Toward high-resolution population genomics using archaeological samples
Identifieur interne : 000016 ( Main/Merge ); précédent : 000015; suivant : 000017Toward high-resolution population genomics using archaeological samples
Auteurs : Irina Morozova [Suisse] ; Pavel Flegontov [République tchèque, Russie] ; Alexander S. Mikheyev [Japon] ; Sergey Bruskin [Russie] ; Hosseinali Asgharian [États-Unis] ; Petr Ponomarenko [États-Unis] ; Vladimir Klyuchnikov [Russie] ; Ganeshprasad Arunkumar [Inde] ; Egor Prokhortchouk [Russie] ; Yuriy Gankin [États-Unis] ; Evgeny Rogaev [Russie, États-Unis] ; Yuri Nikolsky [Russie, États-Unis] ; Ancha Baranova [États-Unis, Russie] ; Eran Elhaik [Royaume-Uni] ; Tatiana V. Tatarinova [Russie, États-Unis]Source :
- DNA Research: An International Journal for Rapid Publication of Reports on Genes and Genomes [ 1340-2838 ] ; 2016.
Abstract
The term ‘ancient DNA’ (aDNA) is coming of age, with over 1,200 hits in the PubMed database, beginning in the early 1980s with the studies of ‘molecular paleontology’. Rooted in cloning and limited sequencing of DNA from ancient remains during the pre-PCR era, the field has made incredible progress since the introduction of PCR and next-generation sequencing. Over the last decade, aDNA analysis ushered in a new era in genomics and became the method of choice for reconstructing the history of organisms, their biogeography, and migration routes, with applications in evolutionary biology, population genetics, archaeogenetics, paleo-epidemiology, and many other areas. This change was brought by development of new strategies for coping with the challenges in studying aDNA due to damage and fragmentation, scarce samples, significant historical gaps, and limited applicability of population genetics methods. In this review, we describe the state-of-the-art achievements in aDNA studies, with particular focus on human evolution and demographic history. We present the current experimental and theoretical procedures for handling and analysing highly degraded aDNA. We also review the challenges in the rapidly growing field of ancient epigenomics. Advancement of aDNA tools and methods signifies a new era in population genetics and evolutionary medicine research.
Url:
DOI: 10.1093/dnares/dsw029
PubMed: 27436340
PubMed Central: 4991838
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PMC:4991838Le document en format XML
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<affiliation wicri:level="2"><nlm:aff id="dsw029-aff14">University of Massachusetts Medical School, Worcester, MA, USA</nlm:aff>
<country xml:lang="fr">États-Unis</country>
<wicri:regionArea>University of Massachusetts Medical School, Worcester, MA</wicri:regionArea>
<placeName><region type="state">Massachusetts</region>
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</author>
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<affiliation wicri:level="3"><nlm:aff id="dsw029-aff5">Vavilov Institute of General Genetics RAS, Moscow, Russia</nlm:aff>
<country xml:lang="fr">Russie</country>
<wicri:regionArea>Vavilov Institute of General Genetics RAS, Moscow</wicri:regionArea>
<placeName><settlement type="city">Moscou</settlement>
<region>District fédéral central</region>
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<affiliation wicri:level="2"><nlm:aff id="dsw029-aff15">F1 Genomics, San Diego, CA, USA</nlm:aff>
<country xml:lang="fr">États-Unis</country>
<wicri:regionArea>F1 Genomics, San Diego, CA</wicri:regionArea>
<placeName><region type="state">Californie</region>
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</affiliation>
<affiliation wicri:level="2"><nlm:aff id="dsw029-aff16">School of Systems Biology, George Mason University, VA, USA</nlm:aff>
<country xml:lang="fr">États-Unis</country>
<wicri:regionArea>School of Systems Biology, George Mason University, VA</wicri:regionArea>
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<country xml:lang="fr">États-Unis</country>
<wicri:regionArea>School of Systems Biology, George Mason University, VA</wicri:regionArea>
<placeName><region type="state">Virginie</region>
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</affiliation>
<affiliation wicri:level="3"><nlm:aff id="dsw029-aff17">Research Centre for Medical Genetics, Moscow, Russia</nlm:aff>
<country xml:lang="fr">Russie</country>
<wicri:regionArea>Research Centre for Medical Genetics, Moscow</wicri:regionArea>
<placeName><settlement type="city">Moscou</settlement>
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<affiliation wicri:level="3"><nlm:aff id="dsw029-aff18">Atlas Biomed Group, Moscow, Russia</nlm:aff>
<country xml:lang="fr">Russie</country>
<wicri:regionArea>Atlas Biomed Group, Moscow</wicri:regionArea>
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<affiliation wicri:level="1"><nlm:aff id="dsw029-aff19">Department of Animal & Plant Sciences, University of Sheffield, Sheffield, South Yorkshire, UK</nlm:aff>
<country xml:lang="fr">Royaume-Uni</country>
<wicri:regionArea>Department of Animal & Plant Sciences, University of Sheffield, Sheffield, South Yorkshire</wicri:regionArea>
<wicri:noRegion>South Yorkshire</wicri:noRegion>
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<author><name sortKey="Tatarinova, Tatiana V" sort="Tatarinova, Tatiana V" uniqKey="Tatarinova T" first="Tatiana V." last="Tatarinova">Tatiana V. Tatarinova</name>
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<country xml:lang="fr">Russie</country>
<wicri:regionArea>Bioinformatics Center, A.A. Kharkevich Institute for Information Transmission Problems, Russian Academy of Sciences, Moscow</wicri:regionArea>
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<affiliation wicri:level="2"><nlm:aff id="dsw029-aff7">Center for Personalized Medicine, Children’s Hospital Los Angeles, Los Angeles, CA, USA</nlm:aff>
<country xml:lang="fr">États-Unis</country>
<wicri:regionArea>Center for Personalized Medicine, Children’s Hospital Los Angeles, Los Angeles, CA</wicri:regionArea>
<placeName><region type="state">Californie</region>
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<affiliation wicri:level="4"><nlm:aff id="dsw029-aff8">Spatial Sciences Institute, University of Southern California, Los Angeles, CA, USA</nlm:aff>
<country xml:lang="fr">États-Unis</country>
<wicri:regionArea>Spatial Sciences Institute, University of Southern California, Los Angeles, CA</wicri:regionArea>
<placeName><region type="state">Californie</region>
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<series><title level="j">DNA Research: An International Journal for Rapid Publication of Reports on Genes and Genomes</title>
<idno type="ISSN">1340-2838</idno>
<idno type="eISSN">1756-1663</idno>
<imprint><date when="2016">2016</date>
</imprint>
</series>
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<profileDesc><textClass></textClass>
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<front><div type="abstract" xml:lang="en"><p>The term ‘ancient DNA’ (aDNA) is coming of age, with over 1,200 hits in the PubMed database, beginning in the early 1980s with the studies of ‘molecular paleontology’. Rooted in cloning and limited sequencing of DNA from ancient remains during the pre-PCR era, the field has made incredible progress since the introduction of PCR and next-generation sequencing. Over the last decade, aDNA analysis ushered in a new era in genomics and became the method of choice for reconstructing the history of organisms, their biogeography, and migration routes, with applications in evolutionary biology, population genetics, archaeogenetics, paleo-epidemiology, and many other areas. This change was brought by development of new strategies for coping with the challenges in studying aDNA due to damage and fragmentation, scarce samples, significant historical gaps, and limited applicability of population genetics methods. In this review, we describe the state-of-the-art achievements in aDNA studies, with particular focus on human evolution and demographic history. We present the current experimental and theoretical procedures for handling and analysing highly degraded aDNA. We also review the challenges in the rapidly growing field of ancient epigenomics. Advancement of aDNA tools and methods signifies a new era in population genetics and evolutionary medicine research.</p>
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