Worldwide patterns of genomic variation and admixture in gray wolves

Genome Research

Volumn 26, Issue 2, 2016, Pages 163-173

  Fan, Zhenxin ^a,b   Silva, Pedro ^c   Gronau, Ilan ^d   Wang, Shuoguo ^e,k   Armero, Aitor Serres ^f   Schweizer, Rena M ^b   Ramirez, Oscar ^f   Pollinger, John ^b   Galaverni, Marco ^g   Del Vecchyo, Diego Ortega ^b   Du, Lianming ^a   Zhang, Wenping ^h   Zhang, Zhihe ^h   Xing, Jinchuan ^e,i   Vilà, Carles ^j   Marques Bonet, Tomas ^f,j   Godinho, Raquel ^c   Yue, Bisong ^a   Wayne, Robert K ^b  

^a SICHUAN UNIVERSITY   (China)

^b UNIVERSITY OF CALIFORNIA   (United States)

^c CENTRO DE INVESTIGAÇÃO EM BIODIVERSIDADE E RECURSOS GENÉTICOS   (Portugal)

^d INTERDISCIPLINARY CENTER   (Israel)

^e RUTGERS UNIVERSITY   (United States)

^f Barcelona Biomedical Research Park   (Spain)

^g INSTITUTE FOR ENVIRONMENTAL PROTECTION AND RESEARCH ISPRA   (Italy)

^h Chengdu Research Base of Giant Panda Breeding   (China)

ⁱ Life Sciences Building Rutgers University   (United States)

^j UNIVERSITY OF BARCELONA   (Spain)

^k ST JUDE CHILDREN S RESEARCH HOSPITAL   (United States)

more..

Author keywords

[No Author keywords available]

Indexed keywords

ADAPTATION; ANCESTRY GROUP; ARTICLE; CANIS LUPUS; CONTROLLED STUDY; DEMOGRAPHY; DOMESTICATION; EXTINCT SPECIES; GENETIC ASSOCIATION; GENETIC VARIABILITY; GENOME; HETEROZYGOSITY; HISTORY; MOLECULAR PHYLOGENY; NONHUMAN; PHYLOGENETIC TREE; PREY; PRIORITY JOURNAL; ANIMAL; BAYES THEOREM; BIOLOGICAL MODEL; DNA SEQUENCE; DOG; FEMALE; GENETICS; HYBRIDIZATION; MALE; MARKOV CHAIN; PHYLOGENY; PRINCIPAL COMPONENT ANALYSIS; SINGLE NUCLEOTIDE POLYMORPHISM; WOLF;

MITOCHONDRIAL DNA;

ANIMALS; BAYES THEOREM; DNA, MITOCHONDRIAL; DOGS; FEMALE; GENOME; HYBRIDIZATION, GENETIC; MALE; MARKOV CHAINS; MODELS, GENETIC; PHYLOGENY; POLYMORPHISM, SINGLE NUCLEOTIDE; PRINCIPAL COMPONENT ANALYSIS; SEQUENCE ANALYSIS, DNA; WOLVES;

EID: 84956876411     PISSN: 10889051     EISSN: 15495469     Source Type: Journal    
DOI: 10.1101/gr.197517.115     Document Type: Article

References (67)

1. Aggarwal RK, Ramadevi J, Singh L. 2003. Ancient origin and evolution of the Indian wolf: evidence from mitochondrial DNA typing of wolves from Trans-Himalayan region and Pennisular India. Genome Biol 4: P6.
2. Aldenderfer M. 2011. Peopling the Tibetan plateau: insights from archaeology. High Alt Med Biol 12: 141-147.
3. Anderson TM, vonHoldt BM, Candille SI, Musiani M, Greco C, Stahler DR, Smith DW, Padhukasahasram B, Randi E, Leonard JA, et al. 2009. Molecular and evolutionary history of melanism in North American gray wolves. Science 323: 1339-1343.
4. Boyko AR, Quignon P, Li L, Schoenebeck J, Degenhardt JD, Lohmueller KE, Zhao K, Brisbin A, Parker HG, vonHoldt BM, et al. 2010. A simple genetic architecture underlies morphological variation in dogs. PLoS Biol 8: e1000451.
5. Brantingham PJ, Rhode D, Madsen DB. 2010. Archaeology augments Tibet's genetic history. Science 329: 1467.
6. Carmichael LE, Nagy JA, Larter NC, Strobeck C. 2001. Prey specialization may influence patterns of gene flow in wolves of the Canadian Northwest. Mol Ecol 10: 2787-2798.
7. Chen FH, Dong GH, Zhang DJ, Liu XY, Jia X, An CB, Ma MM, Xie YW, Barton L, Ren XY, et al. 2015. Agriculture facilitated permanent human occupation of the Tibetan Plateau after 3600 B.P. Science 347: 248-250.
8. Chevalier ML, Hilley G, Tapponnier P, Van der Woerd J, Jing LZ, Finkel RC, Ryerson FJ, Li HB, Liu XH. 2011. Constraints on the late Quaternary gla-ciations in Tibet from cosmogenic exposure ages of moraine surfaces. Quat Sci Rev 30: 528-554.
9. Cho YS, Hu L, Hou H, Lee H, Xu J, Kwon S, Oh S, Kim HM, Jho S, Kim S, et al. 2013. The tiger genome and comparative analysis with lion and snow leopard genomes. Nat Commun 4: 2433.
10. Clark PU, Dyke AS, Shakun JD, Carlson AE, Clark J, Wohlfarth B, Mitrovica JX, Hostetler SW, McCabe AM. 2009. The last glacial maximum. Science 325: 710-714.
11. Coulson T, MacNulty DR, Stahler DR, vonHoldt B, Wayne RK, Smith DW. 2011. Modeling effects of environmental change on wolf population dynamics, trait evolution, and life history. Science 334: 1275-1278.
12. Cronin MA, Cánovas A, Bannasch DL, Oberbauer AM, Medrano JF. 2015. Wolf subspecies: reply to Weckworth, et al. and Fredrickson, et al. J Hered 106: 417-419.
13. Crowther MS, Fillios M, Colman N, Letnic M. 2014. An updated description of the Australian dingo (Canis dingo Meyer, 1793). J Zool 293: 192-203.
14. DePristo MA, Banks E, Poplin R, Garimella KV, Maguire JR, Hartl C, Philippakis AA, del Angel G, Rivas MA, Hanna M, et al. 2011. A framework for variation discovery and genotyping using next-generation DNA sequencing data. Nat Genet 43: 491-498.
15. Ding ZL, Oskarsson M, Ardalan A, Angleby H, Dahlgren LG, Tepeli C, Kirkness E, Savolainen P, Zhang YP. 2012. Origins of domestic dog in southern East Asia is supported by analysis of Y-chromosome DNA. Heredity 108: 507-514.
16. Durand EY, Patterson N, Reich D, Slatkin M. 2011. Testing for ancient admixture between closely related populations. Mol Biol Evol 28: 2239-2252.
17. Fan Z, Zhao G, Li P, Osada N, Xing J, Yi Y, Du L, Silva P, Wang H, Sakate R, et al. 2014. Whole genome sequencing of Tibetan macaque (Macaca thi-betana) provides new insight into the macaque evolutionary history. Mol Biol Evol 31: 1475-1489.
18. Fredrickson RJ, Siminski P, Woolf M, Hedrick PW. 2007. Genetic rescue and inbreeding depression in Mexican wolves. Proc Biol Sci 274: 2365-2371.
19. Freedman AH, Gronau I, Schweizer RM, Ortega-Del Vecchyo D, Han E, Silva PM, Galaverni M, Fan Z, Marx P, Lorente-Galdos B, et al. 2014. Genome sequencing highlights the dynamic early history of dogs. PLoS Genet 10: e1004016.
20. García-Moreno J, Matocq MD, Roy MS, Geffen E, Wayne RK. 1996. Relationships and genetic purity of the endangered Mexican wolf based on analysis of microsatellite loci. Conserv Biol 10: 376-389.
21. Geffen E, Anderson MJ, Wayne RK. 2004. Climate and habitat barriers to dispersal in the highly mobile grey wolf. Mol Ecol 13: 2481-2490.
22. Green RE, Krause J, Briggs AW, Maricic T, Stenzel U, Kircher M, Patterson N, Li H, Zhai W, Fritz MH, et al. 2010. A draft sequence of the Neandertal genome. Science 328: 710-722.
23. Grimm D. 2015. How the wolf became the dog. Science 348: 277.
24. Groenen MA, Archibald AL, Uenishi H, Tuggle CK, Takeuchi Y, Rothschild MF, Rogel-Gaillard C, Park C, Milan D, Megens HJ, et al. 2012. Analyses of pig genomes provide insight into porcine demography and evolution. Nature 491: 393-398.
25. Gronau I, Hubisz MJ, Gulko B, Danko CG, Siepel A. 2011. Bayesian inference of ancient human demography from individual genome sequences. Nat Genet 43: 1031-1034.
26. Hedrick PW, Miller PS, Geffen E, Wayne RK. 1997. Genetic evaluation of the three captive Mexican wolf lineages. Zoo Biology 16: 47-69.
27. Hendricks SA, Clee PR, Harrigan RJ, Pollinger JP, Freedman AH, Callas R, Figura PJ, Wayne RK. 2016. Re-defining historical geographic range in species with sparse records: implications for the Mexican wolf reintro-duction program. Biol Conserv 194: 48-57.
28. Heyman J. 2014. Paleoglaciation of the Tibetan Plateau and surrounding mountains based on exposure ages and ELA depression estimates. Quat Sci Rev 91: 30-41.
29. Koepfli KP, Pollinger J, Godinho R, Robinson J, Lea A, Hendricks S, Schweizer RM, Thalmann O, Silva P, Fan Z, et al. 2015. Genome-wide evidence reveals that African and Eurasian golden jackals are distinct species. Curr Biol 25: 2158-2165.
30. Kurten B, Anderson E. 1980. Pleistocene mammals of North America. Columbia University Press, New York.
31. Langmead B, Salzberg SL. 2012. Fast gapped-read alignment with Bowtie 2. Nat Methods 9: 357-359.
32. Lee TH, Guo H, Wang X, Kim C, Paterson AH. 2014. SNPhylo: a pipeline to construct a phylogenetic tree from huge SNP data. BMC Genomics 15: 162.
33. Leonard JA, Vilà C, Wayne RK. 2005. Legacy lost: genetic variability and population size of extirpated US grey wolves (Canis lupus). Mol Ecol 14: 9-17.
34. Leonard JA, Vilà C, Fox-Dobbs K, Koch PL, Wayne RK, Van Valkenburgh B. 2007. Megafaunal extinctions and the disappearance of a specialized wolf ecomorph. Curr Biol 17: 1146-1150.
35. Levi T, Wilmers CC. 2012. Wolves-coyotes-foxes: a cascade among carnivores. Ecology 93: 921-929.
36. Li H, Durbin R. 2011. Inference of human population history from individual whole-genome sequences. Nature 475: 493-496.
37. Li B, Zhu Li. 2001. "Greatest lake period" and its palaeo-environment on the Tibetan Plateau. J Geogr Sci 11: 34-42.
38. Lindblad-Toh K, Wade CM, Mikkelsen TS, Karlsson EK, Jaffe DB, Kamal M, Clamp M, Chang JL, Kulbokas EJ III, Zody MC, et al. 2005. Genome sequence, comparative analysis and haplotype structure of the domestic dog. Nature 438: 803-819.
39. Lucchini V, Galov A, Randi E. 2004. Evidence of genetic distinction and long-term population decline in wolves (Canis lupus) in the Italian Apennines. Mol Ecol 13: 523-536.
40. Meachen JA, Samuels JX. 2012. Evolution in coyotes (Canis latrans) in response to the megafaunal extinctions. Proc Natl Acad Sci 109: 4191-4196.
41. Miller W, Schuster SC, Welch AJ, Ratan A, Bedoya-Reina OC, Zhao F, Kim HL, Burhans RC, Drautz DI, Wittekindt NE, et al. 2012. Polar and brown bear genomes reveal ancient admixture and demographic footprints of past climate change. Proc Natl Acad Sci 109: E2382-E2390.
42. Musiani M, Leonard JA, Cluff HD, Gates CC, Mariani S, Paquet PC, Vilà C, Wayne RK. 2007. Differentiation of tundra/taiga and boreal coniferous forest wolves: genetics, coat colour and association with migratory caribou. Mol Ecol 16: 4149-4170.
43. Novembre J, Stephens M. 2008. Interpreting principal component analyses of spatial population genetic variation. Nat Genet 40: 646-649.
44. Nowak RM. 1979. North American Quaternary Canis. Monograph of the Museum of Natural History. University of Kansas, Lawrence, KS.
45. Pang JF, Kluetsch C, Zou XJ, Zhang AB, Luo LY, Angleby H, Ardalan A, Ekström C, Sköllermo A, Lundeberg J, et al. 2009. mtDNA data indicate a single origin for dogs south of Yangtze River, less than 16, 300 years ago, from numerous wolves. Mol Biol Evol 26: 2849-2864.
46. Pilot M, Jedrzejewski W, Branicki W, Sidorovich VE, Jedrzejewska B, Stachura K, Funk SM. 2006. Ecological factors influence population genetic structure of European grey wolves. Mol Ecol 15: 4533-4553.
47. Pilot M, Branicki W, Jedrzejewski W, Goszczyński J, Jedrzejewska B, Dykyy I, Shkvyrya M, Tsingarska E. 2010. Phylogeographic history of grey wolves in Europe. BMC Evol Biol 10: 104.
48. Pilot M, Greco C, vonHoldt BM, Jedrzejewska B, Randi E, Jedrzejewski W, Sidorovich VE, Ostrander EA, Wayne RK. 2014. Genome-wide signatures of population bottlenecks and diversifying selection in European wolves. Heredity 112: 428-442.
49. Purcell S, Neale B, Todd-Brown K, Thomas L, Ferreira MA, Bender D, Maller J, Sklar P, de Bakker PI, Daly MJ, et al. 2007. PLINK: a tool set for whole-genome association and population-based linkage analyses. Am J Hum Genet 81: 559-575.
50. Ripple WJ, Estes JA, Beschta RL, Wilmers CC, Ritchie EG, Hebblewhite M, Berger J, Elmhagen B, Letnic M, Nelson MP, et al. 2014. Status and ecological effects of the world's largest carnivores. Science 343: 1241484.
51. Sastre N, Vilà C, Salinas M, Bologov VV, Urios V, Sánchez A, Francino O, Ramírez O. 2011. Signatures of demographic bottlenecks in European wolf populations. Conserv Genet 12: 701-712.
52. Savolainen P, Zhang YP, Luo J, Lundeberg J, Leitner T. 2002. Genetic evi-dencefor an East Asian originof domestic dogs. Science 298: 1610-1613.
53. Shannon LM, Boyko RH, Castelhano M, Corey E, Hayward JJ, McLean C, White ME, Abi Said M, Anita BA, Bondjengo NI, et al. 2015. Genetic structure in village dogs reveals a Central Asian domestication origin. Proc Natl Acad Sci 112: 13639-13644.
54. Shipman P. 2015. The invaders: how humans and their dogs drove Neanderthals to extinction. Belknap Press of Harvard University Press, Cambridge, MA.
55. Skoglund P, Ersmark E, Palkopoulou E, Dalén L. 2015. Ancient wolf genome reveals an early divergence of domestic dog ancestors and admixture into high-latitude breeds. Curr Biol 25: 1515-1519.
56. Thalmann O, Shapiro B, Cui P, Schuenemann VJ, Sawyer SK, Greenfield DL, Germonpré MB, Sablin MV, López-Giráldez F, Domingo-Roura X, et al. 2013. Complete mitochondrial genomes of ancient canids suggest a European origin of domestic dogs. Science 342: 871-874.
57. Van Valkenburgh B, Hayward MW, Ripple WJ, Meloro C, Roth VL. 2015. The impact of large terrestrial carnivores on Pleistocene ecosystems. Proc Natl Acad Sci. doi: 10.1073/pnas.1502554112.
58. Vilà C, Amorim IR, Leonard JA, Posada D, Castroviejo J, Petrucci-Fonseca F, Crandall KA, Ellegren H, Wayne RK. 1999. Mitochondrial DNA phylo-geography and population history of the grey wolf Canis lupus. Mol Ecol 8: 2089-2103.
59. vonHoldt BM, Pollinger JP, Lohmueller KE, Han E, Parker HG, Quignon P, Degenhardt JD, Boyko AR, Earl DA, Auton A, et al. 2010. Genome-wide SNP and haplotype analyses reveal a rich history underlying dog domestication. Nature 464: 898-902.
60. vonHoldt BM, Pollinger JP, Earl DA, Knowles JC, Boyko AR, Parker H, Geffen E, Pilot M, Jedrzejewski W, Jedrzejewska B, et al. 2011. A genome-wide perspective on the evolutionary history of enigmatic wolf-like canids. Genome Res 12: 1294-1305.
61. Wang GD, Zhai W, Yang HC, Fan RX, Cao X, Zhong L, Wang L, Liu F, Wu H, Cheng LG, et al. 2013. The genomics of selection in dogs and the parallel evolution between dogs and humans. Nat Commun 4: 1860.
62. Wayne RK, Hedrick P. 2011. Genetics and wolf conservation in the American West: lessons and challenges. Heredity 107: 16-19.
63. Wayne RK, Ostrander EA. 2007. Lessons learned from the dog genome. Trends Genet 23: 557-567.
64. Wayne RK, Lehman N, Allard MW, Honeycutt RL. 1992. Mitochondrial DNA variability of the gray wolf: genetic consequences of population decline and habitat fragmentation. Conserv Biol 6: 559-569.
65. Xu DM, Shen YP. 1995. On ancient ice-sheet and ice age in the Tibetan plateau. J Glaciol Geocryol 17: 213-229.
66. Yi CL, Cui ZJ, Xiong HG. 2005. Numerical period of Quaternary glaciations in China. Quatern Sci 25: 609-611.
67. Zhang W, Fan Z, Han E, Hou R, Zhang L, Galaverni M, Huang J, Liu H, Silva P, Li P, et al. 2014. Hypoxia adaptations in the grey wolf (Canis lupus chanco) from Qinghai-Tibet Plateau. PLoS Genet 10: e1004466.