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Andrey Epimakhov

Bio: Andrey Epimakhov is an academic researcher from South Ural State University. The author has contributed to research in topics: Bronze Age & Population. The author has an hindex of 10, co-authored 14 publications receiving 1699 citations. Previous affiliations of Andrey Epimakhov include Russian Academy of Sciences & Ural State University.

Papers
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Journal ArticleDOI
11 Jun 2015-Nature
TL;DR: It is shown that the Bronze Age was a highly dynamic period involving large-scale population migrations and replacements, responsible for shaping major parts of present-day demographic structure in both Europe and Asia.
Abstract: The Bronze Age of Eurasia (around 3000-1000 BC) was a period of major cultural changes. However, there is debate about whether these changes resulted from the circulation of ideas or from human migrations, potentially also facilitating the spread of languages and certain phenotypic traits. We investigated this by using new, improved methods to sequence low-coverage genomes from 101 ancient humans from across Eurasia. We show that the Bronze Age was a highly dynamic period involving large-scale population migrations and replacements, responsible for shaping major parts of present-day demographic structure in both Europe and Asia. Our findings are consistent with the hypothesized spread of Indo-European languages during the Early Bronze Age. We also demonstrate that light skin pigmentation in Europeans was already present at high frequency in the Bronze Age, but not lactose tolerance, indicating a more recent onset of positive selection on lactose tolerance than previously thought.

1,088 citations

Journal ArticleDOI
Vagheesh M. Narasimhan1, Nick Patterson2, Nick Patterson3, Priya Moorjani4, Nadin Rohland1, Nadin Rohland2, Rebecca Bernardos1, Swapan Mallick5, Swapan Mallick1, Swapan Mallick2, Iosif Lazaridis1, Nathan Nakatsuka6, Nathan Nakatsuka1, Iñigo Olalde1, Mark Lipson1, Alexander M. Kim1, Luca M. Olivieri, Alfredo Coppa7, Massimo Vidale8, James Mallory9, Vyacheslav Moiseyev10, Egor Kitov10, Egor Kitov11, Janet Monge12, Nicole Adamski1, Nicole Adamski5, Neel Alex4, Nasreen Broomandkhoshbacht1, Nasreen Broomandkhoshbacht5, Francesca Candilio13, Kimberly Callan5, Kimberly Callan1, Olivia Cheronet13, Olivia Cheronet14, Brendan J. Culleton15, Matthew Ferry5, Matthew Ferry1, Daniel Fernandes, Suzanne Freilich14, Beatriz Gamarra13, Daniel Gaudio13, Mateja Hajdinjak16, Eadaoin Harney1, Eadaoin Harney5, Thomas K. Harper15, Denise Keating13, Ann Marie Lawson5, Ann Marie Lawson1, Matthew Mah5, Matthew Mah2, Matthew Mah1, Kirsten Mandl14, Megan Michel5, Megan Michel1, Mario Novak13, Jonas Oppenheimer5, Jonas Oppenheimer1, Niraj Rai17, Niraj Rai18, Kendra Sirak19, Kendra Sirak1, Kendra Sirak13, Viviane Slon16, Kristin Stewardson1, Kristin Stewardson5, Fatma Zalzala1, Fatma Zalzala5, Zhao Zhang1, Gaziz Akhatov, Anatoly N. Bagashev, Alessandra Bagnera, Bauryzhan Baitanayev, Julio Bendezu-Sarmiento20, Arman A. Bissembaev, Gian Luca Bonora, T Chargynov21, T. A. Chikisheva10, Petr K. Dashkovskiy22, Anatoly P. Derevianko10, Miroslav Dobeš23, Katerina Douka24, Katerina Douka16, Nadezhda Dubova10, Meiram N. Duisengali, Dmitry Enshin, Andrey Epimakhov25, Alexey Fribus26, Dorian Q. Fuller27, Dorian Q. Fuller28, Alexander Goryachev, Andrey Gromov10, S. P. Grushin22, Bryan Hanks29, Margaret A. Judd29, Erlan Kazizov, Aleksander Khokhlov30, Aleksander P. Krygin, Elena Kupriyanova31, Pavel Kuznetsov30, Donata Luiselli32, Farhod Maksudov33, Aslan M. Mamedov, Talgat B. Mamirov, Christopher Meiklejohn34, Deborah C. Merrett35, Roberto Micheli, Oleg Mochalov30, Samariddin Mustafokulov33, Ayushi Nayak16, Davide Pettener32, Richard Potts36, Dmitry Razhev, Marina Petrovna Rykun37, Stefania Sarno32, Tatyana M. Savenkova, Kulyan Sikhymbaeva, Sergey Mikhailovich Slepchenko, Oroz A. Soltobaev21, Nadezhda Stepanova10, Svetlana V. Svyatko10, Svetlana V. Svyatko9, Kubatbek Tabaldiev, Maria Teschler-Nicola38, Maria Teschler-Nicola14, Alexey A. Tishkin22, Vitaly V. Tkachev, Sergey Vasilyev10, Petr Velemínský39, Dmitriy Voyakin, Antonina Yermolayeva, Muhammad Zahir16, Muhammad Zahir40, Valery S. Zubkov, A. V. Zubova10, Vasant Shinde41, Carles Lalueza-Fox42, Matthias Meyer16, David W. Anthony43, Nicole Boivin16, Kumarasamy Thangaraj17, Douglas J. Kennett44, Douglas J. Kennett15, Michael D. Frachetti45, Ron Pinhasi13, Ron Pinhasi14, David Reich 
06 Sep 2019-Science
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

Journal ArticleDOI
09 May 2018-Nature
TL;DR: Phylogenies reconstructed using 12 hepatitis B virus genomes, which were recovered from ancient human genome data, reveal a complex history of hepatitis B evolution that is not evident when using only modern samples.
Abstract: Hepatitis B virus (HBV) is a major cause of human hepatitis. There is considerable uncertainty about the timescale of its evolution and its association with humans. Here we present 12 full or partial ancient HBV genomes that are between approximately 0.8 and 4.5 thousand years old. The ancient sequences group either within or in a sister relationship with extant human or other ape HBV clades. Generally, the genome properties follow those of modern HBV. The root of the HBV tree is projected to between 8.6 and 20.9 thousand years ago, and we estimate a substitution rate of 8.04 × 10−6–1.51 × 10−5 nucleotide substitutions per site per year. In several cases, the geographical locations of the ancient genotypes do not match present-day distributions. Genotypes that today are typical of Africa and Asia, and a subgenotype from India, are shown to have an early Eurasian presence. The geographical and temporal patterns that we observe in ancient and modern HBV genotypes are compatible with well-documented human migrations during the Bronze and Iron Ages1,2. We provide evidence for the creation of HBV genotype A via recombination, and for a long-term association of modern HBV genotypes with humans, including the discovery of a human genotype that is now extinct. These data expose a complexity of HBV evolution that is not evident when considering modern sequences alone. Phylogenies reconstructed using 12 hepatitis B virus genomes, which were recovered from ancient human genome data, reveal a complex history of hepatitis B evolution that is not evident when using only modern samples.

148 citations

Journal ArticleDOI
Pablo Librado1, Naveed Khan1, Naveed Khan2, Antoine Fages1  +175 moreInstitutions (72)
01 Jan 2021-Nature
TL;DR: In this article, the authors identify the Western Eurasian steppes, especially the lower Volga-Don region, as the homeland of modern domestic horses and map the population changes accompanying domestication from 273 ancient horse genomes.
Abstract: Domestication of horses fundamentally transformed long-range mobility and warfare1. However, modern domesticated breeds do not descend from the earliest domestic horse lineage associated with archaeological evidence of bridling, milking and corralling2–4 at Botai, Central Asia around 3500 bc3. Other longstanding candidate regions for horse domestication, such as Iberia5 and Anatolia6, have also recently been challenged. Thus, the genetic, geographic and temporal origins of modern domestic horses have remained unknown. Here we pinpoint the Western Eurasian steppes, especially the lower Volga-Don region, as the homeland of modern domestic horses. Furthermore, we map the population changes accompanying domestication from 273 ancient horse genomes. This reveals that modern domestic horses ultimately replaced almost all other local populations as they expanded rapidly across Eurasia from about 2000 bc, synchronously with equestrian material culture, including Sintashta spoke-wheeled chariots. We find that equestrianism involved strong selection for critical locomotor and behavioural adaptations at the GSDMC and ZFPM1 genes. Our results reject the commonly held association7 between horseback riding and the massive expansion of Yamnaya steppe pastoralists into Europe around 3000 bc8,9 driving the spread of Indo-European languages10. This contrasts with the scenario in Asia where Indo-Iranian languages, chariots and horses spread together, following the early second millennium bc Sintashta culture11,12. Analysis of 273 ancient horse genomes reveals that modern domestic horses originated in the Western Eurasian steppes, especially the lower Volga-Don region.

83 citations


Cited by
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01 Jun 2012
TL;DR: SPAdes as mentioned in this paper is a new assembler for both single-cell and standard (multicell) assembly, and demonstrate that it improves on the recently released E+V-SC assembler and on popular assemblers Velvet and SoapDeNovo (for multicell data).
Abstract: The lion's share of bacteria in various environments cannot be cloned in the laboratory and thus cannot be sequenced using existing technologies. A major goal of single-cell genomics is to complement gene-centric metagenomic data with whole-genome assemblies of uncultivated organisms. Assembly of single-cell data is challenging because of highly non-uniform read coverage as well as elevated levels of sequencing errors and chimeric reads. We describe SPAdes, a new assembler for both single-cell and standard (multicell) assembly, and demonstrate that it improves on the recently released E+V-SC assembler (specialized for single-cell data) and on popular assemblers Velvet and SoapDeNovo (for multicell data). SPAdes generates single-cell assemblies, providing information about genomes of uncultivatable bacteria that vastly exceeds what may be obtained via traditional metagenomics studies. SPAdes is available online ( http://bioinf.spbau.ru/spades ). It is distributed as open source software.

10,124 citations

Journal ArticleDOI
TL;DR: Some of the key events in the peopling of the world in the light of the findings of work on ancient DNA are reviewed.
Abstract: Ancient DNA research is revealing a human history far more complex than that inferred from parsimonious models based on modern DNA. Here, we review some of the key events in the peopling of the world in the light of the findings of work on ancient DNA.

1,365 citations

Journal ArticleDOI
11 Jun 2015-Nature
TL;DR: It is shown that the Bronze Age was a highly dynamic period involving large-scale population migrations and replacements, responsible for shaping major parts of present-day demographic structure in both Europe and Asia.
Abstract: The Bronze Age of Eurasia (around 3000-1000 BC) was a period of major cultural changes. However, there is debate about whether these changes resulted from the circulation of ideas or from human migrations, potentially also facilitating the spread of languages and certain phenotypic traits. We investigated this by using new, improved methods to sequence low-coverage genomes from 101 ancient humans from across Eurasia. We show that the Bronze Age was a highly dynamic period involving large-scale population migrations and replacements, responsible for shaping major parts of present-day demographic structure in both Europe and Asia. Our findings are consistent with the hypothesized spread of Indo-European languages during the Early Bronze Age. We also demonstrate that light skin pigmentation in Europeans was already present at high frequency in the Bronze Age, but not lactose tolerance, indicating a more recent onset of positive selection on lactose tolerance than previously thought.

1,088 citations

Journal ArticleDOI
24 Dec 2015-Nature
TL;DR: A genome-wide scan for selection using ancient DNA is reported, capitalizing on the largest ancient DNA data set yet assembled: 230 West Eurasians who lived between 6500 and 300 bc, including 163 with newly reported data.
Abstract: Ancient DNA makes it possible to observe natural selection directly by analysing samples from populations before, during and after adaptation events. Here we report a genome-wide scan for selection using ancient DNA, capitalizing on the largest ancient DNA data set yet assembled: 230 West Eurasians who lived between 6500 and 300 bc, including 163 with newly reported data. The new samples include, to our knowledge, the first genome-wide ancient DNA from Anatolian Neolithic farmers, whose genetic material we obtained by extracting from petrous bones, and who we show were members of the population that was the source of Europe's first farmers. We also report a transect of the steppe region in Samara between 5600 and 300 bc, which allows us to identify admixture into the steppe from at least two external sources. We detect selection at loci associated with diet, pigmentation and immunity, and two independent episodes of selection on height.

1,083 citations

Journal ArticleDOI
25 Aug 2016-Nature
TL;DR: This paper reported genome-wide ancient DNA from 44 ancient Near Easterners ranging in time between ~12,000 and 1,400 bc, from Natufian hunter-gatherers to Bronze Age farmers, showing that the earliest populations of the Near East derived around half their ancestry from a 'Basal Eurasian' lineage that had little if any Neanderthal admixture and that separated from other non-African lineages before their separation from each other.
Abstract: We report genome-wide ancient DNA from 44 ancient Near Easterners ranging in time between ~12,000 and 1,400 bc, from Natufian hunter–gatherers to Bronze Age farmers. We show that the earliest populations of the Near East derived around half their ancestry from a ‘Basal Eurasian’ lineage that had little if any Neanderthal admixture and that separated from other non-African lineages before their separation from each other. The first farmers of the southern Levant (Israel and Jordan) and Zagros Mountains (Iran) were strongly genetically differentiated, and each descended from local hunter–gatherers. By the time of the Bronze Age, these two populations and Anatolian-related farmers had mixed with each other and with the hunter–gatherers of Europe to greatly reduce genetic differentiation. The impact of the Near Eastern farmers extended beyond the Near East: farmers related to those of Anatolia spread westward into Europe; farmers related to those of the Levant spread southward into East Africa; farmers related to those of Iran spread northward into the Eurasian steppe; and people related to both the early farmers of Iran and to the pastoralists of the Eurasian steppe spread eastward into South Asia.

695 citations