (H?)
• 16th-century AD Dobóruszka (U3)
• 19th-century mummies from Vác Dominician Church (H?, H12, N9a. Another mummy was tested, but produced different results for teeth and bone, presumably from contamination. I have not reported these results therefore)

Definitely interesting, but as John Hawks notes: "we need not maintain that the haplogroups presently common in East Asia have necessarily been there all that long."

Ötzi's Y-DNA haplogroup: G2a4

A few days ago a commenter at Dienekes' posted that this information had been revealed by "Dr. Eduard Egarter-Vigl, Head of Conservation and Assistant to research projects of the Archaeological Museum in Bozen [. . .] in a documentary [Ötzi, ein Archäologie-Krimi] broadcast by 3sat on 10th august 2011." Now someone has uploaded the relevant clip:

Subtitles: "Since six months, the full decoding of the genome of the Iceman is done. [. . .] Certain genes that are relevant to the origin, Y-chromosome, for example, can be examined well. [. . .] And the haplogroup to which the Iceman belonged is the haplogroup G2a4. [. . .] And this group is known, that it is now very rare in Europe. Interestingly, it is still in Sardinia. Sardinia is as an island a so-called micro-isolate where the poulation has hardly changed and so has developed genetically fairly constant. But there is this haplogroup in Eurasian regions, ie those from which we know that Europe was actually populated."

Sample size equals one, but the presence of G2a and absence of R1b is consistent with previous ancient DNA findings for Neolithic western and central Europe.

Haplogroup C mtDNA in Caucasoids does not necessarily indicate "Mongoloid" admixture

Dienekes writes:

Jean M links to a Master's thesis, which discovered the following:

While most of our samples possessed mtDNA haplotypes that can be linked to European and Near Eastern populations, three Neolithic and all three Bronze Age individuals belonged to mtDNA haplogroup C, which is common in East Eurasian, particularly South Siberian, populations but exceedingly rare in Europe. Phylogeographic network analysis revealed that our samples are located at or near the ancestral node for haplogroup C and that derived lineages branching from the Neolithic samples were present in Bronze Age Kurgans. In light of the numerous examples of mtDNA admixture that can be found in both Europe and Siberia, it appears that the NPR and South Siberia are located at opposite ends of a genetic continuum established at some point prior to the Neolithic. This migration corridor may have been established during the Last Glacial Maximum due to extensive glaciation in northern Eurasia and a consequent aridization of western Asia. This implies the demographic history for the European gene pool is more complex than previously considered and also has significant implications regarding the origin of Kurgan populations.

[. . .] The Dnieper-Donets population was described as robust Europeoid by Soviet anthropologists as was the Andronovo/Afanasevo tradition further east. It is interesting that Mongoloid admixture has been detected in both groups. I would not have guessed that this would have extended that far west and south. It seems that M. G. Levin may have been right when he stated that the Mongoloid elements penetrated far into eastern Europe.

I see no reason to believe the presence of haplogroup C indicates a "Mongoloid component". Stephen Oppenheimer sees C/Z mtDNA entering Mongoloids as part of an "intrusive" element "likely to have arrived from farther west in Asia, along with the eastern spread of the Upper Palaeolithic technology that appeared in Kara Bom in the Russian Altai 43,000 years ago." If this is correct, the presence of C in robust steppe Caucasoids would not be surprising. Oppenheimer has C/Z originating in western South Asia and entering Central Asia "round the western end of the Himalayas" 40-50,000 years ago, whereas Mongoloids (and "real" East Eurasian haplogroups) ultimately originate in SE Asia. Rather than indicating Mongoloid admixture "penetrated far into Eastern Europe", the presence of C mtDNA this early and this far west means one can't simply write off C and Z lineages in more easterly ancient Caucasoids (like some of those those buried at Xiaohe) -- or in Icelanders, for that matter -- as the product of Mongoloid admixture.

From Oppenheimer's Out of Eden:

Sex Chromosome Evolution and Medicine

A talk from earlier this year by David Page. Slides available here (pdf).

Contra the view promoted by Bryan Sykes, the Y chromosome is not dying.

Greater policing required to enforce cooperation in "diverse" societies

A Test of Evolutionary Policing Theory with Data from Human Societies (PLoS ONE):

In social groups where relatedness among interacting individuals is low, cooperation can often only be maintained through mechanisms that repress competition among group members. Repression-of-competition mechanisms, such as policing and punishment, seem to be of particular importance in human societies, where cooperative interactions often occur among unrelated individuals. In line with this view, economic games have shown that the ability to punish defectors enforces cooperation among humans. Here, I examine a real-world example of a repression-of-competition system, the police institutions common to modern human societies. Specifically, I test evolutionary policing theory by comparing data on policing effort, per capita crime rate, and similarity (used as a proxy for genetic relatedness) among citizens across the 26 cantons of Switzerland. This comparison revealed full support for all three predictions of evolutionary policing theory. First, when controlling for policing efforts, crime rate correlated negatively with the similarity among citizens. This is in line with the prediction that high similarity results in higher levels of cooperative self-restraint (i.e. lower crime rates) because it aligns the interests of individuals. Second, policing effort correlated negatively with the similarity among citizens, supporting the prediction that more policing is required to enforce cooperation in low-similarity societies, where individuals' interests diverge most. Third, increased policing efforts were associated with reductions in crime rates, indicating that policing indeed enforces cooperation. These analyses strongly indicate that humans respond to cues of their social environment and adjust cheating and policing behaviour as predicted by evolutionary policing theory.

Svante Paabo TED talk on Neanderthal admixture

Posting without having watching watched it yet.

"Sharing the results of a massive, worldwide study, geneticist Svante Pääbo shows the DNA proof that early humans mated with Neanderthals after we moved out of Africa. (Yes, many of us have Neanderthal DNA.) He also shows how a tiny bone from a baby finger was enough to identify a whole new humanoid species."

Next PoBI paper should be more interesting

Another ICHG/ASHG 2011 abstract:

People of the British Isles: An analysis of fine-scale population structure in a UK control population. S. Leslie1, B. Winney1, G. Hellenthal2, S. Myers2, A. Boumertit1, T. Day1, K. Hutnik1, E. Royrvik1, D. Lawson3, D. Falush4, P. Donnelly2, W. Bodmer1 1) Department of Oncology, University of Oxford, Oxford, United Kingdom; 2) Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom; 3) Department of Mathematics, University of Bristol, Bristol, United Kingdom; 4) Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany.

There is a great deal of interest in fine scale population structure in the UK, both as a signature of historical immigration events and because of the effect population structure may have on disease association studies. Although population structure appears to have a minor impact on the current generation of genome-wide association studies, it is likely to play a significant part in the next generation of studies designed to search for rare variants. A powerful means of detecting such structure is to control and document carefully the provenance of the samples involved. Here we describe the collection of a cohort of rural UK samples (The People of the British Isles), aimed at providing a well-characterised UK control population that can be used as a resource by the research community as well as providing fine scale genetic information on the British population. So far, some 4000 samples have been collected, the majority of which fit the criteria of coming from a rural area and having all four grandparents from approximately the same area. Three thousand samples were genotyped on the Illumina 1.2M and Affymetrix v6.0 platforms as part of WTCCC2. Using a novel clustering algorithm that takes into account linkage disequilibrium structure, approximately 3000 of the samples were clustered, using these comprehensive genotyping data, into more than 50 groups purely as a function of their genetic similarities without any reference to their know locations. When the appropriate geographical position of each individual within a cluster is plotted on a map of the UK, there is a striking association between clusters and geography, which reflects to a major extent the known history of the British peoples. Thus, for example, even individuals from Cornwall and Devon, the two adjacent counties in the southwestern tip of Britain, fall into different, but coherent clusters. Further details of this comprehensive analysis of the genetic structure of the People of the British Isles, together with a description of the provenance of the samples, will be give in the presentation. We believe that this is the first time that such a detailed fine scale genetic structure of a population of generally very similar individuals has been possible. This has been achieved through, on the one hand, a careful geographically structured collection of samples and, on the other hand, an approach to analysis that takes into account fully the linkage disequilibrium structure of the population.

An estimate of black admixture in white Americans

An ICHG/ASHG 2011 abstract (below) reports some results from a study of the 23andMe database. I see various potential issues with the research as described in the abstract; but while the numbers are not definitive, these estimates are likely to be by far the most accurate to date. What's clear is the overwhelmingly huge majority of white Americans have zero black ancestry. All previous sensible analyses of genetic data agree, and any other result would be difficult to reconcile with American history -- however disappointing that might be to "Multiracial Voice"-types and race denialists.

In 2002, Mark Shriver claimed 30% of white Americans have on average about 2% African ancestry, the average for the population as a whole coming out to about 0.7%. Shortly thereafter, in a different interview, Shriver lowered his estimate, purporting "about 10 percent of [the European-American population] have some African ancestry". Subsequently, another principal of DNAprint revised the estimate still further downward: "Five percent of European Americans exhibit some detectable level of African ancestry". That too was an overestimate. 23andMe, examining the genomes of vastly larger numbers of people using thousands of times as many SNPs, estimates "about 2%" of "European Americans" have any detectable autosomal black ancestry. And three quarters of that 2% have only "about 0.5%" African ancestry (i.e., less than Shriver in 2002 claimed the average American carried).

Exceptions to the "One Drop Rule"? DNA evidence of African ancestry in European Americans. J. L. Mountain1, J. M. Macpherson1, C. B. Do1, B. T. Naughton1, R. A. Kittles2, N. Eriksson1 1) 23andMe, Inc, Mountain View, CA; 2) Institute of Human Genetics, University of Illinois at Chicago, Chicago, IL.

Genetic studies have revealed that most African Americans trace the majority (75-80%, on average) of their ancestry to western Africa. Most of the remaining ancestry traces to Europe, and paternal lines trace to Europe more often than maternal lines. This genetic pattern is consistent with the "One Drop Rule,” a social history wherein children born with at least one ancestor of African descent were considered Black in the United States. The question of how many European Americans have DNA evidence of African ancestry has been studied far less. We examined genetic ancestry for over 77,000 customers of 23andMe who had consented to participate in research. Most live in the United States. A subset of about 60,000 shows genetic evidence of fewer than one in 16 great-great-grandparents tracing ancestry to a continental region other than Europe. They are likely to consider themselves to be entirely of European descent. We conducted two analyses to understand what fraction of this group has genetic evidence of some ancestry tracing recently to Africa. We first identified individuals whose autosomal DNA indicates that they are predominantly of European ancestry, but who carry either a mitochondrial (mt) DNA or Y chromosome haplogroup that is highly likely to have originated in sub-Saharan Africa. Of the 60,000 individuals with 95% or greater European ancestry, close to 1% carry an mtDNA haplogroup indicating African ancestry. Of approximately 33,000 males, about one in 300 trace their paternal line to Africa. We then identified the subset of these European Americans who have estimates of between 0.5% and 5.0% of ancestry tracing to Africa. This subset constitutes about 2% of this set of individuals likely to be aware only of their European ancestry. The majority (75%) of that group has a very small estimated fraction of African ancestry (about 0.5%), likely to reflect African ancestry over seven generations (about 200 years) ago. We estimate that, overall, at least 2-3% of individuals with predominantly European ancestry have genetic patterns suggesting relatively deep ancestry tracing to Africa. This fraction is far lower than the genetic estimates of European ancestry of African Americans, consistent with the social history of the United States, but reveals that a small percentage of “mixed race” individuals were integrating into the European American community (passing for White) over 200 years ago, during the era of slavery in the United States.