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16 results on '"Peter, de Barros Damgaard"'

1. Population genomics of the Viking world

Author

Inna Potekhina, Simon Rasmussen, Maeve Sikora, Sabine Sten, Gordon Turner-Walker, Jörgen Gustafsson, Jade Cheng, Per Holck, Pasquale Favia, Anders Albrechtsen, Julie Gibson, Monika Bajka, Mads Dengsø Jessen, Otto Uldum, Martin Sikora, Ceri Falys, Charlotte Hedenstierna Jonson, Mark Redknap, Tamara Pushkina, Rasmus Nielsen, Claude Bhérer, Enrico Cappellini, Helene Wilhelmson, Morten Søvsø, Wiesław Bogdanowicz, Fernando Racimo, Jan Bill, Ashot Margaryan, Vayacheslav Moiseyev, Marie Allen, Louise Loe, Tom Christensen, Raili Allmäe, Mark Collard, M. Thomas P. Gilbert, Thorfinn Sand Korneliussen, Eske Willerslev, Ida Moltke, Magdalena M. Buś, Ludovic Orlando, Inge Lundstrøm, Alexandra P. Buzhilova, Jette Arneborg, Marie Louise Jørkov, Daniel Lawson, Neil Price, Peter Pentz, Anne Pedersen, Gabriel Renaud, Jilong Ma, Morten E. Allentoft, Ole Kastholm, Ingrid Mainland, Jesper Stenderup, Hugh McColl, J. Víctor Moreno-Mayar, Anna K. Fotakis, Gabriele Scorrano, Allison M. Fox, Thomas Werge, Natalia Grigoreva, Italo M. Muntoni, Sturla Ellingvåg, Símun V. Arge, Niels Lynnerup, Denis Pezhemsky, Andres Ingason, Hildur Gestsdóttir, Linzi Simpson, Katrine Højholt Iversen, Peter de Barros Damgaard, Daniel G. Bradley, Yvonne Magnusson, Caroline Arcini, Jüri Peets, Rui Martiniano, Martyna Molak, Marek Florek, Søren M. Sindbæk, Mikkel Winther Pedersen, Lotte Hedeager, Kristian Kristiansen, Emil Jørsboe, Lara M. Cassidy, Maria Vretemark, Ingrid Gustin, Birgitte Skar, Lisa Strand, Dariusz Błaszczyk, Berit Schütz, Margaryan, Ashot [0000-0002-2576-2429], Lawson, Daniel J [0000-0002-5311-6213], Rasmussen, Simon [0000-0001-6323-9041], Moltke, Ida [0000-0001-7052-8554], Jørsboe, Emil [0000-0002-0593-7906], Korneliussen, Thorfinn [0000-0001-7576-5380], Wilhelmson, Helene [0000-0002-8422-2369], Renaud, Gabriel [0000-0002-0630-027X], Bhérer, Claude [0000-0002-2744-7246], Molak, Martyna [0000-0001-5068-8649], Buzhilova, Alexandra [0000-0001-6398-2177], Albrechtsen, Anders [0000-0001-7306-031X], Falys, Ceri [0000-0003-1903-9573], Strand, Lisa [0000-0002-4245-6298], Florek, Marek [0000-0002-9917-710X], Magnusson, Yvonne [0000-0002-7076-2583], Collard, Mark [0000-0002-2725-4989], Bradley, Daniel G [0000-0001-7335-7092], Nielsen, Rasmus [0000-0003-0513-6591], Werge, Thomas [0000-0003-1829-0766], Willerslev, Eske [0000-0002-7081-6748], Apollo - University of Cambridge Repository, Anthropologie Moléculaire et Imagerie de Synthèse (AMIS), Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS), Centre National de la Recherche Scientifique (CNRS)-Université Toulouse III - Paul Sabatier (UT3), and Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées

Subjects
Gene Flow, Male, [SDV]Life Sciences [q-bio], Human Migration, Population, Greenland, Datasets as Topic, Scandinavian and Nordic Countries, Diaspora, Gene flow, Population genomics, Danish, Evolution, Molecular, 03 medical and health sciences, Young Adult, Spatio-Temporal Analysis, Humans, 0601 history and archaeology, Selection, Genetic, education, ComputingMilieux_MISCELLANEOUS, Alleles, 030304 developmental biology, Lactase, 0303 health sciences, education.field_of_study, Multidisciplinary, 060102 archaeology, Genome, Human, Immunity, 06 humanities and the arts, Genomics, language.human_language, History, Medieval, Geography, Ancient DNA, Genetics, Population, England, Genetic structure, Viking Age, language, Ethnology, Ireland
Abstract

The Viking maritime expansion from Scandinavia (Denmark, Norway, and Sweden) marks one of the swiftest and most far-flung cultural transformations in global history. During this time (c. 750 to 1050 CE), the Vikings reached most of western Eurasia, Greenland, and North America, and left a cultural legacy that persists till today. To understand the genetic structure and influence of the Viking expansion, we sequenced the genomes of 442 ancient humans from across Europe and Greenland ranging from the Bronze Age (c. 2400 BC) to the early Modern period (c. 1600 CE), with particular emphasis on the Viking Age. We find that the period preceding the Viking Age was accompanied by foreign gene flow into Scandinavia from the south and east: spreading from Denmark and eastern Sweden to the rest of Scandinavia. Despite the close linguistic similarities of modern Scandinavian languages, we observe genetic structure within Scandinavia, suggesting that regional population differences were already present 1,000 years ago. We find evidence for a majority of Danish Viking presence in England, Swedish Viking presence in the Baltic, and Norwegian Viking presence in Ireland, Iceland, and Greenland. Additionally, we see substantial foreign European ancestry entering Scandinavia during the Viking Age. We also find that several of the members of the only archaeologically well-attested Viking expedition were close family members. By comparing Viking Scandinavian genomes with present-day Scandinavian genomes, we find that pigmentation-associated loci have undergone strong population differentiation during the last millennia. Finally, we are able to trace the allele frequency dynamics of positively selected loci with unprecedented detail, including the lactase persistence allele and various alleles associated with the immune response. We conclude that the Viking diaspora was characterized by substantial foreign engagement: distinct Viking populations influenced the genomic makeup of different regions of Europe, while Scandinavia also experienced increased contact with the rest of the continent.

Published
2020
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2. Diverse variola virus (smallpox) strains were widespread in northern Europe in the Viking Age

Author

Anders J. Hansen, Yvonne Magnusson, Martin Sikora, Barbara Mühlemann, Ceri Falys, Eske Willerslev, Jan Bill, Peter de Barros Damgaard, Marie Louise Jørkov, Geoffrey L. Smith, Christian Drosten, Lasse Vinner, Morten E. Allentoft, Hannes Schroeder, Alexandra P. Buzhilova, Sofie Holtsmark Nielsen, Vyacheslav Moiseyev, Terry Jones, Ashot Margaryan, Constanza de la Fuente Castro, Lisa Strand, Gerd Sutter, Ron A. M. Fouchier, Tamara Pushkina, Helene Wilhelmson, Palle Østergaard Sørensen, Valeri Khartanovich, Ingrid Gustin, Derek J. Smith, and Virology

Subjects
Most recent common ancestor, viruses, Genome, Viral, Biology, complex mixtures, 03 medical and health sciences, medicine, Smallpox, Humans, 0601 history and archaeology, Clade, 030304 developmental biology, 0303 health sciences, Multidisciplinary, 060102 archaeology, virus diseases, 06 humanities and the arts, Biological evolution, Variola virus, medicine.disease, Virology, Biological Evolution, History, Medieval, 3. Good health, Europe, Viking Age, Host adaptation
Abstract

Humans have a notable capacity to withstand the ravages of infectious diseases. Smallpox killed millions of people but drove Jenner's invention of vaccination, which eventually led to the annihilation of this virus, declared in 1980. To investigate the history of smallpox, Mühlemann et al. obtained high-throughput shotgun sequencing data from 1867 human remains ranging from >31,000 to 150 years ago (see the Perspective by Alcamí). Thirteen positive samples emerged, 11 of which were northern European Viking Age people (6th to 7th century CE). Although the sequences were patchy and incomplete, four could be used to infer a phylogenetic tree. This showed distinct Viking Age lineages with multiple gene inactivations. The analysis pushes back the date of the earliest variola infection in humans by ∼1000 years and reveals the existence of a previously unknown virus clade. This is the author’s version of the work. It is posted here by permission of the AAAS for personal use, not for redistribution.

Published
2020
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3. The population history of northeastern Siberia since the Pleistocene

Author

Vladimir V. Pitulko, Rasmus Nielsen, Michaël Peyrot, Carsten Rahbek, Sergey B. Slobodin, Gabriel Renaud, Charlotte Primeau, Qiaomei Fu, Simon Rasmussen, Sergey Vasilyev, Anna Wessman, Verner Alexandersen, Lasse Vinner, David J. Meltzer, Margarita Gerasimova, Kristian Kristiansen, Vyacheslav G. Chasnyk, Morten Meldgaard, Peter de Barros Damgaard, Karl-Göran Sjögren, Elena Y. Pavlova, Kristiina Mannermaa, P. S. Grebenyuk, Alexander Yu. Fedorchenko, Marta Mirazón Lahr, Hugh McColl, Ashot Margaryan, Constanza de la Fuente Castro, Melinda A. Yang, Pavel A. Nikolskiy, Nurbol Baimukhanov, Mikko Putkonen, Laurent Excoffier, Andrei V. Gromov, Laura Arppe, Eske Willerslev, Vitor C. Sousa, Jukka U. Palo, Boris Malyarchuk, Valeriy I. Khartanovich, Antti Sajantila, Isabelle Dupanloup, Rui Martiniano, David Nogués-Bravo, Ripan S. Malhi, Martin Sikora, A. I. Lebedintsev, Konstantinos Giampoudakis, Vyacheslav Moiseyev, Richard Durbin, Tarja Sundell, Morten E. Allentoft, Elizaveta Veselovskaya, Guus Kroonen, Mirazon Lahr, Mirazon Lahr [0000-0001-5752-5770], Durbin, Richard [0000-0002-9130-1006], Willerslev, Eske [0000-0002-7081-6748], and Apollo - University of Cambridge Repository

Subjects
Male, Neanderthal, Asia, Pleistocene, Human Migration, Population, Archaeological record, Population genetics, 03 medical and health sciences, 0302 clinical medicine, biology.animal, Journal Article, Humans, DNA, Ancient, education, Holocene, History, Ancient, 030304 developmental biology, History, 15th Century, 0303 health sciences, education.field_of_study, Multidisciplinary, biology, Genome, Human, Research Support, Non-U.S. Gov't, Gene Pool, History, Medieval, Europe, Siberia, Geography, Haplotypes, Historical Article, Period (geology), Indians, North American, Biological dispersal, Ethnology, 570 Life sciences, 030217 neurology & neurosurgery
Abstract

Northeastern Siberia has been inhabited by humans for more than 40,000 years but its deep population history remains poorly understood. Here we investigate the late Pleistocene population history of northeastern Siberia through analyses of 34 newly recovered ancient genomes that date to between 31,000 and 600 years ago. We document complex population dynamics during this period, including at least three major migration events: an initial peopling by a previously unknown Palaeolithic population of ‘Ancient North Siberians’ who are distantly related to early West Eurasian hunter-gatherers; the arrival of East Asian-related peoples, which gave rise to ‘Ancient Palaeo-Siberians’ who are closely related to contemporary communities from far-northeastern Siberia (such as the Koryaks), as well as Native Americans; and a Holocene migration of other East Asian-related peoples, who we name ‘Neo-Siberians’, and from whom many contemporary Siberians are descended. Each of these population expansions largely replaced the earlier inhabitants, and ultimately generated the mosaic genetic make-up of contemporary peoples who inhabit a vast area across northern Eurasia and the Americas. Analyses of 34 ancient genomes from northeastern Siberia, dating to between 31,000 and 600 years ago, reveal at least three major migration events in the late Pleistocene population history of the region.

Published
2019
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4. Pretreatment: Improving Endogenous Ancient DNA Yields Using a Simple Enzymatic Predigestion Step

Author

Hannes, Schroeder, Peter, de Barros Damgaard, and Morten E, Allentoft

Subjects
Humans, DNA Contamination, DNA, Ancient, Endopeptidase K, Tooth, Bone and Bones, Edetic Acid
Abstract

Ancient DNA samples generally contain a mixture of both endogenous and exogenous (contaminant) DNA. The authentic endogenous DNA content varies widely between samples and substrates but usually constitutes only a small fraction of the total DNA, while the remainder comprises contamination deriving from bacteria, fungi, and other microorganisms and in some cases also modern human DNA. Recently, several protocols have been developed to improve access to the endogenous DNA fraction by decreasing the exogenous fraction prior to extraction. The most common of these involve pretreatment with single or multiple washes with weak sodium phosphate or sodium hypochlorite (bleach) solutions, as described in Chapter 2 . Here, we present an alternative, less aggressive pretreatment protocol that uses a brief predigestion step in an EDTA-based lysis buffer to increase the endogenous fraction prior to extraction.

Published
2019

5. Shotgun sequencing of clinical biofilm following scanning electron microscopy identifies bacterial community composition

Author

Blaine Gabriel Fritz, Peter de Barros Damgaard, Klaus Qvortrup, Sofie Holtsmark Nielsen, Lars Bjørndal, Thomas Bjarnsholt, Camilla Stavnsbjerg, and Merete Markvart

Subjects
Microbiology (medical), Scanning electron microscope, medicine.disease_cause, Microbiology, 03 medical and health sciences, Microscopy, medicine, Humans, Immunology and Allergy, 030304 developmental biology, 0303 health sciences, Bacteria, General Immunology and Microbiology, biology, 030306 microbiology, Pseudomonas aeruginosa, Shotgun sequencing, Biofilm, Biodiversity, General Medicine, biology.organism_classification, Infectious Diseases, Community composition, Metagenomics, Biofilms, Metagenome
Abstract

Bacterial biofilm infections often involve aggregates of bacteria heterogeneously distributed throughout a tissue or on a surface (such as an implanted medical device). Identification of a biofilm infection requires direct visualization via microscopy, followed by characterization of the microbial community by culturing or sequencing-based approaches. A sample, therefore, must be divided prior to analysis, often leading to inconsistent results. We demonstrate a combined approach, using scanning electron microscopy and next-generation shotgun sequencing, to visually identify a biofilm and characterize the microbial community, without dividing the sample. A clinical sample recovered from a patient following a dental root-filling procedure was prepared and visualized by scanning electron microscopy. DNA was then extracted from the sample several years later and analyzed by shotgun sequencing. The method was subsequently validated on in vitro cultures of Pseudomonas aeruginosa biofilm. Between 19 and 21 different genera and species were identified in the clinical sample with an estimated relative abundance greater than 1% by two different estimation approaches. Only eight genera identified were not associated with endodontic infections. This provides a proof-of-concept for a dual, microscopy and sequencing-based approach to identify and characterize bacterial biofilms, which could also easily be implemented in other scientific fields.

Published
2019
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6. The prehistoric peopling of Southeast Asia

Author

Hsiao-chun Hung, Tadayuki Masuyama, Christophe Pottier, Farhang Aghakhanian, Thi Minh Tran, Anne-Marie Bacon, Lasse Vinner, Andaine Seguin-Orlando, Laura L. Shackelford, Thi Mai Huong Nguyen, Tsunehiko Hanihara, Anh Nguyen, Hajime Ishida, Ashot Margaryan, Yasuhiro Yamada, Thongsa Sayavongkhamdy, Hiroki Shibata, Constanza de la Fuente Castro, Rasmi Shoocongdej, Eske Willerslev, Silas Anselm Rasmussen, Peter de Barros Damgaard, Patcharee Lertrit, Nobuo Shigehara, Marta Mirazón Lahr, Jean Christophe Galipaud, Jean Luc Ponche, Thomas Higham, Shigeki Nakagome, Sally Wasef, Uffe Gram Wilken, David M. Lambert, Thibaut Devièse, Takashi Gakuhari, Robert Foley, George van Driem, Atsushi Tajima, Ludovic Orlando, Bérénice Bellina-Pryce, Morten E. Allentoft, Charles Higham, Hiroki Oota, J. Víctor Moreno-Mayar, Anna-Sapfo Malaspinas, Huu Nghia Truong, Giang Hai Nguyen, Maude E. Phipps, Fernando Racimo, Rebecca Kinaston, Elise Patole-Edoumba, Supannee Kaewsutthi, Ketut Wiradnyana, Ana Prohaska, Fabrice Demeter, Viengkeo Souksavatdy, Shaiful Shahidan, Hugh McColl, Mokhtar Saidin, Hallie R. Buckley, Thorfinn Sand Korneliussen, Minoru Yoneda, Atsushi Toyoda, Takehiro Sato, Hiromi Matsumae, Philippe Duringer, Martin Sikora, Eco-Anthropologie et Ethnobiologie (EAE), Muséum national d'Histoire naturelle (MNHN)-Université Paris Diderot - Paris 7 (UPD7)-Centre National de la Recherche Scientifique (CNRS), Préhistoire et Technologie (PréTech), Université Paris Nanterre (UPN)-Centre National de la Recherche Scientifique (CNRS), Section for GeoGenetics, Globe Institute, Faculty of Health and Medical Sciences, University of Copenhagen = Københavns Universitet (KU)-University of Copenhagen = Københavns Universitet (KU)-Faculty of Health and Medical Sciences, University of Copenhagen = Københavns Universitet (KU)-University of Copenhagen = Københavns Universitet (KU), Université Silpakorn, Department of Museums, Historic Buildings and Archaeology, Ministry of Information and Culture, Département des musées et de l'archéologie, Ministère de la Culture et de l?Information, Kyoto University [Kyoto], Dynamique de l'évolution humaine : individus, populations, espèces [Paris] (DEHIPE), Centre National de la Recherche Scientifique (CNRS), Centre de géochimie de la surface (CGS), Institut national des sciences de l'Univers (INSU - CNRS)-Université Louis Pasteur - Strasbourg I-Centre National de la Recherche Scientifique (CNRS), Institut de chimie et procédés pour l'énergie, l'environnement et la santé (ICPEES), Université de Strasbourg (UNISTRA)-Matériaux et nanosciences d'Alsace (FMNGE), Institut de Chimie du CNRS (INC)-Université de Strasbourg (UNISTRA)-Université de Haute-Alsace (UHA) Mulhouse - Colmar (Université de Haute-Alsace (UHA))-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Chimie du CNRS (INC)-Université de Strasbourg (UNISTRA)-Université de Haute-Alsace (UHA) Mulhouse - Colmar (Université de Haute-Alsace (UHA))-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), University of Illinois at Urbana Champaign (UIUC), University of Illinois at Urbana-Champaign [Urbana], University of Illinois System-University of Illinois System, Museum d'Histoire Naturelle de La Rochelle, Service d'Anatomo-Cyto-Pathologie et de NeuroPathologie [Hôpital de la Timone - APHM] (ACPNP), Aix Marseille Université (AMU)- Hôpital de la Timone [CHU - APHM] (TIMONE), Patrimoines Locaux et Gouvernance (PALOC), Muséum national d'Histoire naturelle (MNHN)-Institut de Recherche pour le Développement (IRD), Archéologies et Sciences de l'Antiquité (ArScAn), Université Paris 1 Panthéon-Sorbonne (UP1)-Université Paris Nanterre (UPN)-Ministère de la Culture et de la Communication (MCC)-Centre National de la Recherche Scientifique (CNRS), Department of Anatomy, University of Otago, Dunedin, University of Otago [Dunedin, Nouvelle-Zélande], École française d'Extrême-Orient (EFEO), Ctr Biol Sequence Anal, Technical University of Denmark [Lyngby] (DTU), Research Laboratory for Archaeology and the History of Art, University of Oxford [Oxford], Institut de Biologia Evolutiva (UPF-CSIC), Max-Planck-Institut für evolutionäre Anthropologie (MPI-EVA), Max-Planck-Gesellschaft, Silpakorn University [Bangkok, Thaïlande], Université Paris Diderot - Paris 7 (UPD7)-Centre National de la Recherche Scientifique (CNRS), Laboratoire d'Analyse et de Mathématiques Appliquées (LAMA), Université Paris-Est Marne-la-Vallée (UPEM)-Fédération de Recherche Bézout-Université Paris-Est Créteil Val-de-Marne - Paris 12 (UPEC UP12)-Centre National de la Recherche Scientifique (CNRS), Centre National de la Recherche Scientifique (CNRS)-Université Louis Pasteur - Strasbourg I-Institut national des sciences de l'Univers (INSU - CNRS), Université de Strasbourg (UNISTRA)-Centre National de la Recherche Scientifique (CNRS)-Matériaux et nanosciences d'Alsace, Université de Strasbourg (UNISTRA)-Université de Haute-Alsace (UHA) Mulhouse - Colmar (Université de Haute-Alsace (UHA))-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Université de Strasbourg (UNISTRA)-Université de Haute-Alsace (UHA) Mulhouse - Colmar (Université de Haute-Alsace (UHA))-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Université Panthéon-Sorbonne (UP1)-Université Paris Nanterre (UPN)-Institut national de recherches archéologiques préventives (Inrap)-Ministère de la Culture et de la Communication (MCC)-Centre National de la Recherche Scientifique (CNRS), Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Haute-Alsace (UHA) Mulhouse - Colmar (Université de Haute-Alsace (UHA))-Université de Strasbourg (UNISTRA)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Haute-Alsace (UHA) Mulhouse - Colmar (Université de Haute-Alsace (UHA))-Université de Strasbourg (UNISTRA), University of Copenhagen = Københavns Universitet (UCPH)-University of Copenhagen = Københavns Universitet (UCPH)-Faculty of Health and Medical Sciences, University of Copenhagen = Københavns Universitet (UCPH)-University of Copenhagen = Københavns Universitet (UCPH), Université de Strasbourg (UNISTRA)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)-Matériaux et nanosciences d'Alsace (FMNGE), Université de Strasbourg (UNISTRA)-Université de Haute-Alsace (UHA) Mulhouse - Colmar (Université de Haute-Alsace (UHA))-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)-Université de Strasbourg (UNISTRA)-Université de Haute-Alsace (UHA) Mulhouse - Colmar (Université de Haute-Alsace (UHA))-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), University of Illinois System, Université Paris 1 Panthéon-Sorbonne (UP1)-Université Paris 8 Vincennes-Saint-Denis (UP8)-Université Paris Nanterre (UPN)-Ministère de la Culture et de la Communication (MCC)-Institut national de recherches archéologiques préventives (Inrap)-Centre National de la Recherche Scientifique (CNRS), Danmarks Tekniske Universitet = Technical University of Denmark (DTU), University of Oxford, Kyoto University, Université de Strasbourg (UNISTRA)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)-Matériaux et Nanosciences Grand-Est (MNGE), Université Paris 1 Panthéon-Sorbonne (UP1)-Université Paris 8 Vincennes-Saint-Denis (UP8)-Université Paris Nanterre (UPN)-Ministère de la Culture et de la Communication (MCC)-Centre National de la Recherche Scientifique (CNRS), McColl, Hugh [0000-0002-7568-4270], Racimo, Fernando [0000-0002-5025-2607], Demeter, Fabrice [0000-0002-1288-5534], Gakuhari, Takashi [0000-0003-1855-8371], Gram Wilken, Uffe [0000-0003-3434-7312], Seguin-Orlando, Andaine [0000-0002-8265-3229], de la Fuente Castro, Constanza [0000-0002-2857-3615], Wasef, Sally [0000-0002-7207-7395], Sayavongkhamdy, Thongsa [0000-0001-9467-0811], Korneliussen, Thorfinn [0000-0001-7576-5380], Prohaska, Ana [0000-0001-5459-6186], Margaryan, Ashot [0000-0002-2576-2429], Kaewsutthi, Supannee [0000-0002-3959-8420], Lertrit, Patcharee [0000-0002-4801-3834], Hung, Hsiao-Chun [0000-0001-5794-3040], Minh Tran, Thi [0000-0001-8833-693X], Nghia Truong, Huu [0000-0003-3291-5646], Shahidan, Shaiful [0000-0002-8367-3539], Matsumae, Hiromi [0000-0003-1858-3833], Ishida, Hajime [0000-0002-5781-7914], Tajima, Atsushi [0000-0001-6808-5491], Toyoda, Atsushi [0000-0002-0728-7548], Nakagome, Shigeki [0000-0001-9613-975X], Deviese, Thibaut [0000-0003-0495-7398], Duringer, Philippe [0000-0001-6213-5726], Patole-Edoumba, Elise [0000-0002-9378-2202], Bellina-Pryce, Bérénice [0000-0001-8790-1394], Galipaud, Jean-Christophe [0000-0003-3546-5265], Kinaston, Rebecca [0000-0001-7697-4950], Higham, Tom [0000-0002-5949-598X], Foley, Robert A [0000-0003-0479-3039], Lahr, Marta Mirazón [0000-0001-5752-5770], Orlando, Ludovic [0000-0003-3936-1850], Sikora, Martin [0000-0003-2818-8319], Lambert, David M [0000-0002-5821-3637], Willerslev, Eske [0000-0002-7081-6748], and Apollo - University of Cambridge Repository

Subjects
0301 basic medicine, [SHS.ARCHEO]Humanities and Social Sciences/Archaeology and Prehistory, Human Migration, Population, Southeast asian, Indigenous, Prehistory, 03 medical and health sciences, 0302 clinical medicine, Asian People, Humans, East Asia, 14. Life underwater, DNA, Ancient, education, Asia, Southeastern, History, Ancient, ComputingMilieux_MISCELLANEOUS, 2. Zero hunger, education.field_of_study, [SDV.GEN]Life Sciences [q-bio]/Genetics, Multidisciplinary, Genome, Human, business.industry, Human migration, Genetic Variation, Sequence Analysis, DNA, Hoabinhian, 030104 developmental biology, Agriculture, Ethnology, [SHS.HIST]Humanities and Social Sciences/History, business, 030217 neurology & neurosurgery
Abstract

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

Published
2018
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7. Ancient Biomolecules and Evolutionary Inference

Author

Richard P. Evershed, Eske Willerslev, Enrico Cappellini, Juergen Cox, Simon Hammann, Lasse Vinner, Morten E. Allentoft, Yucheng Wang, Peter de Barros Damgaard, Martin Sikora, Frido Welker, Mikkel Winther Pedersen, J. Víctor Moreno-Mayar, Julie Dunne, Ana Prohaska, Mélanie Roffet-Salque, Petra Gutenbrunner, Fernando Racimo, and Melissa Ilardo

Subjects
Proteomics, 0301 basic medicine, Computer science, Inference, Extinction, Biological, 01 natural sciences, Biochemistry, paleoproteomics, Evolution, Molecular, 03 medical and health sciences, ancient genomics, ancient lipids, Animals, Humans, ancient proteins, DNA, Ancient, ancient DNA, Phylogeny, Fossils, 010401 analytical chemistry, Paleontology, Proteins, Genomics, Biological Evolution, Lipids, Data science, Field (geography), 0104 chemical sciences, 030104 developmental biology, Ancient DNA, paleogenomics, Experimental methods
Abstract

Over the last decade, studies of ancient biomolecules-particularly ancient DNA, proteins, and lipids-have revolutionized our understanding of evolutionary history. Though initially fraught with many challenges, the field now stands on firm foundations. Researchers now successfully retrieve nucleotide and amino acid sequences, as well as lipid signatures, from progressively older samples, originating from geographic areas and depositional environments that, until recently, were regarded as hostile to long-term preservation of biomolecules. Sampling frequencies and the spatial and temporal scope of studies have also increased markedly, and with them the size and quality of the data sets generated. This progress has been made possible by continuous technical innovations in analytical methods, enhanced criteria for the selection of ancient samples, integrated experimental methods, and advanced computational approaches. Here, we discuss the history and current state of ancient biomolecule research, its applications to evolutionary inference, and future directions for this young and exciting field. Expected final online publication date for the Annual Review of Biochemistry Volume 87 is June 20, 2018. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.

Published
2018
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8. 137 ancient human genomes from across the Eurasian steppes

Author

Karl-Göran Sjögren, Nina Lau, Nikolay N. Kradin, Igor Kukushkin, Arman Beisenov, Kadicha Tashbaeva, Andrey Logvin, Peter de Barros Damgaard, Irina Shevnina, Viktor K. Mertz, Ilya V. Mertz, Alexander Tkachev, Amy Goldberg, Zaruhi Khachatryan, Vyacheslav Moiyesev, Nina Marchi, Valeriy Evdokimov, Gabit Baimbetov, Valeriy Loman, Turaly Tulegenov, Evgeniy Dmitriev, Kasper Nielsen, Diimaajav Erdenebaatar, Lotte Hedeager, Levon Yepiskoposyan, Almaz Aldashev, Egor Kitov, Evelyne Heyer, Kristian Kristiansen, Victor Varfolomeev, Nurbol Baimukhanov, Enkhbayar Mijiddorj, Tereza Štolcová, Melissa A. Wilson Sayres, Sturla Ellingvåg, Dmitriy Voyakin, Gennady Afanasiev, Simon Rasmussen, Anders Gorm Pedersen, Ashyk Alpaslan, Mikkel Winther Pedersen, Ashot Margaryan, Sainbileg Undrakhbold, Z. Orozbekova, Bekmukhanbet Nurmukhanbetov, Tabaldiev Kubatbek, Eske Willerslev, Andrey Gromov, Ruslan Khaskhanov, Hakon Hakonarson, Alina Kolbina, Václav Smrčka, Rasmus Nielsen, Morten E. Allentoft, Gulmira Mukhtarova, Martin Sikora, Gabriel Renaud, J. Víctor Moreno-Mayar, Bazartseren Boldgiv, Angela M. Taravella, Tatyana Hegay, Choduraa Dorzhu, Emma Usmanova, Karol Pieta, Inga Merkyte, Alexey Kukushkin, Michaël Peyrot, Kunbolot Akmatov, Karin Margarita Frei, Vladimir I. Bazaliiskii, Thorfinn Sand Korneliussen, Alexander Goryachev, Ludovic Orlando, Andrzej W. Weber, Irina P. Panyushkina, Rana Dajani, Bazartseren Boldbaatar, Eco-Anthropologie et Ethnobiologie (EAE), Centre National de la Recherche Scientifique (CNRS)-Université Paris Diderot - Paris 7 (UPD7)-Muséum national d'Histoire naturelle (MNHN), Ctr Biol Sequence Anal, Technical University of Denmark [Lyngby] (DTU), Max Planck Institute for Evolutionary Anthropology, Max-Planck-Gesellschaft, Institute of Molecular Biology and Medicine, Irkutsk State University (ISU), The Center for Applied Genomics, Children’s Hospital of Philadelphia (CHOP ), Institute of Immunology, Uzbekistan Academy of Sciences, Laboratory for Tree-Ring Research, University of Arizona, University of Copenhagen = Københavns Universitet (KU), Dept Integrat Biol, Institut de Biologia Evolutiva (UPF-CSIC), Éco-Anthropologie (EA), Muséum national d'Histoire naturelle (MNHN)-Université Paris Diderot - Paris 7 (UPD7)-Centre National de la Recherche Scientifique (CNRS), Section for GeoGenetics, Globe Institute, Faculty of Health and Medical Sciences, University of Copenhagen = Københavns Universitet (KU)-University of Copenhagen = Københavns Universitet (KU)-Faculty of Health and Medical Sciences, University of Copenhagen = Københavns Universitet (KU)-University of Copenhagen = Københavns Universitet (KU), Max Planck Institute for Evolutionary Anthropology [Leipzig], Centre National de la Recherche Scientifique (CNRS)-Muséum national d'Histoire naturelle (MNHN)-Université Paris Diderot - Paris 7 (UPD7), Willerslev, Eske [0000-0002-7081-6748], and Apollo - University of Cambridge Repository

Subjects
0301 basic medicine, Asia, Steppe, Human Migration, Population, [SHS.ANTHRO-BIO]Humanities and Social Sciences/Biological anthropology, Ancient history, Plague (disease), White People, 03 medical and health sciences, Asian People, Bronze Age, Humans, Middle Ages, East Asia, education, History, Ancient, Phylogeny, geography, education.field_of_study, Farmers, Multidisciplinary, geography.geographical_feature_category, Genome, Human, Human migration, business.industry, Grassland, Europe, 030104 developmental biology, Iron Age, business
Abstract

For thousands of years the Eurasian steppes have been a centre of human migrations and cultural change. Here we sequence the genomes of 137 ancient humans (about 1× average coverage), covering a period of 4,000 years, to understand the population history of the Eurasian steppes after the Bronze Age migrations. We find that the genetics of the Scythian groups that dominated the Eurasian steppes throughout the Iron Age were highly structured, with diverse origins comprising Late Bronze Age herders, European farmers and southern Siberian hunter-gatherers. Later, Scythians admixed with the eastern steppe nomads who formed the Xiongnu confederations, and moved westward in about the second or third century bc, forming the Hun traditions in the fourth–fifth century ad, and carrying with them plague that was basal to the Justinian plague. These nomads were further admixed with East Asian groups during several short-term khanates in the Medieval period. These historical events transformed the Eurasian steppes from being inhabited by Indo-European speakers of largely West Eurasian ancestry to the mostly Turkic-speaking groups of the present day, who are primarily of East Asian ancestry. Sequences of 137 ancient and 502 modern human genomes illuminate the population history of the Eurasian steppes after the Bronze Age and document the replacement of Indo-European speakers of West Eurasian ancestry by Turkic-speaking groups of East Asian ancestry.

Published
2018
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9. Physiological and Genetic Adaptations to Diving in Sea Nomads

Author

Melissa Ilardo, Peter de Barros Damgaard, Andaine Seguin-Orlando, Rasmus Nielsen, Fernando Racimo, Inge C.L. van den Munckhof, Jade Cheng, Simon Rasmussen, Eske Willerslev, Martin Sikora, Aaron J. Stern, Mihai G. Netea, Leo A. B. Joosten, Thorfinn Sand Korneliussen, Suhartini Salingkat, Rob ter Horst, and Ida Moltke

Subjects
0301 basic medicine, Adult, Male, Erythrocytes, Adolescent, Diving, Vascular damage Radboud Institute for Health Sciences [Radboudumc 16], lnfectious Diseases and Global Health Radboud Institute for Molecular Life Sciences [Radboudumc 4], Biology, Polymorphism, Single Nucleotide, General Biochemistry, Genetics and Molecular Biology, Indigenous, White People, Southeast asia, Breath Holding, 03 medical and health sciences, Young Adult, All institutes and research themes of the Radboud University Medical Center, 0302 clinical medicine, Asian People, Ethnicity, Humans, 14. Life underwater, Selection, Genetic, Hypoxia, Lung, Mammalian diving reflex, Alleles, Aged, Aged, 80 and over, Natural selection, Phosphoric Diester Hydrolases, Genetic variants, Subsistence agriculture, Genetic Variation, Genomics, Organ Size, Middle Aged, Increased spleen size, Adaptation, Physiological, Oxygen, 030104 developmental biology, Phenotype, Evolutionary biology, Indonesia, Female, Adaptation, 030217 neurology & neurosurgery, Spleen
Abstract

Understanding the physiology and genetics of human hypoxia tolerance has important medical implications, but this phenomenon has thus far only been investigated in high-altitude human populations. Another system, yet to be explored, is humans who engage in breath-hold diving. The indigenous Bajau people ("Sea Nomads") of Southeast Asia live a subsistence lifestyle based on breath-hold diving and are renowned for their extraordinary breath-holding abilities. However, it is unknown whether this has a genetic basis. Using a comparative genomic study, we show that natural selection on genetic variants in the PDE10A gene have increased spleen size in the Bajau, providing them with a larger reservoir of oxygenated red blood cells. We also find evidence of strong selection specific to the Bajau on BDKRB2, a gene affecting the human diving reflex. Thus, the Bajau, and possibly other diving populations, provide a new opportunity to study human adaptation to hypoxia tolerance. VIDEO ABSTRACT.

Published
2018
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10. Ancient hepatitis B viruses from the Bronze Age to the Medieval period

Author

Irina Shevnina, Magdolna Vicze, Dalia Pokutta, Vyacheslav Moiseyev, Eske Willerslev, Anders J. Hansen, Albert D. M. E. Osterhaus, Kristian Kristiansen, Ludovic Orlando, Victor Merz, Kadicha Tashbaeva, Lasse Vinner, Barbara Mühlemann, Karl-Göran Sjögren, Andrey Epimakhov, Peter de Barros Damgaard, Irina P. Panyushkina, Egor Kitov, Nina Lau, Morten E. Allentoft, Ron A. M. Fouchier, Tsevel Bazartseren, Emma Usmanova, Andrey Logvin, Christian Drosten, Terry Jones, Bazartseren Boldgiv, Simon Rasmussen, Václav Smrčka, Dieter Glebe, Martin Sikora, Dmitry Voyakin, Derek J. Smith, T Douglas Price, Virology, Smith, Derek [0000-0002-2393-1890], Willerslev, Eske [0000-0002-7081-6748], and Apollo - University of Cambridge Repository

Subjects
0301 basic medicine, Hepatitis B virus, Asia, Genotype, Human Migration, 030106 microbiology, Biology, medicine.disease_cause, Genome, Evolution, Molecular, 03 medical and health sciences, SDG 3 - Good Health and Well-being, Phylogenetics, Bronze Age, medicine, Animals, Humans, Biologiska vetenskaper, Clade, History, Ancient, Phylogeny, Historia och arkeologi, Recombination, Genetic, Multidisciplinary, History and Archaeology, virus diseases, Hominidae, Hepatitis B, Biological Sciences, medicine.disease, History, Medieval, 3. Good health, Europe, 030104 developmental biology, Evolutionary biology, Africa, Human genome
Abstract

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

Published
2018
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11. Ancient human parvovirus B19 in Eurasia reveals its long-term association with humans

Author

Martin Sikora, Ceri Falys, Václav Smrčka, Anders J. Hansen, Ron A. M. Fouchier, Jette Arneborg, Karl-Göran Sjögren, Barbara Mühlemann, Sabine Sten, Christian Drosten, Vladimir I. Bazaliiskii, Niels Lynnerup, Wiesław Bogdanowicz, Terry Jones, Kadicha Tashbaeva, Peter de Barros Damgaard, Lasse Vinner, Morten E. Allentoft, Derek J. Smith, Ashot Margaryan, Eske Willerslev, Andrzej W. Weber, Martyna Molak, Kristian Kristiansen, Mikhail V. Sablin, Virology, Smith, Derek [0000-0002-2393-1890], Willerslev, Eske [0000-0002-7081-6748], and Apollo - University of Cambridge Repository

Subjects
0301 basic medicine, Most recent common ancestor, Genotype, viruses, 030106 microbiology, Erythema Infectiosum, Genome, Viral, Biology, paleo virology, Genome, Evolution, Molecular, 03 medical and health sciences, Basal (phylogenetics), Phylogenetics, Parvovirus B19, Human, Humans, ancient DNA, Phylogeny, Medicinsk genetik, virus evolution, Multidisciplinary, Phylogenetic tree, parvovirus B19, History, 19th Century, Sequence Analysis, DNA, History, 20th Century, Biological Sciences, 3. Good health, virology, 030104 developmental biology, Ancient DNA, Evolutionary biology, Viral evolution, Medical Genetics
Abstract

Human parvovirus B19 (B19V) is a ubiquitous human pathogen associated with a number of conditions, such as fifth disease in children and arthritis and arthralgias in adults. B19V is thought to evolve exceptionally rapidly among DNA viruses, with substitution rates previously estimated to be closer to those typical of RNA viruses. On the basis of genetic sequences up to similar to 70 years of age, the most recent common ancestor of all B19V has been dated to the early 1800s, and it has been suggested that genotype 1, the most common B19V genotype, only started circulating in the 1960s. Here we present 10 genomes (63.9-99.7% genome coverage) of B19V from dental and skeletal remains of individuals who lived in Eurasia and Greenland from similar to 0.5 to similar to 6.9 thousand years ago (kya). In a phylogenetic analysis, five of the ancient B19V sequences fall within or basal to the modern genotype 1, and five fall basal to genotype 2, showing a long-term association of B19V with humans. The most recent common ancestor of all B19V is placed similar to 12.6 kya, and we find a substitution rate that is an order of magnitude lower than inferred previously. Further, we are able to date the recombination event between genotypes 1 and 3 that formed genotype 2 to similar to 5.0-6.8 kya. This study emphasizes the importance of ancient viral sequences for our understanding of virus evolution and phylogenetics.

Published
2018

12. Population genomics of Bronze Age Eurasia

Author

Valeri Khartanovich, George McGlynn, György Pálfi, Ashot Margaryan, Paweł Dąbrowski, Morten Rasmussen, Thomas Sicheritz-Pontén, N. I. Shishlina, Rasmus Nielsen, Radosław Jarysz, Viktória Kiss, Vajk Szeverényi, Simon Rasmussen, Alexander V. Ebel, Inga Merkyte, Karin Margarita Frei, Synaru V. Trifanova, Thomas Higham, Tomasz Gralak, Jesper Stenderup, Aivar Kriiska, Søren Brunak, Martin Sikora, Paul R. Duffy, Vladislav S. Zhitenev, Niels Lynnerup, Morten E. Allentoft, T. Douglas Price, Torbjörn Ahlström, Irena Lasak, Gusztáv Tóth, Anna-Sapfo Malaspinas, Justyna Baron, Ruzan Mkrtchyan, Lehti Saag, Dalia Pokutta, Levon Yepiskoposyan, Magdolna Vicze, Łukasz Pospieszny, Peter de Barros Damgaard, Karl-Göran Sjögren, Jan Kolář, Václav Smrčka, Tamás Hajdu, Philippe Della Casa, Gisela Grupe, Eske Willerslev, Andrey Gromov, Mikhail V. Sablin, Lise Harvig, Alexandr Khokhlov, Mait Metspalu, Andrey Epimakhov, Algimantas Merkevicius, David Chivall, László Paja, Ludovic Orlando, Vasilii I. Soenov, Vyacheslav Moiseyev, Mirosław Furmanek, Liivi Varul, Kristian Kristiansen, Lasse Vinner, Cristina Longhi, Stanisław Gronkiewicz, and Hannes Schroeder

Subjects
Archaeogenetics, Asia, Human Migration, Light skin, Population, Population genetics, Skin Pigmentation, Polymorphism, Single Nucleotide, White People, Population genomics, Lactose Intolerance, Asian People, Gene Frequency, Bronze Age, Cultural Evolution, Humans, education, History, Ancient, Language, education.field_of_study, Multidisciplinary, Human migration, business.industry, Fossils, Genome, Human, Phenotypic trait, DNA, Genomics, Europe, Genetics, Population, Archaeology, Evolutionary biology, business
Abstract

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

Published
2015
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13. Comparing Ancient DNA Preservation in Petrous Bone and Tooth Cementum

Author

Niels Lynnerup, Henrik B. Hansen, Peter de Barros Damgaard, Eske Willerslev, Ashot Margaryan, Morten E. Allentoft, and Jesper Stenderup

Subjects
0301 basic medicine, Teeth, Dentistry, lcsh:Medicine, Biochemistry, 0302 clinical medicine, Medicine and Health Sciences, lcsh:Science, Musculoskeletal System, Dental Cementum, Multidisciplinary, DNA methylation, Ancient DNA, Anatomy, Skeleton (computer programming), Chromatin, Nuclear DNA, Nucleic acids, medicine.anatomical_structure, Connective Tissue, Epigenetics, DNA modification, Chromatin modification, Research Article, Chromosome biology, Mitochondrial DNA, Cell biology, DNA damage, Biology, DNA, Mitochondrial, 03 medical and health sciences, stomatognathic system, medicine, Genetics, Humans, 030216 legal & forensic medicine, Cementum, DNA, Ancient, Bone, Skeleton, business.industry, lcsh:R, Skull, Biology and Life Sciences, Paleontology, DNA, Earth sciences, 030104 developmental biology, Biological Tissue, Jaw, lcsh:Q, Dental cementum, Gene expression, business, Paleogenetics, Tooth, Digestive System, Head, Petrous Bone
Abstract

Large-scale genomic analyses of ancient human populations have become feasible partly due to refined sampling methods. The inner part of petrous bones and the cementum layer in teeth roots are currently recognized as the best substrates for such research. We present a comparative analysis of DNA preservation in these two substrates obtained from the same human skulls, across a range of different ages and preservation environments. Both substrates display significantly higher endogenous DNA content (average of 16.4% and 40.0% for teeth and petrous bones, respectively) than parietal skull bone (average of 2.2%). Despite sample-to-sample variation, petrous bone overall performs better than tooth cementum (p = 0.001). This difference, however, is driven largely by a cluster of viking skeletons from one particular locality, showing relatively poor molecular tooth preservation (

Published
2016
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14. Improving access to endogenous DNA in ancient bones and teeth

Author

Ludovic Orlando, Morten E. Allentoft, Ashot Margaryan, Peter de Barros Damgaard, Eske Willerslev, and Hannes Schroeder

Subjects
0106 biological sciences, Molecular complexity, Genomic research, Genomic data, Human bone, Genomics, Endogeny, Biology, 010603 evolutionary biology, 01 natural sciences, Genome, DNA, Mitochondrial, Article, Bone and Bones, Standard procedure, Paleontology, 03 medical and health sciences, chemistry.chemical_compound, Bone material, medicine, Humans, Cementum, 030304 developmental biology, 0303 health sciences, Multidisciplinary, Fossils, medicine.anatomical_structure, Ancient DNA, Biochemistry, chemistry, Archaeology, Evolutionary biology, Tooth, DNA
Abstract

Poor DNA preservation is the most limiting factor in ancient genomic research. In the vast majority of ancient bones and teeth, endogenous DNA molecules only represent a minor fraction of the whole DNA extract, rendering traditional shot-gun sequencing approaches cost-ineffective for whole-genome characterization. Based on ancient human bone samples from temperate and tropical environments, we show that an initial EDTA-based enzymatic 'pre-digestion' of powdered bone increases the proportion of endogenous DNA several fold. By performing the pre-digestion step between 30 min and 6 hours on five bones, we identify the optimal pre-digestion time and document an average increase of 2.7 times in the endogenous DNA fraction after 1 hour of pre-digestion. With longer pre-digestion times, the increase is asymptotic while molecular complexity decreases. We repeated the experiment with n=21 and t=15-30', and document a significant increase in endogenous DNA content (one-sided paired t-test: p=0.009). We advocate the implementation of a short pre-digestion step as a standard procedure in ancient DNA extractions from bone material. Finally, we demonstrate on 14 ancient teeth that crushed cementum of the roots contains up to 14 times more endogenous DNA than the dentine. Our presented methodological guidelines considerably advance the ability to characterize ancient genomes.

Published
2015
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15. POPULATION GENETICS. Genomic evidence for the Pleistocene and recent population history of Native Americans

Author

Maanasa, Raghavan, Matthias, Steinrücken, Kelley, Harris, Stephan, Schiffels, Simon, Rasmussen, Michael, DeGiorgio, Anders, Albrechtsen, Cristina, Valdiosera, María C, Ávila-Arcos, Anna-Sapfo, Malaspinas, Anders, Eriksson, Ida, Moltke, Mait, Metspalu, Julian R, Homburger, Jeff, Wall, Omar E, Cornejo, J Víctor, Moreno-Mayar, Thorfinn S, Korneliussen, Tracey, Pierre, Morten, Rasmussen, Paula F, Campos, Peter, de Barros Damgaard, Morten E, Allentoft, John, Lindo, Ene, Metspalu, Ricardo, Rodríguez-Varela, Josefina, Mansilla, Celeste, Henrickson, Andaine, Seguin-Orlando, Helena, Malmström, Thomas, Stafford, Suyash S, Shringarpure, Andrés, Moreno-Estrada, Monika, Karmin, Kristiina, Tambets, Anders, Bergström, Yali, Xue, Vera, Warmuth, Andrew D, Friend, Joy, Singarayer, Paul, Valdes, Francois, Balloux, Ilán, Leboreiro, Jose Luis, Vera, Hector, Rangel-Villalobos, Davide, Pettener, Donata, Luiselli, Loren G, Davis, Evelyne, Heyer, Christoph P E, Zollikofer, Marcia S, Ponce de León, Colin I, Smith, Vaughan, Grimes, Kelly-Anne, Pike, Michael, Deal, Benjamin T, Fuller, Bernardo, Arriaza, Vivien, Standen, Maria F, Luz, Francois, Ricaut, Niede, Guidon, Ludmila, Osipova, Mikhail I, Voevoda, Olga L, Posukh, Oleg, Balanovsky, Maria, Lavryashina, Yuri, Bogunov, Elza, Khusnutdinova, Marina, Gubina, Elena, Balanovska, Sardana, Fedorova, Sergey, Litvinov, Boris, Malyarchuk, Miroslava, Derenko, M J, Mosher, David, Archer, Jerome, Cybulski, Barbara, Petzelt, Joycelynn, Mitchell, Rosita, Worl, Paul J, Norman, Peter, Parham, Brian M, Kemp, Toomas, Kivisild, Chris, Tyler-Smith, Manjinder S, Sandhu, Michael, Crawford, Richard, Villems, David Glenn, Smith, Michael R, Waters, Ted, Goebel, John R, Johnson, Ripan S, Malhi, Mattias, Jakobsson, David J, Meltzer, Andrea, Manica, Richard, Durbin, Carlos D, Bustamante, Yun S, Song, Rasmus, Nielsen, Eske, Willerslev, Raghavan M, Steinrücken M, Harris K, Schiffels S, Rasmussen S, DeGiorgio M, Albrechtsen A, Valdiosera C, Ávila-Arcos MC, Malaspinas AS, Eriksson A, Moltke I, Metspalu M, Homburger JR, Wall J, Cornejo OE, Moreno-Mayar JV, Korneliussen TS, Pierre T, Rasmussen M, Campos PF, Damgaard Pde B, Allentoft ME, Lindo J, Metspalu E, Rodríguez-Varela R, Mansilla J, Henrickson C, Seguin-Orlando A, Malmström H, Stafford T Jr, Shringarpure SS, Moreno-Estrada A, Karmin M, Tambets K, Bergström A, Xue Y, Warmuth V, Friend AD, Singarayer J, Valdes P, Balloux F, Leboreiro I, Vera JL, Rangel-Villalobos H, Pettener D, Luiselli D, Davis LG, Heyer E, Zollikofer CP, Ponce de León MS, Smith CI, Grimes V, Pike KA, Deal M, Fuller BT, Arriaza B, Standen V, Luz MF, Ricaut F, Guidon N, Osipova L, Voevoda MI, Posukh OL, Balanovsky O, Lavryashina M, Bogunov Y, Khusnutdinova E, Gubina M, Balanovska E, Fedorova S, Litvinov S, Malyarchuk B, Derenko M, Mosher MJ, Archer D, Cybulski J, Petzelt B, Mitchell J, Worl R, Norman PJ, Parham P, Kemp BM, Kivisild T, Tyler-Smith C, Sandhu MS, Crawford M, Villems R, Smith DG, Waters MR, Goebel T, Johnson JR, Malhi RS, Jakobsson M, Meltzer DJ, Manica A, Durbin R, Bustamante CD, Song YS, Nielsen R, and Willerslev E

Subjects
Gene Flow, Siberia, Models, Genetic, Athabascans and Amerindians, Human Migration, Genetic history of Native American, Indians, North American, Humans, Genomics, Americas, Population genetic, History, Ancient, Article
Abstract

How and when the Americas were populated remains contentious. Using ancient and modern genome-wide data, we find that the ancestors of all present-day Native Americans, including Athabascans and Amerindians, entered the Americas as a single migration wave from Siberia no earlier than 23 thousand years ago (KYA), and after no more than 8,000-year isolation period in Beringia. Following their arrival to the Americas, ancestral Native Americans diversified into two basal genetic branches around 13 KYA, one that is now dispersed across North and South America and the other is restricted to North America. Subsequent gene flow resulted in some Native Americans sharing ancestry with present-day East Asians (including Siberians) and, more distantly, Australo-Melanesians. Putative ‘Paleoamerican’ relict populations, including the historical Mexican Pericúes and South American Fuego-Patagonians, are not directly related to modern Australo-Melanesians as suggested by the Paleoamerican Model.

Published
2015

16. The first horse herders and the impact of early Bronze Age steppe expansions into Asia

Author

Catriona McKenzie, Vyacheslav Moiseyev, Alan K. Outram, Rui Martiniano, Karl-Göran Sjögren, Ilja Merz, J. Víctor Moreno-Mayar, Olga I. Goriunova, Eske Willerslev, Andrey Gromov, Victor Zaibert, Nazish Gul, Brian E. Hemphill, Vladimir I. Bazaliiskii, Valeriy Loman, Valeriy Evdokimov, Katrine Højholt Iversen, Peter de Barros Damgaard, Abdul Hameed, Ashot Margaryan, Abdul Samad, Süleyman Yücel Senyurt, Martin Sikora, Emma Usmanova, Habib Ahmad, Kristian Kristiansen, Muhammad Hassan Khokhar, John Novembre, Arjun Biddanda, Andrzej W. Weber, Nurbol Baimukhanov, Rasmus Nielsen, Guus Kroonen, Andaine Seguin-Orlando, Hannes Schroeder, Simon Rasmussen, Fulya Eylem Yediay, Gojko Barjamovic, Jack Kamm, Richard Durbin, Michaël Peyrot, Melissa Ilardo, Morten E. Allentoft, Andrei V. Polyakov, Constanza de la Fuente, Jeremy Choin, Inam Ullah, Victor Merz, Sachihiro Omura, Ludovic Orlando, Claus M. Zacho, Martiniano, Rui [0000-0003-0216-778X], Kamm, Jack [0000-0003-2412-756X], Kroonen, Guus [0000-0002-3708-0476], Peyrot, Michaël [0000-0002-5983-9690], Barjamovic, Gojko [0000-0002-7455-946X], Zacho, Claus [0000-0002-6217-4220], Baimukhanov, Nurbol [0000-0003-3617-1007], Biddanda, Arjun [0000-0003-1861-1523], Merz, Ilja [0000-0001-9066-9629], Loman, Valeriy [0000-0001-6951-0509], Seguin-Orlando, Andaine [0000-0002-8265-3229], Yediay, Fulya Eylem [0000-0003-3722-3091], Sjögren, Karl-Göran [0000-0003-1791-3175], de la Fuente, Constanza [0000-0002-2857-3615], Polyakov, Andrei [0000-0002-3418-2469], Omura, Sachihiro [0000-0002-2600-9703], McKenzie, Catriona [0000-0001-7288-1319], Margaryan, Ashot [0000-0002-2576-2429], Novembre, John [0000-0001-5345-0214], Orlando, Ludovic [0000-0003-3936-1850], Nielsen, Rasmus [0000-0003-0513-6591], Sikora, Martin [0000-0003-2818-8319], Outram, Alan K [0000-0003-3360-089X], Durbin, Richard [0000-0002-9130-1006], Willerslev, Eske [0000-0002-7081-6748], and Apollo - University of Cambridge Repository

Subjects
0301 basic medicine, Asia, South asia, Steppe, Human Migration, Population, Ancient history, Inner Asia, DNA, Mitochondrial, Article, Domestication, 03 medical and health sciences, Asian People, Bronze Age, Animals, Humans, Horses, DNA, Ancient, education, History, Ancient, Language, 2. Zero hunger, geography, education.field_of_study, Chromosomes, Human, Y, Multidisciplinary, geography.geographical_feature_category, Whole Genome Sequencing, Genome, Human, Extramural, Genetic Drift, Grassland, Europe, 030104 developmental biology
Abstract

Ancient steppes for human equestrians The Eurasian steppes reach from the Ukraine in Europe to Mongolia and China. Over the past 5000 years, these flat grasslands were thought to be the route for the ebb and flow of migrant humans, their horses, and their languages. de Barros Damgaard et al. probed whole-genome sequences from the remains of 74 individuals found across this region. Although there is evidence for migration into Europe from the steppes, the details of human movements are complex and involve independent acquisitions of horse cultures. Furthermore, it appears that the Indo-European Hittite language derived from Anatolia, not the steppes. The steppe people seem not to have penetrated South Asia. Genetic evidence indicates an independent history involving western Eurasian admixture into ancient South Asian peoples. Science , this issue p. eaar7711

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