The complex admixture history and recent southern origins of Siberian populations

Abstract

Although Siberia was inhabited by modern humans at an early stage, there is still debate over whether this area remained habitable during the extremely cold period of the Last Glacial Maximum or whether it was subsequently repopulated by peoples with a recent shared ancestry. Previous studies of the genetic history of Siberian populations were hampered by the extensive admixture that appears to have taken place among these populations, since commonly used methods assume a tree-like population history and at most single admixture events. We therefore developed a new method based on the covariance of ancestry components, which we validated with simulated data, in order to investigate this potentially complex admixture history and to distinguish the effects of shared ancestry from prehistoric migrations and contact. We furthermore adapted a previously Author SummaryWe developed a new method that lets us disentangle complex admixture events and date the individual episodes of gene flow. We applied this method to a large dataset of genome-wide SNP genotypes from a linguistically diverse sample of populations covering the extent of Siberia. Our results demonstrate that these populations have been in intense contact with each other, with most of them carrying more than two, and up to six different ancestries. 2. CC-BY-NC-ND 4.0 International license not peer-reviewed) is the author/funder. It is made available under a The copyright holder for this preprint (which was . http://dx.doi.org/10.1101/018770 doi: bioRxiv preprint first posted online Apr. 30, 2015; Nevertheless, as shown by the dates we estimate, these various admixture events have taken place over a relatively short time, with the oldest dating to not more than 4500 years ago.Our results emphasize the enormous impact that contact has had on the genetic history of these Siberian populations, and the methods developed here will be of use in the investigation of admixture events in populations around the world.

Siberian genetic diversity reveals complex origins of the Samoyedic‐speaking populations

“…This procedure helps to avoid the potential effect of high relatedness among individuals in isolated populations from Siberia, as well as uneven sample sizes. Our PCA analysis to some extent recaps previously reported patterns of genetic structure across Eurasia (Pugach et al, ; Wong et al, ). PC1 corresponds to west‐east differentiation, while the second PC generally differentiates northern and southern populations.…”

“…In agreement with ROH analysis, the majority of Siberian populations also reveal an increased number of within‐population shared IBD segments with high correlation coefficient between IBD sharing and Ne . Similar to previous studies (Pugach et al, ; Yunusbayev et al, ), Nganasans demonstrates unusually high IBD sharing with other Siberian populations. The fact that a majority of modern Siberian people share excessive IBD sharing (and possibly the same set of ancestors) seems to contradict long‐term isolation and very high genetic differentiation observed within Siberia.…”

“…The majority of previous Siberian population genetic studies have been mostly limited to classical markers, Y‐chromosome and mtDNA surveys, and usually did not include all existing Samoyed populations (Derbeneva, Starikovskaya, Volodko, Wallace, & Sukernik, ; Derenko et al, ; Derenko et al, ; Derenko et al, ; Duggan et al, ; Karafet et al, ; Karafet, Osipova, Kazakovtseva, Posukh, & Hammer, ; Karafet et al, 1999; Lell et al, ; Sukernik, Abanina, Karafet, Osipova, & Galaktionov, ; Sukernik, Karafet, & Osipova, ; Volodko et al, ). Recent studies have analyzed Siberian genome‐wide data, focusing mostly on the history of particular population(s) (Fedorova et al, ; Flegontov et al, ; Yunusbayev et al, ), the evidence of admixture in the history of Siberian aboriginal populations (Pugach et al, ; Wong et al, ), or cold adaptation (Cardona et al, ). The only genetic study that has specifically focused on the history of the Tundra Nentsi, Forest Nentsi, and Selkups from the perspective of male lineage demonstrated that their genetic and linguistic affiliations were not entirely concordant (Karafet, Osipova, Posukh, Wiebe, & Hammer, ).…”

High‐resolution mitochondrial DNA analysis sheds light on human diversity, cultural interactions, and population mobility in Northwestern Amazonia

“…Adding rivers to the regression model resulted in an increase in the amount of variation explained by the model (Table ), with rivers being a significant predictor ( p ‐value = 0.01). We then jack‐knifed over populations (Pugach et al ; Ramachandran et al, ) and identified three populations as outliers—Sikuani, Siona, and Nukak—groups that appeared as outliers in the MDS plot as well (Figure ). We performed the multiple regression analysis excluding the outliers, and this resulted in an increase of 3.4% in the R square value, a better correlation between genetic and geographic distances, and geography becoming a significant predictor factor ( p ‐value < 0.05) (Table and Supporting Information Figure S8), although rivers were no longer a significant predictor of genetic subdivision.…”

“…Furthermore, a multiple regression analysis on distance matrices (MRM) (Goslee and Urban, ) with the form: MRM(as.dist(gen.dist) – as.dist(geo.dist) + as.dist(rivers.dist)) was performed. This analysis takes into consideration a matrix of geographic distances and a matrix of proximity along rivers as predictor variables of the genetic distances (pairwise Φ ST values) between populations (Pugach et al, ; Yunusbayev et al, ). For the matrix of river distances, a value of zero was given to populations living along the same river or on rivers that are closely connected, and a value of one was given to populations living on different rivers.…”