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Gyuris B, Vyazov L, Türk A, Flegontov P, Szeifert B, Langó P, Mende BG, Csáky V, Chizhevskiy AA, Gazimzyanov IR, Khokhlov AA, Kolonskikh AG, Matveeva NP, Ruslanova RR, Rykun MP, Sitdikov A, Volkova EV, Botalov SG, Bugrov DG, Grudochko IV, Komar O, Krasnoperov AA, Poshekhonova OE, Chikunova I, Sungatov F, Stashenkov DA, Zubov S, Zelenkov AS, Ringbauer H, Cheronet O, Pinhasi R, Akbari A, Rohland N, Mallick S, Reich D, Szécsényi-Nagy A. Long shared haplotypes identify the Southern Urals as a primary source for the 10th century Hungarians. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.07.21.599526. [PMID: 39091721 PMCID: PMC11291037 DOI: 10.1101/2024.07.21.599526] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 08/04/2024]
Abstract
During the Hungarian Conquest in the 10th century CE, the early medieval Magyars, a group of mounted warriors from Eastern Europe, settled in the Carpathian Basin. They likely introduced the Hungarian language to this new settlement area, during an event documented by both written sources and archaeological evidence. Previous archaeogenetic research identified the newcomers as migrants from the Eurasian steppe. However, genome-wide ancient DNA from putative source populations has not been available to test alternative theories of their precise source. We generated genome-wide ancient DNA data for 131 individuals from candidate archaeological contexts in the Circum-Uralic region in present-day Russia. Our results tightly link the Magyars to people of the Early Medieval Karayakupovo archaeological horizon on both the European and Asian sides of the southern Urals. Our analyes show that ancestors of the people of the Karayakupovo archaeological horizon were established in the Southern Urals by the Iron Age and that their descendants persisted locally in the Volga-Kama region until at least the 14th century.
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Affiliation(s)
- Balázs Gyuris
- Institute of Archaeogenomics, HUN-REN Research Centre for the Humanities; Budapest, Hungary
- Doctoral School of Biology, ELTE Eötvös Loránd University; Budapest, Hungary
| | - Leonid Vyazov
- Department of Biology and Ecology, Faculty of Science, University of Ostrava; Ostrava, Czechia
- Department of Human Evolutionary Biology, Harvard University; Cambridge, MA, USA
| | - Attila Türk
- Department of Archaeology, Faculty of Humanities and Social Sciences, Pázmány Péter Catholic University; Budapest, Hungary
- Hungarian Prehistory Research group, HUN-REN Research Centre for the Humanities; Budapest, Hungary
| | - Pavel Flegontov
- Department of Biology and Ecology, Faculty of Science, University of Ostrava; Ostrava, Czechia
- Department of Human Evolutionary Biology, Harvard University; Cambridge, MA, USA
| | - Bea Szeifert
- Institute of Archaeogenomics, HUN-REN Research Centre for the Humanities; Budapest, Hungary
| | - Péter Langó
- Institute of Archaeology, HUN-REN Research Centre for the Humanities, Hungarian Research Network (HUN-REN); Budapest, Hungary
- Department of Archaeology, Faculty of Humanities and Social Sciences, Pázmány Péter Catholic University; Budapest, Hungary
| | - Balázs Gusztáv Mende
- Institute of Archaeogenomics, HUN-REN Research Centre for the Humanities; Budapest, Hungary
| | - Veronika Csáky
- Institute of Archaeogenomics, HUN-REN Research Centre for the Humanities; Budapest, Hungary
| | - Andrey A Chizhevskiy
- Institute of Archaeology of the Academy of Sciences of the Republic of Tatarstan; Kazan, Republic of Tatarstan, Russia
| | | | | | - Aleksandr G Kolonskikh
- R.G. Kuzeev Institute of Ethnological Studies, Ufa Federal Research Scientific Center of Russian Academy of Sciences; Ufa, Republic of Bashkortostan, Russia
| | | | - Rida R Ruslanova
- National Museum of the Republic of Bashkortostan; Ufa, Republic of Bashkortostan, Russia
| | | | - Ayrat Sitdikov
- Institute of Archaeology of the Academy of Sciences of the Republic of Tatarstan; Kazan, Republic of Tatarstan, Russia
- Department of Archaeology, Kazan Federal University, Kazan, Republic of Tatarstan, Russia
| | - Elizaveta V Volkova
- Institute of Archaeology of the Academy of Sciences of the Republic of Tatarstan; Kazan, Republic of Tatarstan, Russia
| | - Sergei G Botalov
- South Ural Branch of the Institute of History and Archeology, Ural Branch of the Russian Academy of Sciences; Chelyabinsk, Russia
| | - Dmitriy G Bugrov
- National Museum of Tatarstan Republic; Kazan, Republic of Tatarstan, Russia
| | - Ivan V Grudochko
- South Ural Branch of the Institute of History and Archeology, Ural Branch of the Russian Academy of Sciences; Chelyabinsk, Russia
| | - Oleksii Komar
- Institute of Archaeology, National Academy of Sciences of Ukraine; Kyiv, Ukraine
| | - Alexander A Krasnoperov
- Udmurt Institute of History, Language and Literature, Udmurt Federal Research Center, Ural Branch of the Russian Academy of Sciences; Izhevsk, Udmurt Republic, Russia
| | - Olga E Poshekhonova
- Institute of the Problems of Northern Development, Tyumen Scientific Centre, Siberian Branch of the Russian Academy of Sciences; Tyumen, Russia
| | - Irina Chikunova
- Institute of the Problems of Northern Development, Tyumen Scientific Centre, Siberian Branch of the Russian Academy of Sciences; Tyumen, Russia
| | - Flarit Sungatov
- Institute of History, Language and Literature, Ufa Federal Research Scientific Center of Russian Academy of Sciences; Ufa, Republic of Bashkortostan, Russia
| | - Dmitrii A Stashenkov
- Samara Regional Museum of History and Local Lore named after P. V. Alabin; Samara, Russia
| | - Sergei Zubov
- Research Laboratory of Archeology, Samara National Research University; Samara, Russia
| | | | - Harald Ringbauer
- Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology; Leipzig, Germany
| | - Olivia Cheronet
- Department of Evolutionary Anthropology, University of Vienna; Vienna, Austria
| | - Ron Pinhasi
- Department of Evolutionary Anthropology, University of Vienna; Vienna, Austria
| | - Ali Akbari
- Department of Genetics, Harvard Medical School; Boston, MA 02138, USA
- Broad Institute of MIT and Harvard; Cambridge, MA 02142, USA
| | - Nadin Rohland
- Department of Genetics, Harvard Medical School; Boston, MA 02138, USA
- Broad Institute of MIT and Harvard; Cambridge, MA 02142, USA
| | - Swapan Mallick
- Department of Genetics, Harvard Medical School; Boston, MA 02138, USA
- Broad Institute of MIT and Harvard; Cambridge, MA 02142, USA
- Howard Hughes Medical Institute; Boston, MA 02138, USA
| | - David Reich
- Department of Human Evolutionary Biology, Harvard University; Cambridge, MA, USA
- Department of Genetics, Harvard Medical School; Boston, MA 02138, USA
- Broad Institute of MIT and Harvard; Cambridge, MA 02142, USA
- Howard Hughes Medical Institute; Boston, MA 02138, USA
| | - Anna Szécsényi-Nagy
- Institute of Archaeogenomics, HUN-REN Research Centre for the Humanities; Budapest, Hungary
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2
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Çokoğlu SS, Koptekin D, Fidan FR, Somel M. Investigating food production-associated DNA methylation changes in paleogenomes: Lack of consistent signals beyond technical noise. Evol Appl 2024; 17:e13743. [PMID: 38957308 PMCID: PMC11217591 DOI: 10.1111/eva.13743] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2023] [Revised: 05/29/2024] [Accepted: 06/08/2024] [Indexed: 07/04/2024] Open
Abstract
The Neolithic transition introduced major diet and lifestyle changes to human populations across continents. Beyond well-documented bioarcheological and genetic effects, whether these changes also had molecular-level epigenetic repercussions in past human populations has been an open question. In fact, methylation signatures can be inferred from UDG-treated ancient DNA through postmortem damage patterns, but with low signal-to-noise ratios; it is thus unclear whether published paleogenomes would provide the necessary resolution to discover systematic effects of lifestyle and diet shifts. To address this we compiled UDG-treated shotgun genomes of 13 pre-Neolithic hunter-gatherers (HGs) and 21 Neolithic farmers (NFs) individuals from West and North Eurasia, published by six different laboratories and with coverage c.1×-58× (median = 9×). We used epiPALEOMIX and a Monte Carlo normalization scheme to estimate methylation levels per genome. Our paleomethylome dataset showed expected genome-wide methylation patterns such as CpG island hypomethylation. However, analyzing the data using various approaches did not yield any systematic signals for subsistence type, genetic sex, or tissue effects. Comparing the HG-NF methylation differences in our dataset with methylation differences between hunter-gatherers versus farmers in modern-day Central Africa also did not yield consistent results. Meanwhile, paleomethylome profiles did cluster strongly by their laboratories of origin. Using larger data volumes, minimizing technical noise and/or using alternative protocols may be necessary for capturing subtle environment-related biological signals from paleomethylomes.
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Affiliation(s)
| | - Dilek Koptekin
- Department of BiologyMiddle East Technical UniversityAnkaraTurkey
| | | | - Mehmet Somel
- Department of BiologyMiddle East Technical UniversityAnkaraTurkey
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3
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Cooke NP, Murray M, Cassidy LM, Mattiangeli V, Okazaki K, Kasai K, Gakuhari T, Bradley DG, Nakagome S. Genomic imputation of ancient Asian populations contrasts local adaptation in pre- and post-agricultural Japan. iScience 2024; 27:110050. [PMID: 38883821 PMCID: PMC11176660 DOI: 10.1016/j.isci.2024.110050] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2023] [Revised: 03/25/2024] [Accepted: 05/17/2024] [Indexed: 06/18/2024] Open
Abstract
Early modern humans lived as hunter-gatherers for millennia before agriculture, yet the genetic adaptations of these populations remain a mystery. Here, we investigate selection in the ancient hunter-gatherer-fisher Jomon and contrast pre- and post-agricultural adaptation in the Japanese archipelago. Building on the successful validation of imputation with ancient Asian genomes, we identify selection signatures in the Jomon, particularly robust signals from KITLG variants, which may have influenced dark pigmentation evolution. The Jomon lacks well-known adaptive variants (EDAR, ADH1B, and ALDH2), marking their emergence after the advent of farming in the archipelago. Notably, the EDAR and ADH1B variants were prevalent in the archipelago 1,300 years ago, whereas the ALDH2 variant could have emerged later due to its absence in other ancient genomes. Overall, our study underpins local adaptation unique to the Jomon population, which in turn sheds light on post-farming selection that continues to shape contemporary Asian populations.
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Affiliation(s)
- Niall P Cooke
- School of Medicine, Trinity College Dublin, Dublin, Ireland
| | | | - Lara M Cassidy
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin, Ireland
| | | | - Kenji Okazaki
- Department of Anatomy, Faculty of Medicine, Tottori University, Yonago, Japan
| | - Kenji Kasai
- Toyama Prefectural Center for Archaeological Operations, Toyama, Japan
| | - Takashi Gakuhari
- Institute for the Study of Ancient Civilizations and Cultural Resources, Kanazawa University, Kanazawa, Japan
| | - Daniel G Bradley
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin, Ireland
| | - Shigeki Nakagome
- School of Medicine, Trinity College Dublin, Dublin, Ireland
- Institute for the Study of Ancient Civilizations and Cultural Resources, Kanazawa University, Kanazawa, Japan
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Childebayeva A, Fricke F, Rohrlach AB, Huang L, Schiffels S, Vesakoski O, Mannermaa K, Semerau L, Aron F, Solodovnikov K, Rykun M, Moiseyev V, Khartanovich V, Kovtun I, Krause J, Kuzminykh S, Haak W. Bronze age Northern Eurasian genetics in the context of development of metallurgy and Siberian ancestry. Commun Biol 2024; 7:723. [PMID: 38862782 PMCID: PMC11166947 DOI: 10.1038/s42003-024-06343-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2023] [Accepted: 05/16/2024] [Indexed: 06/13/2024] Open
Abstract
The Eurasian Bronze Age (BA) has been described as a period of substantial human migrations, the emergence of pastoralism, horse domestication, and development of metallurgy. This study focuses on two north Eurasian sites sharing Siberian genetic ancestry. One of the sites, Rostovka, is associated with the Seima-Turbino (ST) phenomenon (~2200-1900 BCE) that is characterized by elaborate metallurgical objects found throughout Northern Eurasia. The genetic profiles of Rostovka individuals vary widely along the forest-tundra Siberian genetic cline represented by many modern Uralic-speaking populations, and the genetic heterogeneity observed is consistent with the current understanding of the ST being a transcultural phenomenon. Individuals from the second site, Bolshoy Oleni Ostrov in Kola, in comparison form a tighter cluster on the Siberian ancestry cline. We further explore this Siberian ancestry profile and assess the role of the ST phenomenon and other contemporaneous BA cultures in the spread of Uralic languages and Siberian ancestry.
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Affiliation(s)
- Ainash Childebayeva
- Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, D-04103, Leipzig, Germany.
- Department of Anthropology, University of Texas at Austin, Austin, TX, 78712, USA.
- Department of Anthropology, University of Kansas, Lawrence, KS, 66044, USA.
| | - Fabian Fricke
- German Archaeological Institute, Eurasia Department, Berlin, 14195, Germany
| | - Adam Benjamin Rohrlach
- Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, D-04103, Leipzig, Germany
- School of Computer and Mathematical Sciences, University of Adelaide, Adelaide, SA, 5005, Australia
| | - Lei Huang
- Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, D-04103, Leipzig, Germany
| | - Stephan Schiffels
- Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, D-04103, Leipzig, Germany
| | - Outi Vesakoski
- Department of Finnish and Finno-Ugric Languages, University of Turku, Turku, 20014, Finland
| | - Kristiina Mannermaa
- Department of Cultures, University of Helsinki, Yliopistonkatu 4, 00100, Helsinki, Finland
| | - Lena Semerau
- Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, D-04103, Leipzig, Germany
| | - Franziska Aron
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena, 07745, Germany
| | - Konstantin Solodovnikov
- Institute of Problems of Northern Development, Tyumen Scientific Center of the Siberian Branch of Russian Academy of Sciences, Tyumen, 625008, Russia
| | - Marina Rykun
- Department of Anthropology and Ethnology, National Research Tomsk State University, Tomsk, 634050, Russia
| | - Vyacheslav Moiseyev
- Peter the Great Museum of Anthropology and Ethnography (Kunstkamera), Russian Academy of Sciences, University Embankment, 3, Saint Petersburg, 199034, Russia
| | - Valery Khartanovich
- Peter the Great Museum of Anthropology and Ethnography (Kunstkamera), Russian Academy of Sciences, University Embankment, 3, Saint Petersburg, 199034, Russia
| | - Igor Kovtun
- Igor V. Kovtun, Independent Researcher, Kemerovo, 650000, Russia
| | - Johannes Krause
- Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, D-04103, Leipzig, Germany
| | - Sergey Kuzminykh
- Russian Academy of Sciences, Institute of Archaeology, Laboratory of Natural Scientific Methods, Moscow, 117292, Russia
| | - Wolfgang Haak
- Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, D-04103, Leipzig, Germany.
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5
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Gill H, Lee J, Jeong C. Reconstructing the Genetic Relationship between Ancient and Present-Day Siberian Populations. Genome Biol Evol 2024; 16:evae063. [PMID: 38526010 PMCID: PMC10999361 DOI: 10.1093/gbe/evae063] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Revised: 02/22/2024] [Accepted: 03/21/2024] [Indexed: 03/26/2024] Open
Abstract
Human populations across a vast area in northern Eurasia, from Fennoscandia to Chukotka, share a distinct genetic component often referred to as the Siberian ancestry. Most enriched in present-day Samoyedic-speaking populations such as Nganasans, its origins and history still remain elusive despite the growing list of ancient and present-day genomes from Siberia. Here, we reanalyze published ancient and present-day Siberian genomes focusing on the Baikal and Yakutia, resolving key questions regarding their genetic history. First, we show a long-term presence of a unique genetic profile in southern Siberia, up to 6,000 yr ago, which distinctly shares a deep ancestral connection with Native Americans. Second, we provide plausible historical models tracing genetic changes in West Baikal and Yakutia in fine resolution. Third, the Middle Neolithic individual from Yakutia, belonging to the Belkachi culture, serves as the best source so far available for the spread of the Siberian ancestry into Fennoscandia and Greenland. These findings shed light on the genetic legacy of the Siberian ancestry and provide insights into the complex interplay between different populations in northern Eurasia throughout history.
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Affiliation(s)
- Haechan Gill
- School of Biological Sciences, Seoul National University, Seoul 08826, Republic of Korea
| | - Juhyeon Lee
- School of Biological Sciences, Seoul National University, Seoul 08826, Republic of Korea
| | - Choongwon Jeong
- School of Biological Sciences, Seoul National University, Seoul 08826, Republic of Korea
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Mallick S, Micco A, Mah M, Ringbauer H, Lazaridis I, Olalde I, Patterson N, Reich D. The Allen Ancient DNA Resource (AADR) a curated compendium of ancient human genomes. Sci Data 2024; 11:182. [PMID: 38341426 PMCID: PMC10858950 DOI: 10.1038/s41597-024-03031-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2023] [Accepted: 01/31/2024] [Indexed: 02/12/2024] Open
Abstract
More than two hundred papers have reported genome-wide data from ancient humans. While the raw data for the vast majority are fully publicly available testifying to the commitment of the paleogenomics community to open data, formats for both raw data and meta-data differ. There is thus a need for uniform curation and a centralized, version-controlled compendium that researchers can download, analyze, and reference. Since 2019, we have been maintaining the Allen Ancient DNA Resource (AADR), which aims to provide an up-to-date, curated version of the world's published ancient human DNA data, represented at more than a million single nucleotide polymorphisms (SNPs) at which almost all ancient individuals have been assayed. The AADR has gone through six public releases at the time of writing and review of this manuscript, and crossed the threshold of >10,000 individuals with published genome-wide ancient DNA data at the end of 2022. This note is intended as a citable descriptor of the AADR.
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Affiliation(s)
- Swapan Mallick
- Department of Genetics, Harvard Medical School, Boston, MA, 02115, USA.
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA.
- Howard Hughes Medical Institute, Boston, MA, 02115, USA.
| | - Adam Micco
- Department of Genetics, Harvard Medical School, Boston, MA, 02115, USA
- Howard Hughes Medical Institute, Boston, MA, 02115, USA
| | - Matthew Mah
- Department of Genetics, Harvard Medical School, Boston, MA, 02115, USA
- Howard Hughes Medical Institute, Boston, MA, 02115, USA
| | - Harald Ringbauer
- Department of Human Evolutionary Biology, Harvard University, Cambridge, MA, 02138, USA
- Max Planck Institute for Evolutionary Anthropology, Leipzig, 04103, Germany
| | - Iosif Lazaridis
- Department of Genetics, Harvard Medical School, Boston, MA, 02115, USA
- Department of Human Evolutionary Biology, Harvard University, Cambridge, MA, 02138, USA
| | - Iñigo Olalde
- Department of Genetics, Harvard Medical School, Boston, MA, 02115, USA
- BIOMICs Research Group, University of the Basque Country, 01006, Vitoria-Gasteiz, Spain
| | - Nick Patterson
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
- Department of Human Evolutionary Biology, Harvard University, Cambridge, MA, 02138, USA
| | - David Reich
- Department of Genetics, Harvard Medical School, Boston, MA, 02115, USA.
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA.
- Howard Hughes Medical Institute, Boston, MA, 02115, USA.
- Department of Human Evolutionary Biology, Harvard University, Cambridge, MA, 02138, USA.
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7
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Ávila-Arcos MC, Raghavan M, Schlebusch C. Going local with ancient DNA: A review of human histories from regional perspectives. Science 2023; 382:53-58. [PMID: 37797024 DOI: 10.1126/science.adh8140] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2023] [Accepted: 09/05/2023] [Indexed: 10/07/2023]
Abstract
Ancient DNA (aDNA) has added a wealth of information about our species' history, including insights on genetic origins, migrations and gene flow, genetic admixture, and health and disease. Much early work has focused on continental-level questions, leaving many regional questions, especially those relevant to the Global South, comparatively underexplored. A few success stories of aDNA studies from smaller laboratories involve more local aspects of human histories and health in the Americas, Africa, Asia, and Oceania. In this Review, we cover some of these contributions by synthesizing finer-scale questions of importance to the archaeogenetics field, as well as to Indigenous and Descendant communities. We further highlight the potential of aDNA to uncover past histories in regions where colonialism has neglected the oral histories of oppressed peoples.
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Affiliation(s)
- María C Ávila-Arcos
- International Laboratory for Human Genome Research, Universidad Nacional Autónoma de México, Querétaro, Mexico
| | - Maanasa Raghavan
- Department of Human Genetics, University of Chicago, Chicago, IL, USA
| | - Carina Schlebusch
- Human Evolution, Department of Organismal Biology, Uppsala University, Uppsala, Sweden
- Palaeo-Research Institute, University of Johannesburg, Johannesburg, South Africa
- SciLifeLab, Uppsala, Sweden
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8
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Derenko M, Denisova G, Litvinov A, Dambueva I, Malyarchuk B. Mitogenomics of the Koryaks and Evens of the northern coast of the Sea of Okhotsk. J Hum Genet 2023; 68:705-712. [PMID: 37316650 DOI: 10.1038/s10038-023-01173-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2023] [Revised: 05/31/2023] [Accepted: 06/07/2023] [Indexed: 06/16/2023]
Abstract
Due to the geographical proximity of the northern coast of the Sea of Okhotsk and Kamchatka Peninsula to the Beringia, the indigenous populations of these territories are of great interest for elucidating the human settlement history of northern Asia and America. Meanwhile, there is a clear shortage of genetic studies of the indigenous populations of the northern coast of the Sea of Okhotsk. Here, in order to examine their fine-scale matrilineal genetic structure, ancestry and relationships with neighboring populations, we analyzed 203 complete mitogenomes (174 of which are new) from population samples of the Koryaks and Evens of the northern coast of the Sea of Okhotsk and the Chukchi of the extreme northeast Asia. The patterns observed underscore the reduced level of genetic diversity found in the Koryak, Even, and Chukchi populations, which, along with the high degree of interpopulation differentiation, may be the result of genetic drift. Our phylogeographic analysis reveals common Paleo-Asiatic ancestry for 51.1% of the Koryaks and 17.8% of the Evens. About third of the mitogenomes found in the Koryaks and Evens might be considered as ethno-specific, as these are virtually absent elsewhere in North, Central and East Asia. Coalescence ages of most of these lineages coincide well with the emergence and development of the Tokarev and Old Koryak archaeological cultures associated with the formation of the Koryaks, as well as with the period of separation and split of the North Tungusic groups migrated northwards from the Lake Baikal or the Amur River area.
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Affiliation(s)
- Miroslava Derenko
- Institute of Biological Problems of the North, Russian Academy of Sciences, Portovaya Street, 18, Magadan, 685000, Russia.
| | - Galina Denisova
- Institute of Biological Problems of the North, Russian Academy of Sciences, Portovaya Street, 18, Magadan, 685000, Russia
| | - Andrey Litvinov
- Institute of Biological Problems of the North, Russian Academy of Sciences, Portovaya Street, 18, Magadan, 685000, Russia
| | - Irina Dambueva
- Institute of Biological Problems of the North, Russian Academy of Sciences, Portovaya Street, 18, Magadan, 685000, Russia
| | - Boris Malyarchuk
- Institute of Biological Problems of the North, Russian Academy of Sciences, Portovaya Street, 18, Magadan, 685000, Russia
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9
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Blöcher J, Brami M, Feinauer IS, Stolarczyk E, Diekmann Y, Vetterdietz L, Karapetian M, Winkelbach L, Kokot V, Vallini L, Stobbe A, Haak W, Papageorgopoulou C, Krause R, Sharapova S, Burger J. Descent, marriage, and residence practices of a 3,800-year-old pastoral community in Central Eurasia. Proc Natl Acad Sci U S A 2023; 120:e2303574120. [PMID: 37603728 PMCID: PMC10483636 DOI: 10.1073/pnas.2303574120] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2023] [Accepted: 07/17/2023] [Indexed: 08/23/2023] Open
Abstract
Our understanding of prehistoric societal organization at the family level is still limited. Here, we generated genome data from 32 individuals from an approximately 3,800-y-old burial mound attributed to the Bronze Age Srubnaya-Alakul cultural tradition at the site of Nepluyevsky, located in the Southern Ural region of Central Eurasia. We found that life expectancy was generally very low, with adult males living on average 8 y longer than females. A total of 35 first-degree, 40 second-degree, and 48 third-degree biological relationships connected 23 of the studied individuals, allowing us to propose a family tree spanning three generations with six brothers at its center. The oldest of these brothers had eight children with two women and the most children overall, whereas the other relationships were monogamous. Notably, related female children above the age of five were completely absent from the site, and adult females were more genetically diverse than males. These results suggest that biological relationships between male siblings played a structural role in society and that descent group membership was based on patrilineality. Women originated from a larger mating network and moved to join the men, with whom they were buried. Finally, the oldest brother likely held a higher social position, which was expressed in terms of fertility.
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Affiliation(s)
- Jens Blöcher
- Institute of Organismic and Molecular Evolution, Palaeogenetics Group, Johannes Gutenberg University, Mainz55128, Germany
| | - Maxime Brami
- Institute of Organismic and Molecular Evolution, Palaeogenetics Group, Johannes Gutenberg University, Mainz55128, Germany
| | - Isabelle Sofie Feinauer
- Institute of Organismic and Molecular Evolution, Palaeogenetics Group, Johannes Gutenberg University, Mainz55128, Germany
- Centre for Palaeogenetics, Stockholm10691, Sweden
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Stockholm10405, Sweden
- Department of Zoology, Stockholm University, Stockholm10691, Sweden
| | - Eliza Stolarczyk
- Institute of Archaeological Sciences, Johann Wolfgang Goethe University, Frankfurt am MainD-60629, Germany
| | - Yoan Diekmann
- Institute of Organismic and Molecular Evolution, Palaeogenetics Group, Johannes Gutenberg University, Mainz55128, Germany
| | - Lisa Vetterdietz
- Institute of Organismic and Molecular Evolution, Palaeogenetics Group, Johannes Gutenberg University, Mainz55128, Germany
| | - Marina Karapetian
- Research Institute and Museum of Anthropology, Lomonosov Moscow State University, Moscow125009, Russia
| | - Laura Winkelbach
- Institute of Organismic and Molecular Evolution, Palaeogenetics Group, Johannes Gutenberg University, Mainz55128, Germany
| | - Vanessa Kokot
- Institute of Organismic and Molecular Evolution, Palaeogenetics Group, Johannes Gutenberg University, Mainz55128, Germany
| | | | - Astrid Stobbe
- Institute of Archaeological Sciences, Johann Wolfgang Goethe University, Frankfurt am MainD-60629, Germany
| | - Wolfgang Haak
- Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, Leipzig04103, Germany
| | - Christina Papageorgopoulou
- Laboratory of Physical Anthropology, Department of History and Ethnology, Democritus University of Thrace, Komotini69100, Greece
| | - Rüdiger Krause
- Institute of Archaeological Sciences, Johann Wolfgang Goethe University, Frankfurt am MainD-60629, Germany
| | - Svetlana Sharapova
- Institute of History and Archaeology, Ural Branch of the Russian Academy of Science, Ekaterinburg620108, Russia
| | - Joachim Burger
- Institute of Organismic and Molecular Evolution, Palaeogenetics Group, Johannes Gutenberg University, Mainz55128, Germany
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10
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Flegontov P, Işıldak U, Maier R, Yüncü E, Changmai P, Reich D. Modeling of African population history using f-statistics is biased when applying all previously proposed SNP ascertainment schemes. PLoS Genet 2023; 19:e1010931. [PMID: 37676865 PMCID: PMC10508636 DOI: 10.1371/journal.pgen.1010931] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2023] [Revised: 09/19/2023] [Accepted: 08/21/2023] [Indexed: 09/09/2023] Open
Abstract
f-statistics have emerged as a first line of analysis for making inferences about demographic history from genome-wide data. Not only are they guaranteed to allow robust tests of the fits of proposed models of population history to data when analyzing full genome sequencing data-that is, all single nucleotide polymorphisms (SNPs) in the individuals being analyzed-but they are also guaranteed to allow robust tests of models for SNPs ascertained as polymorphic in a population that is an outgroup in a phylogenetic sense to all groups being analyzed. True "outgroup ascertainment" is in practice impossible in humans because our species has arisen from a substructured ancestral population that does not descend from a homogeneous ancestral population going back many hundreds of thousands of years into the past. However, initial studies suggested that non-outgroup-ascertainment schemes might produce robust enough results using f-statistics, and that motivated widespread fitting of models to data using non-outgroup-ascertained SNP panels such as the "Affymetrix Human Origins array" which has been genotyped on thousands of modern individuals from hundreds of populations, or the "1240k" in-solution enrichment reagent which has been the source of about 70% of published genome-wide data for ancient humans. In this study, we show that while analyses of population history using such panels work well for studies of relationships among non-African populations and one African outgroup, when co-modeling more than one sub-Saharan African and/or archaic human groups (Neanderthals and Denisovans), fitting of f-statistics to such SNP sets is expected to frequently lead to false rejection of true demographic histories, and failure to reject incorrect models. Analyzing panels of SNPs polymorphic in archaic humans, which has been suggested as a solution for the ascertainment problem, has limited statistical power and retains important biases. However, by carrying out simulations of diverse demographic histories, we show that bias in inferences based on f-statistics can be minimized by ascertaining on variants common in a union of diverse African groups; such ascertainment retains high statistical power while allowing co-analysis of archaic and modern groups.
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Affiliation(s)
- Pavel Flegontov
- Department of Human Evolutionary Biology, Harvard University, Cambridge, Massachusetts, United States of America
- Department of Biology and Ecology, Faculty of Science, University of Ostrava, Ostrava, Czechia
- Kalmyk Research Center of the Russian Academy of Sciences, Elista, Russia
| | - Ulaş Işıldak
- Department of Biology and Ecology, Faculty of Science, University of Ostrava, Ostrava, Czechia
| | - Robert Maier
- Department of Human Evolutionary Biology, Harvard University, Cambridge, Massachusetts, United States of America
| | - Eren Yüncü
- Department of Biology and Ecology, Faculty of Science, University of Ostrava, Ostrava, Czechia
| | - Piya Changmai
- Department of Biology and Ecology, Faculty of Science, University of Ostrava, Ostrava, Czechia
| | - David Reich
- Department of Human Evolutionary Biology, Harvard University, Cambridge, Massachusetts, United States of America
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, United States of America
- Howard Hughes Medical Institute, Harvard Medical School, Boston, Massachusetts, United States of America
- Broad Institute of Harvard and MIT, Cambridge, Massachusetts, United States of America
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11
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Malyarchuk BA. The role of Beringia in human adaptation to Arctic conditions based on results of genomic studies of modern and ancient populations. Vavilovskii Zhurnal Genet Selektsii 2023; 27:373-382. [PMID: 37465192 PMCID: PMC10350865 DOI: 10.18699/vjgb-23-45] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Revised: 10/15/2022] [Accepted: 10/15/2022] [Indexed: 07/20/2023] Open
Abstract
The results of studies in Quaternary geology, archeology, paleoanthropology and human genetics demonstrate that the ancestors of Native Americans arrived in mid-latitude North America mainly along the Pacific Northwest Coast, but had previously inhabited the Arctic and during the last glacial maximum were in a refugium in Beringia, a land bridge connecting Eurasia and North America. The gene pool of Native Americans is represented by unique haplogroups of mitochondrial DNA and the Y chromosome, the evolutionary age of which ranges from 13 to 22 thousand years. The results of a paleogenomic analysis also show that during the last glacial maximum Beringia was populated by human groups that had arisen as a result of interaction between the most ancient Upper Paleolithic populations of Northern Eurasia and newcomer groups from East Asia. Approximately 20 thousand years ago the Beringian populations began to form, and the duration of their existence in relative isolation is estimated at about 5 thousand years. Thus, the adaptation of the Beringians to the Arctic conditions could have taken several millennia. The adaptation of Amerindian ancestors to high latitudes and cold climates is supported by genomic data showing that adaptive genetic variants in Native Americans are associated with various metabolic pathways: melanin production processes in the skin, hair and eyes, the functioning of the cardiovascular system, energy metabolism and immune response characteristics. Meanwhile, the analysis of the existing hypotheses about the selection of some genetic variants in the Beringian ancestors of the Amerindians in connection with adaptation to the Arctic conditions (for example, in the FADS, ACTN3, EDAR genes) shows the ambiguity of the testing results, which may be due to the loss of some traces of the "Beringian" adaptation in the gene pools of modern Native Americans. The most optimal strategy for further research seems to be the search for adaptive variant.
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Affiliation(s)
- B A Malyarchuk
- Institute of Biological Problems of the North, Far-East Branch of the Russian Academy of Sciences, Magadan, Russia N.A. Shilo North-East Interdisciplinary Scientific Research Institute, Far-East Branch of the Russian Academy of Sciences, Magadan, Russia
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12
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Lee J, Miller BK, Bayarsaikhan J, Johannesson E, Ventresca Miller A, Warinner C, Jeong C. Genetic population structure of the Xiongnu Empire at imperial and local scales. SCIENCE ADVANCES 2023; 9:eadf3904. [PMID: 37058560 PMCID: PMC10104459 DOI: 10.1126/sciadv.adf3904] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Accepted: 03/16/2023] [Indexed: 06/19/2023]
Abstract
The Xiongnu established the first nomadic imperial power, controlling the Eastern Eurasian steppe from ca. 200 BCE to 100 CE. Recent archaeogenetic studies identified extreme levels of genetic diversity across the empire, corroborating historical records of the Xiongnu Empire being multiethnic. However, it has remained unknown how this diversity was structured at the local community level or by sociopolitical status. To address this, we investigated aristocratic and local elite cemeteries at the western frontier of the empire. Analyzing genome-wide data from 18 individuals, we show that genetic diversity within these communities was comparable to the empire as a whole, and that high diversity was also observed within extended families. Genetic heterogeneity was highest among the lowest-status individuals, implying diverse origins, while higher-status individuals harbored less genetic diversity, suggesting that elite status and power was concentrated within specific subsets of the broader Xiongnu population.
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Affiliation(s)
- Juhyeon Lee
- School of Biological Sciences, Seoul National University, Seoul 08826, Republic of Korea
| | - Bryan K. Miller
- Max Planck Institute for the Science of Human History, Jena 07745, Germany
- Museum of Anthropological Archaeology, University of Michigan, Ann Arbor, MI 48109, USA
- History of Art, University of Michigan, Ann Arbor, MI 48109, USA
| | - Jamsranjav Bayarsaikhan
- Max Planck Institute for the Science of Human History, Jena 07745, Germany
- National Museum of Mongolia, Ulaanbaatar, Mongolia
| | | | - Alicia Ventresca Miller
- Max Planck Institute for the Science of Human History, Jena 07745, Germany
- Museum of Anthropological Archaeology, University of Michigan, Ann Arbor, MI 48109, USA
- Department of Anthropology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Christina Warinner
- Max Planck Institute for Evolutionary Anthropology, Leipzig 04103, Germany
- Department of Anthropology, Harvard University, Cambridge, MA 02138, USA
| | - Choongwon Jeong
- School of Biological Sciences, Seoul National University, Seoul 08826, Republic of Korea
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13
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Yu HX, Ao C, Wang XP, Zhang XP, Sun J, Li H, Liu KJ, Wei LH. The impacts of bronze age in the gene pool of Chinese: Insights from phylogeographics of Y-chromosomal haplogroup N1a2a-F1101. Front Genet 2023; 14:1139722. [PMID: 36968599 PMCID: PMC10036388 DOI: 10.3389/fgene.2023.1139722] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2023] [Accepted: 02/23/2023] [Indexed: 03/12/2023] Open
Abstract
Objectives: Previous studies of archaeology and history suggested that the rise and prosperity of Bronze Age culture in East Asia had made essential contribution to the formation of early state and civilization in this region. However, the impacts in perspective of genetics remain ambiguous. Previous genetic researches indicated the Y-chromosome Q1a1a-M120 and N1a2a-F1101 may be the two most important paternal lineages among the Bronze Age people in ancient northwest China. Here, we investigated the 9,000-years history of haplogroup N1a2a-F1101 with revised phylogenetic tree and spatial autocorrelation analysis.Materials and Methods: In this study, 229 sequences of N1a2a-F1101 were analyzed. We developed a highly-revised phylogenetic tree with age estimates for N1a2a-F1101. In addition, we also explored the geographical distribution of sub-lineages of N1a2a-F1101, and spatial autocorrelation analysis was conducted for each sub-branch.Results: The initial differentiation location of N1a2a-F1101 and its most closely related branch, N1a2b-P43, a major lineage of Uralic-speaking populations in northern Eurasia, is likely the west part of northeast China. After ~4 thousand years of bottleneck effect period, haplgroup N1a2a-F1101 experienced continuous expansion during the Chalcolithic age (~ 4.5 kya to 4 kya) and Bronze age (~ 4 kya to 2.5 kya) in northern China. Ancient DNA evidence supported that this haplogroup is the lineage of ruling family of Zhou Dynasty (~ 3 kya-2.2 kya) of ancient China.Discussion: In general, we proposed that the Bronze Age people in the border area between the eastern Eurasian steppe and northern China not only played a key role in promoting the early state and civilization of China, but also left significant traces in the gene pool of Chinese people.
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Affiliation(s)
- Hui-Xin Yu
- School of Ethnology and Anthropology, Institute of Humanities and Human Sciences, Inner Mongolia Normal University, Hohhot, China
| | - Cheliger Ao
- School of Ethnology and Anthropology, Institute of Humanities and Human Sciences, Inner Mongolia Normal University, Hohhot, China
| | - Xiao-Peng Wang
- School of Management, Dalian University of Technology, Dalian, China
| | - Xian-Peng Zhang
- School of Ethnology and Anthropology, Institute of Humanities and Human Sciences, Inner Mongolia Normal University, Hohhot, China
| | - Jin Sun
- School of Literature and Media, Xingyi Normal University for Nationalities, Xingyi, China
| | - Hui Li
- MOE Key Laboratory of Contemporary Anthropology, School of Life Sciences, Fudan University, Shanghai, China
- B&R International Joint Laboratory for Eurasian Anthropology, Fudan University, Shanghai, China
| | - Kai-Jun Liu
- School of International Tourism and culture, Guizhou Normal University, Guiyang, China
- *Correspondence: Kai-Jun Liu, ; Lan-Hai Wei,
| | - Lan-Hai Wei
- School of Ethnology and Anthropology, Institute of Humanities and Human Sciences, Inner Mongolia Normal University, Hohhot, China
- B&R International Joint Laboratory for Eurasian Anthropology, Fudan University, Shanghai, China
- *Correspondence: Kai-Jun Liu, ; Lan-Hai Wei,
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14
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Middle Holocene Siberian genomes reveal highly connected gene pools throughout North Asia. Curr Biol 2023; 33:423-433.e5. [PMID: 36638796 DOI: 10.1016/j.cub.2022.11.062] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2022] [Revised: 11/15/2022] [Accepted: 11/28/2022] [Indexed: 01/15/2023]
Abstract
The peopling history of North Asia remains largely unexplored due to the limited number of ancient genomes analyzed from this region. Here, we report genome-wide data of ten individuals dated to as early as 7,500 years before present from three regions in North Asia, namely Altai-Sayan, Russian Far East, and the Kamchatka Peninsula. Our analysis reveals a previously undescribed Middle Holocene Siberian gene pool in Neolithic Altai-Sayan hunter-gatherers as a genetic mixture between paleo-Siberian and ancient North Eurasian (ANE) ancestries. This distinctive gene pool represents an optimal source for the inferred ANE-related population that contributed to Bronze Age groups from North and Inner Asia, such as Lake Baikal hunter-gatherers, Okunevo-associated pastoralists, and possibly Tarim Basin populations. We find the presence of ancient Northeast Asian (ANA) ancestry-initially described in Neolithic groups from the Russian Far East-in another Neolithic Altai-Sayan individual associated with different cultural features, revealing the spread of ANA ancestry ∼1,500 km further to the west than previously observed. In the Russian Far East, we identify 7,000-year-old individuals that carry Jomon-associated ancestry indicating genetic links with hunter-gatherers in the Japanese archipelago. We also report multiple phases of Native American-related gene flow into northeastern Asia over the past 5,000 years, reaching the Kamchatka Peninsula and central Siberia. Our findings highlight largely interconnected population dynamics throughout North Asia from the Early Holocene onward.
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15
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Flegontov P, Işıldak U, Maier R, Yüncü E, Changmai P, Reich D. Modeling of African population history using f -statistics can be highly biased and is not addressed by previously suggested SNP ascertainment schemes. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.01.22.525077. [PMID: 36711923 PMCID: PMC9882349 DOI: 10.1101/2023.01.22.525077] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
f -statistics have emerged as a first line of analysis for making inferences about demographic history from genome-wide data. These statistics can provide strong evidence for either admixture or cladality, which can be robust to substantial rates of errors or missing data. f -statistics are guaranteed to be unbiased under "SNP ascertainment" (analyzing non-randomly chosen subsets of single nucleotide polymorphisms) only if it relies on a population that is an outgroup for all groups analyzed. However, ascertainment on a true outgroup that is not co-analyzed with other populations is often impractical and uncommon in the literature. In this study focused on practical rather than theoretical aspects of SNP ascertainment, we show that many non-outgroup ascertainment schemes lead to false rejection of true demographic histories, as well as to failure to reject incorrect models. But the bias introduced by common ascertainments such as the 1240K panel is mostly limited to situations when more than one sub-Saharan African and/or archaic human groups (Neanderthals and Denisovans) or non-human outgroups are co-modelled, for example, f 4 -statistics involving one non-African group, two African groups, and one archaic group. Analyzing panels of SNPs polymorphic in archaic humans, which has been suggested as a solution for the ascertainment problem, cannot fix all these problems since for some classes of f -statistics it is not a clean outgroup ascertainment, and in other cases it demonstrates relatively low power to reject incorrect demographic models since it provides a relatively small number of variants common in anatomically modern humans. And due to the paucity of high-coverage archaic genomes, archaic individuals used for ascertainment often act as sole representatives of the respective groups in an analysis, and we show that this approach is highly problematic. By carrying out large numbers of simulations of diverse demographic histories, we find that bias in inferences based on f -statistics introduced by non-outgroup ascertainment can be minimized if the derived allele frequency spectrum in the population used for ascertainment approaches the spectrum that existed at the root of all groups being co-analyzed. Ascertaining on sites with variants common in a diverse group of African individuals provides a good approximation to such a set of SNPs, addressing the great majority of biases and also retaining high statistical power for studying population history. Such a "pan-African" ascertainment, although not completely problem-free, allows unbiased exploration of demographic models for the widest set of archaic and modern human populations, as compared to the other ascertainment schemes we explored.
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Affiliation(s)
- Pavel Flegontov
- Department of Human Evolutionary Biology, Harvard University, Cambridge, MA, USA
- Department of Biology and Ecology, Faculty of Science, University of Ostrava, Ostrava, Czechia
- Kalmyk Research Center of the Russian Academy of Sciences, Elista, Russia
| | - Ulaş Işıldak
- Department of Biology and Ecology, Faculty of Science, University of Ostrava, Ostrava, Czechia
| | - Robert Maier
- Department of Human Evolutionary Biology, Harvard University, Cambridge, MA, USA
| | - Eren Yüncü
- Department of Biology and Ecology, Faculty of Science, University of Ostrava, Ostrava, Czechia
| | - Piya Changmai
- Department of Biology and Ecology, Faculty of Science, University of Ostrava, Ostrava, Czechia
| | - David Reich
- Department of Human Evolutionary Biology, Harvard University, Cambridge, MA, USA
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
- Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, USA
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
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16
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Hoffecker JF, Elias SA, Scott GR, O'Rourke DH, Hlusko LJ, Potapova O, Pitulko V, Pavlova E, Bourgeon L, Vachula RS. Beringia and the peopling of the Western Hemisphere. Proc Biol Sci 2023; 290:20222246. [PMID: 36629115 PMCID: PMC9832545 DOI: 10.1098/rspb.2022.2246] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
Did Beringian environments represent an ecological barrier to humans until less than 15 000 years ago or was access to the Americas controlled by the spatial-temporal distribution of North American ice sheets? Beringian environments varied with respect to climate and biota, especially in the two major areas of exposed continental shelf. The East Siberian Arctic Shelf ('Great Arctic Plain' (GAP)) supported a dry steppe-tundra biome inhabited by a diverse large-mammal community, while the southern Bering-Chukchi Platform ('Bering Land Bridge' (BLB)) supported mesic tundra and probably a lower large-mammal biomass. A human population with west Eurasian roots occupied the GAP before the Last Glacial Maximum (LGM) and may have accessed mid-latitude North America via an interior ice-free corridor. Re-opening of the corridor less than 14 000 years ago indicates that the primary ancestors of living First Peoples, who already had spread widely in the Americas at this time, probably dispersed from the NW Pacific coast. A genetic 'arctic signal' in non-arctic First Peoples suggests that their parent population inhabited the GAP during the LGM, before their split from the former. We infer a shift from GAP terrestrial to a subarctic maritime economy on the southern BLB coast before dispersal in the Americas from the NW Pacific coast.
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Affiliation(s)
- John F. Hoffecker
- Institute of Arctic and Alpine Research, University of Colorado, Boulder, CO 80309, USA,Department of Anthropology, University of Kansas, 622 Fraser Hall, 1415 Jayhawk Blvd, Lawrence, KS 66045, USA
| | - Scott A. Elias
- Institute of Arctic and Alpine Research, University of Colorado, Boulder, CO 80309, USA
| | - G. Richard Scott
- Department of Anthropology, University of Nevada-Reno, 1664 N. Virginia Street, Reno, NV 89557, USA
| | - Dennis H. O'Rourke
- Department of Anthropology, University of Kansas, 622 Fraser Hall, 1415 Jayhawk Blvd, Lawrence, KS 66045, USA
| | - Leslea J. Hlusko
- Human Evolution Research Center, University of California-Berkeley, 3101 Valley Life Sciences Building, Berkeley, CA 94720-3140, USA,Centro Nacional de Investigación sobre la Evolución Humana (CENIEH), Burgos, Spain
| | - Olga Potapova
- Pleistocene Park Foundation, Philadelphia, PA 19006, USA,Department of Mammoth Fauna Studies, Academy of Sciences of Sakha, Yakutsk, Russia,The Mammoth Site of Hot Springs, Hot Springs, SD 57747, USA
| | - Vladimir Pitulko
- Institute of the History of Material Culture, Russian Academy of Sciences, Dvortsovaya nab., 18, 191186 St Petersburg, Russia,Peter the Great Museum of Anthropology and Ethnography (Kunstkamera), Russian Academy of Sciences, 3, Universitetskaya nab., St Petersburg 199034, Russian Federation
| | - Elena Pavlova
- Arctic and Antarctic Research Institute, Russian Federal Service for Hydrometeorology and Environmental Monitoring, 38 Bering Street, 199397 St Petersburg, Russia
| | - Lauriane Bourgeon
- Kansas Geological Survey, University of Kansas, 1930 Constant Ave., Lawrence, KS 66047, USA
| | - Richard S. Vachula
- Department of Geosciences, Auburn University, 2050 Beard Eaves Coliseum, Auburn, AL 36849-5305, USA
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17
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Peltola S, Majander K, Makarov N, Dobrovolskaya M, Nordqvist K, Salmela E, Onkamo P. Genetic admixture and language shift in the medieval Volga-Oka interfluve. Curr Biol 2023; 33:174-182.e10. [PMID: 36513080 DOI: 10.1016/j.cub.2022.11.036] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Revised: 09/23/2022] [Accepted: 11/17/2022] [Indexed: 12/14/2022]
Abstract
The Volga-Oka interfluve in northwestern Russia has an intriguing history of population influx and language shift during the Common Era. Today, most inhabitants of the region speak Russian, but until medieval times, northwestern Russia was inhabited by Uralic-speaking peoples.1,2,3 A gradual shift to Slavic languages started in the second half of the first millennium with the expansion of Slavic tribes, which led to the foundation of the Kievan Rus' state in the late 9th century CE. The medieval Rus' was multicultural and multilingual-historical records suggest that its northern regions comprised Slavic and Uralic peoples ruled by Scandinavian settlers.4,5,6 In the 10th-11th centuries, the introduction of Christianity and Cyrillic literature raised the prestige status of Slavic, driving a language shift from Uralic to Slavic.3 This eventually led to the disappearance of the Uralic languages from northwestern Russia. Here, we study a 1,500-year time transect of 30 ancient genomes and stable isotope values from the Suzdal region in the Volga-Oka interfluve. We describe a previously unsampled local Iron Age population and a gradual genetic turnover in the following centuries. Our time transect captures the population shift associated with the spread of Slavic languages and illustrates the ethnically mixed state of medieval Suzdal principality, eventually leading to the formation of the admixed but fully Slavic-speaking population that inhabits the area today. We also observe genetic outliers that highlight the importance of the Suzdal region in medieval times as a hub of long-reaching contacts via trade and warfare.
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Affiliation(s)
- Sanni Peltola
- Faculty of Biological and Environmental Sciences, University of Helsinki, 00014 Helsinki, Finland; Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany.
| | - Kerttu Majander
- Department of Evolutionary Anthropology, University of Vienna, 1030 Vienna, Austria
| | - Nikolaj Makarov
- Institute of Archaeology, Russian Academy of Sciences, 117292 Moscow, Russia
| | - Maria Dobrovolskaya
- Institute of Archaeology, Russian Academy of Sciences, 117292 Moscow, Russia
| | - Kerkko Nordqvist
- Department of Cultures, Archaeology, University of Helsinki, 00014 Helsinki, Finland
| | - Elina Salmela
- Faculty of Biological and Environmental Sciences, University of Helsinki, 00014 Helsinki, Finland; Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany; Department of Biology, University of Turku, 20014 Turku, Finland
| | - Päivi Onkamo
- Department of Biology, University of Turku, 20014 Turku, Finland.
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Fedorova SA, Khusnutdinova EK. Genetic Structure and Genetic History of the Sakha (Yakuts) Population. RUSS J GENET+ 2022. [DOI: 10.1134/s1022795422120031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
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19
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Agdzhoyan AT, Damba LD, Gurianov VM, Zaporozhchenko VV, Balanovsky OP. Phylogenetic Analysis of the South Siberian Q-YP1102 Haplogroup Based on the Data on Y-SNP and Y-STR Markers in Tuvans and Surrounding Populations. RUSS J GENET+ 2021. [DOI: 10.1134/s1022795421120024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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20
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White AE, de-Dios T, Carrión P, Bonora GL, Llovera L, Cilli E, Lizano E, Khabdulina MK, Tleugabulov DT, Olalde I, Marquès-Bonet T, Balloux F, Pettener D, van Dorp L, Luiselli D, Lalueza-Fox C. Genomic Analysis of 18th-Century Kazakh Individuals and Their Oral Microbiome. BIOLOGY 2021; 10:biology10121324. [PMID: 34943238 PMCID: PMC8698332 DOI: 10.3390/biology10121324] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Revised: 12/10/2021] [Accepted: 12/12/2021] [Indexed: 11/16/2022]
Abstract
The Asian Central Steppe, consisting of current-day Kazakhstan and Russia, has acted as a highway for major migrations throughout history. Therefore, describing the genetic composition of past populations in Central Asia holds value to understanding human mobility in this pivotal region. In this study, we analyse paleogenomic data generated from five humans from Kuygenzhar, Kazakhstan. These individuals date to the early to mid-18th century, shortly after the Kazakh Khanate was founded, a union of nomadic tribes of Mongol Golden Horde and Turkic origins. Genomic analysis identifies that these individuals are admixed with varying proportions of East Asian ancestry, indicating a recent admixture event from East Asia. The high amounts of DNA from the anaerobic Gram-negative bacteria Tannerella forsythia, a periodontal pathogen, recovered from their teeth suggest they may have suffered from periodontitis disease. Genomic analysis of this bacterium identified recently evolved virulence and glycosylation genes including the presence of antibiotic resistance genes predating the antibiotic era. This study provides an integrated analysis of individuals with a diet mostly based on meat (mainly horse and lamb), milk, and dairy products and their oral microbiome.
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Affiliation(s)
- Anna E. White
- Institute of Evolutionary Biology, CSIC-Universitat Pompeu Fabra, 08003 Barcelona, Spain; (A.E.W.); (T.d.-D.); (P.C.); (L.L.); (E.L.); (I.O.); (T.M.-B.)
| | - Toni de-Dios
- Institute of Evolutionary Biology, CSIC-Universitat Pompeu Fabra, 08003 Barcelona, Spain; (A.E.W.); (T.d.-D.); (P.C.); (L.L.); (E.L.); (I.O.); (T.M.-B.)
- Estonian Biocentre, Institute of Genomics, University of Tartu, 51010 Tartu, Estonia
| | - Pablo Carrión
- Institute of Evolutionary Biology, CSIC-Universitat Pompeu Fabra, 08003 Barcelona, Spain; (A.E.W.); (T.d.-D.); (P.C.); (L.L.); (E.L.); (I.O.); (T.M.-B.)
| | - Gian Luca Bonora
- ISMEO—International Association for Mediterranean and East Studies, 00186 Rome, Italy;
| | - Laia Llovera
- Institute of Evolutionary Biology, CSIC-Universitat Pompeu Fabra, 08003 Barcelona, Spain; (A.E.W.); (T.d.-D.); (P.C.); (L.L.); (E.L.); (I.O.); (T.M.-B.)
| | - Elisabetta Cilli
- Department of Cultural Heritage, University of Bologna, 48121 Ravenna, Italy;
| | - Esther Lizano
- Institute of Evolutionary Biology, CSIC-Universitat Pompeu Fabra, 08003 Barcelona, Spain; (A.E.W.); (T.d.-D.); (P.C.); (L.L.); (E.L.); (I.O.); (T.M.-B.)
- Institut Català de Paleontologia Miquel Crusafont, Universitat Autònoma de Barcelona, 08193 Cerdanyola del Vallès, Spain
| | - Maral K. Khabdulina
- K.A. Akishev Institute of Archaeology, L.N. Gumilev Eurasian National University, Nur-Sultan 010000, Kazakhstan; (M.K.K.); (D.T.T.)
| | - Daniyar T. Tleugabulov
- K.A. Akishev Institute of Archaeology, L.N. Gumilev Eurasian National University, Nur-Sultan 010000, Kazakhstan; (M.K.K.); (D.T.T.)
| | - Iñigo Olalde
- Institute of Evolutionary Biology, CSIC-Universitat Pompeu Fabra, 08003 Barcelona, Spain; (A.E.W.); (T.d.-D.); (P.C.); (L.L.); (E.L.); (I.O.); (T.M.-B.)
- Centro de Investigación “Lascaray” Ikergunea, BIOMICs Research Group, Universidad del País Vasco, 01006 Vitoria-Gasteiz, Spain
| | - Tomàs Marquès-Bonet
- Institute of Evolutionary Biology, CSIC-Universitat Pompeu Fabra, 08003 Barcelona, Spain; (A.E.W.); (T.d.-D.); (P.C.); (L.L.); (E.L.); (I.O.); (T.M.-B.)
- Institut Català de Paleontologia Miquel Crusafont, Universitat Autònoma de Barcelona, 08193 Cerdanyola del Vallès, Spain
- Catalan Institution of Research and Advanced Studies (ICREA), 08010 Barcelona, Spain
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), 08036 Barcelona, Spain
| | - François Balloux
- UCL Genetics Institute, Department of Genetics Evolution & Environment, University College London, London WC1E 6BT, UK;
| | - Davide Pettener
- Department of Biological, Geological and Environmental Sciences, University of Bologna, 40126 Bologna, Italy;
| | - Lucy van Dorp
- UCL Genetics Institute, Department of Genetics Evolution & Environment, University College London, London WC1E 6BT, UK;
- Correspondence: (L.v.D.); (D.L.); (C.L.-F.); Tel.: +34-617-277-935 (C.L.-F.)
| | - Donata Luiselli
- Department of Cultural Heritage, University of Bologna, 48121 Ravenna, Italy;
- Correspondence: (L.v.D.); (D.L.); (C.L.-F.); Tel.: +34-617-277-935 (C.L.-F.)
| | - Carles Lalueza-Fox
- Institute of Evolutionary Biology, CSIC-Universitat Pompeu Fabra, 08003 Barcelona, Spain; (A.E.W.); (T.d.-D.); (P.C.); (L.L.); (E.L.); (I.O.); (T.M.-B.)
- Correspondence: (L.v.D.); (D.L.); (C.L.-F.); Tel.: +34-617-277-935 (C.L.-F.)
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21
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Ma P, Yang X, Yan S, Li C, Gao S, Han B, Hou K, Robbeets M, Wei LH, Cui Y. Ancient Y-DNA with reconstructed phylogeny provide insights into the demographic history of paternal haplogroup N1a2-F1360. J Genet Genomics 2021; 48:1130-1133. [PMID: 34425243 DOI: 10.1016/j.jgg.2021.07.018] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2021] [Revised: 07/26/2021] [Accepted: 07/27/2021] [Indexed: 11/29/2022]
Affiliation(s)
- Pengcheng Ma
- School of Life Sciences, Jilin University, Changchun 130012, China
| | - Xuan Yang
- School of Life Sciences, Jilin University, Changchun 130012, China
| | - Shi Yan
- School of Ethnology and Sociology, Minzu University of China, Beijing 100081, China
| | - Chunxiang Li
- School of Life Sciences, Jilin University, Changchun 130012, China
| | - Shizhu Gao
- College of Pharmacia Sciences, Jilin University, Changchun 130021, China
| | - Binghua Han
- Shanxi Provincial Institute of Archaeology, Taiyuan 030001, China
| | - Kan Hou
- School of History and Culture, Shanxi University, Taiyuan 030006, China
| | - Martine Robbeets
- Max Planck Institute for the Science of Human History, Jena 07745, Germany
| | - Lan-Hai Wei
- Department of Anthropology and Ethnology, Institute of Anthropology, Xiamen University, Xiamen 361005, China; B&R International Joint Laboratory for Eurasian Anthropology, Fudan University, Shanghai 200438, China.
| | - Yinqiu Cui
- School of Life Sciences, Jilin University, Changchun 130012, China; Research Center for Chinese Frontier Archaeology of Jilin University, Jilin University, Changchun 130012, China.
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22
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Chen J, He G, Ren Z, Wang Q, Liu Y, Zhang H, Yang M, Zhang H, Ji J, Zhao J, Guo J, Zhu K, Yang X, Wang R, Ma H, Wang CC, Huang J. Genomic Insights Into the Admixture History of Mongolic- and Tungusic-Speaking Populations From Southwestern East Asia. Front Genet 2021; 12:685285. [PMID: 34239544 PMCID: PMC8258170 DOI: 10.3389/fgene.2021.685285] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2021] [Accepted: 05/05/2021] [Indexed: 12/17/2022] Open
Abstract
As a major part of the modern Trans-Eurasian or Altaic language family, most of the Mongolic and Tungusic languages were mainly spoken in northern China, Mongolia, and southern Siberia, but some were also found in southern China. Previous genetic surveys only focused on the dissection of genetic structure of northern Altaic-speaking populations; however, the ancestral origin and genomic diversification of Mongolic and Tungusic-speaking populations from southwestern East Asia remain poorly understood because of the paucity of high-density sampling and genome-wide data. Here, we generated genome-wide data at nearly 700,000 single-nucleotide polymorphisms (SNPs) in 26 Mongolians and 55 Manchus collected from Guizhou province in southwestern China. We applied principal component analysis (PCA), ADMIXTURE, f statistics, qpWave/qpAdm analysis, qpGraph, TreeMix, Fst, and ALDER to infer the fine-scale population genetic structure and admixture history. We found significant genetic differentiation between northern and southern Mongolic and Tungusic speakers, as one specific genetic cline of Manchu and Mongolian was identified in Guizhou province. Further results from ADMIXTURE and f statistics showed that the studied Guizhou Mongolians and Manchus had a strong genetic affinity with southern East Asians, especially for inland southern East Asians. The qpAdm-based estimates of ancestry admixture proportion demonstrated that Guizhou Mongolians and Manchus people could be modeled as the admixtures of one northern ancestry related to northern Tungusic/Mongolic speakers or Yellow River farmers and one southern ancestry associated with Austronesian, Tai-Kadai, and Austroasiatic speakers. The qpGraph-based phylogeny and neighbor-joining tree further confirmed that Guizhou Manchus and Mongolians derived approximately half of the ancestry from their northern ancestors and the other half from southern Indigenous East Asians. The estimated admixture time ranged from 600 to 1,000 years ago, which further confirmed the admixture events were mediated via the Mongolians Empire expansion during the formation of the Yuan dynasty.
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Affiliation(s)
- Jing Chen
- Department of Forensic Medicine, Guizhou Medical University, Guiyang, China
| | - Guanglin He
- State Key Laboratory of Cellular Stress Biology, State Key Laboratory of Marine Environmental Science, Department of Anthropology and Ethnology, Institute of Anthropology, National Institute for Data Science in Health and Medicine, Xiamen University, Xiamen, China
| | - Zheng Ren
- Department of Forensic Medicine, Guizhou Medical University, Guiyang, China
| | - Qiyan Wang
- Department of Forensic Medicine, Guizhou Medical University, Guiyang, China
| | - Yubo Liu
- Department of Forensic Medicine, Guizhou Medical University, Guiyang, China
| | - Hongling Zhang
- Department of Forensic Medicine, Guizhou Medical University, Guiyang, China
| | - Meiqing Yang
- Department of Forensic Medicine, Guizhou Medical University, Guiyang, China
| | - Han Zhang
- Department of Forensic Medicine, Guizhou Medical University, Guiyang, China
| | - Jingyan Ji
- Department of Forensic Medicine, Guizhou Medical University, Guiyang, China
| | - Jing Zhao
- State Key Laboratory of Cellular Stress Biology, State Key Laboratory of Marine Environmental Science, Department of Anthropology and Ethnology, Institute of Anthropology, National Institute for Data Science in Health and Medicine, Xiamen University, Xiamen, China
| | - Jianxin Guo
- State Key Laboratory of Cellular Stress Biology, State Key Laboratory of Marine Environmental Science, Department of Anthropology and Ethnology, Institute of Anthropology, National Institute for Data Science in Health and Medicine, Xiamen University, Xiamen, China
| | - Kongyang Zhu
- State Key Laboratory of Cellular Stress Biology, State Key Laboratory of Marine Environmental Science, Department of Anthropology and Ethnology, Institute of Anthropology, National Institute for Data Science in Health and Medicine, Xiamen University, Xiamen, China
| | - Xiaomin Yang
- State Key Laboratory of Cellular Stress Biology, State Key Laboratory of Marine Environmental Science, Department of Anthropology and Ethnology, Institute of Anthropology, National Institute for Data Science in Health and Medicine, Xiamen University, Xiamen, China
| | - Rui Wang
- State Key Laboratory of Cellular Stress Biology, State Key Laboratory of Marine Environmental Science, Department of Anthropology and Ethnology, Institute of Anthropology, National Institute for Data Science in Health and Medicine, Xiamen University, Xiamen, China
| | - Hao Ma
- State Key Laboratory of Cellular Stress Biology, State Key Laboratory of Marine Environmental Science, Department of Anthropology and Ethnology, Institute of Anthropology, National Institute for Data Science in Health and Medicine, Xiamen University, Xiamen, China
| | - Chuan-Chao Wang
- State Key Laboratory of Cellular Stress Biology, State Key Laboratory of Marine Environmental Science, Department of Anthropology and Ethnology, Institute of Anthropology, National Institute for Data Science in Health and Medicine, Xiamen University, Xiamen, China
- School of Basic Medical Sciences, Zhejiang University School of Medicine, Hangzhou, China
| | - Jiang Huang
- Department of Forensic Medicine, Guizhou Medical University, Guiyang, China
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23
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The deep population history of northern East Asia from the Late Pleistocene to the Holocene. Cell 2021; 184:3256-3266.e13. [PMID: 34048699 DOI: 10.1016/j.cell.2021.04.040] [Citation(s) in RCA: 46] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Revised: 01/20/2021] [Accepted: 04/23/2021] [Indexed: 11/22/2022]
Abstract
Northern East Asia was inhabited by modern humans as early as 40 thousand years ago (ka), as demonstrated by the Tianyuan individual. Using genome-wide data obtained from 25 individuals dated to 33.6-3.4 ka from the Amur region, we show that Tianyuan-related ancestry was widespread in northern East Asia before the Last Glacial Maximum (LGM). At the close of the LGM stadial, the earliest northern East Asian appeared in the Amur region, and this population is basal to ancient northern East Asians. Human populations in the Amur region have maintained genetic continuity from 14 ka, and these early inhabitants represent the closest East Asian source known for Ancient Paleo-Siberians. We also observed that EDAR V370A was likely to have been elevated to high frequency after the LGM, suggesting the possible timing for its selection. This study provides a deep look into the population dynamics of northern East Asia.
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