Dental morphological evidence for European admixture in Mongolia and western China

Lee, C. and Scott, G. R. (2011), Brief communication: Two-rooted lower Canines—A European trait and sensitive indicator of admixture across Eurasia. American Journal of Physical Anthropology, 146: 481–485. doi: 10.1002/ajpa.21585
With the exception of Carabelli's trait, the European dentition is better known for the morphological traits that it does not exhibit rather than the ones that it does. One root trait, however, runs counter to the characterization of reduced and simplified European crowns and roots. Although a rare trait in general, two-rooted lower canines are much more common in Europeans than in any other regional grouping and, given adequate sample sizes, can be useful in evaluating gene flow between Europeans and neighboring groups. In European samples, two-rooted lower canines consistently exhibit frequencies of 5–8%. In our sample from northern Spain, the trait attains a frequency of almost 10%. In contrast, in Sub-Saharan Africans the trait is virtually unknown while in Asian and Asian-derived populations, it varies between 0.0 and 1.0%. Here we show that two-rooted canine frequencies for new migrants along the western frontiers of China and Mongolia ranged from 0–4%. These data suggest European-derived populations migrated into western China (Xinjiang Province) and Mongolia (Bayan Olgii Aimag) sometime during the late Bronze age (1000–400 BCE). [. . .]

One of the major concerns of Alexandersen (1963) regarding two-rooted lower canines revolved around the issue of ‘‘atavism.’’ This term, rarely used today, begs the question of whether or not this double rooted form was common at one time, then disappeared, only to reappear sometime later. Swindler (1995) notes that ‘‘the deciduous and permanent canines in the majority of living primates have a single root.’’ This suggests that two-rooted lower canines are not the ancestral condition in anthropoids or hominoids. Rather, the phenotype is a derived condition, found primarily in recent human populations distributed across Western Eurasia.

The presence of the two-rooted canines in East Asia may provide some clue as to the eastward migration of new populations into China and Mongolia. The largest numbers of individuals with this trait are concentrated along the western and northern frontiers of China and Mongolia. Archaeological excavations support the large scale movement of people into this area during the Bronze age (ca. 2200 BCE–400 BCE). Burial artifacts and settlement patterns suggest cultural and technological ties to the Afanasevo culture in Siberia, which in turn is linked archaeologically, linguistically, and genetically with the Indo-European Tocharian populations that appear to have migrated to the Tarim Basin ca. 4,000 years ago (Ma and Sun, 1992; Ma and Wang, 1992; Mallory and Mair, 2000; Romgard, 2008; Keyser et al., 2009; Li et al., 2010).

The appearance of a new population on the western frontier also supports the findings of previous research in cranial metrics, dental nonmetrics, and DNA. Using cranial metrics and archaeological dating, Han (1994) hypothesized the earliest large-scale migration into western China occurred during the early Bronze age (2000 BCE) from Central Asia or southern Siberia. Dental nonmetric data also support multiple migrations into western China (Xinjiang Province) from Central Asia during the Bronze age to Iron age (Lee, 2007; Zhang, 2010). mtDNA studies on archaeological and modern population samples from Xinjiang Province show heterogeneous Asian and European genetic signatures dating from the Bronze age to the present (Yao et al., 2004; Cui et al., 2010; Zhang et al., 2010; Li et al., 2010).

As the frequency of two-rooted canines is highest in European samples and low to nonexistent in Asians, we propose this trait was introduced into East Asia by Indo- European speaking groups or their affines crossing the western frontier of China and Mongolia. Further data are needed to clarify aspects of these population movements, including the identity of the migrants, along with the number, routes, and timing of the migrations.

Although two-rooted lower canines cannot offer the precision of DNA in evaluating the ancestry in individual skulls, this trait is a sensitive indicator of admixture wherever Europeans come in contact with Asian or African populations. As this distinctive trait can be scored with relative ease in large samples, it provides a useful supplemental tool in discerning gene flow between distantly related populations going back many millennia.

Daniel MacArthur twitter commentary from CSHL Personal Genomes meeting

This meeting took place a couple weeks ago -- dgmacarthur is presently posting from ICHG2011.

James Watson is asking a question. At least I think it's a question. #cshlpg
Yes, it was a question: hasn't ELSI just been a huge waste of money? Wait, no - he's back to talking again. #cshlpg

Manfred Kayser is talking about the genetics of human appearance, but his talk is untweetable. #cshlpg
Although Kayser's talk is untweetable it sounds as though a lot of this is close to publication - so stay tuned. #cshlpg

JV [Joris Veltman] discussing published analysis of de novo variants in mental retardation: #cshlpg
JV: total number of de novo coding mutations is not higher in MR patients - but more likely to be in brain genes. #cshlpg

What fraction of the human genome is functional?

What fraction of the human genome is functional?

Chris P. Ponting1,3 and Ross C. Hardison2,3


Many evolutionary studies over the past decade have estimated ?sel, the proportion of all nucleotides in the human genome that are subject to purifying selection because of their biological function. Most of these studies have estimated the nucleotide substitution rates from genome sequence alignments across many diverse mammals. Some ?sel estimates will be affected by the heterogeneity of substitution rates in neutral sequence across the genome. Most will also be inaccurate if change in the functional sequence repertoire occurs rapidly relative to the separation of lineages that are being compared. Evidence gathered from both evolutionary and experimental analyses now indicate that rates of “turnover” of functional, predominantly noncoding, sequence are, indeed, high. They are sufficiently high that an estimated 50% of mouse constrained noncoding sequence is predicted not to be shared with rat, a closely related rodent. The rapidity of turnover results in, at least, a twofold underestimate of ?sel by analyses that measure constraint across the eutherian phylogeny. Approaches that take account of turnover estimate that the steady-state value of ?sel lies between 10% and 15%. Experimental studies corroborate the predicted rates of loss and gain of noncoding functional sites. These studies show the limitations inherent in the use of deep sequence conservation for identifying functional sequence. Experimental investigations focusing on lineage-specific, noncoding, and functional sequence are now essential if we are to appreciate the complete functional repertoire of the human genome.

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.'s "Human Genetic Diversity Project" 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'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'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, 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.