During the last few years, several studies have focused on the Yakuts using genetic analyses to trace their origins [4
]. However, to date the use of ancient DNA has been limited due to small numbers of individuals sampled [37
], in spite of the exceptional taphonomic conditions of Siberia and the possibility of retrieving high quality DNA from remains buried in the permafrost [39
]. Therefore, this study represents the first attempt to trace the origins of the Yakut population by ancient DNA analyses.
Out of the 65 ancient individuals analyzed in this study, 27 complete Y-chromosomal STR haplotypes were obtained from 38 male individuals, and mtDNA sequences were validated for 60 individuals. The quality of the results obtained in our study may be explained by the presence of permafrost which favors the preservation of DNA [41
]. The excavation strategy and the absence of any post-excavation treatment prior to laboratory analyses might have played an important role in the quality of DNA and confirms the statements of Pruvost et al. [31
]. Besides, this limited handling of the ancient remains represents a key factor in the reduction of contamination risk by modern DNA. The combination of the precautions against contamination and the validation strategy (i.e. comparison between the profiles of the samples and the researchers, analyses of different substrates, multiple analysis of one sample, phylogenetic validation of the mtDNA sequences) validate the data presented here, even if not all the traditional criteria [42
] could be met due to the large number of samples.
The Y-chromosome results obtained from our ancient sample are consistent with earlier studies [6
]. The specificity of the male lineages was confirmed by statistical analyses (MDS plot, MJ network) and by individual comparison of the Y-STR haplotypes with the literature data since only three haplotypes were shared with other populations. The high frequency of the haplogroup N1c, which is present from the most ancient graves, and the non-significant Fst values between ancient and present day Yakuts, indicates their stability through time. Thus, this genetic result corroborates the assumption that the Yakuts are a highly homogenous population not only geographically [6
] but also from a chronological standpoint.
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
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
]. 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. Later, the patrilineal clan organization of the Yakuts would have facilitated the diffusion of male lineages borne by the individuals of high social rank. This hypothesis is supported by the fact that the Y-chromosomal haplotypes identified by the warriors of the 15th
centuries were transmitted to the tojons
of the 18th
century. After Russian colonization, the influence of the tojons
was strengthened by the decrees made by the Empress Anna Ivanovna [1
], and this official reinforcement of their power might have increased the spread of a limited number of Y-chromosomal lineages for a second time. Therefore, the early founder effect combined with the Yakutian traditions and the Russian influence would have led to the present day genetic pattern observed for the paternal lineages.
Conversely, the results obtained from the mtDNA analyses revealed a more important diversity and varying origins of the maternal lineages. Indeed, the gene diversity observed in our ancient sample is intermediate compared with the diversity found in small and isolated Siberian groups such as the Chukchi and Mongolian [15
], Buryatian [4
] or Central Asian [23
] populations. The haplogroup distribution observed in our sample matched that found in present day Yakuts and is constituted by distant haplogroups found in Siberian, Mongolian and Central Asian populations. The major haplogroup, C4, indicates more specific affinities with the Evenks [21
]. Nevertheless, the individual comparison of maternal lineages with data from literature allowed us to precise that four out of the six lineages belonging to the C4 haplogroup were present in the Buryat population. Therefore, the Buryat origin of some of the D5 sub-haplogroups found in the Yakuts as demonstrated by Pakendorf et al. [6
] could be expanded to the C4 haplogroup.
The influence of both Buryat and Evenk populations is clearly visible in the mtDNA lineages of the ancient Yakuts. Concerning the contribution of the Evenks to the Yakut's mtDNA gene pool, the admixture might have mostly occurred between Yakut men and Evenk women (as assumed by Pakendorf et al. [6
]) according to the high frequency of the C4 haplogroup in these two groups, and since the Y-chromosomal lineages are highly specific to the Yakuts and the genetic diversity indices are lower for Y chromosome than for mtDNA. Moreover, the number of first settlers who arrived in Central Yakutia was certainly limited and the patrilocal exogamy practiced by the traditional Yakut society [49
] corroborates the inclusion of autochthonous women. This assumption is further confirmed by linguistic data that reveals intermarriages between the Yakuts and Evenks [50
Finally, the stability through time demonstrated by the Y chromosome is also observed in the maternal lineages. Indeed, most of the sequences present in our ancient sample (83%) have been transmitted to the present day population. However, this could signal a small loss in variation over the two last centuries, which could be associated with stochastic processes linked to demographic changes undergone by the Yakut population (plague, smallpox) or other phenomena [51
]. Besides, the Yakuts from all chronological periods are grouped together in the MDS plot and the Fst calculation revealed the absence of significant distances between them. Thus, even if the Russian colonization had an important impact on the expansion of the Yakuts throughout Yakutia [1
], its genetic influence appears to be relatively low.
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. These assumptions are in agreement with archaeological data [54
], the founder effect dates calculated by Pakendorf et al. [6
] and with the recent coalescent simulations of Yakut mtDNA variation by Zlojutro et al. [56
]. The early expansion of the Yakuts was accompanied by intermarriages between Yakut men and Evenk women as evidenced by the migration rates. Our data also suggest that the genetic characteristics of the Yakuts were already well established in the Central Yakutian population during the 15th
century and have remained stable until the present day.