RESEARCH Open Access Between Lake Baikal and the Baltic Sea: genomic history of the gateway to Europe Petr Triska 1† , Nikolay Chekanov 2,3† , Vadim Stepanov 4 , Elza K. Khusnutdinova 5,6 , Ganesh Prasad Arun Kumar 7 , Vita Akhmetova 5 , Konstantin Babalyan 8 , Eugenia Boulygina 9 , Vladimir Kharkov 4 , Marina Gubina 10 , Irina Khidiyatova 5,6 , Irina Khitrinskaya 4 , Ekaterina E. Khrameeva 3,11 , Rita Khusainova 5,6 , Natalia Konovalova 12 , Sergey Litvinov 5 , Andrey Marusin 4 , Alexandr M. Mazur 2 , Valery Puzyrev 4 , Dinara Ivanoshchuk 10 , Maria Spiridonova 4 , Anton Teslyuk 8 , Svetlana Tsygankova 8 , Martin Triska 1 , Natalya Trofimova 5 , Edward Vajda 13 , Oleg Balanovsky 14,15 , Ancha Baranova 14,16,17 , Konstantin Skryabin 2,9,18 , Tatiana V. Tatarinova 15,16,17,19,20*† and Egor Prokhortchouk 2,18*† From Belyaev Conference Novosibirsk, Russia. 07-10 August 2017 Abstract Background: The history of human populations occupying the plains and mountain ridges separating Europe from Asia has been eventful, as these natural obstacles were crossed westward by multiple waves of Turkic and Uralic- speaking migrants as well as eastward by Europeans. Unfortunately, the material records of history of this region are not dense enough to reconstruct details of population history. These considerations stimulate growing interest to obtain a genetic picture of the demographic history of migrations and admixture in Northern Eurasia. Results: We genotyped and analyzed 1076 individuals from 30 populations with geographical coverage spanning from Baltic Sea to Baikal Lake. Our dense sampling allowed us to describe in detail the population structure, provide insight into genomic history of numerous European and Asian populations, and significantly increase quantity of genetic data available for modern populations in region of North Eurasia. Our study doubles the amount of genome-wide profiles available for this region. We detected unusually high amount of shared identical-by-descent (IBD) genomic segments between several Siberian populations, such as Khanty and Ket, providing evidence of genetic relatedness across vast geographic distances and between speakers of different language families. Additionally, we observed excessive IBD sharing between Khanty and Bashkir, a group of Turkic speakers from Southern Urals region. While adding some weight to the “Finno-Ugric” origin of Bashkir, our studies highlighted that the Bashkir genepool lacks the main “core”, being a multi-layered amalgamation of Turkic, Ugric, Finnish and Indo-European contributions, which points at intricacy of genetic interface between Turkic and Uralic populations. Comparison of the genetic structure of Siberian ethnicities and the geography of the region they inhabit point at existence of the “Great Siberian Vortex” directing genetic exchanges in populations across the Siberian part of Asia. Slavic speakers of Eastern Europe are, in general, very similar in their genetic composition. Ukrainians, Belarusians and Russians have almost identical proportions of Caucasus and Northern European components and have virtually (Continued on next page) * Correspondence: ttatarinova@laverne.edu; prokhortchouk@biengi.ac.ru † Equal contributors 15 Vavilov Institute of General Genetics, Moscow, Russia 2 Federal State Institution “Federal Research Centre «Fundamentals of Biotechnology» of the Russian Academy of Sciences”, Moscow, Russia Full list of author information is available at the end of the article © The Author(s). 2017 Open Access This article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated. Triska et al. BMC Genetics 2017, 18(Suppl 1):110 DOI 10.1186/s12863-017-0578-3