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1. Ancient human genome-wide data from a 3000-year interval in the Caucasus corresponds with eco-geographic regions

Author

Chuan-Chao Wang, Sabine Reinhold, Alexey Kalmykov, Antje Wissgott, Guido Brandt, Choongwon Jeong, Olivia Cheronet, Matthew Ferry, Eadaoin Harney, Denise Keating, Swapan Mallick, Nadin Rohland, Kristin Stewardson, Anatoly R. Kantorovich, Vladimir E. Maslov, Vladimira G. Petrenko, Vladimir R. Erlikh, Biaslan Ch. Atabiev, Rabadan G. Magomedov, Philipp L. Kohl, Kurt W. Alt, Sandra L. Pichler, Claudia Gerling, Harald Meller, Benik Vardanyan, Larisa Yeganyan, Alexey D. Rezepkin, Dirk Mariaschk, Natalia Berezina, Julia Gresky, Katharina Fuchs, Corina Knipper, Stephan Schiffels, Elena Balanovska, Oleg Balanovsky, Iain Mathieson, Thomas Higham, Yakov B. Berezin, Alexandra Buzhilova, Viktor Trifonov, Ron Pinhasi, Andrej B. Belinskij, David Reich, Svend Hansen, Johannes Krause, and Wolfgang Haak

Subjects
Science
Abstract

The Caucasus mountain range has impacted on the culture and genetics of the wider region. Here, the authors generate genome-wide SNP data for 45 Eneolithic and Bronze Age individuals across the Caucasus, and find distinct genetic clusters between mountain and steppe zones as well as occasional gene-flow.

Published
2019
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2. Social stratification without genetic differentiation at the site of Kulubnarti in Christian Period Nubia

Author

Nadin Rohland, Kimberly Callan, Ron Pinhasi, Nicole Adamski, Fatma Zalzala, Jonas Oppenheimer, Carla S. Hadden, Eadaoin Harney, Mark Lipson, Rebecca Bernardos, Megan Michel, Matthew Ferry, Kendra Sirak, Iñigo Olalde, Dennis P. Van Gerven, David Reich, Nick Patterson, Matthew Mah, Kristin Stewardson, Jessica C. Thompson, Ann Marie Lawson, Daniel Fernandes, Harald Ringbauer, Swapan Mallick, Nasreen Broomandkhoshbacht, National Science Foundation (US), John Templeton Foundation, Howard Hughes Medical Institute, and Paul G. Allen Family Foundation

Subjects
Male, Population genetics, Science, Genetic genealogy, General Physics and Astronomy, Article, General Biochemistry, Genetics and Molecular Biology, Sudan, Prehistory, Humans, History, Ancient, Sex Characteristics, Multidisciplinary, Fossils, Genome, Human, Genetic Drift, Genetic Variation, Islam, Gene Pool, General Chemistry, Genomics, Social Status, Social stratification, humanities, Genetic differentiation, Genetics, Population, Geography, Period (geology), Ethnology, Egypt, Female, Gene pool, Social status
Abstract

Relatively little is known about Nubia’s genetic landscape prior to the influence of the Islamic migrations that began in the late 1st millennium CE. Here, we increase the number of ancient individuals with genome-level data from the Nile Valley from three to 69, reporting data for 66 individuals from two cemeteries at the Christian Period (~650–1000 CE) site of Kulubnarti, where multiple lines of evidence suggest social stratification. The Kulubnarti Nubians had ~43% Nilotic-related ancestry (individual variation between ~36–54%) with the remaining ancestry consistent with being introduced through Egypt and ultimately deriving from an ancestry pool like that found in the Bronze and Iron Age Levant. The Kulubnarti gene pool – shaped over a millennium – harbors disproportionately female-associated West Eurasian-related ancestry. Genetic similarity among individuals from the two cemeteries supports a hypothesis of social division without genetic distinction. Seven pairs of inter-cemetery relatives suggest fluidity between cemetery groups. Present-day Nubians are not directly descended from the Kulubnarti Nubians, attesting to additional genetic input since the Christian Period., Little is known about the genetic landscape of people living in the Nile region prior to the Islamic migrations of the late 1st millennium CE. Here, the authors report genome-wide data for 66 ancient individuals to investigate the genetic ancestry of a Christian Period group from Kulubnarti.

Published
2021

3. COMBINING ANCIENT DNA AND RADIOCARBON DATING DATA TO INCREASE CHRONOLOGICAL ACCURACY

Author

David Reich, Eadaoin Harney, Nick Patterson, Iñigo Olalde, Jakob Sedig, National Institutes of Health (US), Paul G. Allen Family Foundation, and John Templeton Foundation

Subjects
Radiocarbon dating, Archeology, Ancient DNA, OxCal, Bayesian analysis, food and beverages, Genealogy, humanities, Article, law.invention, Geography, law, Date Range, Physical geography
Abstract

This paper examines how ancient DNA data can enhance radiocarbon dating. Because there is a limit to the number of years that can separate the dates of death of related individuals, the ability to identify relatives through ancient DNA analysis can serve as a constraint on radiocarbon date range estimates. To determine the number of years that can separate related individuals, we modeled maximums derived from biological extremes of human reproduction and death ages and compiled data from historic and genealogical death records. We used these data to jointly study the date ranges of a global dataset of individuals that have been radiocarbon dated and for which ancient DNA analysis identified at least one relative. We found that many of these individuals could have their date uncertainties reduced by building in date of death separation constraints. We examined possible reasons for date discrepancies of related individuals, such as dating of different skeletal elements or wiggles in the radiocarbon curve. We also developed a program, refinedate, which researchers can download and use to help refine the radiocarbon date distributions of related individuals. Our research demonstrates that when combined, radiocarbon dating and ancient DNA analysis can provide a refined and richer view of the past., This work was funded by NIH grant GM100233, the Paul Allen Foundation, John Templeton Foundation (grant number 6122).

Published
2021

4. Ancient DNA from the skeletons of Roopkund Lake reveals Mediterranean migrants in India

Author

Subhash Chandra Diyundi, Megan Michel, Rebecca Bernardos, Kumarasamy Thangaraj, Sachin Kumar, Jonas Oppenheimer, Ayushi Nayak, Kristin Stewardson, Eadaoin Harney, Patrick Roberts, Veena Mushrif-Tripathy, Nadin Rohland, Pramod Joglekar, Douglas J. Kennett, Matthew Ferry, Harashawaradhana, Nicole Boivin, David Reich, Brendan J. Culleton, Maanwendra Singh Bartwal, Swapan Mallick, Nicole Adamski, Zhao Zhang, Niraj Rai, Jakob Sedig, Nick Patterson, Thomas K. Harper, and Nasreen Broomandkhoshbacht

Subjects
0301 basic medicine, Mediterranean climate, South asia, Range (biology), Science, Human Migration, General Physics and Astronomy, India, 02 engineering and technology, Polymorphism, Single Nucleotide, General Biochemistry, Genetics and Molecular Biology, Article, law.invention, 03 medical and health sciences, law, Humans, Radiocarbon dating, Genetic variation, lcsh:Science, Sea level, Multidisciplinary, Fossils, Mediterranean Region, Racial Groups, Radiometric Dating, General Chemistry, DNA, 021001 nanoscience & nanotechnology, Archaeology, Body Remains, Diet, Eastern mediterranean, 030104 developmental biology, Ancient DNA, Geography, lcsh:Q, 0210 nano-technology
Abstract

Situated at over 5,000 meters above sea level in the Himalayan Mountains, Roopkund Lake is home to the scattered skeletal remains of several hundred individuals of unknown origin. We report genome-wide ancient DNA for 38 skeletons from Roopkund Lake, and find that they cluster into three distinct groups. A group of 23 individuals have ancestry that falls within the range of variation of present-day South Asians. A further 14 have ancestry typical of the eastern Mediterranean. We also identify one individual with Southeast Asian-related ancestry. Radiocarbon dating indicates that these remains were not deposited simultaneously. Instead, all of the individuals with South Asian-related ancestry date to ~800 CE (but with evidence of being deposited in more than one event), while all other individuals date to ~1800 CE. These differences are also reflected in stable isotope measurements, which reveal a distinct dietary profile for the two main groups., Remains of several hundred humans are scattered around Roopkund Lake, situated over 5,000 meters above sea level in the Himalayan Mountains. Here the authors analyze genome-wide data from 38 skeletons and find 3 clusters with different ancestries and dates, showing the people were desposited in multiple catastrophic events.

Published
2019

5. Ancient human genome-wide data from a 3000-year interval in the Caucasus corresponds with eco-geographic regions

Author

Alexandra P. Buzhilova, Benik Vardanyan, Harald Meller, Johannes Krause, Kristin Stewardson, Natalia Berezina, Katharina Fuchs, Sabine Reinhold, Andrej Belinskij, Julia Gresky, Eadaoin Harney, Iain Mathieson, Stephan Schiffels, Guido Brandt, Elena Balanovska, Antje Wissgott, Alexey D. Rezepkin, Choongwon Jeong, Denise Keating, Viktor Trifonov, Ron Pinhasi, Olivia Cheronet, Wolfgang Haak, Chuan-Chao Wang, Anatoly R. Kantorovich, Vladimir E. Maslov, Corina Knipper, Oleg Balanovsky, Vladimir R. Erlikh, Swapan Mallick, Thomas Higham, Kurt W. Alt, Matthew Ferry, Rabadan G. Magomedov, Nadin Rohland, Alexey Kalmykov, Claudia Gerling, Philipp L. Kohl, Sandra Pichler, David Reich, Yakov B. Berezin, Larisa Yeganyan, Dirk Mariaschk, Svend Hansen, Vladimira G. Petrenko, and Biaslan Ch. Atabiev

Subjects
0301 basic medicine, Population genetics, Steppe, Science, Pastoralism, General Physics and Astronomy, Evolutionary biology, 02 engineering and technology, General Biochemistry, Genetics and Molecular Biology, Article, Prehistory, 03 medical and health sciences, Bronze Age, Transect, lcsh:Science, 2. Zero hunger, Multidisciplinary, geography.geographical_feature_category, Ecology, Genomics, General Chemistry, Chalcolithic, 15. Life on land, 021001 nanoscience & nanotechnology, 030104 developmental biology, Geography, Archaeology, Anthropology, Human genome, lcsh:Q, 0210 nano-technology, Mountain range
Abstract

Archaeogenetic studies have described the formation of Eurasian ‘steppe ancestry’ as a mixture of Eastern and Caucasus hunter-gatherers. However, it remains unclear when and where this ancestry arose and whether it was related to a horizon of cultural innovations in the 4th millennium BCE that subsequently facilitated the advance of pastoral societies in Eurasia. Here we generated genome-wide SNP data from 45 prehistoric individuals along a 3000-year temporal transect in the North Caucasus. We observe a genetic separation between the groups of the Caucasus and those of the adjacent steppe. The northern Caucasus groups are genetically similar to contemporaneous populations south of it, suggesting human movement across the mountain range during the Bronze Age. The steppe groups from Yamnaya and subsequent pastoralist cultures show evidence for previously undetected farmer-related ancestry from different contact zones, while Steppe Maykop individuals harbour additional Upper Palaeolithic Siberian and Native American related ancestry., The Caucasus mountain range has impacted on the culture and genetics of the wider region. Here, the authors generate genome-wide SNP data for 45 Eneolithic and Bronze Age individuals across the Caucasus, and find distinct genetic clusters between mountain and steppe zones as well as occasional gene-flow.

Published
2019

6. 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

7. A Minimally Destructive Protocol for DNA Extraction from Ancient Teeth

Author

Alexandra Anders, Ann Marie Lawson, Krisztián Kiss, János Dani, Kimberly Callan, Tamás Szeniczey, Jonas Oppenheimer, Eadaoin Harney, Olivia Cheronet, Ágnes Király, Ron Pinhasi, Daniel Fernandes, Cristian Virag, Fatma Zalzala, Kendra Sirak, Magdolna Hellebrandt, Ion Ciobanu, Kitti Köhler, Sergey Vasilyev, Peter Kovacs, Pál Raczky, Rebecca Bernardos, Francesca Candilio, Emese Nagy, Francesco Genchi, Tamás Hajdu, Nasreen Broomandkhoshbacht, Kristin Stewardson, Antónia Horváth, Mihai Constantinescu, Sergiu Popovici, Nadin Rohland, Alfredo Coppa, Zsolt Gallina, Angela Simalcsik, Michaela Lucci, David Reich, Nicole Adamski, Matthew Mah, Barbara Kolozsi, and Ildikó Pap

Subjects
Male, DNA ancient, dental cementum, humans, male, tooth, Dentistry, Method, Biology, 03 medical and health sciences, 0302 clinical medicine, stomatognathic system, Genetics, medicine, Humans, Cementum, DNA, Ancient, Genetics (clinical), 030304 developmental biology, Dental Cementum, High concentration, 0303 health sciences, business.industry, Sampling (statistics), Tooth surface, Light irradiation, Destructive sampling, DNA extraction, stomatognathic diseases, medicine.anatomical_structure, Ancient DNA, Extraction methods, Dental cementum, business, Tooth, 030217 neurology & neurosurgery, Geology, Biomedical engineering
Abstract

Ancient DNA sampling methods—although optimized for efficient DNA extraction—are destructive, relying on drilling or cutting and powdering (parts of) bones and teeth. As the field of ancient DNA has grown, so have concerns about the impact of destructive sampling of the skeletal remains from which ancient DNA is obtained. Due to a particularly high concentration of endogenous DNA, the cementum of tooth roots is often targeted for ancient DNA sampling, but standard destructive sampling methods often result in the loss of at least one entire root. Here, we present a minimally destructive method for extracting ancient DNA from dental cementum present on the surface of tooth roots. This method does not require destructive drilling or grinding, and, following extraction, the tooth remains safe to handle and suitable for most morphological studies, as well as other biochemical studies, such as radiocarbon dating. We extracted and sequenced ancient DNA from 30 teeth (and 9 corresponding petrous bones) using this minimally destructive extraction method in addition to a typical tooth sampling method. We find that the minimally destructive method can provide ancient DNA that is of comparable quality to extracts produced from teeth that have undergone destructive sampling processes. Further, we find that a rigorous cleaning of the tooth surface combining diluted bleach and UV light irradiation seems sufficient to minimize external contaminants usually removed through the physical removal of a superficial layer when sampling through regular powdering methods.

Published
2020

8. 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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9. ContamLD: Estimation of Ancient Nuclear DNA Contamination Using Breakdown of Linkage Disequilibrium

Author

Eadaoin Harney, Nathan Nakatsuka, Nick Patterson, Matthew Mah, Swapan Mallick, and David Reich

Subjects
Linkage disequilibrium, lcsh:QH426-470, Biology, 03 medical and health sciences, chemistry.chemical_compound, 0302 clinical medicine, Contamination, Statistics, DNA, Ancient, lcsh:QH301-705.5, 030304 developmental biology, Autosomal DNA, 0303 health sciences, Ancient DNA, Haplotype, Nuclear DNA, DNA Contamination, Uncorrelated, lcsh:Genetics, Standard error, Haplotypes, lcsh:Biology (General), chemistry, Simulated data, Environmental science, Biological system, Software, 030217 neurology & neurosurgery, DNA
Abstract

We report a method,ContamLD, for estimating autosomal ancient DNA (aDNA) contamination by measuring the breakdown of linkage disequilibrium in a sequenced individual due to the introduction of contaminant DNA, leveraging the idea that contaminants should have haplotypes uncorrelated to those of the studied individual. Using simulated data, we confirm thatContamLDaccurately infers contamination rates with low standard errors (e.g. less than 1.5% standard error in cases with https://github.com/nathan-nakatsuka/ContamLD.

Published
2020

10. 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

11. Human Auditory Ossicles as an Alternative Optimal Source of Ancient DNA

Author

Ron Pinhasi, Michael Pietrusewsky, Lynne S. Bell, Zdeněk Farkaš, Tumen Dashtseveg, Sándor Évinger, Daniel Fernandes, Kimberly Callan, Béla Miklós Szőke, Eadaoin Harney, Juraj Bartík, Andrei Soficaru, Vyacheslav Moiseyev, Tamás Szeniczey, Nicole Adamski, Alfredo Coppa, Mercedes Okumura, Pál Raczky, Jonas Oppenheimer, Kirsten Mandl, Fatma Zalzala, Swapan Mallick, Ann Marie Lawson, Nasreen Broomandkhoshbacht, Matthew Mah, Alexandra Anders, David Reich, Kristin Stewardson, Olivia Cheronet, Alena Šefčáková, Jamsranjav Bayarsaikhan, Francesca Candilio, Sergey Vasilyev, Tamás Hajdu, Kendra Sirak, Lauren McIntyre, Nadin Rohland, Dennis P. Van Gerven, and Ildikó Pap

Subjects
Method, Biology, Dna recovery, 03 medical and health sciences, 0302 clinical medicine, auditory ossicles, ancient DNA, paleogenomic data, DNA optimization, Genetics, medicine, otorhinolaryngologic diseases, Humans, 0601 history and archaeology, Inner ear, Auditory ossicle, DNA, Ancient, Genetics (clinical), Cochlea, Ear Ossicles, 030304 developmental biology, Petrous Bones, 0303 health sciences, 060101 anthropology, Ossicles, Sequence Analysis, DNA, 06 humanities and the arts, Ancient DNA, medicine.anatomical_structure, Evolutionary biology, 030217 neurology & neurosurgery
Abstract

DNA recovery from ancient human remains has revolutionized our ability to reconstruct the genetic landscape of the past. Ancient DNA research has benefited from the identification of skeletal elements, such as the cochlear part of the osseous inner ear, that provide optimal contexts for DNA preservation; however, the rich genetic information obtained from the cochlea must be counterbalanced against the loss of valuable morphological information caused by its sampling. Motivated by similarities in developmental processes and histological properties between the cochlea and auditory ossicles, we evaluated the efficacy of ossicles as an alternative source of ancient DNA. We demonstrate that ossicles perform comparably to the cochlea in terms of DNA recovery, finding no substantial reduction in data quality, quantity, or authenticity across a range of preservation conditions. Ossicles can be sampled from intact skulls or disarticulated petrous bones without damage to surrounding bone, and we argue that, when available, they should be selected over the cochlea to reduce damage to skeletal integrity. These results identify a second optimal skeletal element for ancient DNA analysis and add to a growing toolkit of sampling methods that help to better preserve skeletal remains for future research while maximizing the likelihood that ancient DNA analysis will produce useable results.

Published
2019
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12. Corrigendum: Human auditory ossicles as an alternative optimal source of ancient DNA

Author

Kristin Stewardson, Daniel Fernandes, Tamás Szeniczey, Olivia Cheronet, Zdeněk Farkaš, Nadin Rohland, Tumen Dashtseveg, Jonas Oppenheimer, Francesca Candilio, Michael Pietrusewsky, Juraj Bartík, Sándor Évinger, Alena Šefčáková, Fatma Zalzala, Sergey Vasilyev, Swapan Mallick, Tamás Hajdu, Ron Pinhasi, David Reich, Béla Miklós Szőke, Matthew Mah, Ann Marie Lawson, Eadaoin Harney, Ildikó Pap, Kirsten Mandl, Nicole Adamski, Alexandra Anders, Lynne S. Bell, Mercedes Okumura, Nasreen Broomandkhoshbacht, Dennis P. Van Gerven, Kimberly Callan, Alfredo Coppa, Pál Raczky, Vyacheslav Moiseyev, Kendra Sirak, Jamsranjav Bayarsaikhan, Lauren M. McIntyre, and Andrei Soficaru

Subjects
Ancient DNA, Evolutionary biology, Genetics, Auditory ossicle, Biology, Corrigendum, Genetics (clinical)
Published
2020

13. 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

14. The genetic prehistory of the Greater Caucasus

Author

Philipp L. Kohl, Sandra Pichler, Sabine Reinhold, David Reich, Thomas Higham, Corina Knipper, Svend Hansen, Anatoly R. Kantorovich, Ron Pinhasi, Chuan-Chao Wang, Kurt W. Alt, Julia Gresky, Alexandra P. Buzhilova, Katharina Fuchs, Oleg Balanovsky, Vladimir R. Erlikh, Matthew Ferry, Benik Vardanyan, Wolfgang Haak, Natalia Berezina, Johannes Krause, Choongwon Jeong, Vladimira G. Petrenko, Harald Meller, Antje Wissgott, Guido Brandt, Alexey D. Rezepkin, Denise Keating, Alexey Kalmykov, Rabadan G. Magomedov, Eadaoin Harney, Iain Mathieson, Nadin Rohland, Larisa Yeganyan, Dirk Mariaschk, Yakov B. Berezin, Claudia Gerling, Andrej Belinskij, Biaslan Ch. Atabiev, Vladimir E. Maslov, Swapan Mallick, Kristin Stewardson, Stephan Schiffels, Elena Balanovska, Viktor Trifonov, and Olivia Cheronet

Subjects
Prehistory, Snp data, Geography, geography.geographical_feature_category, Steppe, Ecology, Native american, Pastoralism, Biological dispersal
Abstract

Archaeogenetic studies have described the formation of Eurasian ‘steppe ancestry’ as a mixture of Eastern and Caucasus hunter-gatherers. However, it remains unclear when and where this ancestry arose and whether it was related to a horizon of cultural innovations in the 4thmillennium BCE that subsequently facilitated the advance of pastoral societies likely linked to the dispersal of Indo-European languages. To address this, we generated genome-wide SNP data from 45 prehistoric individuals along a 3000-year temporal transect in the North Caucasus. We observe a genetic separation between the groups of the Caucasus and those of the adjacent steppe. The Caucasus groups are genetically similar to contemporaneous populations south of it, suggesting that – unlike today – the Caucasus acted as a bridge rather than an insurmountable barrier to human movement. The steppe groups from Yamnaya and subsequent pastoralist cultures show evidence for previously undetected farmer-related ancestry from different contact zones, while Steppe Maykop individuals harbour additional Upper Palaeolithic Siberian and Native American related ancestry.

Published
2018
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15. The Genomic Formation of South and Central Asia

Author

Nadezhda Stepanova, Ron Pinhasi, Enshin Dmitry, Bryan Hanks, Iñigo Olalde, Nasreen Broomandkhoshbacht, Sergey Vasilyev, Eadaoin Harney, James Mallory, Daniel Fernandes, Dorian Q. Fuller, Nicole Boivin, Richard Potts, Rebecca Bernardos, Elena Kupriyanova, Aleksander Khokhlov, Anatoly N. Bagashev, Farhad Maksudov, Margaret A. Judd, Priya Moorjani, Mateja Hajdinjak, Mario Novak, David W. Anthony, Francesca Candilio, Gaziz Akhatov, Baurzhan Baitanayev, Sergey M. Slepchenko, Svetlana V. Svyatko, Nick Patterson, Zhao Zhang, Olivia Cheronet, Nadin Rohland, Pavel Kuznetsov, Beatriz Gamarra, Katerina Douka, Ann-Marie Lawson, Oleg Mochalov, Thomas K. Harper, Nathan Nakatsuka, Jonas Oppenheimer, Antonina Yermolayeva, Alexander Goryachev, Egor Kitov, David Reich, Swapan Mallick, T. A. Chikisheva, Brendan J. Culleton, Vasant Shinde, Stefania Sarno, Deborah C. Merrett, Matthew Ferry, Ayushi Nayak, Matthias Meyer, Daniel Gaudio, Andrey Epimakhov, Vagheesh M. Narasimhan, Kendra Sirak, Nicole Adamski, Kulyan Sikhymbaevae, Alfredo Coppa, Denise Keating, Erlan Kazizov, Lipson Mark, Muhammad Zahir, Gian Luca Bonora, Massimo Vidale, Christopher Meiklejohn, Samridin Mustafakulov, Iosif Lazaridis, Kristin Stewardson, Davide Pettner, Andrey Gromov, Dmitry Razhev, Viviane Slon, Roberto Micheli, Kumarasmy Thangaraj, Donata Luiselli, Luca M. Olivieri, Niraj Rai, Rykun M Petrovna, Megan Michel, Nadezhda Dubova, Suzanne Freilich, Janet Monge, Anatoly P. Derevianko, Carles Lalueza-Fox, Vyacheslav Moiseyev, Dima Voyakin, Michael D. Frachetti, Alexander M. Kim, Douglas J. Kennett, and A. V. Zubova

Subjects
0303 health sciences, Civilization, South asia, geography.geographical_feature_category, Steppe, media_common.quotation_subject, Indus, 030305 genetics & heredity, Central asia, Pastoralism, 15. Life on land, Prehistory, 03 medical and health sciences, Geography, Bronze Age, Ethnology, 030304 developmental biology, media_common
Abstract

The genetic formation of Central and South Asian populations has been unclear because of an absence of ancient DNA. To address this gap, we generated genome-wide data from 362 ancient individuals, including the first from eastern Iran, Turan (Uzbekistan, Turkmenistan, and Tajikistan), Bronze Age Kazakhstan, and South Asia. Our data reveal a complex set of genetic sources that ultimately combined to form the ancestry of South Asians today. We document a southward spread of genetic ancestry from the Eurasian Steppe, correlating with the archaeologically known expansion of pastoralist sites from the Steppe to Turan in the Middle Bronze Age (2300-1500 BCE). These Steppe communities mixed genetically with peoples of the Bactria Margiana Archaeological Complex (BMAC) whom they encountered in Turan (primarily descendants of earlier agriculturalists of Iran), but there is no evidence that the main BMAC population contributed genetically to later South Asians. Instead, Steppe communities integrated farther south throughout the 2nd millennium BCE, and we show that they mixed with a more southern population that we document at multiple sites as outlier individuals exhibiting a distinctive mixture of ancestry related to Iranian agriculturalists and South Asian hunter-gathers. We call this groupIndus Peripherybecause they were found at sites in cultural contact with the Indus Valley Civilization (IVC) and along its northern fringe, and also because they were genetically similar to post-IVC groups in the Swat Valley of Pakistan. By co-analyzing ancient DNA and genomic data from diverse present-day South Asians, we show thatIndus Periphery-related people are the single most important source of ancestry in South Asia—consistent with the idea that theIndus Peripheryindividuals are providing us with the first direct look at the ancestry of peoples of the IVC—and we develop a model for the formation of present-day South Asians in terms of the temporally and geographically proximate sources ofIndus Periphery-related, Steppe, and local South Asian hunter-gatherer-related ancestry. Our results show how ancestry from the Steppe genetically linked Europe and South Asia in the Bronze Age, and identifies the populations that almost certainly were responsible for spreading Indo-European languages across much of Eurasia.One Sentence SummaryGenome wide ancient DNA from 357 individuals from Central and South Asia sheds new light on the spread of Indo-European languages and parallels between the genetic history of two sub-continents, Europe and South Asia.

Published
2018
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16. 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

17. 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

18. 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

19. 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

20. 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

21. 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

22. The genetic structure of the world’s first farmers

Author

György Lengyel, Ahuva-Sivan Mizrahi, Nick Patterson, David Comas, Darren McGettigan, Ron Pinhasi, Deborah C. Merrett, Shona M. Kerr, Peter Kovacs, Qiaomei Fu, Kendra Sirak, Daniel Fernandes, Beatriz Gamarra, Christopher Meiklejohn, Michael Merrigan, Archie Campbell, Songül Alpaslan Roodenberg, Martin B. Richards, Gary O. Rollefson, Kristin Stewardson, Eadaoin Harney, Michael Stumvoll, David Reich, Michel Shamoon-Pour, Philippe Froguel, Michael Gregg, Mario Novak, Johannes Krause, Iosif Lazaridis, Seamus O’Reilly, Gloria Gonzalez-Fortes, Swapan Mallick, Gheorghe Stefanescu, Sarah Connell, Gianpero Cavalleri, Vered Eshed, Anke Tönjes, Nelli Hovhannisyan, Fokke Gerritsen, Nadin Rohland, Edmund Gilbert, Dani Nadel, Matthias Blueher, Fanny Bocquentin, James F. Wilson, Boris Gasparian, Antonio Torroni, Janet Monge, Luminita Bejenaru, Loic Yengo, Ornella Semino, and D. Andrew Merriwether

Subjects
2. Zero hunger, 0303 health sciences, geography.geographical_feature_category, Middle East, Neanderthal, Southern Levant, biology, Steppe, Pastoralism, 15. Life on land, Archaeology, 03 medical and health sciences, 0302 clinical medicine, Geography, Ancient DNA, Bronze Age, biology.animal, Genetic structure, 030217 neurology & neurosurgery, 030304 developmental biology
Abstract

We report genome-wide ancient DNA from 44 ancient Near Easterners ranging in time between ~12,000-1,400 BCE, 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 prior to 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 drastically 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 from 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.

Published
2016
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23. 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

24. Genomic insights into the origin of farming in the ancient Near East

Author

Peter Kovacs, Dani Nadel, Eppie R. Jones, James F. Wilson, Gary O. Rollefson, Christopher Meiklejohn, Beatriz Gamarra, Songül Alpaslan Roodenberg, Anke Tönjes, Edmund Gilbert, Eadaoin Harney, Darren McGettigan, Mario Novak, Shona M. Kerr, Michael Stumvoll, Michael Gregg, György Lengyel, Antonio Torroni, Nadin Rohland, Matthias Blüher, Loic Yengo, Daniel Fernandes, Nick Patterson, David Comas, David Reich, Qiaomei Fu, Janet Monge, Archie Campbell, Vered Eshed, Deborah C. Merrett, Ron Pinhasi, Michael Merrigan, Seamus O’Reilly, Kristin Stewardson, Gianpiero L. Cavalleri, Martin B. Richards, Philippe Froguel, Gheorghe Stefanescu, Fokke Gerritsen, Swapan Mallick, Michel Shamoon-Pour, Luminita Bejenaru, Ahuva Sivan Mizrahi, Boris Gasparian, Fanny Bocquentin, Kendra Sirak, Johannes Krause, Iosif Lazaridis, Gloria Gonzalez-Fortes, Sarah Connell, Nelli Hovhannisyan, D. Andrew Merriwether, Ornella Semino, Art and Culture, History, Antiquity, CLUE+, Irish Research Council, Irish Research Council for the Humanities and Social Sciences, European Research Council, Chinese Academy of Sciences, National Natural Science Foundation of China, Scottish Government, Scottish Funding Council, German Research Foundation, Wenner-Gren Foundation, National Science Foundation (US), Federal Ministry of Education and Research (Germany), European Commission, Leverhulme Trust, Università degli studi di Pavia, Ministero dell'Istruzione, dell'Università e della Ricerca, National Geographic Society, Irene Levi Sala Care Archaeological Foundation, Israel Science Foundation, Howard Hughes Medical Institute, Department of Genetics [Boston], Harvard Medical School [Boston] (HMS), Broad Institute of MIT and Harvard (BROAD INSTITUTE), Harvard Medical School [Boston] (HMS)-Massachusetts Institute of Technology (MIT)-Massachusetts General Hospital [Boston], Zinman Institute of Archaeology [Haifa], University of Haifa [Haifa], Whitman College, Simon Fraser University (SFU.ca), Howard Hughes Medical Institute [Boston] (HHMI), Howard Hughes Medical Institute (HHMI)-Harvard Medical School [Boston] (HMS), University College Dublin [Dublin] (UCD), Research Centre for Anthropology and Health (CIAS), Department of Life Sciences, Universidade de Coimbra, Coimbra, Portugal., Institute for Anthropological Research, 10000 Zagreb, Croatia., Emory University [Atlanta, GA], Department of Organismic and Evolutionary Biology [Cambridge] (OEB), Harvard University [Cambridge], Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology [Leipzig], Max-Planck-Gesellschaft-Max-Planck-Gesellschaft, Key Laboratory of Vertebrate Evolution and Human Origins of Chinese Academy of Sciences, Institute of Vertebrate Paleontology and Paleoanthropology, Biology and Evolution, University of Ferrara, Università degli Studi di Ferrara (UniFE), Department of Zoology [Cambridge], University of Cambridge [UK] (CAM), University of Miskolc, Ethnologie préhistorique, 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)-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), National Academy of Sciences of the Republic of Armenia [Yerevan] (NAS RA), University of Pennsylvania Museum of Archaeology and Anthropology (Penn Museum), israel Antiquities Authority, University of Winnipeg, Netherlands Institute in Turkey, Alexandru Ioan Cuza University of Iași [Romania], Clinic of Endocrinology and Nephrology [Leipzig], University of Edinburgh, Royal College of Surgeons in Ireland (RCSI), Institut de Biologia Evolutiva (CSIC-UPF), Universitat Pompeu Fabra [Barcelona] (UPF), Metabolic functional (epi)genomics and molecular mechanisms involved in type 2 diabetes and related diseases - UMR 8199 - UMR 1283 (GI3M), Institut Pasteur de Lille, Réseau International des Instituts Pasteur (RIIP)-Réseau International des Instituts Pasteur (RIIP)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Lille-Centre National de la Recherche Scientifique (CNRS), Imperial College London, Universityhospital of Leipzig, Max Planck Institute for the Science of Human History (MPI-SHH), Max-Planck-Gesellschaft, Genealogical Society of Ireland, Binghamton University [SUNY], State University of New York (SUNY), University of Huddersfield, Università degli Studi di Pavia, Institutul de Cercetari Biologice, Usher Institute of Population Health Sciences and Informatics [Edinburgh, U.K.], MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine (MRC), Edinburgh University, Yerevan State University, Harvard University, Università degli Studi di Ferrara = University of Ferrara (UniFE), 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)-Centre National de la Recherche Scientifique (CNRS)-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)-Centre National de la Recherche Scientifique (CNRS), Metabolic functional (epi)genomics and molecular mechanisms involved in type 2 diabetes and related diseases - UMR 8199 - UMR 1283 (EGENODIA (GI3M)), Università degli Studi di Pavia = University of Pavia (UNIPV), 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 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), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Lille-Centre National de la Recherche Scientifique (CNRS)-Institut Pasteur de Lille, and Réseau International des Instituts Pasteur (RIIP)-Réseau International des Instituts Pasteur (RIIP)

Subjects
0301 basic medicine, History, Neanderthal, Turkey, Steppe, Migració humana -- Història, Eastern, Iran, Israel, History, Ancient, Phylogeny, Neanderthals, 2. Zero hunger, Multidisciplinary, geography.geographical_feature_category, Middle East, biology, Continental Population Groups, Agriculture, Genomics, Africa, Eastern, Armenia, Europe, Phylogeography, Archaeogenetics, Asia, Southern Levant, [SHS.ARCHEO]Humanities and Social Sciences/Archaeology and Prehistory, Human Migration, Pastoralism, Animals, DNA, Humans, Hybridization, Genetic, Jordan, Article, Ancient, ancient DNA, Near East, hunter-gatherers, early farmers, Filogènia, 03 medical and health sciences, Genetic, Bronze Age, biology.animal, QH426, Hybridization, Agricultura -- Història, geography, QH, Racial Groups, Ambientale, 15. Life on land, Archaeology, Genòmica, 030104 developmental biology, Ancient DNA, Africa, Genètica
Abstract

Lazaridis, Iosif et al., 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., D.F. and M.N. were supported by Irish Research Council grants GOIPG/2013/36 and GOIPD/2013/1, respectively. S.C. was funded by the Irish Research Council for Humanities and Social Sciences (IRCHSS) ERC Support Programme. Q.F. was funded by the Bureau of International Cooperation of the Chinese Academy of Sciences, the National Natural Science Foundation of China (L1524016) and the Chinese Academy of Sciences Discipline Development Strategy Project (2015-DX-C-03). The Scottish diversity data was funded by the Chief Scientist Office of the Scottish Government Health Directorates (CZD/16/6), the Scottish Funding Council (HR03006), and a project grant from the Scottish Executive Health Department, Chief Scientist Office (CZB/4/285). M.S., A.Tön., M.B. and P.K. were supported by the German Research Foundation (CRC 1052; B01, B03, C01). M.S.-P. was funded by a Wenner-Gren Foundation Dissertation Fieldwork grant (9005), and by the National Science Foundation DDRIG (BCS-1455744). P.K. was funded by the Federal Ministry of Education and Research, Germany (FKZ: 01EO1501). J.F.W. acknowledge the MRC ‘QTL in Health and Disease’ programme grant. The Romanian diversity data was supported by the EC Commission, Directorate General XII (Supplementary Agreement ERBCIPDCT 940038 to the Contract ERBCHRXCT 920032, coordinated by A. Piazza, Turin, Italy). M.R. received support from the Leverhulme Trust’s Doctoral Scholarship programme. O.S. and A.Tor. were supported by the University of Pavia (MIGRAT-IN-G) and the Italian Ministry of Education, University and Research: Progetti Ricerca Interesse Nazionale 2012. The Raqefet Cave Natufian project was supported by funds from the National Geographic Society (grant 8915-11), the Wenner-Gren Foundation (grant 7481) and the Irene Levi-Sala CARE Foundation, while radiocarbon dating on the samples was funded by the Israel Science Foundation (grant 475/10; E. Boaretto). R.P. was supported by ERC starting grant ADNABIOARC (263441). D.R. was supported by NIH grant GM100233, by NSF HOMINID BCS-1032255, and is a Howard Hughes Medical Institute investigator.

Published
2016

25. 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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26. 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

27. 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

28. Social stratification without genetic differentiation at the site of Kulubnarti in Christian Period Nubia

Author

Kendra A. Sirak, Daniel M. Fernandes, Mark Lipson, Swapan Mallick, Matthew Mah, Iñigo Olalde, Harald Ringbauer, Nadin Rohland, Carla S. Hadden, Éadaoin Harney, Nicole Adamski, Rebecca Bernardos, Nasreen Broomandkhoshbacht, Kimberly Callan, Matthew Ferry, Ann Marie Lawson, Megan Michel, Jonas Oppenheimer, Kristin Stewardson, Fatma Zalzala, Nick Patterson, Ron Pinhasi, Jessica C. Thompson, Dennis Van Gerven, and David Reich

Subjects
Science
Abstract

Little is known about the genetic landscape of people living in the Nile region prior to the Islamic migrations of the late 1st millennium CE. Here, the authors report genome-wide data for 66 ancient individuals to investigate the genetic ancestry of a Christian Period group from Kulubnarti.

Published
2021
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29. ContamLD: estimation of ancient nuclear DNA contamination using breakdown of linkage disequilibrium

Author

Nathan Nakatsuka, Éadaoin Harney, Swapan Mallick, Matthew Mah, Nick Patterson, and David Reich

Subjects
Ancient DNA, Linkage disequilibrium, Contamination, Autosomal DNA, Nuclear DNA, Biology (General), QH301-705.5, Genetics, QH426-470
Abstract

Abstract We report a method called ContamLD for estimating autosomal ancient DNA (aDNA) contamination by measuring the breakdown of linkage disequilibrium in a sequenced individual due to the introduction of contaminant DNA. ContamLD leverages the idea that contaminants should have haplotypes uncorrelated to those of the studied individual. Using simulated data, we confirm that ContamLD accurately infers contamination rates with low standard errors: for example, less than 1.5% standard error in cases with less than 10% contamination and 500,000 sequences covering SNPs. This method is optimized for application to aDNA, taking advantage of characteristic aDNA damage patterns to provide calibrated contamination estimates, and is available at https://github.com/nathan-nakatsuka/ContamLD .

Published
2020
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30. Ancient DNA from the skeletons of Roopkund Lake reveals Mediterranean migrants in India

Author

Éadaoin Harney, Ayushi Nayak, Nick Patterson, Pramod Joglekar, Veena Mushrif-Tripathy, Swapan Mallick, Nadin Rohland, Jakob Sedig, Nicole Adamski, Rebecca Bernardos, Nasreen Broomandkhoshbacht, Brendan J. Culleton, Matthew Ferry, Thomas K. Harper, Megan Michel, Jonas Oppenheimer, Kristin Stewardson, Zhao Zhang, Harashawaradhana, Maanwendra Singh Bartwal, Sachin Kumar, Subhash Chandra Diyundi, Patrick Roberts, Nicole Boivin, Douglas J. Kennett, Kumarasamy Thangaraj, David Reich, and Niraj Rai

Subjects
Science
Abstract

Remains of several hundred humans are scattered around Roopkund Lake, situated over 5,000 meters above sea level in the Himalayan Mountains. Here the authors analyze genome-wide data from 38 skeletons and find 3 clusters with different ancestries and dates, showing the people were desposited in multiple catastrophic events.

Published
2019
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31. Ancient DNA from Chalcolithic Israel reveals the role of population mixture in cultural transformation

Author

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

Subjects
Science
Abstract

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

Author

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

Subjects
Science
Abstract

In the original version of this Article, references in the format ‘First author et al.’ were inappropriately deleted. These errors have been corrected in the PDF and HTML versions of the Article.

Published
2018
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