1932

Abstract

Ancient DNA provides a unique means to record genetic change through time and directly observe evolutionary and ecological processes. Although mostly based on mitochondrial DNA, the increasing availability of genomic sequences is leading to unprecedented levels of resolution. Temporal studies of population genetics have revealed dynamic patterns of change in many large vertebrates, featuring localized extinctions, migrations, and population bottlenecks. The pronounced climate cycles of the Late Pleistocene have played a key role, reducing the taxonomic and genetic diversity of many taxa and shaping modern populations. Importantly, the complex series of events revealed by ancient DNA data is seldom reflected in current biogeographic patterns. DNA preserved in ancient sediments and coprolites has been used to characterize a range of paleoenvironments and reconstruct functional relationships in paleoecological systems. In the near future, genome-level surveys of ancient populations will play an increasingly important role in revealing, calibrating, and testing evolutionary processes.

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2014-11-23
2024-05-28
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Literature Cited

  1. Adler CJ, Dobney K, Weyrich LS, Kaidonis J, Walker AW. et al. 2013. Sequencing ancient calcified dental plaque shows changes in oral microbiota with dietary shifts of the Neolithic and Industrial revolutions. Nat. Genet. 45:450–55 [Google Scholar]
  2. Andersen K, Bird KL, Rasmussen M, Haile JS, Breuning-Madsen H. et al. 2011. Meta-barcoding of ‘dirt’ DNA from soil reflects vertebrate biodiversity. Mol. Ecol. 21:1966–79 [Google Scholar]
  3. Anderson CN, Ramakrishnan U, Chan YL, Hadly EA. 2005. Serial SimCoal: a population genetics model for data from multiple populations and points in time. Bioinformatics 21:1733–34 [Google Scholar]
  4. Anderson-Carpenter LL, McLachlan JS, Jackson ST, Kuch M, Lumibao CY, Poinar HN. 2011. Ancient DNA from lake sediments: bridging the gap between paleoecology and genetics. BMC Evol. Biol. 11:30 [Google Scholar]
  5. Arnold LJ, Roberts RG, Macphee RDE, Haile JS, Brock F. et al. 2011. Paper II—dirt, dates and DNA: OSL and radiocarbon chronologies of perennially frozen sediments in Siberia, and their implications for sedimentary ancient DNA studies. Boreas 40:417–45 [Google Scholar]
  6. Austin JJ, Ross AJ, Smith AB, Fortey RA, Thomas RH. 1997. Problems of reproducibility—does geologically ancient DNA survive in amber-preserved insects?. Proc. Biol. Sci. 264:467–74 [Google Scholar]
  7. Austin JJ, Soubrier J, Prevosti FJ, Prates L, Trejo V. et al. 2013. The origins of the enigmatic Falkland Islands wolf. Nat. Commun. 4:1552 [Google Scholar]
  8. Axelsson E, Willerslev E, Gilbert MT, Nielsen R. 2008. The effect of ancient DNA damage on inferences of demographic histories. Mol. Biol. Evol. 25:2181–87 [Google Scholar]
  9. Barnes I, Matheus P, Shapiro B, Jensen D, Cooper A. 2002. Dynamics of Pleistocene population extinctions in Beringia brown bears. Science 295:2267–70 [Google Scholar]
  10. Barnett R, Phillips MJ, Martin LD, Harington CR, Leonard JA, Cooper A. 2005. Evolution of the extinct sabre-tooths and the American cheetahlike cat. Curr. Biol. 15:R1–2 [Google Scholar]
  11. Barnett R, Shapiro B, Barnes I, Ho SY, Burger J. et al. 2009. Phylogeography of lions (Panthera leo ssp.) reveals three distinct taxa and a late Pleistocene reduction in genetic diversity. Mol. Ecol. 18:1668–77 [Google Scholar]
  12. Barnosky AD, Matzke N, Tomiya S, Wogan GO, Swartz B. et al. 2001. Has the Earth's sixth mass extinction already arrived?. Nature 471:51–57 [Google Scholar]
  13. Beaumont MA, Zhang W, Balding DJ. 2002. Approximate Bayesian computation in population genetics. Genetics 162:2025–35 [Google Scholar]
  14. Beaumont MA. 2008. Joint determination of topology, divergence time and immigration in population trees. Simulations, Genetics and Human Prehistory S Matsumura, P Forster, C Renfrew 135–54 Cambridge, UK: McDonald Inst. Archaeol. Res. [Google Scholar]
  15. Bellemain E, Davey ML, Kauserud H, Epp LS, Boessenkool S. et al. 2013. Fungal palaeodiversity revealed using high-throughput metabarcoding of ancient DNA from arctic permafrost. Environ. Microbiol. 15:1176–89 [Google Scholar]
  16. Bertorelle G, Benazzo A, Mona S. 2010. ABC as a flexible framework to estimate demography over space and time: some cons, many pros. Mol. Ecol. 19:2609–25 [Google Scholar]
  17. Bi K, Linderoth T, Vanderpool D, Good JM, Nielsen R, Moritz C. 2013. Unlocking the vault: next-generation museum population genomics. Mol. Ecol. 22:6018–32 [Google Scholar]
  18. Boessenkool S, McGlynn G, Epp LS, Taylor D, Pimentel M. et al. 2013. Use of ancient sedimentary DNA as a novel conservation tool for high-altitude tropical biodiversity. Conserv. Biol. 28:446–55 [Google Scholar]
  19. Bon C, Berthonaud V, Maksud F, Labadie K, Poulain J. et al. 2012. Coprolites as a source of information on the genome and diet of the cave hyena. Proc. Biol. Sci. 279:2825–30 [Google Scholar]
  20. Brace S, Palkopoulou E, Dalén L, Lister AM, Miller R. et al. 2012. Serial population extinctions in a small mammal indicate Late Pleistocene ecosystem instability. Proc. Natl. Acad. Sci. USA 109:20532–36 [Google Scholar]
  21. Brandt G, Haak W, Adler CJ, Roth C, Szécsényi-Nagy A. et al. 2013. Ancient DNA reveals key stages in the formation of central European mitochondrial genetic diversity. Science 342:257–61 [Google Scholar]
  22. Briggs AW, Stenzel U, Meyer M, Krause J, Kircher M, Pääbo S. 2010. Removal of deaminated cytosines and detection of in vivo methylation in ancient DNA. Nucleic Acids Res. 38:e87 [Google Scholar]
  23. Bunce M, Worthy TH, Hoppitt W, Ford T, Willerslev E. et al. 2003. Extreme reversed sexual size dimorphism in the extinct New Zealand moa Dinornis. Nature 425:172–75 [Google Scholar]
  24. Burbano HA, Hodges E, Green RE, Briggs AW, Krause J. et al. 2010. Targeted investigation of the Neandertal genome by array-based sequence capture. Science 328:723–25 [Google Scholar]
  25. Cahill JA, Green RE, Fulton TL, Stiller M, Jay F. et al. 2013. Genomic evidence for island population conversion resolves conflicting theories of polar bear evolution. PLOS Genet. 9:e1003345 [Google Scholar]
  26. Calvignac S, Hughes S, Tougard C, Michaux J, Thevenot M. et al. 2008. Ancient DNA evidence for the loss of a highly divergent brown bear clade during historical times. Mol. Ecol. 17:1962–70 [Google Scholar]
  27. Campbell KL, Roberts JE, Watson LN, Stetefeld J, Sloan AM. et al. 2010. Substitutions in woolly mammoth hemoglobin confer biochemical properties adaptive for cold tolerance. Nat. Genet. 42:536–40 [Google Scholar]
  28. Campos PF, Willerslev E, Sher A, Orlando L, Axelsson E. et al. 2010. Ancient DNA analyses exclude humans as the driving force behind late Pleistocene musk ox (Ovibos moschatus) population dynamics. Proc. Natl. Acad. Sci. USA 107:5675–80 [Google Scholar]
  29. Collins MJ, Penkman KE, Rohland N, Shapiro B, Dobberstein RC. et al. 2009. Is amino-acid racemization a useful tool for screening for ancient DNA in bone?. Proc. R. Soc. B-Biol. Sci. 276:2971–77 [Google Scholar]
  30. Cooper A, Poinar HN. 2000. Ancient DNA: Do it right or not at all. Science 289:1139 [Google Scholar]
  31. Cooper A, Turney C, Brook BW, McDonald HG, Hughen KA, Bradshaw CJA. 2014. Climate-associated megafaunal turnover in Late Pleistocene Eurasia and North America revealed by high-resolution timescale. Science. In press
  32. Cornuet JM, Pudlo P, Veyssier J, Dehne-Garcia A, Gauier M. et al. 2014. DIYABC v2.0: a software to make approximate Bayesian computation inferences about population history using single nucleotide polymorphism, DNA sequence and microsatellite data. Bioinformatics 30:1187–89 [Google Scholar]
  33. Cornuet JM, Santos F, Beaumont MA, Robert CP, Marin JM. et al. 2008. Inferring population history with DYI ABC: a user-friendly approach to approximate Bayesian computation. Bioinformatics 24:2713–19 [Google Scholar]
  34. Csillery K, Blum MG, Gaggiotti OE, Francois O. 2010. Approximate Bayesian Computation (ABC) in practice. Trends Ecol. Evol. 25:410–18 [Google Scholar]
  35. Csillery K, Francois O, Blum MG. 2012. abc: an R package for approximate Bayesian computation (ABC). Methods Ecol. Evol. 3:475–79 [Google Scholar]
  36. Dabney J, Knapp M, Glocke I, Gansauge MT, Weihmann A. et al. 2013. Complete mitochondrial genome sequence of a Middle Pleistocene cave bear reconstructed from ultrashort DNA fragments. Proc. Natl. Acad. Sci. USA 110:15758–63 [Google Scholar]
  37. Dalén L, Nyström V, Valdiosera C, Germonpré M, Sablin M. et al. 2007. Ancient DNA reveals lack of postglacial habitat tracking in the arctic fox. Proc. Natl. Acad. Sci. USA 104:6726–29 [Google Scholar]
  38. Debruyne R, Chu G, King CE, Bos K, Kuch M. et al. 2008. Out of America: ancient DNA evidence for a new world origin of late quaternary woolly mammoths. Curr. Biol. 18:1320–26 [Google Scholar]
  39. Depaulis F, Orlando L, Hanni C. 2009. Using classical population genetics tools with heterochroneous data: time matters. ! PLOS ONE 4:e5541 [Google Scholar]
  40. Der Sarkissian C, Ermini L, Jónsson H, Alekseev AN, Crubezy E. et al. 2014. Shotgun microbial profiling of fossil remains. Mol. Ecol. 23:180–98 [Google Scholar]
  41. Drummond AJ, Rambaut A, Shapiro B, Pybus OG. 2005. Bayesian coalescent inference of past population dynamics from molecular sequences. Mol. Biol. Evol. 22:1185–92 [Google Scholar]
  42. Drummond AJ, Suchard MA, Xie D, Rambaut A. 2012. Bayesian phylogenetics with BEAUti and the BEAST 1.7. Mol. Biol. Evol. 29:1969–73 [Google Scholar]
  43. Edwards CJ, Suchard MA, Lemey P, Welch JJ, Barnes I. et al. 2011. Ancient hybridization and an Irish origin for the modern polar bear matriline. Curr. Biol. 21:1251–58 [Google Scholar]
  44. Enard W, Gehre S, Hammerschmidt K, Hölter SM, Blass T. et al. 2009. A humanized version of Foxp2 affects cortico-basal ganglia circuits in mice. Cell 137:961–71 [Google Scholar]
  45. Epp LA, Boessenkool S, Bellemain EP, Haile J, Esposito A. et al. 2012. New environmental metabarcodes for analyzing soil DNA: potential for studying past and present ecosystems. Mol. Ecol. 21:1821–33 [Google Scholar]
  46. Excoffier L, Foll M. 2011. Fastsimcoal: a continuous-time coalescent simulator of genomic diversity under arbitrarily complex evolutionary scenarios. Bioinformatics 27:1332–34 [Google Scholar]
  47. Fu Q, Meyer M, Gao X, Stenzel U, Burbano HA. et al. 2013a. DNA analysis of an early modern human from Tianyuan Cave, China. Proc. Natl. Acad. Sci. USA 110:2223–27 [Google Scholar]
  48. Fu Q, Mittnik A, Johnson PL, Bos K, Lari M. et al. 2013b. A revised timescale for human evolution based on ancient mitochondrial genomes. Curr. Biol. 23:553–59 [Google Scholar]
  49. Giguet-Covex C, Pansu J, Arnaud F, Rey PJ, Griggo C. et al. 2014. Long livestock farming history and human landscape shaping revealed by lake sediment DNA. Nat. Commun. 5:3211 [Google Scholar]
  50. Gilbert MT, Drautz DI, Lesk AM, Ho SY, Qi J. et al. 2008. Intraspecific analysis of Siberian woolly mammoths using complete mitochondrial genomes. Proc. Natl. Acad. Sci. USA 105:8327–32 [Google Scholar]
  51. Gill MS, Lemey P, Faria NR, Rambaut A, Shapiro B, Suchard MA. 2013. Improving Bayesian population dynamics inference: a coalescent-based model for multiple loci. Mol. Biol. Evol. 30:713–24 [Google Scholar]
  52. Ginolhac A, Rasmussen M, Gilbert MT, Willerslev E, Orlando L. 2011. mapDamage testing for damage patterns in ancient DNA sequences. Bioinformatics 27:2153–55 [Google Scholar]
  53. Gokhman D, Lavi E, Prüfer K, Fraga MF, Riancho JA. et al. 2014. Reconstructing the DNA methylation maps of the Neandertal and the Denisovan. Science 344:523–27 [Google Scholar]
  54. Gongora J, Rawlence NJ, Mobegi VA, Jianlin H, Alcalde JA. et al. 2008. Indo-European and Asian origins for Chilean and Pacific chickens revealed by mtDNA. Proc. Natl. Acad. Sci. USA 105:10308–13 [Google Scholar]
  55. Green RE, Krause J, Briggs AW, Maricic T, Stenzel U. et al. 2010. A draft sequence of the Neandertal genome. Science 328:710–22 [Google Scholar]
  56. Guthrie RD. 1990. Frozen Fauna of the Mammoth Steppe Chicago: Univ. Chicago Press
  57. Haile J, Froese DG, Macphee RD, Roberts RG, Arnold LJ. et al. 2009. Ancient DNA reveals late survival of mammoth and horse in interior Alaska. Proc. Natl. Acad. Sci. USA 106:22352–57 [Google Scholar]
  58. Haile J, Holdaway R, Oliver K, Bunce M, Gilbert MTP. et al. 2007. Ancient DNA chronology within sediment deposits: Are paleobiological reconstructions possible and is DNA leaching a factor?. Mol. Biol. Evol. 24:982–89 [Google Scholar]
  59. Hein J, Schierup MH, Wiuf C. 2005. Gene Genealogies, Variation and Evolution: A Primer in Coalescent Theory Oxford, UK: Oxford Univ. Press
  60. Helled J, Drummond AJ. 2010. Bayesian inference of species trees from multilocus data. Mol. Biol. Evol. 27:570–80 [Google Scholar]
  61. Heller R, Chikhi L, Siegismund HR. 2013. The confounding effect of population structure on Bayesian skyline plot inferences of demographic histories. PLOS ONE 8:e62992 [Google Scholar]
  62. Higuchi R, Bowman B, Freiberger M, Ryder OA, Wilson AC. 1984. DNA sequences from the quagga, an extinct member of the horse family. Nature 312:282–84 [Google Scholar]
  63. Ho SYW, Kolokotronis SO, Allaby RG. 2007a. Elevated substitution rates estimated from ancient DNA. Biol. Lett. 3:702–5 [Google Scholar]
  64. Ho SYW, Lanfear R, Bromham L, Phillips MJ, Soubrier J. et al. 2011. Time dependent rates of molecular evolution. Mol. Ecol. 20:3087–101 [Google Scholar]
  65. Ho SYW, Phillips MJ, Cooper A, Drummond AJ. 2005. Time dependency of molecular rate estimates and systematic overestimation of recent divergence times. Mol. Biol. Evol. 22:1561–68 [Google Scholar]
  66. Ho SYW, Shapiro B. 2011. Skyline-plot methods for estimating demographic history from nucleotide sequences. Mol. Ecol. Resour. 11:423–34 [Google Scholar]
  67. Ho SYW, Shapiro S, Phillips MJ, Cooper A, Drummond AJ. 2007b. Evidence for time dependency of molecular rate estimates. Syst. Biol. 56:515–22 [Google Scholar]
  68. Hofreiter M, Capelli C, Krings M, Waits L, Conard N. et al. 2002. Ancient DNA analyses reveal high mitochondrial DNA sequence diversity and parallel morphological evolution of Late Pleistocene cave bears. Mol. Biol. Evol. 19:1244–50 [Google Scholar]
  69. Hofreiter M, Mead JI, Martin P, Poinar HN. 2003. Molecular caving. Curr. Biol. 13:R693–95 [Google Scholar]
  70. Hofreiter M, Münzel S, Conard NJ, Pollack J, Slatkin M. et al. 2007. Sudden replacement of cave bear mitochondrial DNA in the Late Pleistocene. Curr. Biol. 17:R122–23 [Google Scholar]
  71. Hofreiter M, Poinar HN, Spaulding WG, Bauer K, Martin PS. et al. 2000. A molecular analysis of ground sloth diet through the last glaciation. Mol. Ecol. 9:1975–84 [Google Scholar]
  72. Hofreiter M, Rabeder G, Jaenicke-Després V, Withalm G, Nagel D. et al. 2004a. Evidence for reproductive isolation between cave bear populations. Curr. Biol. 14:40–43 [Google Scholar]
  73. Hofreiter M, Serre D, Rohland N, Rabeder G, Nagel D. et al. 2004b. Lack of phylogeography in European mammals before the last glaciation. Proc. Natl. Acad. Sci. USA 101:12963–68 [Google Scholar]
  74. Huson DH, Auch AF, Qi J, Schuster SC. 2007. MEGAN analysis of metagenomic data. Genome Res. 17:377–86 [Google Scholar]
  75. Huson DH, Weber N. 2013. Microbial community analysis using MEGAN. Methods Enzymol. 531:465–85 [Google Scholar]
  76. Huynen L, Millar CD, Scofield RP, Lambert DM. 2003. Nuclear DNA sequences detect species limits in ancient moa. Nature 425:175–78 [Google Scholar]
  77. Jakobsson M. 2009. COMPASS: a program for generating serial samples under an infinite site model. Bioinformatics 25:2845–47 [Google Scholar]
  78. Jónsson H, Ginolhac A, Schubert M, Johnson PL, Orlando L. 2013. mapDamage2.0: fast approximate Bayesian estimates of ancient DNA damage parameters. Bioinformatics 29:1682–84 [Google Scholar]
  79. Jørgensen T, Haile J, Moller P, Andreev A, Boessenkool S. et al. 2012a. A comparative study of ancient sedimentary DNA, pollen and macrofossils from permafrost sediments of northern Siberia reveals long-term vegetational stability. Mol. Ecol. 21:1989–2003 [Google Scholar]
  80. Jørgensen T, Kjaer KH, Haile J, Rasmussen M, Boessenkool S. et al. 2012b. Islands in the ice: detecting past vegetation on Greenlandic nunataks using historical records. Mol. Ecol. 21:1980–88 [Google Scholar]
  81. Juck DF, Whissell G, Steven B, Pollard W, McKay CP. et al. 2005. Utilization of fluorescent microspheres and a green fluorescent protein-marked strain for assessment of microbiological contamination of permafrost and ground ice core samples from the Canadian High Arctic. Appl. Environ. Microbiol. 71:1035–41 [Google Scholar]
  82. Keller A, Graefen A, Ball M, Matzas M, Boisguerin V. et al. 2012. New insights into the Tyrolean Iceman's origin and phenotype as inferred by whole-genome sequencing. Nat. Commun. 3:698 [Google Scholar]
  83. Kircher M, Sawyer S, Meyer M. 2012. Double indexing overcomes inaccuracies in multiplex sequencing on the Illumina platform. Nucleic Acids Res. 40:e3 [Google Scholar]
  84. Knapp M, Rohland N, Weinstock J, Baryshnikov G, Sher A. et al. 2009. First DNA sequences from Asian cave bear fossils reveal deep divergences and complex phylogeographic patterns. Mol. Ecol. 18:1225–38 [Google Scholar]
  85. Koch PL, Barnosky AD. 2006. Late Quaternary extinctions: state of the debate. Annu. Rev. Ecol. Evol. Syst. 37:215–50 [Google Scholar]
  86. Krause J, Dear PH, Pollack JL, Slatkin M, Spriggs H. et al. 2006. Multiplex amplification of the mammoth mitochondrial genome and the evolution of Elephantidae. Nature 439:724–27 [Google Scholar]
  87. Krause J, Lalueza-Fox C, Orlando L, Enard W, Green RE. et al. 2007. The derived FOXP2 variant of modern humans was shared with Neandertals. Curr. Biol. 17:1908–12 [Google Scholar]
  88. Lalueza-Fox C, Römpler H, Caramelli D, Stäubert C, Catalano G. et al. 2007. A melanocortin 1 receptor allele suggests varying pigmentation among Neanderthals. Science 318:1453–55 [Google Scholar]
  89. Leonard JA, Shanks O, Hofreiter M, Kreuz E, Hodges L. et al. 2007a. Animal DNA in PCR reagents plagues ancient DNA research. J. Arch. Sci. 34:1361–66 [Google Scholar]
  90. Leonard JA, Vilà C, Fox-Dobbs K, Koch PL, Wayne RK, Van Valkenburgh B. 2007b. Megafaunal exinctions and the disappearance of a specialized wolf ecomorph. Curr. Biol. 17:1146–50 [Google Scholar]
  91. Leuenberger C, Wegmann D. 2010. Bayesian computation and model selection without likelihoods. Genetics 184:243–52 [Google Scholar]
  92. Li H, Durbin R. 2011. Inference of human population history from individual whole-genome sequences. Nature 475:493–96 [Google Scholar]
  93. Lister AM, Stuart AJ. 2008. The impact of climate change on large mammal distribution and extinction: evidence from the last glacial/interglacial transition. C. R. Geosci. 340:615–20 [Google Scholar]
  94. Llamas B, Holland ML, Chen K, Cropley JE, Cooper A, Suter CM. 2012. High-resolution analysis of cytosine methylation in ancient DNA. PLOS ONE 7:e30226 [Google Scholar]
  95. Loreille O, Orlando L, Patou-Mathis M, Philippe M, Taberlet P, Hänni C. 2001. Ancient DNA analysis reveals divergence of the cave bear, Ursus spelaeus, and brown bear, Ursus arctos, lineages. Curr. Biol. 11:200–3 [Google Scholar]
  96. Lorenzen ED, Nogués-Bravo D, Orlando L, Weinstock J, Binladen J. et al. 2011. Species-specific responses of Late Quaternary megafauna to climate and humans. Nature 479:359–64 [Google Scholar]
  97. Lydolph MC, Jacobsen J, Arctander P, Gilbert MTP, Gilichinsky DA. et al. 2005. Beringia paleoecology inferred from permafrost-preserved fungal DNA. App. Environ. Microbiol. 71:1012 [Google Scholar]
  98. Maricic T, Günther V, Georgiev O, Gehre S, Curlin M. et al. 2013. A recent evolutionary change affects a regulatory element in the human FOXP2 gene. Mol. Biol. Evol. 30:844–52 [Google Scholar]
  99. Maricic T, Whitten M, Pääbo S. 2010. Multiplex DNA sequence capture of mitochondrial genomes using PCR products. PLOS ONE 5:e14004 [Google Scholar]
  100. Meiri M, Lister AM, Collins MJ, Tuross N, Goebel T. et al. 2013. Faunal record identifies Bering isthmus conditions as constraint to end-Pleistocene migration to the New World. Proc. R. Soc. B-Biol. Sci. 281:20132167 [Google Scholar]
  101. Mellows A, Barnett R, Dalén L, Sandoval-Castellanos E, Linderholm A. et al. 2012. The impact of past climate change on genetic variation and population connectivity in the Icelandic arctic fox. Proc. R. Soc. B-Biol. Sci. 279:4568–73 [Google Scholar]
  102. Metcalf JL, Prost S, Nogués-Bravo D, DeChaine EG, Anderson C. et al. 2014. Integrating multiple lines of evidence into historical biogeography hypothesis testing: a Bison bison case study. Proc. R. Soc. B-Biol. Sci. 281:20132782 [Google Scholar]
  103. Meyer M, Fu Q, Aximu-Petri A, Glocke I, Nickel B. et al. 2014. A mitochondrial genome sequence of a hominin from Sima de los Huesos. Nature 505:403–6 [Google Scholar]
  104. Meyer M, Kircher M, Gansauge MT, Li H, Racimo F. et al. 2012. A high-coverage genome sequence from an archaic Denisovan individual. Science 338:222–26 [Google Scholar]
  105. Miller W, Drautz DI, Ratan A, Pusey B, Qi J. et al. 2008. Sequencing the nuclear genome of the extinct woolly mammoth. Nature 456:387–90 [Google Scholar]
  106. Miller W, Schuster SC, Welch AJ, Ratan A, Bedoya-Reina OC. et al. 2012. Polar and brown bear genomes reveal ancient admixture and demographic footprints of past climate change. Proc. Natl. Acad. Sci. USA 109:E2382–90 [Google Scholar]
  107. Mourier T, Ho SY, Gilbert MT, Willerslev E, Orlando L. 2012. Statistical guidelines for detecting past population shifts using ancient DNA. Mol. Biol. Evol. 29:2241–51 [Google Scholar]
  108. Munch K, Boomsma W, Huelsenbeck J, Willerslev E, Nielsen R. 2008. Statistical assignment of DNA sequences using Bayesian phylogenetics. Syst. Biol. 57:750–57 [Google Scholar]
  109. Navascues M, Emerson BC. 2009. Elevated substitution rate estimates from ancient DNA: model violation and bias of Bayesian methods. Mol. Ecol. 18:4390–97 [Google Scholar]
  110. Navascues M, Depaulis F, Emerson BC. 2010. Combining contemporary and ancient DNA in population genetic and phylogeographical studies. Mol. Ecol. Resour. 10:760–72 [Google Scholar]
  111. Nicholls H. 2008. Darwin 200: Let's make a mammoth. Nature 456:310–14 [Google Scholar]
  112. Nielsen R, Beaumont MA. 2009. Statistical inferences in phylogeography. Mol. Ecol. 18:1034–47 [Google Scholar]
  113. Nyström V, Dalén L, Vartanyan S, Lidén K, Ryman N, Angerbjörn A. 2010. Temporal genetic change in the last remaining population of woolly mammoth. Proc. R. Soc. B-Biol. Sci. 277:2331–37 [Google Scholar]
  114. Nyström V, Humphrey J, Skoglund P, McKeown NJ, Vartanyan S. et al. 2012. Microsatellite genotyping reveals end-Pleistocene decline in mammoth autosomal genetic variation. Mol. Ecol. 21:3391–402 [Google Scholar]
  115. Olalde I, Allentoft ME, Sánchez-Quinto F, Santpere G, Chiang CW. et al. 2014. Derived immune and ancestral pigmentation alleles in a 7,000-year-old Mesolithic European. Nature 507:225–28 [Google Scholar]
  116. Orlando L, Bonjean D, Bocherens H, Thénot A, Argant A. et al. 2002. Ancient DNA and the population genetics of cave bears (Ursus spelaeus) through space and time. Mol. Biol. Evol. 19:1920–33 [Google Scholar]
  117. Orlando L, Ginolhac A, Zhang G, Froese D, Albrechtsen A. et al. 2013. Recalibrating Equus evolution using the genome sequence of an early Middle Pleistocene horse. Nature 499:74–78 [Google Scholar]
  118. Orlando L, Male D, Alberdi MT, Prado JL, Prieto A. et al. 2008. Ancient DNA clarifies the evolutionary history of American Late Pleistocene equids. J. Mol. Evol. 66:533–38 [Google Scholar]
  119. Orlando L, Metcalf J, Alberdi MT, Telles-Antunes M, Bonjean D. et al. 2009. Revising the recent evolutionary history of equids using ancient DNA. Proc. Natl. Acad. Sci. USA 106:21754–59 [Google Scholar]
  120. Orlando L, Willerslev E. 2014. Evolution: an epigenetic window into the past?. Science 345:511–12 [Google Scholar]
  121. Pääbo S. 1985. Molecular cloning of Ancient Egyptian mummy DNA. Nature 314:644–45 [Google Scholar]
  122. Pääbo S, Higuchi RG, Wilson AC. 1989. Ancient DNA and the polymerase chain reaction. The emerging field of molecular archaeology. J. Biol. Chem. 264:9709–12 [Google Scholar]
  123. Palkopoulou E, Dalén L, Lister AM, Vartanyan S, Sablin M. et al. 2013. Holarctic genetic structure and range dynamics in the woolly mammoth. Proc. R. Soc. B-Biol. Sci. 280:20131910 [Google Scholar]
  124. Parducci L, Jørgensen T, Tollefsrud MM, Elverland E, Alm T. et al. 2011. Glacial survival of boreal trees in northern Scandinavia. Science 335:1083–86 [Google Scholar]
  125. Paxinos EE, James HF, Olson SL, Ballou JD, Leonard JA, Fleischer RC. 2002. Prehistoric decline of genetic diversity in the nene. Science 296:1827 [Google Scholar]
  126. Pedersen JS, Valen E, Velazquez AM, Parker BJ, Rasmussen M. et al. 2014. Genome-wide nucleosome map and cytosine methylation levels of an ancient human genome. Genome Res. 24:454–66 [Google Scholar]
  127. Pedersen MW, Ginolhac A, Orlando L, Olsen J, Andersen K. et al. 2013. A comparative study of ancient environmental DNA to pollen and macrofossils from lake sediments reveals taxonomic overlap and additional plant taxa. Quat. Sci. Rev. 75:161–68 [Google Scholar]
  128. Phillips MJ, Gibb GC, Crimp EA, Penny D. 2010. Tinamous and moa flock together: mitochondrial genome sequence analysis reveals independent losses of flight among ratites. Syst. Biol. 59:90–107 [Google Scholar]
  129. Prost S, Smirnov N, Fedorov VB, Sommer RS, Stiller M. et al. 2010. Influence of climate warming on arctic mammals? New insights from ancient DNA studies of the collared lemming Dicrostonyx torquatus. PLOS ONE 5:e10447 [Google Scholar]
  130. Prüfer K, Racimo F, Patterson N, Jay F, Sankararaman S. et al. 2014. The complete genome sequence of a Neanderthal from the Altai Mountains. Nature 505:43–49 [Google Scholar]
  131. Raghavan M, Sloglund P, Graf KE, Metspalu M, Albrechtsen A. et al. 2014. Upper Palaeolithic Siberian genome reveals dual ancestry of Native Americans. Nature 505:87–91 [Google Scholar]
  132. Ramakrishnan U, Hadly EA, Mountain JL. 2005. Detecting past bottlenecks using temporal genetic data. Mol. Ecol. 14:2915–22 [Google Scholar]
  133. Rambaut A, Ho SY, Drummond AJ, Shapiro B. 2009. Accommodating the effect of ancient DNA damage on inferences of demographic histories. Mol. Biol. Evol. 26:245–48 [Google Scholar]
  134. Rasmussen M, Anzick SL, Waters MR, Skoglund P, DeGiorgio M. et al. 2014. The genome of a Late Pleistocene human from a Clovis burial site in western Montana. Nature 506:225–29 [Google Scholar]
  135. Rasmussen M, Guo X, Wang Y, Lohmueller KE, Rasmussen S. et al. 2011. An Aboriginal Australian genome reveals separate human dispersals into Asia. Science 334:94–98 [Google Scholar]
  136. Rasmussen M, Li Y, Lindgreen S, Pedersen JS, Albrechtsen A. et al. 2010. Ancient human genome sequence of an extinct Palaeo-Eskimo. Nature 463:757–62 [Google Scholar]
  137. Reich D, Green RE, Kircher M, Krause J, Patterson N. et al. 2010. Genetic history of an archaic hominin group from Denisova Cave in Siberia. Nature 468:1053–60 [Google Scholar]
  138. Reimers-Kipping S, Hevers W, Pääbo S, Enard W. 2011. Humanized Foxp2 specifically affects cortico-basal ganglia circuits. Neuroscience 175:75–84 [Google Scholar]
  139. Römpler H, Rohland N, Lalueza-Fox C, Willerslev E, Kuznetsova T. et al. 2006. Nuclear gene indicates coat-color polymorphism in mammoths. Science 313:62 [Google Scholar]
  140. Santiago-Rodriguez TM, Patrício AR, Rivera JI, Coradin M, Gonzalez A. et al. 2014. luxS in bacteria isolated from 25- to 40-million-year-old amber. FEMS Microbiol. Lett. 350:117–24 [Google Scholar]
  141. Scally A, Durbin R. 2012. Revising the human mutation rate: implications for understanding human evolution. Nat. Rev. Genet. 13:745–53 [Google Scholar]
  142. Shapiro B, Drummond AJ, Rambaut A, Wilson MC, Matheus PE. et al. 2004. Rise and fall of the Beringian steppe bison. Science 306:1561–65 [Google Scholar]
  143. Shapiro B, Hofreiter M. 2014. A paleogenomic perspective on evolution and gene function: new insights from ancient DNA. Science 343:1236573 [Google Scholar]
  144. Sheehan S, Harris K, Song YS. 2013. Estimating variable effective population size from multiple genomes: a sequentially Markov Conditional Sampling Distribution Approach. Genetics 194:647–62 [Google Scholar]
  145. Sheng GL, Soubrier J, Liu JY, Werdelin L, Llamas B. et al. 2014. Pleistocene Chinese cave hyenas and the recent Eurasian history of the spotted hyena, Crocuta crocuta. Mol. Ecol. 23:522–33 [Google Scholar]
  146. Smith CI, Chamberlain AT, Riley MS, Stringer CB, Collins MJ. 2003. The thermal history of human fossils and the likelihood of successful DNA amplification. J. Hum. Evol. 45:203–17 [Google Scholar]
  147. Soubrier J, Steel M, Lee MS, Der Sarkissian C, Guindon S. et al. 2012. The influence of rate heterogeneity among sites on the time dependence of molecular rates. Mol. Biol. Evol. 29:3345–58 [Google Scholar]
  148. Stewart JR, Lister AM. 2001. Cryptic northern refugia and the origins of the modern biota. Trends Ecol. Evol. 16:608–13 [Google Scholar]
  149. Stewart JR, Lister AM, Barnes I, Dalén L. 2010. Refugia revisited: individualistic responses of species in space and time. Proc. R. Soc. B-Biol. Sci. 277:661–71 [Google Scholar]
  150. Stiller M, Baryshnikov G, Bocherens H, Grandal d'Anglade A, Hilpert B. et al. 2010. Withering away—25,000 years of genetic decline preceded cave bear extinction. Mol. Biol. Evol. 27:975–78 [Google Scholar]
  151. Storey AA, Ramírez JM, Quiroz D, Burley DV, Addison DJ. et al. 2007. Radiocarbon and DNA evidence for a pre-Columbian introduction of Polynesian chickens to Chile. Proc. Natl. Acad. Sci. USA 104:10335–39 [Google Scholar]
  152. Stuart AJ, Lister AM. 2007. Patterns of Late Quaternary megafaunal extinctions in Europe and northern Asia. Cour. Forsch.-Inst. Senckenberg 259:289–99 [Google Scholar]
  153. Stuart AJ, Lister AM. 2012. Extinction chronology of the woolly rhinoceros Coelodonta antiquitatis in the context of late Quaternary megafaunal extinctions in northern Eurasia. Quat. Sci. Rev. 51:1–17 [Google Scholar]
  154. Thomson VA, Lebrasseur O, Austin JJ, Hunt T, Burney D. et al. 2014. Using ancient DNA to study the origins and dispersal of ancestral Polynesian chickens across the Pacific. Proc. Natl. Acad. Sci. USA 111:4821–31 [Google Scholar]
  155. Valdiosera CE, Garcia N, Anderung C, Dalén L, Cregut-Bonnoure E. et al. 2007. Staying out in the cold: glacial refugia and mitochondrial DNA phylogeography in ancient European brown bears. Mol. Ecol. 16:5140–48 [Google Scholar]
  156. Valdiosera CE, Garcia-Garitagoitia JL, Garcia N, Doadrio I, Thomas MG. et al. 2008. Surprising migration and population size dynamics in ancient Iberian brown bears (Ursus arctos). Proc. Natl. Acad. Sci. USA 105:5123–28 [Google Scholar]
  157. Waits LP, Talbot SL, Ward RH, Shields GF. 1998. Mitochondrial DNA phylogeography of the North American brown bear and implications for conservation. Conserv. Biol. 12:408–17 [Google Scholar]
  158. Wall JD, Kim SK. 2007. Inconsistencies in Neanderthal genomic DNA sequences. PLOS Genet. 3:1862–66 [Google Scholar]
  159. Warinner C, Rodrigues JF, Vyas R, Trachsel C, Shved N. et al. 2014. Pathogens and host immunity in the ancient human oral cavity. Nat. Genet. 46:336–44 [Google Scholar]
  160. Wegmann D, Excoffier L. 2008. Efficient Approximate Bayesian Computation coupled with Markov Chain Monte Carlo without likelihood. Genetics 182:1207–18 [Google Scholar]
  161. Wegmann D, Leuenberger C, Neuenschwander S, Excoffier L. 2010. ABCtoolbox: a versatile toolkit for approximate Bayesian computations. BMC Bioinform. 11:116 [Google Scholar]
  162. Weinstock J, Willerslev E, Sher A, Tong W, Ho SY. et al. 2005. Evolution, systematics, and phylogeography of Pleistocene horses in the new world: a molecular perspective. PLOS Biol. 3:e241 [Google Scholar]
  163. Welch AJ, Wiley AE, James HF, Ostrom PH, Stafford TW Jr, Fleischer RC. 2012. Ancient DNA reveals genetic stability despite demographic decline: 3,000 years of population history in the endemic Hawaiian petrel. Mol. Biol. Evol. 29:3729–40 [Google Scholar]
  164. Willerslev E, Cappellini E, Boomsma W, Nielsen R, Hebsgaard MB. et al. 2007. Ancient biomolecules from deep ice cores reveal a forested southern Greenland. Science 317:111–14 [Google Scholar]
  165. Willerslev E, Davison J, Moora M, Zobel M, Coissac E. et al. 2014. Fifty thousand years of Arctic vegetation and megafaunal diet. Nature 506:47–51 [Google Scholar]
  166. Willerslev E, Hansen A, Binladen J, Brand TB, Gilbert MT. et al. 2003. Diverse plant and animal genetic records from Holocene and Pleistocene sediments. Science 300:791–95 [Google Scholar]
  167. Willerslev E, Hansen AJ, Rønn R, Brand TB, Barnes I. et al. 2004. Long-term persistence of bacterial DNA. Curr. Biol. 14:R9–10 [Google Scholar]
  168. Wood JR, Rawlence NJ, Rogers GM, Austin JJ. et al. 2008. Coprolite deposits reveal the diet and ecology of the extinct New Zealand megaherbivore moa (Aves, Dinornithiformes). Quat. Sci. Rev. 27:2593–602 [Google Scholar]
  169. Wood JR, Wilmshurst JM, Richardson SJ, Rawlence NJ, Wagstaff SJ. et al. 2013. Resolving lost herbivore community structure using coprolites of four sympatric moa species (Aves: Dinornithiformes). Proc. Natl. Acad. Sci. USA 110:16910–15 [Google Scholar]
  170. Wood JR, Wilmshurst JM, Worthy TH, Holzapfel AS, Cooper A. 2012. A lost link between a flightless parrot and a parasitic plant and the potential role of coprolites in conservation paleobiology. Conserv. Biol. 26:1091–99 [Google Scholar]
  171. Yuan Y, Shen TJ, Gupta P, Ho NT, Simplaceanu V. et al. 2011. A biochemical-biophysical study of hemoglobins from woolly mammoth, Asian elephant, and humans. Biochemistry 50:7350–60 [Google Scholar]
  172. Zhang H, Paijmans JL, Chang F, Wu X, Chen G. et al. 2013. Morphological and genetic evidence for early Holocene cattle management in northeastern China. Nat. Commun. 4:2755 [Google Scholar]
  173. Zischler H, Höss M, Handt O, von Haeseler A, van der Kuyl AC, Goudsmit J. 1995. Detecting dinosaur DNA. Science 268:1192–93 [Google Scholar]
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