The evolutionary and phylogeographic history of woolly mammoths: a comprehensive mitogenomic analysis.
Near the end of the Pleistocene epoch, populations of the woolly mammoth (Mammuthus primigenius) were distributed across parts of three continents, from western Europe and northern Asia through Beringia to the Atlantic seaboard of North America. Nonetheless, questions about the connectivity and temporal continuity of mammoth populations and species remain unanswered. We use a combination of targeted enrichment and high-throughput sequencing to assemble and interpret a data set of 143 mammoth mitochondrial genomes, sampled from fossils recovered from across their Holarctic range. Our dataset includes 54 previously unpublished mitochondrial genomes and significantly increases the coverage of the Eurasian range of the species. The resulting global phylogeny confirms that the Late Pleistocene mammoth population comprised three distinct mitochondrial lineages that began to diverge ~1.0-2.0 million years ago (Ma). We also find that mammoth mitochondrial lineages were strongly geographically partitioned throughout the Pleistocene. In combination, our genetic results and the pattern of morphological variation in time and space suggest that male-mediated gene flow, rather than large-scale dispersals, was important in the Pleistocene evolutionary history of mammoths.
Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, Santa Cruz, CA 95064, USA.
Dan
D
Chang
Department of Anatomy, University of Otago, 270 Great King Street, Dunedin 9016, New Zealand.
Michael
M
Knapp
McMaster Ancient DNA Centre, Department of Anthropology, McMaster University, 1280 Main Street West, Hamilton, Ontario L8S 4L9, Canada.
Jacob
J
Enk
Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, Leipzig D04103, Germany.
Sebastian
S
Lippold
Department of Genome Sciences, University of Washington, 3720 15th Ave NE, Seattle, WA 98195-5065, USA.
Martin
M
Kircher
Department of Earth Sciences, The Natural History Museum, Cromwell Road, London SW7 5BD, UK.
Adrian
A
Lister
Department of Mammalogy, American Museum of Natural History, 200 Central Park West, New York NY, 10024, USA.
Ross D E
RD
MacPhee
Center of Excellence in Paleontology, East Tennessee State University, 1212 Sunset Dr., Gray, TN 37615, USA.
Christopher
C
Widga
Antarctic Biological Research Initiative, 31 Jobson Road, SA 5110, Australia.
Paul
P
Czechowski
Department of Zoology, Institute of Biosciences, University of Rostock, Universitätsplatz 2, Rostock D-18055, Germany.
Robert
R
Sommer
Department of Biochemistry, Vanderbilt University School of Medicine, 2215 Garland Ave, Nashville, TN 37232, USA.
Emily
E
Hodges
Staatliches Naturhistorisches Museum Braunschweig, Pockelstrasse 10, Braunschweig 38106, Germany.
Nikolaus
N
Stümpel
Department of Earth Sciences, The Natural History Museum, Cromwell Road, London SW7 5BD, UK.
Ian
I
Barnes
Swedish Museum of Natural History, Department of Bioinformatics and Genetics, S-104 05 Stockholm, P.O. Box 50007, Sweden.
Love
L
Dalén
Institute of Archaeology and Ethnography, Siberian Branch, Russian Academy of Sciences, 17, Novosibirsk, Akademia Lavrentieva, 630090, Russia.
Anatoly
A
Derevianko
Operational Directorate "Earth and History of Life", Royal Belgian Institute of Natural Sciences, Vautierstraat 29, Brussels 1000, Belgium.
Mietje
M
Germonpré
"Emil Racoviţă" Institute of Speleology, Frumoasă 31, Bucharest, 01906, Romania.
Alexandra
A
Hillebrand-Voiculescu
"Emil Racoviţă" Institute of Speleology, Frumoasă 31, Bucharest, 01906, Romania.
Silviu
S
Constantin
Department of Palaeontology, Faculty of Geology, Moscow State University, ul. Leninskiye Gory, 1, Moscow, 119991, Russia.
Tatyana
T
Kuznetsova
Mammuthus Club International, Gudumholm 41, Hoofddorp, HG 2133, Netherlands.
Dick
D
Mol
Staatliches Museum für Naturkunde Stuttgart Rosenstein, Gewann 1, Stuttgart 70191, Germany.
Thomas
T
Rathgeber
Department "World Cultures and Environment", Reiss-Engelhorn-Museen, C 5, Zeughaus, Mannheim, 68159, Germany.
Wilfried
W
Rosendahl
Zoological Institute Russian Academy of Sciences, Universitetskaya nab., 1 Saint-Petersburg 199034, Russia.|Institute of Applied Ecology of the North, North-Eastern Federal University, Lenina 1, Yakutsk, Russia.
Alexey N
AN
Tikhonov
Centre for GeoGenetics, Copenhagen University, Nørregade '10, Copenhagen, 1165, Denmark.|Department of Zoology, University of Cambridge, Downing St. Cambridge, CB2 3EJ, UK.|Sanger Institute, Wellcome Trust Genome Campus, Hinxton, CB10 1SA, UK.
Eske
E
Willerslev
CRUK Cambridge Institute, University of Cambridge, Robinson Way, Cambridge, CB2 0RE, UK.
Greg
G
Hannon
Institute of Evolutionary Biology (CSIC-UPF), Doctor Aiguader, 88, Barcelona, 08003, Spain.
Carles
C
Lalueza-Fox
Staatliches Naturhistorisches Museum Braunschweig, Pockelstrasse 10, Braunschweig 38106, Germany.
Ulrich
U
Joger
McMaster Ancient DNA Centre, Department of Anthropology, McMaster University, 1280 Main Street West, Hamilton, Ontario L8S 4L9, Canada.
Hendrik
H
Poinar
Department of Mathematics and Natural Sciences, Evolutionary Adaptive Genomics, Institute for Biochemistry and Biology, University of Potsdam, Karl-Liebknecht-Str. 24-25, Potsdam, 14476, Germany.
Michael
M
Hofreiter
Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, Santa Cruz, CA 95064, USA.
Beth
B
Shapiro
D063147:Animal Distribution; D000818:Animals; D001208:Asia; D005075:Biological Evolution; D004272:DNA, Mitochondrial / Q000235:genetics*; D005060:Europe; D053476:Extinction, Biological; D005260:Female; D005580:Fossils; D051456:Gene Flow; D054629:Genome, Mitochondrial; D008297:Male; D056665:Mammoths / Q000145:classification / Q000235:genetics*; D009656:North America; D010802:Phylogeny; D058974:Phylogeography; D017422:Sequence Analysis, DNA
D004272:DNA, Mitochondrial