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1. Assessing the performance of qpAdm: a statistical tool for studying population admixture

Author

David Reich, John Wakeley, Eadaoin Harney, and Nick Patterson

Subjects
AcademicSubjects/SCI01140, AcademicSubjects/SCI00010, Population, Biology, AcademicSubjects/SCI01180, Gene flow, Source Population, Evolution, Molecular, Statistics, Genetics, Animals, Humans, DNA, Ancient, education, Population and Evolutionary Genetics, Investigation, High rate, education.field_of_study, Single model, simulation, Missing data, Pedigree, AdmixTools, Geography, Genetics, Population, Ancient DNA, Practice Guidelines as Topic, AcademicSubjects/SCI00960, qpAdm, admixture, Software
Abstract

qpAdm is a statistical tool for studying the ancestry of populations with histories that involve admixture between two or more source populations. Using qpAdm, it is possible to identify plausible models of admixture that fit the population history of a group of interest and to calculate the relative proportion of ancestry that can be ascribed to each source population in the model. Although qpAdm is widely used in studies of population history of human (and nonhuman) groups, relatively little has been done to assess its performance. We performed a simulation study to assess the behavior of qpAdm under various scenarios in order to identify areas of potential weakness and establish recommended best practices for use. We find that qpAdm is a robust tool that yields accurate results in many cases, including when data coverage is low, there are high rates of missing data or ancient DNA damage, or when diploid calls cannot be made. However, we caution against co-analyzing ancient and present-day data, the inclusion of an extremely large number of reference populations in a single model, and analyzing population histories involving extended periods of gene flow. We provide a user guide suggesting best practices for the use of qpAdm.

Published
2021

2. A Paleogenomic Reconstruction of the Deep Population History of the Andes

Author

Maria Ines Barreto, José M. Capriles, Douglas J. Kennett, Lucy C. Salazar, Brendan J. Culleton, Karina Aranda Álvarez, Carlos Lémuz Aguirre, Johannes Krause, Ricardo Fujita, Matthew Ferry, Megan Michel, Alan Cooper, Guido Valverde, Marta Alfonso Durruty, Lars Fehren-Schmitz, Kelly Harkins-Kinkaid, Pablo Geronimo Messineo, David Reich, Chiara Barbieri, George Lau, Pontus Skoglund, Iosif Lazaridis, Jannine Novak-Forst, Elsa Tomasto-Cagigao, Sergio Calla Maldonado, Kurt Rademaker, Frank Meddens, Eadaoin Harney, Wolfgang Haak, Vivien G. Standen, José R. Sandoval, Thomas K. Harper, Markus Reindel, Isabel Flores Espinoza, Steven A. LeBlanc, Calogero M. Santoro, Johny Isla, Nadine Rohland, Jeffrey Quilter, Richard L. Burger, Bastien Llamas, Kristin Stewardson, Gustavo G. Politis, David Beresford-Jones, Swapan Mallick, Nathan Nakatsuka, Mario A. Rivera, Nahuel A. Scheifler, Lauren Cadwallader, Cosimo Posth, Beresford-Jones, David [0000-0003-2427-7007], Cadwallader, Lauren [0000-0002-7571-3502], and Apollo - University of Cambridge Repository

Subjects
Gene Flow, media_common.quotation_subject, Population, Andes, Biology, DNA, Mitochondrial, General Biochemistry, Genetics and Molecular Biology, Article, 03 medical and health sciences, 0302 clinical medicine, State (polity), POPULATION GENETICS, ANCIENT DNA, Humans, ANDES, ARCHAEOLOGY, Cosmopolitanism, DNA, Ancient, education, ancient DNA, 030304 developmental biology, media_common, purl.org/becyt/ford/6 [https], 0303 health sciences, education.field_of_study, population genetics, archaeology, Central America, Sequence Analysis, DNA, South America, FOS: Sociology, Ancient DNA, Genetics, Population, Haplotypes, Anthropology, Genetic structure, Period (geology), Ethnology, ANTHROPOLOGY, purl.org/becyt/ford/6.1 [https], 030217 neurology & neurosurgery, Amazon basin
Abstract

Summary There are many unanswered questions about the population history of the Central and South Central Andes, particularly regarding the impact of large-scale societies, such as the Moche, Wari, Tiwanaku, and Inca. We assembled genome-wide data on 89 individuals dating from ∼9,000-500 years ago (BP), with a particular focus on the period of the rise and fall of state societies. Today’s genetic structure began to develop by 5,800 BP, followed by bi-directional gene flow between the North and South Highlands, and between the Highlands and Coast. We detect minimal admixture among neighboring groups between ∼2,000–500 BP, although we do detect cosmopolitanism (people of diverse ancestries living side-by-side) in the heartlands of the Tiwanaku and Inca polities. We also highlight cases of long-range mobility connecting the Andes to Argentina and the Northwest Andes to the Amazon Basin. Video Abstract, Graphical Abstract, Highlights • Ancient DNA transect reveals north-south substructure of Andean highlands by 5,800 BP • After 5,800 BP, gene flow mixed highland people with their neighbors • After 2,000 BP, striking genetic continuity through rise and fall of major cultures, Genome-wide data from 89 ancient humans illuminates the changes to the genetic landscape in the Central Andes over 9,000 years, revealing large-scale gene flow and cosmopolitan societies in the Tiwanaku and Inca polities.

Published
2020
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3. The genomic history of Southern Europe

Author

Richard Cottiaux, Eadaoin Harney, Iain Mathieson, Elizaveta Veselovskaya, Corinne Thevenet, Georgi Ganetsovski, Philipp W. Stockhammer, Petar Stanev, Douglas J. Kennett, Stefan Chohadzhiev, Adina Boroneanţ, Domenico Lo Vetro, Megan Michel, Nicholas J. Conard, Maleen Leppek, Fanica Veljanovska, Harald Meller, Martina Lari, Clive Bonsall, Michael Bolus, Thomas Higham, Andrej Starović, Darko Komšo, Mario Novak, Ivaylo Lozanov, Maja Čuka, Vanya Petrova, Krum Bacvarov, Alicja Budnik, Cosimo Posth, Cristian Virag, Stanislav Iliev, Wolfgang Haak, Francesca Candilio, Iñigo Olalde, Tamás Hajdu, David Caramelli, Raiko Krauß, Ivor Janković, Swapan Mallick, Matthew Ferry, Ben Krause-Kyora, Maria Teschler-Nicola, Kristin Stewardson, Cătălin Lazăr, Anastasia Papathanasiou, Giulio Catalano, Veneta Handzhyiska, Kendra Sirak, Kathrin Nägele, Kurt W. Alt, Bernard Gély, Ivor Karavanić, Svetlana Venelinova, Nedko Elenski, Dragana Antonović, Ron Pinhasi, Maria Malina, Inna Potekhina, Ivan Valchev, Alexey G. Nikitin, Kath McSweeney, Dusan Boric, Alissa Mittnik, Nick Patterson, Saskia Pfrengle, Angela Simalcsik, Anna Szécsényi-Nagy, Abigail Ash, Malcolm Lillie, Mario Šlaus, Fabio Martini, David Reich, Johannes Krause, Tamás Szeniczey, Bence Viola, Dženi Los, Luca Sineo, Hervé Bocherens, Christophe Cupillard, Yavor Boyadzhiev, Pavel Mirea, Sahra Talamo, Alexandra Kozak, Katerina Harvati, Songül Alpaslan-Roodenberg, Nasreen Broomandkhoshbacht, Marko Menđušić, Gunita Zariņa, Olivia Cheronet, Isil Kucukkalipci, Denise Keating, Dorothée G. Drucker, Stefan Alexandrov, Vladimir Slavchev, Radian Andreescu, Eppie R. Jones, Beatriz Gamarra, Michael Francken, Nadin Rohland, Gloria G. Fortes, Jonas Oppenheimer, Stefania Vai, T. Douglas Price, Sergey Vasilyev, Borislava Galabova, Krassimir Leshtakov, Bisserka Gaydarska, Mende Balázs Gusztáv, Joško Zaninović, Nadezhda Atanassova, Vyacheslav Moiseyev, Josip Burmaz, Daniel Fernandes, Steve Zäuner, Damian Labuda, Frédérique Valentin, Iain Mathieson, Songül Alpaslan-Roodenberg, Cosimo Posth, Anna Szécsényi-Nagy, Nadin Rohland1, Swapan Mallick, Iigo Olalde, Nasreen Broomandkhoshbacht, Francesca Candilio, Olivia Cheronet, Daniel Fernandes, Matthew Ferry, Beatriz Gamarra, Gloria González Fortes, Wolfgang Haak, Eadaoin Harney, Eppie Jones, Denise Keating, Ben Krause-Kyora, Isil Kucukkalipci, Megan Michel, Alissa Mittnik, Kathrin N.gele, Mario Novak, Jonas Oppenheimer, Nick Patterson, Saskia Pfrengle, Kendra Sirak, Kristin Stewardson, Stefania Vai, Stefan Alexandrov, Kurt W. Alt, Radian Andreescu, Dragana Antonovic′, Abigail Ash, Nadezhda Atanassova, Krum Bacvarov, Mende Balázs Gusztáv, Hervé Bocherens, Michael Bolus, Adina Boroneant., Yavor Boyadzhiev, Alicja Budnik, Josip Burmaz, Stefan Chohadzhiev, Nicholas J. Conard, Richard Cottiaux, Maja Cuka, Christophe Cupillard, Dorothée G. Drucker, Nedko Elenski, Michael Francken, Borislava Galabova, Georgi Ganetsovski, Bernard Gély, Tamás Hajdu, Veneta Handzhyiska, Katerina Harvati, Thomas Higham, Stanislav Iliev, Ivor Jankovic′, Ivor Karavanic, Douglas J. Kennett, Darko Komšo, Alexandra Kozak, Damian Labuda, Martina Lari, Catalin Lazar, Maleen Leppek, Krassimir Leshtakov, Domenico Lo Vetro, Dženi Los, Ivaylo Lozanov, Maria Malina, Fabio Martini, Kath McSweeney, Harald Meller, Marko Mendˉušic, Pavel Mirea, Vyacheslav Moiseyev, Vanya Petrova, T. Douglas Price, Angela Simalcsik, Luca Sineo, Mario Šlaus, Vladimir Slavchev, Petar Stanev, Andrej Starovic′, Tamás Szeniczey, Sahra Talamo, Maria Teschler-Nicola, Corinne Thevenet, Ivan Valchev, Frédérique Valentin, Sergey Vasilyev, Fanica Veljanovska, Svetlana Venelinova, Elizaveta Veselovskaya, Bence Viola, Cristian Virag, Joško Zaninovic′, Steve Zuner, Philipp W. Stockhammer, Giulio Catalano, Raiko Krau, David Caramelli, Gunita Zarin, Bisserka Gaydarska, Malcolm Lillie, Alexey G. Nikitin, Inna Potekhina, Anastasia Papathanasiou, Dušan Boric, Clive Bonsall, Johannes Krause, Ron Pinhasi, David Reich, Laboratoire Chrono-environnement - CNRS - UBFC (UMR 6249) (LCE), Centre National de la Recherche Scientifique (CNRS)-Université de Franche-Comté (UFC), Université Bourgogne Franche-Comté [COMUE] (UBFC)-Université Bourgogne Franche-Comté [COMUE] (UBFC), Mathieson I., Alpaslan-Roodenberg S., Posth C., Szecsenyi-Nagy A., Rohland N., Mallick S., Olalde I., Broomandkhoshbacht N., Candilio F., Cheronet O., Fernandes D., Ferry M., Gamarra B., Fortes G.G., Haak W., Harney E., Jones E., Keating D., Krause-Kyora B., Kucukkalipci I., Michel M., Mittnik A., Nagele K., Novak M., Oppenheimer J., Patterson N., Pfrengle S., Sirak K., Stewardson K., Vai S., Alexandrov S., Alt K.W., Andreescu R., Antonovic D., Ash A., Atanassova N., Bacvarov K., Gusztav M.B., Bocherens H., Bolus M., Boroneant A., Boyadzhiev Y., Budnik A., Burmaz J., Chohadzhiev S., Conard N.J., Cottiaux R., Cuka M., Cupillard C., Drucker D.G., Elenski N., Francken M., Galabova B., Ganetsovski G., Gely B., Hajdu T., Handzhyiska V., Harvati K., Higham T., Iliev S., Jankovic I., Karavanic I., Kennett D.J., Komso D., Kozak A., Labuda D., Lari M., Lazar C., Leppek M., Leshtakov K., Vetro D.L., Los D., Lozanov I., Malina M., Martini F., McSweeney K., Meller H., Mentusic M., Mirea P., Moiseyev V., Petrova V., Douglas Price T., Simalcsik A., Sineo L., Slaus M., Slavchev V., Stanev P., Starovic A., Szeniczey T., Talamo S., Teschler-Nicola M., Thevenet C., Valchev I., Valentin F., Vasilyev S., Veljanovska F., Venelinova S., Veselovskaya E., Viola B., Virag C., Zaninovic J., Zauner S., Stockhammer P.W., Catalano G., Krauss R., Caramelli D., Zarina G., Gaydarska B., Lillie M., Nikitin A.G., Potekhina I., Papathanasiou A., Boric D., Bonsall C., Krause J., Pinhasi R., Reich D., Université de Franche-Comté (UFC), and Université Bourgogne Franche-Comté [COMUE] (UBFC)-Université Bourgogne Franche-Comté [COMUE] (UBFC)-Centre National de la Recherche Scientifique (CNRS)

Subjects
0301 basic medicine, Male, History, Steppe, 01 natural sciences, genome wide ancient DNA, 0302 clinical medicine, population dynamics, ComputingMilieux_MISCELLANEOUS, History, Ancient, 2. Zero hunger, 0303 health sciences, education.field_of_study, Multidisciplinary, geography.geographical_feature_category, Farmers, Genome, Agriculture, Cline (biology), Genomics, Grassland, Europe, Geography, Western europe, Ethnology, Female, southeastern Europe, Human, Archaeogenetics, 010506 paleontology, Asia, [SHS.ARCHEO]Humanities and Social Sciences/Archaeology and Prehistory, Human Migration, Population, Settore BIO/08 - Antropologia, Indigenous, Article, Ancient, 03 medical and health sciences, genetic variation, genomics, prehistoric Europe, prehistoric archeology, bioarchaeology, Bioarchaeology, Genetics, Humans, HUMANISTIC SCIENCES. Archeology, Farmer, DNA, Ancient, Sex Distribution, education, Mesolithic, 030304 developmental biology, 0105 earth and related environmental sciences, HUMANISTIČKE ZNANOSTI. Arheologija, Extramural, business.industry, Genome, Human, Ambientale, DNA, Archaeology, PRIRODNE ZNANOSTI. Biologija. Genetika, evolucija i filogenija, 030104 developmental biology, Ancient DNA, Genetics, Population, Ancient DNA, Genomics, Southeastern Europe, Genetic Variation, business, NATURAL SCIENCES. Biology. Genetics, Evolution and Phylogenetics, 030217 neurology & neurosurgery
Abstract

Farming was first introduced to southeastern Europe in the mid-7th millennium BCE - brought by migrants from Anatolia who settled in the region before spreading throughout Europe. However, the dynamics of the interaction between the first farmers and the indigenous hunter-gatherers remain poorly understood because of the near absence of ancient DNA from the region. We report new genome-wide ancient DNA data from 204 individuals-65 Paleolithic and Mesolithic, 93 Neolithic, and 46 Copper, Bronze and Iron Age-who lived in southeastern Europe and surrounding regions between about 12,000 and 500 BCE. We document that the hunter-gatherer populations of southeastern Europe, the Baltic, and the North Pontic Steppe were distinctive from those of western Europe, with a West-East cline of ancestry. We show that the people who brought farming to Europe were not part of a single population, as early farmers from southern Greece are not descended from the Neolithic population of northwestern Anatolia that was ancestral to all other European farmers. The ancestors of the first farmers of northern and western Europe passed through southeastern Europe with limited admixture with local hunter-gatherers, but we show that some groups that remained in the region mixed extensively with local hunter-gatherers, with relatively sex-balanced admixture compared to the male-biased hunter-gatherer admixture that we show prevailed later in the North and West. After the spread of farming, southeastern Europe continued to be a nexus between East and West, with intermittent steppe ancestry, including in individuals from the Varna I cemetery and associated with the Cucuteni-Trypillian archaeological complex, up to 2,000 years before the Steppe migration that replaced much of northern Europe9s population.

Published
2018

4. Publisher Correction: Ancient DNA from Chalcolithic Israel reveals the role of population mixture in cultural transformation

Author

Susanne Nordenfelt, Eadaoin Harney, Kristin Stewardson, Rachel Sarig, Israel Hershkovitz, Nadin Rohland, Swapan Mallick, Nick Patterson, Iosif Lazaridis, Hila May, Dina Shalem, and David Reich

Subjects
education.field_of_study, Multidisciplinary, History, Science, Published Erratum, Population, General Physics and Astronomy, General Chemistry, Chalcolithic, Article, General Biochemistry, Genetics and Molecular Biology, Genealogy, Transformation (music), Ancient DNA, Data_FILES, ComputingMethodologies_DOCUMENTANDTEXTPROCESSING, lcsh:Q, lcsh:Science, education
Abstract

The material culture of the Late Chalcolithic period in the southern Levant (4500–3900/3800 BCE) is qualitatively distinct from previous and subsequent periods. Here, to test the hypothesis that the advent and decline of this culture was influenced by movements of people, we generated genome-wide ancient DNA from 22 individuals from Peqi’in Cave, Israel. These individuals were part of a homogeneous population that can be modeled as deriving ~57% of its ancestry from groups related to those of the local Levant Neolithic, ~17% from groups related to those of the Iran Chalcolithic, and ~26% from groups related to those of the Anatolian Neolithic. The Peqi’in population also appears to have contributed differently to later Bronze Age groups, one of which we show cannot plausibly have descended from the same population as that of Peqi’in Cave. These results provide an example of how population movements propelled cultural changes in the deep past., The Late Chalcolithic material culture in the southern Levant has unique attributes that suggest spread of people or culture. Here, the authors use genome-wide ancient DNA data from 22 individuals from a Chalcolithic site and show evidence of complex population movements and turnovers.

Published
2018

5. Ancient genomes document multiple waves of migration in Southeast Asian prehistory

Author

Hoang Hiep Trinh, Kate Domett, Beatriz Gamarra, Thomas Oliver Pryce, David Reich, Mark Lipson, Olivia Cheronet, Eadaoin Harney, Ron Pinhasi, Aung Aung Kyaw, Piya Changmai, Mario Novak, Nadin Rohland, Pavel Flegontov, Anna Willis, Nasreen Broomandkhoshbacht, Zhao Zhang, Hallie R. Buckley, Daniel Fernandes, Kristin Stewardson, Francesca Candilio, Baptiste Pradier, Hirofumi Matsumura, Wibhu Kutanan, Swapan Mallick, Matthew Ferry, Marc Oxenham, Giang Hai Nguyen, Jonas Oppenheimer, Jatupol Kampuansai, Kendra Sirak, Tin Tin Win, Michael Pietrusewsky, Megan Michel, Harvard School of Public Health, Department of Anthropology [University of Vienna], University of Vienna [Vienna], School of Archaeology [Dublin], University College Dublin [Dublin] (UCD), School of Archaeology & Anthropology, Australian National University (ANU), Department of Anthropology University of Hawai'i at Manoa, University of Hawai‘i [Mānoa] (UHM), Laboratoire Archéomatériaux et Prévision de l'Altération (LAPA - UMR 3685), Nanosciences et Innovation pour les Matériaux, la Biomédecine et l'Energie (ex SIS2M) (NIMBE UMR 3685), Institut Rayonnement Matière de Saclay (IRAMIS), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)-Institut Rayonnement Matière de Saclay (IRAMIS), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS), Préhistoire et Technologie (PréTech), Université Paris Nanterre (UPN)-Centre National de la Recherche Scientifique (CNRS), Sapporo Medical University, Department of Anatomy, University of Otago, Dunedin, University of Otago [Dunedin, Nouvelle-Zélande], James Cook University (JCU), Vietnam Institute of Archaeology, Hanoi, Vietnam., Department of Archaeology, Ministry of Culture, Ministry of Religious Affairs and Culture, Howard Hughes Medical Institute [Boston] (HHMI), Howard Hughes Medical Institute (HHMI)-Harvard Medical School [Boston] (HMS), Department of Anthropology [University of Pennsylvania], University of Pennsylvania [Philadelphia], Ostravská univerzita / University of Ostrava, Chiang Mai University (CMU), Khon Kaen University [Thailand] (KKU), Iowa State University (ISU), Department of Epidemiology and Public Health [university of Ostrava], Lékařská fakulta / Faculty of Medicine [University of Ostrava], Ostravská univerzita / University of Ostrava-Ostravská univerzita / University of Ostrava, School of Archaeology, Broad Institute of MIT and Harvard (BROAD INSTITUTE), Harvard Medical School [Boston] (HMS)-Massachusetts Institute of Technology (MIT)-Massachusetts General Hospital [Boston], and University of Pennsylvania

Subjects
0301 basic medicine, human migration, Asia, Population, [SHS.ANTHRO-BIO]Humanities and Social Sciences/Biological anthropology, Southeastern, Southeast asian, Article, [SHS]Humanities and Social Sciences, radiometric dating, Prehistory, 03 medical and health sciences, Asian People, Bronze Age, genetic variation, genomics, migration, South East Asian prehistory, prehistoric archaeology, bioarchaeology, 0601 history and archaeology, East Asia, human, DNA, Ancient, agriculture, Asian continental ancestry group, DNA, ancient, history, humans, language, genome, multidisciplinary, education, Asia, Southeastern, History, Ancient, 030304 developmental biology, 0303 health sciences, education.field_of_study, 060101 anthropology, 060102 archaeology, Human migration, business.industry, Genome, Human, 06 humanities and the arts, 030104 developmental biology, Geography, Ancient DNA, Iron Age, Period (geology), Ethnology, business
Abstract

Ancient migrations in Southeast Asia The past movements and peopling of Southeast Asia have been poorly represented in ancient DNA studies (see the Perspective by Bellwood). Lipson et al. generated sequences from people inhabiting Southeast Asia from about 1700 to 4100 years ago. Screening of more than a hundred individuals from five sites yielded ancient DNA from 18 individuals. Comparisons with present-day populations suggest two waves of mixing between resident populations. The first mix was between local hunter-gatherers and incoming farmers associated with the Neolithic spreading from South China. A second event resulted in an additional pulse of genetic material from China to Southeast Asia associated with a Bronze Age migration. McColl et al. sequenced 26 ancient genomes from Southeast Asia and Japan spanning from the late Neolithic to the Iron Age. They found that present-day populations are the result of mixing among four ancient populations, including multiple waves of genetic material from more northern East Asian populations. Science , this issue p. 92 , p. 88 ; see also p. 31

Published
2018

6. Ancient DNA from Chalcolithic Israel reveals the role of population mixture in cultural transformation

Author

Kristin Stewardson, Susanne Nordenfelt, Nick Patterson, Rachel Sarig, Iosif Lazaridis, Eadaoin Harney, Israel Hershkovitz, Nadin Rohland, Swapan Mallick, David Reich, Hila May, and Dina Shalem

Subjects
0301 basic medicine, 010506 paleontology, Geologic Sediments, Southern Levant, Science, Population, Culture, General Physics and Astronomy, Ancient history, 01 natural sciences, General Biochemistry, Genetics and Molecular Biology, 03 medical and health sciences, Genetic Heterogeneity, Cave, Bronze Age, Humans, DNA, Ancient, Israel, lcsh:Science, education, 0105 earth and related environmental sciences, education.field_of_study, Multidisciplinary, geography.geographical_feature_category, Genetic Variation, General Chemistry, Chalcolithic, Caves, 030104 developmental biology, Geography, Ancient DNA, Genetics, Population, Homogeneous, Mutation, Period (geology), lcsh:Q
Abstract

The material culture of the Late Chalcolithic period in the southern Levant (4500–3900/3800 BCE) is qualitatively distinct from previous and subsequent periods. Here, to test the hypothesis that the advent and decline of this culture was influenced by movements of people, we generated genome-wide ancient DNA from 22 individuals from Peqi’in Cave, Israel. These individuals were part of a homogeneous population that can be modeled as deriving ~57% of its ancestry from groups related to those of the local Levant Neolithic, ~17% from groups related to those of the Iran Chalcolithic, and ~26% from groups related to those of the Anatolian Neolithic. The Peqi’in population also appears to have contributed differently to later Bronze Age groups, one of which we show cannot plausibly have descended from the same population as that of Peqi’in Cave. These results provide an example of how population movements propelled cultural changes in the deep past.

Published
2017

7. Reconstructing Prehistoric African Population Structure

Author

Saioa López, Audax Mabulla, Douglas J. Kennett, Elizabeth Gomani-Chindebvu, Svante Pääbo, Kendra Sirak, Iñigo Olalde, Mateja Hajdinjak, Mark Horton, Chrissy Chiumia, Johannes Krause, Mary E. Prendergast, Ceri Shipton, Eadaoin Harney, David Reich, Alison Crowther, Anja Heinze, Pontus Skoglund, Richard F. Helm, Matthew Ferry, Nick Patterson, Jessica I. Cerezo-Román, Kristin Stewardson, Ron Pinhasi, Nicole Boivin, Menno Welling, Mark G. Thomas, Alexander Peltzer, Megan Michel, Agness Gidna, Katherine M. Grillo, Ruth Tibesasa, Vanessa M. Hayes, John Parkington, Nadin Rohland, I. Taneli Helenius, Swapan Mallick, Raj Ramesar, Alissa Mittnik, Garrett Hellenthal, Jessica C. Thompson, Alan G. Morris, Tasneem Salie, and Matthias Meyer

Subjects
0301 basic medicine, Male, Genetics, Medical, Pastoralism, Population, Population genetics, Black People, Biology, General Biochemistry, Genetics and Molecular Biology, Article, Bone and Bones, Lineage (anthropology), Prehistory, 03 medical and health sciences, 0302 clinical medicine, parasitic diseases, Humans, DNA, Ancient, education, Life Style, education.field_of_study, Fossils, Genome, Human, Population ecology, biology.organism_classification, 030104 developmental biology, Ancient DNA, Tanzania, Genetics, Population, Africa, Ethnology, Female, 030217 neurology & neurosurgery, Genome-Wide Association Study
Abstract

We assembled genome-wide data from 16 prehistoric Africans. We show that the anciently divergent lineage that comprises the primary ancestry of the southern African San had a wider distribution in the past, contributing approximately two-thirds of the ancestry of Malawi hunter-gatherers ∼8,100-2,500 years ago and approximately one-third of the ancestry of Tanzanian hunter-gatherers ∼1,400 years ago. We document how the spread of farmers from western Africa involved complete replacement of local hunter-gatherers in some regions, and we track the spread of herders by showing that the population of a ∼3,100-year-old pastoralist from Tanzania contributed ancestry to people from northeastern to southern Africa, including a ∼1,200-year-old southern African pastoralist. The deepest diversifications of African lineages were complex, involving either repeated gene flow among geographically disparate groups or a lineage more deeply diverging than that of the San contributing more to some western African populations than to others. We finally leverage ancient genomes to document episodes of natural selection in southern African populations. PAPERCLIP.

Published
2017

8. Parallel paleogenomic transects reveal complex genetic history of early European farmers

Author

José Antonio Mujika-Alustiza, Eadaoin Harney, Carmen Alonso Fernández, Annamária Pósa, László Márk, Tibor Paluch, Béla Melegh, Swapan Mallick, Victoria Keerl, Ferenc Horváth, Matthew Ferry, Zoltán Toldi, Anna Szécsényi-Nagy, Zsolt Bánfai, László Domboróczki, Susanne Nordenfelt, Nasreen Broomandkhoshbacht, Alan Cooper, Alexandra Anders, János Dani, Ruth Bollongino, Jörg Orschiedt, Judit Koós, Megan Michel, János Jakucs, Judit P. Barna, Kristin Stewardson, Javier Fernández-Eraso, Katalin Sebők, Carles Lalueza-Fox, Wolfgang Haak, Emese Gyöngyvér Nagy, Szilvia Fábián, Eszter Bánffy, Harald Meller, Kurt W. Alt, Gábor Serlegi, Erika Molnár, Nadin Rohland, Bastien Llamas, György Pálfi, Javier Jiménez Echevarría, Mária Bondár, Balázs Gusztáv Mende, Piroska Csengeri, Kerstin Schierhold, Judit Regenye, Joachim Burger, Pál Raczky, Balázs Stégmár, Krisztián Oross, Mark Lipson, Tibor Marton, Kitti Köhler, Anett Osztás, David Reich, and Jonas Oppenheimer

Subjects
0301 basic medicine, Gene Flow, Male, 0106 biological sciences, Human Migration, Population Dynamics, Population, Datasets as Topic, 010603 evolutionary biology, 01 natural sciences, Article, Gene flow, Prehistory, 03 medical and health sciences, Spatio-Temporal Analysis, Germany, Genetic variation, Humans, DNA, Ancient, education, Transect, History, Ancient, 030304 developmental biology, Hungary, 0303 health sciences, education.field_of_study, Genetic diversity, Multidisciplinary, Farmers, Human migration, business.industry, Ecology, Genetic Variation, Chalcolithic, 030104 developmental biology, Ancient DNA, Geography, Spain, Period (geology), Ethnology, Female, business
Abstract

In European Neolithic populations, the arrival of farmers prompted admixture with local hunter-gatherers over many centuries, resulting in distinct signatures in each region due to a complex series of interactions. David Reich and colleagues analyse genome-wide data from 180 individuals from the Neolithic and Chalcolithic periods of Hungary, Germany and Spain to study the population dynamics of Neolithization in European prehistory. They examine how gene flow reshaped European populations during the Neolithic period, including pervasive admixture—the interbreeding between previously isolated populations—between groups with different ancestry profiles. In each region, they find that the arrival of farmers prompted admixture with local hunter-gatherers, over the course of 3,000 years. Ancient DNA studies have established that Neolithic European populations were descended from Anatolian migrants1,2,3,4,5,6,7,8 who received a limited amount of admixture from resident hunter-gatherers3,4,5,9. Many open questions remain, however, about the spatial and temporal dynamics of population interactions and admixture during the Neolithic period. Here we investigate the population dynamics of Neolithization across Europe using a high-resolution genome-wide ancient DNA dataset with a total of 180 samples, of which 130 are newly reported here, from the Neolithic and Chalcolithic periods of Hungary (6000–2900 bc, n = 100), Germany (5500–3000 bc, n = 42) and Spain (5500–2200 bc, n = 38). We find that genetic diversity was shaped predominantly by local processes, with varied sources and proportions of hunter-gatherer ancestry among the three regions and through time. Admixture between groups with different ancestry profiles was pervasive and resulted in observable population transformation across almost all cultural transitions. Our results shed new light on the ways in which gene flow reshaped European populations throughout the Neolithic period and demonstrate the potential of time-series-based sampling and modelling approaches to elucidate multiple dimensions of historical population interactions.

Published
2017

9. The beaker phenomenon and the Genomic transformations of Northwest Europe

Author

Matthew Ferry, Nasreen Broomandkhoshbacht, Anna Endrődi, César Heras Martínez, Balázs Gusztáv Mende, Fraser Brown, András Czene, Morten E. Allentoft, Anna Szécsényi-Nagy, Ian Barnes, Roberto Risch, Milan Kuchařík, Clive Waddington, Benjamin Neil, Róbert Patay, Ignacio Soriano, Jocelyne Desideri, Luc Vergnaud, Gordon Cook, Denise Keating, Francesca Candilio, Karl-Göran Sjögren, Iosif Lazaridis, Kristin Stewardson, Harry Fokkens, Virginia Galera Olmo, Tamás Hajdu, David Caramelli, Aurore Schmitt, Philippe Lefranc, Maya Hoole, Stephany Leach, Megan Michel, Alessandra Modi, Daniel Fernandes, Viktória Kiss, João Luís Cardoso, Václav Smrčka, Swapan Mallick, Zuzana Faltyskova, Wolfgang Haak, Eszter Bánffy, David Billoin, Ron Pinhasi, T. Douglas Price, Ian Armit, Michiel Gazenbeek, Piotr Włodarczak, Eadaoin Harney, Marie Besse, Tim Allen, Douglas J. Kennett, Christopher Evans, Carles Lalueza-Fox, Alessandro Zanini, Selina Brace, Manuel Ángel Rojo Guerra, Philipp W. Stockhammer, Mike Luke, Zsolt Bernert, Peter de Knijff, Richard Mortimer, Michal Ernée, Gill Hey, Emiliano Carnieri, Elżbieta Haduch, Kitti Köhler, Laura Bonsall, João Zilhão, Thomas J. Booth, Mike Parker Pearson, Germán Delibes, Yoan Diekmann, Olivier Lemercier, Iñigo Olalde, János Dani, Eveline Altena, Alistair Barclay, Ken Massy, Sebastiano Tusa, Antonella Valenti, David Reich, Jonas Oppenheimer, Nadin Rohland, Clive Bonsall, Ana Maria Silva, Pierre-Jérôme Rey, Joaquín Lomba Maurandi, Alison Sheridan, Tona Majó, Chris Fowler, Petr Velemínský, Natasha Dodwell, Luigi Lentini, Katina T. Lillios, Miroslav Dobeš, Azucena Avilés Fernández, Olivia Cheronet, Mark G. Thomas, Ana-Mercedes Herrero-Corral, María Haber-Uriarte, Maria Bernabò-Brea, Agata Hałuszko, Ana Bastida Ramírez, Concepción Blasco, Alissa Mittnik, Roberto Menduiña García, Marcus Brittain, Nick Patterson, Tamás Szeniczey, Maksym Mackiewicz, Raúl Flores Fernández, Sophie Carver, Timothy D J Knowles, Volker M Heyd, Rafael Garrido Pena, Arnaud Lefebvre, Kathleen McSweeney, Lindsey Büster, Joël Serralongue, Mirosław Furmanek, Laura Castells Navarro, Kirsten Egging Dinwiddy, Artur Rapiński, Thomas K. Harper, Corina Liesau, Kristian Kristiansen, Barry Cunliffe, Oliver E. Craig, Patricia Ríos, Gabriella Kulcsár, Joan Francès Farré, Pilar Prieto, Jorge Vega de Miguel, Johannes Krause, Saskia Pfrengle, Thomas Higham, Elisa Guerra-Doce, Anthony Denaire, Nick Jowett, Kurt W. Alt, Mark Lipson, Jacqueline I. McKinley, Günter Brücken, Universitat Pompeu Fabra [Barcelona] (UPF), Egham TW20 0EX, Middlesex University, Max Planck Institute for Evolutionary Anthropology [Leipzig], Max-Planck-Gesellschaft, Harvard School of Public Health, Max Planck Institute for the Science of Human History (MPI-SHH), Broad Institute of MIT and Harvard (BROAD INSTITUTE), Harvard Medical School [Boston] (HMS)-Massachusetts Institute of Technology (MIT)-Massachusetts General Hospital [Boston], School of Archaeology [Dublin], University College Dublin [Dublin] (UCD), Center for Human and Clinical Genetics, Leiden University Medical Center (LUMC), Institut national de recherches archéologiques préventives (Inrap), Haematology, St James' Institute of Oncology, Etude des Civilisations de l'Antiquité (UMR 7044), Centre National de la Recherche Scientifique (CNRS)-Université Marc Bloch - Strasbourg II-Université de Haute-Alsace (UHA) Mulhouse - Colmar (Université de Haute-Alsace (UHA)), Department of Psychiatry and Biobehavioral Sciences, University of California [Los Angeles] (UCLA), University of California-University of California-Shirley and Stefan Hatos Center for Neuropharmacology, Archéologie, Terre, Histoire, Sociétés [Dijon] (ARTeHiS), Ministère de la Culture et de la Communication (MCC)-Université de Bourgogne (UB)-Centre National de la Recherche Scientifique (CNRS), Université de Rouen Normandie (UNIROUEN), Normandie Université (NU), Institute of Archaeology [Budapest], Research Centre for The Humanities [Budapest], Hungarian Academy of Sciences (MTA)-Hungarian Academy of Sciences (MTA), Department of Anthropology [University of Vienna], University of Vienna [Vienna], Department of Anthropology, Národní muzeum, Università degli Studi di Roma 'La Sapienza' = Sapienza University [Rome], Laboratoire d'archéologie préhistorique et anthropologie, Université de Genève (UNIGE), Instytut Archeologii Uniwersytetu Wrocławskiego, Institute for Health and Consumer Protection, European Commission - Joint Research Centre, Environnements, Dynamiques et Territoires de la Montagne (EDYTEM), Centre National de la Recherche Scientifique (CNRS)-Université Savoie Mont Blanc (USMB [Université de Savoie] [Université de Chambéry]), Universidad de Valladolid [Valladolid] (UVa), Anthropologie bio-culturelle, Droit, Ethique et Santé (ADES), Aix Marseille Université (AMU)-EFS ALPES MEDITERRANEE-Centre National de la Recherche Scientifique (CNRS), Service archéologique de la Haute-Savoie, Office départemental d'animation culturelle de la Haute-Savoie, University of Minho [Braga], Department of Archaeology and Anthropology, University of Bristol [Bristol], Laboratorio di Antropologia, Università degli Studi di Firenze = University of Florence [Firenze] (UNIFI), Oxford Radiocarbon Accelerator Unit, RLAHA, National Museums of Scotland, Department of Archaeogenetics [Jena] (DAG), Max-Planck-Gesellschaft-Max-Planck-Gesellschaft, School of Archaeology, Departament de biologia animal, Universitad de barcelona, Universiteit Leiden-Universiteit Leiden, Étude des Civilisations de l'Antiquité : de la Préhistoire à Byzance (ARCHIMEDE), Université de Haute-Alsace (UHA) Mulhouse - Colmar (Université de Haute-Alsace (UHA))-Université Marc Bloch - Strasbourg II-Centre National de la Recherche Scientifique (CNRS), University of California (UC)-University of California (UC)-Shirley and Stefan Hatos Center for Neuropharmacology, Università degli Studi di Roma 'La Sapienza' = Sapienza University [Rome] (UNIROMA), Université de Genève = University of Geneva (UNIGE), Environnements, Dynamiques et Territoires de Montagne (EDYTEM), Université Savoie Mont Blanc (USMB [Université de Savoie] [Université de Chambéry])-Centre National de la Recherche Scientifique (CNRS), Università degli Studi di Firenze = University of Florence (UniFI), National Museums Scotland (NMS), Repositório da Universidade de Lisboa, Universitat de Barcelona, Desideri, Jocelyne, and Besse, Marie

Subjects
Male, 0301 basic medicine, Steppe, ADN, Néolithique, Bell Beaker, Arqueologia, Bell Beaker culture, genome wide ancient DNA, 0302 clinical medicine, Archéologie, Phenomenon, ddc:550, 0601 history and archaeology, Suisse, History, Ancient, 0303 health sciences, education.field_of_study, geography.geographical_feature_category, Multidisciplinary, 060102 archaeology, [SDE.IE]Environmental Sciences/Environmental Engineering, Human migration, Préhistoire, Neolithic period, Gene Pool, Genomics, [SHS.GEO]Humanities and Social Sciences/Geography, 06 humanities and the arts, bell Beaker, Europe, Geography, Archaeology, Ceràmica, Ethnology, Mégalithisme, Archaeogenetics, Campaniforme, Pottery, Human Migration, [SDE.MCG]Environmental Sciences/Global Changes, Population, Ancient history, Article, 03 medical and health sciences, Spatio-Temporal Analysis, popular genetics, Bronze Age, Beaker, Cultural Evolution, Neolític, genomics, Humans, DNA, Ancient, education, 030304 developmental biology, Chromosomes, Human, Y, Genome, Human, business.industry, Northwest Europe, Chalcolithic, [SDE.ES]Environmental Sciences/Environmental and Society, Ancient DNA, Genetics, Population, 030104 developmental biology, Haplotypes, Period (geology), Genomic, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, business, 030217 neurology & neurosurgery
Abstract

Bell Beaker pottery spread across western and central Europe beginning around 2750 BCE before disappearing between 2200–1800 BCE. The mechanism of its expansion is a topic of long-standing debate, with support for both cultural diffusion and human migration. We present new genome-wide ancient DNA data from 170 Neolithic, Copper Age and Bronze Age Europeans, including 100 Beaker-associated individuals. In contrast to the Corded Ware Complex, which has previously been identified as arriving in central Europe following migration from the east, we observe limited genetic affinity between Iberian and central European Beaker Complex-associated individuals, and thus exclude migration as a significant mechanism of spread between these two regions. However, human migration did have an important role in the further dissemination of the Beaker Complex, which we document most clearly in Britain using data from 80 newly reported individuals dating to 3900–1200 BCE. British Neolithic farmers were genetically similar to contemporary populations in continental Europe and in particular to Neolithic Iberians, suggesting that a portion of the farmer ancestry in Britain came from the Mediterranean rather than the Danubian route of farming expansion. Beginning with the Beaker period, and continuing through the Bronze Age, all British individuals harboured high proportions of Steppe ancestry and were genetically closely related to Beaker-associated individuals from the Lower Rhine area. We use these observations to show that the spread of the Beaker Complex to Britain was mediated by migration from the continent that replaced >90% of Britain’s Neolithic gene pool within a few hundred years, continuing the process that brought Steppe ancestry into central and northern Europe 400 years earlier.

Published
2017

10. Multi-layered population structure in Island Southeast Asians

Author

Joseph Wee, Toomas Kivisild, Bryndis Yngvadottir, Pradiptajati Kusuma, S M Abdullah, Tiago Antao, Denis Pierron, Eadaoin Harney, Nicolas Brucato, Thierry Letellier, Cristina Castillo, Luca Pagani, François-Xavier Ricaut, Alexander Mörseburg, Mait Metspalu, Alexia Cardona, Tom Hoogervorst, Human Genetics, Centre National de la Recherche Scientifique (CNRS), Department of Genetics [Boston], Harvard Medical School [Boston] (HMS), University College of London [London] (UCL), Anthropologie Moléculaire et Imagerie de Synthèse (AMIS), Centre National de la Recherche Scientifique (CNRS)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées, Physiopathologie mitochondriale, Université Bordeaux Segalen - Bordeaux 2-Institut National de la Santé et de la Recherche Médicale (INSERM), University of Tartu, Leverhulme Centre for Human Evolutionary Studies University of Cambridge, University of Cambridge [UK] (CAM), Université Toulouse III - Paul Sabatier (UT3), and Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)

Subjects
0301 basic medicine, Genetics, Genetics (clinical), Vietnamese, Human Migration, Population, [SHS.ANTHRO-BIO]Humanities and Social Sciences/Biological anthropology, 030105 genetics & heredity, Southeast asian, Article, Burmese, 03 medical and health sciences, Asian People, parasitic diseases, Humans, education, Asia, Southeastern, Malay, Islands, education.field_of_study, Human migration, business.industry, language.human_language, 030104 developmental biology, Geography, language, Biological dispersal, Ethnology, Mainland, business
Abstract

International audience; The history of human settlement in Southeast Asia has been complex and involved several distinct dispersal events. Here, we report the analyses of 1825 individuals from Southeast Asia including new genome-wide genotype data for 146 individuals from three Mainland Southeast Asian (Burmese, Malay and Vietnamese) and four Island Southeast Asian (Dusun, Filipino, Kankanaey and Murut) populations. While confirming the presence of previously recognised major ancestry components in the Southeast Asian population structure, we highlight the Kankanaey Igorots from the highlands of the Philippine Mountain Province as likely the closest living representatives of the source population that may have given rise to the Austronesian expansion. This conclusion rests on independent evidence from various analyses of autosomal data and uniparental markers. Given the extensive presence of trade goods, cultural and linguistic evidence of Indian influence in Southeast Asia starting from 2.5 kya, we also detect traces of a South Asian signature in different populations in the region dating to the last couple of thousand years.

Published
2016

11. Genomic insights into the peopling of the Southwest Pacific

Author

Eadaoin Harney, Murray P. Cox, Joseph Wee, Nadine Rohland, Qiaomei Fu, Toomas Kivisild, Stuart Bedford, Swapan Mallick, Kristin Stewardson, Matthew Spriggs, David Reich, Pontus Skoglund, Christian Reepmeyer, Mario Novak, Fiona Petchey, Cosimo Posth, Jonathan S. Friedlaender, Daniel Fernandes, Pradiptajati Kusuma, Nick Patterson, S M Abdullah, Ron Pinhasi, Françoise R. Friedlaender, Johannes Krause, George Koki, Geoffrey Clark, D. Andrew Merriwether, Mark Lipson, Frédérique Valentin, François-X Ricaut, Kendra Sirak, Max Planck Institute for the Science of Human History (MPI-SHH), Max-Planck-Gesellschaft, University College Dublin [Dublin] (UCD), Australian National University (ANU), Archéologies et Sciences de l'Antiquité (ArScAn), Université Paris 1 Panthéon-Sorbonne (UP1)-Université Paris Nanterre (UPN)-Ministère de la Culture et de la Communication (MCC)-Centre National de la Recherche Scientifique (CNRS), James Cook University (JCU), Radiocarbon Dating Laboratory, University of Waikato, University of Waikato [Hamilton], School of Archaeology [Dublin], Department of Genetics [Boston], Harvard Medical School [Boston] (HMS), Harvard School of Public Health, Department of Evolutianory Genetics, Max-Planck-Institut, Leverhulme Centre for Human Evolutionary Studies University of Cambridge, University of Cambridge [UK] (CAM), Anthropologie Moléculaire et Imagerie de Synthèse (AMIS), Centre National de la Recherche Scientifique (CNRS)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées, Centre National de la Recherche Scientifique (CNRS), Department of Archaeogenetics [Jena] (DAG), Max-Planck-Gesellschaft-Max-Planck-Gesellschaft, School of Archaeology, Broad Institute of MIT and Harvard (BROAD INSTITUTE), Harvard Medical School [Boston] (HMS)-Massachusetts Institute of Technology (MIT)-Massachusetts General Hospital [Boston], Université Paris 1 Panthéon-Sorbonne (UP1)-Université Paris 8 Vincennes-Saint-Denis (UP8)-Université Paris Nanterre (UPN)-Ministère de la Culture et de la Communication (MCC)-Institut national de recherches archéologiques préventives (Inrap)-Centre National de la Recherche Scientifique (CNRS), Université Toulouse III - Paul Sabatier (UT3), and Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)

Subjects
0301 basic medicine, Male, Native Hawaiian or Other Pacific Islander, Remote Oceania, Human Migration, Population, [SHS.ANTHRO-BIO]Humanities and Social Sciences/Biological anthropology, Indigenous, Polynesia, Article, 03 medical and health sciences, Asian People, Vanuatu, parasitic diseases, Humans, 0601 history and archaeology, East Asia, education, History, Ancient, Phylogeny, education.field_of_study, New Guinea, Multidisciplinary, 060102 archaeology, Genome, Human, Tonga, New guinea, peopling, South Pacific, aDNA, genetic variation, 06 humanities and the arts, Genomics, Before Present, 030104 developmental biology, Ancient DNA, Genetics, Population, Ethnology, Biological dispersal, Female
Abstract

International audience; The appearance of people associated with the Lapita culture in the South Pacific around 3,000 years ago marked the beginning of the last major human dispersal to unpopulated lands. However, the relationship of these pioneers to the long-established Papuan people of the New Guinea region is unclear. Here we present genome-wide ancient DNA data from three individuals from Vanuatu (about 3,100-2,700 years before present) and one from Tonga (about 2,700-2,300 years before present), and analyse them with data from 778 present-day East Asians and Oceanians. Today, indigenous people of the South Pacific harbour a mixture of ancestry from Papuans and a population of East Asian origin that no longer exists in unmixed form, but is a match to the ancient individuals. Most analyses have interpreted the minimum of twenty-five per cent Papuan ancestry in the region today as evidence that the first humans to reach Remote Oceania, including Polynesia, were derived from population mixtures near New Guinea, before their further expansion into Remote Oceania. However, our finding that the ancient individuals had little to no Papuan ancestry implies that later human population movements spread Papuan ancestry through the South Pacific after the first peopling of the islands.

Published
2016

12. Eight thousand years of natural selection in Europe

Author

Harald Meller, Bastien Llamas, Johannes Krause, de Castro Jmb, Roodenberg J, David Reich, Fokke Gerritsen, Kristin Stewardson, Pavel Kuznetsov, Joseph K. Pickrell, Mario Novak, Eppie R. Jones, David W. Anthony, Rojo Guerra Ma, Alpaslan Roodenberg S, Eadaoin Harney, Josep Maria Vergès, Iain Mathieson, Oleg Mochalov, Kurt W. Alt, Moiseyev, Ron Pinhasi, Carles Lalueza-Fox, Eudald Carbonell, Marina Lozano, Nadine Rohland, Cristina Gamba, Dorcas Brown, Daniel Fernandes, Mallick S, Wolfgang Haak, Kendra Sirak, Stanislav Dryomov, Aleksander Khokhlov, Iosif Lazaridis, Alan Cooper, Juan Luis Arsuaga, and Nick Patterson

Subjects
Genetics, 0303 health sciences, education.field_of_study, Natural selection, Population, Biology, Indirect evidence, 03 medical and health sciences, 0302 clinical medicine, Ancient DNA, Evolutionary biology, Genetic variation, Adaptation, education, Social organization, 030217 neurology & neurosurgery, Selection (genetic algorithm), 030304 developmental biology
Abstract

The arrival of farming in Europe around 8,500 years ago necessitated adaptation to new environments, pathogens, diets, and social organizations. While indirect evidence of adaptation can be detected in patterns of genetic variation in present-day people, ancient DNA makes it possible to witness selection directly by analyzing samples from populations before, during and after adaptation events. Here we report the first genome-wide scan for selection using ancient DNA, capitalizing on the largest genome-wide dataset yet assembled: 230 West Eurasians dating to between 6500 and 1000 BCE, including 163 with newly reported data. The new samples include the first genome-wide data from the Anatolian Neolithic culture, who we show were members of the population that was the source of Europe's first farmers, and whose genetic material we extracted by focusing on the DNA-rich petrous bone. We identify genome-wide significant signatures of selection at loci associated with diet, pigmentation and immunity, and two independent episodes of selection on height.

Published
2015
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13. Massive migration from the steppe was a source for Indo-European languages in Europe

Author

David Reich, Valery Khartanovich, Wolfgang Haak, Anna Szécsényi-Nagy, Roberto Risch, Iosif Lazaridis, Eadaoin Harney, Matthias Meyer, Aleksandr Khokhlov, Harald Meller, Susanne Friederich, Johannes Krause, Guido Brandt, Christina Roth, Rafael Garrido Pena, Qiaomei Fu, Vayacheslav Moiseyev, Eszter Bánffy, Michael Kunst, Pavel Kuznetsov, Michael Francken, Sandra Pichler, Kurt W. Alt, Nadin Rohland, David W. Anthony, Alan Cooper, Alissa Mittnik, Nick Patterson, Joachim Wahl, Oleg Mochalov, Manuel Ángel Rojo Guerra, Christos Economou, Kristin Stewardson, Bastien Llamas, Swapan Mallick, Fredrik Hallgren, Nicole Nicklisch, Dorcas Brown, and Susanne Nordenfelt

Subjects
Male, Archaeogenetics, Steppe, Human Migration, Population Dynamics, Population, Ancient history, Corded Ware culture, Indigenous, Article, Russia, 03 medical and health sciences, Cultural Evolution, Humans, 0601 history and archaeology, Quantitative Biology - Populations and Evolution, education, History, Ancient, Language, 030304 developmental biology, 0303 health sciences, geography, education.field_of_study, Polymorphism, Genetic, Multidisciplinary, geography.geographical_feature_category, 060102 archaeology, Genome, Human, Indo-European languages, Populations and Evolution (q-bio.PE), Languages of Europe, 06 humanities and the arts, Grassland, Europe, Eastern european, Ancient DNA, FOS: Biological sciences, Period (geology), Ethnology
Abstract

We generated genome-wide data from 69 Europeans who lived between 8,000-3,000 years ago by enriching ancient DNA libraries for a target set of almost four hundred thousand polymorphisms. Enrichment of these positions decreases the sequencing required for genome-wide ancient DNA analysis by a median of around 250-fold, allowing us to study an order of magnitude more individuals than previous studies and to obtain new insights about the past. We show that the populations of western and far eastern Europe followed opposite trajectories between 8,000-5,000 years ago. At the beginning of the Neolithic period in Europe, ~8,000-7,000 years ago, closely related groups of early farmers appeared in Germany, Hungary, and Spain, different from indigenous hunter-gatherers, whereas Russia was inhabited by a distinctive population of hunter-gatherers with high affinity to a ~24,000 year old Siberian6. By ~6,000-5,000 years ago, a resurgence of hunter-gatherer ancestry had occurred throughout much of Europe, but in Russia, the Yamnaya steppe herders of this time were descended not only from the preceding eastern European hunter-gatherers, but from a population of Near Eastern ancestry. Western and Eastern Europe came into contact ~4,500 years ago, as the Late Neolithic Corded Ware people from Germany traced ~3/4 of their ancestry to the Yamnaya, documenting a massive migration into the heartland of Europe from its eastern periphery. This steppe ancestry persisted in all sampled central Europeans until at least ~3,000 years ago, and is ubiquitous in present-day Europeans. These results provide support for the theory of a steppe origin of at least some of the Indo-European languages of Europe.

Published
2015

14. Genome-wide patterns of selection in 230 ancient Eurasians

Author

Jacob Roodenberg, Swapan Mallick, Dorcas Brown, Ron Pinhasi, Juan Luis Arsuaga, Alan Cooper, Nick Patterson, Songül Alpaslan Roodenberg, Eadaoin Harney, Johannes Krause, Iain Mathieson, Manuel Ángel Rojo Guerra, Iosif Lazaridis, Oleg Mochalov, Wolfgang Haak, Eudald Carbonell, David W. Anthony, Cristina Gamba, Vayacheslav Moiseyev, Josep Maria Vergès, Marina Lozano, Carles Lalueza-Fox, José María Bermúdez de Castro, Kendra Sirak, Aleksandr Khokhlov, Joseph K. Pickrell, Fokke Gerritsen, Bastien Llamas, Kurt W. Alt, Mario Novak, Kristin Stewardson, Nadin Rohland, Harald Meller, Daniel Fernandes, Pavel Kuznetsov, Eppie R. Jones, Stanislav Dryomov, David Reich, Irish Research Council for the Humanities and Social Sciences, Netherlands Organization for Scientific Research, Russian Foundation for Basic Research, Ministry of Education and Science of the Russian Federation, German Research Foundation, European Research Council, Ministerio de Economía y Competitividad (España), Australian Research Council, National Science Foundation (US), National Institutes of Health (US), Howard Hughes Medical Institute, Art and Culture, History, Antiquity, and CLUE+

Subjects
Male, Multifactorial Inheritance, Archaeogenetics, Asia, Population, Biology, Genome, Article, Bone and Bones, 03 medical and health sciences, 0302 clinical medicine, Humans, Selection, Genetic, education, History, Ancient, Selection (genetic algorithm), 030304 developmental biology, Genetics, 0303 health sciences, education.field_of_study, Multidisciplinary, Natural selection, ancient DNA, prehistory, Eurasia, natural selection, Genome, Human, Pigmentation, Immunity, Agriculture, DNA, Sequence Analysis, DNA, 15. Life on land, Body Height, Diet, 3. Good health, Europe, Genetics, Population, Ancient DNA, Haplotypes, Evolutionary biology, Human genome, Adaptation, 030217 neurology & neurosurgery
Abstract

Mathieson, Iain et al., 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., I.M. was supported by the Human Frontier Science Program LT001095/2014-L. C.G. was supported by the Irish Research Council for Humanities and Social Sciences (IRCHSS). F.G. was supported by a grant of the Netherlands Organization for Scientific Research, no. 380-62-005. A.K., P.K. and O.M. were supported by RFBR no. 15-06-01916 and RFH no. 15-11-63008 and O.M. by a state grant of the Ministry of Education and Science of the Russia Federation no. 33.1195.2014/k. J.K. was supported by ERC starting grant APGREID and DFG grant KR 4015/1-1. K.W.A. was supported by DFG grant AL 287 / 14-1. C.L.-F. was supported by a BFU2015-64699-P grant from the Spanish government. W.H. and B.L. were supported by Australian Research Council DP130102158. R.P. was supported by ERC starting grant ADNABIOARC (263441), and an Irish Research Council ERC support grant. D.R. was supported by US National Science Foundation HOMINID grant BCS-1032255, US National Institutes of Health grant GM100233, and the Howard Hughes Medical Institute.

Published
2015

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