Author
Nurbol Baimukhanov
Bio: Nurbol Baimukhanov is an academic researcher. The author has contributed to research in topics: Population & Bronze Age. The author has an hindex of 5, co-authored 6 publications receiving 759 citations.
Topics: Population, Bronze Age, Domestication, Steppe, Ancient DNA
Papers
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University of Copenhagen1, Paris Diderot University2, Technical University of Denmark3, Leiden University4, University of Cambridge5, Stanford University6, Karagandy State University7, University of Oslo8, Russian Academy of Sciences9, National Academy of Sciences10, Irkutsk State University11, Mongolian State University of Agriculture12, National University of Mongolia13, Tuvan State University14, Radcliffe Institute for Advanced Study15, Hashemite University16, Children's Hospital of Philadelphia17, Russian-Armenian (Slavonic) University18, Armenian National Academy of Sciences19, University of Arizona20, Slovak Academy of Sciences21, First Faculty of Medicine, Charles University in Prague22, University of Gothenburg23, Arizona State University24, University of Alberta25, Paul Sabatier University26, University of California, Berkeley27, Wellcome Trust Sanger Institute28
TL;DR: The genomes of 137 ancient and 502 modern human genomes illuminate the population history of the Eurasian steppes after the Bronze Age and document the replacement of Indo-European speakers of West Eurasian ancestry by Turkic-speaking groups of East Asian ancestry.
Abstract: For thousands of years the Eurasian steppes have been a centre of human migrations and cultural change. Here we sequence the genomes of 137 ancient humans (about 1× average coverage), covering a period of 4,000 years, to understand the population history of the Eurasian steppes after the Bronze Age migrations. We find that the genetics of the Scythian groups that dominated the Eurasian steppes throughout the Iron Age were highly structured, with diverse origins comprising Late Bronze Age herders, European farmers and southern Siberian hunter-gatherers. Later, Scythians admixed with the eastern steppe nomads who formed the Xiongnu confederations, and moved westward in about the second or third century bc, forming the Hun traditions in the fourth–fifth century ad, and carrying with them plague that was basal to the Justinian plague. These nomads were further admixed with East Asian groups during several short-term khanates in the Medieval period. These historical events transformed the Eurasian steppes from being inhabited by Indo-European speakers of largely West Eurasian ancestry to the mostly Turkic-speaking groups of the present day, who are primarily of East Asian ancestry. Sequences of 137 ancient and 502 modern human genomes illuminate the population history of the Eurasian steppes after the Bronze Age and document the replacement of Indo-European speakers of West Eurasian ancestry by Turkic-speaking groups of East Asian ancestry.
280 citations
University of Copenhagen1, Wellcome Trust Sanger Institute2, University of Cambridge3, Leiden University4, Harvard University5, Technical University of Denmark6, Al-Farabi University7, University of Chicago8, Karagandy State University9, University of Alaska Fairbanks10, Istanbul University11, Hazara University12, University of Gothenburg13, Russian Academy of Sciences14, Gazi University15, Islamia College University16, University of Exeter17, Government of Khyber Pakhtunkhwa18, Irkutsk State University19, University of Alberta20, Paul Sabatier University21, University of California, Berkeley22
TL;DR: Analysis of ancient whole-genome sequences from across Inner Asia and Anatolia shows that the Botai people associated with the earliest horse husbandry derived from a hunter-gatherer population deeply diverged from the Yamnaya, and suggests distinct migrations bringing West Eurasian ancestry into South Asia before and after, but not at the time of, YamNaya culture.
Abstract: The Yamnaya expansions from the western steppe into Europe and Asia during the Early Bronze Age (~3000 BCE) are believed to have brought with them Indo-European languages and possibly horse husbandry. We analyze 74 ancient whole-genome sequences from across Inner Asia and Anatolia and show that the Botai people associated with the earliest horse husbandry derived from a hunter-gatherer population deeply diverged from the Yamnaya. Our results also suggest distinct migrations bringing West Eurasian ancestry into South Asia before and after but not at the time of Yamnaya culture. We find no evidence of steppe ancestry in Bronze Age Anatolia from when Indo-European languages are attested there. Thus, in contrast to Europe, Early Bronze Age Yamnaya-related migrations had limited direct genetic impact in Asia.
273 citations
University of Copenhagen1, Russian Academy of Sciences2, Swiss Institute of Bioinformatics3, University of Bern4, University of Lisbon5, Technical University of Denmark6, University of Chicago7, Chinese Academy of Sciences8, Leiden University9, Arctic and Antarctic Research Institute10, University of Cambridge11, University of Greenland12, American Museum of Natural History13, National Institutes of Health14, University of Helsinki15, University of Illinois at Urbana–Champaign16, University of Gothenburg17, University of Turku18, Wellcome Trust Sanger Institute19, University of California, Berkeley20, Southern Methodist University21
TL;DR: Analysis of 34 newly recovered ancient genomes from northeastern Siberia reveal at least three major migration events in the late Pleistocene population history of the region, including an initial peopling by a previously unknown Palaeolithic population of ‘Ancient North Siberians’ and a Holocene migration of other East Asian-related peoples, which generated the mosaic genetic make-up of contemporary peoples.
Abstract: Northeastern Siberia has been inhabited by humans for more than 40,000 years but its deep population history remains poorly understood. Here we investigate the late Pleistocene population history of northeastern Siberia through analyses of 34 newly recovered ancient genomes that date to between 31,000 and 600 years ago. We document complex population dynamics during this period, including at least three major migration events: an initial peopling by a previously unknown Palaeolithic population of ‘Ancient North Siberians’ who are distantly related to early West Eurasian hunter-gatherers; the arrival of East Asian-related peoples, which gave rise to ‘Ancient Palaeo-Siberians’ who are closely related to contemporary communities from far-northeastern Siberia (such as the Koryaks), as well as Native Americans; and a Holocene migration of other East Asian-related peoples, who we name ‘Neo-Siberians’, and from whom many contemporary Siberians are descended. Each of these population expansions largely replaced the earlier inhabitants, and ultimately generated the mosaic genetic make-up of contemporary peoples who inhabit a vast area across northern Eurasia and the Americas. Analyses of 34 ancient genomes from northeastern Siberia, dating to between 31,000 and 600 years ago, reveal at least three major migration events in the late Pleistocene population history of the region.
211 citations
American Museum of Natural History1, Paul Sabatier University2, University of Copenhagen3, Abdul Wali Khan University Mardan4, University of Cambridge5, University of Exeter6, University of Veterinary Medicine Vienna7, Centre national de la recherche scientifique8, Max Planck Society9, University of Tehran10, Tarbiat Modares University11, King Saud University12, Deutsches Archäologisches Institut13, University of Kansas14, Hartwick College15, Ludwig Maximilian University of Munich16, Russian Academy of Sciences17, University of Potsdam18, Tallinn University19, Istanbul University20, National University of Mongolia21, Leibniz Association22, Al-Farabi University23, Wellcome Trust24
TL;DR: Data indicate that Przewalski’s horses are the feral descendants of horses herded at Botai and not truly wild horses, which indicates that a massive genomic turnover underpins the expansion of the horse stock that gave rise to modern domesticates, which coincides with large-scale human population expansions during the Early Bronze Age.
Abstract: The Eneolithic Botai culture of the Central Asian steppes provides the earliest archaeological evidence for horse husbandry, ~5500 years ago, but the exact nature of early horse domestication remains controversial. We generated 42 ancient-horse genomes, including 20 from Botai. Compared to 46 published ancient- and modern-horse genomes, our data indicate that Przewalski's horses are the feral descendants of horses herded at Botai and not truly wild horses. All domestic horses dated from ~4000 years ago to present only show ~2.7% of Botai-related ancestry. This indicates that a massive genomic turnover underpins the expansion of the horse stock that gave rise to modern domesticates, which coincides with large-scale human population expansions during the Early Bronze Age.
209 citations
University of Copenhagen1, Paul Sabatier University2, Abdul Wali Khan University Mardan3, University of Cambridge4, Stanford University5, King Saud University6, University of Barcelona7, Hartwick College8, McDonald Institute for Archaeological Research9, Deutsches Archäologisches Institut10, Autonomous University of Madrid11, University of Oslo12, National University of Mongolia13, University of Vienna14, University of Mainz15, Tarbiat Modares University16, Spanish National Research Council17, University of Lisbon18, Ludwig Maximilian University of Munich19, University of Tehran20, Facultad de Filosofía y Letras21, Pablo de Olavide University22, Royal Belgian Institute of Natural Sciences23, Agricultural University of Iceland24, University of Potsdam25, Russian Academy of Sciences26, University of Gothenburg27, Pompeu Fabra University28, Samara State University29, Tallinn University30, Humboldt University of Berlin31, Leibniz Association32, ISCTE – University Institute of Lisbon33, University of Oxford34, Centre national de la recherche scientifique35, Istanbul University36, Tbilisi State University37, University of Bordeaux38, Indian Council of Agricultural Research39, University of Edinburgh40, Martin Luther University of Halle-Wittenberg41, University of California, Santa Cruz42, University of Kashan43, University of California, Irvine44, University of Nottingham45, University of Exeter46, Max Planck Society47, University of Zagreb48, Karagandy State University49, University of Southampton50, Al-Farabi University51, deCODE genetics52, Université Paris-Saclay53
TL;DR: This extensive dataset allows us to assess the modern legacy of past equestrian civilizations and finds that two extinct horse lineages existed during early domestication, and the development of modern breeding impacted genetic diversity more dramatically than the previous millennia of human management.
174 citations
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TL;DR: An overview on how EnteroBase works, what it can do, and its future prospects is provided.
Abstract: EnteroBase is an integrated software environment that supports the identification of global population structures within several bacterial genera that include pathogens. Here, we provide an overview of how EnteroBase works, what it can do, and its future prospects. EnteroBase has currently assembled more than 300,000 genomes from Illumina short reads from Salmonella, Escherichia, Yersinia, Clostridioides, Helicobacter, Vibrio, and Moraxella and genotyped those assemblies by core genome multilocus sequence typing (cgMLST). Hierarchical clustering of cgMLST sequence types allows mapping a new bacterial strain to predefined population structures at multiple levels of resolution within a few hours after uploading its short reads. Case Study 1 illustrates this process for local transmissions of Salmonella enterica serovar Agama between neighboring social groups of badgers and humans. EnteroBase also supports single nucleotide polymorphism (SNP) calls from both genomic assemblies and after extraction from metagenomic sequences, as illustrated by Case Study 2 which summarizes the microevolution of Yersinia pestis over the last 5000 years of pandemic plague. EnteroBase can also provide a global overview of the genomic diversity within an entire genus, as illustrated by Case Study 3, which presents a novel, global overview of the population structure of all of the species, subspecies, and clades within Escherichia.
469 citations
Harvard University1, Broad Institute2, University of Tübingen3, Max Planck Society4, University of Mainz5, University of Washington6, University of California, Berkeley7, Massachusetts Institute of Technology8, Stockholm University9, University of Adelaide10, The Heritage Foundation11, National Museum of Natural History12, Sultan Qaboos University13, University of Edinburgh14, University of Costa Rica15, University of Antioquia16, Rambam Health Care Campus17, University of Pécs18, Al Akhawayn University19, Catholic University of the Sacred Heart20, University of Oxford21, Belgorod State University22, University of Toronto23, University of Buenos Aires24, University of Bern25, Russian Academy of Sciences26, Paul Sabatier University27, North-Eastern Federal University28, University of Chicago29, University of Arizona30, Stony Brook University31, University of Bergen32, Illumina33, Sofia Medical University34, Bashkir State University35, University of Cambridge36, Vilnius University37, Estonian Biocentre38, University of Strasbourg39, Amgen40, University College London41, Gladstone Institutes42, University of Tartu43, University of Oulu44, Muhimbili University of Health and Allied Sciences45, University of Palermo46, University of Chile47, University of Tarapacá48, Academy of Sciences of Uzbekistan49, Armenian National Academy of Sciences50, University of North Texas51, University of Santiago de Compostela52, University of Kharkiv53, Higher University of San Andrés54, Novosibirsk State University55, Leidos56, Lebanese American University57, University of Split58, University of Pennsylvania59, Banaras Hindu University60, Centre for Cellular and Molecular Biology61, Estonian Academy of Sciences62, Pompeu Fabra University63, Howard Hughes Medical Institute64
TL;DR: The authors showed that most present-day Europeans derive from at least three highly differentiated populations: west European hunter-gatherers, ancient north Eurasians related to Upper Palaeolithic Siberians, who contributed to both Europeans and Near Easterners; and early European farmers, who were mainly of Near Eastern origin but also harboured west European hunters-gatherer related ancestry.
Abstract: We sequenced the genomes of a ∼7,000-year-old farmer from Germany and eight ∼8,000-year-old hunter-gatherers from Luxembourg and Sweden. We analysed these and other ancient genomes with 2,345 contemporary humans to show that most present-day Europeans derive from at least three highly differentiated populations: west European hunter-gatherers, who contributed ancestry to all Europeans but not to Near Easterners; ancient north Eurasians related to Upper Palaeolithic Siberians, who contributed to both Europeans and Near Easterners; and early European farmers, who were mainly of Near Eastern origin but also harboured west European hunter-gatherer related ancestry. We model these populations' deep relationships and show that early European farmers had ∼44% ancestry from a 'basal Eurasian' population that split before the diversification of other non-African lineages.
442 citations
Harvard University1, Broad Institute2, Radcliffe Institute for Advanced Study3, University of California, Berkeley4, Howard Hughes Medical Institute5, Massachusetts Institute of Technology6, Sapienza University of Rome7, University of Padua8, Queen's University Belfast9, Russian Academy of Sciences10, Al-Farabi University11, University of Pennsylvania12, University College Dublin13, University of Vienna14, Pennsylvania State University15, Max Planck Society16, Birbal Sahni Institute of Palaeobotany17, Centre for Cellular and Molecular Biology18, Emory University19, Centre national de la recherche scientifique20, Kyrgyz National University21, Altai State University22, Academy of Sciences of the Czech Republic23, University of Oxford24, South Ural State University25, Kemerovo State University26, University College London27, Northwest University (China)28, University of Pittsburgh29, Samara State University30, Chelyabinsk State University31, University of Bologna32, Academy of Sciences of Uzbekistan33, University of Winnipeg34, Simon Fraser University35, National Museum of Natural History36, Tomsk State University37, Naturhistorisches Museum38, Národní muzeum39, Hazara University40, Deccan College Post-Graduate and Research Institute41, Pompeu Fabra University42, Hartwick College43, University of California, Santa Barbara44, Washington University in St. Louis45
TL;DR: It is shown that Steppe ancestry then integrated further south in the first half of the second millennium BCE, contributing up to 30% of the ancestry of modern groups in South Asia, supporting the idea that the archaeologically documented dispersal of domesticates was accompanied by the spread of people from multiple centers of domestication.
Abstract: By sequencing 523 ancient humans, we show that the primary source of ancestry in modern South Asians is a prehistoric genetic gradient between people related to early hunter-gatherers of Iran and Southeast Asia. After the Indus Valley Civilization's decline, its people mixed with individuals in the southeast to form one of the two main ancestral populations of South Asia, whose direct descendants live in southern India. Simultaneously, they mixed with descendants of Steppe pastoralists who, starting around 4000 years ago, spread via Central Asia to form the other main ancestral population. The Steppe ancestry in South Asia has the same profile as that in Bronze Age Eastern Europe, tracking a movement of people that affected both regions and that likely spread the distinctive features shared between Indo-Iranian and Balto-Slavic languages.
354 citations
University of Copenhagen1, University of Cambridge2, Wellcome Trust Sanger Institute3, Leiden University4, Harvard University5, Technical University of Denmark6, Al-Farabi University7, University of Chicago8, Karagandy State University9, University of Alaska Fairbanks10, Istanbul University11, Hazara University12, University of Gothenburg13, Russian Academy of Sciences14, Gazi University15, Islamia College University16, University of Exeter17, Government of Khyber Pakhtunkhwa18, Irkutsk State University19, University of Alberta20, Paul Sabatier University21, University of California, Berkeley22
TL;DR: Analysis of ancient whole-genome sequences from across Inner Asia and Anatolia shows that the Botai people associated with the earliest horse husbandry derived from a hunter-gatherer population deeply diverged from the Yamnaya, and suggests distinct migrations bringing West Eurasian ancestry into South Asia before and after, but not at the time of, YamNaya culture.
Abstract: The Yamnaya expansions from the western steppe into Europe and Asia during the Early Bronze Age (~3000 BCE) are believed to have brought with them Indo-European languages and possibly horse husbandry. We analyze 74 ancient whole-genome sequences from across Inner Asia and Anatolia and show that the Botai people associated with the earliest horse husbandry derived from a hunter-gatherer population deeply diverged from the Yamnaya. Our results also suggest distinct migrations bringing West Eurasian ancestry into South Asia before and after but not at the time of Yamnaya culture. We find no evidence of steppe ancestry in Bronze Age Anatolia from when Indo-European languages are attested there. Thus, in contrast to Europe, Early Bronze Age Yamnaya-related migrations had limited direct genetic impact in Asia.
273 citations