Mammuthus Population Dynamics in Late Pleistocene North America: Divergence, Phylogeography, and Introgression

Jacob Enk1,2,3, Alison Devault1,3, Chris Widga4, Jeffrey J. Saunders4, Paul Szpak5, John Southon6, Jean‐Marie Rouillard3, Beth Shapiro7, G. Brian Golding2, Grant D. Zazula8, Duane G. Froese9,10, Daniel C. Fisher11, R. D. E. MacPhee12, Hendrik N. Poinar1,2,13
1Department of Anthropology, McMaster Ancient DNA Centre, McMaster University, Hamilton, ON, Canada
2Department of Biology, McMaster University, Hamilton, ON, Canada
3MYcroarray, Ann Arbor, MI, USA
4Geology Section, Illinois State Museum Research and Collections Center, Springfield, IL, USA
5Department of Anthropology, University of British Columbia, Vancouver, BC, Canada
6Keck Carbon Cycle Accelerator Mass Spectrometer, Earth Systems Science Department, University of California, Irvine, Irvine, CA, USA
7Ecology and Evolutionary Biology, University of California, Santa Cruz, Santa Cruz, CA, USA
8Yukon Palaeontology Program, Department of Tourism and Culture, Yukon Government, Whitehorse, YT, Canada
9Department of Earth and Atmospheric Sciences, University of Alberta, Edmonton, AB, Canada
10Museum of Paleontology and Department of Geological Sciences, University of Michigan, Ann Arbor, MI, USA
11Museum of Paleontology and Department of Earth and Environmental Sciences, University of Michigan, Ann Arbor, MI, USA
12Division of Vertebrate Zoology/Mammalogy, American Museum of Natural History, New York, NY, USA
13Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, ON, Canada

Tóm tắt

Từ khóa


Tài liệu tham khảo

Agenbroad, 2005, North American proboscideans: mammoths: the state of knowledge, 2003, Quat. Int., 126, 10.1016/j.quaint.2004.04.016

Ávila-Arcos, 2011, Application and comparison of large-scale solution-based DNA capture-enrichment methods on ancient DNA, Sci. Rep., 1, 74, 10.1038/srep00074

Bandelt, 2008, Clock debate: when times are a-changin': time dependency of molecular rate estimates: tempest in a teacup, Heredity (Edinb.), 100, 1, 10.1038/sj.hdy.6801054

Barnes, 2007, Genetic structure and extinction of the woolly mammoth, Mammuthus primigenius, Curr. Biol., 17, 1072, 10.1016/j.cub.2007.05.035

Beaumont, 2010, Bone preparation at the KCCAMS laboratory, Nucl. Instrum. Methods Phys. Res. B, 268, 906, 10.1016/j.nimb.2009.10.061

Bos, 2011, A draft genome of Yersinia pestis from victims of the Black Death, Nature, 478, 506, 10.1038/nature10549

Briggs, 2009, Primer extension capture: targeted sequence retrieval from heavily degraded DNA sources, J. Vis. Exp., 31, e1573, 10.3791/1573

Burbano, 2010, Targeted investigation of the Neandertal genome by array-based sequence capture, Science, 328, 723, 10.1126/science.1188046

Carpenter, 2013, Pulling out the 1%: whole-genome capture for the targeted enrichment of ancient DNA sequencing libraries, Am. J. Hum. Genet., 93, 852, 10.1016/j.ajhg.2013.10.002

Dabney, 2013, Complete mitochondrial genome sequence of a Middle Pleistocene cave bear reconstructed from ultrashort DNA fragments, Proc. Natl. Acad. Sci. U.S.A., 110, 15758, 10.1073/pnas.1314445110

Daley, 2013, Predicting the molecular complexity of sequencing libraries, Nat. Methods, 10, 325, 10.1038/nmeth.2375

Darriba, 2012, jModelTest 2: more models, new heuristics and parallel computing, Nat. Methods, 9, 772, 10.1038/nmeth.2109

Debruyne, 2008, Out of America: Ancient DNA evidence for a new world origin of late quaternary woolly mammoths, Curr. Biol., 18, 1320, 10.1016/j.cub.2008.07.061

Debruyne, 2009, Time dependency of molecular rates in ancient DNA data sets, a sampling artifact?, Syst. Biol., 58, 348, 10.1093/sysbio/syp028

Drummond, 2012, Bayesian phylogenetics with BEAUti and the BEAST 1.7, Mol. Biol. Evol., 29, 1969, 10.1093/molbev/mss075

Emerson, 2007, Alarm bells for the molecular clock? No support for Ho et al.'s model of time-dependent molecular rate estimates, Syst. Biol., 56, 337, 10.1080/10635150701258795

Enk, 2011, Complete Columbian mammoth mitogenome suggests interbreeding with woolly mammoths, Genome Biol., 12, R51, 10.1186/gb-2011-12-5-r51

Enk, 2013, Quantitative PCR as a predictor of aligned ancient DNA read counts following targeted enrichment, Biotechniques, 55, 300, 10.2144/000114114

Fisher, 2009, Paleobiology and extinction of proboscideans in the Great Lakes region of North America, American Megafaunal Extinctions at the End of the Pleistocene, 55, 10.1007/978-1-4020-8793-6_4

Gilbert, 2008, Intraspecific phylogenetic analysis of Siberian woolly mammoths using complete mitochondrial genomes, Proc. Natl. Acad. Sci. U.S.A., 105, 8327, 10.1073/pnas.0802315105

Gilbert, 2007, Whole-genome shotgun sequencing of mitochondria from ancient hair shafts, Science, 317, 1927, 10.1126/science.1146971

Gill, 2013, Improving Bayesian population dynamics inference: a coalescent-based model for multiple loci, Mol. Biol. Evol., 30, 713, 10.1093/molbev/mss265

Hagelberg, 1994, DNA from ancient mammoth bones, Nature, 370, 333, 10.1038/370333b0

Haile, 2009, Ancient DNA reveals late survival of mammoth and horse in interior Alaska, Proc. Natl. Acad. Sci. U.S.A., 106, 22352, 10.1073/pnas.0912510106

Harington, 1984, Mammoths, bison and time in North America, Dev. Palaeontol. Stratigr., 7, 299, 10.1016/S0920-5446(08)70078-5

Ho, 2005, Time dependency of molecular rate estimates and systematic overestimation of recent divergence times, Mol. Biol. Evol., 22, 1561, 10.1093/molbev/msi145

Ho, 2008, The effect of inappropriate calibration: three case studies in molecular ecology, PLoS ONE, 3, e1615, 10.1371/journal.pone.0001615

Ho, 2007, Evidence for time dependency of molecular rate estimates, Syst. Biol., 56, 515, 10.1080/10635150701435401

Höss, 1994, Mammoth DNA-Sequences, Nature, 370, 333, 10.1038/370333a0

Hoyle, 2004, Late Pleistocene mammoth remains from Coastal Maine, USA, Quat. Res., 61, 277, 10.1016/j.yqres.2004.02.006

Hurvich, 1989, Regression and time-series model selection in small samples, Biometrika, 76, 297, 10.1093/biomet/76.2.297

Kearse, 2012, Geneious Basic: an integrated and extendable desktop software platform for the organization and analysis of sequence data, Bioinformatics, 28, 1647, 10.1093/bioinformatics/bts199

Kircher, 2012, Analysis of high-throughput ancient DNA sequencing data, Methods Mol. Biol., 840, 197, 10.1007/978-1-61779-516-9_23

Kircher, 2012, Double indexing overcomes inaccuracies in multiplex sequencing on the Illumina platform, Nucleic Acids Res., 40, e3, 10.1093/nar/gkr771

Krause, 2006, Multiplex amplification of the mammoth mitochondrial genome and the evolution of Elephantidae, Nature, 439, 724, 10.1038/nature04432

Li, 2009, Fast and accurate short read alignment with Burrows-Wheeler transform, Bioinformatics, 25, 1754, 10.1093/bioinformatics/btp324

Lister, 2007, Mammoths: Giants of the Ice Age.

Lister, 1996, Evolution and taxonomy of Eurasian mammoths, The Proboscidea: Evolution and Palaeoecology of Elephants and Their Relatives, 203, 10.1093/oso/9780198546528.003.0020

Lister, 2001, The origin and evolution of the woolly mammoth, Science, 294, 1094, 10.1126/science.1056370

Lister, 2015, Evolution and dispersal of mammoths across the Northern Hemisphere, Science, 350, 805, 10.1126/science.aac5660

Maglio, 1973, Origin and evolution of the Elephantidae, Transactions of the American Philosophical Society held at Philadelphia for Promoting Useful Knowledge, 1

Meyer, 2014, A mitochondrial genome sequence of a hominin from Sima de los Huesos, Nature, 505, 403, 10.1038/nature12788

Meyer, 2010, Illumina sequencing library preparation for highly multiplexed target capture and sequencing, Cold Spring Harb. Protoc., 10.1101/pdb.prot5448

Minh, 2013, Ultrafast approximation for phylogenetic bootstrap, Mol. Biol. Evol., 30, 1188, 10.1093/molbev/mst024

Mitchell, 2005, Damage and repair of ancient DNA, Mutat. Res., 571, 265, 10.1016/j.mrfmmm.2004.06.060

Mokry, 2010, Accurate SNP and mutation detection by targeted custom microarray-based genomic enrichment of short-fragment sequencing libraries, Nucleic Acids Res., 38, e116, 10.1093/nar/gkq072

Neph, 2012, BEDOPS: high-performance genomic feature operations, Bioinformatics, 28, 1919, 10.1093/bioinformatics/bts277

Nystrom, 2010, Temporal genetic change in the last remaining population of woolly mammoth, Proc. R. Soc. B Biol. Sci., 277, 2331, 10.1098/rspb.2010.0301

Orlando, 2013, Recalibrating Equus evolution using the genome sequence of an early Middle Pleistocene horse, Nature, 499, 74, 10.1038/nature12323

Ozawa, 1997, Phylogenetic position of Mammoth and Steller's sea cow within Tethytheria demonstrated by mitochondrial DNA sequences, J. Mol. Evol., 44, 406, 10.1007/PL00006160

Palkopoulou, 2013, Holarctic genetic structure and range dynamics in the woolly mammoth, Proc. Biol. Sci., 280, 20131910, 10.1098/rspb.2013.1910

Ramsey, 2013, Recent and planned developments of the program oxcal, Radiocarbon, 55, 720, 10.2458/azu_js_rc.55.16215

Reimer, 2013, Intcal13 and Marine13 radiocarbon age calibration curves 0-50,000 Years Cal Bp, Radiocarbon, 1869

Roca, 2005, Cytonuclear genomic dissociation in African elephant species, Nat. Genet., 37, 96, 10.1038/ng1485

Rogaev, 2006, Complete mitochondrial genome and phylogeny of Pleistocene mammoth Mammuthus primigenius, PLoS Biol., 4, e73, 10.1371/journal.pbio.0040073

Rohland, 2007, Proboscidean mitogenomics: Chronology and mode of elephant evolution using mastodon as outgroup, PLoS Biol., 5, e207, 10.1371/journal.pbio.0050207

Saunders, 2010, Paradigms and proboscideans in the southern Great Lakes region, USA, Quat. Int., 217, 175, 10.1016/j.quaint.2009.07.031

Sanders, 2010, Cenozoic Mammals of Africa.

Schubert, 2012, Improving ancient DNA read mapping against modern reference genomes, BMC Genomics, 13, 178, 10.1186/1471-2164-13-178

Sher, 2005, Early Siberian mammoths in Northern Yukon, The World of Elephants: 2nd International Congress, 154

Skeels, 1962, The mastodons and mammoths of Michigan, Acad. Sci. Arts. Lett., 101

Smith, 2003, The thermal history of human fossils and the likelihood of successful DNA amplification, J. Hum. Evol., 45, 203, 10.1016/S0047-2484(03)00106-4

Stuart, 2002, The latest woolly mammoths (Mammuthus primigenius Blumenbach) in Europe and Asia: a review of the current evidence, Quat. Sci. Rev., 21, 1559, 10.1016/S0277-3791(02)00026-4

Tamura, 1993, Estimation of the Number of Nucleotide Substitutions in the Control Region of Mitochondrial-DNA in Humans and Chimpanzees, Mol. Biol. Evol., 10, 512

Todd, 1996, Origin and radiation of the Elephantidae, The Proboscidea: Evolution and Palaeoecology of Elephants and Their Relatives, 193, 10.1093/oso/9780198546528.003.0019

Wagner, 2014, Yersinia pestis and the Plague of Justinian 541–543 AD: a genomic analysis, Lancet Infect. Dis, 14, 319, 10.1016/S1473-3099(13)70323-2

Westgate, 2013, Tephrochronology, magnetostratigraphy and mammalian faunas of middle and early pleistocene sediments at two sites on the Old Crow River, Northern Yukon Territory, Canada, Quat. Res., 79, 75, 10.1016/j.yqres.2012.09.003

Woodhams, 2006, Can deleterious mutations explain the time dependency of molecular rate estimates?, Mol. Biol. Evol., 23, 2271, 10.1093/molbev/msl107