More excerpts from Chris Stringer's "The Origin of Our Species"

I read this a few months ago, but never got around to posting anything on it.

On group selection:

However, more recently, biologists and anthropologists such as Paul Bingham and Samuel Bowles have returned to the issue by recruiting weaponry and genes to the cause of group selection. The argument goes that by joining together to use effective projectile weaponry, individual risks were reduced, and thus coalitions of warriors would have been advantageous for group defence and offence. Bingham proposed that this development would also have been important within societies by deterring free-riders who tried to reap the rewards of group membership without contributing their fair share of commitment to the associated costs or risks. However strong individually, they could soon be brought into line when faced with a coalition of spear-armed peers, who could act as general enforcers of within-group rules and solidarity. Bowles posited the idea that if Palaeolithic groups were relatively inbred and genetically distinct from each other, and warfare between groups was prevalent, then group selection via collaborative defence and attack could evolve and be maintained. Without warfare, a gene with a self-sacrificial cost of only 3 per cent would disappear in a few millennia, but with warfare, Bowles's model showed that even levels of self-sacrifice of up to 13 per cent could be sustained. He used archaeological data (although mainly post-Palaeolithic) to argue that lethal warfare was indeed widespread in prehistory, and that altruistic group-beneficial behaviours that damaged the survival chances of individuals but improved the group's chances of winning a conflict could emerge and even thrive by group selection. Moreover, the model could work whether the behaviour in question was genetically based or was a cultural trait such as a shared belief system. As mentioned above, Bowles's archaeological data do not come from the Palaeolithic, but there is one observation that does resonate with his views: the French archaeologist Nicolas Teyssandier has noted that the period of overlap of the last Neanderthals and first moderns in Europe was characterized by a profusion of different styles of stone points. This might reflect a sort of arms race to perfect the tips of spears, perhaps to hunt more efficiently, but equally, this could suggest heightened intergroup conflict.
On modern behavior:
In terms of innovation, we saw in chapter 1 that the apparently sudden florescence of the rich Upper Palaeolithic societies of Europe seduced many in the last century to consider that this period marked the real arrival of fully modern humans, even if areas like the Middle East or Africa had been rehearsal grounds for the revolution that was to be finally expressed in the caves of France. But as we have also seen, this Eurocentric viewpoint that the Cro-Magnons were the first "modern" people has been largely abandoned, although that is not to deny that something special did happen in the Upper Palaeolithic of Europe. If Africa was actually at the forefront of Palaeolithic innovations more than 40,000 years ago, why was that? As anthropologist Rob Foley has pointed out, the sheer size of Africa (one could easily fit China, India and Europe into its surface area), and its position straddling the tropics, certainly gave it advantages over any other area inhabited by early humans. The rapidity and repetition of climatic oscillations outside of Africa probably continually disrupted long-term adaptations by human populations in those regions. Thus Neanderthals in Europe and the descendants of Homo erectus in northern China were constantly faced with sudden range contractions and the extinction of large parts of their populations every time temperatures sank rapidly, as they often did. [. . .]

The complex climates of Africa may also explain why there seems to be no single centre of origin for the earliest signals of behavioural modernity. Perhaps North Africa (and the Middle East?) led the way 120,000 years ago, but as conditions deteriorated, populations there shrank back or even became extinct, as favoured environments rapidly vanished. Perhaps the torch of modernity was then kept alive further south at sites like Blombos and Klasies River Mouth, as conditions favoured that region for a while (give or take the interruption of events like the Toba eruption).Waves of population expansion and contraction could explain the brief but extensive florescence of the Still Bay culture with its rich symbolism, and the subsequent rise and fall of the Howieson's Poort with its innovative tiny hafted blades and engraved ostrich eggshells (recently described from Diepkloof rock shelter) more than 5,000 years later. And it is my guess (though we lack much data to support it) that East Africa became one of the next centres for behavioural evolution, about 60,000 years ago, as it was from there that modern humans (and their developing suite of modern behaviours) made their way out of Africa. [. . .]

The big picture is that we are predominantly of recent African origin, so is there a special reason for this? Overall, I think that the pre-eminence of Africa in the story of modern human origins was a question of its larger geographical and human population size, which gave greater opportunities for morphological and behavioural variations, and for innovations to develop and be conserved, rather than the result of a special evolutionary pathway. "Modernity" was not a package that had a unique African origin in one time, place and population, but was a composite whose elements appeared at different times and places, and were then gradually assembled to assume the form we recognize today.

On genetic evidence for archaic admixture:
Up to now, the big picture, from our autosomal, mitochondrial and Y-chromosome DNA, has generally lacked signs of introgression from other human species, although scientists such as John Relethford, Vinayak Eswaran, Henry Harpending and Alan Templeton have argued that indications were indeed there. Short branches in our gene trees, particularly in Y and mtDNA, have pointed to a simple, recent African origin, and simulations from mtDNA data of the level of possible Neanderthal and Cro-Magnon admixture had suggested that it was either zero or very close to zero. However, despite the fact that mtDNA and Y-DNA provide such clear genealogical signals, they constitute only about 1 per cent of our total DNA, and signs of hybridization were clearly lurking in the rest of our genome. [. . .]

A recent example of such work is the study by Jeffrey Wall and colleagues of 222 SNPs (see chapters 7 and 8) in the genes of people from West Africa (Yoruba), China and Europe. Many of the SNPs were tightly clustered, and so deviations from the expectation of them all sharing the same pattern of inheritance from a single recent African ancestral population should have shown up clearly. The majority met Out of Africa expectations, but analysis suggested that the populations did display unusual mutations in some genes, and these had different histories from each other, and when compared between the geographical samples. Wall argued that the most likely explanation was that there was not a single ancestral population for all the SNPs -- most fitted the bill, but some were apparently descended from ancestral groups that had been isolated from each other long enough to develop separate SNP mutational patterns, which had then been bequeathed in slightly different ways to the modern regional populations. Interestingly, although each showed a signal of some "archaic" (rather than recent African) genetic contribution, the strongest pattern was not in Europe (where the Neanderthals might have been the source), nor in China (where it might have come from Denisovans), but in West Africa -- a puzzling result. The work has been criticized because some of the anomalous genes might have developed via recent drift or strong selection, if the mutations were regionally advantageous, but enough have been found to convince sceptics like me that there probably was ancient admixture in Africa as well.

On Iwo Eleru:
West Africa, where the oldest known fossil, from the Iwo Eleru rock shelter in Nigeria, is thought to be less than 15,000 years old. This poorly preserved skeleton was excavated from basal sediments at Iwo Eleru in 1965 by archaeologist Thurstan Shaw and his team, and was associated with Later Stone Age tools. That latter fact alone would suggest a relatively young age, and a radiocarbon date on a piece of charcoal suggested an age of about 13,000 years. The skeleton, and particularly the skull and jaw, was studied in 1971 by Don Brothwell, my predecessor at the Natural History Museum, and he argued that while the specimen could be related to recent populations in West Africa, it actually looked rather different from them. I studied the skull for my Ph.D., with surprising results. I also found that it did not closely resemble recent African populations, but in its long and low shape it was actually closer to early moderns such as those from Skhul, and even to more primitive specimens such as Omo 2. This was decidedly odd for such a young skeleton, and so I recently collaborated in a new study of the specimen with archaeologist Philip Allsworth-Jones, dating expert Rainer Gruen and anthropologist Katerina Harvati. We first checked with Thurstan Shaw whether there were any hints that the skull could have been much older than previously suggested, and there were none. With the help of Nigerian archaeologist Philip Oyelaran, I obtained a fragment of bone from the skeleton and passed it to Gruen in order to check its age directly. His determination from a direct uranium-series age estimate is that the bone is unlikely to be older than 20,000 years, consistent with the stratigraphy, and associated archaeology and radiocarbon date. Finally, could Brothwell and I have been wrong about the unusual shape of the skull? Harvati used state-of-the-art geometric morphometric scanning techniques on an exact replica of the skull (which is now in Nigeria), and found, as we did, that it was quite distinct from recent African crania, and indeed from any modern specimen in her comparative sample. Her results placed the skull closest to late archaic African fossils such as Ngaloba, Jebel Irhoud and Omo 2 -- all thought to be at least 140,000 years old. So what does this mean? Because of the poor preservation of Pleistocene bones in West Africa, we have no other data on the physical form of the inhabitants of the region during the whole of the Pleistocene, so we have to be careful in interpreting an isolated specimen such as Iwo Eleru. But it does not seem to be diseased or distorted, and does indeed seem to indicate that Africa contained archaic-looking people in some areas when, and even long after, the first modern-looking humans had appeared. Support for this view comes from the work of anthropologist Isabelle Crevecoeur. Her restudy of the numerous Ishango fossils from the Congo has shown that these Later Stone Age humans were not only similar to Iwo Eleru in age, but also in the surprisingly archaic features found in their skulls, jaws and skeletons. [. . .]

Africa today has the greatest internal genetic variation of any inhabited continent, and its skull shapes show the highest variation. This is usually attributed to its greater size, larger ancient populations and deepest timelines for humanity. But could those timelines go back even further than we thought? Did the early modern morphology evolve gradually, and then spread outwards from a region like East Africa, completely replacing archaic forms within Africa, and then outside (as mtDNA data would suggest)? Or, could there have been a version of assimilation or multiregional evolution within Africa, with modern genes, morphology and behaviour coalescing from partly isolated populations across the continent? Given its huge size, complex climates and patchworks of environments, Africa could have secreted distinct human populations just as easily as the rest of the inhabited world. So was the origin of modern humans there characterized by long periods of fission and fusion between populations, rather than representing a sudden single event? And was the replacement of the preceding late archaic peoples not absolute, so that they were partly absorbed by the evolving moderns rather than completely dying out? In which case, did early Homo sapiens forms, and even the preceding species, Homo heidelbergensis, survive alongside descendant modern humans?

Possible reason we don't have pigmentation genes from Neanderthals:
If the interbreeding actually happened earlier, in a warmer region or a warmer period, maybe the Neanderthals involved were not light-skinned and cold-adapted European examples? In fact, the interbreeding might even have happened when people like those from Skhul-Qafzeh and Tabun were in the Middle East 120,000 years ago. If a thousand of those early moderns mixed with just fifty Neanderthals and then survived somewhere in Arabia or North Africa, could they have subsequently interbred with the Out of Africa emigrants 60,000 years later, and passed on their hidden component of Neanderthal genes?

Out of Eurasia

From Chris Stringer's most recent book ("The Origin of Our Species"):
And the evidence from Dmanisi is now being added to this rethink, since the lack of very ancient fossil human evidence from Asia, apart from Dmanisi, is considered by archaeologists like Robin Dennell and Wil Roebroeks to reflect a lack of preservation and discovery, rather than a real absence. Combining the primitiveness of the Dmanisi specimens and tools with a similar view of the Liang Bua finds, it is argued that there was a widespread phase of human evolution in Eurasia about 2 million years ago, which is now only represented by the isolated Dmanisi and "Hobbit" fossils. This alternative scenario has a small-brained and small-bodied pre-erectus species, perhaps comparable to Homo habilis or even a late australopithecine, dispersing from Africa with primitive tools over 2 million years ago, reaching the Far East and, eventually, Flores. In Asia, this ancestral species then gave rise to the Dmanisi people and Homo erectus, while Dmanisi-like people reentered Africa about 1.8 million years ago, and evolved into later populations there -- including, eventually, Homo sapiens. So the orthodoxy of Out of Africa 1 is being challenged because of new evidence, and new interpretations of old evidence.

Ancestry.com's "Human Genetic Diversity Project"

Ancestry.com will apparently be offering autosomal DNA testing soon. They just gave away 2000 free "upgrades" to people who had previously done Y or mtDNA tests through Ancestry DNA, evidently for a forthcoming service along the lines of 23andMe's Relative Finder.
What You'll Get
Your Genetic Ethnicity
By testing over 700,000 of your DNA markers, you'll see the mix of ethnicities you have in your genes and how they relate to your family tree.
More comprehensive DNA matching
Find more and closer relatives, overcome brick walls, confirm relationships and find common ancestors. Enhanced, simple web site tools
The consent form contains some additional details, which I haven't seen discussed elsewhere:
1. What is the research project?

The Ancestry DNA's Human Genetic Diversity Project ("The Project") will collect, preserve and analyze genetic information, genealogical pedigrees, historical records, surveys, and other information (collectively, "Information") from people all around the world in order to better understand human evolution and migration, population genetics, ethnographic diversity and boundaries, genealogy, and the history of our species. Researchers hope that the Project will be an invaluable genealogic tool for future generations and will engage the interest of a wide range of scholars interested in genealogy, anthropology, evolution, languages, cultures, medicine, and other topics. The Information will not be used for medical purposes in the treatment or diagnosis of any individuals. [. . .]

2. What information will be collected?

The Project will collect genetic, genealogical and health information that has been stripped of any personally identifiable information in order to study the history of our species. Genes are in your cells, and they are what make you different from anyone else. Some genes control things like the color of your hair or eyes. Genetic information includes your genotype that is discovered when Ancestry DNA processes your saliva or is otherwise provided by you to Ancestry DNA (the "Genetic Information") when you choose to use the Ancestry DNA service. Genealogical information is your pedigree, ethnicity, family history, and other information about you that is either provided by you or is gleaned from publicly available documents on Ancestry.com's website and other locations (the "Genealogical Information"). Health information includes self-reported information from you such as medical conditions, diseases, other health-related information, personal traits, and other information that is either provided by you or is gleaned from publicly available documents on Ancestry.com's website and other locations (the "Health Information").

In all cases for this Project, personally identifiable information about specific study participants (such as name and birth date) is removed from the Information before it is compiled as part of this Project.

The Project will take all of this information (that is already stripped of personally identifiable information) and compile it into a single data summary to minimize the possibility that any individual participant can be identified by any researcher or other individual from the Information.

3. How will the information be used?

Your Information will be combined with others and used to further the Project's objectives of increasing our understanding the components that define the history of our species. Discoveries made as a result of this research could be used in the study of genealogy, anthropology, evolution, languages, cultures, medicine, and other topics.

Previously, ancestry.com have advertised for a PhD population geneticist:
The right person will be using a huge dataset of information from all over the world, developing methods and experimental design to improve results in genotyping data to inform pedigrees. This is not (yet) for medical research and, as such, is not regulated by the FDA. [ . . .] We are mounting a major effort to use genomics to shed light on human diversity, origins and relatedness. The successful candidate will join our efforts to develop and apply analysis pipelines to exploit genotyping data in order to provide information about countries of origin, relatedness and apply genetic information to the construction of human pedigrees. In this position, you will develop, implement and improve methods to use SNP data to provide information on relatedness and genetic origins of humans. You will work closely with other biologists in analyzing data as well as with members of the product development team. This position offers an exciting opportunity to apply cutting edge computational approaches to an unprecedented, large-scale set of pedigreed human genome data. Characteristic duties will include: • Develop, benchmark and implement data analysis pipelines for SNP genotyping data • Evaluate significance of results and recommend changes in experimental design to improve results • Develop, benchmark and implement methods to use genotyping data to inform pedigrees. • Identify new experimental and/or analytic approaches that will improve the outcome of the study • Manage collaborations with laboratory and informatics staff • Successfully communicate scientific concepts to a diverse community of scientists and laypeople Key Responsibilities / Performance Requirements: • Doctorate degree in statistical genetics, population genetics, statistics or a related field. • Candidates should have a track record of productive research in statistical and population genetics • Experience in human population genetics and genotyping • Ability to manipulate large data sets • Programming skills in UNIX/LINUX operating systems, and fluency in standard genetic analytic software (such as R/Bioconductor, EIGENSOFT, MACH, PLINK, ADMIXMAP) • Experience in molecular biology and high-throughput environments would be a significant advantage. • Excellent organizational skills • Superior oral and written English communication skills required. • Must be able to manage multiple simultaneous long-term projects while meeting frequent project deadlines in a fast-paced environment. • Must be able to translate high-level biological questions into concrete tasks.

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.

Was there ever a Ruling Class? 1000 years of Social Mobility

According to Gregory Clark, because of regression to the mean and the lack of any (e.g., racial) barrier preventing gene flow across classes, there was never a persistent ruling class in England.

Notes from a presentation by Clark last year containing "work in progress from a planned book on social mobility over the long run" (pdf):

What is the fundamental nature of human society? Is it stratified into enduring layers of privilege and want, with some mobility between the layers, but permanent social classes? Or is there, over generations, complete mobility between all ranks in the social hierarchy, and complete long run equal opportunity? [. . .]

This book systematically exploits a new method of tracing social mobility over many generations, surnames, to measure the persistence of classes over as much as 800 years, 24 generations. It looks at societies where surnames are inherited, unchanged, by children from fathers. In such cases they thus serve as a tracer of the distant social origins of the modern population (and interestingly also as a tracer of the Y chromosome).

In this role surnames are a surprisingly powerful instrument for measuring long run social mobility. The results they reveal are clear, powerful, and a shock to our casual intuitions.

(1) In England, where we can trace social mobility back to 1066 using surnames, there were never any long persistent ruling and lower classes for the indigenous population: not in medieval England, and not now. About 5-6 generations were, and are, enough to erase most echoes of initial advantage or want. For the English class is, and always was, an illusion. Histories such as those of the Stanley family turn out to be rare exceptions, not the rule.

(2) Paradoxically, while England reveals complete long run mobility, the rates of social mobility per generation, better measured by looking over multiple generations, turn out to be lower than is conventionally estimated. But the mathematics of mobility is such that even such slow regression to the mean, over time, will completely erase initial advantage and want.

(3) The rate of social mobility in England was as high in the middle ages as it is now. The arrival of the whole apparatus of free public education in the late nineteenth century, and the elimination of nepotism in government and private firms, has not improved the rate of social mobility.

(4) The extraordinarily complete long run mobility of England is likely typical of other western European societies. But other countries, in contrast, do exhibit persistent social classes over hundreds of years. In the US, for example, the Black population has persisted at the bottom of the social order, and the Jewish population at the top. In Chile surname evidence shows the indigenous population has remained at the bottom since the Spanish conquest of 1541. [. . .]

(7) Though parents at the top of the economic ladder in any generation in preindustrial England did not derive any lasting advantage for their progeny, there was one odd effect. Surname frequencies show was that there was a permanent increase in the share of the DNA in England from rich parents before 1850. After 1850 a frequency effect operated, but in reverse. Surname frequencies show the DNA share of families in England who were rich in 1850 declined relative to that of poor families of the same generation by 2010. [. . .]

What is the meaning and explanation of these results? This is a much more contentious and difficult area. The book argues for the following conclusions:

A. Why can’t the ruling class in a place like England defend itself against downwards mobility? If the main determinants of economic and social success were wealth, education and connections then there would be no explanation of the consistent tendency of the rich to regress to the society mean. Only if genetics is the main element in determining economic success, if nature trumps nurture, is there a built-in mechanism that ensures the observed regression. That mechanism is the intermarriage of the rich with those from the lower classes. Even though there is strong assortative mating, since this is based on the phenotype created in part by chance and luck, those of higher than average innate talent tend to systematically mate with those of lesser ability and regress to the mean.

B. Racial, ethnic and religious differences allow long persisting social stratification through the barriers they create to this intermarriage. Thus for a society to achieve complete social mobility it must achieve cultural homogeneity. Multiculturalism is the enemy of long run equality.

On the Normans:

Another R1b paper

The peopling of Europe and the cautionary tale of Y chromosome lineage R-M269 (full text freely accessible):
Recently, the debate on the origins of the major European Y chromosome haplogroup R1b1b2-M269 has reignited, and opinion has moved away from Palaeolithic origins to the notion of a younger Neolithic spread of these chromosomes from the Near East. Here, we address this debate by investigating frequency patterns and diversity in the largest collection of R1b1b2-M269 chromosomes yet assembled. Our analysis reveals no geographical trends in diversity, in contradiction to expectation under the Neolithic hypothesis, and suggests an alternative explanation for the apparent cline in diversity recently described. We further investigate the young, STR-based time to the most recent common ancestor estimates proposed so far for R-M269-related lineages and find evidence for an appreciable effect of microsatellite choice on age estimates. As a consequence, the existing data and tools are insufficient to make credible estimates for the age of this haplogroup, and conclusions about the timing of its origin and dispersal should be viewed with a large degree of caution.
I find it hard to get too excited about this paper. As discussed previously, amateurs looking at more finely-resolved subclades using larger numbers of STRs do find trends in diversity that seem to point to an E. European origin for W. European R1b. I expect we'll have to wait a couple years, for overwhelming evidence to accumulate in the form of ancient DNA results and SNP-based dating, before seeing the correct route and timing of the entry of R1b into Europe widely agreed upon by academics. BBC article:
The extent to which modern Europeans are descended from these early farmers versus the indigenous hunter-gatherers who settled the continent thousands of years previously is a matter of heated debate. [. . .]

More than 100 million European men carry a type called R-M269, so identifying when this genetic group spread out is vital to understanding the peopling of Europe. [. . .]

A more recent origin for R-M269 than the Neolithic is also possible. But researchers point out that after the advent of agriculture, populations in Europe exploded, meaning that it would have been more difficult for incoming migrants to displace local people.

From the paper:
If the R-M269 lineage is more recent in origin than the Neolithic expansion, then its current distribution would have to be the result of major population movements occurring since that origin. For this haplogroup to be so ubiquitous, the population carrying R-S127 would have displaced most of the populations present in western Europe after the Neolithic agricultural transition.
Although the debate is commonly framed as Paleolithic vs. Neolithic, many lines of evidence suggest the correct answer is the third option: major post-Neolithic population movement.

Adaptive introgression of Denisovan HLA alleles across Asia?

John Hawks:
If it turns out that we have widespread adaptive introgression in Asia today from Denisovans, that will change the game of studying the origins of these populations. Based on the genome-wide comparison, it looks like the genetic interaction that led to the habitation of Asia did not involve Denisovans, who contributed only to populations at the most eastern extreme of habitation in island Southeast Asia. But the only Denisovans we know about lived near the geographic center of the Asian landmass, not at the extreme southeastern extreme.

The HLA pattern may suggest a more widespread pattern of mixture across Asia, which was later overwritten by population movements of people who didn't have Denisovan ancestry. That means that the habitation of Asia was a process of successive migrations and replacements, which imperfectly covered up the evidence of archaic intermixture. The genes that remain as signs of this intermixture are those that had selective advantages in later populations.

The paper: The Shaping of Modern Human Immune Systems by Multiregional Admixture with Archaic Humans

Deary / Visscher IQ paper

Those who read Sailer learned of this study a couple weeks ago. I've finally gotten around to looking at the actual paper, which seems convincing enough to me in doing what it says it does -- demonstrating "human intelligence is highly heritable and polygenic".

TGGP draws attention to comments by a blogger (Kevin Mitchell) who claims the paper "failed to establish the polygenic nature of the trait", but I don't see that Mitchell has a case. Mitchell:

I would interpret these findings very differently. What the authors do is analyse GWAS data in a very unusual way – they are not interested in finding specific SNPs affecting the trait, they simply use the SNPs to measure genetic relatedness between individuals.

As Mitchell then acknowledges, the paper does include a standard GWAS, the results of which are negative: at the level of individual SNPs not a single "replicable genome-wide significant association" is found. This is not surprising given the relatively small sample size and the (for me) expected polygenic nature of intelligence, but it (along with previous negative findings) tends to rule out any significant role for common variants of large effect in determining IQ.

The study uses SNPs across the genome to measure this relatedness and then shows it correlates with phenotypic similarity – i.e., the trait is heritable. We knew that already.

What they claim is that you can break down this effect by chromosome or by subregion. When they use the SNPs along longer chromosomes they seem to get a bigger effect – “explaining more of the phenotypic variance”. The inference is that thousands of SNPs, scattered across the whole genome, contribute to the trait or, more specifically to variance in the trait across the population (the implication is that they contribute to the value of the trait in individuals).

There is an alternative explanation for this effect, however, which is that using more SNPs simply gives a better estimate of genetic relatedness. So, the SNPs on chromosomes 1 (the longest) give a better estimate than those on chromosome 21 (the shortest) – they index relatedness with more precision. As a result, they correlate better with phenotypic similarity – this looks like you have “explained more of the variance”. In fact, getting such a signal from SNPs on chromosome 1 does not mean that any of the causal variants are actually on chromosome 1. Nor does the fact that such signals can be derived from anywhere in the genome mean that there are thousands of variants across the genome affecting the trait.

What Mitchell is claiming here is that the results could be explained by cryptic relatedness and/or population structure. However, the researchers address both issues, by excluding samples that appear to be related to other samples nearer than the level of 4th cousins and by including as covariates in their models the first few components of an MDS analysis. For non-close relatives in unstructured populations, how similar two individuals are on chromosome 1 tells us nothing about how similar they are on any other chromosome. Visscher was more explicit on this point in a commentary on the height paper:

What is the evidence that population structure is not causing the observed effects?

We took several steps to avoid population structure inflating the estimate of the variance explained by the SNPs. We excluded one individual from any pair that had an estimated relationship > 0.025 (approximately equivalent to between 3rd and 4th cousins). We fitted the first 20 principal components from the relationship matrix in the statistical model so that any population substructure that they picked up was excluded from the variance explained by the SNPs. Critically, we then estimated the correlation between the relationship matrices estimated from different chromosomes and did not find significant correlation. We tested a set of SNPs that are ancestry-informative in Europe for association with height and did not observe inflation of the test-statistics.

For the purpose of this paper, we performed an additional simulation experiment (inspired by comments from Dan Stram) by assuming that the causal variants were all carried on one set of chromosomes (odd numbers) and another set of chromosomes (even numbers) carried SNPs from which we estimated relatedness. If there is structure in the population then this would imply that a pair of individuals that are closely related on odd chromosomes will also be closely related on even chromosomes. We used the observed genotype data of 3,925 individuals and 295K SNPs as the basis of the simulation, and simulated 1,000 causal variants on the odd chromosomes with a total heritability of 80%. Then we performed a restricted maximum likelihood (REML) analysis of the simulated phenotypes on the genetic relationship matrix estimated from the SNPs on the even chromosomes. The estimates and standard errors (SEs) from 10 simulation replicates are shown in Table 1. Since REML estimates of variance are always positive, if the true variance explained is zero, we expect half the replicates to return an estimate of 0.0 and half to return an estimate with mean value 0.8 times the standard error. This is exactly what happened. Therefore we conclude (again) that there is no structure in the data that would inflate the estimate of the variance explained by the SNPs.

Steve Hsu correctly points out:

If I understand correctly, you want to claim that the observed population variation could be due to a few rare variants of large effect. But then it would be surprising for this study to have found .5 of the total variation to be associated with SNPs — compare to earlier studies using twins/adoptions/siblings that found narrow sense heritability of about .6 or so. I would not expect the rare alleles you hypothesize to be in good LD with SNPs (which are designed to tag common variants), so we would expect to lose a big chunk of the .6 additive heritability.

For example, in the Visscher paper on height they had to hand wave about imperfect LD to recover the full .8 or so of heritability. In this case the global fit comes out very close to .6, which suggests common rather than rare variants (at least, they are well tagged by SNPs). But if they are common variants their individual effect sizes must be small and there are a lot of them. Let me know if I am missing something.

Mitchell:

I don’t think the population variation is caused by “a few” rare variants – I think it is (or could be at least) caused by a larger number of rare variants – different ones in different people.

This is getting to be a pretty silly argument: "different ones in different people" would add up to a very large number, which sounds "polygenic" enough to me (regardless of how many people have the major allele at most variable sites). And again: rare variants will be tagged less effectively (if at all) by common SNPs, so the causal variants whose effects are being estimated in this study can't be too rare. The contribution of rare variants to variability in intelligence is likely largely on top of the effect identified here, and probably mostly negative: an unusually high number of rare, deleterious mutations will tend to interfere with brain development and diminish IQ; an unusually low number will result in a higher IQ on average, explaining at least in part the associations commonly found between intelligence and other markers of "good genes" (health, physical attractiveness, and so on). A priori, though, it makes no sense to expect this type of variation to be the only or overwhelming source of genetic variability in IQ. Clearly, a very large number of genes affect brain development, and I expect pretty much all of these genes to be polymorphic. It's also clear tradeoffs affecting IQ exist (such as between brain size and energy expenditure) and that specific IQ-influencing alleles will have varying effects on fitness in different times and places. So it seems obvious to me common variants should be expected to play a major role in inter-individual and inter-population IQ differences.

Incidentally, looking again at the supplementary material for the height paper recently, I noticed the following addition:

In the version of this supplementary file originally posted online, Supplementary Fig. 2a and 2b were incorrect. The legend stated that in Supplementary Fig. 2a, PC1 versus PC2 was plotted when in fact PC2 versus PC3 was shown. Similarly, in Supplementary Fig. 2b, PC4 versus PC5 was plotted rather than PC3 versus PC4 as stated. This error is purely graphical and does not in any way affect the results or conclusions presented in the article.
Dasein spotted the strange-looking PCA at the time. I didn't think it materially affected that paper's conclusion, but I'm pleased to see that confirmed and the issue resolved.

Y haplogroup R1b and light hair in Italy

Via Italian Wikipedia.
 

Update addressing some questions/comments:

(1) The map specifically shows the frequency of blond hair; so yes the frequency of light hair in general will be higher.

(2) The map is adapted from Biasutti's Razze e popoli della Terra. The data was originally collected by Ridolfo Livi in 1859-1863.

(3) The Biasutti/Livi map shows a higher frequency of blond hair in Corsica than in Sardinia. In keeping with the apparent pattern elsewhere in Italy, the frequency of R1b appears to be markedly higher in Corsicans than in Sardinians (in this paper, "HG 1" in combination with "HG 22" roughly corresponds to R1b).

(4) "Does R1b necessarily correlate with light hair?" In Italy it pretty clearly does. If you mean am I suggesting a strict correspondence between light hair and haplogroup R1b, obviously I am not. Looking at Europe as a whole, I doubt much of a correlation exists. But the evidence is consistent with the bearers of R1b (or more specifically subclades of R-L11) being lighter than the previous inhabitants of Italy. This doesn't mean the original carriers of R-M417 and some subclades of I weren't probably also lighter-haired, or that as R1b spread throughout Europe and mixing occurred, R1b always remained associated with light hair. It does tend to add yet more weight against attempts to link R1b in Europe to migration of Neolithic farmers from Anatolia, but dispensing with that question for good awaits large, high-resolution studies of ancient and modern DNA.

"haplogroup R1b is found in some of it's highest concentrations among European peoples in Spain and Portugal -- two countries hardly known for blondes."

Within Iberia, though, it's certainly possible the pattern will hold. Among Iberians, Basques have some of the highest frequencies of both R1b and blondism. According to Coon: 'The French Basques are by no means all brunet; Collignon finds 22 per cent of blue eyes, 44 per cent of "medium," and 34 per cent of dark. Black hair is found in 7 per cent of the group, brown in 77 per cent, and light brown to blond in 16 per cent. Among the Spanish Basques the incidence of blondism is somewhat lower, but the Basques are still light when compared to most other inhabitants of Spain.'

Variance of R-P312 lineages highest in eastern Europe

I take this as further evidence most R1b arrived in western Europe by way of eastern (but not southeastern) Europe:

Recently-revealed structure in Y haplogroup R1a

Posters at dna-forums.com using data from the 1000 Genomes Project to identify new Y subclades have arrived at the following structure below M417:

Early results from commercial and academic testing suggest the bulk of Central Asian, Middle Eastern, and South Asian R1a will turn out to be Z93+ and L342.2+. An academic, posting at dna-forums:
It appears that Z93 and Z95, which, according to the heuristic tree from the 1K genomes project, are above L342.2 do separate most of the Europeans who are ancestral for Z93 and Z95 from the Pakistanis, Indians, Iranians, Ashkenazi Levites and the Eastern Turks (probably Kurds). [. . .] We do have some very preliminary results on Z93 and Z95 that would indicate that almost all Balkan and East European R1a1's are ancestral for Z93 and Z95. Also most of Western Turkey but not Eastern Turkey. I think that the Tuscans who are derived for Z93 and Z95 must be originally of Ashkenazi ancestry (perhaps also the Iberian).
Note: Ashkenazi Levite R1a is L342.2+. I can see no reasonable grounds on which to propose the Z93+ L342.2- TSI and IBS samples are of Jewish origin. More from the academic:
Most Pakistanis are Z93/Z95. We haven't tested many Indians, but the few we have are Z93/Z95. We haven't genotyped any other Z or L SNPs on R1a1 backgrounds. What amazes me is the clear geographic bifurcation between Middle East/South Asian Z93/Z95 (and by inference L342.2) and European markers such as M458. This points to a vary old what we term vicariance pattern between Europe and the Middle East with respect to R1a1. Maybe the original source of R1a1 is somewhere in the middle such as Armenia or Turkey and some R1a1 moved to Europe to become M458 and other newly discovered L# lineages and other R1a1's move to Iran/Pakistan/India/Central Asia to become Z93/Z95. I think that this bifurcation occurred at least 10,000 years ago, but then of course we tend to use the evolutionary mutation rates on YSTRs.
Another poster points out: "Dividing by 3 [to bring the estimate more in line with real mutation rates] gives an age of 3300 years, almost exactly the estimate from Nordtvedt's spreadsheet." Someone else recently estimated the TMRCA for L342.2+ at around 3,600 years. So: if current patterns hold, the bulk of South Asian R1a unambiguously falls within European R1a variation. While I fully expect, when we eventually see results for these markers in large academic samples published, the papers will feature evolutionary mutation rates and less than parsimonious attempts to fit the distribution of M417 sublineages to archaeology, it's pretty clear to me Z93 and L342.2 originated on the Steppe within the past 4000 years or so and spread with Indo-Iranian.

Swedish McDonald's