101
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Grogan KE, Perry GH. Studying human and nonhuman primate evolutionary biology with powerful in vitro and in vivo functional genomics tools. Evol Anthropol 2020; 29:143-158. [PMID: 32142200 PMCID: PMC10574139 DOI: 10.1002/evan.21825] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2019] [Revised: 09/18/2019] [Accepted: 02/06/2020] [Indexed: 12/19/2022]
Abstract
In recent years, tools for functional genomic studies have become increasingly feasible for use by evolutionary anthropologists. In this review, we provide brief overviews of several exciting in vitro techniques that can be paired with "-omics" approaches (e.g., genomics, epigenomics, transcriptomics, proteomics, and metabolomics) for potentially powerful evolutionary insights. These in vitro techniques include ancestral protein resurrection, cell line experiments using primary, immortalized, and induced pluripotent stem cells, and CRISPR-Cas9 genetic manipulation. We also discuss how several of these methods can be used in vivo, for transgenic organism studies of human and nonhuman primate evolution. Throughout this review, we highlight example studies in which these approaches have already been used to inform our understanding of the evolutionary biology of modern and archaic humans and other primates while simultaneously identifying future opportunities for anthropologists to use this toolkit to help answer additional outstanding questions in evolutionary anthropology.
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Affiliation(s)
- Kathleen E. Grogan
- Department of Anthropology, Pennsylvania State University, University Park, PA 16802
- Department of Biology, Pennsylvania State University, University Park, PA 16802
| | - George H. Perry
- Department of Anthropology, Pennsylvania State University, University Park, PA 16802
- Department of Biology, Pennsylvania State University, University Park, PA 16802
- Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA 16802
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102
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Pierini F, Nutsua M, Böhme L, Özer O, Bonczarowska J, Susat J, Franke A, Nebel A, Krause-Kyora B, Lenz TL. Targeted analysis of polymorphic loci from low-coverage shotgun sequence data allows accurate genotyping of HLA genes in historical human populations. Sci Rep 2020; 10:7339. [PMID: 32355290 PMCID: PMC7193575 DOI: 10.1038/s41598-020-64312-w] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2019] [Accepted: 04/14/2020] [Indexed: 01/15/2023] Open
Abstract
The highly polymorphic human leukocyte antigen (HLA) plays a crucial role in adaptive immunity and is associated with various complex diseases. Accurate analysis of HLA genes using ancient DNA (aDNA) data is crucial for understanding their role in human adaptation to pathogens. Here, we describe the TARGT pipeline for targeted analysis of polymorphic loci from low-coverage shotgun sequence data. The pipeline was successfully applied to medieval aDNA samples and validated using both simulated aDNA and modern empirical sequence data from the 1000 Genomes Project. Thus the TARGT pipeline enables accurate analysis of HLA polymorphisms in historical (and modern) human populations.
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Affiliation(s)
- Federica Pierini
- Research Group for Evolutionary Immunogenomics, Max Planck Institute for Evolutionary Biology, 24306, Ploen, Germany.,Université Paris-Saclay, CNRS, Inria, Laboratoire de recherche en informatique, 91405, Orsay, France
| | - Marcel Nutsua
- Institute of Clinical Molecular Biology, Kiel University, 24105, Kiel, Germany
| | - Lisa Böhme
- Institute of Clinical Molecular Biology, Kiel University, 24105, Kiel, Germany
| | - Onur Özer
- Research Group for Evolutionary Immunogenomics, Max Planck Institute for Evolutionary Biology, 24306, Ploen, Germany
| | - Joanna Bonczarowska
- Institute of Clinical Molecular Biology, Kiel University, 24105, Kiel, Germany
| | - Julian Susat
- Institute of Clinical Molecular Biology, Kiel University, 24105, Kiel, Germany
| | - Andre Franke
- Institute of Clinical Molecular Biology, Kiel University, 24105, Kiel, Germany
| | - Almut Nebel
- Institute of Clinical Molecular Biology, Kiel University, 24105, Kiel, Germany
| | - Ben Krause-Kyora
- Institute of Clinical Molecular Biology, Kiel University, 24105, Kiel, Germany
| | - Tobias L Lenz
- Research Group for Evolutionary Immunogenomics, Max Planck Institute for Evolutionary Biology, 24306, Ploen, Germany.
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103
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Abstract
The domestication of animals led to a major shift in human subsistence patterns, from a hunter-gatherer to a sedentary agricultural lifestyle, which ultimately resulted in the development of complex societies. Over the past 15,000 years, the phenotype and genotype of multiple animal species, such as dogs, pigs, sheep, goats, cattle and horses, have been substantially altered during their adaptation to the human niche. Recent methodological innovations, such as improved ancient DNA extraction methods and next-generation sequencing, have enabled the sequencing of whole ancient genomes. These genomes have helped reconstruct the process by which animals entered into domestic relationships with humans and were subjected to novel selection pressures. Here, we discuss and update key concepts in animal domestication in light of recent contributions from ancient genomics.
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104
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Vai S, Amorim CEG, Lari M, Caramelli D. Kinship Determination in Archeological Contexts Through DNA Analysis. Front Ecol Evol 2020. [DOI: 10.3389/fevo.2020.00083] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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105
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Machnik M, Oleksiewicz U. Dynamic Signatures of the Epigenome: Friend or Foe? Cells 2020; 9:cells9030653. [PMID: 32156057 PMCID: PMC7140607 DOI: 10.3390/cells9030653] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2020] [Revised: 02/24/2020] [Accepted: 03/04/2020] [Indexed: 12/12/2022] Open
Abstract
Highly dynamic epigenetic signaling is influenced mainly by (micro)environmental stimuli and genetic factors. The exact mechanisms affecting particular epigenomic patterns differ dependently on the context. In the current review, we focus on the causes and effects of the dynamic signatures of the human epigenome as evaluated with the high-throughput profiling data and single-gene approaches. We will discuss three different aspects of phenotypic outcomes occurring as a consequence of epigenetics interplaying with genotype and environment. The first issue is related to the cases of environmental impacts on epigenetic profile, and its adverse and advantageous effects related to human health and evolutionary adaptation. The next topic will present a model of the interwoven co-evolution of genetic and epigenetic patterns exemplified with transposable elements (TEs) and their epigenetic repressors Krüppel-associated box zinc finger proteins (KRAB–ZNFs). The third aspect concentrates on the mitosis-based microevolution that takes place during carcinogenesis, leading to clonal diversity and expansion of tumor cells. The whole picture of epigenome plasticity and its role in distinct biological processes is still incomplete. However, accumulating data define epigenomic dynamics as an essential co-factor driving adaptation at the cellular and inter-species levels with a benefit or disadvantage to the host.
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Affiliation(s)
- Marta Machnik
- Department of Cancer Immunology, Poznan University of Medical Sciences, 60-806 Poznan, Poland;
- Department of Cancer Diagnostics and Immunology, Greater Poland Cancer Centre, 61-866 Poznan, Poland
| | - Urszula Oleksiewicz
- Department of Cancer Immunology, Poznan University of Medical Sciences, 60-806 Poznan, Poland;
- Department of Cancer Diagnostics and Immunology, Greater Poland Cancer Centre, 61-866 Poznan, Poland
- Correspondence:
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106
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Sirak K, Fernandes D, Cheronet O, Harney E, Mah M, Mallick S, Rohland N, Adamski N, Broomandkhoshbacht N, Callan K, Candilio F, Lawson AM, Mandl K, Oppenheimer J, Stewardson K, Zalzala F, Anders A, Bartík J, Coppa A, Dashtseveg T, Évinger S, Farkaš Z, Hajdu T, Bayarsaikhan J, McIntyre L, Moiseyev V, Okumura M, Pap I, Pietrusewsky M, Raczky P, Šefčáková A, Soficaru A, Szeniczey T, Szőke BM, Van Gerven D, Vasilyev S, Bell L, Reich D, Pinhasi R. Human auditory ossicles as an alternative optimal source of ancient DNA. Genome Res 2020. [PMID: 32098773 DOI: 10.1101/654749] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
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 provides optimal contexts for DNA preservation; however, the rich genetic information obtained from the cochlea must be counterbalanced against the loss of morphological information caused by its sampling. Motivated by similarities in developmental processes and histological properties between the cochlea and auditory ossicles, we evaluate the ossicles as an alternative source of ancient DNA. We show that ossicles perform comparably to the cochlea in terms of DNA recovery, finding no substantial reduction in data quantity and minimal differences in data quality across preservation conditions. Ossicles can be sampled from intact skulls or disarticulated petrous bones without damage to surrounding bone, and we argue that they should be used when available to reduce damage to human remains. Our results identify another 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.
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Affiliation(s)
- Kendra Sirak
- Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA
- Earth Institute and School of Archaeology, University College Dublin, Dublin 4, Ireland
| | - Daniel Fernandes
- Earth Institute and School of Archaeology, University College Dublin, Dublin 4, Ireland
- Department of Evolutionary Anthropology, University of Vienna, Vienna, 1090, Austria
- CIAS, Department of Life Sciences, University of Coimbra, 3000-456 Coimbra, Portugal
| | - Olivia Cheronet
- Earth Institute and School of Archaeology, University College Dublin, Dublin 4, Ireland
- Department of Evolutionary Anthropology, University of Vienna, Vienna, 1090, Austria
| | - Eadaoin Harney
- Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts 02138, USA
- The Max Planck-Harvard Research Center for the Archaeoscience of the Ancient Mediterranean, Cambridge, Massachusetts 02138, USA and Jena, D-07745, Germany
| | - Matthew Mah
- Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA
- Broad Institute of Harvard and MIT, Cambridge, Massachusetts 02142, USA
- Howard Hughes Medical Institute, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Swapan Mallick
- Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA
- Broad Institute of Harvard and MIT, Cambridge, Massachusetts 02142, USA
- Howard Hughes Medical Institute, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Nadin Rohland
- Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Nicole Adamski
- Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA
- Howard Hughes Medical Institute, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Nasreen Broomandkhoshbacht
- Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA
- Howard Hughes Medical Institute, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Kimberly Callan
- Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA
- Howard Hughes Medical Institute, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Francesca Candilio
- Earth Institute and School of Archaeology, University College Dublin, Dublin 4, Ireland
| | - Ann Marie Lawson
- Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA
- Howard Hughes Medical Institute, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Kirsten Mandl
- Department of Evolutionary Anthropology, University of Vienna, Vienna, 1090, Austria
| | - Jonas Oppenheimer
- Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA
- Howard Hughes Medical Institute, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Kristin Stewardson
- Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA
- Howard Hughes Medical Institute, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Fatma Zalzala
- Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA
- Howard Hughes Medical Institute, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Alexandra Anders
- Institute of Archaeological Sciences, Eötvös Loránd University, H-1088 Budapest, Hungary
| | - Juraj Bartík
- Slovak National Museum-Archaeological Museum, 810 06 Bratislava 16, Slovak Republic
| | - Alfredo Coppa
- Dipartimento di Biologia Ambientale, Sapienza Università di Roma, Rome 00185, Italy
| | - Tumen Dashtseveg
- Department of Anthropology and Archaeology, National University of Mongolia, Ulaanbaatar 14200, Mongolia
| | - Sándor Évinger
- Department of Anthropology, Hungarian Natural History Museum, H-1083 Budapest, Hungary
| | - Zdeněk Farkaš
- Slovak National Museum-Archaeological Museum, 810 06 Bratislava 16, Slovak Republic
| | - Tamás Hajdu
- Department of Anthropology, Hungarian Natural History Museum, H-1083 Budapest, Hungary
- Department of Biological Anthropology, Institute of Biology, Faculty of Science, Eötvös Loránd University Budapest, H-1117 Budapest, Hungary
| | - Jamsranjav Bayarsaikhan
- Department of Anthropology and Archaeology, National University of Mongolia, Ulaanbaatar 14200, Mongolia
- National Museum of Mongolia, Ulaanbaatar 210146, Mongolia
| | | | - Vyacheslav Moiseyev
- Peter the Great Museum of Anthropology and Ethnography (Kunstkamera), Russian Academy of Science, St. Petersburg 199034, Russia
| | - Mercedes Okumura
- Department of Genetics and Evolutionary Biology, Institute of Biosciences, University of São Paulo, Cidade Universitária 05508-090 São Paulo, Brazil
| | - Ildikó Pap
- Department of Anthropology, Hungarian Natural History Museum, H-1083 Budapest, Hungary
| | - Michael Pietrusewsky
- Department of Anthropology, University of Hawai'i at Mānoa, Honolulu, Hawaii 96822, USA
| | - Pál Raczky
- Institute of Archaeological Sciences, Eötvös Loránd University, H-1088 Budapest, Hungary
| | - Alena Šefčáková
- Department of Anthropology, Slovak National Museum-Natural History Museum, 810 06 Bratislava 16, Slovak Republic
| | - Andrei Soficaru
- "Fr. J. Rainer" Institute of Anthropology, Romanian Academy, 050474 Bucharest, Romania
| | - Tamás Szeniczey
- Department of Anthropology, Hungarian Natural History Museum, H-1083 Budapest, Hungary
- Department of Biological Anthropology, Institute of Biology, Faculty of Science, Eötvös Loránd University Budapest, H-1117 Budapest, Hungary
| | - Béla Miklós Szőke
- Institute of Archaeology, Research Centre for the Humanities, Hungarian Academy of Sciences, H-1097 Budapest, Hungary
| | - Dennis Van Gerven
- Department of Anthropology, University of Colorado at Boulder, Boulder, Colorado 80309, USA
| | - Sergey Vasilyev
- Institute of Ethnology and Anthropology, RAS, Moscow, 119991, Russia
| | - Lynne Bell
- Centre for Forensic Research, Simon Fraser University, Burnaby, British Columbia, V5A 1S6, Canada
| | - David Reich
- Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA
- Broad Institute of Harvard and MIT, Cambridge, Massachusetts 02142, USA
- Howard Hughes Medical Institute, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Ron Pinhasi
- Department of Evolutionary Anthropology, University of Vienna, Vienna, 1090, Austria
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107
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McGaughran A. Effects of sample age on data quality from targeted sequencing of museum specimens: what are we capturing in time? BMC Genomics 2020; 21:188. [PMID: 32111157 PMCID: PMC7048091 DOI: 10.1186/s12864-020-6594-0] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2019] [Accepted: 02/19/2020] [Indexed: 01/04/2023] Open
Abstract
Background Next generation sequencing (NGS) can recover DNA data from valuable extant and extinct museum specimens. However, archived or preserved DNA is difficult to sequence because of its fragmented, damaged nature, such that the most successful NGS methods for preserved specimens remain sub-optimal. Improving wet-lab protocols and comprehensively determining the effects of sample age on NGS library quality are therefore of vital importance. Here, I examine the relationship between sample age and several indicators of library quality following targeted NGS sequencing of ~ 1300 loci using 271 samples of pinned moth specimens (Helicoverpa armigera) ranging in age from 5 to 117 years. Results I find that older samples have lower DNA concentrations following extraction and thus require a higher number of indexing PCR cycles during library preparation. When sequenced reads are aligned to a reference genome or to only the targeted region, older samples have a lower number of sequenced and mapped reads, lower mean coverage, and lower estimated library sizes, while the percentage of adapters in sequenced reads increases significantly as samples become older. Older samples also show the poorest capture success, with lower enrichment and a higher improved coverage anticipated from further sequencing. Conclusions Sample age has significant, measurable impacts on the quality of NGS data following targeted enrichment. However, incorporating a uracil-removing enzyme into the blunt end-repair step during library preparation could help to repair DNA damage, and using a method that prevents adapter-dimer formation may result in improved data yields.
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Affiliation(s)
- Angela McGaughran
- Australian National University, Research School of Biology, Division of Ecology and Evolution, Acton, Canberra, ACT, 2600, Australia. .,CSIRO Land and Water, Integrated Omics Team, Black Mountain Laboratories, Canberra, ACT, 2600, Australia.
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108
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Sirak K, Fernandes D, Cheronet O, Harney E, Mah M, Mallick S, Rohland N, Adamski N, Broomandkhoshbacht N, Callan K, Candilio F, Lawson AM, Mandl K, Oppenheimer J, Stewardson K, Zalzala F, Anders A, Bartík J, Coppa A, Dashtseveg T, Évinger S, Farkaš Z, Hajdu T, Bayarsaikhan J, McIntyre L, Moiseyev V, Okumura M, Pap I, Pietrusewsky M, Raczky P, Šefčáková A, Soficaru A, Szeniczey T, Szőke BM, Van Gerven D, Vasilyev S, Bell L, Reich D, Pinhasi R. Human auditory ossicles as an alternative optimal source of ancient DNA. Genome Res 2020; 30:427-436. [PMID: 32098773 PMCID: PMC7111520 DOI: 10.1101/gr.260141.119] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2019] [Accepted: 02/11/2020] [Indexed: 12/29/2022]
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 provides optimal contexts for DNA preservation; however, the rich genetic information obtained from the cochlea must be counterbalanced against the loss of morphological information caused by its sampling. Motivated by similarities in developmental processes and histological properties between the cochlea and auditory ossicles, we evaluate the ossicles as an alternative source of ancient DNA. We show that ossicles perform comparably to the cochlea in terms of DNA recovery, finding no substantial reduction in data quantity and minimal differences in data quality across preservation conditions. Ossicles can be sampled from intact skulls or disarticulated petrous bones without damage to surrounding bone, and we argue that they should be used when available to reduce damage to human remains. Our results identify another 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.
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Affiliation(s)
- Kendra Sirak
- Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA.,Earth Institute and School of Archaeology, University College Dublin, Dublin 4, Ireland
| | - Daniel Fernandes
- Earth Institute and School of Archaeology, University College Dublin, Dublin 4, Ireland.,Department of Evolutionary Anthropology, University of Vienna, Vienna, 1090, Austria.,CIAS, Department of Life Sciences, University of Coimbra, 3000-456 Coimbra, Portugal
| | - Olivia Cheronet
- Earth Institute and School of Archaeology, University College Dublin, Dublin 4, Ireland.,Department of Evolutionary Anthropology, University of Vienna, Vienna, 1090, Austria
| | - Eadaoin Harney
- Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA.,Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts 02138, USA.,The Max Planck-Harvard Research Center for the Archaeoscience of the Ancient Mediterranean, Cambridge, Massachusetts 02138, USA and Jena, D-07745, Germany
| | - Matthew Mah
- Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA.,Broad Institute of Harvard and MIT, Cambridge, Massachusetts 02142, USA.,Howard Hughes Medical Institute, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Swapan Mallick
- Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA.,Broad Institute of Harvard and MIT, Cambridge, Massachusetts 02142, USA.,Howard Hughes Medical Institute, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Nadin Rohland
- Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Nicole Adamski
- Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA.,Howard Hughes Medical Institute, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Nasreen Broomandkhoshbacht
- Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA.,Howard Hughes Medical Institute, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Kimberly Callan
- Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA.,Howard Hughes Medical Institute, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Francesca Candilio
- Earth Institute and School of Archaeology, University College Dublin, Dublin 4, Ireland
| | - Ann Marie Lawson
- Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA.,Howard Hughes Medical Institute, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Kirsten Mandl
- Department of Evolutionary Anthropology, University of Vienna, Vienna, 1090, Austria
| | - Jonas Oppenheimer
- Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA.,Howard Hughes Medical Institute, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Kristin Stewardson
- Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA.,Howard Hughes Medical Institute, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Fatma Zalzala
- Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA.,Howard Hughes Medical Institute, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Alexandra Anders
- Institute of Archaeological Sciences, Eötvös Loránd University, H-1088 Budapest, Hungary
| | - Juraj Bartík
- Slovak National Museum-Archaeological Museum, 810 06 Bratislava 16, Slovak Republic
| | - Alfredo Coppa
- Dipartimento di Biologia Ambientale, Sapienza Università di Roma, Rome 00185, Italy
| | - Tumen Dashtseveg
- Department of Anthropology and Archaeology, National University of Mongolia, Ulaanbaatar 14200, Mongolia
| | - Sándor Évinger
- Department of Anthropology, Hungarian Natural History Museum, H-1083 Budapest, Hungary
| | - Zdeněk Farkaš
- Slovak National Museum-Archaeological Museum, 810 06 Bratislava 16, Slovak Republic
| | - Tamás Hajdu
- Department of Anthropology, Hungarian Natural History Museum, H-1083 Budapest, Hungary.,Department of Biological Anthropology, Institute of Biology, Faculty of Science, Eötvös Loránd University Budapest, H-1117 Budapest, Hungary
| | - Jamsranjav Bayarsaikhan
- Department of Anthropology and Archaeology, National University of Mongolia, Ulaanbaatar 14200, Mongolia.,National Museum of Mongolia, Ulaanbaatar 210146, Mongolia
| | | | - Vyacheslav Moiseyev
- Peter the Great Museum of Anthropology and Ethnography (Kunstkamera), Russian Academy of Science, St. Petersburg 199034, Russia
| | - Mercedes Okumura
- Department of Genetics and Evolutionary Biology, Institute of Biosciences, University of São Paulo, Cidade Universitária 05508-090 São Paulo, Brazil
| | - Ildikó Pap
- Department of Anthropology, Hungarian Natural History Museum, H-1083 Budapest, Hungary
| | - Michael Pietrusewsky
- Department of Anthropology, University of Hawai'i at Mānoa, Honolulu, Hawaii 96822, USA
| | - Pál Raczky
- Institute of Archaeological Sciences, Eötvös Loránd University, H-1088 Budapest, Hungary
| | - Alena Šefčáková
- Department of Anthropology, Slovak National Museum-Natural History Museum, 810 06 Bratislava 16, Slovak Republic
| | - Andrei Soficaru
- "Fr. J. Rainer" Institute of Anthropology, Romanian Academy, 050474 Bucharest, Romania
| | - Tamás Szeniczey
- Department of Anthropology, Hungarian Natural History Museum, H-1083 Budapest, Hungary.,Department of Biological Anthropology, Institute of Biology, Faculty of Science, Eötvös Loránd University Budapest, H-1117 Budapest, Hungary
| | - Béla Miklós Szőke
- Institute of Archaeology, Research Centre for the Humanities, Hungarian Academy of Sciences, H-1097 Budapest, Hungary
| | - Dennis Van Gerven
- Department of Anthropology, University of Colorado at Boulder, Boulder, Colorado 80309, USA
| | - Sergey Vasilyev
- Institute of Ethnology and Anthropology, RAS, Moscow, 119991, Russia
| | - Lynne Bell
- Centre for Forensic Research, Simon Fraser University, Burnaby, British Columbia, V5A 1S6, Canada
| | - David Reich
- Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA.,Broad Institute of Harvard and MIT, Cambridge, Massachusetts 02142, USA.,Howard Hughes Medical Institute, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Ron Pinhasi
- Department of Evolutionary Anthropology, University of Vienna, Vienna, 1090, Austria
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109
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The spread of steppe and Iranian-related ancestry in the islands of the western Mediterranean. Nat Ecol Evol 2020; 4:334-345. [PMID: 32094539 PMCID: PMC7080320 DOI: 10.1038/s41559-020-1102-0] [Citation(s) in RCA: 65] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2019] [Accepted: 01/08/2020] [Indexed: 11/08/2022]
Abstract
Steppe-pastoralist-related ancestry reached Central Europe by at least 2500 BC, whereas Iranian farmer-related ancestry was present in Aegean Europe by at least 1900 BC. However, the spread of these ancestries into the western Mediterranean, where they have contributed to many populations that live today, remains poorly understood. Here, we generated genome-wide ancient-DNA data from the Balearic Islands, Sicily and Sardinia, increasing the number of individuals with reported data from 5 to 66. The oldest individual from the Balearic Islands (~2400 BC) carried ancestry from steppe pastoralists that probably derived from west-to-east migration from Iberia, although two later Balearic individuals had less ancestry from steppe pastoralists. In Sicily, steppe pastoralist ancestry arrived by ~2200 BC, in part from Iberia; Iranian-related ancestry arrived by the mid-second millennium BC, contemporary to its previously documented spread to the Aegean; and there was large-scale population replacement after the Bronze Age. In Sardinia, nearly all ancestry derived from the island's early farmers until the first millennium BC, with the exception of an outlier from the third millennium BC, who had primarily North African ancestry and who-along with an approximately contemporary Iberian-documents widespread Africa-to-Europe gene flow in the Chalcolithic. Major immigration into Sardinia began in the first millennium BC and, at present, no more than 56-62% of Sardinian ancestry is from its first farmers. This value is lower than previous estimates, highlighting that Sardinia, similar to every other region in Europe, has been a stage for major movement and mixtures of people.
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110
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Key FM, Posth C, Esquivel-Gomez LR, Hübler R, Spyrou MA, Neumann GU, Furtwängler A, Sabin S, Burri M, Wissgott A, Lankapalli AK, Vågene ÅJ, Meyer M, Nagel S, Tukhbatova R, Khokhlov A, Chizhevsky A, Hansen S, Belinsky AB, Kalmykov A, Kantorovich AR, Maslov VE, Stockhammer PW, Vai S, Zavattaro M, Riga A, Caramelli D, Skeates R, Beckett J, Gradoli MG, Steuri N, Hafner A, Ramstein M, Siebke I, Lösch S, Erdal YS, Alikhan NF, Zhou Z, Achtman M, Bos K, Reinhold S, Haak W, Kühnert D, Herbig A, Krause J. Emergence of human-adapted Salmonella enterica is linked to the Neolithization process. Nat Ecol Evol 2020; 4:324-333. [PMID: 32094538 PMCID: PMC7186082 DOI: 10.1038/s41559-020-1106-9] [Citation(s) in RCA: 48] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2019] [Accepted: 01/08/2020] [Indexed: 11/13/2022]
Abstract
It has been hypothesized that the Neolithic transition towards an
agricultural and pastoralist economy facilitated the emergence of human adapted
pathogens. Here, we recovered eight Salmonella enterica subsp.
enterica genomes from human skeletons of transitional
foragers, pastoralists, and agro-pastoralists in western Eurasia that were up to
6,500 years old. Despite the high genetic diversity of S.
enterica all ancient bacterial genomes clustered in a single
previously uncharacterized branch that contains S. enterica
adapted to multiple mammalian species. All ancient bacterial genomes from
prehistoric (agro-)pastoralists fall within a part of this branch that also
includes the human-specific S. enterica Paratyphi C,
illustrating the evolution of a human pathogen over a period of five thousand
years. Bacterial genomic comparisons suggest that the earlier ancient strains
were not host specific, differed in pathogenic potential, and experienced
convergent pseudogenization that accompanied their downstream host adaptation.
These observations support the concept that the emergence of human adapted
S. enterica is linked to human cultural
transformations.
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Affiliation(s)
- Felix M Key
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena, Germany. .,Institute for Medical Engineering and Sciences, Massachusetts Institute of Technology, Cambridge, MA, USA. .,Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA.
| | - Cosimo Posth
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena, Germany
| | - Luis R Esquivel-Gomez
- Transmission, Infection, Diversification & Evolution Group, Max Planck Institute for the Science of Human History, Jena, Germany
| | - Ron Hübler
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena, Germany
| | - Maria A Spyrou
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena, Germany
| | - Gunnar U Neumann
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena, Germany
| | - Anja Furtwängler
- Institute for Archaeological Sciences, Archaeo- and Palaeogenetics, University of Tuebingen, Tuebingen, Germany
| | - Susanna Sabin
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena, Germany
| | - Marta Burri
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena, Germany
| | - Antje Wissgott
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena, Germany
| | - Aditya Kumar Lankapalli
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena, Germany
| | - Åshild J Vågene
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena, Germany
| | - Matthias Meyer
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Sarah Nagel
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Rezeda Tukhbatova
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena, Germany.,Laboratory of Structural Biology, Kazan Federal University, Kazan, Russian Federation
| | - Aleksandr Khokhlov
- Samara State University of Social Sciences and Education, Samara, Russian Federation
| | - Andrey Chizhevsky
- Institute of Archaeology named after A.Kh. Khalikov of the Academy of Sciences of the Republic of Tatarstan, Kazan, Russian Federation
| | - Svend Hansen
- Eurasia Department, German Archaeological Institute, Berlin, Germany
| | | | - Alexey Kalmykov
- 'Nasledie' Cultural Heritage Unit, Stavropol, Russian Federation
| | - Anatoly R Kantorovich
- Department of Archaeology, Faculty of History, Lomonosov Moscow State University, Moscow, Russian Federation
| | | | - Philipp W Stockhammer
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena, Germany.,Institute for Pre- and Protohistoric Archaeology and Archaeology of the Roman Provinces, Ludwig Maximilian University Munich, Munich, Germany
| | - Stefania Vai
- Department of Biology, University of Florence, Florence, Italy
| | - Monica Zavattaro
- Museum of Anthropology and Ethnology, Museum System of the University of Florence, Florence, Italy
| | - Alessandro Riga
- Department of Biology, University of Florence, Florence, Italy
| | - David Caramelli
- Department of Biology, University of Florence, Florence, Italy
| | - Robin Skeates
- Department of Archaeology, Durham University, Durham, UK
| | | | | | - Noah Steuri
- Institute of Archaeological Sciences and Oeschger Centre for Climate Change Research, University of Bern, Bern, Switzerland
| | - Albert Hafner
- Institute of Archaeological Sciences and Oeschger Centre for Climate Change Research, University of Bern, Bern, Switzerland
| | | | - Inga Siebke
- Department of Physical Anthropology Institute of Forensic Medicine, University of Bern, Bern, Switzerland
| | - Sandra Lösch
- Department of Physical Anthropology Institute of Forensic Medicine, University of Bern, Bern, Switzerland
| | | | | | - Zhemin Zhou
- Warwick Medical School, University of Warwick, Coventry, UK
| | - Mark Achtman
- Warwick Medical School, University of Warwick, Coventry, UK
| | - Kirsten Bos
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena, Germany
| | - Sabine Reinhold
- Eurasia Department, German Archaeological Institute, Berlin, Germany
| | - Wolfgang Haak
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena, Germany
| | - Denise Kühnert
- Transmission, Infection, Diversification & Evolution Group, Max Planck Institute for the Science of Human History, Jena, Germany
| | - Alexander Herbig
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena, Germany.
| | - Johannes Krause
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena, Germany.
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111
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Andermann T, Torres Jiménez MF, Matos-Maraví P, Batista R, Blanco-Pastor JL, Gustafsson ALS, Kistler L, Liberal IM, Oxelman B, Bacon CD, Antonelli A. A Guide to Carrying Out a Phylogenomic Target Sequence Capture Project. Front Genet 2020; 10:1407. [PMID: 32153629 PMCID: PMC7047930 DOI: 10.3389/fgene.2019.01407] [Citation(s) in RCA: 52] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2019] [Accepted: 12/24/2019] [Indexed: 12/17/2022] Open
Abstract
High-throughput DNA sequencing techniques enable time- and cost-effective sequencing of large portions of the genome. Instead of sequencing and annotating whole genomes, many phylogenetic studies focus sequencing effort on large sets of pre-selected loci, which further reduces costs and bioinformatic challenges while increasing coverage. One common approach that enriches loci before sequencing is often referred to as target sequence capture. This technique has been shown to be applicable to phylogenetic studies of greatly varying evolutionary depth. Moreover, it has proven to produce powerful, large multi-locus DNA sequence datasets suitable for phylogenetic analyses. However, target capture requires careful considerations, which may greatly affect the success of experiments. Here we provide a simple flowchart for designing phylogenomic target capture experiments. We discuss necessary decisions from the identification of target loci to the final bioinformatic processing of sequence data. We outline challenges and solutions related to the taxonomic scope, sample quality, and available genomic resources of target capture projects. We hope this review will serve as a useful roadmap for designing and carrying out successful phylogenetic target capture studies.
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Affiliation(s)
- Tobias Andermann
- Department of Biological and Environmental Sciences, University of Gothenburg, Gothenburg, Sweden
- Gothenburg Global Biodiversity Centre, Gothenburg, Sweden
| | - Maria Fernanda Torres Jiménez
- Department of Biological and Environmental Sciences, University of Gothenburg, Gothenburg, Sweden
- Gothenburg Global Biodiversity Centre, Gothenburg, Sweden
| | - Pável Matos-Maraví
- Department of Biological and Environmental Sciences, University of Gothenburg, Gothenburg, Sweden
- Gothenburg Global Biodiversity Centre, Gothenburg, Sweden
- Institute of Entomology, Biology Centre of the Czech Academy of Sciences, České Budějovice, Czechia
| | - Romina Batista
- Gothenburg Global Biodiversity Centre, Gothenburg, Sweden
- Programa de Pós-Graduação em Genética, Conservação e Biologia Evolutiva, PPG GCBEv–Instituto Nacional de Pesquisas da Amazônia—INPA Campus II, Manaus, Brazil
- Coordenação de Zoologia, Museu Paraense Emílio Goeldi, Belém, Brazil
| | - José L. Blanco-Pastor
- Department of Biological and Environmental Sciences, University of Gothenburg, Gothenburg, Sweden
- INRAE, Centre Nouvelle-Aquitaine-Poitiers, Lusignan, France
| | | | - Logan Kistler
- Department of Anthropology, National Museum of Natural History, Smithsonian Institution, Washington, DC, United States
| | - Isabel M. Liberal
- Department of Biological and Environmental Sciences, University of Gothenburg, Gothenburg, Sweden
| | - Bengt Oxelman
- Department of Biological and Environmental Sciences, University of Gothenburg, Gothenburg, Sweden
- Gothenburg Global Biodiversity Centre, Gothenburg, Sweden
| | - Christine D. Bacon
- Department of Biological and Environmental Sciences, University of Gothenburg, Gothenburg, Sweden
- Gothenburg Global Biodiversity Centre, Gothenburg, Sweden
| | - Alexandre Antonelli
- Department of Biological and Environmental Sciences, University of Gothenburg, Gothenburg, Sweden
- Gothenburg Global Biodiversity Centre, Gothenburg, Sweden
- Royal Botanic Gardens, Kew, Richmond-Surrey, United Kingdom
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112
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Liu Y, Weyrich LS, Llamas B. More Arrows in the Ancient DNA Quiver: Use of Paleoepigenomes and Paleomicrobiomes to Investigate Animal Adaptation to Environment. Mol Biol Evol 2020; 37:307-319. [PMID: 31638147 DOI: 10.1093/molbev/msz231] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Whether and how epigenetic mechanisms and the microbiome play a role in mammalian adaptation raised considerable attention and controversy, mainly because they have the potential to add new insights into the Modern Synthesis. Recent attempts to reconcile neo-Darwinism and neo-Lamarckism in a unified theory of molecular evolution give epigenetic mechanisms and microbiome a prominent role. However, supporting empirical data are still largely missing. Because experimental studies using extant animals can hardly be done over evolutionary timescales, we propose that advances in ancient DNA techniques provide a valid alternative. In this piece, we evaluate 1) the possible roles of epigenomes and microbiomes in animal adaptation, 2) advances in the retrieval of paleoepigenome and paleomicrobiome data using ancient DNA techniques, and 3) the plasticity of either and interactions between the epigenome and the microbiome, while emphasizing that it is essential to take both into account, as well as the underlying genetic factors that may confound the findings. We propose that advanced ancient DNA techniques should be applied to a wide range of past animals, so novel dynamics in animal evolution and adaption can be revealed.
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Affiliation(s)
- Yichen Liu
- Australian Centre for Ancient DNA, School of Biological Sciences, Environment Institute, University of Adelaide, Adelaide, South Australia, Australia
| | - Laura S Weyrich
- Australian Centre for Ancient DNA, School of Biological Sciences, Environment Institute, University of Adelaide, Adelaide, South Australia, Australia
| | - Bastien Llamas
- Australian Centre for Ancient DNA, School of Biological Sciences, Environment Institute, University of Adelaide, Adelaide, South Australia, Australia
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113
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Wagner S, Plomion C, Orlando L. Uncovering Signatures of DNA Methylation in Ancient Plant Remains From Patterns of Post-mortem DNA Damage. Front Ecol Evol 2020. [DOI: 10.3389/fevo.2020.00011] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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114
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Lipson M, Ribot I, Mallick S, Rohland N, Olalde I, Adamski N, Broomandkhoshbacht N, Lawson AM, López S, Oppenheimer J, Stewardson K, Asombang RN, Bocherens H, Bradman N, Culleton BJ, Cornelissen E, Crevecoeur I, de Maret P, Fomine FLM, Lavachery P, Mindzie CM, Orban R, Sawchuk E, Semal P, Thomas MG, Van Neer W, Veeramah KR, Kennett DJ, Patterson N, Hellenthal G, Lalueza-Fox C, MacEachern S, Prendergast ME, Reich D. Ancient West African foragers in the context of African population history. Nature 2020; 577:665-670. [PMID: 31969706 PMCID: PMC8386425 DOI: 10.1038/s41586-020-1929-1] [Citation(s) in RCA: 51] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2018] [Accepted: 11/29/2019] [Indexed: 12/31/2022]
Abstract
Our knowledge of ancient human population structure in sub-Saharan Africa, particularly prior to the advent of food production, remains limited. Here we report genome-wide DNA data from four children-two of whom were buried approximately 8,000 years ago and two 3,000 years ago-from Shum Laka (Cameroon), one of the earliest known archaeological sites within the probable homeland of the Bantu language group1-11. One individual carried the deeply divergent Y chromosome haplogroup A00, which today is found almost exclusively in the same region12,13. However, the genome-wide ancestry profiles of all four individuals are most similar to those of present-day hunter-gatherers from western Central Africa, which implies that populations in western Cameroon today-as well as speakers of Bantu languages from across the continent-are not descended substantially from the population represented by these four people. We infer an Africa-wide phylogeny that features widespread admixture and three prominent radiations, including one that gave rise to at least four major lineages deep in the history of modern humans.
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Affiliation(s)
- Mark Lipson
- Department of Genetics, Harvard Medical School, Boston, MA, USA.
| | - Isabelle Ribot
- Département d'Anthropologie, Université de Montréal, Montreal, Quebec, Canada
| | - Swapan Mallick
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- Medical and Population Genetics Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, USA
| | - Nadin Rohland
- Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Iñigo Olalde
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- Institute of Evolutionary Biology (CSIC-UPF), Barcelona, Spain
| | - Nicole Adamski
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, USA
| | - Nasreen Broomandkhoshbacht
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, USA
- Department of Anthropology, University of California, Santa Cruz, CA, USA
| | - Ann Marie Lawson
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, USA
| | - Saioa López
- UCL Genetics Institute, University College London, London, UK
| | - Jonas Oppenheimer
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, USA
- Department of Biomolecular Engineering, University of California, Santa Cruz, CA, USA
| | - Kristin Stewardson
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, USA
| | | | - Hervé Bocherens
- Department of Geosciences, Biogeology, University of Tübingen, Tübingen, Germany
- Senckenberg Research Centre for Human Evolution and Palaeoenvironment, University of Tübingen, Tübingen, Germany
| | - Neil Bradman
- UCL Genetics Institute, University College London, London, UK
- The Henry Stewart Group, London, UK
| | - Brendan J Culleton
- Institutes of Energy and the Environment, Pennsylvania State University, University Park, PA, USA
| | - Els Cornelissen
- Department of Cultural Anthropology and History, Royal Museum for Central Africa, Tervuren, Belgium
| | | | - Pierre de Maret
- Faculté de Philosophie et Sciences Sociales, Université Libre de Bruxelles, Brussels, Belgium
| | | | - Philippe Lavachery
- Agence Wallonne du Patrimoine, Service Public de Wallonie, Namur, Belgium
| | | | - Rosine Orban
- Royal Belgian Institute of Natural Sciences, Brussels, Belgium
| | - Elizabeth Sawchuk
- Department of Anthropology, Stony Brook University, Stony Brook, NY, USA
| | - Patrick Semal
- Royal Belgian Institute of Natural Sciences, Brussels, Belgium
| | - Mark G Thomas
- UCL Genetics Institute, University College London, London, UK
- Department of Genetics, Evolution and Environment, University College London, London, UK
| | - Wim Van Neer
- Royal Belgian Institute of Natural Sciences, Brussels, Belgium
- Department of Biology, University of Leuven, Leuven, Belgium
| | - Krishna R Veeramah
- Department of Ecology and Evolution, Stony Brook University, Stony Brook, NY, USA
| | - Douglas J Kennett
- Department of Anthropology, University of California, Santa Barbara, CA, USA
| | - Nick Patterson
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- Department of Human Evolutionary Biology, Harvard University, Cambridge, MA, USA
| | - Garrett Hellenthal
- UCL Genetics Institute, University College London, London, UK
- Department of Genetics, Evolution and Environment, University College London, London, UK
| | | | - Scott MacEachern
- Division of Social Science, Duke Kunshan University, Kunshan, China
| | - Mary E Prendergast
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- Department of Sociology and Anthropology, Saint Louis University, Madrid, Spain
| | - David Reich
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- Medical and Population Genetics Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, USA
- Department of Human Evolutionary Biology, Harvard University, Cambridge, MA, USA
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115
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Ngatia JN, Lan TM, Ma Y, Dinh TD, Wang Z, Dahmer TD, Chun Xu Y. Distinguishing extant elephants ivory from mammoth ivory using a short sequence of cytochrome b gene. Sci Rep 2019; 9:18863. [PMID: 31827140 PMCID: PMC6906310 DOI: 10.1038/s41598-019-55094-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2019] [Accepted: 11/14/2019] [Indexed: 11/08/2022] Open
Abstract
Trade in ivory from extant elephant species namely Asian elephant (Elephas maximus), African savanna elephant (Loxodonta africana) and African forest elephant (Loxodonta cyclotis) is regulated internationally, while the trade in ivory from extinct species of Elephantidae, including woolly mammoth, is unregulated. This distinction creates opportunity for laundering and trading elephant ivory as mammoth ivory. The existing morphological and molecular genetics methods do not reliably distinguish the source of ivory items that lack clear identification characteristics or for which the quality of extracted DNA cannot support amplification of large gene fragments. We present a PCR-sequencing method based on 116 bp target sequence of the cytochrome b gene to specifically amplify elephantid DNA while simultaneously excluding non-elephantid species and ivory substitutes, and while avoiding contamination by human DNA. The partial Cytochrome b gene sequence enabled accurate association of ivory samples with their species of origin for all three extant elephants and from mammoth. The detection limit of the PCR system was as low as 10 copy numbers of target DNA. The amplification and sequencing success reached 96.7% for woolly mammoth ivory and 100% for African savanna elephant and African forest elephant ivory. This is the first validated method for distinguishing elephant from mammoth ivory and it provides forensic support for investigation of ivory laundering cases.
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Affiliation(s)
- Jacob Njaramba Ngatia
- College of Wildlife and Protected Areas, Northeast Forestry University, Harbin, 150040, China
| | - Tian Ming Lan
- BGI - Shenzhen, Shenzhen, 518083, China
- Laboratory of Genomics and Molecular Biomedicine, Department of Biology, University of Copenhagen, Copenhagen, DK-2100, Denmark
- China National GeneBank, BGI - Shenzhen, Shenzhen, 518083, China
| | - Yue Ma
- College of Wildlife and Protected Areas, Northeast Forestry University, Harbin, 150040, China
- State Forestry and Grassland Administration Detecting Center of Wildlife, Harbin, 150040, China
| | - Thi Dao Dinh
- College of Wildlife and Protected Areas, Northeast Forestry University, Harbin, 150040, China
| | - Zhen Wang
- College of Wildlife and Protected Areas, Northeast Forestry University, Harbin, 150040, China
- State Forestry and Grassland Administration Detecting Center of Wildlife, Harbin, 150040, China
| | - Thomas D Dahmer
- Ecosystems Ltd, No. 40 Shek Pai Wan Road, Aberdeen, Hong Kong, China
| | - Yan Chun Xu
- College of Wildlife and Protected Areas, Northeast Forestry University, Harbin, 150040, China.
- State Forestry and Grassland Administration Detecting Center of Wildlife, Harbin, 150040, China.
- State Forestry and Grassland Administration Research Center of Engineering Technology for Wildlife Conservation and Utilization of China, Harbin, 150040, China.
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116
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Rubi TL, Knowles LL, Dantzer B. Museum epigenomics: Characterizing cytosine methylation in historic museum specimens. Mol Ecol Resour 2019; 20:1161-1170. [DOI: 10.1111/1755-0998.13115] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2019] [Revised: 10/23/2019] [Accepted: 11/01/2019] [Indexed: 11/28/2022]
Affiliation(s)
- Tricia L. Rubi
- Department of Psychology University of Michigan Ann Arbor MI USA
- Department of Biology University of Victoria Victoria BC Canada
| | - L. Lacey Knowles
- Department of Ecology and Evolutionary Biology University of Michigan Ann Arbor MI USA
| | - Ben Dantzer
- Department of Psychology University of Michigan Ann Arbor MI USA
- Department of Ecology and Evolutionary Biology University of Michigan Ann Arbor MI USA
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117
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Abstract
Motivation The study of ancient genomes can elucidate the evolutionary past. However, analyses are complicated by base-modifications in ancient DNA molecules that result in errors in DNA sequences. These errors are particularly common near the ends of sequences and pose a challenge for genotype calling. Results I describe an iterative method that estimates genotype frequencies and errors along sequences to allow for accurate genotype calling from ancient sequences. The implementation of this method, called snpAD, performs well on high-coverage ancient data, as shown by simulations and by subsampling the data of a high-coverage Neandertal genome. Although estimates for low-coverage genomes are less accurate, I am able to derive approximate estimates of heterozygosity from several low-coverage Neandertals. These estimates show that low heterozygosity, compared to modern humans, was common among Neandertals. Availability and implementation The C++ code of snpAD is freely available at http://bioinf.eva.mpg.de/snpAD/. Supplementary information Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Kay Prüfer
- Department for Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
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118
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Spyrou MA, Keller M, Tukhbatova RI, Scheib CL, Nelson EA, Andrades Valtueña A, Neumann GU, Walker D, Alterauge A, Carty N, Cessford C, Fetz H, Gourvennec M, Hartle R, Henderson M, von Heyking K, Inskip SA, Kacki S, Key FM, Knox EL, Later C, Maheshwari-Aplin P, Peters J, Robb JE, Schreiber J, Kivisild T, Castex D, Lösch S, Harbeck M, Herbig A, Bos KI, Krause J. Phylogeography of the second plague pandemic revealed through analysis of historical Yersinia pestis genomes. Nat Commun 2019; 10:4470. [PMID: 31578321 PMCID: PMC6775055 DOI: 10.1038/s41467-019-12154-0] [Citation(s) in RCA: 69] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2018] [Accepted: 08/15/2019] [Indexed: 12/30/2022] Open
Abstract
The second plague pandemic, caused by Yersinia pestis, devastated Europe and the nearby regions between the 14th and 18th centuries AD. Here we analyse human remains from ten European archaeological sites spanning this period and reconstruct 34 ancient Y. pestis genomes. Our data support an initial entry of the bacterium through eastern Europe, the absence of genetic diversity during the Black Death, and low within-outbreak diversity thereafter. Analysis of post-Black Death genomes shows the diversification of a Y. pestis lineage into multiple genetically distinct clades that may have given rise to more than one disease reservoir in, or close to, Europe. In addition, we show the loss of a genomic region that includes virulence-related genes in strains associated with late stages of the pandemic. The deletion was also identified in genomes connected with the first plague pandemic (541-750 AD), suggesting a comparable evolutionary trajectory of Y. pestis during both events.
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Affiliation(s)
- Maria A Spyrou
- Max Planck Institute for the Science of Human History, 07745, Jena, Germany.
- Institute for Archaeological Sciences, University of Tübingen, 72070, Tübingen, Germany.
| | - Marcel Keller
- Max Planck Institute for the Science of Human History, 07745, Jena, Germany
- SNSB, State Collection for Anthropology and Palaeoanatomy Munich, 80333, Munich, Germany
| | - Rezeda I Tukhbatova
- Max Planck Institute for the Science of Human History, 07745, Jena, Germany
- Laboratory of Structural Biology, Kazan Federal University, Kazan, Russian Federation, 420008
| | | | - Elizabeth A Nelson
- Max Planck Institute for the Science of Human History, 07745, Jena, Germany
- Institute for Archaeological Sciences, University of Tübingen, 72070, Tübingen, Germany
| | | | - Gunnar U Neumann
- Max Planck Institute for the Science of Human History, 07745, Jena, Germany
| | - Don Walker
- MOLA (Museum of London Archaeology), London, N1 7ED, UK
| | - Amelie Alterauge
- Department of Physical Anthropology, Institute for Forensic Medicine, University of Bern, 3007, Bern, Switzerland
| | - Niamh Carty
- MOLA (Museum of London Archaeology), London, N1 7ED, UK
| | - Craig Cessford
- Department of Archaeology, University of Cambridge, Downing St, Cambridge, CB2 3ER, UK
| | - Hermann Fetz
- Archaeological Service, State Archive Nidwalden, 6371, Nidwalden, Switzerland
| | - Michaël Gourvennec
- Archeodunum SAS, Agency Toulouse, 8 allée Michel de Montaigne, 31770, Colomiers, France
| | - Robert Hartle
- MOLA (Museum of London Archaeology), London, N1 7ED, UK
| | | | - Kristin von Heyking
- SNSB, State Collection for Anthropology and Palaeoanatomy Munich, 80333, Munich, Germany
| | - Sarah A Inskip
- McDonald Institute for Archaeological Research, University of Cambridge, Downing St, Cambridge, CB2 3ER, UK
| | - Sacha Kacki
- PACEA, CNRS Institute, Université de Bordeaux, 33615, Pessac, France
- Department of Archaeology, Durham University, South Rd, Durham, DH1 3LE, UK
| | - Felix M Key
- Institute for Medical Engineering and Sciences, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | | | - Christian Later
- Bavarian State Department of Monuments and Sites, 80539, Munich, Germany
| | | | - Joris Peters
- SNSB, State Collection for Anthropology and Palaeoanatomy Munich, 80333, Munich, Germany
- ArchaeoBioCenter and Department of Veterinary Sciences, Institute of Palaeoanatomy, Domestication Research and the History of Veterinary Medicine, Ludwig Maximilian University Munich, Kaulbachstr. 37/III, 80539, Munich, Germany
| | - John E Robb
- Department of Archaeology, University of Cambridge, Downing St, Cambridge, CB2 3ER, UK
| | | | - Toomas Kivisild
- Institute of Genomics, University of Tartu, Riia 23b, 51010, Tartu, Estonia
- Department of Human Genetics, Katholieke Universiteit Leuven, 3000, Leuven, Belgium
| | - Dominique Castex
- PACEA, CNRS Institute, Université de Bordeaux, 33615, Pessac, France
| | - Sandra Lösch
- Department of Physical Anthropology, Institute for Forensic Medicine, University of Bern, 3007, Bern, Switzerland
| | - Michaela Harbeck
- SNSB, State Collection for Anthropology and Palaeoanatomy Munich, 80333, Munich, Germany
| | - Alexander Herbig
- Max Planck Institute for the Science of Human History, 07745, Jena, Germany
| | - Kirsten I Bos
- Max Planck Institute for the Science of Human History, 07745, Jena, Germany.
| | - Johannes Krause
- Max Planck Institute for the Science of Human History, 07745, Jena, Germany.
- Institute for Archaeological Sciences, University of Tübingen, 72070, Tübingen, Germany.
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119
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Tsai WLE, Schedl ME, Maley JM, McCormack JE. More than skin and bones: Comparing extraction methods and alternative sources of DNA from avian museum specimens. Mol Ecol Resour 2019; 20:1220-1227. [PMID: 31478338 DOI: 10.1111/1755-0998.13077] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2019] [Revised: 07/11/2019] [Accepted: 07/23/2019] [Indexed: 11/28/2022]
Abstract
Next-generation sequencing has greatly expanded the utility and value of museum collections by revealing specimens as genomic resources. As the field of museum genomics grows, so does the need for extraction methods that maximize DNA yields. For avian museum specimens, the established method of extracting DNA from toe pads works well for most specimens. However, for some specimens, especially those of birds that are very small or very large, toe pads can be a poor source of DNA. In this study, we apply two DNA extraction methods (phenol-chloroform and silica column) to three different sources of DNA (toe pad, skin punch and bone) from 10 historical avian museum specimens. We show that a modified phenol-chloroform protocol yielded significantly more DNA than a silica column protocol (e.g., Qiagen DNeasy Blood & Tissue Kit) across all tissue types. However, extractions using the silica column protocol contained longer fragments on average than those using the phenol-chloroform protocol, probably as a result of loss of small fragments through the silica column. While toe pads yielded more DNA than skin punches and bone fragments, skin punches proved to be a reliable alternative source of DNA and might be especially appealing when toe pad extractions are impractical. Overall, we found that historical bird museum specimens contain substantial amounts of DNA for genomic studies under most extraction scenarios, but that a phenol-chloroform protocol consistently provides the high quantities of DNA required for most current genomic protocols.
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Affiliation(s)
- Whitney L E Tsai
- Moore Laboratory of Zoology, Occidental College, Los Angeles, California
| | - Margaret E Schedl
- Moore Laboratory of Zoology, Occidental College, Los Angeles, California
| | - James M Maley
- Moore Laboratory of Zoology, Occidental College, Los Angeles, California
| | - John E McCormack
- Moore Laboratory of Zoology, Occidental College, Los Angeles, California.,Biology Department, Occidental College, Los Angeles, California
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120
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Chen SG, Li J, Zhang F, Xiao B, Hu JM, Cui YQ, Hofreiter M, Hou XD, Sheng GL, Lai XL, Yuan JX. Different maternal lineages revealed by ancient mitochondrial genome of Camelus bactrianus from China. Mitochondrial DNA A DNA Mapp Seq Anal 2019; 30:786-793. [PMID: 31542986 DOI: 10.1080/24701394.2019.1659250] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Domestic Bactrian camel (Camelus bactrianus) used to be one of the most important livestock species in Chinese history, as well as the major transport carrier on the ancient Silk Road. However, archeological studies on Chinese C. bactrianus are still limited, and molecular biology research on this species is mainly focused on modern specimens. In this study, we retrieved the complete mitochondrial genome from a C. bactrianus specimen, which was excavated from northwestern China and dated at 1290-1180 cal. years before present (yBP). Phylogenetic analyses using 18 mitochondrial genomes indicated that the C. bactrianus clade was divided into two maternal lineages. The majority of samples originating from Iran to Japan and Mongolia belong to subclade A1, while our sample together with two Mongolian individuals formed the much smaller subclade A2. Furthermore, the divergence time of these two maternal lineages was estimated as 165 Kya (95% credibility interval 117-222 Kya), this might indicate that several different evolutionary lineages were incorporated into the domestic gene pool during the initial domestication process. Bayesian skyline plot (BSP) analysis suggest a slow increase in female effective population size of C. bactrianus from 5000 years ago, which corresponds to the beginning of domestication of C. bactrianus. The present study also revealed that there were extensive exchanges of genetic information among C. bactrianus populations in regions along the Silk Road.
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Affiliation(s)
- Shun-Gang Chen
- Faculty of Materials Science and Chemistry, China University of Geosciences , Wuhan , China.,State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences , Wuhan , China
| | - Ji Li
- Insitute of Silk Road Studies, Northwest University , Xi'an , China
| | - Fan Zhang
- Ancient DNA Lab, School of Life Science, Jilin University , Changchun , China
| | - Bo Xiao
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences , Wuhan , China
| | - Jia-Ming Hu
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences , Wuhan , China
| | - Yin-Qiu Cui
- Ancient DNA Lab, School of Life Science, Jilin University , Changchun , China
| | - Michael Hofreiter
- Institute for Biochemistry and Biology, University of Potsdam, Karl-Liebknecht-Strasse , Potsdam , Germany
| | - Xin-Dong Hou
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences , Wuhan , China
| | - Gui-Lian Sheng
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences , Wuhan , China
| | - Xu-Long Lai
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences , Wuhan , China
| | - Jun-Xia Yuan
- Faculty of Materials Science and Chemistry, China University of Geosciences , Wuhan , China.,State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences , Wuhan , China
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121
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Cappellini E, Welker F, Pandolfi L, Ramos-Madrigal J, Samodova D, Rüther PL, Fotakis AK, Lyon D, Moreno-Mayar JV, Bukhsianidze M, Rakownikow Jersie-Christensen R, Mackie M, Ginolhac A, Ferring R, Tappen M, Palkopoulou E, Dickinson MR, Stafford TW, Chan YL, Götherström A, Nathan SKSS, Heintzman PD, Kapp JD, Kirillova I, Moodley Y, Agusti J, Kahlke RD, Kiladze G, Martínez-Navarro B, Liu S, Sandoval Velasco M, Sinding MHS, Kelstrup CD, Allentoft ME, Orlando L, Penkman K, Shapiro B, Rook L, Dalén L, Gilbert MTP, Olsen JV, Lordkipanidze D, Willerslev E. Early Pleistocene enamel proteome from Dmanisi resolves Stephanorhinus phylogeny. Nature 2019; 574:103-107. [PMID: 31511700 PMCID: PMC6894936 DOI: 10.1038/s41586-019-1555-y] [Citation(s) in RCA: 67] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2018] [Accepted: 08/12/2019] [Indexed: 11/10/2022]
Abstract
Ancient DNA (aDNA) sequencing has enabled reconstruction of speciation, migration, and admixture events for extinct taxa1. Outside the permafrost, however, irreversible aDNA post-mortem degradation2 has so far limited aDNA recovery to the past ~0.5 million years (Ma)3. Contrarily, tandem mass spectrometry (MS) allowed sequencing ~1.5 million year (Ma) old collagen type I (COL1)4 and suggested the presence of protein residues in Cretaceous fossil remains5, although with limited phylogenetic use6. In the absence of molecular evidence, the speciation of several Early and Middle Pleistocene extinct species remain contentious. In this study, we address the phylogenetic relationships of the Eurasian Pleistocene Rhinocerotidae7–9 using a ~1.77 Ma old dental enamel proteome of a Stephanorhinus specimen from the Dmanisi archaeological site in Georgia (South Caucasus)10. Molecular phylogenetic analyses place the Dmanisi Stephanorhinus as a sister group to the woolly (Coelodonta antiquitatis) and Merck’s rhinoceros (S. kirchbergensis) clade. We show that Coelodonta evolved from an early Stephanorhinus lineage and that the latter includes at least two distinct evolutionary lines. As such, the genus Stephanorhinus is currently paraphyletic and its systematic revision is therefore needed. We demonstrate that Early Pleistocene dental enamel proteome sequencing overcomes the limits of ancient collagen- and aDNA-based phylogenetic inference. It also provides additional information about the sex and taxonomic assignment of the specimens analysed. Dental enamel, the hardest tissue in vertebrates11, is highly abundant in the fossil record. Our findings reveal that palaeoproteomic investigation of this material can push biomolecular investigation further back into the Early Pleistocene.
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Affiliation(s)
- Enrico Cappellini
- Lundbeck Foundation GeoGenetics Centre, Globe Institute, University of Copenhagen, Copenhagen, Denmark. .,Evolutionary Genomics Section, Globe Institute, University of Copenhagen, Copenhagen, Denmark.
| | - Frido Welker
- Evolutionary Genomics Section, Globe Institute, University of Copenhagen, Copenhagen, Denmark.,Department of Human Evolution, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Luca Pandolfi
- Dipartimento di Scienze della Terra, Università degli Studi di Firenze, Florence, Italy
| | - Jazmín Ramos-Madrigal
- Evolutionary Genomics Section, Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | - Diana Samodova
- Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Copenhagen, Denmark
| | - Patrick L Rüther
- Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Copenhagen, Denmark
| | - Anna K Fotakis
- Evolutionary Genomics Section, Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | - David Lyon
- Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Copenhagen, Denmark
| | - J Víctor Moreno-Mayar
- Lundbeck Foundation GeoGenetics Centre, Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | | | | | - Meaghan Mackie
- Evolutionary Genomics Section, Globe Institute, University of Copenhagen, Copenhagen, Denmark.,Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Copenhagen, Denmark
| | - Aurélien Ginolhac
- Life Sciences Research Unit, University of Luxembourg, Belvaux, Luxembourg
| | - Reid Ferring
- Department of Geography and Environment, University of North Texas, Denton, TX, USA
| | - Martha Tappen
- Department of Anthropology, University of Minnesota, Minneapolis, MN, USA
| | | | | | | | - Yvonne L Chan
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Stockholm, Sweden
| | - Anders Götherström
- Department of Archaeology and Classical Studies, Stockholm University, Stockholm, Sweden
| | | | - Peter D Heintzman
- Department of Ecology and Evolutionary Biology, University of California Santa Cruz, Santa Cruz, CA, USA.,Tromsø University Museum, The Arctic University of Norway (UiT), Tromsø, Norway
| | - Joshua D Kapp
- Department of Ecology and Evolutionary Biology, University of California Santa Cruz, Santa Cruz, CA, USA
| | - Irina Kirillova
- Ice Age Museum, National Alliance of Shidlovskiy 'Ice Age', Moscow, Russia
| | - Yoshan Moodley
- Department of Zoology, University of Venda, Thohoyandou, South Africa
| | - Jordi Agusti
- Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain.,Institut Català de Paleoecologia Humana i Evolució Social, Universitat Rovira i Virgili, Tarragona, Spain
| | | | - Gocha Kiladze
- Geology Department, Tbilisi State University, Tbilisi, Georgia
| | - Bienvenido Martínez-Navarro
- Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain.,Institut Català de Paleoecologia Humana i Evolució Social, Universitat Rovira i Virgili, Tarragona, Spain.,Departament d'Història i Geografia, Universitat Rovira i Virgili, Tarragona, Spain
| | - Shanlin Liu
- Evolutionary Genomics Section, Globe Institute, University of Copenhagen, Copenhagen, Denmark.,BGI Shenzhen, Shenzen, China
| | | | - Mikkel-Holger S Sinding
- Evolutionary Genomics Section, Globe Institute, University of Copenhagen, Copenhagen, Denmark.,Greenland Institute of Natural Resources, Nuuk, Greenland
| | - Christian D Kelstrup
- Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Copenhagen, Denmark
| | - Morten E Allentoft
- Lundbeck Foundation GeoGenetics Centre, Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | - Ludovic Orlando
- Lundbeck Foundation GeoGenetics Centre, Globe Institute, University of Copenhagen, Copenhagen, Denmark.,Laboratoire d'Anthropobiologie Moléculaire et d'Imagerie de Synthèse, Université Paul Sabatier, Toulouse, France
| | | | - Beth Shapiro
- Department of Ecology and Evolutionary Biology, University of California Santa Cruz, Santa Cruz, CA, USA.,Howard Hughes Medical Institute, University of California Santa Cruz, Santa Cruz, CA, USA
| | - Lorenzo Rook
- Dipartimento di Scienze della Terra, Università degli Studi di Firenze, Florence, Italy
| | - Love Dalén
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Stockholm, Sweden
| | - M Thomas P Gilbert
- Evolutionary Genomics Section, Globe Institute, University of Copenhagen, Copenhagen, Denmark.,University Museum, Norwegian University of Science and Technology, Trondheim, Norway
| | - Jesper V Olsen
- Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Copenhagen, Denmark.
| | | | - Eske Willerslev
- Lundbeck Foundation GeoGenetics Centre, Globe Institute, University of Copenhagen, Copenhagen, Denmark. .,Department of Zoology, University of Cambridge, Cambridge, UK. .,Wellcome Trust Sanger Institute, Hinxton, UK. .,Danish Institute for Advanced Study, University of Southern Denmark, Odense, Denmark.
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122
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Olalde I, Mallick S, Patterson N, Rohland N, Villalba-Mouco V, Silva M, Dulias K, Edwards CJ, Gandini F, Pala M, Soares P, Ferrando-Bernal M, Adamski N, Broomandkhoshbacht N, Cheronet O, Culleton BJ, Fernandes D, Lawson AM, Mah M, Oppenheimer J, Stewardson K, Zhang Z, Jiménez Arenas JM, Toro Moyano IJ, Salazar-García DC, Castanyer P, Santos M, Tremoleda J, Lozano M, García Borja P, Fernández-Eraso J, Mujika-Alustiza JA, Barroso C, Bermúdez FJ, Viguera Mínguez E, Burch J, Coromina N, Vivó D, Cebrià A, Fullola JM, García-Puchol O, Morales JI, Oms FX, Majó T, Vergès JM, Díaz-Carvajal A, Ollich-Castanyer I, López-Cachero FJ, Silva AM, Alonso-Fernández C, Delibes de Castro G, Jiménez Echevarría J, Moreno-Márquez A, Pascual Berlanga G, Ramos-García P, Ramos-Muñoz J, Vijande Vila E, Aguilella Arzo G, Esparza Arroyo Á, Lillios KT, Mack J, Velasco-Vázquez J, Waterman A, Benítez de Lugo Enrich L, Benito Sánchez M, Agustí B, Codina F, de Prado G, Estalrrich A, Fernández Flores Á, Finlayson C, Finlayson G, Finlayson S, Giles-Guzmán F, Rosas A, Barciela González V, García Atiénzar G, Hernández Pérez MS, Llanos A, Carrión Marco Y, Collado Beneyto I, López-Serrano D, Sanz Tormo M, Valera AC, Blasco C, Liesau C, Ríos P, Daura J, de Pedro Michó MJ, Diez-Castillo AA, Flores Fernández R, Francès Farré J, Garrido-Pena R, Gonçalves VS, Guerra-Doce E, Herrero-Corral AM, Juan-Cabanilles J, López-Reyes D, McClure SB, Merino Pérez M, Oliver Foix A, Sanz Borràs M, Sousa AC, Vidal Encinas JM, Kennett DJ, Richards MB, Werner Alt K, Haak W, Pinhasi R, Lalueza-Fox C, Reich D. The genomic history of the Iberian Peninsula over the past 8000 years. Science 2019; 363:1230-1234. [PMID: 30872528 DOI: 10.1126/science.aav4040] [Citation(s) in RCA: 192] [Impact Index Per Article: 38.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2018] [Accepted: 01/30/2019] [Indexed: 12/18/2022]
Abstract
We assembled genome-wide data from 271 ancient Iberians, of whom 176 are from the largely unsampled period after 2000 BCE, thereby providing a high-resolution time transect of the Iberian Peninsula. We document high genetic substructure between northwestern and southeastern hunter-gatherers before the spread of farming. We reveal sporadic contacts between Iberia and North Africa by ~2500 BCE and, by ~2000 BCE, the replacement of 40% of Iberia's ancestry and nearly 100% of its Y-chromosomes by people with Steppe ancestry. We show that, in the Iron Age, Steppe ancestry had spread not only into Indo-European-speaking regions but also into non-Indo-European-speaking ones, and we reveal that present-day Basques are best described as a typical Iron Age population without the admixture events that later affected the rest of Iberia. Additionally, we document how, beginning at least in the Roman period, the ancestry of the peninsula was transformed by gene flow from North Africa and the eastern Mediterranean.
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Affiliation(s)
- Iñigo Olalde
- Department of Genetics, Harvard Medical School, Boston, MA, USA.
| | - Swapan Mallick
- Department of Genetics, Harvard Medical School, Boston, MA, USA.,Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, USA
| | | | - Nadin Rohland
- Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Vanessa Villalba-Mouco
- Max Planck Institute for the Science of Human History, Jena, Germany.,Departamento de Ciencias de la Antigüedad, Grupo Primeros Pobladores del Valle del Ebro (PPVE), Instituto de Investigación en Ciencias Ambientales (IUCA), Universidad de Zaragoza, Zaragoza, Spain
| | - Marina Silva
- Department of Biological and Geographical Sciences, School of Applied Sciences, University of Huddersfield, Huddersfield, UK
| | - Katharina Dulias
- Department of Biological and Geographical Sciences, School of Applied Sciences, University of Huddersfield, Huddersfield, UK
| | - Ceiridwen J Edwards
- Department of Biological and Geographical Sciences, School of Applied Sciences, University of Huddersfield, Huddersfield, UK
| | - Francesca Gandini
- Department of Biological and Geographical Sciences, School of Applied Sciences, University of Huddersfield, Huddersfield, UK
| | - Maria Pala
- Department of Biological and Geographical Sciences, School of Applied Sciences, University of Huddersfield, Huddersfield, UK
| | - Pedro Soares
- Centre of Molecular and Environmental Biology, Department of Biology, University of Minho, Braga, Portugal
| | | | - Nicole Adamski
- Department of Genetics, Harvard Medical School, Boston, MA, USA.,Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, USA
| | - Nasreen Broomandkhoshbacht
- Department of Genetics, Harvard Medical School, Boston, MA, USA.,Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, USA
| | - Olivia Cheronet
- Department of Evolutionary Anthropology, University of Vienna, Vienna, Austria
| | - Brendan J Culleton
- Department of Anthropology and Institutes of Energy and the Environment, The Pennsylvania State University, University Park, PA, USA
| | - Daniel Fernandes
- Department of Evolutionary Anthropology, University of Vienna, Vienna, Austria.,Research Center for Anthropology and Health, Department of Life Science, University of Coimbra, Coimbra, Portugal
| | - Ann Marie Lawson
- Department of Genetics, Harvard Medical School, Boston, MA, USA.,Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, USA
| | - Matthew Mah
- Department of Genetics, Harvard Medical School, Boston, MA, USA.,Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, USA
| | - Jonas Oppenheimer
- Department of Genetics, Harvard Medical School, Boston, MA, USA.,Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, USA
| | - Kristin Stewardson
- Department of Genetics, Harvard Medical School, Boston, MA, USA.,Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, USA
| | - Zhao Zhang
- Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Juan Manuel Jiménez Arenas
- Departamento de Prehistoria y Arqueología, Universidad de Granada, Granada, Spain.,Instituto Universitario de la Paz y los Conflictos, Universidad de Granada, Granada, Spain.,Department of Anthropology - Anthropologisches Institut and Museum, Universität Zürich, Zürich, Switzerland
| | | | - Domingo C Salazar-García
- Departamento de Geografía, Prehistoria y Arqueología, Grupo de Investigación en Prehistoria, (UPV-EHU)/IKERBASQUE-Basque Foundation for Science, Vitoria, Spain
| | - Pere Castanyer
- Museu d'Arqueologia de Catalunya-Empúries, L'Escala, Spain
| | - Marta Santos
- Museu d'Arqueologia de Catalunya-Empúries, L'Escala, Spain
| | | | - Marina Lozano
- Institut Català de Paleoecologia Humana i Evolució Social (IPHES), Tarragona, Spain.,Àrea de Prehistòria, Universitat Rovira i Virgili (URV), Tarragona, Spain
| | - Pablo García Borja
- Departamento de Prehistoria e Historia Antigua, Universidad Nacional de Educación a Distancia, Valencia, Spain
| | - Javier Fernández-Eraso
- Departamento de Geografía, Prehistoria y Arqueología, Universidad del País Vasco, Vitoria, Spain
| | | | - Cecilio Barroso
- Fundación Instituto de Investigación de Prehistoria y Evolución Humana (FIPEH), Lucena, Spain
| | - Francisco J Bermúdez
- Fundación Instituto de Investigación de Prehistoria y Evolución Humana (FIPEH), Lucena, Spain
| | | | - Josep Burch
- Institut de Recerca Històrica, Universitat de Girona, Girona, Spain
| | - Neus Coromina
- Institut de Recerca Històrica, Universitat de Girona, Girona, Spain
| | - David Vivó
- Institut de Recerca Històrica, Universitat de Girona, Girona, Spain
| | - Artur Cebrià
- SERP, Departament d'Història i Arqueologia, Facultat de Geografia i Història, Universitat de Barcelona, Barcelona, Spain
| | - Josep Maria Fullola
- SERP, Departament d'Història i Arqueologia, Facultat de Geografia i Història, Universitat de Barcelona, Barcelona, Spain
| | - Oreto García-Puchol
- PREMEDOC Research Group, Departament de Prehistòria, Arqueologia i Historia Antiga, Universitat de València, València, Spain
| | - Juan Ignacio Morales
- SERP, Departament d'Història i Arqueologia, Facultat de Geografia i Història, Universitat de Barcelona, Barcelona, Spain
| | - F Xavier Oms
- SERP, Departament d'Història i Arqueologia, Facultat de Geografia i Història, Universitat de Barcelona, Barcelona, Spain
| | - Tona Majó
- Archaeom. Departament de Prehistòria, Universitat Autònoma de Barcelona, Cerdanyola del Vallès, Spain
| | - Josep Maria Vergès
- Institut Català de Paleoecologia Humana i Evolució Social (IPHES), Tarragona, Spain.,Àrea de Prehistòria, Universitat Rovira i Virgili (URV), Tarragona, Spain
| | | | | | - F Javier López-Cachero
- SERP, Departament d'Història i Arqueologia, Facultat de Geografia i Història, Universitat de Barcelona, Barcelona, Spain
| | - Ana Maria Silva
- Laboratory of Prehistory, Research Center for Anthropology and Health, Department of Life Sciences, University of Coimbra, Coimbra, Portugal.,UNIARQ, Faculdade de Letras, Universidade de Lisboa, Lisboa, Portugal.,CEF, Department of Life Sciences, University of Coimbra, Coimbra, Portugal
| | | | - Germán Delibes de Castro
- Departamento de Prehistoria, Facultad de Filosofía y Letras, Universidad de Valladolid, Valladolid, Spain
| | | | - Adolfo Moreno-Márquez
- Departamento de Historia, Geografía y Filosofía, Universidad de Cádiz, Cádiz, Spain.,Departamento de Geografía, Historia y Humanidades, Universidad de Almería, Almería, Spain
| | | | | | - José Ramos-Muñoz
- Departamento de Historia, Geografía y Filosofía, Universidad de Cádiz, Cádiz, Spain
| | - Eduardo Vijande Vila
- Departamento de Historia, Geografía y Filosofía, Universidad de Cádiz, Cádiz, Spain
| | - Gustau Aguilella Arzo
- Servicio de Investigaciones Arqueológicas y Prehistóricas de la Diputación de Castellón, Castelló de la Plana, Spain
| | - Ángel Esparza Arroyo
- GIR PrehUSAL, Departamento de Prehistoria, Historia Antigua y Arqueología, Universidad de Salamanca, Salamanca, Spain
| | - Katina T Lillios
- Department of Anthropology, University of Iowa, Iowa City, IA, USA
| | - Jennifer Mack
- Office of the State Archaeologist, University of Iowa, Iowa City, IA, USA
| | - Javier Velasco-Vázquez
- Departamento de Ciencias Históricas, Universidad de Las Palmas de Gran Canaria, Las Palmas, Spain
| | | | - Luis Benítez de Lugo Enrich
- Departamento de Prehistoria y Arqueología, Universidad Autónoma de Madrid, Madrid, Spain.,Departamento de Prehistoria y Arqueología, Universidad Nacional de Educación a Distancia, Madrid, Spain
| | - María Benito Sánchez
- Departamento de Medicina Legal, Psiquiatría y Anatomía Patológica, Universidad Complutense de Madrid, Madrid, Spain
| | - Bibiana Agustí
- INSITU S.C.P., Centelles, Spain.,Museu d'Arqueologia de Catalunya-Ullastret, Ullastret, Spain
| | - Ferran Codina
- Museu d'Arqueologia de Catalunya-Ullastret, Ullastret, Spain
| | | | - Almudena Estalrrich
- Instituto Internacional de Investigaciones Prehistóricas de Cantabria IIIPC (Universidad de Cantabria-Gobierno de Cantabria-Santander), Santander, Spain
| | | | - Clive Finlayson
- The Gibraltar National Museum, Gibraltar.,Department of Anthropology, University of Toronto, Toronto, ON, Canada.,School of Natural Sciences and Psychology, Liverpool John Moores University, Liverpool, UK.,Institute of Life and Earth Sciences, University of Gibraltar, Gibraltar
| | - Geraldine Finlayson
- The Gibraltar National Museum, Gibraltar.,School of Natural Sciences and Psychology, Liverpool John Moores University, Liverpool, UK.,Institute of Life and Earth Sciences, University of Gibraltar, Gibraltar
| | - Stewart Finlayson
- The Gibraltar National Museum, Gibraltar.,Department of Life Sciences, Anglia Ruskin University, Cambridge, UK
| | | | - Antonio Rosas
- Paleoanthropology Group, Department of Paleobiology, Museo Nacional de Ciencias Naturales (MNCN)-Consejo Superior de Investigaciones Científicas (CSIC), Madrid, Spain
| | - Virginia Barciela González
- Departamento de Prehistoria, Arqueología e Historia Antigua, Facultad de Filosofía y Letras, Universidad de Alicante, San Vicente del Raspeig, Spain.,Instituto Universitario de Investigación en Arqueología y Patrimonio Histórico (INAPH), San Vicente del Raspeig, Spain
| | - Gabriel García Atiénzar
- Departamento de Prehistoria, Arqueología e Historia Antigua, Facultad de Filosofía y Letras, Universidad de Alicante, San Vicente del Raspeig, Spain.,Instituto Universitario de Investigación en Arqueología y Patrimonio Histórico (INAPH), San Vicente del Raspeig, Spain
| | - Mauro S Hernández Pérez
- Departamento de Prehistoria, Arqueología e Historia Antigua, Facultad de Filosofía y Letras, Universidad de Alicante, San Vicente del Raspeig, Spain.,Instituto Universitario de Investigación en Arqueología y Patrimonio Histórico (INAPH), San Vicente del Raspeig, Spain
| | | | - Yolanda Carrión Marco
- Departament de Prehistòria, Arqueologia i Historia Antiga, Universitat de València, València, Spain
| | | | | | | | | | - Concepción Blasco
- Departamento de Prehistoria y Arqueología, Universidad Autónoma de Madrid, Madrid, Spain
| | - Corina Liesau
- Departamento de Prehistoria y Arqueología, Universidad Autónoma de Madrid, Madrid, Spain
| | - Patricia Ríos
- Departamento de Prehistoria y Arqueología, Universidad Autónoma de Madrid, Madrid, Spain
| | - Joan Daura
- SERP, Departament d'Història i Arqueologia, Facultat de Geografia i Història, Universitat de Barcelona, Barcelona, Spain
| | | | - Agustín A Diez-Castillo
- GRAM Research Group, Departament de Prehistòria, Arqueologia i Historia Antiga, Universitat de València, València, Spain
| | | | | | - Rafael Garrido-Pena
- Departamento de Prehistoria y Arqueología, Universidad Autónoma de Madrid, Madrid, Spain
| | | | - Elisa Guerra-Doce
- Departamento de Prehistoria, Facultad de Filosofía y Letras, Universidad de Valladolid, Valladolid, Spain
| | | | | | | | - Sarah B McClure
- Department of Anthropology, University of California, Santa Barbara, CA, USA
| | - Marta Merino Pérez
- Unitat d'Antropologia Física, Departament de Biologia Animal, Facultat de Biologia, Universitat de Barcelona, Barcelona, Spain
| | - Arturo Oliver Foix
- Servicio de Investigaciones Arqueológicas y Prehistóricas de la Diputación de Castellón, Castelló de la Plana, Spain
| | - Montserrat Sanz Borràs
- SERP, Departament d'Història i Arqueologia, Facultat de Geografia i Història, Universitat de Barcelona, Barcelona, Spain
| | | | | | - Douglas J Kennett
- Department of Anthropology and Institutes of Energy and the Environment, The Pennsylvania State University, University Park, PA, USA.,Department of Anthropology, University of California, Santa Barbara, CA, USA
| | - Martin B Richards
- Department of Biological and Geographical Sciences, School of Applied Sciences, University of Huddersfield, Huddersfield, UK
| | - Kurt Werner Alt
- Center of Natural and Cultural Human History, Danube Private University, Krems, Austria.,Department of Biomedical Engineering and Integrative Prehistory and Archaeological Science, Basel University, Basel, Switzerland
| | - Wolfgang Haak
- Max Planck Institute for the Science of Human History, Jena, Germany.,School of Biological Sciences, University of Adelaide, Adelaide, Australia
| | - Ron Pinhasi
- Department of Evolutionary Anthropology, University of Vienna, Vienna, Austria
| | - Carles Lalueza-Fox
- Institute of Evolutionary Biology, CSIC-Universitat Pompeu Fabra, Barcelona, Spain.
| | - David Reich
- Department of Genetics, Harvard Medical School, Boston, MA, USA. .,Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, USA
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Abstract
Over the past decade, a genomics revolution, made possible through the development of high-throughput sequencing, has triggered considerable progress in the study of ancient DNA, enabling complete genomes of past organisms to be reconstructed. A newly established branch of this field, ancient pathogen genomics, affords an in-depth view of microbial evolution by providing a molecular fossil record for a number of human-associated pathogens. Recent accomplishments include the confident identification of causative agents from past pandemics, the discovery of microbial lineages that are now extinct, the extrapolation of past emergence events on a chronological scale and the characterization of long-term evolutionary history of microorganisms that remain relevant to public health today. In this Review, we discuss methodological advancements, persistent challenges and novel revelations gained through the study of ancient pathogen genomes.
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124
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Gutaker RM, Weiß CL, Ellis D, Anglin NL, Knapp S, Luis Fernández-Alonso J, Prat S, Burbano HA. The origins and adaptation of European potatoes reconstructed from historical genomes. Nat Ecol Evol 2019; 3:1093-1101. [PMID: 31235927 DOI: 10.1038/s41559-019-0921-3] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2019] [Accepted: 05/10/2019] [Indexed: 12/30/2022]
Abstract
Potato, one of the most important staple crops, originates from the highlands of the equatorial Andes. There, potatoes propagate vegetatively via tubers under short days, constant throughout the year. After their introduction to Europe in the sixteenth century, potatoes adapted to a shorter growing season and to tuber formation under long days. Here, we traced the demographic and adaptive history of potato introduction to Europe. To this end, we sequenced 88 individuals that comprise landraces, modern cultivars and historical herbarium samples, including specimens collected by Darwin during the voyage of the Beagle. Our findings show that European potatoes collected during the period 1650-1750 were closely related to Andean landraces. After their introduction to Europe, potatoes admixed with Chilean genotypes. We identified candidate genes putatively involved in long-day pre-adaptation, and showed that the 1650-1750 European individuals were not long-day adapted through previously described allelic variants of the CYCLING DOF FACTOR1 gene. Such allelic variants were detected in Europe during the nineteenth century. Our study highlights the power of combining contemporary and historical genomes to understand the complex evolutionary history of crop adaptation to new environments.
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Affiliation(s)
- Rafal M Gutaker
- Research Group for Ancient Genomics and Evolution, Department of Molecular Biology, Max Planck Institute for Developmental Biology, Tuebingen, Germany
| | - Clemens L Weiß
- Research Group for Ancient Genomics and Evolution, Department of Molecular Biology, Max Planck Institute for Developmental Biology, Tuebingen, Germany
| | | | | | - Sandra Knapp
- Department of Life Sciences, Natural History Museum, London, UK
| | | | - Salomé Prat
- Departamento de Genética Molecular de Plantas, Centro Nacional de Biotecnología-CSIC, Madrid, Spain
| | - Hernán A Burbano
- Research Group for Ancient Genomics and Evolution, Department of Molecular Biology, Max Planck Institute for Developmental Biology, Tuebingen, Germany.
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125
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Keller M, Spyrou MA, Scheib CL, Neumann GU, Kröpelin A, Haas-Gebhard B, Päffgen B, Haberstroh J, Ribera I Lacomba A, Raynaud C, Cessford C, Durand R, Stadler P, Nägele K, Bates JS, Trautmann B, Inskip SA, Peters J, Robb JE, Kivisild T, Castex D, McCormick M, Bos KI, Harbeck M, Herbig A, Krause J. Ancient Yersinia pestis genomes from across Western Europe reveal early diversification during the First Pandemic (541-750). Proc Natl Acad Sci U S A 2019; 116:12363-12372. [PMID: 31164419 PMCID: PMC6589673 DOI: 10.1073/pnas.1820447116] [Citation(s) in RCA: 52] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The first historically documented pandemic caused by Yersinia pestis began as the Justinianic Plague in 541 within the Roman Empire and continued as the so-called First Pandemic until 750. Although paleogenomic studies have previously identified the causative agent as Y. pestis, little is known about the bacterium's spread, diversity, and genetic history over the course of the pandemic. To elucidate the microevolution of the bacterium during this time period, we screened human remains from 21 sites in Austria, Britain, Germany, France, and Spain for Y. pestis DNA and reconstructed eight genomes. We present a methodological approach assessing single-nucleotide polymorphisms (SNPs) in ancient bacterial genomes, facilitating qualitative analyses of low coverage genomes from a metagenomic background. Phylogenetic analysis on the eight reconstructed genomes reveals the existence of previously undocumented Y. pestis diversity during the sixth to eighth centuries, and provides evidence for the presence of multiple distinct Y. pestis strains in Europe. We offer genetic evidence for the presence of the Justinianic Plague in the British Isles, previously only hypothesized from ambiguous documentary accounts, as well as the parallel occurrence of multiple derived strains in central and southern France, Spain, and southern Germany. Four of the reported strains form a polytomy similar to others seen across the Y. pestis phylogeny, associated with the Second and Third Pandemics. We identified a deletion of a 45-kb genomic region in the most recent First Pandemic strains affecting two virulence factors, intriguingly overlapping with a deletion found in 17th- to 18th-century genomes of the Second Pandemic.
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Affiliation(s)
- Marcel Keller
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745 Jena, Germany;
- State Collection of Anthropology and Palaeoanatomy Munich, Staatliche Naturwissenschaftliche Sammlungen Bayerns, 80333 Munich, Germany
| | - Maria A Spyrou
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745 Jena, Germany
| | - Christiana L Scheib
- Department of Archaeology, University of Cambridge, Cambridge CB2 3ER, United Kingdom
- Institute of Genomics, University of Tartu, 51010 Tartu, Estonia
| | - Gunnar U Neumann
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745 Jena, Germany
| | - Andreas Kröpelin
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745 Jena, Germany
- Friedrich Schiller University Jena, 07743 Jena, Germany
| | | | - Bernd Päffgen
- Institute for Pre- and Protohistoric Archaeology and Archaeology of the Roman Provinces, Ludwig Maximilian University Munich, 80799 Munich, Germany
| | - Jochen Haberstroh
- Bavarian State Department of Monuments and Sites, 80539 Munich, Germany
| | | | - Claude Raynaud
- CNRS, UMR5140, Archéologie des Sociétés Méditerranéennes, 34199 Montpellier, France
| | - Craig Cessford
- Department of Archaeology, University of Cambridge, Cambridge CB2 3ER, United Kingdom
| | - Raphaël Durand
- Service d'Archéologie Préventive de l'Agglomération de Bourges Plus, 18023 Bourges Cedex, France
| | - Peter Stadler
- Department of Pre- and Protohistory, University of Vienna, 1190 Vienna, Austria
| | - Kathrin Nägele
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745 Jena, Germany
| | - Jessica S Bates
- Department of Archaeology, University of Cambridge, Cambridge CB2 3ER, United Kingdom
| | - Bernd Trautmann
- State Collection of Anthropology and Palaeoanatomy Munich, Staatliche Naturwissenschaftliche Sammlungen Bayerns, 80333 Munich, Germany
| | - Sarah A Inskip
- McDonald Institute for Archaeological Research, University of Cambridge, Cambridge CB2 3ER, United Kingdom
| | - Joris Peters
- State Collection of Anthropology and Palaeoanatomy Munich, Staatliche Naturwissenschaftliche Sammlungen Bayerns, 80333 Munich, Germany
- ArchaeoBioCenter, Ludwig Maximilian University Munich, 80539 Munich, Germany
- Department of Veterinary Sciences, Institute of Palaeoanatomy, Domestication Research and the History of Veterinary Medicine, Ludwig Maximilian University Munich, 80539 Munich, Germany
| | - John E Robb
- Department of Archaeology, University of Cambridge, Cambridge CB2 3ER, United Kingdom
| | - Toomas Kivisild
- Department of Archaeology, University of Cambridge, Cambridge CB2 3ER, United Kingdom
- Department of Human Genetics, Katholieke Universiteit Leuven, 3000 Leuven, Belgium
| | | | - Michael McCormick
- Initiative for the Science of the Human Past, Department of History, Harvard University, Cambridge, MA 02138
- Max Planck-Harvard Research Center for the Archaeoscience of the Ancient Mediterranean, 07745 Jena, Germany
| | - Kirsten I Bos
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745 Jena, Germany
| | - Michaela Harbeck
- State Collection of Anthropology and Palaeoanatomy Munich, Staatliche Naturwissenschaftliche Sammlungen Bayerns, 80333 Munich, Germany;
| | - Alexander Herbig
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745 Jena, Germany;
| | - Johannes Krause
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745 Jena, Germany;
- Max Planck-Harvard Research Center for the Archaeoscience of the Ancient Mediterranean, 07745 Jena, Germany
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126
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Fages A, Hanghøj K, Khan N, Gaunitz C, Seguin-Orlando A, Leonardi M, McCrory Constantz C, Gamba C, Al-Rasheid KAS, Albizuri S, Alfarhan AH, Allentoft M, Alquraishi S, Anthony D, Baimukhanov N, Barrett JH, Bayarsaikhan J, Benecke N, Bernáldez-Sánchez E, Berrocal-Rangel L, Biglari F, Boessenkool S, Boldgiv B, Brem G, Brown D, Burger J, Crubézy E, Daugnora L, Davoudi H, de Barros Damgaard P, de Los Ángeles de Chorro Y de Villa-Ceballos M, Deschler-Erb S, Detry C, Dill N, do Mar Oom M, Dohr A, Ellingvåg S, Erdenebaatar D, Fathi H, Felkel S, Fernández-Rodríguez C, García-Viñas E, Germonpré M, Granado JD, Hallsson JH, Hemmer H, Hofreiter M, Kasparov A, Khasanov M, Khazaeli R, Kosintsev P, Kristiansen K, Kubatbek T, Kuderna L, Kuznetsov P, Laleh H, Leonard JA, Lhuillier J, Liesau von Lettow-Vorbeck C, Logvin A, Lõugas L, Ludwig A, Luis C, Arruda AM, Marques-Bonet T, Matoso Silva R, Merz V, Mijiddorj E, Miller BK, Monchalov O, Mohaseb FA, Morales A, Nieto-Espinet A, Nistelberger H, Onar V, Pálsdóttir AH, Pitulko V, Pitskhelauri K, Pruvost M, Rajic Sikanjic P, Rapan Papeša A, Roslyakova N, Sardari A, Sauer E, Schafberg R, Scheu A, Schibler J, Schlumbaum A, Serrand N, Serres-Armero A, Shapiro B, Sheikhi Seno S, Shevnina I, Shidrang S, Southon J, Star B, Sykes N, Taheri K, Taylor W, Teegen WR, Trbojević Vukičević T, Trixl S, Tumen D, Undrakhbold S, Usmanova E, Vahdati A, Valenzuela-Lamas S, Viegas C, Wallner B, Weinstock J, Zaibert V, Clavel B, Lepetz S, Mashkour M, Helgason A, Stefánsson K, Barrey E, Willerslev E, Outram AK, Librado P, Orlando L. Tracking Five Millennia of Horse Management with Extensive Ancient Genome Time Series. Cell 2019; 177:1419-1435.e31. [PMID: 31056281 PMCID: PMC6547883 DOI: 10.1016/j.cell.2019.03.049] [Citation(s) in RCA: 113] [Impact Index Per Article: 22.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2018] [Revised: 02/14/2019] [Accepted: 03/27/2019] [Indexed: 11/30/2022]
Abstract
Horse domestication revolutionized warfare and accelerated travel, trade, and the geographic expansion of languages. Here, we present the largest DNA time series for a non-human organism to date, including genome-scale data from 149 ancient animals and 129 ancient genomes (≥1-fold coverage), 87 of which are new. This extensive dataset allows us to assess the modern legacy of past equestrian civilizations. We find that two extinct horse lineages existed during early domestication, one at the far western (Iberia) and the other at the far eastern range (Siberia) of Eurasia. None of these contributed significantly to modern diversity. We show that the influence of Persian-related horse lineages increased following the Islamic conquests in Europe and Asia. Multiple alleles associated with elite-racing, including at the MSTN "speed gene," only rose in popularity within the last millennium. Finally, the development of modern breeding impacted genetic diversity more dramatically than the previous millennia of human management.
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Affiliation(s)
- Antoine Fages
- Laboratoire d'Anthropobiologie Moléculaire et d'Imagerie de Synthèse, CNRS UMR 5288, Université de Toulouse, Université Paul Sabatier, 31000 Toulouse, France; Lundbeck Foundation GeoGenetics Center, University of Copenhagen, 1350K Copenhagen, Denmark
| | - Kristian Hanghøj
- Laboratoire d'Anthropobiologie Moléculaire et d'Imagerie de Synthèse, CNRS UMR 5288, Université de Toulouse, Université Paul Sabatier, 31000 Toulouse, France; Lundbeck Foundation GeoGenetics Center, University of Copenhagen, 1350K Copenhagen, Denmark
| | - Naveed Khan
- Lundbeck Foundation GeoGenetics Center, University of Copenhagen, 1350K Copenhagen, Denmark; Department of Biotechnology, Abdul Wali Khan University, Mardan, Pakistan
| | - Charleen Gaunitz
- Lundbeck Foundation GeoGenetics Center, University of Copenhagen, 1350K Copenhagen, Denmark
| | - Andaine Seguin-Orlando
- Laboratoire d'Anthropobiologie Moléculaire et d'Imagerie de Synthèse, CNRS UMR 5288, Université de Toulouse, Université Paul Sabatier, 31000 Toulouse, France; Lundbeck Foundation GeoGenetics Center, University of Copenhagen, 1350K Copenhagen, Denmark
| | - Michela Leonardi
- Lundbeck Foundation GeoGenetics Center, University of Copenhagen, 1350K Copenhagen, Denmark; Evolutionary Ecology Group, Department of Zoology, University of Cambridge, Cambridge CB2 3EJ, UK
| | - Christian McCrory Constantz
- Lundbeck Foundation GeoGenetics Center, University of Copenhagen, 1350K Copenhagen, Denmark; Institute for Immunity, Transplantation and Infection, Stanford University, Stanford, CA 94305, USA
| | - Cristina Gamba
- Lundbeck Foundation GeoGenetics Center, University of Copenhagen, 1350K Copenhagen, Denmark
| | - Khaled A S Al-Rasheid
- Zoology Department, College of Science, King Saud University, Riyadh 11451, Saudi Arabia
| | - Silvia Albizuri
- Seminari d'Estudis i Recerques Prehistoriques, HAR2017-87695-P, Universitat de Barcelona, Barcelona, Spain
| | - Ahmed H Alfarhan
- Zoology Department, College of Science, King Saud University, Riyadh 11451, Saudi Arabia
| | - Morten Allentoft
- Lundbeck Foundation GeoGenetics Center, University of Copenhagen, 1350K Copenhagen, Denmark
| | - Saleh Alquraishi
- Zoology Department, College of Science, King Saud University, Riyadh 11451, Saudi Arabia
| | - David Anthony
- Anthropology Department, Hartwick College 1, Oneonta, NY 13820, USA
| | | | - James H Barrett
- McDonald Institute for Archaeological Research, Department of Archaeology, University of Cambridge, Cambridge CB2 3ER, UK
| | | | - Norbert Benecke
- Deutsches Archäologisches Institut (DAI), 14195 Berlin, Germany
| | - Eloísa Bernáldez-Sánchez
- Laboratorio de Paleontologia y Paleobiologia, Instituto Andaluz del Patrimonio Historico, Sevilla, Spain
| | - Luis Berrocal-Rangel
- Departamento de Prehistoria y Arqueología, Universidad Autónoma de Madrid, Madrid, Spain
| | - Fereidoun Biglari
- Department of Paleolithic, National Museum of Iran, 1136918111, Tehran, Iran
| | - Sanne Boessenkool
- Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences, University of Oslo, Postbox 1066, Blindern, 0316 Oslo, Norway
| | - Bazartseren Boldgiv
- Ecology Group, Department of Biology, School of Arts and Sciences, National University of Mongolia, Ulaanbaatar 14201, Mongolia
| | - Gottfried Brem
- Institute of Animal Breeding and Genetics, Department of Biomedical Sciences, Veterinary University of Vienna, 1210 Vienna, Austria
| | - Dorcas Brown
- Anthropology Department, Hartwick College 1, Oneonta, NY 13820, USA
| | - Joachim Burger
- Palaeogenetics Group, Institute of Organismic and Molecular Evolution (iOME), Johannes Gutenberg-University Mainz, 55099 Mainz, Germany
| | - Eric Crubézy
- Laboratoire d'Anthropobiologie Moléculaire et d'Imagerie de Synthèse, CNRS UMR 5288, Université de Toulouse, Université Paul Sabatier, 31000 Toulouse, France
| | - Linas Daugnora
- Osteological material research laboratory, Klaipėda university, Klaipėda 92294, Lithuania
| | - Hossein Davoudi
- Department of Osteology, National Museum of Iran, 1136918111, Tehran, Iran; Department of Archaeology, Faculty of Humanities, Tarbiat Modares University, Tehran, Iran
| | | | | | - Sabine Deschler-Erb
- Integrative prähistorische und naturwissenschaftliche Archäologie (IPNA), 4055 Basel, Switzerland
| | - Cleia Detry
- Uniarq, Centro de Arqueologia da Universidade de Lisboa, Faculdade de Letras da Universidade de Lisboa, 1600-214 Lisboa, Portugal
| | - Nadine Dill
- Integrative prähistorische und naturwissenschaftliche Archäologie (IPNA), 4055 Basel, Switzerland
| | - Maria do Mar Oom
- CE3C-Centre for Ecology, Evolution and Environmental Changes, Faculdade de Ciências, Universidade de Lisboa, 1749-016 Lisboa, Portugal
| | - Anna Dohr
- Institute for Pre- and Protohistoric Archaeology and Archaeology of the Roman Provinces, Ludwig-Maximilians-University Munich, 80539 München, Germany; ArchaeoBioCenter, Ludwig-Maximilians-University Munich, 80539 München, Germany; Institute of Palaeoanatomy, Domestication Research and History of Veterinary Medicine, Ludwig-Maximilians-University Munich, 80539 München, Germany
| | | | | | - Homa Fathi
- Department of Osteology, National Museum of Iran, 1136918111, Tehran, Iran; Archaezoology section, Bioarchaeology Laboratory of the Central Laboratory, University of Tehran, Tehran CP1417634934, Iran
| | - Sabine Felkel
- Institute of Animal Breeding and Genetics, Department of Biomedical Sciences, Veterinary University of Vienna, 1210 Vienna, Austria
| | | | - Esteban García-Viñas
- Departamento de Sistemas Físicos, Químicos y Naturales, Universidad Pablo de Olavide, 41013 Sevilla, Spain
| | - Mietje Germonpré
- Operational Direction, Earth and History of Life, Royal Belgian Institute of Natural Sciences, 1000, Brussels, Belgium
| | - José D Granado
- Integrative prähistorische und naturwissenschaftliche Archäologie (IPNA), 4055 Basel, Switzerland
| | - Jón H Hallsson
- Faculty of Agricultural and Environmental Sciences, The Agricultural University of Iceland, Keldnaholti - Árleyni 22, 112 Reykjavík, Iceland
| | - Helmut Hemmer
- Palaeogenetics Group, Institute of Organismic and Molecular Evolution (iOME), Johannes Gutenberg-University Mainz, 55099 Mainz, Germany
| | - Michael Hofreiter
- University of Potsdam, Faculty of Mathematics and Natural Sciences, Institute for Biochemistry and Biology, 14476 Potsdam, Germany
| | - Aleksei Kasparov
- Institute for the History of Material Culture, Russian Academy of Sciences, St. Petersburg 191186, Russia
| | | | - Roya Khazaeli
- Department of Osteology, National Museum of Iran, 1136918111, Tehran, Iran; Archaezoology section, Bioarchaeology Laboratory of the Central Laboratory, University of Tehran, Tehran CP1417634934, Iran
| | - Pavel Kosintsev
- Institute of Plant and Animal Ecology, Urals Branch of the Russian Academy of Sciences, Ekaterinburg 620144, Russia
| | | | - Tabaldiev Kubatbek
- Department of History, Kyrgyz-Turkish Manas University, Bishkek, Kyrgyzstan
| | - Lukas Kuderna
- Institut de Biologia Evolutiva, (CSIC-Universitat Pompeu Fabra), PRBB, Barcelona, Catalonia 08003, Spain
| | - Pavel Kuznetsov
- Samara State University of Social Science and Education, Samara, Russia
| | - Haeedeh Laleh
- Archaezoology section, Bioarchaeology Laboratory of the Central Laboratory, University of Tehran, Tehran CP1417634934, Iran; Department of Archaeology, Faculty of Humanities, University of Tehran, Iran
| | - Jennifer A Leonard
- Conservation and Evolutionary Genetics Group, Estación Biológica de Doñana (EBD-CSIC), 41092 Sevilla, Spain
| | - Johanna Lhuillier
- Laboratoire Archéorient, UMR 5133, Maison de l'Orient et de la Méditerranée, 69365 Lyon Cedex 7, France
| | | | - Andrey Logvin
- Laboratory for Archaeological Research, Faculty of History and Law, Kostanay State University, Kostanay, Kazakhstan
| | - Lembi Lõugas
- Archaeological Research Collection, Tallinn University, 10130 Tallinn, Estonia
| | - Arne Ludwig
- Department of Evolutionary Genetics, Leibniz Institute for Zoo and Wildlife Research, 10315 Berlin, Germany; Faculty of Life Sciences, Albrecht Daniel Thaer-Institute, Humboldt University Berlin, 10115 Berlin, Germany
| | - Cristina Luis
- Museu Nacional de História Natural e da Ciência, Universidade de Lisboa, Lisboa, Portugal; Centro Interuniversitário de História das Ciências e da Tecnologia (CIUHCT), Faculdade de Ciências, Universidade de Lisboa, Lisboa, Portugal; Instituto Universitário de Lisboa (ISCTE-IUL), CIES-IUL, Lisboa, Portugal
| | - Ana Margarida Arruda
- Uniarq, Centro de Arqueologia da Universidade de Lisboa, Faculdade de Letras da Universidade de Lisboa, 1600-214 Lisboa, Portugal
| | - Tomas Marques-Bonet
- Institut de Biologia Evolutiva, (CSIC-Universitat Pompeu Fabra), PRBB, Barcelona, Catalonia 08003, Spain; Catalan Institution of Research and Advanced Studies (ICREA), 08010 Barcelona, Spain; CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), 08028 Barcelona, Spain; Institut Català de Paleontologia Miquel Crusafont, Universitat Autònoma de Barcelona, Edifici ICTA-ICP, c/ Columnes s/n, 08193, Cerdanyola del Vallès, Barcelona, Spain
| | | | - Victor Merz
- S.Toraighyrov Pavlodar State University, Joint Research Center for Archeological Studies, 637000 Pavlodar, Kazakhstan
| | - Enkhbayar Mijiddorj
- Department of Archaeology, Ulaanbaatar State University, Ulaanbaatar 51, Mongolia
| | - Bryan K Miller
- University of Oxford, Faculty of History, George Street, Oxford, OX1 2RL, UK
| | - Oleg Monchalov
- Samara State University of Social Science and Education, Samara, Russia
| | - Fatemeh A Mohaseb
- Department of Osteology, National Museum of Iran, 1136918111, Tehran, Iran; Archaezoology section, Bioarchaeology Laboratory of the Central Laboratory, University of Tehran, Tehran CP1417634934, Iran; Centre National de la Recherche Scientifique, Muséum National d'Histoire Naturelle, Archéozoologie, Archéobotanique, Sociétés, Pratiques et Environnements (UMR 7209), 75005 Paris, France
| | - Arturo Morales
- Laboratory of Archaeozoology, Department Biología, Universidad Autónoma de Madrid, Madrid, Spain
| | - Ariadna Nieto-Espinet
- Archaeology of Social Dynamics Group (ADS), Institució Milà i Fontanals-Consejo Superior de Investigaciones Científicas (IMF-CSIC), 08001 Barcelona, Spain; Grup d'Investigació Prehistòrica, HAR2016-78277-R, Universitat de Lleida, 25003 Lleida, Spain
| | - Heidi Nistelberger
- Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences, University of Oslo, Postbox 1066, Blindern, 0316 Oslo, Norway
| | - Vedat Onar
- Osteoarchaeology Practice and Research Center and Department of Anatomy, Faculty of Veterinary Medicine, Istanbul University-Cerrahpaşa, 34320, Avcılar, Istanbul, Turkey
| | - Albína H Pálsdóttir
- Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences, University of Oslo, Postbox 1066, Blindern, 0316 Oslo, Norway; Faculty of Agricultural and Environmental Sciences, The Agricultural University of Iceland, Keldnaholti - Árleyni 22, 112 Reykjavík, Iceland
| | - Vladimir Pitulko
- Institute for the History of Material Culture, Russian Academy of Sciences, St. Petersburg 191186, Russia
| | | | - Mélanie Pruvost
- Université de Bordeaux, CNRS, UMR 5199-PACEA, 33615 Pessac Cedex, France
| | | | | | | | - Alireza Sardari
- Iranian Center for Archaeological Research (ICAR), Iranian Cultural Heritage, Handicrafts, and Tourism Organization (ICHHTO), 1136918111, Tehran, Iran
| | - Eberhard Sauer
- School of History, Classics and Archaeology, The University of Edinburgh, Edinburgh, EH8 9AG, UK
| | - Renate Schafberg
- Central Natural Science Collections (ZNS), Martin Luther University Halle-Wittenberg, Domplatz 4, 06108 Halle (Saale), Germany
| | - Amelie Scheu
- Palaeogenetics Group, Institute of Organismic and Molecular Evolution (iOME), Johannes Gutenberg-University Mainz, 55099 Mainz, Germany
| | - Jörg Schibler
- Integrative prähistorische und naturwissenschaftliche Archäologie (IPNA), 4055 Basel, Switzerland
| | - Angela Schlumbaum
- Integrative prähistorische und naturwissenschaftliche Archäologie (IPNA), 4055 Basel, Switzerland
| | - Nathalie Serrand
- Centre National de la Recherche Scientifique, Muséum National d'Histoire Naturelle, Archéozoologie, Archéobotanique, Sociétés, Pratiques et Environnements (UMR 7209), 75005 Paris, France; INRAP Guadeloupe, Centre de recherches archéologiques, UMR 7209 CNRS/MNHN, 97113 Gourbeyre, Guadeloupe
| | - Aitor Serres-Armero
- Institut de Biologia Evolutiva, (CSIC-Universitat Pompeu Fabra), PRBB, Barcelona, Catalonia 08003, Spain
| | - Beth Shapiro
- Department of Ecology and Evolutionary Biology and Howard Hughes Medical Institute, University of California, Santa Cruz, Santa Cruz, CA 95060, USA
| | - Shiva Sheikhi Seno
- Department of Osteology, National Museum of Iran, 1136918111, Tehran, Iran; Archaezoology section, Bioarchaeology Laboratory of the Central Laboratory, University of Tehran, Tehran CP1417634934, Iran; Centre National de la Recherche Scientifique, Muséum National d'Histoire Naturelle, Archéozoologie, Archéobotanique, Sociétés, Pratiques et Environnements (UMR 7209), 75005 Paris, France
| | - Irina Shevnina
- Laboratory for Archaeological Research, Faculty of History and Law, Kostanay State University, Kostanay, Kazakhstan
| | - Sonia Shidrang
- Saeedi Institute for Advanced Studies, University of Kashan, Kashan 87317-51167, Iran
| | - John Southon
- Department Earth System Science, University of California, Irvine, Irvine, CA 92697, USA
| | - Bastiaan Star
- Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences, University of Oslo, Postbox 1066, Blindern, 0316 Oslo, Norway
| | - Naomi Sykes
- Department of Archaeology, University of Nottingham, Nottingham, NG7 2RD, UK; Department of Archaeology, University of Exeter, Exeter, EX4 4QE, UK
| | - Kamal Taheri
- Kermanshah Regional Water Authority, Kermanshah 67145-1466, Iran
| | - William Taylor
- Max Planck Institute for the Science of Human History, 07745 Jena, Germany
| | - Wolf-Rüdiger Teegen
- Institute for Pre- and Protohistoric Archaeology and Archaeology of the Roman Provinces, Ludwig-Maximilians-University Munich, 80539 München, Germany; ArchaeoBioCenter, Ludwig-Maximilians-University Munich, 80539 München, Germany
| | - Tajana Trbojević Vukičević
- Department of Anatomy, Histology and Embryology, Faculty of Veterinary Medicine, University of Zagreb, 10 000 Zagreb, Croatia
| | - Simon Trixl
- Institute of Palaeoanatomy, Domestication Research and History of Veterinary Medicine, Ludwig-Maximilians-University Munich, 80539 München, Germany
| | - Dashzeveg Tumen
- Department of Anthropology and Archaeology, School of Arts and Sciences, National University of Mongolia, Ulaanbaatar 14201, Mongolia
| | - Sainbileg Undrakhbold
- Ecology Group, Department of Biology, School of Arts and Sciences, National University of Mongolia, Ulaanbaatar 14201, Mongolia
| | - Emma Usmanova
- Saryarka Archaeological Institute of Buketov Karaganda State University, Karaganda 100074, Kazakhstan
| | - Ali Vahdati
- Iranian Center for Archaeological Research (ICAR), Iranian Cultural Heritage, Handicrafts, and Tourism Organization (ICHHTO), 1136918111, Tehran, Iran
| | - Silvia Valenzuela-Lamas
- Archaeology of Social Dynamics Group (ADS), Institució Milà i Fontanals-Consejo Superior de Investigaciones Científicas (IMF-CSIC), 08001 Barcelona, Spain
| | - Catarina Viegas
- Uniarq, Centro de Arqueologia da Universidade de Lisboa, Faculdade de Letras da Universidade de Lisboa, 1600-214 Lisboa, Portugal
| | - Barbara Wallner
- Institute of Animal Breeding and Genetics, Department of Biomedical Sciences, Veterinary University of Vienna, 1210 Vienna, Austria
| | - Jaco Weinstock
- Faculty of Humanities (Archaeology), University of Southampton, Avenue Campus, Highfield, Southampton SO17 1BF, UK
| | - Victor Zaibert
- Scientific Research Institute of Archaeology and Steppe Civilizations, Al Farabi Kazakh National University, 050040 Almaty, Kazakhstan
| | - Benoit Clavel
- Centre National de la Recherche Scientifique, Muséum National d'Histoire Naturelle, Archéozoologie, Archéobotanique, Sociétés, Pratiques et Environnements (UMR 7209), 75005 Paris, France
| | - Sébastien Lepetz
- Centre National de la Recherche Scientifique, Muséum National d'Histoire Naturelle, Archéozoologie, Archéobotanique, Sociétés, Pratiques et Environnements (UMR 7209), 75005 Paris, France
| | - Marjan Mashkour
- Department of Osteology, National Museum of Iran, 1136918111, Tehran, Iran; Archaezoology section, Bioarchaeology Laboratory of the Central Laboratory, University of Tehran, Tehran CP1417634934, Iran; Centre National de la Recherche Scientifique, Muséum National d'Histoire Naturelle, Archéozoologie, Archéobotanique, Sociétés, Pratiques et Environnements (UMR 7209), 75005 Paris, France
| | | | | | - Eric Barrey
- GABI UMR1313, INRA, AgroParisTech, Université Paris-Saclay, Jouy-en-Josas, France
| | - Eske Willerslev
- Lundbeck Foundation GeoGenetics Center, University of Copenhagen, 1350K Copenhagen, Denmark
| | - Alan K Outram
- Department of Archaeology, University of Exeter, Exeter, EX4 4QE, UK
| | - Pablo Librado
- Laboratoire d'Anthropobiologie Moléculaire et d'Imagerie de Synthèse, CNRS UMR 5288, Université de Toulouse, Université Paul Sabatier, 31000 Toulouse, France; Lundbeck Foundation GeoGenetics Center, University of Copenhagen, 1350K Copenhagen, Denmark
| | - Ludovic Orlando
- Laboratoire d'Anthropobiologie Moléculaire et d'Imagerie de Synthèse, CNRS UMR 5288, Université de Toulouse, Université Paul Sabatier, 31000 Toulouse, France; Lundbeck Foundation GeoGenetics Center, University of Copenhagen, 1350K Copenhagen, Denmark.
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127
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Hanghøj K, Renaud G, Albrechtsen A, Orlando L. DamMet: ancient methylome mapping accounting for errors, true variants, and post-mortem DNA damage. Gigascience 2019; 8:giz025. [PMID: 31004132 PMCID: PMC6474913 DOI: 10.1093/gigascience/giz025] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2018] [Revised: 02/07/2019] [Accepted: 02/27/2019] [Indexed: 01/10/2023] Open
Abstract
BACKGROUND Recent computational advances in ancient DNA research have opened access to the detection of ancient DNA methylation footprints at the genome-wide scale. The most commonly used approach infers the methylation state of a given genomic region on the basis of the amount of nucleotide mis-incorporations observed at CpG dinucleotide sites. However, this approach overlooks a number of confounding factors, including the presence of sequencing errors and true variants. The scale and distribution of the inferred methylation measurements are also variable across samples, precluding direct comparisons. FINDINGS Here, we present DamMet, an open-source software program retrieving maximum likelihood estimates of regional CpG methylation levels from ancient DNA sequencing data. It builds on a novel statistical model of post-mortem DNA damage for dinucleotides, accounting for sequencing errors, genotypes, and differential post-mortem cytosine deamination rates at both methylated and unmethylated sites. To validate DamMet, we extended gargammel, a sequence simulator for ancient DNA data, by introducing methylation-dependent features of post-mortem DNA decay. This new simulator provides direct validation of DamMet predictions. Additionally, the methylation levels inferred by DamMet were found to be correlated to those inferred by epiPALEOMIX and both on par and directly comparable to those measured from whole-genome bisulphite sequencing experiments of fresh tissues. CONCLUSIONS DamMet provides genuine estimates for local DNA methylation levels in ancient individual genomes. The returned estimates are directly cross-sample comparable, and the software is available as an open-source C++ program hosted at https://gitlab.com/KHanghoj/DamMet along with a manual and tutorial.
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Affiliation(s)
- Kristian Hanghøj
- Lundbeck Foundation GeoGenetics Center, University of Copenhagen, Øster Voldgade 5-7, 1350K Copenhagen, Denmark
- Laboratoire d’Anthropobiologie Moléculaire et d’Imagerie de Synthèse, CNRS UMR 5288, Université de Toulouse III, Paul Sabatier (UPS), 31000 Toulouse, France
| | - Gabriel Renaud
- Lundbeck Foundation GeoGenetics Center, University of Copenhagen, Øster Voldgade 5-7, 1350K Copenhagen, Denmark
| | - Anders Albrechtsen
- Computational and RNA Biology, Department of Biology, University of Copenhagen, 2200 Copenhagen, Denmark, Øster voldgade 5-7, 1350k
| | - Ludovic Orlando
- Lundbeck Foundation GeoGenetics Center, University of Copenhagen, Øster Voldgade 5-7, 1350K Copenhagen, Denmark
- Laboratoire d’Anthropobiologie Moléculaire et d’Imagerie de Synthèse, CNRS UMR 5288, Université de Toulouse III, Paul Sabatier (UPS), 31000 Toulouse, France
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128
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Eisenhofer R, Weyrich LS. Assessing alignment-based taxonomic classification of ancient microbial DNA. PeerJ 2019; 7:e6594. [PMID: 30886779 PMCID: PMC6420809 DOI: 10.7717/peerj.6594] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2018] [Accepted: 02/09/2019] [Indexed: 11/20/2022] Open
Abstract
The field of palaeomicrobiology-the study of ancient microorganisms-is rapidly growing due to recent methodological and technological advancements. It is now possible to obtain vast quantities of DNA data from ancient specimens in a high-throughput manner and use this information to investigate the dynamics and evolution of past microbial communities. However, we still know very little about how the characteristics of ancient DNA influence our ability to accurately assign microbial taxonomies (i.e. identify species) within ancient metagenomic samples. Here, we use both simulated and published metagenomic data sets to investigate how ancient DNA characteristics affect alignment-based taxonomic classification. We find that nucleotide-to-nucleotide, rather than nucleotide-to-protein, alignments are preferable when assigning taxonomies to short DNA fragment lengths routinely identified within ancient specimens (<60 bp). We determine that deamination (a form of ancient DNA damage) and random sequence substitutions corresponding to ∼100,000 years of genomic divergence minimally impact alignment-based classification. We also test four different reference databases and find that database choice can significantly bias the results of alignment-based taxonomic classification in ancient metagenomic studies. Finally, we perform a reanalysis of previously published ancient dental calculus data, increasing the number of microbial DNA sequences assigned taxonomically by an average of 64.2-fold and identifying microbial species previously unidentified in the original study. Overall, this study enhances our understanding of how ancient DNA characteristics influence alignment-based taxonomic classification of ancient microorganisms and provides recommendations for future palaeomicrobiological studies.
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Affiliation(s)
- Raphael Eisenhofer
- Australian Centre for Ancient DNA, University of Adelaide, Adelaide, SA, Australia.,Centre of Excellence for Australia Biodiversity and Heritage, University of Adelaide, Adelaide, SA, Australia
| | - Laura Susan Weyrich
- Australian Centre for Ancient DNA, University of Adelaide, Adelaide, SA, Australia.,Centre of Excellence for Australia Biodiversity and Heritage, University of Adelaide, Adelaide, SA, Australia
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129
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Renaud G, Schubert M, Sawyer S, Orlando L. Authentication and Assessment of Contamination in Ancient DNA. Methods Mol Biol 2019; 1963:163-194. [PMID: 30875054 DOI: 10.1007/978-1-4939-9176-1_17] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Contamination from both present-day humans and postmortem microbial sources is a common challenge in ancient DNA studies. Here we present a suite of tools to assist in the assessment of contamination in ancient DNA data sets. These tools perform standard tests of authenticity of ancient DNA data including detecting the presence of postmortem damage signatures in sequence alignments and quantifying the amount of present-day human contamination.
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Affiliation(s)
- Gabriel Renaud
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen K, Denmark
| | - Mikkel Schubert
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen K, Denmark
| | - Susanna Sawyer
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen K, Denmark
| | - Ludovic Orlando
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen K, Denmark.
- Laboratoire d'Anthropobiologie Moléculaire et d'Imagerie de Synthèse, CNRS UMR 5288, Université de Toulouse, University Paul Sabatier, Toulouse, France.
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130
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Historical Genomes Reveal the Genomic Consequences of Recent Population Decline in Eastern Gorillas. Curr Biol 2018; 29:165-170.e6. [PMID: 30595519 DOI: 10.1016/j.cub.2018.11.055] [Citation(s) in RCA: 91] [Impact Index Per Article: 15.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2018] [Revised: 11/12/2018] [Accepted: 11/21/2018] [Indexed: 12/30/2022]
Abstract
Many endangered species have experienced severe population declines within the last centuries [1, 2]. However, despite concerns about negative fitness effects resulting from increased genetic drift and inbreeding, there is a lack of empirical data on genomic changes in conjunction with such declines [3-7]. Here, we use whole genomes recovered from century-old historical museum specimens to quantify the genomic consequences of small population size in the critically endangered Grauer's and endangered mountain gorillas. We find a reduction of genetic diversity and increase in inbreeding and genetic load in the Grauer's gorilla, which experienced severe population declines in recent decades. In contrast, the small but relatively stable mountain gorilla population has experienced little genomic change during the last century. These results suggest that species histories as well as the rate of demographic change may influence how population declines affect genome diversity.
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131
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Kistler L, Maezumi SY, Gregorio de Souza J, Przelomska NAS, Malaquias Costa F, Smith O, Loiselle H, Ramos-Madrigal J, Wales N, Ribeiro ER, Morrison RR, Grimaldo C, Prous AP, Arriaza B, Gilbert MTP, de Oliveira Freitas F, Allaby RG. Multiproxy evidence highlights a complex evolutionary legacy of maize in South America. Science 2018; 362:1309-1313. [DOI: 10.1126/science.aav0207] [Citation(s) in RCA: 123] [Impact Index Per Article: 20.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2018] [Accepted: 10/22/2018] [Indexed: 12/14/2022]
Abstract
Domesticated maize evolved from wild teosinte under human influences in Mexico beginning around 9000 years before the present (yr B.P.), traversed Central America by ~7500 yr B.P., and spread into South America by ~6500 yr B.P. Landrace and archaeological maize genomes from South America suggest that the ancestral population to South American maize was brought out of the domestication center in Mexico and became isolated from the wild teosinte gene pool before traits of domesticated maize were fixed. Deeply structured lineages then evolved within South America out of this partially domesticated progenitor population. Genomic, linguistic, archaeological, and paleoecological data suggest that the southwestern Amazon was a secondary improvement center for partially domesticated maize. Multiple waves of human-mediated dispersal are responsible for the diversity and biogeography of modern South American maize.
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132
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Gaudin M, Desnues C. Hybrid Capture-Based Next Generation Sequencing and Its Application to Human Infectious Diseases. Front Microbiol 2018; 9:2924. [PMID: 30542340 PMCID: PMC6277869 DOI: 10.3389/fmicb.2018.02924] [Citation(s) in RCA: 62] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2018] [Accepted: 11/14/2018] [Indexed: 01/12/2023] Open
Abstract
This review describes target-enrichment approaches followed by next generation sequencing and their recent application to the research and diagnostic field of modern and past infectious human diseases caused by viruses, bacteria, parasites and fungi.
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Affiliation(s)
- Maxime Gaudin
- IRD 198, CNRS FRE2013, Assistance-Publique des Hôpitaux de Marseille, UMR Microbes, Evolution, Phylogeny and Infections (MEPHI), IHU Méditerranée Infection, Aix-Marseille Université, Marseille, France
| | - Christelle Desnues
- IRD 198, CNRS FRE2013, Assistance-Publique des Hôpitaux de Marseille, UMR Microbes, Evolution, Phylogeny and Infections (MEPHI), IHU Méditerranée Infection, Aix-Marseille Université, Marseille, France
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133
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Posth C, Nakatsuka N, Lazaridis I, Skoglund P, Mallick S, Lamnidis TC, Rohland N, Nägele K, Adamski N, Bertolini E, Broomandkhoshbacht N, Cooper A, Culleton BJ, Ferraz T, Ferry M, Furtwängler A, Haak W, Harkins K, Harper TK, Hünemeier T, Lawson AM, Llamas B, Michel M, Nelson E, Oppenheimer J, Patterson N, Schiffels S, Sedig J, Stewardson K, Talamo S, Wang CC, Hublin JJ, Hubbe M, Harvati K, Nuevo Delaunay A, Beier J, Francken M, Kaulicke P, Reyes-Centeno H, Rademaker K, Trask WR, Robinson M, Gutierrez SM, Prufer KM, Salazar-García DC, Chim EN, Müller Plumm Gomes L, Alves ML, Liryo A, Inglez M, Oliveira RE, Bernardo DV, Barioni A, Wesolowski V, Scheifler NA, Rivera MA, Plens CR, Messineo PG, Figuti L, Corach D, Scabuzzo C, Eggers S, DeBlasis P, Reindel M, Méndez C, Politis G, Tomasto-Cagigao E, Kennett DJ, Strauss A, Fehren-Schmitz L, Krause J, Reich D. Reconstructing the Deep Population History of Central and South America. Cell 2018; 175:1185-1197.e22. [PMID: 30415837 PMCID: PMC6327247 DOI: 10.1016/j.cell.2018.10.027] [Citation(s) in RCA: 138] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2018] [Revised: 09/15/2018] [Accepted: 10/11/2018] [Indexed: 01/16/2023]
Abstract
We report genome-wide ancient DNA from 49 individuals forming four parallel time transects in Belize, Brazil, the Central Andes, and the Southern Cone, each dating to at least ∼9,000 years ago. The common ancestral population radiated rapidly from just one of the two early branches that contributed to Native Americans today. We document two previously unappreciated streams of gene flow between North and South America. One affected the Central Andes by ∼4,200 years ago, while the other explains an affinity between the oldest North American genome associated with the Clovis culture and the oldest Central and South Americans from Chile, Brazil, and Belize. However, this was not the primary source for later South Americans, as the other ancient individuals derive from lineages without specific affinity to the Clovis-associated genome, suggesting a population replacement that began at least 9,000 years ago and was followed by substantial population continuity in multiple regions.
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Affiliation(s)
- Cosimo Posth
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena 07745, Germany; Institute for Archaeological Sciences, Archaeo- and Palaeogenetics, University of Tübingen, Tübingen 72070, Germany.
| | - Nathan Nakatsuka
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA; Harvard-MIT Division of Health Sciences and Technology, Boston, MA 02115, USA.
| | - Iosif Lazaridis
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Pontus Skoglund
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA; Francis Crick Institute, London NW1 1AT, UK
| | - Swapan Mallick
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA; Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA; Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Thiseas C Lamnidis
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena 07745, Germany
| | - Nadin Rohland
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Kathrin Nägele
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena 07745, Germany
| | - Nicole Adamski
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA; Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Emilie Bertolini
- Dipartimento di Biologia e Biotecnologie, Università di Pavia, Pavia 27100, Italy
| | - Nasreen Broomandkhoshbacht
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA; Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Alan Cooper
- Australian Centre for Ancient DNA, School of Biological Sciences and The Environment Institute, Adelaide University, Adelaide, SA 5005, Australia
| | - Brendan J Culleton
- Department of Anthropology, The Pennsylvania State University, University Park, PA 16802, USA; Institutes of Energy and the Environment, The Pennsylvania State University, University Park, PA 16802, USA
| | - Tiago Ferraz
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena 07745, Germany; Departamento de Genética e Biologia Evolutiva, Universidade de São Paulo, São Paulo 05508-090, Brazil
| | - Matthew Ferry
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA; Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Anja Furtwängler
- Institute for Archaeological Sciences, Archaeo- and Palaeogenetics, University of Tübingen, Tübingen 72070, Germany
| | - Wolfgang Haak
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena 07745, Germany
| | - Kelly Harkins
- UCSC Paleogenomics, University of California, Santa Cruz, Santa Cruz, CA 95064, USA
| | - Thomas K Harper
- Department of Anthropology, The Pennsylvania State University, University Park, PA 16802, USA
| | - Tábita Hünemeier
- Departamento de Genética e Biologia Evolutiva, Universidade de São Paulo, São Paulo 05508-090, Brazil
| | - Ann Marie Lawson
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA; Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Bastien Llamas
- Australian Centre for Ancient DNA, School of Biological Sciences and The Environment Institute, Adelaide University, Adelaide, SA 5005, Australia
| | - Megan Michel
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA; Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Elizabeth Nelson
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena 07745, Germany; Institute for Archaeological Sciences, Archaeo- and Palaeogenetics, University of Tübingen, Tübingen 72070, Germany
| | - Jonas Oppenheimer
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA; Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Nick Patterson
- Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | - Stephan Schiffels
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena 07745, Germany
| | - Jakob Sedig
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Kristin Stewardson
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA; Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Sahra Talamo
- Department of Human Evolution, Max Planck Institute for Evolutionary Anthropology, Leipzig 04103, Germany
| | - Chuan-Chao Wang
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena 07745, Germany; Department of Anthropology and Ethnology, Xiamen University, Xiamen 361005, China
| | - Jean-Jacques Hublin
- Department of Human Evolution, Max Planck Institute for Evolutionary Anthropology, Leipzig 04103, Germany
| | - Mark Hubbe
- Department of Anthropology, The Ohio State University, Columbus, OH 43210, USA; Instituto de Arqueología y Antropología, Universidad Católica del Norte, San Pedro de Atacama, Región de Antofagasta, Antofagasta CP 1410000, Chile
| | - Katerina Harvati
- Institute for Archaeological Sciences, Palaeoanthropology and Senckenberg Centre for Human Evolution and Palaeoenvironment, University of Tuebingen, Tübingen 72070, Germany; DFG Center for Advanced Studies, "Words, Bones, Genes, Tools," University of Tübingen, Tübingen 72070, Germany
| | | | - Judith Beier
- Institute for Archaeological Sciences, Palaeoanthropology and Senckenberg Centre for Human Evolution and Palaeoenvironment, University of Tuebingen, Tübingen 72070, Germany
| | - Michael Francken
- Institute for Archaeological Sciences, Palaeoanthropology and Senckenberg Centre for Human Evolution and Palaeoenvironment, University of Tuebingen, Tübingen 72070, Germany
| | - Peter Kaulicke
- Pontifical Catholic University of Peru, San Miguel, Lima 32, Peru
| | - Hugo Reyes-Centeno
- Institute for Archaeological Sciences, Palaeoanthropology and Senckenberg Centre for Human Evolution and Palaeoenvironment, University of Tuebingen, Tübingen 72070, Germany; DFG Center for Advanced Studies, "Words, Bones, Genes, Tools," University of Tübingen, Tübingen 72070, Germany
| | - Kurt Rademaker
- Department of Anthropology, Michigan State University, East Lansing, MI 48824, USA
| | - Willa R Trask
- Central Identification Laboratory, Defense POW/MIA Accounting Agency, Department of Defense, Joint Base Pearl Harbor-Hickam, HI 96853, USA
| | - Mark Robinson
- Department of Archaeology, Exeter University, Exeter EX4 4QJ, UK
| | | | - Keith M Prufer
- Department of Anthropology, University of New Mexico, Albuquerque, NM 87131, USA; Center for Stable Isotopes, University of New Mexico, Albuquerque, NM 87131, USA
| | - Domingo C Salazar-García
- Department of Human Evolution, Max Planck Institute for Evolutionary Anthropology, Leipzig 04103, Germany; Grupo de Investigación en Prehistoria IT-622-13 (UPV-EHU), IKERBASQUE-Basque Foundation for Science, Vitoria, Spain
| | - Eliane N Chim
- Museu de Arqueologia e Etnologia, Universidade de São Paulo, São Paulo 05508-070, Brazil
| | | | - Marcony L Alves
- Museu de Arqueologia e Etnologia, Universidade de São Paulo, São Paulo 05508-070, Brazil
| | - Andersen Liryo
- Museu Nacional da Universidade Federal do Rio de Janeiro, Rio de Janeiro 20940-040, Brazil
| | - Mariana Inglez
- Departamento de Genética e Biologia Evolutiva, Universidade de São Paulo, São Paulo 05508-090, Brazil
| | - Rodrigo E Oliveira
- Departamento de Genética e Biologia Evolutiva, Universidade de São Paulo, São Paulo 05508-090, Brazil; Departamento de Estomatologia, Faculdade de Odontologia, Universidade de São Paulo, São Paulo 05508-000, Brazil
| | - Danilo V Bernardo
- Laboratório de Estudos em Antropologia Biológica, Bioarqueologia e Evolução Humana, Instituto de Ciências Humanas e da Informação, Universidade Federal do Rio Grande, Rio Grande do Sul 96203-900, Brazil
| | - Alberto Barioni
- Faculdade de Filosofia Ciencias e Letras, Universidade de São Paulo, São Paulo 05508-080, Brazil
| | - Veronica Wesolowski
- Museu de Arqueologia e Etnologia, Universidade de São Paulo, São Paulo 05508-070, Brazil
| | - Nahuel A Scheifler
- INCUAPA-CONICET, Facultad de Ciencias Sociales, Universidad Nacional del Centro de la Provincia de Buenos Aires, Olavarría 7400, Argentina
| | - Mario A Rivera
- Comité Chileno del Consejo Internacional de Monumentos y Sitios, Santiago 8320000, Chile; Field Museum of Natural History, Chicago, IL 60605, USA; Universidad de Magallanes, Punta Arenas 6200000, Chile
| | - Claudia R Plens
- Escola De Filosofia, Letras E Ciências Humanas, Universidade Federal de São Paulo, São Paulo 07252-312, Brazil
| | - Pablo G Messineo
- INCUAPA-CONICET, Facultad de Ciencias Sociales, Universidad Nacional del Centro de la Provincia de Buenos Aires, Olavarría 7400, Argentina
| | - Levy Figuti
- Museu de Arqueologia e Etnologia, Universidade de São Paulo, São Paulo 05508-070, Brazil
| | - Daniel Corach
- Servicio de Huellas Digitales Genéticas, School of Pharmacy and Biochemistry, Universidad de Buenos Aires y CONICET, Ciudad Autonoma de Buenos Aires, Junin 954, Argentina
| | - Clara Scabuzzo
- CONICET-División Arqueología, Facultad de Ciencias Naturales y Museo, La Plata 1900, Argentina
| | - Sabine Eggers
- Departamento de Genética e Biologia Evolutiva, Universidade de São Paulo, São Paulo 05508-090, Brazil; Naturhistorisches Museum Wien, Vienna 1010, Austria
| | - Paulo DeBlasis
- Museu de Arqueologia e Etnologia, Universidade de São Paulo, São Paulo 05508-070, Brazil
| | - Markus Reindel
- German Archaeological Institute, Commission for Archaeology of Non-European Cultures, Bonn 53173, Germany
| | - César Méndez
- Centro de Investigación en Ecosistemas de la Patagonia, Coyhaique 5951601, Chile
| | - Gustavo Politis
- INCUAPA-CONICET, Facultad de Ciencias Sociales, Universidad Nacional del Centro de la Provincia de Buenos Aires, Olavarría 7400, Argentina
| | | | - Douglas J Kennett
- Department of Anthropology, The Pennsylvania State University, University Park, PA 16802, USA; Institutes of Energy and the Environment, The Pennsylvania State University, University Park, PA 16802, USA
| | - André Strauss
- Departamento de Genética e Biologia Evolutiva, Universidade de São Paulo, São Paulo 05508-090, Brazil; Institute for Archaeological Sciences, Palaeoanthropology and Senckenberg Centre for Human Evolution and Palaeoenvironment, University of Tuebingen, Tübingen 72070, Germany; Museu de Arqueologia e Etnologia, Universidade de São Paulo, São Paulo 05508-070, Brazil; Centro de Arqueologia Annette Laming Emperaire, Miguel A Salomão, Lagoa Santa, MG 33400-000, Brazil
| | - Lars Fehren-Schmitz
- UCSC Paleogenomics, University of California, Santa Cruz, Santa Cruz, CA 95064, USA; UCSC Genomics Institute, University of California, Santa Cruz, Santa Cruz, CA 95064, USA
| | - Johannes Krause
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena 07745, Germany; Institute for Archaeological Sciences, Archaeo- and Palaeogenetics, University of Tübingen, Tübingen 72070, Germany
| | - David Reich
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA; Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA; Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02115, USA.
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134
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Oben B, Cosemans C, Arijs I, Linsen L, Daniëls A, Declercq J, Maes B, Vanhees K, Froyen G, Rummens JL. Archival May-Grünwald-Giemsa-Stained Bone Marrow Smears Are an Eligible Source for Molecular DNA Research. Biopreserv Biobank 2018; 17:274-281. [PMID: 30412415 DOI: 10.1089/bio.2018.0062] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
Abstract
Biobanking is increasingly important in studying complex heterogeneous diseases. Therefore, it is essential to ensure the sample quality after long-term storage for reliable downstream analyses. The Clinical Biobank of the Jessa Hospital and the University Biobank Limburg (UBiLim) hold a continuously growing collection of hematological samples, including May-Grünwald-Giemsa (MGG)- and Perls' Prussian Blue (PPB)-stained bone marrow (BM) smears, stored at room temperature (RT) for up to 20 years. In this study, we investigated the effect of short- and long-term storage on the quality of DNA and RNA extracted from these BM smears to assess their fitness-for-purpose in downstream molecular applications, including agarose gel electrophoresis, bio-analyzer analysis, quantitative polymerase chain reaction (qPCR), and targeted next-generation sequencing (NGS). The RNA quality was very low for all samples, independent of storage time or staining method. The DNA from PPB-stained BM smears was already degraded after 1 year of storage and correspondingly could not be used for reliable downstream molecular analysis. In contrast, DNA extracted from MGG-stained BM smears stored for up to 10 years was able to generate high-quality data in qPCR and targeted NGS analyses. Longer storage periods (>15 years) of these samples revealed a high degree of degradation and a significant amount of DNA transitions and transversions. In conclusion, the DNA extracted from archival MGG-stained BM smears with a storage time up to at least 10 years was qualitatively good and fit for downstream analysis, including targeted NGS. This indicates that these samples are an eligible source for molecular DNA research and for studying complex diseases.
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Affiliation(s)
- Bénedith Oben
- 1Department of Experimental Hematology, Jessa Hospital, Hasselt, Belgium.,2Faculty of Medicine and Life Sciences, Hasselt University, Hasselt, Belgium
| | - Charlotte Cosemans
- 1Department of Experimental Hematology, Jessa Hospital, Hasselt, Belgium.,2Faculty of Medicine and Life Sciences, Hasselt University, Hasselt, Belgium
| | - Ingrid Arijs
- 1Department of Experimental Hematology, Jessa Hospital, Hasselt, Belgium.,2Faculty of Medicine and Life Sciences, Hasselt University, Hasselt, Belgium
| | - Loes Linsen
- 1Department of Experimental Hematology, Jessa Hospital, Hasselt, Belgium.,2Faculty of Medicine and Life Sciences, Hasselt University, Hasselt, Belgium.,3University Biobank Limburg (UBiLim) and Clinical Biobank Jessa Hospital, Hasselt, Belgium
| | - Annick Daniëls
- 1Department of Experimental Hematology, Jessa Hospital, Hasselt, Belgium
| | - Jeroen Declercq
- 1Department of Experimental Hematology, Jessa Hospital, Hasselt, Belgium.,2Faculty of Medicine and Life Sciences, Hasselt University, Hasselt, Belgium
| | - Brigitte Maes
- 1Department of Experimental Hematology, Jessa Hospital, Hasselt, Belgium.,2Faculty of Medicine and Life Sciences, Hasselt University, Hasselt, Belgium.,4Department of Clinical Biology, Jessa Hospital, Hasselt, Belgium
| | - Kimberly Vanhees
- 2Faculty of Medicine and Life Sciences, Hasselt University, Hasselt, Belgium.,3University Biobank Limburg (UBiLim) and Clinical Biobank Jessa Hospital, Hasselt, Belgium
| | - Guy Froyen
- 1Department of Experimental Hematology, Jessa Hospital, Hasselt, Belgium.,2Faculty of Medicine and Life Sciences, Hasselt University, Hasselt, Belgium.,4Department of Clinical Biology, Jessa Hospital, Hasselt, Belgium
| | - Jean-Luc Rummens
- 1Department of Experimental Hematology, Jessa Hospital, Hasselt, Belgium.,2Faculty of Medicine and Life Sciences, Hasselt University, Hasselt, Belgium.,3University Biobank Limburg (UBiLim) and Clinical Biobank Jessa Hospital, Hasselt, Belgium.,4Department of Clinical Biology, Jessa Hospital, Hasselt, Belgium
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135
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Moreno-Mayar JV, Vinner L, de Barros Damgaard P, de la Fuente C, Chan J, Spence JP, Allentoft ME, Vimala T, Racimo F, Pinotti T, Rasmussen S, Margaryan A, Iraeta Orbegozo M, Mylopotamitaki D, Wooller M, Bataille C, Becerra-Valdivia L, Chivall D, Comeskey D, Devièse T, Grayson DK, George L, Harry H, Alexandersen V, Primeau C, Erlandson J, Rodrigues-Carvalho C, Reis S, Bastos MQR, Cybulski J, Vullo C, Morello F, Vilar M, Wells S, Gregersen K, Hansen KL, Lynnerup N, Mirazón Lahr M, Kjær K, Strauss A, Alfonso-Durruty M, Salas A, Schroeder H, Higham T, Malhi RS, Rasic JT, Souza L, Santos FR, Malaspinas AS, Sikora M, Nielsen R, Song YS, Meltzer DJ, Willerslev E. Early human dispersals within the Americas. Science 2018; 362:science.aav2621. [DOI: 10.1126/science.aav2621] [Citation(s) in RCA: 102] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2018] [Accepted: 10/30/2018] [Indexed: 12/16/2022]
Abstract
Studies of the peopling of the Americas have focused on the timing and number of initial migrations. Less attention has been paid to the subsequent spread of people within the Americas. We sequenced 15 ancient human genomes spanning from Alaska to Patagonia; six are ≥10,000 years old (up to ~18× coverage). All are most closely related to Native Americans, including those from an Ancient Beringian individual and two morphologically distinct “Paleoamericans.” We found evidence of rapid dispersal and early diversification that included previously unknown groups as people moved south. This resulted in multiple independent, geographically uneven migrations, including one that provides clues of a Late Pleistocene Australasian genetic signal, as well as a later Mesoamerican-related expansion. These led to complex and dynamic population histories from North to South America.
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136
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Intragenus (Homo) variation in a chemokine receptor gene (CCR5). PLoS One 2018; 13:e0204989. [PMID: 30278065 PMCID: PMC6168169 DOI: 10.1371/journal.pone.0204989] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2017] [Accepted: 09/18/2018] [Indexed: 01/04/2023] Open
Abstract
Humans have a comparatively higher rate of more polymorphisms in regulatory regions of the primate CCR5 gene, an immune system gene with both general and specific functions. This has been interpreted as allowing flexibility and diversity of gene expression in response to varying disease loads. A broad expression repertoire is useful to humans-the only globally distributed primate-due to our unique adaptive pattern that increased pathogen exposure and disease loads (e.g., sedentism, subsistence practices). The main objective of the study was to determine if the previously observed human pattern of increased variation extended to other members of our genus, Homo. The data for this study are mined from the published genomes of extinct hominins (four Neandertals and two Denisovans), an ancient human (Ust'-Ishim), and modern humans (1000 Genomes). An average of 15 polymorphisms per individual were found in human populations (with a total of 262 polymorphisms). There were 94 polymorphisms identified across extinct Homo (an average of 13 per individual) with 41 previously observed in modern humans and 53 novel polymorphisms (32 in Denisova and 21 in Neandertal). Neither the frequency nor distribution of polymorphisms across gene regions exhibit significant differences within the genus Homo. Thus, humans are not unique with regards to the increased frequency of regulatory polymorphisms and the evolution of variation patterns across CCR5 gene appears to have originated within the genus. A broader evolutionary perspective on regulatory flexibility may be that it provided an advantage during the transition to confrontational foraging (and later hunting) that altered human-environment interaction as well as during migration to Eurasia and encounters with novel pathogens.
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137
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Daly KG, Maisano Delser P, Mullin VE, Scheu A, Mattiangeli V, Teasdale MD, Hare AJ, Burger J, Verdugo MP, Collins MJ, Kehati R, Erek CM, Bar-Oz G, Pompanon F, Cumer T, Çakırlar C, Mohaseb AF, Decruyenaere D, Davoudi H, Çevik Ö, Rollefson G, Vigne JD, Khazaeli R, Fathi H, Doost SB, Rahimi Sorkhani R, Vahdati AA, Sauer EW, Azizi Kharanaghi H, Maziar S, Gasparian B, Pinhasi R, Martin L, Orton D, Arbuckle BS, Benecke N, Manica A, Horwitz LK, Mashkour M, Bradley DG. Ancient goat genomes reveal mosaic domestication in the Fertile Crescent. Science 2018; 361:85-88. [PMID: 29976826 DOI: 10.1126/science.aas9411] [Citation(s) in RCA: 69] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2018] [Revised: 02/13/2018] [Accepted: 06/04/2018] [Indexed: 12/16/2022]
Abstract
Current genetic data are equivocal as to whether goat domestication occurred multiple times or was a singular process. We generated genomic data from 83 ancient goats (51 with genome-wide coverage) from Paleolithic to Medieval contexts throughout the Near East. Our findings demonstrate that multiple divergent ancient wild goat sources were domesticated in a dispersed process that resulted in genetically and geographically distinct Neolithic goat populations, echoing contemporaneous human divergence across the region. These early goat populations contributed differently to modern goats in Asia, Africa, and Europe. We also detect early selection for pigmentation, stature, reproduction, milking, and response to dietary change, providing 8000-year-old evidence for human agency in molding genome variation within a partner species.
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Affiliation(s)
- Kevin G Daly
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin 2, Ireland
| | - Pierpaolo Maisano Delser
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin 2, Ireland.,Department of Zoology, University of Cambridge, Cambridge CB2 3EJ, UK
| | - Victoria E Mullin
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin 2, Ireland.,Department of Earth Sciences, Natural History Museum, London SW7 5BD, UK
| | - Amelie Scheu
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin 2, Ireland.,Palaeogenetics Group, Institute of Organismic and Molecular Evolution (iOME), Johannes Gutenberg University Mainz, 55099 Mainz, Germany
| | | | - Matthew D Teasdale
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin 2, Ireland.,BioArCh, University of York, York YO10 5DD, UK
| | - Andrew J Hare
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin 2, Ireland
| | - Joachim Burger
- Palaeogenetics Group, Institute of Organismic and Molecular Evolution (iOME), Johannes Gutenberg University Mainz, 55099 Mainz, Germany
| | | | - Matthew J Collins
- BioArCh, University of York, York YO10 5DD, UK.,Museum of Natural History, University of Copenhagen, Copenhagen, Denmark
| | - Ron Kehati
- National Natural History Collections, Faculty of Life Sciences, The Hebrew University, Jerusalem, Israel
| | | | - Guy Bar-Oz
- Zinman Institute of Archaeology, University of Haifa, Mount Carmel, Haifa, Israel
| | - François Pompanon
- Université Grenoble Alpes, Univ. Savoie Mont Blanc, CNRS, LECA, F-38000 Grenoble, France
| | - Tristan Cumer
- Université Grenoble Alpes, Univ. Savoie Mont Blanc, CNRS, LECA, F-38000 Grenoble, France
| | - Canan Çakırlar
- Groningen Institute of Archaeology, Groningen University, Groningen, Netherlands
| | - Azadeh Fatemeh Mohaseb
- Archéozoologie, Archéobotanique (UMR 7209), CNRS, MNHN, UPMC, Sorbonne Universités, Paris, France.,Archaeozoology section, Archaeometry Laboratory, University of Tehran, Tehran, Iran
| | - Delphine Decruyenaere
- Archéozoologie, Archéobotanique (UMR 7209), CNRS, MNHN, UPMC, Sorbonne Universités, Paris, France
| | - Hossein Davoudi
- Department of Archaeology, Faculty of Humanities, Tarbiat Modares University, Tehran, Iran.,Osteology Department, National Museum of Iran, Tehran, Iran
| | - Özlem Çevik
- Trakya Universitesi, Edebiyat Fakültesi, Arkeoloi Bölümü, Edirne, Turkey
| | - Gary Rollefson
- Department of Anthropology, Whitman College, Walla Walla, WA 99362, USA
| | - Jean-Denis Vigne
- Archéozoologie, Archéobotanique (UMR 7209), CNRS, MNHN, UPMC, Sorbonne Universités, Paris, France
| | - Roya Khazaeli
- Archaeozoology section, Archaeometry Laboratory, University of Tehran, Tehran, Iran
| | - Homa Fathi
- Archaeozoology section, Archaeometry Laboratory, University of Tehran, Tehran, Iran
| | - Sanaz Beizaee Doost
- Archaeozoology section, Archaeometry Laboratory, University of Tehran, Tehran, Iran
| | | | - Ali Akbar Vahdati
- Provincial Office of the Iranian Center for Cultural Heritage, Handicrafts and Tourism Organisation, North Khorassan, Bojnord, Iran
| | - Eberhard W Sauer
- School of History, Classics and Archaeology, University of Edinburgh, William Robertson Wing, Old Medical School, Edinburgh EH8 9AG, UK
| | | | - Sepideh Maziar
- Institut für Archäologische Wissenschaften, Goethe Universität, Frankfurt am Main, Germany
| | - Boris Gasparian
- Institute of Archaeology and Ethnology, National Academy of Sciences of the Republic of Armenia, Yerevan 0025, Republic of Armenia
| | - Ron Pinhasi
- Department of Anthropology, University of Vienna, 1090 Vienna, Austria
| | - Louise Martin
- Institute of Archeology, University College London, London, UK
| | - David Orton
- BioArCh, University of York, York YO10 5DD, UK
| | - Benjamin S Arbuckle
- Department of Anthropology, University of North Carolina, Chapel Hill, NC, USA
| | - Norbert Benecke
- Department of Natural Sciences, German Archaeological Institute, 14195 Berlin, Germany
| | - Andrea Manica
- Department of Zoology, University of Cambridge, Cambridge CB2 3EJ, UK
| | - Liora Kolska Horwitz
- National Natural History Collections, Faculty of Life Sciences, The Hebrew University, Jerusalem, Israel
| | - Marjan Mashkour
- Archéozoologie, Archéobotanique (UMR 7209), CNRS, MNHN, UPMC, Sorbonne Universités, Paris, France.,Archaeozoology section, Archaeometry Laboratory, University of Tehran, Tehran, Iran.,Osteology Department, National Museum of Iran, Tehran, Iran
| | - Daniel G Bradley
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin 2, Ireland.
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138
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Wright PGR, Mathews F, Schofield H, Morris C, Burrage J, Smith A, Dempster EL, Hamilton PB. Application of a novel molecular method to age free-living wild Bechstein's bats. Mol Ecol Resour 2018; 18:1374-1380. [PMID: 29981199 DOI: 10.1111/1755-0998.12925] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2018] [Revised: 04/21/2018] [Accepted: 05/02/2018] [Indexed: 11/26/2022]
Abstract
The age profile of populations fundamentally affects their conservation status. Yet, age is frequently difficult to assess in wild animals. Here, we assessed the use of DNA methylation of homologous genes to establish the age structure of a rare and elusive wild mammal: the Bechstein's bat (Myotis bechsteinii). We collected 62 wing punches from individuals whose ages were known as a result of a long-term banding study. DNA methylation was measured at seven CpG sites from three genes, which have previously shown age-associated changes in humans and laboratory mice. All CpG sites from the tested genes showed a significant relationship between DNA methylation and age, both individually and in combination (multiple linear regression R2 = 0.58, p < 0.001). Despite slight approximation around estimates, the approach is sufficiently precise to place animals into practically useful age cohorts. This method is of considerable practical benefit as it can reliably age individual bats. It is also much faster than traditional capture-mark-recapture techniques, with the potential to collect information on the age structure of an entire colony from a single sampling session to better inform conservation actions for Bechstein's bats. By identifying three genes where DNA methylation correlates with age across distantly related species, this study also suggests that the technique can potentially be applied across a wide range of mammals.
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Affiliation(s)
- Patrick G R Wright
- Bioscience, College of Life and Environmental Sciences, University of Exeter, Exeter, UK
| | - Fiona Mathews
- College of Life Sciences, University of Sussex, Falmer, UK
| | | | - Colin Morris
- The Vincent Wildlife Trust, Ledbury, Herefordshire, UK
| | - Joe Burrage
- Exeter Medical School, University of Exeter, Exeter, UK
| | - Adam Smith
- Exeter Medical School, University of Exeter, Exeter, UK
| | | | - Patrick B Hamilton
- Bioscience, College of Life and Environmental Sciences, University of Exeter, Exeter, UK
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139
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McColl H, Racimo F, Vinner L, Demeter F, Gakuhari T, Moreno-Mayar JV, van Driem G, Gram Wilken U, Seguin-Orlando A, de la Fuente Castro C, Wasef S, Shoocongdej R, Souksavatdy V, Sayavongkhamdy T, Saidin MM, Allentoft ME, Sato T, Malaspinas AS, Aghakhanian FA, Korneliussen T, Prohaska A, Margaryan A, de Barros Damgaard P, Kaewsutthi S, Lertrit P, Nguyen TMH, Hung HC, Minh Tran T, Nghia Truong H, Nguyen GH, Shahidan S, Wiradnyana K, Matsumae H, Shigehara N, Yoneda M, Ishida H, Masuyama T, Yamada Y, Tajima A, Shibata H, Toyoda A, Hanihara T, Nakagome S, Deviese T, Bacon AM, Duringer P, Ponche JL, Shackelford L, Patole-Edoumba E, Nguyen AT, Bellina-Pryce B, Galipaud JC, Kinaston R, Buckley H, Pottier C, Rasmussen S, Higham T, Foley RA, Lahr MM, Orlando L, Sikora M, Phipps ME, Oota H, Higham C, Lambert DM, Willerslev E. The prehistoric peopling of Southeast Asia. Science 2018; 361:88-92. [DOI: 10.1126/science.aat3628] [Citation(s) in RCA: 216] [Impact Index Per Article: 36.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2018] [Accepted: 05/29/2018] [Indexed: 12/11/2022]
Abstract
The human occupation history of Southeast Asia (SEA) remains heavily debated. Current evidence suggests that SEA was occupied by Hòabìnhian hunter-gatherers until ~4000 years ago, when farming economies developed and expanded, restricting foraging groups to remote habitats. Some argue that agricultural development was indigenous; others favor the “two-layer” hypothesis that posits a southward expansion of farmers giving rise to present-day Southeast Asian genetic diversity. By sequencing 26 ancient human genomes (25 from SEA, 1 Japanese Jōmon), we show that neither interpretation fits the complexity of Southeast Asian history: Both Hòabìnhian hunter-gatherers and East Asian farmers contributed to current Southeast Asian diversity, with further migrations affecting island SEA and Vietnam. Our results help resolve one of the long-standing controversies in Southeast Asian prehistory.
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Affiliation(s)
- Hugh McColl
- Centre for GeoGenetics, Natural History Museum of Denmark, Copenhagen, Denmark
| | - Fernando Racimo
- Centre for GeoGenetics, Natural History Museum of Denmark, Copenhagen, Denmark
| | - Lasse Vinner
- Centre for GeoGenetics, Natural History Museum of Denmark, Copenhagen, Denmark
| | - Fabrice Demeter
- Centre for GeoGenetics, Natural History Museum of Denmark, Copenhagen, Denmark
- National Museum of Natural History, Ecoanthropology and Ethnobiology, Musée de l’Homme, Paris, France
| | - Takashi Gakuhari
- Center for Cultural Resource Studies, Kanazawa University, Kanazawa, Japan
- Kitasato University School of Medicine, Sagamihara, Kanagawa, Japan
| | | | - George van Driem
- Institut für Sprachwissenschaft, Universität Bern, Bern, Switzerland
- University of New England, Armidale, NSW, Australia
| | - Uffe Gram Wilken
- Centre for GeoGenetics, Natural History Museum of Denmark, Copenhagen, Denmark
| | - Andaine Seguin-Orlando
- Centre for GeoGenetics, Natural History Museum of Denmark, Copenhagen, Denmark
- Laboratoire AMIS, Université Paul Sabatier (UPS), Toulouse, France
| | | | - Sally Wasef
- Australian Research Centre for Human Evolution, Griffith University, Nathan, QLD, Australia
| | - Rasmi Shoocongdej
- Department of Archaeology, Faculty of Archaeology, Silpakorn University, Bangkok, Thailand
| | - Viengkeo Souksavatdy
- Department of Heritage, Ministry of Information, Culture and Tourism, Vientiane, Lao People’s Democratic Republic
| | - Thongsa Sayavongkhamdy
- Department of Heritage, Ministry of Information, Culture and Tourism, Vientiane, Lao People’s Democratic Republic
| | - Mohd Mokhtar Saidin
- Centre for Global Archaeological Research, Universiti Sains Malaysia, Penang, Malaysia
| | - Morten E. Allentoft
- Centre for GeoGenetics, Natural History Museum of Denmark, Copenhagen, Denmark
| | - Takehiro Sato
- Department of Bioinformatics and Genomics, Graduate School of Advanced Preventive Medical Sciences, Kanazawa University, Kanazawa, Japan
| | - Anna-Sapfo Malaspinas
- Department of Computational Biology, University of Lausanne and SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Farhang A. Aghakhanian
- Jeffrey Cheah School of Medicine & Health Sciences, Monash University Malaysia, Jalan Lagoon Selatan, Sunway City, Selangor, Malaysia
| | | | - Ana Prohaska
- Department of Zoology, University of Cambridge, Cambridge, UK
| | - Ashot Margaryan
- Centre for GeoGenetics, Natural History Museum of Denmark, Copenhagen, Denmark
- Institute of Molecular Biology, National Academy of Sciences, Yerevan, Armenia
| | | | - Supannee Kaewsutthi
- Department of Biochemistry, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Patcharee Lertrit
- Department of Biochemistry, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Thi Mai Huong Nguyen
- Anthropological and Paleoenvironmental Department, Institute of Archaeology, Hanoi, Vietnam
| | - Hsiao-chun Hung
- Department of Archaeology and Natural History, Australian National University, Canberra, ACT, Australia
| | - Thi Minh Tran
- Anthropological and Paleoenvironmental Department, Institute of Archaeology, Hanoi, Vietnam
| | - Huu Nghia Truong
- Anthropological and Paleoenvironmental Department, Institute of Archaeology, Hanoi, Vietnam
| | - Giang Hai Nguyen
- Anthropological and Paleoenvironmental Department, Institute of Archaeology, Hanoi, Vietnam
| | - Shaiful Shahidan
- Centre for Global Archaeological Research, Universiti Sains Malaysia, Penang, Malaysia
| | | | - Hiromi Matsumae
- Kitasato University School of Medicine, Sagamihara, Kanagawa, Japan
| | - Nobuo Shigehara
- Nara National Research Institute for Cultural Properties, Nara, Japan
| | - Minoru Yoneda
- University Museum, University of Tokyo, Tokyo, Japan
| | - Hajime Ishida
- Graduate School of Medicine, University of the Ryukyus, Nishihara, Okinawa, Japan
| | | | | | - Atsushi Tajima
- Department of Bioinformatics and Genomics, Graduate School of Advanced Preventive Medical Sciences, Kanazawa University, Kanazawa, Japan
| | - Hiroki Shibata
- Division of Genomics, Medical Institute of Bioregulation, Kyushu University, Fukuoka, Japan
| | - Atsushi Toyoda
- Center for Information Biology, National Institute of Genetics, Mishima, Japan
| | | | - Shigeki Nakagome
- School of Medicine, Trinity College Dublin, University of Dublin, Dublin, Ireland
| | - Thibaut Deviese
- Oxford Radiocarbon Accelerator Unit (ORAU), University of Oxford, Oxford, UK
| | - Anne-Marie Bacon
- Laboratoire AMIS, Université Paris Descartes, Faculté de Chirurgie Dentaire, Montrouge, France
| | - Philippe Duringer
- École et Observatoire des Sciences de la Terre, Université de Strasbourg, Strasbourg, France
- Institut de Physique du Globe de Strasbourg (IPGS) (CNRS/UDS UMR 7516), Strasbourg, France
| | - Jean-Luc Ponche
- Laboratory “Image Ville et Environnement LIVE,” UMR7362, CNRS and Université de Strasbourg, Strasbourg, France
| | - Laura Shackelford
- Department of Anthropology, University of Illinois at Urbana-Champaign, Champaign, IL, USA
| | | | - Anh Tuan Nguyen
- Anthropological and Paleoenvironmental Department, Institute of Archaeology, Hanoi, Vietnam
| | - Bérénice Bellina-Pryce
- CNRS, UMR7055 “Préhistoire et Technologie,” Maison Archéologie et Ethnologie, Nanterre, France
| | - Jean-Christophe Galipaud
- Research Institute for Development, National Museum of Natural History, UMR Paloc, Paris, France
| | - Rebecca Kinaston
- Department of Anatomy, School of Biomedical Sciences, University of Otago, Dunedin, New Zealand
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena, Germany
| | - Hallie Buckley
- Department of Anatomy, School of Biomedical Sciences, University of Otago, Dunedin, New Zealand
| | | | - Simon Rasmussen
- Department of Bio and Health Informatics, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Tom Higham
- Oxford Radiocarbon Accelerator Unit (ORAU), University of Oxford, Oxford, UK
| | - Robert A. Foley
- Leverhulme Centre for Human Evolutionary Studies, Department of Archaeology, University of Cambridge, Cambridge, UK
| | - Marta Mirazón Lahr
- Leverhulme Centre for Human Evolutionary Studies, Department of Archaeology, University of Cambridge, Cambridge, UK
| | - Ludovic Orlando
- Centre for GeoGenetics, Natural History Museum of Denmark, Copenhagen, Denmark
- Laboratoire AMIS, Université Paul Sabatier (UPS), Toulouse, France
| | - Martin Sikora
- Centre for GeoGenetics, Natural History Museum of Denmark, Copenhagen, Denmark
| | - Maude E. Phipps
- Jeffrey Cheah School of Medicine & Health Sciences, Monash University Malaysia, Jalan Lagoon Selatan, Sunway City, Selangor, Malaysia
| | - Hiroki Oota
- Kitasato University School of Medicine, Sagamihara, Kanagawa, Japan
| | - Charles Higham
- Department of Anthropology and Archaeology, University of Otago, Dunedin, New Zealand
- St. Catharine’s College, University of Cambridge, Cambridge, UK
| | - David M. Lambert
- Australian Research Centre for Human Evolution, Griffith University, Nathan, QLD, Australia
| | - Eske Willerslev
- Centre for GeoGenetics, Natural History Museum of Denmark, Copenhagen, Denmark
- Department of Zoology, University of Cambridge, Cambridge, UK
- Wellcome Trust Sanger Institute, Hinxton, UK
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140
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Alberti F, Gonzalez J, Paijmans JLA, Basler N, Preick M, Henneberger K, Trinks A, Rabeder G, Conard NJ, Münzel SC, Joger U, Fritsch G, Hildebrandt T, Hofreiter M, Barlow A. Optimized DNA sampling of ancient bones using Computed Tomography scans. Mol Ecol Resour 2018; 18:1196-1208. [DOI: 10.1111/1755-0998.12911] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2017] [Revised: 03/14/2018] [Accepted: 03/19/2018] [Indexed: 11/28/2022]
Affiliation(s)
- Federica Alberti
- Institute for Biochemistry and Biology; University of Potsdam; Potsdam Germany
| | - Javier Gonzalez
- Institute for Biochemistry and Biology; University of Potsdam; Potsdam Germany
| | | | - Nikolas Basler
- Institute for Biochemistry and Biology; University of Potsdam; Potsdam Germany
| | - Michaela Preick
- Institute for Biochemistry and Biology; University of Potsdam; Potsdam Germany
| | - Kirstin Henneberger
- Institute for Biochemistry and Biology; University of Potsdam; Potsdam Germany
| | - Alexandra Trinks
- Institute for Biochemistry and Biology; University of Potsdam; Potsdam Germany
- Evolutionary Biology; IRI for the Life Sciences; Humboldt University Berlin; Berlin Germany
| | - Gernot Rabeder
- Department of Palaeontology; Geozentrum; University of Vienna; Vienna Austria
| | - Nicholas J. Conard
- Institute for Archaeological Sciences; Archaeozoology; University of Tübingen; Tübingen Germany
| | - Susanne C. Münzel
- Institute for Archaeological Sciences; Archaeozoology; University of Tübingen; Tübingen Germany
| | - Ulrich Joger
- Staatliches Naturhistorisches Museum Braunschweig; Braunschweig Germany
| | - Guido Fritsch
- Leibniz Institute for Zoo and Wildlife Research; Berlin Germany
| | | | - Michael Hofreiter
- Institute for Biochemistry and Biology; University of Potsdam; Potsdam Germany
| | - Axel Barlow
- Institute for Biochemistry and Biology; University of Potsdam; Potsdam Germany
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141
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Spyrou MA, Tukhbatova RI, Wang CC, Valtueña AA, Lankapalli AK, Kondrashin VV, Tsybin VA, Khokhlov A, Kühnert D, Herbig A, Bos KI, Krause J. Analysis of 3800-year-old Yersinia pestis genomes suggests Bronze Age origin for bubonic plague. Nat Commun 2018; 9:2234. [PMID: 29884871 PMCID: PMC5993720 DOI: 10.1038/s41467-018-04550-9] [Citation(s) in RCA: 85] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2017] [Accepted: 04/27/2018] [Indexed: 12/23/2022] Open
Abstract
The origin of Yersinia pestis and the early stages of its evolution are fundamental subjects of investigation given its high virulence and mortality that resulted from past pandemics. Although the earliest evidence of Y. pestis infections in humans has been identified in Late Neolithic/Bronze Age Eurasia (LNBA 5000–3500y BP), these strains lack key genetic components required for flea adaptation, thus making their mode of transmission and disease presentation in humans unclear. Here, we reconstruct ancient Y. pestis genomes from individuals associated with the Late Bronze Age period (~3800 BP) in the Samara region of modern-day Russia. We show clear distinctions between our new strains and the LNBA lineage, and suggest that the full ability for flea-mediated transmission causing bubonic plague evolved more than 1000 years earlier than previously suggested. Finally, we propose that several Y. pestis lineages were established during the Bronze Age, some of which persist to the present day. Yersinia pestis has caused infections (plague) in humans since the Early Bronze Age (5000 years ago). Here, Spyrou et al. reconstruct Y. pestis genomes from Late Bronze Age individuals, and find genomic evidence compatible with flea-mediated transmission causing bubonic plague.
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Affiliation(s)
- Maria A Spyrou
- Max Planck Institute for the Science of Human History, Kahlaische Str. 10, 07745, Jena, Germany. .,Institute for Archaeological Sciences, University of Tübingen, Rümelinstrasse 23, 72070, Tübingen, Germany.
| | - Rezeda I Tukhbatova
- Max Planck Institute for the Science of Human History, Kahlaische Str. 10, 07745, Jena, Germany.,Center of Excellence "Archaeometry", Kazan Federal University, Kazan, 420008, Russian Federation
| | - Chuan-Chao Wang
- Max Planck Institute for the Science of Human History, Kahlaische Str. 10, 07745, Jena, Germany.,Department of Anthropology and Ethnology, Xiamen University, 361005, Xiamen, China
| | - Aida Andrades Valtueña
- Max Planck Institute for the Science of Human History, Kahlaische Str. 10, 07745, Jena, Germany
| | - Aditya K Lankapalli
- Max Planck Institute for the Science of Human History, Kahlaische Str. 10, 07745, Jena, Germany
| | | | - Victor A Tsybin
- State Institute of Culture, Agency for Preservation of the Historical and Cultural Heritage of the Samara Region, Samara, 443010, Russia
| | - Aleksandr Khokhlov
- Samara State University of Social Sciences and Education, Maxim Gorky Str., Samara, 443090, Russia
| | - Denise Kühnert
- Max Planck Institute for the Science of Human History, Kahlaische Str. 10, 07745, Jena, Germany.,Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, 8091, Zurich, Switzerland
| | - Alexander Herbig
- Max Planck Institute for the Science of Human History, Kahlaische Str. 10, 07745, Jena, Germany
| | - Kirsten I Bos
- Max Planck Institute for the Science of Human History, Kahlaische Str. 10, 07745, Jena, Germany.
| | - Johannes Krause
- Max Planck Institute for the Science of Human History, Kahlaische Str. 10, 07745, Jena, Germany. .,Institute for Archaeological Sciences, University of Tübingen, Rümelinstrasse 23, 72070, Tübingen, Germany.
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142
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Schuenemann VJ, Kumar Lankapalli A, Barquera R, Nelson EA, Iraíz Hernández D, Acuña Alonzo V, Bos KI, Márquez Morfín L, Herbig A, Krause J. Historic Treponema pallidum genomes from Colonial Mexico retrieved from archaeological remains. PLoS Negl Trop Dis 2018; 12:e0006447. [PMID: 29927932 PMCID: PMC6013024 DOI: 10.1371/journal.pntd.0006447] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2018] [Accepted: 04/12/2018] [Indexed: 12/20/2022] Open
Abstract
Treponema pallidum infections occur worldwide causing, among other diseases, syphilis and yaws. In particular sexually transmitted syphilis is regarded as a re-emerging infectious disease with millions of new infections annually. Here we present three historic T. pallidum genomes (two from T. pallidum ssp. pallidum and one from T. pallidum ssp. pertenue) that have been reconstructed from skeletons recovered from the Convent of Santa Isabel in Mexico City, operational between the 17th and 19th century. Our analyses indicate that different T. pallidum subspecies caused similar diagnostic presentations that are normally associated with syphilis in infants, and potential evidence of a congenital infection of T. pallidum ssp. pertenue, the causative agent of yaws. This first reconstruction of T. pallidum genomes from archaeological material opens the possibility of studying its evolutionary history at a resolution previously assumed to be out of reach.
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Affiliation(s)
- Verena J. Schuenemann
- Institute for Archaeological Sciences, University of Tübingen, Tübingen, Germany
- Senckenberg Center for Human Evolution and Paleoenvironment, University of Tübingen, Tübingen, Germany
- Institute of Evolutionary Medicine, University of Zurich, Zurich, Switzerland
| | - Aditya Kumar Lankapalli
- Department for Archaeogenetics, Max Planck Institute for the Science of Human History, Jena, Germany
| | - Rodrigo Barquera
- Department for Archaeogenetics, Max Planck Institute for the Science of Human History, Jena, Germany
- Molecular Genetics Laboratory, National School of Anthropology and History, Mexico City, Mexico
| | - Elizabeth A. Nelson
- Department for Archaeogenetics, Max Planck Institute for the Science of Human History, Jena, Germany
| | - Diana Iraíz Hernández
- Department for Archaeogenetics, Max Planck Institute for the Science of Human History, Jena, Germany
- Molecular Genetics Laboratory, National School of Anthropology and History, Mexico City, Mexico
| | - Víctor Acuña Alonzo
- Molecular Genetics Laboratory, National School of Anthropology and History, Mexico City, Mexico
| | - Kirsten I. Bos
- Department for Archaeogenetics, Max Planck Institute for the Science of Human History, Jena, Germany
| | | | - Alexander Herbig
- Department for Archaeogenetics, Max Planck Institute for the Science of Human History, Jena, Germany
| | - Johannes Krause
- Institute for Archaeological Sciences, University of Tübingen, Tübingen, Germany
- Senckenberg Center for Human Evolution and Paleoenvironment, University of Tübingen, Tübingen, Germany
- Department for Archaeogenetics, Max Planck Institute for the Science of Human History, Jena, Germany
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143
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Lipson M, Cheronet O, Mallick S, Rohland N, Oxenham M, Pietrusewsky M, Pryce TO, Willis A, Matsumura H, Buckley H, Domett K, Nguyen GH, Trinh HH, Kyaw AA, Win TT, Pradier B, Broomandkhoshbacht N, Candilio F, Changmai P, Fernandes D, Ferry M, Gamarra B, Harney E, Kampuansai J, Kutanan W, Michel M, Novak M, Oppenheimer J, Sirak K, Stewardson K, Zhang Z, Flegontov P, Pinhasi R, Reich D. Ancient genomes document multiple waves of migration in Southeast Asian prehistory. Science 2018; 361:92-95. [PMID: 29773666 DOI: 10.1126/science.aat3188] [Citation(s) in RCA: 154] [Impact Index Per Article: 25.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2018] [Accepted: 05/03/2018] [Indexed: 12/18/2022]
Abstract
Southeast Asia is home to rich human genetic and linguistic diversity, but the details of past population movements in the region are not well known. Here, we report genome-wide ancient DNA data from 18 Southeast Asian individuals spanning from the Neolithic period through the Iron Age (4100 to 1700 years ago). Early farmers from Man Bac in Vietnam exhibit a mixture of East Asian (southern Chinese agriculturalist) and deeply diverged eastern Eurasian (hunter-gatherer) ancestry characteristic of Austroasiatic speakers, with similar ancestry as far south as Indonesia providing evidence for an expansive initial spread of Austroasiatic languages. By the Bronze Age, in a parallel pattern to Europe, sites in Vietnam and Myanmar show close connections to present-day majority groups, reflecting substantial additional influxes of migrants.
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Affiliation(s)
- Mark Lipson
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA.
| | - Olivia Cheronet
- Department of Anthropology, University of Vienna, 1090 Vienna, Austria.,Earth Institute, University College Dublin, Dublin 4, Ireland.,School of Archaeology, University College Dublin, Dublin 4, Ireland
| | - Swapan Mallick
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA.,Medical and Population Genetics Program, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Nadin Rohland
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Marc Oxenham
- School of Archaeology and Anthropology, Australian National University, Canberra, ACT 0200, Australia
| | - Michael Pietrusewsky
- Department of Anthropology, University of Hawai'i at Mānoa, Honolulu, Hawai'i 96822, USA
| | - Thomas Oliver Pryce
- Centre National de la Recherche Scientifique, 75016 Paris, France.,UMR 7055 Préhistoire et Technologie, Université Paris Nanterre, 92023 Nanterre, France.,CEA/CNRS UMR 3685 NIMBE, 91191 Gif-sur-Yvette, France
| | - Anna Willis
- College of Arts, Society and Education, James Cook University, Townsville, Queensland 4811, Australia
| | - Hirofumi Matsumura
- School of Health Science, Sapporo Medical University, Sapporo 060-8556, Japan
| | - Hallie Buckley
- Department of Anatomy, University of Otago, Dunedin 9054, New Zealand
| | - Kate Domett
- Division of Tropical Health and Medicine, College of Medicine and Dentistry, James Cook University, Townsville, Queensland 4811, Australia
| | - Giang Hai Nguyen
- Department of Prehistoric Archaeology, Vietnam Institute of Archaeology, Hanoi, Vietnam
| | - Hoang Hiep Trinh
- Department of Prehistoric Archaeology, Vietnam Institute of Archaeology, Hanoi, Vietnam
| | - Aung Aung Kyaw
- Department of Archaeology, Ministry of Religious Affairs and Culture, Mandalay, Myanmar
| | - Tin Tin Win
- Department of Archaeology, Ministry of Religious Affairs and Culture, Mandalay, Myanmar
| | - Baptiste Pradier
- UMR 7055 Préhistoire et Technologie, Université Paris Nanterre, 92023 Nanterre, France
| | - Nasreen Broomandkhoshbacht
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA.,Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Francesca Candilio
- Soprintendenza Archeologia Belle Arti e Paesaggio per la Città Metropolitana di Cagliari e per le Province di Oristano e Sud Sardegna, 09124 Cagliari, Italy.,Physical Anthropology Section, University of Pennsylvania Museum of Archaeology and Anthropology, Philadelphia, PA 19104, USA
| | - Piya Changmai
- Department of Biology and Ecology, Faculty of Science, University of Ostrava, 70103 Ostrava, Czech Republic
| | - Daniel Fernandes
- Department of Anthropology, University of Vienna, 1090 Vienna, Austria.,Earth Institute, University College Dublin, Dublin 4, Ireland.,CIAS, Department of Life Sciences, University of Coimbra, Coimbra 3000-456, Portugal
| | - Matthew Ferry
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA.,Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Beatriz Gamarra
- Earth Institute, University College Dublin, Dublin 4, Ireland.,School of Archaeology, University College Dublin, Dublin 4, Ireland
| | - Eadaoin Harney
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA.,Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Jatupol Kampuansai
- Department of Biology, Faculty of Science, Chiang Mai University, Chiang Mai 50200, Thailand.,Center of Excellence in Bioresources for Agriculture, Industry and Medicine, Chiang Mai University, Chiang Mai 50200, Thailand
| | - Wibhu Kutanan
- Department of Biology, Faculty of Science, Khon Kaen University, Khon Kaen, 40002, Thailand
| | - Megan Michel
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA.,Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Mario Novak
- Earth Institute, University College Dublin, Dublin 4, Ireland.,Institute for Anthropological Research, 10000 Zagreb, Croatia
| | - Jonas Oppenheimer
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA.,Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Kendra Sirak
- Earth Institute, University College Dublin, Dublin 4, Ireland.,Department of Anthropology, Emory University, Atlanta, GA 30322, USA
| | - Kristin Stewardson
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA.,Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Zhao Zhang
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Pavel Flegontov
- Department of Biology and Ecology, Faculty of Science, University of Ostrava, 70103 Ostrava, Czech Republic.,Institute of Parasitology, Biology Centre, Czech Academy of Sciences, 37005 České Budějovice, Czech Republic
| | - Ron Pinhasi
- Department of Anthropology, University of Vienna, 1090 Vienna, Austria. .,Earth Institute, University College Dublin, Dublin 4, Ireland
| | - David Reich
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA. .,Medical and Population Genetics Program, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.,Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02115, USA
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144
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Banerjee N, Polushina T, Bettella F, Giddaluru S, Steen VM, Andreassen OA, Le Hellard S. Recently evolved human-specific methylated regions are enriched in schizophrenia signals. BMC Evol Biol 2018; 18:63. [PMID: 29747567 PMCID: PMC5946405 DOI: 10.1186/s12862-018-1177-2] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2017] [Accepted: 04/11/2018] [Indexed: 01/10/2023] Open
Abstract
Background One explanation for the persistence of schizophrenia despite the reduced fertility of patients is that it is a by-product of recent human evolution. This hypothesis is supported by evidence suggesting that recently-evolved genomic regions in humans are involved in the genetic risk for schizophrenia. Using summary statistics from genome-wide association studies (GWAS) of schizophrenia and 11 other phenotypes, we tested for enrichment of association with GWAS traits in regions that have undergone methylation changes in the human lineage compared to Neanderthals and Denisovans, i.e. human-specific differentially methylated regions (DMRs). We used analytical tools that evaluate polygenic enrichment of a subset of genomic variants against all variants. Results Schizophrenia was the only trait in which DMR SNPs showed clear enrichment of association that passed the genome-wide significance threshold. The enrichment was not observed for Neanderthal or Denisovan DMRs. The enrichment seen in human DMRs is comparable to that for genomic regions tagged by Neanderthal Selective Sweep markers, and stronger than that for Human Accelerated Regions. The enrichment survives multiple testing performed through permutation (n = 10,000) and bootstrapping (n = 5000) in INRICH (p < 0.01). Some enrichment of association with height was observed at the gene level. Conclusions Regions where DNA methylation modifications have changed during recent human evolution show enrichment of association with schizophrenia and possibly with height. Our study further supports the hypothesis that genetic variants conferring risk of schizophrenia co-occur in genomic regions that have changed as the human species evolved. Since methylation is an epigenetic mark, potentially mediated by environmental changes, our results also suggest that interaction with the environment might have contributed to that association. Electronic supplementary material The online version of this article (10.1186/s12862-018-1177-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Niladri Banerjee
- NORMENT - K.G. Jebsen Center for Psychosis Research, Department of Clinical Science, University of Bergen, Bergen, Norway.,Dr. Einar Martens Research Group for Biological Psychiatry, Center for Medical Genetics and Molecular Medicine, Haukeland University Hospital, Bergen, Norway
| | - Tatiana Polushina
- NORMENT - K.G. Jebsen Center for Psychosis Research, Department of Clinical Science, University of Bergen, Bergen, Norway.,Dr. Einar Martens Research Group for Biological Psychiatry, Center for Medical Genetics and Molecular Medicine, Haukeland University Hospital, Bergen, Norway
| | - Francesco Bettella
- NORMENT - K.G. Jebsen Center for Psychosis Research, Institute of Clinical Medicine, University of Oslo, Oslo, Norway.,NORMENT - K.G. Jebsen Centre, Division of Mental Health and Addiction, Oslo University Hospital, Oslo, Norway
| | - Sudheer Giddaluru
- NORMENT - K.G. Jebsen Center for Psychosis Research, Department of Clinical Science, University of Bergen, Bergen, Norway.,Dr. Einar Martens Research Group for Biological Psychiatry, Center for Medical Genetics and Molecular Medicine, Haukeland University Hospital, Bergen, Norway
| | - Vidar M Steen
- NORMENT - K.G. Jebsen Center for Psychosis Research, Department of Clinical Science, University of Bergen, Bergen, Norway.,Dr. Einar Martens Research Group for Biological Psychiatry, Center for Medical Genetics and Molecular Medicine, Haukeland University Hospital, Bergen, Norway
| | - Ole A Andreassen
- NORMENT - K.G. Jebsen Center for Psychosis Research, Institute of Clinical Medicine, University of Oslo, Oslo, Norway.,NORMENT - K.G. Jebsen Centre, Division of Mental Health and Addiction, Oslo University Hospital, Oslo, Norway
| | - Stephanie Le Hellard
- NORMENT - K.G. Jebsen Center for Psychosis Research, Department of Clinical Science, University of Bergen, Bergen, Norway. .,Dr. Einar Martens Research Group for Biological Psychiatry, Center for Medical Genetics and Molecular Medicine, Haukeland University Hospital, Bergen, Norway. .,Department of Clinical Medicine, Laboratory Building, Haukeland University Hospital, N-5021, Bergen, Norway.
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145
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Schuenemann VJ, Avanzi C, Krause-Kyora B, Seitz A, Herbig A, Inskip S, Bonazzi M, Reiter E, Urban C, Dangvard Pedersen D, Taylor GM, Singh P, Stewart GR, Velemínský P, Likovsky J, Marcsik A, Molnár E, Pálfi G, Mariotti V, Riga A, Belcastro MG, Boldsen JL, Nebel A, Mays S, Donoghue HD, Zakrzewski S, Benjak A, Nieselt K, Cole ST, Krause J. Ancient genomes reveal a high diversity of Mycobacterium leprae in medieval Europe. PLoS Pathog 2018; 14:e1006997. [PMID: 29746563 PMCID: PMC5944922 DOI: 10.1371/journal.ppat.1006997] [Citation(s) in RCA: 62] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2017] [Accepted: 03/28/2018] [Indexed: 11/19/2022] Open
Abstract
Studying ancient DNA allows us to retrace the evolutionary history of human pathogens, such as Mycobacterium leprae, the main causative agent of leprosy. Leprosy is one of the oldest recorded and most stigmatizing diseases in human history. The disease was prevalent in Europe until the 16th century and is still endemic in many countries with over 200,000 new cases reported annually. Previous worldwide studies on modern and European medieval M. leprae genomes revealed that they cluster into several distinct branches of which two were present in medieval Northwestern Europe. In this study, we analyzed 10 new medieval M. leprae genomes including the so far oldest M. leprae genome from one of the earliest known cases of leprosy in the United Kingdom-a skeleton from the Great Chesterford cemetery with a calibrated age of 415-545 C.E. This dataset provides a genetic time transect of M. leprae diversity in Europe over the past 1500 years. We find M. leprae strains from four distinct branches to be present in the Early Medieval Period, and strains from three different branches were detected within a single cemetery from the High Medieval Period. Altogether these findings suggest a higher genetic diversity of M. leprae strains in medieval Europe at various time points than previously assumed. The resulting more complex picture of the past phylogeography of leprosy in Europe impacts current phylogeographical models of M. leprae dissemination. It suggests alternative models for the past spread of leprosy such as a wide spread prevalence of strains from different branches in Eurasia already in Antiquity or maybe even an origin in Western Eurasia. Furthermore, these results highlight how studying ancient M. leprae strains improves understanding the history of leprosy worldwide.
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Affiliation(s)
- Verena J. Schuenemann
- Institute for Archaeological Sciences, University of Tübingen, Tübingen, Germany
- Senckenberg Centre for Human Evolution and Palaeoenvironment, University of Tübingen, Tübingen, Germany
- Institute of Evolutionary Medicine, University of Zurich, Zurich, Switzerland
| | - Charlotte Avanzi
- Global Health Institute, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Ben Krause-Kyora
- Institute of Clinical Molecular Biology, Kiel University, Kiel, Germany
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena, Germany
| | - Alexander Seitz
- Center for Bioinformatics, University of Tübingen, Tübingen, Germany
| | - Alexander Herbig
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena, Germany
| | - Sarah Inskip
- McDonald Institute for Archaeological Research, University of Cambridge, Cambridge, United Kingdom
| | - Marion Bonazzi
- Institute of Clinical Molecular Biology, Kiel University, Kiel, Germany
| | - Ella Reiter
- Institute for Archaeological Sciences, University of Tübingen, Tübingen, Germany
| | - Christian Urban
- Institute for Archaeological Sciences, University of Tübingen, Tübingen, Germany
| | - Dorthe Dangvard Pedersen
- Unit of Anthropology (ADBOU), Department of Forensic Medicine, University of Southern Denmark, Odense S, Denmark
| | - G. Michael Taylor
- Department of Microbial Sciences, Faculty of Health and Medical Sciences, University of Surrey, Guildford, United Kingdom
| | - Pushpendra Singh
- Global Health Institute, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
- Department of Microbiology and Biotechnology Centre, The Maharaja Sayajirao University of Baroda, Vadodara, India
| | - Graham R. Stewart
- Department of Microbial Sciences, Faculty of Health and Medical Sciences, University of Surrey, Guildford, United Kingdom
| | - Petr Velemínský
- Department of Anthropology, National Museum, Prague, Czech Republic
| | - Jakub Likovsky
- Department of Archaeology of Landscape and Archaeobiology, Institute of Archaeology of the Czech Academy of Sciences, Prague, Czech Republic
| | - Antónia Marcsik
- Department of Biological Anthropology, University of Szeged, Szeged, Hungary
| | - Erika Molnár
- Department of Biological Anthropology, University of Szeged, Szeged, Hungary
| | - György Pálfi
- Department of Biological Anthropology, University of Szeged, Szeged, Hungary
| | - Valentina Mariotti
- Department of Biological, Geological and Environmental Sciences, Bologna, Italy
- ADES AMU-CNRS- EFS: Anthropology and Health, Aix-Marseille Université, Marseille, France
| | - Alessandro Riga
- Department of Biology, University of Florence, Firenze, Italy
| | - M. Giovanna Belcastro
- Department of Biological, Geological and Environmental Sciences, Bologna, Italy
- ADES AMU-CNRS- EFS: Anthropology and Health, Aix-Marseille Université, Marseille, France
| | - Jesper L. Boldsen
- Unit of Anthropology (ADBOU), Department of Forensic Medicine, University of Southern Denmark, Odense S, Denmark
| | - Almut Nebel
- Institute of Clinical Molecular Biology, Kiel University, Kiel, Germany
| | - Simon Mays
- Historic England, Portsmouth, United Kingdom
| | - Helen D. Donoghue
- Centre for Clinical Microbiology, Division of Infection and Immunity, University College London, London, United Kingdom
| | - Sonia Zakrzewski
- Department of Archaeology, University of Southampton, Southampton, United Kingdom
| | - Andrej Benjak
- Global Health Institute, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Kay Nieselt
- Center for Bioinformatics, University of Tübingen, Tübingen, Germany
- * E-mail: (KN); (STC); (JK)
| | - Stewart T. Cole
- Global Health Institute, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
- Institut Pasteur, Paris, France
- * E-mail: (KN); (STC); (JK)
| | - Johannes Krause
- Institute for Archaeological Sciences, University of Tübingen, Tübingen, Germany
- Senckenberg Centre for Human Evolution and Palaeoenvironment, University of Tübingen, Tübingen, Germany
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena, Germany
- * E-mail: (KN); (STC); (JK)
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146
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Mühlemann B, Jones TC, Damgaard PDB, Allentoft ME, Shevnina I, Logvin A, Usmanova E, Panyushkina IP, Boldgiv B, Bazartseren T, Tashbaeva K, Merz V, Lau N, Smrčka V, Voyakin D, Kitov E, Epimakhov A, Pokutta D, Vicze M, Price TD, Moiseyev V, Hansen AJ, Orlando L, Rasmussen S, Sikora M, Vinner L, Osterhaus ADME, Smith DJ, Glebe D, Fouchier RAM, Drosten C, Sjögren KG, Kristiansen K, Willerslev E. Ancient hepatitis B viruses from the Bronze Age to the Medieval period. Nature 2018; 557:418-423. [PMID: 29743673 DOI: 10.1038/s41586-018-0097-z] [Citation(s) in RCA: 123] [Impact Index Per Article: 20.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2017] [Accepted: 04/06/2018] [Indexed: 12/16/2022]
Abstract
Hepatitis B virus (HBV) is a major cause of human hepatitis. There is considerable uncertainty about the timescale of its evolution and its association with humans. Here we present 12 full or partial ancient HBV genomes that are between approximately 0.8 and 4.5 thousand years old. The ancient sequences group either within or in a sister relationship with extant human or other ape HBV clades. Generally, the genome properties follow those of modern HBV. The root of the HBV tree is projected to between 8.6 and 20.9 thousand years ago, and we estimate a substitution rate of 8.04 × 10-6-1.51 × 10-5 nucleotide substitutions per site per year. In several cases, the geographical locations of the ancient genotypes do not match present-day distributions. Genotypes that today are typical of Africa and Asia, and a subgenotype from India, are shown to have an early Eurasian presence. The geographical and temporal patterns that we observe in ancient and modern HBV genotypes are compatible with well-documented human migrations during the Bronze and Iron Ages1,2. We provide evidence for the creation of HBV genotype A via recombination, and for a long-term association of modern HBV genotypes with humans, including the discovery of a human genotype that is now extinct. These data expose a complexity of HBV evolution that is not evident when considering modern sequences alone.
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Affiliation(s)
- Barbara Mühlemann
- Center for Pathogen Evolution, Department of Zoology, University of Cambridge, Cambridge, UK
| | - Terry C Jones
- Center for Pathogen Evolution, Department of Zoology, University of Cambridge, Cambridge, UK.,Institute of Virology, Charité, Universitätsmedizin Berlin, Berlin, Germany
| | | | - Morten E Allentoft
- Centre for GeoGenetics, Natural History Museum, University of Copenhagen, Copenhagen, Denmark
| | - Irina Shevnina
- Archaeological Laboratory, Faculty of History and Law, A. A. Baitursynov Kostanay State University, Kostanay, Kazakhstan
| | - Andrey Logvin
- Archaeological Laboratory, Faculty of History and Law, A. A. Baitursynov Kostanay State University, Kostanay, Kazakhstan
| | - Emma Usmanova
- Saryarka Archaeological Institute, Karaganda State University, Karaganda, Kazakhstan
| | | | - Bazartseren Boldgiv
- Department of Biology, School of Arts and Sciences, National University of Mongolia, Ulaanbaatar, Mongolia
| | - Tsevel Bazartseren
- Laboratory of Virology, Institute of Veterinary Medicine, Mongolian University of Life Sciences, Ulaanbaatar, Mongolia
| | | | - Victor Merz
- Pavlodar State University, Pavlodar, Kazakhstan
| | - Nina Lau
- Centre for Baltic and Scandinavian Archaeology, Schleswig, Germany
| | - Václav Smrčka
- Institute for History of Medicine and Foreign Languages of the First Faculty of Medicine, Charles University, Prague, Czech Republic
| | | | - Egor Kitov
- N. N. Miklouho-Maklay Institute of Ethnology and Anthropology, Russian Academy of Sciences, Moscow, Russia
| | - Andrey Epimakhov
- South Ural Department, Institute of History and Archaeology UBRAS, South Ural State University, Chelyabinsk, Russia
| | - Dalia Pokutta
- Department of Archaeology and Classical Studies, Stockholm University, Stockholm, Sweden
| | | | - T Douglas Price
- Department of Historical Studies, University of Gothenburg, Gothenburg, Sweden
| | - Vyacheslav Moiseyev
- Department of Physical Anthropology, Peter the Great Museum of Anthropology and Ethnography, Saint-Petersburg, Russia
| | - Anders J Hansen
- Centre for GeoGenetics, Natural History Museum, University of Copenhagen, Copenhagen, Denmark
| | - Ludovic Orlando
- Centre for GeoGenetics, Natural History Museum, University of Copenhagen, Copenhagen, Denmark.,Laboratoire d'Anthropobiologie Moléculaire et d'Imagerie de Synthèse, CNRS UMR 5288, Université de Toulouse, Université Paul Sabatier, Toulouse, France
| | - Simon Rasmussen
- Department of Bio and Health Informatics, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Martin Sikora
- Centre for GeoGenetics, Natural History Museum, University of Copenhagen, Copenhagen, Denmark
| | - Lasse Vinner
- Centre for GeoGenetics, Natural History Museum, University of Copenhagen, Copenhagen, Denmark
| | - Albert D M E Osterhaus
- Research Center for Emerging Infections and Zoonoses, University of Veterinary Medicine Hannover, Hannover, Germany
| | - Derek J Smith
- Center for Pathogen Evolution, Department of Zoology, University of Cambridge, Cambridge, UK
| | - Dieter Glebe
- Institute of Medical Virology, Justus Liebig University of Giessen, Giessen, Germany.,National Reference Centre for Hepatitis B and D Viruses, German Center for Infection Research (DZIF), Giessen, Germany
| | - Ron A M Fouchier
- Department of Viroscience, Erasmus Medical Centre, Rotterdam, The Netherlands
| | - Christian Drosten
- Institute of Virology, Charité, Universitätsmedizin Berlin, Berlin, Germany.,German Center for Infection Research (DZIF), Braunschweig, Germany
| | - Karl-Göran Sjögren
- Department of Historical Studies, University of Gothenburg, Gothenburg, Sweden
| | | | - Eske Willerslev
- Centre for GeoGenetics, Natural History Museum, University of Copenhagen, Copenhagen, Denmark. .,Cambridge GeoGenetics Group, Department of Zoology, University of Cambridge, Cambridge, UK. .,Wellcome Trust Sanger Institute, Hinxton, UK.
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147
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Mak SST, Gopalakrishnan S, Carøe C, Geng C, Liu S, Sinding MHS, Kuderna LFK, Zhang W, Fu S, Vieira FG, Germonpré M, Bocherens H, Fedorov S, Petersen B, Sicheritz-Pontén T, Marques-Bonet T, Zhang G, Jiang H, Gilbert MTP. Comparative performance of the BGISEQ-500 vs Illumina HiSeq2500 sequencing platforms for palaeogenomic sequencing. Gigascience 2018; 6:1-13. [PMID: 28854615 PMCID: PMC5570000 DOI: 10.1093/gigascience/gix049] [Citation(s) in RCA: 109] [Impact Index Per Article: 18.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2017] [Accepted: 06/20/2017] [Indexed: 12/30/2022] Open
Abstract
Ancient DNA research has been revolutionized following development of next-generation sequencing platforms. Although a number of such platforms have been applied to ancient DNA samples, the Illumina series are the dominant choice today, mainly because of high production capacities and short read production. Recently a potentially attractive alternative platform for palaeogenomic data generation has been developed, the BGISEQ-500, whose sequence output are comparable with the Illumina series. In this study, we modified the standard BGISEQ-500 library preparation specifically for use on degraded DNA, then directly compared the sequencing performance and data quality of the BGISEQ-500 to the Illumina HiSeq2500 platform on DNA extracted from 8 historic and ancient dog and wolf samples. The data generated were largely comparable between sequencing platforms, with no statistically significant difference observed for parameters including level (P = 0.371) and average sequence length (P = 0718) of endogenous nuclear DNA, sequence GC content (P = 0.311), double-stranded DNA damage rate (v. 0.309), and sequence clonality (P = 0.093). Small significant differences were found in single-strand DNA damage rate (δS; slightly lower for the BGISEQ-500, P = 0.011) and the background rate of difference from the reference genome (θ; slightly higher for BGISEQ-500, P = 0.012). This may result from the differences in amplification cycles used to polymerase chain reaction–amplify the libraries. A significant difference was also observed in the mitochondrial DNA percentages recovered (P = 0.018), although we believe this is likely a stochastic effect relating to the extremely low levels of mitochondria that were sequenced from 3 of the samples with overall very low levels of endogenous DNA. Although we acknowledge that our analyses were limited to animal material, our observations suggest that the BGISEQ-500 holds the potential to represent a valid and potentially valuable alternative platform for palaeogenomic data generation that is worthy of future exploration by those interested in the sequencing and analysis of degraded DNA.
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Affiliation(s)
- Sarah Siu Tze Mak
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen, Denmark
| | - Shyam Gopalakrishnan
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen, Denmark
| | - Christian Carøe
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen, Denmark.,DTU Bioinformatics, Department of Bio and Health Informatics, Technical University of Denmark, Building 208, DK-2800 Lyngby, Denmark
| | | | - Shanlin Liu
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen, Denmark.,China National GeneBank, BGI-Shenzhen, Shenzhen 518083, China
| | - Mikkel-Holger S Sinding
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen, Denmark.,Natural History Museum, University of Oslo, PO Box 1172 Blindern, N-0318 Oslo, Norway.,The Qimmeq Project, University of Greenland, Manutooq 1, PO Box 1061, 3905 Nuussuaq, Greenland
| | - Lukas F K Kuderna
- Institute of Evolutionary Biology (UPF-CSIC), PRBB, Dr. Aiguader 88, 08003 Barcelona, Spain.,CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Baldiri i Reixac 4, 08028 Barcelona, Spain
| | | | - Shujin Fu
- BGI-Shenzhen, Shenzhen 518083, China
| | - Filipe G Vieira
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen, Denmark
| | - Mietje Germonpré
- OD Earth and History of Life, Royal Belgian Institute of Natural Sciences, Vautierstraat 29, 1000 Brussels, Belgium
| | - Hervé Bocherens
- Department of Geosciences, Palaeobiology, University of Tübingen, Tübingen, Germany.,Senckenberg Centre for Human Evolution and Palaeoenvironment, University of Tübingen, Tübingen, Germany
| | - Sergey Fedorov
- Mammoth Museum, Institute of Applied Ecology of the North of the North-Eastern Federal University, ul. Kulakovskogo 48, 677980 Yakutsk, Russia
| | - Bent Petersen
- DTU Bioinformatics, Department of Bio and Health Informatics, Technical University of Denmark, Building 208, DK-2800 Lyngby, Denmark
| | - Thomas Sicheritz-Pontén
- DTU Bioinformatics, Department of Bio and Health Informatics, Technical University of Denmark, Building 208, DK-2800 Lyngby, Denmark
| | - Tomas Marques-Bonet
- Institute of Evolutionary Biology (UPF-CSIC), PRBB, Dr. Aiguader 88, 08003 Barcelona, Spain.,CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Baldiri i Reixac 4, 08028 Barcelona, Spain.,Catalan Institution of Research and Advanced Studies (ICREA), Passeig de Lluís Companys, 23, 08010, Barcelona, Spain
| | - Guojie Zhang
- China National GeneBank, BGI-Shenzhen, Shenzhen 518083, China.,Centre for Social Evolution, Department of Biology, Universitetsparken 15, University of Copenhagen, Copenhagen DK-2100, Denmark
| | - Hui Jiang
- BGI-Shenzhen, Shenzhen 518083, China
| | - M Thomas P Gilbert
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen, Denmark.,Trace and Environmental DNA Laboratory, Department of Environment and Agriculture, Curtin University, 6102 Perth, Australia.,Norwegian University of Science and Technology, University Museum, 7491 Trondheim, Norway
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148
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Gorden EM, Sturk-Andreaggi K, Marshall C. Repair of DNA damage caused by cytosine deamination in mitochondrial DNA of forensic case samples. Forensic Sci Int Genet 2018; 34:257-264. [DOI: 10.1016/j.fsigen.2018.02.015] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2017] [Revised: 02/01/2018] [Accepted: 02/17/2018] [Indexed: 01/14/2023]
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149
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Monroy Kuhn JM, Jakobsson M, Günther T. Estimating genetic kin relationships in prehistoric populations. PLoS One 2018; 13:e0195491. [PMID: 29684051 PMCID: PMC5912749 DOI: 10.1371/journal.pone.0195491] [Citation(s) in RCA: 151] [Impact Index Per Article: 25.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2017] [Accepted: 03/23/2018] [Indexed: 12/21/2022] Open
Abstract
Archaeogenomic research has proven to be a valuable tool to trace migrations of historic and prehistoric individuals and groups, whereas relationships within a group or burial site have not been investigated to a large extent. Knowing the genetic kinship of historic and prehistoric individuals would give important insights into social structures of ancient and historic cultures. Most archaeogenetic research concerning kinship has been restricted to uniparental markers, while studies using genome-wide information were mainly focused on comparisons between populations. Applications which infer the degree of relationship based on modern-day DNA information typically require diploid genotype data. Low concentration of endogenous DNA, fragmentation and other post-mortem damage to ancient DNA (aDNA) makes the application of such tools unfeasible for most archaeological samples. To infer family relationships for degraded samples, we developed the software READ (Relationship Estimation from Ancient DNA). We show that our heuristic approach can successfully infer up to second degree relationships with as little as 0.1x shotgun coverage per genome for pairs of individuals. We uncover previously unknown relationships among prehistoric individuals by applying READ to published aDNA data from several human remains excavated from different cultural contexts. In particular, we find a group of five closely related males from the same Corded Ware culture site in modern-day Germany, suggesting patrilocality, which highlights the possibility to uncover social structures of ancient populations by applying READ to genome-wide aDNA data. READ is publicly available from https://bitbucket.org/tguenther/read.
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Affiliation(s)
- Jose Manuel Monroy Kuhn
- Uppsala University, Evolutionary Biology Centre, Department of Organismal Biology, Norbyvägen 18C, SE-752 36 Uppsala, Sweden
| | - Mattias Jakobsson
- Uppsala University, Evolutionary Biology Centre, Department of Organismal Biology, Norbyvägen 18C, SE-752 36 Uppsala, Sweden
- Uppsala University, SciLifeLab, Norbyvägen 18C, SE-752 36 Uppsala, Sweden
- * E-mail: (MJ); (TG)
| | - Torsten Günther
- Uppsala University, Evolutionary Biology Centre, Department of Organismal Biology, Norbyvägen 18C, SE-752 36 Uppsala, Sweden
- * E-mail: (MJ); (TG)
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150
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Olalde I, Brace S, Allentoft ME, Armit I, Kristiansen K, Booth T, Rohland N, Mallick S, Szécsényi-Nagy A, Mittnik A, Altena E, Lipson M, Lazaridis I, Harper TK, Patterson N, Broomandkhoshbacht N, Diekmann Y, Faltyskova Z, Fernandes D, Ferry M, Harney E, de Knijff P, Michel M, Oppenheimer J, Stewardson K, Barclay A, Alt KW, Liesau C, Ríos P, Blasco C, Miguel JV, García RM, Fernández AA, Bánffy E, Bernabò-Brea M, Billoin D, Bonsall C, Bonsall L, Allen T, Büster L, Carver S, Navarro LC, Craig OE, Cook GT, Cunliffe B, Denaire A, Dinwiddy KE, Dodwell N, Ernée M, Evans C, Kuchařík M, Farré JF, Fowler C, Gazenbeek M, Pena RG, Haber-Uriarte M, Haduch E, Hey G, Jowett N, Knowles T, Massy K, Pfrengle S, Lefranc P, Lemercier O, Lefebvre A, Martínez CH, Olmo VG, Ramírez AB, Maurandi JL, Majó T, McKinley JI, McSweeney K, Mende BG, Modi A, Kulcsár G, Kiss V, Czene A, Patay R, Endrődi A, Köhler K, Hajdu T, Szeniczey T, Dani J, Bernert Z, Hoole M, Cheronet O, Keating D, Velemínský P, Dobeš M, Candilio F, Brown F, Fernández RF, Herrero-Corral AM, Tusa S, Carnieri E, Lentini L, Valenti A, Zanini A, Waddington C, Delibes G, Guerra-Doce E, Neil B, Brittain M, Luke M, Mortimer R, Desideri J, Besse M, Brücken G, Furmanek M, Hałuszko A, Mackiewicz M, Rapiński A, Leach S, Soriano I, Lillios KT, Cardoso JL, Pearson MP, Włodarczak P, Price TD, Prieto P, Rey PJ, Risch R, Rojo Guerra MA, Schmitt A, Serralongue J, Silva AM, Smrčka V, Vergnaud L, Zilhão J, Caramelli D, Higham T, Thomas MG, Kennett DJ, Fokkens H, Heyd V, Sheridan A, Sjögren KG, Stockhammer PW, Krause J, Pinhasi R, Haak W, Barnes I, Lalueza-Fox C, Reich D. The Beaker phenomenon and the genomic transformation of northwest Europe. Nature 2018; 555:190-196. [PMID: 29466337 PMCID: PMC5973796 DOI: 10.1038/nature25738] [Citation(s) in RCA: 255] [Impact Index Per Article: 42.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2017] [Accepted: 01/04/2018] [Indexed: 12/19/2022]
Abstract
From around 2750 to 2500 bc, Bell Beaker pottery became widespread across western and central Europe, before it disappeared between 2200 and 1800 bc. The forces that propelled its expansion are a matter of long-standing debate, and there is support for both cultural diffusion and migration having a role in this process. Here we present genome-wide data from 400 Neolithic, Copper Age and Bronze Age Europeans, including 226 individuals associated with Beaker-complex artefacts. We detected limited genetic affinity between Beaker-complex-associated individuals from Iberia and central Europe, and thus exclude migration as an important mechanism of spread between these two regions. However, migration had a key role in the further dissemination of the Beaker complex. We document this phenomenon most clearly in Britain, where the spread of the Beaker complex introduced high levels of steppe-related ancestry and was associated with the replacement of approximately 90% of Britain's gene pool within a few hundred years, continuing the east-to-west expansion that had brought steppe-related ancestry into central and northern Europe over the previous centuries.
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Affiliation(s)
- Iñigo Olalde
- Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Selina Brace
- Department of Earth Sciences, Natural History Museum, London SW7 5BD, UK
| | - Morten E Allentoft
- Centre for GeoGenetics, Natural History Museum, University of Copenhagen, Copenhagen 1350, Denmark
| | - Ian Armit
- School of Archaeological and Forensic Sciences, University of Bradford, Bradford BD7 1DP, UK
| | | | - Thomas Booth
- Department of Earth Sciences, Natural History Museum, London SW7 5BD, UK
| | - Nadin Rohland
- Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Swapan Mallick
- Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA
- Howard Hughes Medical Institute, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Anna Szécsényi-Nagy
- Laboratory of Archaeogenetics, Institute of Archaeology, Research Centre for the Humanities, Hungarian Academy of Sciences, Budapest 1097, Hungary
| | - Alissa Mittnik
- Institute for Archaeological Sciences, Archaeo- and Palaeogenetics, University of Tübingen, Tübingen 72070, Germany
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena 07745, Germany
| | - Eveline Altena
- Department of Human Genetics, Leiden University Medical Center, Leiden 2333 ZC, The Netherlands
| | - Mark Lipson
- Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Iosif Lazaridis
- Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA
| | - Thomas K Harper
- Department of Anthropology, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
| | - Nick Patterson
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA
| | - Nasreen Broomandkhoshbacht
- Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA
- Howard Hughes Medical Institute, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Yoan Diekmann
- Research Department of Genetics, Evolution and Environment, University College London, London WC1E 6BT, UK
| | - Zuzana Faltyskova
- Research Department of Genetics, Evolution and Environment, University College London, London WC1E 6BT, UK
| | - Daniel Fernandes
- Earth Institute, University College Dublin, Dublin 4, Ireland
- Department of Anthropology, University of Vienna, Vienna 1090, Austria
- Research Center for Anthropology and Health, Department of Life Science, University of Coimbra, Coimbra 3000-456, Portugal
| | - Matthew Ferry
- Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA
- Howard Hughes Medical Institute, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Eadaoin Harney
- Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Peter de Knijff
- Department of Human Genetics, Leiden University Medical Center, Leiden 2333 ZC, The Netherlands
| | - Megan Michel
- Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA
- Howard Hughes Medical Institute, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Jonas Oppenheimer
- Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA
- Howard Hughes Medical Institute, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Kristin Stewardson
- Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA
- Howard Hughes Medical Institute, Harvard Medical School, Boston, Massachusetts 02115, USA
| | | | - Kurt Werner Alt
- Center of Natural and Cultural History of Man, Danube Private University, Krems 3500, Austria
- Department of Biomedical Engineering, Basel University, Basel 4123, Switzerland
- Integrative Prehistory and Archaeological Science, Basel University, Basel, Switzerland
| | - Corina Liesau
- Departamento de Prehistoria y Arqueología, Universidad Autónoma de Madrid, Madrid 28049, Spain
| | - Patricia Ríos
- Departamento de Prehistoria y Arqueología, Universidad Autónoma de Madrid, Madrid 28049, Spain
| | - Concepción Blasco
- Departamento de Prehistoria y Arqueología, Universidad Autónoma de Madrid, Madrid 28049, Spain
| | | | | | | | - Eszter Bánffy
- Institute of Archaeology, Research Centre for the Humanities, Hungarian Academy of Sciences, Budapest 1097, Hungary
- Romano-Germanic Commission, German Archaeological Institute, Frankfurt am Main 60325, Germany
| | | | - David Billoin
- INRAP, Institut National de Recherches Archéologiques Préventives, Buffard 25440, France
| | - Clive Bonsall
- School of History, Classics and Archaeology, University of Edinburgh, Edinburgh EH8 9AG, UK
| | | | - Tim Allen
- Oxford Archaeology, Oxford OX2 0ES, UK
| | - Lindsey Büster
- School of Archaeological and Forensic Sciences, University of Bradford, Bradford BD7 1DP, UK
| | - Sophie Carver
- Department of Archaeology and Anthropology, University of Bristol, Bristol BS8 1UU, UK
| | - Laura Castells Navarro
- School of Archaeological and Forensic Sciences, University of Bradford, Bradford BD7 1DP, UK
| | - Oliver E Craig
- BioArCh, Department of Archaeology, University of York, York YO10 5DD, UK
| | - Gordon T Cook
- Scottish Universities Environmental Research Centre, East Kilbride G75 0QF, UK
| | - Barry Cunliffe
- Institute of Archaeology, University of Oxford, Oxford OX1 2PG, UK
| | | | | | | | - Michal Ernée
- Institute of Archaeology, Czech Academy of Sciences, Prague 118 01, Czech Republic
| | - Christopher Evans
- Cambridge Archaeological Unit, Department of Archaeology, University of Cambridge, Cambridge CB3 0DT, UK
| | | | - Joan Francès Farré
- Museu i Poblat Ibèric de Ca n'Oliver, Cerdanyola del Vallès 08290, Spain
| | - Chris Fowler
- School of History, Classics & Archaeology, Newcastle University, Newcastle upon Tyne NE1 7RU, UK
| | - Michiel Gazenbeek
- INRAP, Institut National de Recherches Archéologiques Préventives, Nice 06300, France
| | - Rafael Garrido Pena
- Departamento de Prehistoria y Arqueología, Universidad Autónoma de Madrid, Madrid 28049, Spain
| | | | - Elżbieta Haduch
- Institute of Zoology and Biomedical Research, Jagiellonian University, Kraków 31-007, Poland
| | - Gill Hey
- Oxford Archaeology, Oxford OX2 0ES, UK
| | - Nick Jowett
- Great Orme Mines, Great Orme, Llandudno LL30 2XG, UK
| | - Timothy Knowles
- Bristol Radiocarbon Accelerator Mass Spectrometry Facility, University of Bristol, Bristol BS8 1UU, UK
| | - Ken Massy
- Institut für Vor- und Frühgeschichtliche Archäologie und Provinzialrömische Archäologie, Ludwig-Maximilians-Universität München, Munich 80539, Germany
| | - Saskia Pfrengle
- Institute for Archaeological Sciences, Archaeo- and Palaeogenetics, University of Tübingen, Tübingen 72070, Germany
| | - Philippe Lefranc
- INRAP, Institut National de Recherches Archéologiques Préventives, Strasbourg 67100, France
| | - Olivier Lemercier
- Université Paul-Valéry - Montpellier 3, UMR 5140 ASM, Montpellier 34199, France
| | - Arnaud Lefebvre
- INRAP, Institut National de Recherches Archéologiques Préventives, Metz 57063, France
- UMR 5199, Pacea, équipe A3P, Université de Bordeaux, Talence 33400, France
| | - César Heras Martínez
- TRÉBEDE, Patrimonio y Cultura SL, Torres de la Alameda 28813, Spain
- Departamento de Ciencias de la Vida, Universidad de Alcalá, Alcalá de Henares 28801, Spain
- Instituto Universitario de Investigación en Ciencias Policiales (IUICP), Alcalá de Henares 28801, Spain
| | - Virginia Galera Olmo
- Departamento de Ciencias de la Vida, Universidad de Alcalá, Alcalá de Henares 28801, Spain
- Instituto Universitario de Investigación en Ciencias Policiales (IUICP), Alcalá de Henares 28801, Spain
| | | | | | - Tona Majó
- Archaeom, Departament de Prehistòria, Universitat Autònoma de Barcelona, Cerdanyola del Vallès 08193, Spain
| | | | - Kathleen McSweeney
- School of History, Classics and Archaeology, University of Edinburgh, Edinburgh EH8 9AG, UK
| | - Balázs Gusztáv Mende
- Laboratory of Archaeogenetics, Institute of Archaeology, Research Centre for the Humanities, Hungarian Academy of Sciences, Budapest 1097, Hungary
| | - Alessandra Modi
- Department of Biology, University of Florence, Florence 50121, Italy
| | - Gabriella Kulcsár
- Institute of Archaeology, Research Centre for the Humanities, Hungarian Academy of Sciences, Budapest 1097, Hungary
| | - Viktória Kiss
- Institute of Archaeology, Research Centre for the Humanities, Hungarian Academy of Sciences, Budapest 1097, Hungary
| | | | - Róbert Patay
- Ferenczy Museum Center, Szentendre 2100, Hungary
| | | | - Kitti Köhler
- Institute of Archaeology, Research Centre for the Humanities, Hungarian Academy of Sciences, Budapest 1097, Hungary
| | - Tamás Hajdu
- Department of Biological Anthropology, Eötvös Loránd University, Budapest 1117, Hungary
- Hungarian Natural History Museum, Budapest 1083, Hungary
| | - Tamás Szeniczey
- Department of Biological Anthropology, Eötvös Loránd University, Budapest 1117, Hungary
| | | | - Zsolt Bernert
- Hungarian Natural History Museum, Budapest 1083, Hungary
| | - Maya Hoole
- Historic Environment Scotland, Edinburgh EH9 1SH, UK
| | - Olivia Cheronet
- Earth Institute, University College Dublin, Dublin 4, Ireland
- Department of Anthropology, University of Vienna, Vienna 1090, Austria
| | - Denise Keating
- Humanities Institute, University College Dublin, Dublin 4, Ireland
| | - Petr Velemínský
- Department of Anthropology, National Museum, Prague 115 79, Czech Republic
| | - Miroslav Dobeš
- Institute of Archaeology, Czech Academy of Sciences, Prague 118 01, Czech Republic
| | - Francesca Candilio
- Soprintendenza Archeologia belle arti e paesaggio per la città metropolitana di Cagliari e per le province di Oristano e Sud Sardegna, Cagliari 9124, Italy
- Physical Anthropology Section, University of Philadelphia Museum of Archaeology and Anthropology, Philadelphia, Pennsylvania 19104, USA
- Department of Environmental Biology, Sapienza University of Rome, Rome 00185, Italy
| | | | | | | | | | - Emiliano Carnieri
- Facoltà di Lettere e Filosofia, Università di Palermo, Palermo 90133, Italy
| | - Luigi Lentini
- Soprintendenza per i beni culturali e ambientali di Trapani, Trapani 91100, Italy
| | | | | | | | - Germán Delibes
- Departamento de Prehistoria, Facultad de Filosofía y Letras, Universidad de Valladolid, Valladolid 47011, Spain
| | - Elisa Guerra-Doce
- Departamento de Prehistoria, Facultad de Filosofía y Letras, Universidad de Valladolid, Valladolid 47011, Spain
| | - Benjamin Neil
- Cambridge Archaeological Unit, Department of Archaeology, University of Cambridge, Cambridge CB3 0DT, UK
| | - Marcus Brittain
- Cambridge Archaeological Unit, Department of Archaeology, University of Cambridge, Cambridge CB3 0DT, UK
| | - Mike Luke
- Albion Archaeology, Bedford MK42 0AS, UK
| | | | - Jocelyne Desideri
- Laboratory of Prehistoric Archaeology and Anthropology, Department F.-A. Forel for Environmental and Aquatic Sciences, University of Geneva, Geneva 4, Switzerland
| | - Marie Besse
- Laboratory of Prehistoric Archaeology and Anthropology, Department F.-A. Forel for Environmental and Aquatic Sciences, University of Geneva, Geneva 4, Switzerland
| | - Günter Brücken
- General Department of Cultural Heritage Rhineland Palatinate, Department of Archaeology, Mainz 55116, Germany
| | - Mirosław Furmanek
- Institute of Archaeology, University of Wroclaw, Wrocław 50-137, Poland
| | - Agata Hałuszko
- Institute of Archaeology, University of Wroclaw, Wrocław 50-137, Poland
| | - Maksym Mackiewicz
- Institute of Archaeology, University of Wroclaw, Wrocław 50-137, Poland
| | - Artur Rapiński
- Institute of Archaeology, Silesian University in Opava, Opava 746 01, Czech Republic
| | - Stephany Leach
- Department of Archaeology, University of Exeter, Exeter EX4 4QE, UK
| | - Ignacio Soriano
- Departament de Prehistòria, Universitat Autònoma de Barcelona, Cerdanyola del Vallès 08193, Spain
| | - Katina T Lillios
- Department of Anthropology, University of Iowa, Iowa City, Iowa 52240, USA
| | - João Luís Cardoso
- Centro de Arqueologia, Universidade de Lisboa, Lisboa 1600-214, Portugal
- Universidade Aberta, Lisboa 1269-001, Portugal
| | | | - Piotr Włodarczak
- Institute of Archaeology and Ethnology, Polish Academy of Sciences, Kraków 31-016, Poland
| | - T Douglas Price
- Laboratory for Archaeological Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
| | - Pilar Prieto
- University of Santiago de Compostela, Santiago de Compostela 15782, Spain
| | - Pierre-Jérôme Rey
- UMR 5204 Laboratoire Edytem, Université Savoie Mont Blanc, Chambéry 73376, France
| | - Roberto Risch
- Departament de Prehistòria, Universitat Autònoma de Barcelona, Cerdanyola del Vallès 08193, Spain
| | - Manuel A Rojo Guerra
- Department of Prehistory and Archaeology, Faculty of Philosophy and Letters, Valladolid University, Valladolid 47011, Spain
| | - Aurore Schmitt
- UMR 7268 ADES, CNRS, Aix-Marseille Univ, EFS, Faculté de médecine Nord, Marseille 13015, France
| | - Joël Serralongue
- Service archéologique, Conseil Général de la Haute-Savoie, Annecy 74000, France
| | - Ana Maria Silva
- Laboratory of Prehistory, Research Center for Anthropology and Health, Department of Life Science, University of Coimbra, Coimbra 3000-456, Portugal
| | - Václav Smrčka
- Institute for History of Medicine and Foreign Languages, First Faculty of Medicine, Charles University, Prague 121 08, Czech Republic
| | - Luc Vergnaud
- ANTEA Bureau d'étude en Archéologie, Habsheim 68440, France
| | - João Zilhão
- Centro de Arqueologia, Universidade de Lisboa, Lisboa 1600-214, Portugal
- Institució Catalana de Recerca i Estudis Avançats, Barcelona 08010, Spain
- Departament d'Història i Arqueologia, Universitat de Barcelona, Barcelona 08001, Spain
| | - David Caramelli
- Department of Biology, University of Florence, Florence 50121, Italy
| | - Thomas Higham
- Oxford Radiocarbon Accelerator Unit, RLAHA, University of Oxford, Oxford OX1 3QY, UK
| | - Mark G Thomas
- Research Department of Genetics, Evolution and Environment, University College London, London WC1E 6BT, UK
| | - Douglas J Kennett
- Department of Anthropology & Institute for Energy and the Environment, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
| | - Harry Fokkens
- Faculty of Archaeology, Leiden University, 2333 CC Leiden, The Netherlands
| | - Volker Heyd
- Department of Archaeology and Anthropology, University of Bristol, Bristol BS8 1UU, UK
- Department of Philosophy, History, Culture and Art Studies, Section of Archaeology, University of Helsinki, Helsinki 00014, Finland
| | | | | | - Philipp W Stockhammer
- Institut für Vor- und Frühgeschichtliche Archäologie und Provinzialrömische Archäologie, Ludwig-Maximilians-Universität München, Munich 80539, Germany
- Max Planck Institute for the Science of Human History, Jena 07745, Germany
| | - Johannes Krause
- Max Planck Institute for the Science of Human History, Jena 07745, Germany
| | - Ron Pinhasi
- Earth Institute, University College Dublin, Dublin 4, Ireland
- Department of Anthropology, University of Vienna, Vienna 1090, Austria
| | - Wolfgang Haak
- Max Planck Institute for the Science of Human History, Jena 07745, Germany
- Australian Centre for Ancient DNA, School of Biological Sciences, University of Adelaide, Adelaide 5005, South Australia, Australia
| | - Ian Barnes
- Department of Earth Sciences, Natural History Museum, London SW7 5BD, UK
| | - Carles Lalueza-Fox
- Institute of Evolutionary Biology, CSIC-Universitat Pompeu Fabra, Barcelona 08003, Spain
| | - David Reich
- Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA
- Howard Hughes Medical Institute, Harvard Medical School, Boston, Massachusetts 02115, USA
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