March 28, 2014

Oldest modern human genome from Siberia ~45 thousand years ago

Just a teaser from Ann Gibbons in Science:
In 2008, Siberian ivory carver Nikolay Peristov was searching for ancient mammoth tusks eroding from the banks of the Irtysh River in western Siberia, when he found fossilized bones instead. Back in his workshop in Omsk, he showed the bones to local paleontologist Aleksey Bondarev, who recognized a human thighbone. Bondarev in turn showed it to an anthropologist friend, and it was passed on up the chain to some of the world's top experts in human evolution. They dated it to 45,000 years ago, making it one of the oldest known modern humans in northern Asia and Europe.

Now, the bone has opened a window on the genetics of our species at a crucial moment: soon after their arrival in northern Eurasia. At a meeting* here last week, paleogeneticist Svante Pääbo of the Max Planck Institute for Evolutionary Anthropology in Leipzig, Germany, announced that his team has sequenced the thighbone's entire nuclear genome to high accuracy—an astonishing 42x coverage. "This is by far the oldest sequenced genome of a modern human," he said.

Because all living people in Europe and Asia carry roughly the same amount of Neandertal DNA, Pääbo's team thought that the interbreeding probably took place in the Middle East, as moderns first made their way out of Africa. Middle Eastern Neandertal sites are close to Skhul and Qafzeh, so some researchers suspected that those populations were the ones that mingled. But the team's analysis favors a more recent rendezvous. The femur belonged to an H. sapiens man who had slightly more Neandertal DNA, distributed in different parts of his genome, than do living Europeans and Asians. His Neandertal DNA is also concentrated into longer chunks than in living people, Pääbo reported. That indicates that the sequences were recently introduced: With each passing generation, any new segment of DNA gets broken up into shorter chunks as chromosomes from each parent cross over and exchange DNA. Both features of the Neandertal DNA in the femur suggest that the Ust-Ishim man lived soon after the interbreeding, which Pääbo estimated at 50,000 to 60,000 years ago.
The higher Neandertal DNA in the Ust-Ishim sample might be explainable by the negative selection against Neandertal material recently documented.  At 45kya, this sample is right around the time of the Early Upper Paleolithic at Kara-Bom in Siberia (and indeed anywhere), so this will be a hugely interesting sample when it is finally published.

Here is the program of the symposium on which this was apparently discussed (pdf). There seem to be quite a few interesting titles (but no abstracts).

March 27, 2014

Major new article on the deep origins of Y-haplogroup R1a (Underhill et al. 2014)

Five years ago, Underhill et al. (2009) presented a major advance in the study of haplogroup R1a. Much new knowledge was added in the interim by genetic genealogists and some scientists,  and now a major new paper by Peter Underhill comes to update our knowledge of this important and widely spread human lineage.

The shallow coalescence time within R1a will not surprise many genetic genealogists while its diversification in the vicinity of present-day Iran might. A ~5-7kyBP coalescence would make the expansion of R1a lineages presumably visible to future ancient DNA studies which will probably be the final arbiter of the veracity of the date estimate in this paper and its postulated place of origin.

I'll try to digest what the new information has to say about Eurasian prehistory, but in the meantime...

... I will, however, take some time to highlight the passing of the guard from Y-STRs to Y-SNPs which I had long ago anticipated. There is some lingering controversy about the substitution rate on the Y chromosome is, but it is hopeful that this will be resolved before not too long as the price of whole genome sequencing is always dropping and the samples sequenced in this study are probably the first of many to come.

In any case:
Our phylogeographic data lead us to conclude that the initial episodes of R1a-M420 diversification occurred in the vicinity of Iran and Eastern Turkey, and we estimate that diversification downstream of M417/Page7 occurred ~5800 years ago. This suggests the possibility that R1a lineages accompanied demic expansions initiated during the Copper, Bronze, and Iron ages, partially replacing previous Y-chromosome strata, an interpretation consistent with albeit limited ancient DNA evidence.54, 60 However, our data do not enable us to directly ascribe the patterns of R1a geographic spread to specific prehistoric cultures or more recent demographic events. High-throughput sequencing studies of more R1a lineages will lead to further insight into the structure of the underlying tree, and ancient DNA specimens will help adjudicate the molecular clock calibration. Together these advancements will yield more refined inferences about pre-historic dispersals of peoples, their material cultures, and languages.
It would of course be great to get some ancient DNA data from Iran and Eastern Turkey:
Among the 120 populations with sample sizes of at least 50 individuals and with at least 10% occurrence of R1a, just 6 met these criteria, and 5 of these 6 populations reside in modern-day Iran. Haplogroup diversities among the six populations ranged from 0.78 to 0.86 (Supplementary Table 4). Of the 24 R1a-M420*(xSRY10831.2) chromosomes in our data set, 18 were sampled in Iran and 3 were from eastern Turkey. Similarly, five of the six observed R1a1-SRY10831.2*(xM417/Page7) chromosomes were also from Iran, with the sixth occurring in a Kabardin individual from the Caucasus. Owing to the prevalence of basal lineages and the high levels of haplogroup diversities in the region, we find a compelling case for the Middle East, possibly near present-day Iran, as the geographic origin of hg R1a.
Also, the finding that...
The four subhaplogroups of Z93 (branches 9-M582, 10-M560, 12-Z2125, and 17-M780, L657) constitute a multifurcation unresolved by 10 Mb of sequencing; it is likely that no further resolution of this part of the tree will be possible with current technology. Similarly, the shared European branch has just three SNPs.
... seems to imply some Copper-to-Bronze Age guys did more than their fair share of fathering.

European Journal of Human Genetics , (26 March 2014) | doi:10.1038/ejhg.2014.50

The phylogenetic and geographic structure of Y-chromosome haplogroup R1a

Peter A Underhill et al.

R1a-M420 is one of the most widely spread Y-chromosome haplogroups; however, its substructure within Europe and Asia has remained poorly characterized. Using a panel of 16 244 male subjects from 126 populations sampled across Eurasia, we identified 2923 R1a-M420 Y-chromosomes and analyzed them to a highly granular phylogeographic resolution. Whole Y-chromosome sequence analysis of eight R1a and five R1b individuals suggests a divergence time of ~25 000 (95% CI: 21 300–29 000) years ago and a coalescence time within R1a-M417 of ~5800 (95% CI: 4800–6800) years. The spatial frequency distributions of R1a sub-haplogroups conclusively indicate two major groups, one found primarily in Europe and the other confined to Central and South Asia. Beyond the major European versus Asian dichotomy, we describe several younger sub-haplogroups. Based on spatial distributions and diversity patterns within the R1a-M420 clade, particularly rare basal branches detected primarily within Iran and eastern Turkey, we conclude that the initial episodes of haplogroup R1a diversification likely occurred in the vicinity of present-day Iran.


Haplogroup E and Afroasiatic

This is an open access article.

European Journal of Human Genetics advance online publication 26 March 2014; doi: 10.1038/ejhg.2014.41

Y-chromosome E haplogroups: their distribution and implication to the origin of Afro-Asiatic languages and pastoralism

Eyoab I Gebremeskel and Muntaser E Ibrahim

Archeological and paleontological evidences point to East Africa as the likely area of early evolution of modern humans. Genetic studies also indicate that populations from the region often contain, but not exclusively, representatives of the more basal clades of mitochondrial and Y-chromosome phylogenies. Most Y-chromosome haplogroup diversity in Africa, however, is present within macrohaplogroup E that seem to have appeared 21 000–32 000 YBP somewhere between the Red Sea and Lake Chad. The combined analysis of 17 bi-allelic markers in 1214 Y chromosomes together with cultural background of 49 populations displayed in various metrics: network, multidimensional scaling, principal component analysis and neighbor-joining plots, indicate a major contribution of East African populations to the foundation of the macrohaplogroup, suggesting a diversification that predates the appearance of some cultural traits and the subsequent expansion that is more associated with the cultural and linguistic diversity witnessed today. The proto-Afro-Asiatic group carrying the E-P2 mutation may have appeared at this point in time and subsequently gave rise to the different major population groups including current speakers of the Afro-Asiatic languages and pastoralist populations.


Origins of the Tharu

European Journal of Human Genetics advance online publication 26 March 2014; doi: 10.1038/ejhg.2014.36

Unravelling the distinct strains of Tharu ancestry

Gyaneshwer Chaubey et al.

The northern region of the Indian subcontinent is a vast landscape interlaced by diverse ecologies, for example, the Gangetic Plain and the Himalayas. A great number of ethnic groups are found there, displaying a multitude of languages and cultures. The Tharu is one of the largest and most linguistically diverse of such groups, scattered across the Tarai region of Nepal and bordering Indian states. Their origins are uncertain. Hypotheses have been advanced postulating shared ancestry with Austroasiatic, or Tibeto-Burman-speaking populations as well as aboriginal roots in the Tarai. Several Tharu groups speak a variety of Indo-Aryan languages, but have traditionally been described by ethnographers as representing East Asian phenotype. Their ancestry and intra-population diversity has previously been tested only for haploid (mitochondrial DNA and Y-chromosome) markers in a small portion of the population. This study presents the first systematic genetic survey of the Tharu from both Nepal and two Indian states of Uttarakhand and Uttar Pradesh, using genome-wide SNPs and haploid markers. We show that the Tharu have dual genetic ancestry as up to one-half of their gene pool is of East Asian origin. Within the South Asian proportion of the Tharu genetic ancestry, we see vestiges of their common origin in the north of the South Asian Subcontinent manifested by mitochondrial DNA haplogroup M43.


March 16, 2014

Lactase persistence and pastoralism in Africa

AJHG doi:10.1016/j.ajhg.2014.02.009

Genetic Origins of Lactase Persistence and the Spread of Pastoralism in Africa

Alessia Ranciaro et al.

In humans, the ability to digest lactose, the sugar in milk, declines after weaning because of decreasing levels of the enzyme lactase-phlorizin hydrolase, encoded by LCT. However, some individuals maintain high enzyme amounts and are able to digest lactose into adulthood (i.e., they have the lactase-persistence [LP] trait). It is thought that selection has played a major role in maintaining this genetically determined phenotypic trait in different human populations that practice pastoralism. To identify variants associated with the LP trait and to study its evolutionary history in Africa, we sequenced MCM6 introns 9 and 13 and ∼2 kb of the LCT promoter region in 819 individuals from 63 African populations and in 154 non-Africans from nine populations. We also genotyped four microsatellites in an ∼198 kb region in a subset of 252 individuals to reconstruct the origin and spread of LP-associated variants in Africa. Additionally, we examined the association between LP and genetic variability at candidate regulatory regions in 513 individuals from eastern Africa. Our analyses confirmed the association between the LP trait and three common variants in intron 13 (C-14010, G-13907, and G-13915). Furthermore, we identified two additional LP-associated SNPs in intron 13 and the promoter region (G-12962 and T-956, respectively). Using neutrality tests based on the allele frequency spectrum and long-range linkage disequilibrium, we detected strong signatures of recent positive selection in eastern African populations and the Fulani from central Africa. In addition, haplotype analysis supported an eastern African origin of the C-14010 LP-associated mutation in southern Africa.


Back-migration of Yeniseian into Asia from Beringia

PLOS One DOI: 10.1371/journal.pone.0091722

Linguistic Phylogenies Support Back-Migration from Beringia to Asia

Mark A. Sicoli, Gary Holton

Recent arguments connecting Na-Dene languages of North America with Yeniseian languages of Siberia have been used to assert proof for the origin of Native Americans in central or western Asia. We apply phylogenetic methods to test support for this hypothesis against an alternative hypothesis that Yeniseian represents a back-migration to Asia from a Beringian ancestral population. We coded a linguistic dataset of typological features and used neighbor-joining network algorithms and Bayesian model comparison based on Bayes factors to test the fit between the data and the linguistic phylogenies modeling two dispersal hypotheses. Our results support that a Dene-Yeniseian connection more likely represents radiation out of Beringia with back-migration into central Asia than a migration from central or western Asia to North America.


March 10, 2014

Dark pigmentation of Eneolithic and Bronze Age kurgan groups from eastern Europe

This is a very exciting new study that seems to parallel some results from early west Europeans. The authors invoke selection as a possible cause for the massive change in frequency between the Bronze Age and present-day Ukrainians.

An invocation of selection as an explanation requires evidence population continuity, otherwise changes in allele frequency may involve migration of a new frequency-differentiated new population; for example, the massive change in pigmentation in North America over the last 500 years is not due to selection but to migration of Europeans. The authors cannot reject population continuity on the basis of mtDNA haplogroup frequencies, although autosomal data may be more informative for that purpose.

In any case, the fact that the limited sample from western Europe and the much more extensive sample from eastern Europe both show a darker pigmentation than modern Europeans does suggest that interesting changes happened in Europe over the last few thousand years and samples from more recent time periods may better determine the pace of this change.

From the paper:
In sum, a combination of selective pressures associated with living in northern latitudes, the adoption of an agriculturalist diet, and assortative mating may sufficiently explain the observed change from a darker phenotype during the Eneolithic/Early Bronze age to a generally lighter one in modern Eastern Europeans, although other selective factors cannot be discounted. The selection coefficients inferred directly from serially sampled data at these pigmentation loci range from 2 to 10% and are among the strongest signals of recent selection in humans.

The classical Greeks did of course notice that the inhabitants of the north Pontic hinterland, collectively known as Scythians, were extraordinarily light-pigmented. This would imply that major pigmentation change occurred in the steppe over a time span of Bronze Age-Classical Antiquity rather than Bronze Age-present; this would imply even higher selection coefficients (if selection over a population exhibiting continuity is at play).

The Scythians were also thought to be recent arrivals from the east so it is not clear if they were descended from the Bronze Age population of eastern Europe; the crazy selection coefficients that would need to be assumed if there was indeed population continuity might imply that Herodotus got it right again, and the Scythians did in fact arrive from elsewhere. That would of course also imply that people from Central Asia and Siberia (where the Scythians may have come from) were originally lighter than Europeans which does find support from an older study on southern Siberian remains. Ironically, if that is the case, it would mean that the famous light-pigmented mummies of different parts of Inner Asia may not be long-lost European descendants -- as it has sometimes been presumed on the basis of modern-day clines of pigmentation. As usual, ancient DNA continues to surprise.

PNAS doi: 10.1073/pnas.1316513111

Direct evidence for positive selection of skin, hair, and eye pigmentation in Europeans during the last 5,000 y

Sandra Wilde et al.

Eye, hair, and skin pigmentation are highly variable in humans, particularly in western Eurasian populations. This diversity may be explained by population history, the relaxation of selection pressures, or positive selection. To investigate whether positive natural selection is responsible for depigmentation within Europe, we estimated the strength of selection acting on three genes known to have significant effects on human pigmentation. In a direct approach, these estimates were made using ancient DNA from prehistoric Europeans and computer simulations. This allowed us to determine selection coefficients for a precisely bounded period in the deep past. Our results indicate that strong selection has been operating on pigmentation-related genes within western Eurasia for the past 5,000 y.


March 09, 2014

The place of the Armenian language in the Indo-European family

A very interesting talk at the Library of Congress making a good case for a Greek-Phrygian-Armenian clade within the Indo-European family.

Of course the testimony of Herodotus is -at least for me- the most convincing argument for an ultimately Balkan origin of the Phrygo-Armenians.

Modern Armenians are quite distinct from modern populations of the Balkans but who knows how both they and the populations of the Balkans have changed since the beginning of the Iron Age when the Phrygians established themselves in Asia Minor? The recent study by Hellenthal et al. did not find any good evidence for recent admixture in Armenians but this might be due to (i) Armenians being unmixed descendants of Proto-Armenians, (ii) Armenians being near-unmixed descendants of pre-Armenians, or (iii) the method not having enough power to detect admixture.

My guess is that the relative remoteness of the Armenian highlands coupled with the heterodox position of the Armenian church hindered substantial gene flow into the Armenian population over at least the last 1,500 years.

Green Arabia 2014 conference

The program of an upcoming conference that will take in about a month. I don't see abstracts but the list of talks seems interesting and hopefully there will be a twitter stream by attendees in April.

March 06, 2014

Chauvet cave art not the work of earliest Europeans

Many of you may have watched Cave of Forgotten Dreams, a great documentary about the paintings of Chauvet cave in France. It now turns out that the extraordinary art preserved in the cave may not date to ~36,000 years but rather to the Gravettian or Solutrean period.

 L'Anthropologie Available online 11 February 2014

New investigations into the cultural and stylistic identity of the Chauvet cave and its radiocarbon dating

Jean Combiera, Guy Jouve

The discovery of Chauvet cave, at Vallon-Pont-d’Arc (Ardèche), in 1994, was an important event for our knowledge of palaeolithic parietal art as a whole. Its painted and engraved figures, thanks to their number (425 graphic units), and their excellent state of preservation, provide a documentary thesaurus comparable to that of the greatest sites known, and far beyond what had already been found in the group of Rhône valley caves (Ardèche and Gard). But its study – when one places it in its natural regional, cultural and thematic framework – makes it impossible to see it as an isolated entity of astonishing precocity. This needs to be reconsidered, and the affinities that our research has brought to light are clearly incompatible with the very early age which has been attributed to it. And if one extends this examination to the whole of the Franco-Cantabrian domain, the conclusion is inescapable: although Chauvet cave displays some unique characteristics (like every decorated cave), it belongs to an evolved phase of parietal art that is far removed from the motifs of its origins (known from art on blocks and on shelter walls dated by stratigraphy to the Aurignacian, in France and Cantabrian Spain). The majority of its works are therefore to be placed, quite normally, within the framework of the well-defined artistic creations of the Gravettian and Solutrean. Moreover, this phase of the Middle Upper Palaeolithic (26,000–18,000) coincides with a particularly intensive and diversified local human occupation, unknown in earlier periods and far less dense afterwards in the Magdalenian. A detailed critique of the treatment of the samples subjected to AMS radiocarbon dating makes it impossible to retain the very early age (36,000 cal BP) attributed by some authors to the painted and engraved figures of Chauvet cave.


Middle Neolithic European archers from France

Am J Phys Anthropol DOI: 10.1002/ajpa.22504

Bioarchaeology of the middle Neolithic: Evidence for archery among early european farmers

Aline Thomas

This article focuses on Neolithic skeletons associated with the first monumental cemeteries of Western Europe and specifically those of the Cerny culture (Paris Basin, France). While this cultural context is an agrarian one, numerous arrowheads derived from complete hunting equipment are present in numerous graves. The goal of this work is to evaluate the morphological and pathological differences among the individuals according to the presence of arrowheads in their graves. It is postulated that those buried with such artifacts practiced archery, unlike their counterparts. Only adult males were selected for study to limit the effect of non-mechanical factors such as age- and sex-related modifications. The corpus consists of 36 males reliably identified among the 101 Cerny adults currently available. Thirteen men are associated with arrowheads. Variations in morphology and robusticity are evaluated on the basis of the external geometric properties of the appendicular skeleton. Entheseal changes to fibrocartilaginous attachment sites of upper and lower limbs are also examined. Both nonpathological skeletal adaptations and pathological indicators are consistent and reveal significant differences between the two groups compared. Functional adaptation is observed in the forearm bones and the clavicle in response to mechanical loads, and enthesopathies suggest repeated forceful use of upper limb muscles. These osteological changes specifically reflect the higher intensity upper limb activity of the men buried with arrowheads and correspond with the medical data on known archers, suggesting that this specific forceful task is linked to the practice of archery.


March 04, 2014

Admixture in US populations

An interesting blog post from 23andMe:
In an update to that work, our researcher Kasia Bryc found that about about 4 percent of whites have at least 1 percent or more African ancestry.

Although it is a relatively small percentage, the percentage indicates that an individual with at least 1 percent African ancestry had an African ancestor within the last six generations, or in the last 200 years. This data also suggests that individuals with mixed parentage at some point were absorbed into the white population.

Looking a little more deeply into the data, Kasia also found that the percentage of whites with hidden African ancestry differed significantly from state-to-state. Southern states with the highest African American populations, tended to have the highest percentages of hidden African ancestry. In South Carolina at least 13 percent of self-identified whites have 1 percent or more African ancestry, while in Louisiana the number is a little more than 12 percent. In Georgia and Alabama the number is about 9 percent. The differences perhaps point to different social and cultural histories within the south.
Previous published studies estimate that on average African Americans had about 82 percent African ancestry and about 18 percent European ancestry. But in self-identified African Americans in 23andMe’s database, Kasia found the average amount of African ancestry was closer to 73 percent.
I don't think that is necessarily the average percentage in the general African American population as the subset of African Americans who take 23andMe tests may not be representative (e.g., it may come more from cities where African Americans may have more opportunity to admix with European Americans).

On average Latinos had about 70 percent European ancestry, 14 percent Native American ancestry and 6 percent African ancestry. The remainder ancestry is difficult to assign because the DNA is either shared by a number of different populations around the world, or because it’s from understudied populations, such as Native Americans. Obviously that large “unassigned” percentage means that those “averages” could be higher. As with African Americans, looking at the regional and state-to-state numbers for self-identified Latinos, the differences are striking. 

For example, some Latinos have no discernible Native American ancestry, while in others have as much as 50 percent of the ancestry being Native American. Latinos in states in the Southwest, bordering Mexico — New Mexico, Texas, California and Arizona — have the greatest percentage of Native American ancestry. Latinos in states with the largest proportion of African Americans in their population — South Carolina, Louisiana and Alabama — have the highest percentage of African Ancestry.
23andMe may have a couple of orders of magnitude more sampled individuals than anything that appears in most published studies and it's great to see this being put to good use.

It'd be great if someone at 23andMe did some more analyses over their huge database. I can only imagine what a flashPCA with half a million individuals from around the world would look like; even if it told us nothing new about human history it would be quite a cool picture to look at.