Reconstructing genetic history of Siberian and Northeastern European populations

Abstract

Siberia and Northwestern Russia are home to over 40 culturally and linguistically diverse indigenous ethnic groups, yet genetic variation and histories of peoples from this region are largely uncharacterized. We present deep whole-genome sequencing data (∼38×) from 28 individuals belonging to 14 distinct indigenous populations from that region. We combined these data sets with additional 32 modern-day and 46 ancient human genomes to reconstruct genetic histories of several indigenous Northern Eurasian populations. We found that Siberian and East Asian populations shared 38% of their ancestry with a 45,000-yr-old Ust’-Ishim individual who was previously believed to have no modern-day descendants. Western Siberians trace 57% of their ancestry to ancient North Eurasians, represented by the 24,000-yr-old Siberian Mal'ta boy MA-1. Eastern Siberian populations formed a distinct sublineage that separated from other East Asian populations ∼10,000 yr ago. In addition, we uncovered admixtures between Siberians and Eastern European hunter-gatherers from Samara, Karelia, Hungary, and Sweden (from 8000–6600 yr ago); Yamnaya people (5300–4700 yr ago); and modern-day Northeastern Europeans. Our results provide new insights into genetic histories of Siberian and Northeastern European populations and evidence of ancient gene flow from Siberia into Europe.

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.…”

“…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, ).…”

“…His genome diverged from the ancestors of present‐day west Eurasian and east Eurasian populations before—or simultaneously with—their divergence from each other. Recently it was discovered that Siberian and East Asian populations share 38% of their ancestry with the Ust’‐Ishim individual (Wong et al, ). A 24 000‐year‐old Siberian from south‐central Siberia (Mal'ta) was found to be basal to modern‐day western Eurasians and genetically closely related to modern‐day Native Americans, with little if any genetic affinity with East Asians (Raghavan et al, ).…”

Nasal cavity and maxillary sinuses form variation among modern humans of Asian descent

“…It has been noted in many old and recent works to the topic that ecogeographic patterns of variation are more evident at the continental rather than the world‐wide level (Davies, ; Evteev et al, ; Hubbe et al, ). But despite this clear biological relatedness, both genetic and morphological variation among these populations is outstanding compared to western Eurasians (Evteev & Grosheva, ; Relethford, ; Wong et al, ; Woo & Morant, ). Second, many of these populations inhabit the zones of extremely cold climate, virtually absent in Europe or the Americas, which seems to trigger substantial adaptive change in the face of North Asians and the Inuit (see, for instance, Evteev et al, ; Harvati & Weaver, ; Roseman, ).…”

Have we already tested the aquatic ape hypothesis?

“…Similar situations are found in other indigenous populations. For example, although living in far distance, Siberians (northeastern Asian) and Europeans have genetic affinity (e.g., Lamnidis et al 2018, Wong et al 2017). Generally speaking, genetic studies give superior pictures of human migrations, and they may reveal that gene flows in and between current ethnic groups were more frequent than expected.…”