Toward high-resolution population genomics using archaeological samples
Identifieur interne : 000332 ( Pmc/Curation ); précédent : 000331; suivant : 000333Toward 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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<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>
</div>
</front>
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<pmc article-type="research-article"><pmc-dir>properties open_access</pmc-dir>
<front><journal-meta><journal-id journal-id-type="nlm-ta">DNA Res</journal-id>
<journal-id journal-id-type="iso-abbrev">DNA Res</journal-id>
<journal-id journal-id-type="publisher-id">dnares</journal-id>
<journal-id journal-id-type="hwp">dnares</journal-id>
<journal-title-group><journal-title>DNA Research: An International Journal for Rapid Publication of Reports on Genes and Genomes</journal-title>
</journal-title-group>
<issn pub-type="ppub">1340-2838</issn>
<issn pub-type="epub">1756-1663</issn>
<publisher><publisher-name>Oxford University Press</publisher-name>
</publisher>
</journal-meta>
<article-meta><article-id pub-id-type="pmid">27436340</article-id>
<article-id pub-id-type="pmc">4991838</article-id>
<article-id pub-id-type="doi">10.1093/dnares/dsw029</article-id>
<article-id pub-id-type="publisher-id">dsw029</article-id>
<article-categories><subj-group subj-group-type="heading"><subject>Invited Review</subject>
</subj-group>
<series-title>Editor's Choice</series-title>
</article-categories>
<title-group><article-title>Toward high-resolution population genomics using archaeological samples</article-title>
</title-group>
<contrib-group><contrib contrib-type="author"><name><surname>Morozova</surname>
<given-names>Irina</given-names>
</name>
<xref ref-type="aff" rid="dsw029-aff1"><sup>1</sup>
</xref>
<xref ref-type="corresp" rid="dsw029-cor1">*</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Flegontov</surname>
<given-names>Pavel</given-names>
</name>
<xref ref-type="aff" rid="dsw029-aff2"><sup>2</sup>
</xref>
<xref ref-type="aff" rid="dsw029-aff3"><sup>3</sup>
</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Mikheyev</surname>
<given-names>Alexander S.</given-names>
</name>
<xref ref-type="aff" rid="dsw029-aff4"><sup>4</sup>
</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Bruskin</surname>
<given-names>Sergey</given-names>
</name>
<xref ref-type="aff" rid="dsw029-aff5"><sup>5</sup>
</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Asgharian</surname>
<given-names>Hosseinali</given-names>
</name>
<xref ref-type="aff" rid="dsw029-aff6"><sup>6</sup>
</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Ponomarenko</surname>
<given-names>Petr</given-names>
</name>
<xref ref-type="aff" rid="dsw029-aff7"><sup>7</sup>
</xref>
<xref ref-type="aff" rid="dsw029-aff8"><sup>8</sup>
</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Klyuchnikov</surname>
<given-names>Vladimir</given-names>
</name>
<xref ref-type="aff" rid="dsw029-aff9"><sup>9</sup>
</xref>
</contrib>
<contrib contrib-type="author"><name><surname>ArunKumar</surname>
<given-names>GaneshPrasad</given-names>
</name>
<xref ref-type="aff" rid="dsw029-aff10"><sup>10</sup>
</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Prokhortchouk</surname>
<given-names>Egor</given-names>
</name>
<xref ref-type="aff" rid="dsw029-aff11"><sup>11</sup>
</xref>
<xref ref-type="aff" rid="dsw029-aff12"><sup>12</sup>
</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Gankin</surname>
<given-names>Yuriy</given-names>
</name>
<xref ref-type="aff" rid="dsw029-aff13"><sup>13</sup>
</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Rogaev</surname>
<given-names>Evgeny</given-names>
</name>
<xref ref-type="aff" rid="dsw029-aff5"><sup>5</sup>
</xref>
<xref ref-type="aff" rid="dsw029-aff14"><sup>14</sup>
</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Nikolsky</surname>
<given-names>Yuri</given-names>
</name>
<xref ref-type="aff" rid="dsw029-aff5"><sup>5</sup>
</xref>
<xref ref-type="aff" rid="dsw029-aff15"><sup>15</sup>
</xref>
<xref ref-type="aff" rid="dsw029-aff16"><sup>16</sup>
</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Baranova</surname>
<given-names>Ancha</given-names>
</name>
<xref ref-type="aff" rid="dsw029-aff16"><sup>16</sup>
</xref>
<xref ref-type="aff" rid="dsw029-aff17"><sup>17</sup>
</xref>
<xref ref-type="aff" rid="dsw029-aff18"><sup>18</sup>
</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Elhaik</surname>
<given-names>Eran</given-names>
</name>
<xref ref-type="aff" rid="dsw029-aff19"><sup>19</sup>
</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Tatarinova</surname>
<given-names>Tatiana V.</given-names>
</name>
<xref ref-type="aff" rid="dsw029-aff3"><sup>3</sup>
</xref>
<xref ref-type="aff" rid="dsw029-aff7"><sup>7</sup>
</xref>
<xref ref-type="aff" rid="dsw029-aff8"><sup>8</sup>
</xref>
<xref ref-type="corresp" rid="dsw029-cor1">*</xref>
</contrib>
<aff id="dsw029-aff1"><sup>1</sup>
Institute of Evolutionary Medicine, University of Zurich, Zurich, Switzerland</aff>
<aff id="dsw029-aff2"><sup>2</sup>
Department of Biology and Ecology, Faculty of Science, University of Ostrava, Ostrava, Czech Republic</aff>
<aff id="dsw029-aff3"><sup>3</sup>
Bioinformatics Center, A.A. Kharkevich Institute for Information Transmission Problems, Russian Academy of Sciences, Moscow, Russian Federation</aff>
<aff id="dsw029-aff4"><sup>4</sup>
Ecology and Evolution Unit, Okinawa Institute of Science and Technology Graduate University, Okinawa, Japan</aff>
<aff id="dsw029-aff5"><sup>5</sup>
Vavilov Institute of General Genetics RAS, Moscow, Russia</aff>
<aff id="dsw029-aff6"><sup>6</sup>
Department of Computational and Molecular Biology, University of Southern California, Los Angeles, CA, USA</aff>
<aff id="dsw029-aff7"><sup>7</sup>
Center for Personalized Medicine, Children’s Hospital Los Angeles, Los Angeles, CA, USA</aff>
<aff id="dsw029-aff8"><sup>8</sup>
Spatial Sciences Institute, University of Southern California, Los Angeles, CA, USA</aff>
<aff id="dsw029-aff9"><sup>9</sup>
Donskaya Archeologia, Rostov, Russia</aff>
<aff id="dsw029-aff10"><sup>10</sup>
School of Chemical and Biotechnology, SASTRA University, Tanjore, India</aff>
<aff id="dsw029-aff11"><sup>11</sup>
Research Center of Biotechnology RAS, Moscow, Russia</aff>
<aff id="dsw029-aff12"><sup>12</sup>
Department of Biology, Lomonosov Moscow State University, Russia</aff>
<aff id="dsw029-aff13"><sup>13</sup>
EPAM Systems, Newtown, PA, USA</aff>
<aff id="dsw029-aff14"><sup>14</sup>
University of Massachusetts Medical School, Worcester, MA, USA</aff>
<aff id="dsw029-aff15"><sup>15</sup>
F1 Genomics, San Diego, CA, USA</aff>
<aff id="dsw029-aff16"><sup>16</sup>
School of Systems Biology, George Mason University, VA, USA</aff>
<aff id="dsw029-aff17"><sup>17</sup>
Research Centre for Medical Genetics, Moscow, Russia</aff>
<aff id="dsw029-aff18"><sup>18</sup>
Atlas Biomed Group, Moscow, Russia</aff>
<aff id="dsw029-aff19"><sup>19</sup>
Department of Animal & Plant Sciences, University of Sheffield, Sheffield, South Yorkshire, UK</aff>
</contrib-group>
<author-notes><corresp id="dsw029-cor1">*To whom correspondence should be addressed. Tel. +310 266 8024 (cell), +323 361 8086 (work). Fax: +323 361 1183. E-mail: <email>tatiana.tatarinova@usc.edu</email>
; <email>irina.morozova@iem.uzh.ch</email>
</corresp>
<fn id="dsw029-FM1"><p>Edited by Dr Katsumi Isono</p>
</fn>
</author-notes>
<pub-date pub-type="ppub"><month>8</month>
<year>2016</year>
</pub-date>
<pub-date pub-type="epub"><day>19</day>
<month>7</month>
<year>2016</year>
</pub-date>
<pub-date pub-type="pmc-release"><day>19</day>
<month>7</month>
<year>2016</year>
</pub-date>
<pmc-comment> PMC Release delay is 0 months and 0 days and was based on the . </pmc-comment>
<volume>23</volume>
<issue>4</issue>
<fpage>295</fpage>
<lpage>310</lpage>
<history><date date-type="received"><day>22</day>
<month>11</month>
<year>2015</year>
</date>
<date date-type="accepted"><day>22</day>
<month>5</month>
<year>2016</year>
</date>
</history>
<permissions><copyright-statement>© The Author 2016. Published by Oxford University Press on behalf of Kazusa DNA Research Institute.</copyright-statement>
<copyright-year>2016</copyright-year>
<license xlink:href="http://creativecommons.org/licenses/by-nc/4.0/" license-type="creative-commons"><license-p>This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (<ext-link ext-link-type="uri" xlink:href="http://creativecommons.org/licenses/by-nc/4.0/">http://creativecommons.org/licenses/by-nc/4.0/</ext-link>
), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact journals.permissions@oup.com</license-p>
</license>
</permissions>
<abstract><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>
</abstract>
<kwd-group kwd-group-type="author"><kwd>ancient DNA</kwd>
<kwd>bioinformatics</kwd>
<kwd>epigenetics</kwd>
<kwd>population genetics</kwd>
<kwd>next-generation sequencing</kwd>
</kwd-group>
<counts><page-count count="16"></page-count>
</counts>
</article-meta>
</front>
</pmc>
</record>
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