Sakha origins

An interesting quote from the paper:

Although the genetic heritage of the native populations of Sakha is mostly of East Asian ancestry, analyses of autosomal SNP data as well as haploid loci also show a minor West  Eurasian genetic component. The patchy presence of the “European” (blue) component in the  ADMIXTURE plot (Figure 6), most pronounced in Yukaghirs, probably testifies to recent  admixture with Europeans. In addition, the presence of European-specific paternal lineages  R1a-M458, I1 and I2a among Yakuts, Dolgans, Evenks and Yukaghirs likely points to a  recent gene flow from East Europeans. Although only individuals with self-reported unadmixed ancestry for at least two generations were included in the study of haploid loci,  mistakes in ethnic self-identification cannot be entirely excluded. One of the main sources of  gene flow has likely been Russians who accounted for 37.8% of the population of Sakha in  2010 [61]. The migration of Russians (at first mainly men) to eastern Siberia started already  in the 17th century, when Yakutia was incorporated into the Russian Empire [62]. 

But:

The mtDNA haplogroup J detected in the remains from a Yakut burial site dated to the  beginning of the 17th century [41], long before the beginning of the settlement of Russian  families in the 18th century [63], clearly points to more ancient gene flow from western  Eurasia. The presence of haplogroups H8, H20 and HV1a1a among the Yakuts, Dolgans and  Evenks (Figure 1) also suggests gene flow other than from Russians, because these  haplogroups are rare (H8 and H20) or even absent (HV1a1a) among Russians [64-67], but are  common among southern Siberian populations as well as in the Caucasus, the Middle and  Near East [19,68-70]. Moreover, the HVSI haplotypes of H8, H20a and HV1a1a in our  sample exactly match those in the Buryats from the Buryat Republic [19]. Similarly, the Ychromosome haplogroup J in Dolgans and Evens very likely testifies to gene flow through  South Siberia, as it is present among native South Siberian populations [47,71]. The scenario  of ancient gene flow from West Eurasia is supported by ancient DNA data, which show that  in the Bronze and Iron Ages, South Siberia, including the Altai region, was an area of  overwhelmingly predominant western Eurasian settlement [72,73], and the Indo-European  migration even reached northeastern Mongolia [74]. To summarize, the West Eurasian  genetic component in Sakha may originate from recent admixture with East Europeans,  whereas more ancient gene flow from West Eurasia through Central Asia and South Siberia is  also probable. 

BMC Evolutionary Biology 2013, 13:127 doi:10.1186/1471-2148-13-127

Autosomal and uniparental portraits of the native populations of Sakha (Yakutia): implications for the peopling of Northeast Eurasia

Sardana A Fedorova et al.

Abstract (provisional)

Background

Sakha -- an area connecting South and Northeast Siberia -- is significant for understanding the history of peopling of Northeast Eurasia and the Americas. Previous studies have shown a genetic contiguity between Siberia and East Asia and the key role of South Siberia in the colonization of Siberia.

Results

We report the results of a high-resolution phylogenetic analysis of 701 mtDNAs and 318 Y chromosomes from five native populations of Sakha (Yakuts, Evenks, Evens, Yukaghirs and Dolgans) and of the analysis of more than 500,000 autosomal SNPs of 758 individuals from 55 populations, including 40 previously unpublished samples from Siberia. Phylogenetically terminal clades of East Asian mtDNA haplogroups C and D and Y-chromosome haplogroups N1c, N1b and C3, constituting the core of the gene pool of the native populations from Sakha, connect Sakha and South Siberia. Analysis of autosomal SNP data confirms the genetic continuity between Sakha and South Siberia. Maternal lineages D5a2a2, C4a1c, C4a2, C5b1b and the Yakut-specific STR sub-clade of Y-chromosome haplogroup N1c can be linked to a migration of Yakut ancestors, while the paternal lineage C3c was most likely carried to Sakha by the expansion of the Tungusic people. MtDNA haplogroups Z1a1b and Z1a3, present in Yukaghirs, Evens and Dolgans, show traces of different and probably more ancient migration(s). Analysis of both haploid loci and autosomal SNP data revealed only minor genetic components shared between Sakha and the extreme Northeast Siberia. Although the major part of West Eurasian maternal and paternal lineages in Sakha could originate from recent admixture with East Europeans, mtDNA haplogroups H8, H20a and HV1a1a, as well as Y-chromosome haplogroup J, more probably reflect an ancient gene flow from West Eurasia through Central Asia and South Siberia.

Conclusions

Our high-resolution phylogenetic dissection of mtDNA and Y-chromosome haplogroups as well as analysis of autosomal SNP data suggests that Sakha was colonized by repeated expansions from South Siberia with minor gene flow from the Lower Amur/Southern Okhotsk region and/or Kamchatka. The minor West Eurasian component in Sakha attests to both recent and ongoing admixture with East Europeans and an ancient gene flow from West Eurasia.

Link

ESHG 2011 abstracts are online

From here. I didn't find much of interest this year, except a long-overdue look at Bulgarian Y-chromosomes but with not a very informative abstract.

Y-Chromosome genetic variation of modern Bulgarians
S. Karachanak et al.

To date, Bulgarian Y chromosomes have been studied only in macrogeographic context or in the lineage-based approach. Therefore, in order to comprehensively characterize Bulgarian Y-chromosome variation, we have performed high-resolution phylogenetic analysis of 812 healthy,unrelated Bulgarian males and compared the results with Y-chromosome data from other Eurasian populations.
The genotyping of 60 biallelic markers was performed in hierarchical order by RFLP and DHPLC analyses. The position of Bulgarians among other populations was visualized by Principal Component (PC) analysis.
About 80% of the total genetic variation in Bulgarians falls within haplogroups E-M35, I-M170, J-M172, R-M17 and R-M269. This finding shows that the Bulgarian haplogroup profile is congruent with those described for most European populations.
Among the prehistoric events marked by the observed haplogroups, the greatest contribution comes from the range expansion of local Mesolithic foragers triggered by adoption of agriculture introduced by a cadre of Near Eastern farmers. The Bulgarian Y chromosome gene pool also bears signals of the recolonization from different glacial refugia, the spread of agriculture from the Near East and the expansion of early farmers along the Central and East European river basins.
As for the interpopulation analysis, similarly to mtDNA, Bulgarians belong to the cluster of European populations, still being slightly distant from them. Bulgarians are distant from Turks (despite geographical proximity), Arabic and Caucasus populations and Indians. These trends in the PCA graph likely reflect not only prehistoric, but also more recent demographic events that have shaped the Y chromosome structure of modern Bulgarians.

An abstract on Yakuts seems to report the link between the Altaic-Turkic Yakut and the Altaic-Tungusic Evenk that I also discovered recently.

Autosomal and uniparental genetic diversity of the populations of Sakha (Yakutia): Implications for the peopling of Northeast Eurasia
S. A. Fedorov et al.

Sakha Autonomous Republic occupies a quarter of Siberian total land area in its northeastern part, is an important region for understanding the colonization of the Northern Eurasia by anatomically modern humans. To characterize the genetic variation in Sakha both the haploid mitochondrial DNA (mtDNA) and Y chromosomal as well as diploid autosomal loci (650 000 SNPs) of genome were analyzed in five native populations of Sakha (Yakuts, Evenks, Evens, Dolgans and Yukaghirs).
While striking prevalence of Y chromosome haplogroup N1c in gene pool differentiates Yakuts from other populations, the mtDNA and autosomal analyses demonstrate genetic similarity of all native populations of Sakha, in particular Yakuts and Evenks. The results also demonstrate closest genetic proximity of the populations of Sakha with southern Siberians. Both mtDNA and autosomal analyses reveal deep genetic discontinuity between Siberian and Beringian populations. MtDNA haplogroups A2 and G1b, prevalent in Beringian populations, are either minor or even absent in Sakha, where haplogroups C and D dominate. Autosomal analysis also differentiates Beringian populations from those of Sakha. Our results support the scenario that the territory of Sakha was colonized from the regions west and eastward of Lake Baikal with only minor gene flow from Lower Amur/Southern Okhotsk region and/or Kamchatka.

An abstract on Lithuanian Y-chromosomes

The place of the population of Lithuania between Northern and Eastern Europe: Y chromosome analysis
I. Uktverytė et al.

The population of Lithuania is constituted of 6 dialectal groups which form two major ethno-linguistic groups known as Aukštaitish and Žemaitish, both speaking Baltic languages of Indo-European family. Neighbouring Finno-Ugric (Northern and Eastern Europe), Slavonic (Eastern Europe) and Germanic (Northern Europe) populations surrounding the Baltic sea region influenced historical formation of Lithuanian ethno-linguistic groups. Analysis of the Lithuanian population genetic composition helps to understand the origin, history and place among other populations.
Y chromosome analysis was performed for 301 individuals from 6 dialectal groups. 25 SNPs were genotyped (TaqMan) to determine Y haplogroup and 17 STR were analysed to determine haplotype for each individual. Most frequent haplogroups in the population of Lithuania are R1a1a (42.2%, R1a1a1g compose 8.97% in studied population) and N1c1 (40.5%) and less frequent haplogroups are R1b1b1, I1, I2a, E1b1b1 (<5% each). AMOVA showed no statistically significant differences between two major ethno-linguistic groups Aukštaitish and Žemaitish (among groups p-value=0.897, among population within groups p-value=0.194, within populations p-value=0.282 based on 10100 permutations). MDS of genetic distances based on Y-biallelic markers showed that Lithuanians are closer to Latvian and Estonian populations than to Slavic populations (European part of Russia, Poland, Ukraine, Belorussia, stress=0.029). According to the frequencies of haplogroups, no statistically significant differences between ethno-linguistic groups were detected (p>0.05), moreover, MDS analysis sets the population of Lithuania between Northern and Eastern European populations.

An abstract on Sardinian population structure.

A genome-wide analysis of Sardinian population structure
M. Steri et al.

Sardinia is particular attractive for human genetic studies, being one of the larger isolated populations and thus suitable for large-scale studies. Several attempts have been made to explore its genetic structure, but they either analyzed a large set of markers in very few samples or thousands of individuals at specific loci. Here we genotyped 2,615 individuals with the Affymetrix 6.0 array. Samples were recruited from the north, south and central east areas of the Island, and initially considered as 3 distinct populations. Genotype calling was performed with Birdseed-v2, considering all samples as a unique cluster to avoid batch effects. Subsequently, we applied standard filters for samples and SNP quality, and used IBD sharing to detect, and discard, hidden relatives. Using principal component analysis, we identified outliers and reassigned each individual accordingly. An analysis of molecular variance indicated that only 0.21% of the variability could be attributable to inter-population variation (Fst=0.002), confirming a lack of large-scale substructure. We thus considered the Sardinians as a unique sample. Compared to HapMap3 populations, as expected, higher similarity was observed with Tuscany and CEPH samples (Fst=0.005 and 0.010, respectively). A genome-wide search for SNPs highly differentiated between Sardinians and these European populations confirmed the specialness of HLA and LCT regions, and also showed elevated Fst values (>0.27) at the CR1 gene, known to be related to malaria severity. We are now integrating sequencing data of many individuals to provide a more comprehensive analysis of variants in addition to the common SNPs in current genotyping platforms.

A major new study on Arabian mtDNA

Phylogeographic analyses; mitochondrial DNA; Arabian Peninsula
V. Fernandes et al.

Phylogeographic analyses of mitochondrial DNA (mtDNA) provide insights into modern human evolution. In recent years, worldwide studies of contemporary mtDNAs have indicated that modern humans left Africa ~60,000-70,000 years ago along the “southern coastal route”, across the Red Sea and via the Arabian Peninsula. Yet no obvious signs of the passage though Arabia have been found in genetics and archaeology fields. The aims of this work are to seek for possible mtDNA relicts of the initial dispersal from Africa in Arabia and to investigate the origins of lineages that arrived later. We are doing this by sequencing the complete mtDNA molecule (~16,568 bp) from unclassified lineages (referred to as the paraphyletic clusters L3*, N* and R*) and poorly studied haplogroups within the Eurasian macrohaplogroup N, which is predominant in Arabian populations today (86% in Saudi Arabia, 66% in Yemen and 79% in Dubai), in 90 samples from Dubai, Yemen, North/East Africa, the Near East and Europe. Our results will allow to test hypotheses about the settlement of the Arabian Peninsula.

Of Cattle and Men (Edwards et al. 2010)

From the paper:

Apparently, the expansion of the dairy breeds have created, or largely maintained, a sharp genetic contrast of northern and southern Europe, which divides both France and Germany. It may be hypothesised that the northern landscapes, with large flat meadows, are suitable for large-scale farming with specialised dairy cattle (Niederungsvieh, lowland cattle), whilst the mixed-purpose or beef cattle (Höhenvieh, highland cattle) are better suited to the smaller farms and hilly regions of the south. However, it is also remarkable that in both France and Germany the bovine genetic boundary coincides with historic linguistic and cultural boundaries. In France, the Frankish invasion in the north created the difference between the northern langue d'oïl and the southern langue d'oc. The German language is still divided into the southern Hochdeutsch and northern Niederdeutsch dialects, which also correlates with the distribution of the Catholic and Protestant religions. On a larger scale, it is tempting to speculate that the difference between two types of European cattle reflects, and has even reinforced, the traditional and still visible contrast of Roman and Germanic Europe.

UPDATE: I wish there'd be some data points for the vast area between Eastern Europe and Yakutia. There might be a simple (and recent) expalanation for why Northeastern Europe is mostly "green" and Yakutia "red", but it would be nice to have actual datapoints in the quadrilater between NE Europe ("green"), SW Asia (mostly "red"), S Asia (zebu "black") and Yakutia.

PLoS ONE 6(1): e15922. doi:10.1371/journal.pone.0015922

Dual Origins of Dairy Cattle Farming – Evidence from a Comprehensive Survey of European Y-Chromosomal Variation

Ceiridwen J. Edwards et al.

Abstract
Background
Diversity patterns of livestock species are informative to the history of agriculture and indicate uniqueness of breeds as relevant for conservation. So far, most studies on cattle have focused on mitochondrial and autosomal DNA variation. Previous studies of Y-chromosomal variation, with limited breed panels, identified two Bos taurus (taurine) haplogroups (Y1 and Y2; both composed of several haplotypes) and one Bos indicus (indicine/zebu) haplogroup (Y3), as well as a strong phylogeographic structuring of paternal lineages.

Methodology and Principal Findings
Haplogroup data were collected for 2087 animals from 138 breeds. For 111 breeds, these were resolved further by genotyping microsatellites INRA189 (10 alleles) and BM861 (2 alleles). European cattle carry exclusively taurine haplotypes, with the zebu Y-chromosomes having appreciable frequencies in Southwest Asian populations. Y1 is predominant in northern and north-western Europe, but is also observed in several Iberian breeds, as well as in Southwest Asia. A single Y1 haplotype is predominant in north-central Europe and a single Y2 haplotype in central Europe. In contrast, we found both Y1 and Y2 haplotypes in Britain, the Nordic region and Russia, with the highest Y-chromosomal diversity seen in the Iberian Peninsula.

Conclusions
We propose that the homogeneous Y1 and Y2 regions reflect founder effects associated with the development and expansion of two groups of dairy cattle, the pied or red breeds from the North Sea and Baltic coasts and the spotted, yellow or brown breeds from Switzerland, respectively. The present Y1-Y2 contrast in central Europe coincides with historic, linguistic, religious and cultural boundaries.

Link

Multidimensional scaling and ADMIXTURE across Northern Eurasia corresponds to geography and language

Here is a multi-dimensional scaling plot of a number of North Eurasian populations. In comparison to my previous post, I have excluded Americans and Greenlanders, and added several other populations from Central Asia and West Eurasia.

Population labels have been printed in the co-ordinates of the population averages; these largely correspond with identifiable blobs of colored points, but note that some populations have several outliers, so labels appear in white space. Most notable in that respect are the Koryak, Chukchi, and the Nganasan, all of whom have some apparently European-admixed individuals.

"Mongol" corresponds to Rasmussen et al. (2010) Mongol sample, while "Mongola" to the HGDP-CEPH one. The population codes on the left may not be clearly visible as they overlap with each other and are CEU, LT, HU (relatively unadmixed Caucasoids), FI/RU (Uralian-admixed northern Caucasoids), IR/TR (Altaic-admixed southern Caucasoids). The West Eurasian part of the plot can be seen blown up on the right.

The correspondence with geography and language is striking. Siberian isolates from the extreme north and east, Koryak and Chuckhi are on top; HapMap Chinese at the bottom. Between them are Uralians (Selkup, Yukagir, Nganassan) and Altaics (Mongol-Tungus-Turkic people).

Below is ADMIXTURE analysis for the same set of populations, for K=7:

Finns and Russians seem to have an excess of the "Nganasan" component over the Altaic, while Turks have the opposite. Below is a table of Fst distances between components:

The close relationship between the two Caucasoid components is apparent (Fst=0.033), but note fairly large Fst divergences between the morphologically Mongoloid groups. I attribute this mostly to the very low population sizes of these groups, which have probably affected them by drift. For the less demographically constrained Altaic and East Asian components, Fst=0.044.

If you are not familiar with these ethnic groups, the Red Book of the Peoples of the Russian Empire and the Ethnologue indexes on Altaic and Uralic are invaluable, as are the portraits of ethnic groups of China. On the right a picture of a Nganasan.

UPDATE: Also, a past post from the blog, collating Y-haplogroup N frequencies with anthropological descriptions. Nganasans apparently belong to haplogroup N at a frequency of 92.1%!

ADMIXTURE across Eurasia: from Anatolia to Siberia

(Last Update: Oct 17)

Here is a result of an ADMIXTURE run of a few populations from Eurasia (left to right: Turks, Armenians, Georgians, followed by a mix of Uygur, Mongolians, Yakut, Hezhen in no order), combining the HGDP dataset with that of Behar et al. (2010).

It's more of a test, rather than a final result, as I've just finished integrating the two datasets, but it's a nice comparison of a wide assortment of linguistic families.

Notice Turks and Armenians being quite similar to each other, (green+blue), although Turks are differentiated by the presence of an east Eurasian component (5.5%). On the basis of uniparental markers, five years ago, I estimated this component as 6.2% which seems to be right on the money. In the combined Armenian/Georgian sample this admixture is only 0.14% and as can be seen is limited to a handful of Georgian individuals.

It is interesting that Georgians belong semi-uniquely to the green cluster. Turks' non-Mongoloid ancestors were Indo-European speaking like the Armenians still are. It would be tempting to see in the blue-green contrast an Indo-European/Caucasian one, especially as the Caucasoid component further east seems to be mainly blue, in agreement with the idea that it was Indo-Europeans (in particular mainly Iranic speakers) who brought Caucasoid genes to the heartland of Asia.

UPDATE I (Oct 17):

Moving to the north, we see (left-to-right) Han (red), Hungarian/Belorussian (blue), Chuvash (first red "step"), Uzbek (second red "step"). Unlike the Turks, the Hungarians, who also speak a language that came from the east, seem to lack a noticeable east Eurasian component.

Their linguistic conversion was one of elite dominance, where a handful of Mongoloid and quasi-Mongoloid upper echelons left their language but not their genes:

According to his observations, the “overlords” were characterized by Turanid, Uralian and Pamir race elements and also by certain long-headed components. The “middle layer” or “warriors’ layer”, however, showed an anthropological profile distinctly different from that of the overlords. It was essentially constituted by Mediterraneans, Nordoids (who might also have been tall robust Mediterraneans) and Pamir component while the absence of Turanid and Uralian race characteristics was remarkable. As regards the third layer, the so-called “common folk”, they were dominated, just as the middle layer was, by Mediterranean and Nordoid elements but, in addition, the Cromagnoid ones were also significant.

The Chuvash are Turkic and live in Europe, while the Uzbeks, closer to the Altaic homeland in Asia are also Turkic, and have a predictable higher percentage of east Eurasian genes.

Comparison between morphological and genetic data for Egyin Gol Mongolians

I had first blogged about Egyin Gol in 2003, that paper is freely available here. From the current paper:

The Egyin Gol necropolis is located in the Egyin Gol Valley (northern Mongolia), near the Egyin Gol River, close to its confluence with the Selenge, a main tributary of Lake Baikal (see Fig. 1). This site has been the subject of a French-Mongolian interdisciplinary research project from 1997 to 1999, which allowed the excavation of 84 graves containing skeletal remains of 99 individuals buried from the third century B.C. to the second century A.D. The graves were organized in three main sectors (A, B, and C) that, based on AMS carbon-14 dating of human bones, progressively expanded from south to north (i.e., Sector A is the oldest followed by Sector B and Sector C). The development of Sector C corresponds to the end of the necropolis and may reflect a Turkish influence on the Xiongnu tribe (Keyser-Tracqui et al., 2003).

and:

The results showed, however, that individuals buried in sector C represent a specific kin group clearly differentiated from the rest of the necropolis based on nonmetric
data (Table 4), and confirmed by the genetic data. This might be explained on the basis that these individuals are suggested to be of Turkish origin, based on their shared single paternal lineage, unique in the necropolis and affiliated with Turkish populations (Keyser-Tracqui et al., 2003). However, the sector C individuals share the same maternal lineages with individuals buried in sectors A and B, which could explain the global homogeneity of the population as a whole. The particular characteristics of the sample from sector C suggests a possible shift in the population demographics, caused by the emergence of a Turkish component in the Xiongnu population at the end of the necropolis use and at the end of the first steppe empire led by the Xiongnu. The fact that this particular subgroup of the population buried in sector C was detected by nonmetric traits analysis demonstrated that nonmetric traits are an efficient tool when analyzing population microevolution.

The Y chromosome results are found in Table 2 of the original paper.

I ran the Y-STR profile of the shared patrilineage over the haplogroup predictor, but I don't get a clear estimate for the Y-STR profile (grave 46 in Table 2).

A YHRD search gave the following results:
The high frequency in Kazakhs and Yakuts, with a little spillover in both China and eastern Europe is certainly consistent with a Turkic origin of this haplotype.

Finally, I gave it a try at ysearch, getting a match with a Pole and a 1-step match with a Czech, both of which are listed as C3-tested.

So, there you have it, archaeology, non-metric data, Y-chromosomes, and a little use of online tools gives us a first glimpse on what may have been a group of ancient Turkic individuals. Of course here are theories-a-plenty about what language the Xiongnu originally spoke, so it would be premature to arrive at any firm conclusions.

Interestingly, C3 is also present in a different 2,000-year old Xiongnu individual from NE Mongolia from the Duurlig Nars site, but an earlier group of Xiongnu-related individuals from China (Pengyang) belonged to haplogroup Q.

American Journal of Physical Anthropology doi:10.1002/ajpa.21322

Comparison between morphological and genetic data to estimate biological relationship: The case of the Egyin Gol necropolis (Mongolia)

François-X. Ricaut et al.

Osseous and dental nonmetric (discrete) traits have long been used to assess population variability and affinity in anthropological and archaeological contexts. However, the full extent to which nonmetric traits can reliably be used as a proxy for genetic data when assessing close or familial relationships is currently poorly understood. This study represents the unique opportunity to directly compare genetic and nonmetric data for the same individuals excavated from the Egyin Gol necropolis, Mongolia. These data were analyzed to consider the general efficacy of nonmetric traits for detecting familial groupings in the absence of available genetic data. The results showed that the Egyin Gol population is quite homogenous both metrically and genetically confirming a previous suggestion that the same people occupied the necropolis throughout the five centuries of its existence. Kinship analysis detected the presence of potential family burials in the necropolis. Moreover, individuals buried in one sector of the necropolis were differentiated from other sectors on the basis of nonmetric data. This separation is likely due to an outside Turkish influence in the paternal line, as indicated by the results of Y-chromosome analysis. Affinity matrices based on nonmetric and genetic data were correlated demonstrating the potential of nonmetric traits for detecting relationships in the absence of genetic data. However, the strengths of the correlations were relatively low, cautioning against the use of nonmetric traits when the resolution of the familial relationships is low. Am J Phys Anthropol 2010. © 2010 Wiley-Liss, Inc.

Link

Abstracts from AAPA 2010

Some abstracts from the upcoming (April 14-17) meeting of the American Association of Physical Anthropologists.

Why are pygmies small? An anthropometrical and anthropogenetical question

NOEMIE BECKER et al.

Pygmy populations from central Africa have the shortest stature worldwide. The name “pygmy” indeed comes from the Greek “pugmaios” that is a measure of length. This reduced stature has been the subject of numerous endocrinological studies and many evolutionary hypotheses have suggested that this phenotype was an adaptation to the rainforest (hot, humid and dense environment), to alimentation or due to life history trade-offs (high mortality). We have anthropometrical data for a sample of more than 1000 individuals from 7 pygmy populations and 3 neighbouring farmer populations from Gabon, Cameroon and Central African Republic. DNA samples are also available for a large number of individuals. The analysis of anthropometrical data shows that all pygmy groups have a male mean stature under 160 cm (this was used in the definition settled by Cavalli-Sforza in1986) and that a high variability exists between various pygmy populations. Verdu et al. (2009) published a genetic analysis based on neutral microsatellites on the same populations and found that pygmies present a variable admixture proportion with nonpygmies. Comparing this data with our anthropometrical data at the individual level we find a strong correlation between level of admixture and stature, thus strongly supporting the existence of a genetic component in pygmy short stature. We developed a candidate-gene approach to search for such genetic factor and will present current results on various genes located in the GH-IGF1 axis.

New evidence on headshaping from the Early Byzantine Maroneia in Thrace, Greece.

PARASKEVI TRITSAROLI

The first case of headshaping from Early Byzantine Greece was identified in 2006 at the cemetery of Maroneia (5th-6th c. A.D.). Biocultural evidence suggested the presence of a female individual culturally linked to Hunic traditions. This paper analyzes the second case of headshaping on a female skeleton uncovered in 2009 and allows for the wider discussion of the presence of a larger group related to the Huns in the city of Maroneia. The skull was examined by combining macroscopic observation and x-ray. Points of pressure are recorded in the frontal, post-coronal and occipital regions resulting in an undulation of diploic bone. Possible bilateral pressure on the frontal bone has produced an artificially narrowed frontal. The skull extends posterosuperiorly. These features suggest the application of bandaging producing circular modification. Both headshaped skulls exhibit the same type of modification. Similarly, both women were buried in a supine position, without offerings, just like the remaining 36 deceased individuals in the cemetery of Maroneia. Headshaping was unknown among Byzantine customs. On the contrary, the Huns who attacked the Balkans twice and who unsuccessfully threatened Maroneia in 411 practiced a pronounced form of circular headshaping. Consequently, biocultural evidence strongly supports the hypothesis that a group linked to the Huns was installed at the city and was assimilated into this Early Byzantine society. Future biogeochemical analysis needs to be undertaken in order to investigate migration patterns. However, headshaping reflects the cosmopolitan character of Maroneia, an important urban center in a province of the Byzantine Empire.

The genetic legacy of indigenous Caribbean peoples: Evidence from autosomal and mitochondrial data.

JADA BENN TORRES et al.

Archeological evidence suggests that autochthonous peoples began to migrate into the eastern island chain in the Caribbean, known as the Lesser Antilles, as early as 7200 years BP. Upon the arrival of Europeans, an estimated 2-4 million people lived on these islands. Within 32 years of contact, the native populations had virtually disappeared from the region due to European-introduced disease, abuse, and genocide. This lead many scholars to conclude that indigenous Caribbean people had become extinct. However, small pockets of indigenous communities have survived and are present today on several Lesser Antillean islands. Furthermore, ethnohistoric data suggests that gene flow occurred between autochthonous peoples and enslaved Africans beginning in the colonial period. In this study, we examine the genetic legacy of autochthonous Caribbean peoples from the Lesser Antilles in contemporary African- Caribbean populations as evidenced from mitochondrial data and novel autosomal data. A total of 516 individuals from eight Caribbean islands were typed for 109 ancestry informative markers and a subset of individuals were also typed for their mitochondrial haplogroup. Mitochondrial haplogroups indicate that 5% of the sample has indigenous ancestry while admixture estimates from autosomal markers show 4% indigenous ancestry. Both lines of data suggest that despite the dramatic postcontact decline in population size, indigenous Caribbean people have made notable genetic contributions to contemporary African-Caribbean populations. Furthermore, these genetic contributions vary according to the genetic system typed and across the islands.

Chuvash origins: Evidence frommtDNA Markers.

ORION M. GRAF et al.

A sample of 96 unrelated individuals from Chuvashia, Russia was sequenced for hypervariable region-I (HVR-I) of the mtDNA molecule. The Chuvash speak a Turkic language that is not mutually intelligible to other extant Turkish groups, and their genetics are distinct from Turkic-speaking Altaic groups. Some scholars have suggested that they are remnants of the Golden Horde, while others have advocated that they are the products of admixture between Turkic and Finno-Ugric speakers who came into contact during the 13th century. Earlier genetic research using autosomal DNA markers suggested a Finno-Ugric origin for the Chuvash. This study examines non-recombining DNA markers to better elucidate their origins. The majority of individuals in this sample exhibit haplogroups H (31%), U (22%), and K (11%), all representative of western and northern Europeans, but absent in Altaic or Mongolian populations. Multidimensional scaling (MDS) was used to examine distances between the Chuvash and 8 reference populations compiled from the literature. Mismatch analysis showed a unimodal distribution. Along with neutrality tests (Tajima’s D (-1.43365) p less than 0.05, Fu’s FS (-25.50518) p less than 0.001), the mismatch distribution is suggestive of an expanding population. These tests suggest that the Chuvash are not related to the Altai and Mongolia along their maternal line but supports the “Elite” hypothesis that their language was imposed by a conquering group-- leaving Chuvash mtDNA largely of Eurasian origin with a small amount of Central Asian gene flow. Their maternal markers appear to most closely resemble Finno-Ugric speakers rather than fellow Turkic speakers.

Population history and substructure of Anatolia and Turkey as evidenced by craniofacial diversity.

NORIKO SEGUCHI et al.

Anatolia, the Asian segment of Turkey, is an area of evolutionary importance for human groups who used this corridor as a bridge for migration between the Caucasus, Western Asia and Europe since Lower Paleolithic times. Historically, Anatolia has been occupied by diverse civilizations, including the Byzantine and Ottoman Empires. This study is an attempt to understand Turkish population substructure and history by examining craniofacial diversity through several temporal periods framed within a population genetic model. If the region of Anatolia has been used as a migratory corridor for peoples spanning disparate geographic areas (Balkans, Central Asia, and East Asia), then gradual craniofacial change is expected due to these migrations coupled with extensive admixture. Studies using mtDNA indicate a pre-Neolithic expansion resulting in extensive migration, while Y chromosome studies reveal haplogroup clustering and gene flow from the Caucus with less admixture from Central and East Asia. Overall, our results indicate minimal Turkish population substructure. When crania were separated into sex, our results are consistent with uniparental marker population history. Female crania show a distinctness with modern groups and are actually more similar to Neolithic European and Near Eastern populations. This would indicate a relatively stable female population in Anatolia since Neolithic times. Male crania are more heterogeneous and cluster within a larger geographic zone of Eurasia and the Near East consistent with greater male migration. There is little support for admixture from Central or East Asian groups. These results support the hypothesis for a Turkic language displacement with insignificant genetic exchange.

Genetic analyses reveal a history of serial founder effects, admixture between longseparated founding populations in Oceania, and interbreeding with archaic humans.

SARAH JOYCE, KEITH HUNLEY

Genetic anthropologists continue to debate whether human neutral genetic variation primarily reflects a continuum of demes connected by local gene flow or colonization and serial founder effects. A second unresolved issue concerns the genetic contribution of archaic species to the modern human gene pool. Some studies suggest that this contribution was substantial and that it played an important role in human adaptation. These issues remain unresolved because of inadequacies and biases in datasets, problems in statistical methodology, and the failure to recognize that different evolutionary processes may produce similar outcomes. This study redresses these limitations by analyzing gene identity within and between populations in a dataset comprised of 614 STRs assayed in 1,983 people from 99 widespread populations. Our strategy is to fit hierarchical models to these data and examine residual deviations from the models. Each model involves nesting smaller units such as populations into larger units such as continental regions. It is possible to restate many of these models as either expansions or reductions of each other and thereby identify aspects of population structure that have had a major impact on the overall pattern of diversity. The strong fit of a model estimated using the Neighbor Joining algorithm indicates that human genetic diversity primarily reflects a history of successive founder effects associated with our exodus from Africa, not a continuum of demes connected by gene flow. Residual deviations from the model suggest: 1) the genomes of Oceanic peoples are the product of two independent waves of migration to the region and admixture, and 2) genetic exchange occurred between archaic and modern humans after their initial divergence.

Correlations between genetic ancestry and superficial traits indicate substantial admixture stratification in Brazil.

LAUREL N. PEARSON et al.

Brazil is one of the most admixed countries in the world. How this admixture affected the distribution of genetic ancestry across Brazilian ethnic (“Color”) groups is a fundamental question which to date has only received minimal attention. In an effort to systematically study variation in genetic ancestry in Brazil, we collected DNA and various phenotypic measures from 596 volunteers in Brasilia, Brazil. Participants were asked to provide their self-described “Color” as defined by the Brazilian census (Preta/Black, Parda/Brown, Branca/White, Indigena/Indigenous, Amarela/Yellow). Phenotype data was collected from each subject including hair texture, highresolution eye photographs, skin and hair color by reflectometry, and three-dimensional facial photographs. To estimate genomic ancestry, DNA from each participant was genotyped using 176 ancestry informative markers (AIMs), autosomal SNPs with large frequency differences between parental populations known to contribute to Brazilian admixture (West African, East Asian, European and Indigenous American). Although genomic ancestry shows significant overlap across “Color” groups, there are highly significant differences in average proportional ancestry. Additionally, analyses comparing trait values and genetic ancestry show significant correlations consistent with expectations of populations stratified with respect to genetic ancestry. Ethnographic research indicates that designations of “Color” are fluid and largely based on physical traits as opposed to known ancestry. This likely contributes to the observed ancestry overlap between ethnic groups and the strong association between phenotype and group. This study emphasizes the importance of genetic marker based estimates of ancestry as well as objective assessment of superficial traits in understanding the admixture process.

Geographic structure of genetic variation in North America: Population fissions and European admixture.

KARI BRITT SCHROEDER et al.

A satisfactory understanding of how modern Native North America populations are biologically related to each other requires increased sampling of populations and/or genetic markers and testing of the fit of different models of population structure. To this end, we combine new autosomal microsatellite data from Native North American populations with previously published data. Using J.C. Long’s Generalized Hierarchical Modeling software, we evaluate the fit of different trees to the data. Although we observe a correlation between population pairwise genetic and geographic distances, as expected with a long-term process of isolation by distance, we show that this correlation likely results from geographically-structured population fissions. This pattern could result from the initial peopling of North America or from a later process. The magnitude of European ancestry in the sampled populations, as estimated with the software structure, varies drastically among geographic regions, and may limit our ability to use modern genetic variation to investigate Native North American prehistory.This study was funded by the Wenner-Gren Foundation for Anthropological Research, grant number 7580 to K.B. Schroeder and D.G. Smith, and by the National Science Foundation, grant BCS- 0422144 to R.S. Malhi, B.M. Kemp, and D.G. Smith.

Coalescent modeling of Yakut origins points to small founding population based on mtDNA variation.

MARK ZLOJUTRO et al.

Based on archaeological and ethnohistorical evidence, the Yakut people of northeastern Siberia are considered to be descendants of ancient Turkic-speaking populations once living in the distant Altai- Sayan region on the Russian- Mongolian border. The results of phylogeographic studies on Siberian mtDNA variation have been generally concordant with a southern Yakut origin, although the timing of the northern migration, the size of the founder group and the degree of genetic admixture with non-Turkic Siberian populations are less apparent. In an effort to better understand Yakut origins, we modeled 25 demographic scenarios, including parameters such as effective population size, growth rate and gene flow, and tested by coalescent simulation whether any are consistent with the patterns of mtDNA diversity observed in present-day Yakuts. The models consist of either two simulated demes that represent Yakuts and a South Siberian ancestral population, or three demes that also include a regional Northeast Siberian population that served as a source of localized gene flow into the Yakut deme. The model that produced the best fit to the observed data defined a founder group with an effective female population size of only 150 individuals, migrating northwards approximately 1,000 years BP and undergoing significant admixture with neighboring populations in Northeastern Siberia. These simulation results indicate a pronounced founder effect that was primarily kin-structured and reconcile reported discrepancies between Yakut mtDNA and Y chromosome diversity levels.

The role of selection-nominated candidate genes in determining Indigenous American skin pigmentation.

ELLEN E QUILLEN et al.

World-wide variability in skin pigmentation has been a subject of anthropological inquiry from the beginning of our discipline. Recent genomic studies indicate that skin pigmentation is one of the most rapidly evolving phenotypes in many human populations and that genes underlying skin pigmentation have been subject to some of the most extreme selective pressures of any genes in the human genome. Unlike previous research, this study both identifies pigmentation genes that have undergone selection in Indigenous American populations and tests the influences of these genes on skin color in admixed individuals. 906,600 single nucleotide polymorphisms (SNPs) were surveyed for signatures of selection in indigenous populations from Central and South America. Evidence of selection was identified by comparison to HapMap Phase I populations using reduction in heterozygosity (lnRH), Locus- Specific Branch Length (LSBL), Tajima’s D, and haplotype block structure. In the 12 pigmentation candidate genes that show the strongest evidence of selection (ADAM17, POMC, AP3B1, OPRM1, SILV, OCA2/HERC, PLDN, MYO5A, RAB27A, CYP1A2, ATRN, and ASIP), 48 SNPs selected to represent the overall variation in the selection nominated candidate genes were genotyped in individuals of admixed Indigenous American and European ancestry. These SNPs show substantial allele frequency differences between the parental populations. Using admixture based regression model analyses, genes contributing to darker skin pigmentation in Indigenous Americans were found. This study not only identified skin pigmentation genes contributing to skin color variation in previously understudied Indigenous American populations, it validated the usefulness of using population genetic tests of selection to identify functional genes. This study was generously funded by the National Science Foundation Dissertation Improvement Grant 0925976

Ancient DNA from frozen Yakuts

From the paper:

Sixty one percent (8 out of 13) of the haplotypes (Ht1, Ht2, Yaka56, 65, 71, 80, 81, 86) were affiliated to the N1c (TAT-C) haplogroup on the basis of the SNP analyses. This haplogroup is considered as the most frequent in the Yakut population, and its frequency varies across studies from 75% [12] to 100% [13]. Sample YAKa26 was affiliated to haplogroups K . The SNP typing was inconclusive for 5 individuals (YAKa17, 19, 47, 49 and 57); nevertheless the affiliation to N1c was excluded on the basis of the absence of the TAT-C mutation.

and:

The origin of the most frequent Y-chromosomal haplotypes (Ht1 and Ht2) was difficult to establish on the basis of genetic information. Indeed, these two lineages belonging to haplogroup N1c seem to be restricted to Yakut populations, and were probably present since the period they were first located in Central Yakutia. Interestingly, the comparison with archaeological data revealed that the male individuals (YAKa34, 39, 40, 69, 78) at the beginning of the 18th century, identified as Clan Chiefs (or tojons) on the basis of their grave goods (weapons, jewelry, silk clothes, richly ornamented saddles and signet rings), belonged to these two haplotypes. Therefore, archaeological data could bring interesting information in tracing back the origin of these enigmatic male lineages. Indeed, the grave goods of the 15th/17th centuries (weapons and horse harnesses) and the construction of coffins with an empty trunk from the 18th century are similar to the burial customs of the Cis-Baïkal area [44] and of the Egyin Gol Necropolis during the 3rd century BC [45-47]. This suggests that the male ancestors of the Yakuts were probably formed of a small group of horse-riders originating from Northern Mongolia or the Baïkal Lake.

and:

Based on the analyses of the maternal and paternal lineages of ancient Yakuts, we were able to demonstrate that the formation of this population started before the 15th century, with a small group of settlers composed of horse-riders from the Cis-Baïkal region and a small number of women from different South Siberian origins.

BMC Evolutionary Biology doi:10.1186/1471-2148-10-25

Human evolution in Siberia: from frozen bodies to ancient DNA

Eric Crubezy et al.

Abstract (provisional)

Background
The Yakuts contrast strikingly with other populations from Siberia due to their cattle- and horse-breeding economy as well as their Turkic language. On the basis of ethnological and linguistic criteria as well as population genetic studies, it has been assumed that they originated from South Siberian populations. However, many questions regarding the origins of this intriguing population still need to be clarified (e.g. precise origin of paternal lineages and admixture rate with indigenous populations). This study attempts to better understand the origins of the Yakuts, by performing genetic analyses on 58 mummified frozen bodies dated from the 15th to the 19th century, excavated from Yakutia (Eastern Siberia).

Results
High quality data were obtained for the autosomal STRs, Y-chromosomal STRs and SNPs and mtDNA due to exceptional sample preservation. A comparison with the same markers on seven museum specimens excavated 3 to 15 years ago showed significant differences in DNA quantity and quality. Direct access to ancient genetic data from these molecular markers combined with the archaeological evidence, demographical studies and comparisons with 166 contemporary individuals from the same location as the frozen bodies, helped us to clarify the microevolution of this intriguing population.

Conclusion
We were able to trace the origins of the male lineages to a small group of horse-riders from the Cis-Baikal area. Furthermore, mtDNA data showed that intermarriages between the first settlers with Evenks women led to the establishment of genetic characteristics during the 15th century that are still observed today.

Link (pdf)