We tested between-group differences in both AR and H e using the Wilcoxon's signed-rank test, with locus-specific estimates taken as replicate observations. We tested heterogeneity in both AR and H e across the five groups of Eurasian populations using the Kruskal—Wallis test, taking locus-specific estimates as replicate observations.
When significant differences among groups were found, we ran the Tukey's range test to find which group statistics were significantly different from one another. All statistical analyses were performed with the software package — JMP5.
The least-cost distances, which account for the cost of the movement through the slopes in the landscape, were calculated from the digital elevation model GTOPO30 of the Earth Resources Observation and Science Center.
Each Markov chain was run for 10 6 steps, after a 10 5 -step burn-in period. In each case, the results were checked to ensure consistency over 40 independent runs. All chains were run using the F model for correlations of allele frequencies across clusters.
The Central Asian genetic pool may be more than just the result of admixture from Eurasian populations, but we were nonetheless interested in investigating the potential origins of Central Asian populations among all Eurasian populations. Average AR and expected heterozygosity for each of the 26 Central Asian populations and across regions are given in Table 2. Central Asia therefore showed neither higher nor lower diversity than the rest of Eurasia. These significant estimates mainly corresponded to pairwise comparisons between one Turkic and one Indo-Iranian population, as well as to comparisons between two Indo-Iranian populations.
The first two factorial components FC accounted for The first two FC accounted for Interestingly, the Hazaras from Pakistan, who claim to be direct male-line descendants of Genghis Khan, 40 , 41 as well as the Uygurs, clustered together with the Turkic-speaking populations of Central Asia. Correspondence analysis CA based on the table of allele counts in Central Asia a.
The first two factorial components FC are represented, and their relative contribution to the total inertia are indicated. Colors indicate language affiliation; blue: Indo-Iranian speakers; orange: Turkic speakers. CA based on the table of allele counts in Eurasian populations b. The two latter clusters were found almost exclusively in Central Asian populations.
Most Turkic-speaking populations showed a contribution from the East-Asian cluster in red , and most Indo-Iranian populations showed a contribution from Europe and Middle East in green. It is worth noting that Uygur and Hazara populations showed the same pattern as the Turkic-speaking populations from Central Asia. K represents the number of putative clusters. Each individual is represented by a vertical line, divided into up to K colored segments, each of which represents the individual's estimated membership fraction to that cluster.
Most Turkic-speaking populations had a large East-Asian ancestral contribution, which represented in general It is worth noting that, in general, many geographically close populations that speak different languages showed contrasted admixture proportions see, eg, UZT and TJU in Table 4 , which supports the idea that language is a major determinant of population differentiation in Central Asia.
We found a high level of autosomal genetic diversity in Central Asia, consistent with previous observations, 3 , 16 and similar in extent to other major regions in Eurasia Table 2. Most importantly, the observed diversity was mainly owing to the differentiation into two main groups of populations Figure 3 : on the one hand, Indo-Iranian-speaking populations which include Tajiks and three Uzbek populations that are genetically closer to populations from Western Eurasia, and on the other hand, Turkic-speaking populations which include Karakalpaks, Kazakhs, Kyrgyz and two other Uzbek populations that are closer to Eastern Asian populations with the exception of the Turkmen.
This pattern was also apparent in the CA Figure 2b , and consistent with the significant differentiation of almost all pairwise comparisons between an Indo-Iranian- and a Turkic-speaking population Supplementary Table 1.
Although several studies have shown that geography is, in general, a better predictor of genetic differentiation than ethnicity and linguistics, 42 , 43 language affiliation appears as the most important factor explaining the distribution of genetic diversity in Central Asia Table 3.
We found no evidence of a correlation between geography and genetics within each of the Indo-Iranian or Turkic groups of Central Asian populations. However, more striking is the fact that no geographic pattern of genetic variation was found among sedentary Indo-Iranian speakers either. The clustering analysis showed that most individuals from the Indo-Iranian-speaking populations had large membership coefficients into two clusters light blue and beige in Figure 3 that were found mostly in these populations.
Altogether, the significant pairwise F ST estimates between almost all pairs of Indo-Iranian-speaking populations Supplementary Table 1 , the high level of diversity across Indo-Iranian populations Table 2 and the variable level of admixture from the putative parental populations Table 4 seem consistent with the premise that Indo-Iranian speakers are long-term settled populations in the area. This latter hypothesis is strongly supported by archeological evidence.
Our study further shed some light on the origins of the Turkic-speaking populations in Central Asia. The clustering analyses indeed showed that most individuals from the Turkic-speaking populations had large membership coefficients into one Central Asian cluster in orange in Figure 3 and smaller membership coefficients into the East-Asian cluster in red in Figure 3 , thus confirming the result of Li et al 45 based on a small central Asian cluster for Uygur, Kazakh and Khanty.
This pattern likely reflects the existence of an ancestral group of Turkic speakers orange cluster in Figure 3 , which popular Turkic culture considers as originating from the Altai region. The East-Asian ancestry of Turkic-speaking populations red cluster in Figure 3 may then correspond to the westward expansions of nomadic groups form East Asia during historical times.
The Westernized view of westward invasions usually emphasizes the extreme violence and cruelty of the hordes led by Attila the Hun AD — , or that from the Mongolian empire led by Genghis Khan. However, our results somehow challenge this view and rather suggest that these more recent expansions did not lead to the massacre and complete replacement of the locally settled populations, but rather to partial admixture.
We found almost no eastern ancestry in Indo-Iranian-speaking populations see Figure 3 , which suggests that the group of people from which the current-day Tajik and Turkmen populations would be the descendants did not suffer from the westward expansions of eastern nomadic groups.
Furthermore, the present finding that the partial admixture with eastern nomadic groups concerned almost exclusively the Turkic-speaking populations is consistent with the fact that Turks and Mongols share cultural traditions and lifestyle, which may have facilitated inter-groups marriages. Our study also contradicts the claim that these westward invasions resulted in founder effects.
Overall, our results are partly consistent with Comas et al 's hypothesis 11 that Central Asia has been a contact zone between two differentiated groups. Our study suggests that one of these groups is a long-lasting group of settled populations, now represented by Tajiks and Turkmen, although the origin of this group is difficult to infer; the second of these groups is likely to have a more recent origin, resulting from the movements of eastern nomadic Turkic-speaking groups. Interestingly, we found almost no African ancestry in the genetic pool of Central Asian population from clustering analyses Figure 3.
Yet, with the same level of clustering, we found no African ancestry either in Europe or in East-Asia. Further work is therefore required to infer the more ancient peopling of Central Asia, after the spread of modern humans out of Africa.
We found that the Uzbek populations were scattered across Turkic- and Indo-Iranian-speaking populations Figure 2b. This is consistent with the fact that Uzbek populations include the seventeenth century Uzbeks, which were nomadic herders before they sedentarized around the sixteenth century, 10 and the former Chagatai Turk groups who were already settled in Uzbekistan. We found two presumable cases of linguistic replacements in Central Asia. The Uzbek population UZA, a currently Turkic-speaking population, is indeed genetically more similar to Indo-Iranian speakers, which suggests a linguistic shift in this population.
Concerning the Turkmen, their genetic similarity with Tajiks see also Table 4 is consistent with the hypothesis that they may be the present-day descendants of populations established over long periods of time. A recent linguistic replacement in the TUR population would then explain the observed pattern of a Turkic-speaking population clustering with Indo-Iranian speakers. Our study confirms the results of Li et al 's study 48 that cluster the Hazara population with Central Asian populations, rather than Mongolian populations, which is consistent with ethnological studies.
Google Scholar. Mol Biol Evol ; 10 : — Am J Hum Genet ; 63 : — Science ; : Kazakhstan is a country of transit and destination for migrant workers from Central Asia, while Kyrgyzstan and Tajikistan lead in the world in dependency on remittances from labour migration.
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