. 2021 Jan 6;7(2):eabc4587.

doi: 10.1126/sciadv.abc4587. Print 2021 Jan.

Human population dynamics and Yersinia pestis in ancient northeast Asia

Gülşah Merve Kılınç^{1

2}, Natalija Kashuba^{3

4}, Dilek Koptekin⁵, Nora Bergfeldt^{6

7}, Handan Melike Dönertaş⁸, Ricardo Rodríguez-Varela^{3

7}, Dmitrij Shergin⁹, Grigorij Ivanov¹⁰, Dmitrii Kichigin¹¹, Kjunnej Pestereva¹², Denis Volkov¹³, Pavel Mandryka¹⁴, Artur Kharinskii¹¹, Alexey Tishkin¹⁵, Evgenij Ineshin⁹, Evgeniy Kovychev¹⁶, Aleksandr Stepanov¹⁷, Love Dalén^{6

7}, Torsten Günther¹⁸, Emrah Kırdök^{7

19}, Mattias Jakobsson¹⁸, Mehmet Somel²⁰, Maja Krzewińska^{3

7}, Jan Storå²¹, Anders Götherström^{1

7}

Affiliations

¹ Archaeological Research Laboratory, Department of Archaeology and Classical Studies, Stockholm University, 10691 Stockholm, Sweden. anders.gotherstrom@arklab.su.se jan.stora@ofl.su.se gulsahkilinc@hacettepe.edu.tr.
² Department of Bioinformatics, Graduate School of Health Sciences, Hacettepe University, 06100 Ankara, Turkey.
³ Archaeological Research Laboratory, Department of Archaeology and Classical Studies, Stockholm University, 10691 Stockholm, Sweden.
⁴ Department of Archaeology and Ancient History, Uppsala University, 75126 Uppsala, Sweden.
⁵ Department of Health Informatics, Middle East Technical University, 06800 Ankara, Turkey.
⁶ Department of Zoology, Stockholm University, 10691 Stockholm, Sweden.
⁷ Centre for Palaeogenetics, 10691 Stockholm, Sweden.
⁸ European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, CB10 1SD Cambridge, UK.
⁹ Laboratory of Archaeology and Ethnography, Faculty of History and Methods, Department of Humanitarian and Aesthetic Education, Pedagogical Institute, Irkutsk State University, Irkutsk, 664011 Irkutsk Oblast, Russia.
¹⁰ Irkutsk Museum of Regional Studies, Irkutsk, 664003 Irkutsk Oblast, Russia.
¹¹ Irkutsk National Research Technical University, Laboratory of Archaeology, Paleoecology and the Subsistence Strategies of the Peoples of Northern Asia, Irkutsk State Technical University, Irkutsk, 664074 Irkutsk Oblast, Russia.
¹² Faculty of History, Federal State Autonomous Educational Institution of Higher Education "M. K. Ammosov North-Eastern Federal University," Yakutsk, 677000 Sakha Republic, Russia.
¹³ The Center for Preservation of Historical and Cultural Heritage of the Amur Region, Blagoveshchensk, 675000 Amur Oblast, Russia.
¹⁴ Siberian Federal University, Krasnoyarsk, 660041 Krasnoyarskiy Kray, Russia.
¹⁵ Department of Archaeology, Ethnography and Museology, Altai State University, Barnaul, Altaiskiy Kray, Russia.
¹⁶ Faculty of History, Transbaikal State University, Chita, 672039 Zabaykalsky Kray, Russia.
¹⁷ Museum of Archaeology and Ethnography, Federal State Autonomous Educational Institution of Higher Education "M. K. Ammosov North-Eastern Federal University," Yakutsk, 677000 Sakha Republic, Russia.
¹⁸ Department of Organismal Biology and SciLife Lab, Uppsala University, Norbyvägen 18 A, SE-752 36 Uppsala, Sweden.
¹⁹ Department of Biotechnology, Mersin University, 33343 Mersin, Turkey.
²⁰ Department of Biological Sciences, Middle East Technical University, 06800 Ankara, Turkey.
²¹ Osteoarchaeological Research Laboratory, Department of Archaeology and Classical Studies, Stockholm University, 10691 Stockholm, Sweden. anders.gotherstrom@arklab.su.se jan.stora@ofl.su.se gulsahkilinc@hacettepe.edu.tr.

PMID: 33523963
PMCID: PMC7787494
DOI: 10.1126/sciadv.abc4587

Human population dynamics and Yersinia pestis in ancient northeast Asia

Gülşah Merve Kılınç et al. Sci Adv. 2021.

. 2021 Jan 6;7(2):eabc4587.

doi: 10.1126/sciadv.abc4587. Print 2021 Jan.

Authors

Affiliations

¹ Archaeological Research Laboratory, Department of Archaeology and Classical Studies, Stockholm University, 10691 Stockholm, Sweden. anders.gotherstrom@arklab.su.se jan.stora@ofl.su.se gulsahkilinc@hacettepe.edu.tr.
² Department of Bioinformatics, Graduate School of Health Sciences, Hacettepe University, 06100 Ankara, Turkey.
³ Archaeological Research Laboratory, Department of Archaeology and Classical Studies, Stockholm University, 10691 Stockholm, Sweden.
⁴ Department of Archaeology and Ancient History, Uppsala University, 75126 Uppsala, Sweden.
⁵ Department of Health Informatics, Middle East Technical University, 06800 Ankara, Turkey.
⁶ Department of Zoology, Stockholm University, 10691 Stockholm, Sweden.
⁷ Centre for Palaeogenetics, 10691 Stockholm, Sweden.
⁸ European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, CB10 1SD Cambridge, UK.
⁹ Laboratory of Archaeology and Ethnography, Faculty of History and Methods, Department of Humanitarian and Aesthetic Education, Pedagogical Institute, Irkutsk State University, Irkutsk, 664011 Irkutsk Oblast, Russia.
¹⁰ Irkutsk Museum of Regional Studies, Irkutsk, 664003 Irkutsk Oblast, Russia.
¹¹ Irkutsk National Research Technical University, Laboratory of Archaeology, Paleoecology and the Subsistence Strategies of the Peoples of Northern Asia, Irkutsk State Technical University, Irkutsk, 664074 Irkutsk Oblast, Russia.
¹² Faculty of History, Federal State Autonomous Educational Institution of Higher Education "M. K. Ammosov North-Eastern Federal University," Yakutsk, 677000 Sakha Republic, Russia.
¹³ The Center for Preservation of Historical and Cultural Heritage of the Amur Region, Blagoveshchensk, 675000 Amur Oblast, Russia.
¹⁴ Siberian Federal University, Krasnoyarsk, 660041 Krasnoyarskiy Kray, Russia.
¹⁵ Department of Archaeology, Ethnography and Museology, Altai State University, Barnaul, Altaiskiy Kray, Russia.
¹⁶ Faculty of History, Transbaikal State University, Chita, 672039 Zabaykalsky Kray, Russia.
¹⁷ Museum of Archaeology and Ethnography, Federal State Autonomous Educational Institution of Higher Education "M. K. Ammosov North-Eastern Federal University," Yakutsk, 677000 Sakha Republic, Russia.
¹⁸ Department of Organismal Biology and SciLife Lab, Uppsala University, Norbyvägen 18 A, SE-752 36 Uppsala, Sweden.
¹⁹ Department of Biotechnology, Mersin University, 33343 Mersin, Turkey.
²⁰ Department of Biological Sciences, Middle East Technical University, 06800 Ankara, Turkey.
²¹ Osteoarchaeological Research Laboratory, Department of Archaeology and Classical Studies, Stockholm University, 10691 Stockholm, Sweden. anders.gotherstrom@arklab.su.se jan.stora@ofl.su.se gulsahkilinc@hacettepe.edu.tr.

PMID: 33523963
PMCID: PMC7787494
DOI: 10.1126/sciadv.abc4587

Abstract

We present genome-wide data from 40 individuals dating to c.16,900 to 550 years ago in northeast Asia. We describe hitherto unknown gene flow and admixture events in the region, revealing a complex population history. While populations east of Lake Baikal remained relatively stable from the Mesolithic to the Bronze Age, those from Yakutia and west of Lake Baikal witnessed major population transformations, from the Late Upper Paleolithic to the Neolithic, and during the Bronze Age, respectively. We further locate the Asian ancestors of Paleo-Inuits, using direct genetic evidence. Last, we report the most northeastern ancient occurrence of the plague-related bacterium, Yersinia pestis Our findings indicate the highly connected and dynamic nature of northeast Asia populations throughout the Holocene.

Copyright © 2021 The Authors, some rights reserved; exclusive licensee American Association for the Advancement of Science. No claim to original U.S. Government Works. Distributed under a Creative Commons Attribution NonCommercial License 4.0 (CC BY-NC).

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Figures

**Fig. 1. Geographical and chronological information concerning the ancient individuals.**
(A) Geographical map showing the locations of the individuals sequenced in this study (orange, blue, and red). Genomes published elsewhere are shown as black (see table S2 for information about all published individuals used in comparative analysis). (B) Timeline showing the ages of the ancient individuals as calibrated years before the present.

**Fig. 2. PCA and ADMIXTURE analysis.**
(A) PCA calculated using a set of world populations. Ancient individuals were projected onto the inferred PC space (see table S2 for information about individuals). Arrows indicate the direction of population changes in time. Asterisk denotes being published in (16). (B) A subset of ADMIXTURE result for K = 14 clusters showing the ancestral composition of investigated ancient individuals.

**Fig. 3. Key f₄-statistics summarizing the population transitions across the Lake Baikal area.**
(A) *f₄(Yoruba, Trans-Baikal_8515_8380_BP; PopX, Yakutia_Lena_6850_6190_BP)*. (B) *f₄(Yoruba, Trans-Baikal_8345_3000_BP; PopX, Cis-Baikal_8980_8640_BP)*. (C) *f₄(Yoruba, Cis-Baikal_8980_8640_BP; PopX, Trans-Baikal_8345_3000_BP)*.

**Fig. 4. Estimating the level of genetic diversity and population size changes in time.**
(A) Heterozygosity estimates. (B) Amount of short RoH in the genomes of Lake Baikal and Yakutia individuals. Mb, megabase. (C) Effective population size change in time estimated using MSMC.

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Human population dynamics and Yersinia pestis in ancient northeast Asia

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Human population dynamics and Yersinia pestis in ancient northeast Asia

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