Polar and brown bear genomes reveal ancient admixture and demographic footprints of past climate change

Proceedings of the National Academy of Sciences of the United States of America

Volumn 109, Issue 36, 2012, Pages

  Miller, Webb ^a   Schuster, Stephan C ^a,b   Welch, Andreanna J ^c   Ratan, Aakrosh ^a   Bedoya Reinaa, Oscar C ^a   Zhao, Fangqing ^b,d   Kim, Hie Lim ^a   Burhans, Richard C ^a   Drautz, Daniela I ^b   Wittekindt, Nicola E ^b   Tomsho, Lynn P ^a   Ibarra Laclette, Enrique ^e   Herrera Estrella, Luis ^e   Peacock, Elizabeth ^f   Farley, Sean ^g   Sage, George K ^f   Rode, Karyn ^h   Obbard, Martyn ⁱ   Montiel, Rafael ^e   Bachmann, Lutz ^j   Ingólfsson, Ólafur ^k,l   Aars, Jon ^m   Mailund, Thomas ⁿ   Wiig, Øystein ^j   Talbot, Sandra L ^f   Lindqvist, Charlotte ^c   more..

^a PENNSYLVANIA STATE UNIVERSITY   (United States)

^b NANYANG TECHNOLOGICAL UNIVERSITY   (Singapore)

^c UNIVERSITY AT BUFFALO   (United States)

^d INSTITUTE OF GEOLOGY AND GEOPHYSICS   (China)

^e DEPARTAMENTO DE FÍSICA   (Mexico)

^f U S GEOLOGICAL SURVEY   (United States)

^g ALASKA DEPARTMENT OF FISH AND GAME   (United States)

^h U S FISH AND WILDLIFE SERVICE   (United States)

ⁱ ONTARIO MINISTRY OF NATURAL RESOURCES   (Canada)

^j UNIVERSITY OF OSLO   (Norway)

^k UNIVERSITY OF ICELAND   (Iceland)

^l UNIVERSITY CENTRE IN SVALBARD   (Norway)

^m NORWEGIAN POLAR INSTITUTE   (Norway)

ⁿ AARHUS UNIVERSITY   (Denmark)

more..

Author keywords

Demographic history; Hybridization; Mammalian genomics; Phylogenetics

Indexed keywords

ARCTIC CLIMATE; ARTICLE; BEAR; BLACK BEAR; BROWN BEAR; CLIMATE CHANGE; DEMOGRAPHY; EVOLUTION; GENE SEQUENCE; GENETIC VARIABILITY; GENOME; GENOMICS; NONHUMAN; PHENOTYPE; PHYLOGENY; POLAR BEAR; PRIORITY JOURNAL; UNITED STATES;

ADAPTATION, BIOLOGICAL; ANIMALS; ARCTIC REGIONS; BASE SEQUENCE; CLIMATE CHANGE; EVOLUTION, MOLECULAR; GENETIC MARKERS; GENETICS, POPULATION; GENOME; HISTORY, ANCIENT; MOLECULAR SEQUENCE DATA; POPULATION DENSITY; POPULATION DYNAMICS; SEQUENCE ANALYSIS, DNA; SPECIES SPECIFICITY; URSIDAE;

MAMMALIA; URSUS AMERICANUS; URSUS ARCTOS; URSUS MARITIMUS;

EID: 84865964725     PISSN: 00278424     EISSN: 10916490     Source Type: Journal    
DOI: 10.1073/pnas.1210506109     Document Type: Article

References (59)

1. Green RE, et al. (2010) A draft sequence of the Neandertal genome. Science 328:710-722.
2. Reich D, et al. (2010) Genetic history of an archaic hominin group from Denisova Cave in Siberia. Nature 468:1053-1060.
3. vonHoldt BM, et al. (2011) A genome-wide perspective on the evolutionary history of enigmatic wolf-like canids. Genome Res 21:1294-1305.
4. Lindqvist C, et al. (2010) Complete mitochondrial genome of a Pleistocene jawbone unveils the origin of polar bear. Proc Natl Acad Sci USA 107:5053-5057.
5. Stirling I (2011) Polar Bears: A Natural History of a Threatened Species (Fitzhenry and Whiteside, Brighton, MA).
6. Doupé JP, England JH, Furze M, Paetkau D (2007) Most northerly observation of a grizzly bear (Ursus arctos) in Canada: Photographic and DNA evidence from Melville Island, Northwest Territories. Arctic 60:271-276.
7. Gray AP (1972) Mammalian Hybrids. A Check-List With Bibliography (Commonwealth Agricultural Bureaux, Slough, UK), 2nd Ed.
8. Edwards CJ, et al. (2011) Ancient hybridization and an Irish origin for the modern polar bear matriline. Curr Biol 21:1251-1258.
9. Hailer F, et al. (2012) Nuclear genomic sequences reveal that polar bears are an old and distinct bear lineage. Science 336:344-347.
10. Miller W, et al. (2011) Genetic diversity and population structure of the endangered marsupial Sarcophilus harrisii (Tasmanian devil). Proc Natl Acad Sci USA 108:12348-12353.
11. Perry GH, et al. (2012) A genome sequence resource for the aye-aye (Daubentonia madagascariensis), a nocturnal lemur from Madagascar. Genome Biol Evol 4:126-135.
12. Li R, et al. (2010) De novo assembly of human genomes with massively parallel short read sequencing. Genome Res 20:265-272.
13. Li R, et al. (2010) The sequence and de novo assembly of the giant panda genome. Nature 463:311-317.
14. Ballard JWO, Whitlock MC (2004) The incomplete natural history of mitochondria. Mol Ecol 13:729-744. (Pubitemid 38390584)
15. Mailund T, Dutheil JY, Hobolth A, Lunter G, Schierup MH (2011) Estimating divergence time and ancestral effective population size of Bornean and Sumatran orangutan subspecies using a coalescent hidden Markov model. PLoS Genet 7:e1001319.
16. Krause J, et al. (2008) Mitochondrial genomes reveal an explosive radiation of extinct and extant bears near the Miocene-Pliocene boundary. BMC Evol Biol 8:220.
17. Polyak L, et al. (2010) History of sea ice in the Arctic. Quat Sci Rev 29:1757-1778.
18. Paschou P, et al. (2007) PCA-correlated SNPs for structure identification in worldwide human populations. PLoS Genet 3:1672-1686. (Pubitemid 47510260)
19. Bryc K, et al. (2010) Genome-wide patterns of population structure and admixture in West Africans and African Americans. Proc Natl Acad Sci USA 107:786-791.
20. Pugach I, Matveyev R, Wollstein A, Kayser M, Stoneking M (2011) Dating the age of admixture via wavelet transform analysis of genome-wide data. Genome Biol 12:R19.
21. Tang H, et al. (2007) Recent genetic selection in the ancestral admixture of Puerto Ricans. Am J Hum Genet 81:626-633. (Pubitemid 47330221)
22. Abi-Rached L, et al. (2011) The shaping of modern human immune systems by multiregional admixture with archaic humans. Science 334:89-94.
23. Brocker C, et al. (2010) Aldehyde dehydrogenase 7A1 (ALDH7A1) is a novel enzyme involved in cellular defense against hyperosmotic stress. J Biol Chem 285:18452-18463.
24. Paetkau D, et al. (1999) Genetic structure of the world's polar bear populations. Mol Ecol 8:1571-1584. (Pubitemid 29514698)
25. Li H, Durbin R (2011) Inference of human population history from individual whole-genome sequences. Nature 475:493-496.
26. Lisiecki LE, Raymo ME (2005) A Pliocene-Pleistocene stack of 57 globally distributed benthic δ18O records. Paleoceanography 20:PA103.
27. Howard WR (1997) Palaeoclimatology: A warm future in the past. Nature 388:418-419.
28. Øritsland NA (1970) Temperature regulation of the polar bear (Thalarctos maritimus). Comp Biochem Physiol 37:225.
29. Harington CR (2008) The evolution of Arctic marine mammals. Ecol Appl 18(2, Suppl):S23-S40.
30. Bruce DS, et al. (1990) Is the polar bear (Ursus maritimus) a hibernator? Continued studies on opioids and hibernation. Pharmacol Biochem Behav 35:705-711. (Pubitemid 20115761)
31. Akey JM, Zhang G, Zhang K, Jin L, Shriver MD (2002) Interrogating a high-density SNP map for signatures of natural selection. Genome Res 12:1805-1814. (Pubitemid 35469929)
32. Ibraghimov-Beskrovnaya O, et al. (1992) Primary structure of dystrophin-associated glycoproteins linking dystrophin to the extracellular matrix. Nature 355:696-702.
33. Harlow HJ, Lohuis T, Beck TDI, Iaizzo PA (2001) Muscle strength in overwintering bears. Nature 409:997. (Pubitemid 32204040)
34. Barboza PS, Farley SD, Robbins CT (1997) Whole-body urea cycling and protein turnover during hyperphagia and dormancy in growing bears (Ursus americanus and U. arctos). Can J Zool 75:2129-2136. (Pubitemid 28159377)
35. Ogg SL, Weldon AK, Dobbie L, Smith AJH, Mather IH (2004) Expression of butyrophilin (Btn1a1) in lactating mammary gland is essential for the regulated secretion of milk-lipid droplets. Proc Natl Acad Sci USA 101:10084-10089. (Pubitemid 38891198)
36. Qu Y, et al. (2011) Novel SNPs of butyrophilin (BTN1A1) and milk fat globule epidermal growth factor (EGF) 8 (MFG-E8) are associated with milk traits in dairy goat. Mol Biol Rep 38:371-377.
37. Fischer J, et al. (2009) Inactivation of the Fto gene protects from obesity. Nature 458:894-898.
38. Kaser S, et al. (2004) Effects of weight loss on PLTP activity and HDL particle size. Int J Obes Relat Metab Disord 28:1280-1282. (Pubitemid 39389585)
39. Miljkovic I, et al. (2009) Association of the CPT1B gene with skeletal muscle fat infiltration in Afro-Caribbean men. Obesity (Silver Spring) 17:1396-1401.
40. Soupene E, Dinh NP, Siliakus M, Kuypers FA (2010) Activity of the acyl-CoA synthetase ACSL6 isoforms: Role of the fatty acid Gate-domains. BMC Biochem 11:18.
41. Shin MK, Levorse JM, Ingram RS, Tilghman SM (1999) The temporal requirement for endothelin receptor-B signalling during neural crest development. Nature 402:496-501.
42. Cieslak M, Reissmann M, Hofreiter M, Ludwig A (2011) Colours of domestication. Biol Rev Camb Philos Soc 86:885-899.
43. Hedrick PW, Ritland K (2012) Population genetics of the white-phased "Spirit" black bear of British Columbia. Evolution 66:305-313.
44. Bellone RR, et al. (2008) Differential gene expression of TRPM1, the potential cause of congenital stationary night blindness and coat spotting patterns (LP) in the Appaloosa horse (Equus caballus). Genetics 179:1861-1870.
45. Mallet J (2005) Hybridization as an invasion of the genome. Trends Ecol Evol 20:229-237.
46. Stewart JR, Stringer CB (2012) Human evolution out of Africa: The role of refugia and climate change. Science 335:1317-1321.
47. Hansen J, et al. (2006) Global temperature change. Proc Natl Acad Sci USA 103:14288-14293. (Pubitemid 44484742)
48. Hunter CM, et al. (2010) Climate change threatens polar bear populations: A stochastic demographic analysis. Ecology 91:2883-2897.
49. Wiig Ø, Aars J, Born EW (2008) Effects of climate change on polar bears. Sci Prog 91:151-173.
50. Patterson N, Richter DJ, Gnerre S, Lander ES, Reich D (2006) Genetic evidence for complex speciation of humans and chimpanzees. Nature 441:1103-1108. (Pubitemid 43990725)
51. MacDonald GM (2010) Global warming and the Arctic: A new world beyond the reach of the Grinnellian niche? J Exp Biol 213:855-861.
52. Kelly BP, Whiteley A, Tallmon D (2010) The Arctic melting pot. Nature 468:891.
53. Li H, Durbin R (2009) Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics 25:1754-1760.
54. Harris RS (2007) Improved pairwise alignment of genomic DNA. PhD dissertation (Pennsylvania State Univ, University Park, PA).
55. Drummond AJ, Rambaut A (2007) BEAST: Bayesian evolutionary analysis by sampling trees. BMC Evol Biol 7:214.
56. Woolley S, Johnson J, Smith MJ, Crandall KA, McClellan DA (2003) TreeSAAP: Selection on amino acid properties using phylogenetic trees. Bioinformatics 19:671-672. (Pubitemid 36417070)
57. Peakall R, Smouse PE (2006) GENALEX 6: Genetic analysis in Excel. Population genetic software for teaching and research. Mol Ecol Notes 6:288-295. (Pubitemid 43373825)
58. Pritchard JK, Stephens M, Donnelly P (2000) Inference of population structure using multilocus genotype data. Genetics 155:945-959. (Pubitemid 30397141)
59. Adzhubei IA, et al. (2010) A method and server for predicting damaging missense mutations. Nat Methods 7:248-249.