title: Toward high-resolution population genomics using archaeological samples.
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.
authors.affiliation: Institute of Evolutionary Medicine, University of Zurich, Zurich, Switzerland tatiana.tatarinova@usc.edu irina.morozova@iem.uzh.ch.
authors.forename: Irina
authors.initials: I
authors.lastname: Morozova
authors.affiliation: Department of Biology and Ecology, Faculty of Science, University of Ostrava, Ostrava, Czech Republic Bioinformatics Center, A.A. Kharkevich Institute for Information Transmission Problems, Russian Academy of Sciences, Moscow, Russian Federation.
authors.forename: Pavel
authors.initials: P
authors.lastname: Flegontov
authors.affiliation: Ecology and Evolution Unit, Okinawa Institute of Science and Technology Graduate University, Okinawa, Japan.
authors.forename: Alexander S
authors.initials: AS
authors.lastname: Mikheyev
authors.affiliation: Vavilov Institute of General Genetics RAS, Moscow, Russia.
authors.forename: Sergey
authors.initials: S
authors.lastname: Bruskin
authors.affiliation: Department of Computational and Molecular Biology, University of Southern California, Los Angeles, CA, USA.
authors.forename: Hosseinali
authors.initials: H
authors.lastname: Asgharian
authors.affiliation: Center for Personalized Medicine, Children's Hospital Los Angeles, Los Angeles, CA, USA Spatial Sciences Institute, University of Southern California, Los Angeles, CA, USA.
authors.forename: Petr
authors.initials: P
authors.lastname: Ponomarenko
authors.affiliation: Donskaya Archeologia, Rostov, Russia.
authors.forename: Vladimir
authors.initials: V
authors.lastname: Klyuchnikov
authors.affiliation: School of Chemical and Biotechnology, SASTRA University, Tanjore, India.
authors.forename: GaneshPrasad
authors.initials: G
authors.lastname: ArunKumar
authors.affiliation: Research Center of Biotechnology RAS, Moscow, Russia Department of Biology, Lomonosov Moscow State University, Russia.
authors.forename: Egor
authors.initials: E
authors.lastname: Prokhortchouk
authors.affiliation: EPAM Systems, Newtown, PA, USA.
authors.forename: Yuriy
authors.initials: Y
authors.lastname: Gankin
authors.affiliation: Vavilov Institute of General Genetics RAS, Moscow, Russia University of Massachusetts Medical School, Worcester, MA, USA.
authors.forename: Evgeny
authors.initials: E
authors.lastname: Rogaev
authors.affiliation: Vavilov Institute of General Genetics RAS, Moscow, Russia F1 Genomics, San Diego, CA, USA School of Systems Biology, George Mason University, VA, USA.
authors.forename: Yuri
authors.initials: Y
authors.lastname: Nikolsky
authors.affiliation: School of Systems Biology, George Mason University, VA, USA Research Centre for Medical Genetics, Moscow, Russia Atlas Biomed Group, Moscow, Russia.
authors.forename: Ancha
authors.initials: A
authors.lastname: Baranova
authors.affiliation: Department of Animal & Plant Sciences, University of Sheffield, Sheffield, South Yorkshire, UK.
authors.forename: Eran
authors.initials: E
authors.lastname: Elhaik
authors.affiliation: Bioinformatics Center, A.A. Kharkevich Institute for Information Transmission Problems, Russian Academy of Sciences, Moscow, Russian Federation Center for Personalized Medicine, Children's Hospital Los Angeles, Los Angeles, CA, USA Spatial Sciences Institute, University of Southern California, Los Angeles, CA, USA tatiana.tatarinova@usc.edu irina.morozova@iem.uzh.ch.
authors.forename: Tatiana V
authors.initials: TV
authors.lastname: Tatarinova
mesh_terms: D000818:Animals; D000072441:DNA, Ancient; D019143:Evolution, Molecular; D005828:Genetics, Population / Q000379:methods*; D015894:Genome, Human; D023281:Genomics / Q000379:methods*; D006801:Humans; D017422:Sequence Analysis, DNA / Q000379:methods*
chemical_list: D000072441:DNA, Ancient
keywords: ancient DNA; bioinformatics; epigenetics; next-generation sequencing; population genetics