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Paleogenomics pp 393–418Cite as

Genomics of Extinction

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Part of the book series: Population Genomics ((POGE))

Abstract

Many species went extinct during the Late Pleistocene, including a large proportion of the Earth’s megafauna. Recent research on Pleistocene extinctions has started to reveal that species responded individualistically to environmental fluctuations and human interference. Through paleogenomics, it is now possible to study the extinction process in more detail, which could help disentangle why some species went extinct while others did not. Several species seem to have gone through a sudden decline right before extinction, whereas others reached the point of extinction via a gradual decline. In addition, some species experienced an initial severe bottleneck but survived for thousands of years more at reduced numbers before their final extinction. The use of temporally spaced complete genomes allows for a more direct examination of changes in genomic parameters through time, such as declines in standing genetic variation and accumulation of deleterious mutations, as a consequence of these pre-extinction processes. Additionally, the increasing access to complete ancient genomes will in the future allow researchers to investigate whether species were capable of adapting to environmental changes as well as the small population size that they were subject to prior to the extinction.

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References

  • Barnes I, Matheus P, Shapiro B, Jensen D, Cooper A. Dynamics of Pleistocene population extinctions in Beringian brown bears. Science. 2002;295:2267–70.

    Article  CAS  PubMed  Google Scholar 

  • Barnosky AD, Koch PL, Feranec RS, Wing SL, Shabel AB. Assessing the causes of Late Pleistocene extinctions on the continents. Science. 2004;306:70–5.

    Article  CAS  PubMed  Google Scholar 

  • Barrett SCH, Charlesworth D. Effects of a change in the level of inbreeding on the genetic load. Nature. 1991;352:522–4.

    Article  CAS  PubMed  Google Scholar 

  • Bernatchez L, Landry C. MHC studies in nonmodel vertebrates: what have we learned aboutnatural selection in 15 years? J Evol Biol. 2003;16:363–77.

    Article  CAS  PubMed  Google Scholar 

  • Bocherens H, Fizet M, Mariotti A. Diet, physiology and ecology of fossil mammals as inferred from stable carbon and nitrogen isotope biogeochemistry: implications for Pleistocene bears. Palaeogeogr Palaeoclimatol Palaeoecol. 1994;107:213–25.

    Article  Google Scholar 

  • Bolger AM, Lohse M, Usade B. Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics. 2014;30:2114–20.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Brace S, Palkopoulou E, Dalen L, Lister AM, Miller R, Otte M, Germonpré M, Blockley SPE, Stewart JR, Barnes I. Serial population extinctions in a small mammal indicate Late Pleistocene ecosystem instability. Proc Natl Acad Sci U S A. 2012;109:20532–6.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Broman KW, Weber JL. Long homozygous chromosomal segments in reference families from the centre d’Etude du polymorphisme humain. Am J Hum Genet. 1999;65:1493–500.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Brooks TM, Pimm SL, Oyugi JO. Time lag between deforestation and bird extinciton in tropical forest fragments. Conserv Biol. 1999;13:1140–50.

    Article  Google Scholar 

  • Bryant EH, Meffert LM, McCommas SA. Fitness rebound in serially bottlenecked populations of the house fly. Am Nat. 1990;136:542–9.

    Article  Google Scholar 

  • Bucher EH. The causes of extinction of the passenger pigeon. Curr Ornithol. 1992;9:1–36.

    Google Scholar 

  • Campbell DL, Whittle PM. Three case studies: aurochs, mammoths and passenger pigeons. In: Resurrecting extinct species. Cham: Palgrave MacMillan; 2017.

    Chapter  Google Scholar 

  • Campos PF, Willerslev E, Sher A, Orlando L, Axelsson E, Tikhonov A, Aaris-Sorensen K, Greenwood AD, Kahlke RD, Kosintsev P, Krakhmalnaya T, Kuznetsova T, Lemey P, MacPhee R, Norris CA, Shepherd K, Suchard MA, Zazula GD, Shapiro B, Gilbert MTP. Ancient DNA analyses exclude humans as the driving force behind late Pleistocene musk ox (Ovibos moschatus) population dynamics. Proc Natl Acad Sci U S A. 2010;107:5675–80.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Carrington M, Nelson GW, Martin MP, Kissner T, Vlahov D, Goedert JJ, Kaslow R, Buchbinder S, Hoots K, O’Brien SJ. HLA and HIV-1: heterozygote advantage and B*35-Cw*04 disadvantage. Science. 1999;283:1748–52.

    Article  CAS  PubMed  Google Scholar 

  • Caughley G. Directions in conservation biology. J Anim Ecol. 1994;63:215–44.

    Article  Google Scholar 

  • Chang D, Shapiro B. Using ancient DNA and coalescent-based methods to infer extinction. Biol Lett. 2016;12:20150822.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Charlesworth B, Charlesworth D. The genetic basis of inbreeding depression. Genet Res. 1999;74:329–40.

    Article  CAS  PubMed  Google Scholar 

  • Charlesworth D, Willis JH. The genetics of inbreeding depression. Nat Rev Genet. 2009;10:783–96.

    Article  CAS  PubMed  Google Scholar 

  • Cho YS, Hu L, Hou H, Lee H, Xu J, Kwon S, Oh S, Kim HM, Jho S, Kim S, Shin YA, Kim BC, Kim H, Kim CU, Luo SJ, Johnson WE, Koepfli KP, Schmidt-Kuntzel A, Turner JA, Marker L, Harper C, Miller SM, Jacobs W, Bertola LD, Kim TH, Lee S, Zhou Q, Jung HJ, Xu X, Gadhvi P, Xu P, Xiong Y, Luo Y, Pan S, Gou C, Chu X, Zhang J, Liu S, He J, Chen Y, Yang L, Yang Y, He J, Liu S, Wang J, Kim CH, Kwak H, Kim JS, Hwang S, Ko J, Kim CB, Kim S, Bayarlkhagva D, Paek WK, Kim SJ, O’Brien SJ, Wang J, Bhak J. The tiger genome and comparative analysis with lion and snow leopard genomes. Nat Commun. 2013;4:2433.

    Article  PubMed  CAS  Google Scholar 

  • Clayton DA. Replication of animal mitochondrial DNA. Cell. 1982;28:693–705.

    Article  CAS  PubMed  Google Scholar 

  • Cooper A, Turney C, Hughen KA, Brook BW, McDonald HG, Bradshaw CJA. Abrupt warming events drove Late Pleistocene Holarctic megafaunal turnover. Science. 2015;349:602–6.

    Article  CAS  PubMed  Google Scholar 

  • Crow JF. Wright and fisher on inbreeding and random drift. Genetics. 2010;184:609–11.

    Article  PubMed  PubMed Central  Google Scholar 

  • Dalén L, Orlando L, Shapiro B, Brandström-Durling M, Quam R, Gilbert MTP, Fernández-Lomana JCD, Willerslev E, Arsuaga JL, Götherström A. Partial genetic turnover in neandertals: continuity in the east and population replacement in the west. Mol Biol Evol. 2012;29:1893–7.

    Article  PubMed  CAS  Google Scholar 

  • DePristo MA, Banks E, Poplin R, Garimella KV, Maguire JR, Hartl C, Philippakis AA, del Angel G, Rivas MA, Hanna M, McKenna A, Fennell TJ, Kernytsky AM, Sivachenko AY, Cibulskis K, Gabriel SB, Altshuler D, Daly MJ. A framework for variation discovery and genotyping using next-generation DNA sequencing data. Nat Genet. 2011;43:491–8.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Díez-del-Molino D, Sánchez-Barreiro F, Barnes I, Gilbert MTP, Dalén L. Quantifying temporal genomic erosion in endangered species. Trends Ecol Evol. 2018;33:176–85.

    Article  PubMed  Google Scholar 

  • Dixo M, Metzger JP, Morgante JS, Zamudio KR. Habitat fragmentation reduces genetic diversity and connectivity among toad populations in the Brazilian Atlantic Coastal Forest. Biol Conserv. 2009;142:1560–9.

    Article  Google Scholar 

  • Dobrynin P, Liu S, Tamazian G, Xiong Z, Yurchenko AA, Krasheninnikova K, Kliver S, Schmidt-Kuntzel A, Koepfli KP, Johnson W, Kuderna LF, Garcia-Perez R, Manuel M, Godinez R, Komissarov A, Makunin A, Brukhin V, Qiu W, Zhou L, Li F, Yi J, Driscoll C, Antunes A, Oleksyk TK, Eizirik E, Perelman P, Roelke M, Wildt D, Diekhans M, Marques-Bonet T, Marker L, Bhak J, Wang J, Zhang G, O’Brien SJ. Genomic legacy of the African cheetah, Acinonyx jubatus. Genome Biol. 2015;16:277.

    Article  PubMed  PubMed Central  Google Scholar 

  • Drummond AJ, Rambaut A, Shapiro B, Pybus OG. Bayesian coalescent inference of past population dynamics from molecular sequences. Mol Biol Evol. 2005;22:1185–92.

    Article  CAS  PubMed  Google Scholar 

  • Emerson BC, Paradis E, Thébaud C. Revealing the demographic histories of species using DNA sequences. Trends Ecol Evol. 2001;16:707–16.

    Article  Google Scholar 

  • Feigin CY, Newton AH, Doronina L, Schmitz J, Hipsley CA, Mitchell KJ, Gower G, Llamas B, Soubrier J, Heider TN, Menzies BR, Cooper A, O’Neill RJ, Pask AJ. Genome of the Tasmanian tiger provides insights into the evolution and demography of an extinct marsupial carnivore. Nat Ecol Evol. 2017;2:182–92.

    Article  PubMed  Google Scholar 

  • Fisher RA. The genetical theory of natural selection. Oxford: Clarendon Press; 1930.

    Book  Google Scholar 

  • Folch J, Cocero MJ, Chesné P, Alabart JL, Dominguez V, Cognie Y, Roche A, Fernandez-Arias A, Marti JI, Sanchez P, Echegoyen E, Beckers JF, Bonastre AS, Vignon X. First birth of an animal from an extinct subspecies (Capra pyrenaica pyrenaica) by cloning. Theriogenology. 2009;71:1026–34.

    Article  CAS  PubMed  Google Scholar 

  • Fortes GG, Grandal-d'Anglade A, Kolbe B, Fernandes D, Meleg IN, Garcia-Vazquez A, Pinto-Llona AC, Constantin S, de Torres TJ, Ortiz JE, Frischauf C, Rabeder G, Hofreiter M, Barlow A. Ancient DNA reveals differences in behaviour and sociality between brown bears and extinct cave bears. Mol Ecol. 2016;25:4907–18.

    Article  CAS  PubMed  Google Scholar 

  • Frankham R. Effective population size/adult population size in wildlife: a review. Genet Res. 1995;66:95–107.

    Article  Google Scholar 

  • Frankham R. Do island populations have less genetic variation than mainland populations? Heredity. 1997;78:311–27.

    Article  PubMed  Google Scholar 

  • Frankham R. Inbreeding and extinction: island populations. Conserv Biol. 1998;12:665–75.

    Article  Google Scholar 

  • Frankham R. Genetics and extinction. Biol Conserv. 2005;126:131–40.

    Article  Google Scholar 

  • Frankham R, Ballou JD, Ralls K, Eldridge M, Dudash MR, Fenster CB, Lacy RC, Sunnucks P. Genetic management of fragmented animal and plant populations. Oxford: Oxford University Press; 2017.

    Book  Google Scholar 

  • Fu Q, Posth C, Hajdinjak M, Petr M, Mallick S, Fernandes D, Furtwangler A, Haak W, Meyer M, Mittnik A, Nickel B, Peltzer A, Rohland N, Slon V, Talamo S, Lazaridis I, Lipson M, Mathieson I, Schiffels S, Skoglund P, Derevianko AP, Drozdov N, Slavinsky V, Tsybankov A, Cremonesi RG, Mallegni F, Gely B, Vacca E, Morales MR, Straus LG, Neugebauer-Maresch C, Teschler-Nicola M, Constantin S, Moldovan OT, Benazzi S, Peresani M, Coppola D, Lari M, Ricci S, Ronchitelli A, Valentin F, Thevenet C, Wehrberger K, Grigorescu D, Rougier H, Crevecoeur I, Flas D, Semal P, Mannino MA, Cupillard C, Bocherens H, Conard NJ, Harvati K, Moiseyev V, Drucker DG, Svoboda J, Richards MP, Caramelli D, Pinhasi R, Kelso J, Patterson N, Krause J, Paabo S, Reich D. The genetic history of Ice Age Europe. Nature. 2016;534:200–5.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Fulton TL, Wagner SM, Fisher C, Shapiro B. Nuclear DNA from the extinct Passenger Pigeon (Ectopistes migratorius) confirms a single origin of New World pigeons. Ann Anat. 2012;194:52–7.

    Article  CAS  PubMed  Google Scholar 

  • Gaggiotti OE. Genetic threats to population persistence. Ann Zool Fenn. 2003;40:155–68.

    Google Scholar 

  • Galtier N, Nabholz B, Glemin S, Hurst GD. Mitochondrial DNA as a marker of molecular diversity: a reappraisal. Mol Ecol. 2009;18:4541–50.

    Article  CAS  PubMed  Google Scholar 

  • Gibson J, Morton NE, Collins A. Extended tracts of homozygosity in outbred human populations. Hum Mol Genet. 2006;15:789–95.

    Article  CAS  PubMed  Google Scholar 

  • Goossens B, Chikhi L, Jalil MF, Ancrenaz M, Lackman-Ancrenaz I, Mohamed M, Andau P, Bruford MW. Patterns of genetic diversity and migration in increasingly fragmented and declining orang-utan (Pongo pygmaeus) populations from Sabah, Malaysia. Mol Ecol. 2005;14:441–56.

    Article  CAS  PubMed  Google Scholar 

  • Gordon D, Huddleston J, Chaisson MJP, Hill CM, Kronenberg ZN, Munson KM, Malig M, Raja A, Fiddes I, Hillier LW, Dunn C, Baker C, Armstrong J, Diekhans M, Paten B, Shendure J, Wilson RK, Haussler D, Chin C-S, Eichler EE. Long-read sequence assembly of the gorilla genome. Science. 2016;352:aae0344.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Grayson DK, Delpech F. Ungulates and the middle-to-upper Paleolithic transition at Grotte XVI (Dordogne, France). J Archaeol Sci. 2003;30:1633–48.

    Article  Google Scholar 

  • Haddad NM, Brudvig LA, Clobert J, Davies KF, Gonzalez A, Holt RD, Lovejoy TE, Sexton JO, Austin MP, Collins CD, Cook WM, Damschen EI, Ewers RM, Foster BL, Jenkins CN, King AJ, Laurance WF, Levey DJ, Margules CR, Melbourne BA, Nicholls AO, Orrock JL, Song D-X, Townshend JR. Habitat fragmentation and its lasting impact on Earth’s ecosystems. Sci Adv. 2015;1:e1500052.

    Article  PubMed  PubMed Central  Google Scholar 

  • Hajdinjak M, Fu Q, Hubner A, Petr M, Mafessoni F, Grote S, Skoglund P, Narasimham V, Rougier H, Crevecoeur I, Semal P, Soressi M, Talamo S, Hublin JJ, Gusic I, Kucan Z, Rudan P, Golovanova LV, Doronichev VB, Posth C, Krause J, Korlevic P, Nagel S, Nickel B, Slatkin M, Patterson N, Reich D, Prufer K, Meyer M, Paabo S, Kelso J. Reconstructing the genetic history of late Neanderthals. Nature. 2018;555:652–6.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Haubold B, Pfaffelhuber P, Lynch M. mlRho – a program for estimating the population mutation and recombination rates from shotgun-sequenced diploid genomes. Mol Ecol. 2010;19(Suppl 1):277–84.

    Article  PubMed  PubMed Central  Google Scholar 

  • Hedrick PW. Purging inbreeding depression and the probability of extinction: full-sib mating. Heredity. 1994;73:363–72.

    Article  PubMed  Google Scholar 

  • Hedrick PW, Kalinowski ST. Inbreeding depression in conservation biology. Annu Rev Ecol Syst. 2000;31:139–62.

    Article  Google Scholar 

  • Hedrick PW, Miller PS. Conservation genetics – techniques and fundamentals. Ecol Appl. 1992;2:30–46.

    Article  PubMed  Google Scholar 

  • Heintzman PD, Zazula GD, Cahill JA, Reyes AV, MacPhee RD, Shapiro B. Genomic data from extinct North American Camelops revise camel evolutionary history. Mol Biol Evol. 2015;32:2433–40.

    Article  CAS  PubMed  Google Scholar 

  • Heled J, Drummond AJ. Bayesian inference of population size history from multiple loci. BMC Evol Biol. 2008;8:289.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Hofreiter M, Serre D, Rohland N, Rabeder G, Nagel D, Conard N, Munzel S, Paabo S. Lack of phylogeography in European mammals before the last glaciation. Proc Natl Acad Sci U S A. 2004;101:12963–8.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Hofreiter M, Muenzel S, Conard NJ, Pollack J, Slatkin M, Weiss G, Paabo S. Sudden replacement of cave bear mitochondrial DNA in the Late Pleistocene. Curr Biol. 2007;17:R122–3.

    Article  CAS  PubMed  Google Scholar 

  • Hung CM, Shaner PJL, Zink RM, Liu WC, Chu TC, Huang WS, Li SH. Drastic population fluctuations explain the rapid extinction of the passenger pigeon. Proc Natl Acad Sci U S A. 2014;111:10636–41.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • IUCN. The IUCN red list of threatened species 2016. 2016.

    Google Scholar 

  • Jinek M, Chylinski K, Fonfara I, Hauer M, Doudna JA, Charpentier E. A programmable dual-RNA-guided DNA endonuclease in adaptive bacterial immunity. Science. 2012;337:816–21.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • John JS. SeqPrep. 2011. https://github.com/jstjohn/SeqPrep.

  • Johnson RN, O’Meally D, Chen Z, Etherington GJ, Ho SYW, Nash WJ, Grueber CE, Cheng Y, Whittington CM, Dennison S, Peel E, Haerty W, O’Neill RJ, Colgan D, Russell TL, Alquezar-Planas DE, Attenbrow V, Bragg JG, Brandies PA, Chong AY-Y, Deakin JE, Di Palma F, Duda Z, Eldridge MDB, Ewart KM, Hogg CJ, Frankham GJ, Georges A, Gillett AK, Govendir M, Greenwood AD, Hayakawa T, Helgen KM, Hobbs M, Holleley CE, Heider TN, Jones EA, King A, Madden D, Graves JAM, Morris KM, Neaves LE, Patel HR, Polkinghorne A, Renfree MB, Robin C, Salinas R, Tsangaras K, Waters PD, Waters SA, Wright B, Wilkins MR, Timms P, Belov K. Adaptation and conservation insights from the koala genome. Nat Genet. 2018;50:1102–11.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Kalinowski ST, Hedrick PW, Miller PS. Inbreeding depression in the Speke’s gazelle captive breeding program. Conserv Biol. 2000;14:1375–84.

    Article  Google Scholar 

  • Kardos M, Taylor HR, Ellegren H, Luikart G, Allendorf FW. Genomics advances the study of inbreeding depression in the wild. Evol Appl. 2016;9:1205–18.

    Article  PubMed  PubMed Central  Google Scholar 

  • Kimura M. The neutral theory of molecular evolution. New York: Cambridge University Press; 1983.

    Book  Google Scholar 

  • Kingman JFC. On the genealogy of large populations. J Appl Probab. 1982a;19A:27–43.

    Article  Google Scholar 

  • Kingman JFC. The coalescent. Stoch Process Appl. 1982b;13:235–48.

    Article  Google Scholar 

  • Kohn MH, Murphy WJ, Ostrander EA, Wayne RK. Genomics and conservation genetics. Trends Ecol Evol. 2006;21:629–37.

    Article  PubMed  Google Scholar 

  • Kurtén B. The cave bear story. New York: Columbia University Press; 1976.

    Google Scholar 

  • Lee BC, Kim MK, Jang G, Oh HJ, Yuda F, Kim HJ, Hossein MS, Kim JJ, Kang SK, Schatten G, Hwang WS. Dogs cloned from adult somatic cells. Nature. 2005;436:641.

    Article  CAS  PubMed  Google Scholar 

  • Leffler EM, Bullaughey K, Matute DR, Meyer WK, Ségurel L, Venkat A, Andolfatto P, Przeworski M. Revisiting an old riddle: what determines genetic diversity levels within species? PLoS Biol. 2012;10:e1001388.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Leonard JA, Vila C, Fox-Dobbs K, Koch PL, Wayne RK, Van Valkenburgh B. Megafaunal extinctions and the disappearance of a specialized wolf ecomorph. Curr Biol. 2007;17:1146–50.

    Article  CAS  PubMed  Google Scholar 

  • Li H. Aligning sequence reads, clone sequences and assembly contigs with BWA-MEM. arXiv:1303.3997 [q-bio.GN]. 2013.

    Google Scholar 

  • Li H, Durbin R. Inference of human population history from individual whole-genome sequences. Nature. 2011;475:493–6.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, Marth G, Abecasis G, Durbin R, 1000 Genome Project Data Processing Subgroup. The sequence alignment/map format and SAMtools. Bioinformatics. 2009;25:2078–9.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Li Y, Hu Y, Bolund L, Wang J. State of the art de novo assembly of human genomes from massively parallel sequencing data. Hum Genomics. 2010;4:271–7.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Lindahl T. Instability and decay of the primary structure of DNA. Nature. 1993;362:709–15.

    Article  CAS  PubMed  Google Scholar 

  • Lister AM, Stuart AJ. The impact of climate change on large mammal distribution and extinction: evidence from the last glacial/interglacial transition. Compt Rendus Geosci. 2008;340:615–20.

    Article  Google Scholar 

  • Lorenzen ED, Nogues-Bravo D, Orlando L, Weinstock J, Binladen J, Marske KA, Ugan A, Borregaard MK, Gilbert MTP, Nielsen R, Ho SYW, Goebel T, Graf KE, Byers D, Stenderup JT, Rasmussen M, Campos PF, Leonard JA, Koepfli KP, Froese D, Zazula G, Stafford TW, Aaris-Sorensen K, Batra P, Haywood AM, Singarayer JS, Valdes PJ, Boeskorov G, Burns JA, Davydov SP, Haile J, Jenkins DL, Kosintsev P, Kuznetsova T, Lai XL, Martin LD, McDonald HG, Mol D, Meldgaard M, Munch K, Stephan E, Sablin M, Sommer RS, Sipko T, Scott E, Suchard MA, Tikhonov A, Willerslev R, Wayne RK, Cooper A, Hofreiter M, Sher A, Shapiro B, Rahbek C, Willerslev E. Species-specific responses of Late Quaternary megafauna to climate and humans. Nature. 2011;479:359–U195.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Lunter G, Goodson M. Stampy: a statistical algorithm for sensitive and fast mapping of Illumina sequence reads. Genome Res. 2011;21:936–9.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Lynch M, Gabriel W. Mutational load and the survival of small populations. Evolution. 1990;44:1725–37.

    Article  PubMed  Google Scholar 

  • Lynch M, Conery J, Bürger R. Mutational meltdowns in sexual populations. Evolution. 1995a;49:1067–80.

    Article  PubMed  Google Scholar 

  • Lynch M, Conery J, Burger R. Mutation accumulation and the extinction of small populations. Am Nat. 1995b;146:489–518.

    Article  Google Scholar 

  • McKenna A, Hanna M, Banks E, Sivachenko A, Cibulskis K, Kernytsky A, Garimella K, Altshuler D, Gabriel S, Daly M, DePristo MA. The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data. Genome Res. 2010;20:1297–303.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • McQuillan R, Leutenegger AL, Abdel-Rahman R, Franklin CS, Pericic M, Barac-Lauc L, Smolej-Narancic N, Janicijevic B, Polasek O, Tenesa A, Macleod AK, Farrington SM, Rudan P, Hayward C, Vitart V, Rudan I, Wild SH, Dunlop MG, Wright AF, Campbell H, Wilson JF. Runs of homozygosity in European populations. Am J Hum Genet. 2008;83:359–72.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Meyer M, Kircher M, Gansauge M-T, Li H, Racimo F, Mallick S, Schraiber JG, Jay F, Prüfer K, de Filippo C, Sudmant PH, Alkan C, Fu Q, Do R, Rohland N, Tandon A, Siebauer M, Green RE, Bryc K, Briggs AW, Stenzel U, Dabney J, Shendure J, Kitzman J, Hammer MF, Shunkov MV, Derevianko AP, Patterson N, Andrés AM, Eichler EE, Slatkin M, Reich D, Kelso J, Pääbo S. A high-coverage genome sequence from an archaic Denisovan individual. Science. 2012;338:222–6.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Millberg P, Tyrberg T. Naïve birds and noble savages – a review of man-caused prehistoric extinctions of island bird. Ecography. 1993;16:229–50.

    Article  Google Scholar 

  • Miller W, Drautz DI, Ratan A, Pusey B, Qi J, Lesk AM, Tomsho LP, Packard MD, Zhao F, Sher A, Tikhonov A, Raney B, Patterson N, Lindblad-Toh K, Lander ES, Knight JR, Irzyk GP, Fredrikson KM, Harkins TT, Sheridan S, Pringle T, Schuster SC. Sequencing the nuclear genome of the extinct woolly mammoth. Nature. 2008;456:387–90.

    Article  CAS  PubMed  Google Scholar 

  • Milot E, Weimerskirch H, Duchesne P, Bernatchez L. Surviving with low genetic diversity: the case of albatrosses. Proc Biol Sci. 2007;274:779–87.

    CAS  PubMed  PubMed Central  Google Scholar 

  • Minin VN, Bloomquist EW, Suchard MA. Smooth skyride through a rough skyline: Bayesian coalescent-based inference of population dynamics. Mol Biol Evol. 2008;25:1459–71.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Mourier T, Ho SY, Gilbert MT, Willerslev E, Orlando L. Statistical guidelines for detecting past population shifts using ancient DNA. Mol Biol Evol. 2012;29:2241–51.

    Article  CAS  PubMed  Google Scholar 

  • Murray GGR, Soares AER, Novak BJ, Schaefer NK, Cahill J, Baker AJ, Demboski JR, Doll A, Da Fonseca RR, Fulton TL, Gilbert TP, Heintzman PD, Letts B, McIntosh G, O’Connell BL, Peck M, Pipes M-L, Rice ES, Santos KM, Sohrweide AG, Vohr SH, Corbett-Detig RB, Green RE, Shapiro B. Natural selection shaped the rise and fall of passenger pigeon genomic diversity. Sci Rep. 2017;358:951–4.

    CAS  Google Scholar 

  • Nelson DE, Angerbjorn A, Liden K, Turk I. Stable isotopes and the metabolism of the European cave bear. Oecologia. 1998;116:177–81.

    Article  CAS  PubMed  Google Scholar 

  • Nikolskiy PA, Sulerzhitsky LD, Pitulko VV. Last straw versus Blitzkrieg overkill: climate-driven changes in the Arctic Siberian mammoth population and the Late Pleistocene extinction problem. Quat Sci Rev. 2011;30:2309–28.

    Article  Google Scholar 

  • Opgen-Rhein R, Fahrmeir L, Strimmer K. Inference of demographic history from genealogical trees using reversible jump Markov chain Monte Carlo. BMC Evol Biol. 2005;5:6.

    Article  PubMed  PubMed Central  Google Scholar 

  • Orlando L, Cooper A. Using ancient DNA to understand evolutionary and ecological processes. Annu Rev Ecol Evol Syst. 2014;45(45):573–98.

    Article  Google Scholar 

  • Pääbo S. Ancient DNA: extraction, characterization, molecular cloning, and enzymatic amplification. Proc Natl Acad Sci U S A. 1989;86:1939–43.

    Article  PubMed  PubMed Central  Google Scholar 

  • Pääbo S, Poinar H, Serre D, Jaenicke-Despres V, Hebler J, Rohland N, Kuch M, Krause J, Vigilant L, Hofreiter M. Genetic analyses from ancient DNA. Annu Rev Genet. 2004;38:645–79.

    Article  PubMed  CAS  Google Scholar 

  • Pacher M, Stuart AJ. Extinction chronology and palaeobiology of the cave bear (Ursus spelaeus). Boreas. 2009;38:189–206.

    Article  Google Scholar 

  • Palkopoulou E, Dalen L, Lister AM, Vartanyan S, Sablin M, Sher A, Edmark VN, Brandstrom MD, Germonpre M, Barnes I, Thomas JA. Holarctic genetic structure and range dynamics in the woolly mammoth. Proc R Soc B Biol Sci. 2013;280:20131910.

    Article  Google Scholar 

  • Palkopoulou E, Mallick S, Skoglund P, Enk J, Rohland N, Li H, Omrak A, Vartanyan S, Poinar H, Gotherstrom A, Reich D, Dalen L. Complete genomes reveal signatures of demographic and genetic declines in the woolly mammoth. Curr Biol. 2015;25:1395–400.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Palkopoulou E, Baca M, Abramson NI, Sablin M, Socha P, Nadachowski A, Prost S, Germonpre M, Kosintsev P, Smirnov NG, Vartanyan S, Ponomarev D, Nystrom J, Nikolskiy P, Jass CN, Litvinov YN, Kalthoff DC, Grigoriev S, Fadeeva T, Douka A, Higham TFG, Ersmark E, Pitulko V, Pavlova E, Stewart JR, Weglenski P, Stankovic A, Dalen L. Synchronous genetic turnovers across Western Eurasia in Late Pleistocene collared lemmings. Glob Chang Biol. 2016;22:1710–21.

    Article  PubMed  Google Scholar 

  • Park SDE, Magee DA, McGettigan PA, Teasdale MD, Edwards CJ, Lohan AJ, Murphy A, Braud M, Donoghue MT, Liu Y, Chamberlain AT, Rue-Albrecht K, Schroeder S, Spillane C, Tai SS, Bradley DG, Sonstegard TS, Loftus BJ, MacHugh DE. Genome sequencing of the extinct Eurasian wild aurochs, Bos primigenius, illuminates the phylogeography and evolution of cattle. Genome Biol. 2015;16:234.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Pečnerová P, Díez-del-Molino D, Vartanyan S, Dalén L. Changes in variation at the MHC class II DQA locus during the final demise of the woolly mammoth. Sci Rep. 2016;6:25274.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Peltzer A, Jäger G, Herbig A, Seitz A, Kniep C, Krause J, Nieselt K. EAGER: efficient ancient genome reconstruction. Genome Biol. 2016;17:60.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Perry GLW, Wheeler AB, Wood JR, Wilmshurst JM. A high-precision chronology for the rapid extinction of New Zealand moa (Aves, Dinornithiformes). Quat Sci Rev. 2014;105:126–35.

    Article  Google Scholar 

  • Posth C, Renaud G, Mittnik A, Drucker DG, Rougier H, Cupillard C, Valentin F, Thevenet C, Furtwangler A, Wissing C, Francken M, Malina M, Bolus M, Lari M, Gigli E, Capecchi G, Crevecoeur I, Beauval C, Flas D, Germonpre M, van der Plicht J, Cottiaux R, Gely B, Ronchitelli A, Wehrberger K, Grigorescu D, Svoboda J, Semal P, Caramelli D, Bocherens H, Harvati K, Conard NJ, Haak W, Powell A, Krause J. Pleistocene mitochondrial genomes suggest a single major dispersal of non-Africans and a Late Glacial population turnover in Europe. Curr Biol. 2016;26:827–33.

    Article  CAS  PubMed  Google Scholar 

  • Prado-Martinez J, Sudmant PH, Kidd JM, Li H, Kelley JL, Lorente-Galdos B, Veeramah KR, Woerner AE, O’Connor TD, Santpere G, Cagan A, Theunert C, Casals F, Laayouni H, Munch K, Hobolth A, Halager AE, Malig M, Hernandez-Rodriguez J, Hernando-Herraez I, Prufer K, Pybus M, Johnstone L, Lachmann M, Alkan C, Twigg D, Petit N, Baker C, Hormozdiari F, Fernandez-Callejo M, Dabad M, Wilson ML, Stevison L, Camprubi C, Carvalho T, Ruiz-Herrera A, Vives L, Mele M, Abello T, Kondova I, Bontrop RE, Pusey A, Lankester F, Kiyang JA, Bergl RA, Lonsdorf E, Myers S, Ventura M, Gagneux P, Comas D, Siegismund H, Blanc J, Agueda-Calpena L, Gut M, Fulton L, Tishkoff SA, Mullikin JC, Wilson RK, Gut IG, Gonder MK, Ryder OA, Hahn BH, Navarro A, Akey JM, Bertranpetit J, Reich D, Mailund T, Schierup MH, Hvilsom C, Andres AM, Wall JD, Bustamante CD, Hammer MF, Eichler EE, Marques-Bonet T. Great ape genetic diversity and population history. Nature. 2013;499:471–5.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Prowse TA, Johnson CN, Lacy RC, Bradshaw CJ, Pollak JP, Watts MJ, Brook BW. No need for disease: testing extinction hypotheses for the thylacine using multi-species metamodels. J Anim Ecol. 2013;82:355–64.

    Article  PubMed  Google Scholar 

  • Prüfer K, Stenzel U, Hofreiter M, Pääbo S, Kelso J, Green RE. Computantional challenges in the analysis of ancient DNA. Genome Biol. 2010;11:R47.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Prufer K, Racimo F, Patterson N, Jay F, Sankararaman S, Sawyer S, Heinze A, Renaud G, Sudmant PH, de Filippo C, Li H, Mallick S, Dannemann M, Fu Q, Kircher M, Kuhlwilm M, Lachmann M, Meyer M, Ongyerth M, Siebauer M, Theunert C, Tandon A, Moorjani P, Pickrell J, Mullikin JC, Vohr SH, Green RE, Hellmann I, Johnson PL, Blanche H, Cann H, Kitzman JO, Shendure J, Eichler EE, Lein ES, Bakken TE, Golovanova LV, Doronichev VB, Shunkov MV, Derevianko AP, Viola B, Slatkin M, Reich D, Kelso J, Paabo S. The complete genome sequence of a Neanderthal from the Altai Mountains. Nature. 2014;505:43–9.

    Article  PubMed  CAS  Google Scholar 

  • Purvis A, Gittleman JL, Cowlishaw G, Mace GM. Predicting extinction risk in declining species. Proc Biol Sci. 2000;267:1947–52.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Pybus OG, Rambaut A, Harvey PH. An integrated framework for the inference of viral population history from reconstructed genealogies. Genetics. 2000;155:1429–37.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Rasmussen M, Li Y, Lindgreen S, Pedersen JS, Albrechtsen A, Moltke I, Metspalu M, Metspalu E, Kivisild T, Gupta R, Bertalan M, Nielsen K, Gilbert MT, Wang Y, Raghavan M, Campos PF, Kamp HM, Wilson AS, Gledhill A, Tridico S, Bunce M, Lorenzen ED, Binladen J, Guo X, Zhao J, Zhang X, Zhang H, Li Z, Chen M, Orlando L, Kristiansen K, Bak M, Tommerup N, Bendixen C, Pierre TL, Gronnow B, Meldgaard M, Andreasen C, Fedorova SA, Osipova LP, Higham TF, Ramsey CB, Hansen TV, Nielsen FC, Crawford MH, Brunak S, Sicheritz-Ponten T, Villems R, Nielsen R, Krogh A, Wang J, Willerslev E. Ancient human genome sequence of an extinct Palaeo-Eskimo. Nature. 2010;463:757–62.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Richmond DJ, Sinding M-HS, Gilbert MTP. The potential and pitfalls of de-extinction. Zool Scr. 2016;45:22–36.

    Article  Google Scholar 

  • Robinson JA, Ortega-Del Vecchyo D, Fan Z, Kim BY, von Holdt BM, Marsden CD, Lohmueller KE, Wayne RK. Genomic flatlining in the endangered island fox. Curr Biol. 2016;26:1183–9.

    Article  CAS  PubMed  Google Scholar 

  • Rogers RL, Slatkin M. Excess of genomic defects in a woolly mammoth on Wrangel island. PLoS Genet. 2017;13:e1006601.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Saltre F, Rodriguez-Rey M, Brook BW, Johnson CN, Turney CS, Alroy J, Cooper A, Beeton N, Bird MI, Fordham DA, Gillespie R, Herrando-Perez S, Jacobs Z, Miller GH, Nogues-Bravo D, Prideaux GJ, Roberts RG, Bradshaw CJ. Climate change not to blame for Late Quaternary megafauna extinctions in Australia. Nat Commun. 2016;7:10511.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Sax DF, Gaines SD. Colloquium paper: species invasions and extinction: the future of native biodiversity on islands. Proc Natl Acad Sci U S A. 2008;105(Suppl 1):11490–7.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Schorger AW. The passenger pigeon: its natural history and extinction. Whitefish: Literary Licensing, LLC; 1955.

    Google Scholar 

  • Schubert M, Ermini L, Der Sarkissian C, Jonsson H, Ginolhac A, Schaefer R, Martin MD, Fernandez R, Kircher M, McCue M, Willerslev E, Orlando L. Characterization of ancient and modern genomes by SNP detection and phylogenomic and metagenomic analysis using PALEOMIX. Nat Protoc. 2014;9:1056–82.

    Article  CAS  PubMed  Google Scholar 

  • Shapiro B. Pathways to de-extinction: how close can we get to resurrection of an extinct species? Funct Ecol. 2017;31:996–1002.

    Article  Google Scholar 

  • Shapiro B, Hofreiter M. A paleogenomic perspective on evolution and gene function: new insights from ancient DNA. Science. 2014;343:1236573.

    Article  CAS  PubMed  Google Scholar 

  • Siddle HV, Marzec J, Cheng Y, Jones M, Belov K. MHC gene copy number variation in Tasmanian devils: implications for the spread of a contagious cancer. Proc Biol Sci. 2010;277:2001–6.

    CAS  PubMed  PubMed Central  Google Scholar 

  • Skoglund P, Malmström H, Raghavan M, Storå J, Hall P, Willerslev E, Gilbert TP, Götherström A, Jakobsson M. Origins and genetic legacy of neolithic farmers and hunter-gatherers in Europe. Science. 2012;336:466–9.

    Article  CAS  PubMed  Google Scholar 

  • Skoglund P, Northoff BH, Shunkov MV, Derevianko AP, Paabo S, Krause J, Jakobsson M. Separating endogenous ancient DNA from modern day contamination in a Siberian Neandertal. Proc Natl Acad Sci U S A. 2014;111:2229–34.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Skoglund P, Ersmark E, Palkopoulou E, Dalen L. Ancient wolf genome reveals an early divergence of domestic dog ancestors and admixture into high-latitude breeds. Curr Biol. 2015;25:1515–9.

    Article  CAS  PubMed  Google Scholar 

  • Spurgin LG, Richardson DS. How pathogens drive genetic diversity: MHC, mechanisms and misunderstandings. Proc Biol Sci. 2010;277:979–88.

    CAS  PubMed  PubMed Central  Google Scholar 

  • Stiller M, Baryshnikov G, Bocherens H, Grandal d'Anglade A, Hilpert B, Munzel SC, Pinhasi R, Rabeder G, Rosendahl W, Trinkaus E, Hofreiter M, Knapp M. Withering away – 25,000 years of genetic decline preceded cave bear extinction. Mol Biol Evol. 2010;27:975–8.

    Article  CAS  PubMed  Google Scholar 

  • Strimmer K, Pybus OG. Exploring the demographic history of DNA sequences using the generalized skyline plot. Mol Biol Evol. 2001;18:2298–305.

    Article  CAS  PubMed  Google Scholar 

  • Tallmon DA, Luikart G, Waples RS. The alluring simplicity and complex reality of genetic rescue. Trends Ecol Evol. 2004;19:489–96.

    Article  PubMed  Google Scholar 

  • Tilman D, May RM, Lehman CL, Nowak MA. Habitat destruction and the extinction debt. Nature. 1994;371:65.

    Article  Google Scholar 

  • Treangen TJ, Salzberg SL. Erratum: repetitive DNA and next-generation sequencing: computational challenges and solutions. Nat Rev Genet. 2012;13:146.

    Article  CAS  Google Scholar 

  • Valdiosera CE, Garcia N, Anderung C, Dalen L, Cregut-Bonnoure E, Kahlke RD, Stiller M, Brandstrom M, Thomas MG, Arsuaga JL, Gotherstrom A, Barnes I. Staying out in the cold: glacial refugia and mitochondrial DNA phylogeography in ancient European brown bears. Mol Ecol. 2007;16:5140–8.

    Article  CAS  PubMed  Google Scholar 

  • Vartanyan S, Garutt VE, Sher AV. Holocene dwarf mammoths from Wrangel Island in the Siberian Arctic. Nature. 1993;362:337–40.

    Article  CAS  PubMed  Google Scholar 

  • Veltre DW, Yesner DR, Crossen KJ, Graham RW, Coltrain JB. Patterns of faunal extinction and paleoclimatic change from mid-Holocene mammoth and polar bear remains, Pribilof Islands, Alaska. Quat Res. 2017;70:40–50.

    Article  Google Scholar 

  • Vucetich JA, Waite TA, Nunney L. Fluctuating population size and the ratio of effective to census population size. Evolution. 1997;51:2017–21.

    Article  PubMed  Google Scholar 

  • Wakayama S, Ohta H, Hikichi T, Mizutani E, Iwaki T, Kanagawa O, Wakayama T. Production of healthy cloned mice from bodies frozen at −20°C for 16 years. Proc Natl Acad Sci U S A. 2008;105:17318–22.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Wandeler P, Hoeck PE, Keller LF. Back to the future: museum specimens in population genetics. Trends Ecol Evol. 2007;22:634–42.

    Article  PubMed  Google Scholar 

  • Wang J, Hill WG, Charlesworth D, Charlesworth B. Dynamics of inbreeding depression due to deleterious mutations in small populations: mutation parameters and inbreeding rate. Genet Res. 1999;74:165–78.

    Article  CAS  PubMed  Google Scholar 

  • Willi Y, van Buskirk J, Hoffmann AA. Limits to the adaptive potential of small populations. Annu Rev Ecol Evol Syst. 2006;37:433–58.

    Article  Google Scholar 

  • Wright S. Evolution in Mendelian populations. Genetics. 1931;16:139–56.

    Article  Google Scholar 

  • Wright S. Size of population and breeding structure in relation to evolution. Science. 1938;87:430–1.

    Google Scholar 

  • Wright S. Genetical structure of populations. Nature. 1950;166:247–9.

    Article  CAS  PubMed  Google Scholar 

  • Zimov SA, Zimov NS, Tikhonov AN, Chapin FS. Mammoth steppe: a high-productivity phenomenon. Quat Sci Rev. 2012;57:26–45.

    Article  Google Scholar 

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Authors and Affiliations

  1. Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Stockholm, Sweden

    Johanna von Seth & Love Dalén

  2. Division of Systematics and Evolution, Department of Zoology, Stockholm University, Stockholm, Sweden

    Johanna von Seth

  3. Centre for GeoGenetics, Natural History Museum of Denmark, Copenhagen, Denmark

    Jonas Niemann

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Correspondence to Love Dalén .

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  1. Department of Biological Sciences, University at Buffalo (SUNY), Buffalo, NY, USA

    Charlotte Lindqvist

  2. Faculty of Forestry and Environmental Management, University of New Brunswick, Fredericton, NB, Canada

    Om P. Rajora

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von Seth, J., Niemann, J., Dalén, L. (2018). Genomics of Extinction. In: Lindqvist, C., Rajora, O. (eds) Paleogenomics. Population Genomics. Springer, Cham. https://doi.org/10.1007/13836_2018_53

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