Single nucleotide polymorphism (SNP) variation of wolves (Canis lupus) in Southeast Alaska and comparison with wolves, dogs, and Coyotes in North America

Journal of Heredity

Volumn 106, Issue 1, 2015, Pages 26-36

  Cronin, Matthew A ^a   Cánovas, Angela ^b   Bannasch, Danika L ^b   Oberbauer, Anita M ^b   MeDrano, Juan F ^b   Ostrander, Elaine ^c  

^a UNIVERSITY OF ALASKA FAIRBANKS   (United States)

^b UNIVERSITY OF CALIFORNIA   (United States)

^c University of California Davis ^*

Author keywords

Coyote; Dog; Genetic variation; Single nucleotide polymorphism; SNP; Wolf

Indexed keywords

ANIMAL EXPERIMENT; ANIMAL GENETICS; ANIMAL TISSUE; ARTICLE; CANADA; CANIS LUPUS; COMPARATIVE STUDY; CONTROLLED STUDY; COYOTE; DOG; GENE FREQUENCY; GENE LINKAGE DISEQUILIBRIUM; GENETIC DISTANCE; GENETIC VARIABILITY; GENOTYPE; HETEROZYGOSITY; MAXIMUM LIKELIHOOD METHOD; NONHUMAN; NORTH AMERICA; PRIORITY JOURNAL; SINGLE NUCLEOTIDE POLYMORPHISM; SPECIES DIFFERENTIATION; SUBSPECIES; UNITED STATES; ANIMAL; ANIMAL DISPERSAL; CLUSTER ANALYSIS; GENETICS; HETEROZYGOTE; PHYLOGENY; POPULATION GENETICS; SPECIES DIFFERENCE; WOLF;

ALASKA; ANIMAL DISTRIBUTION; ANIMALS; CLUSTER ANALYSIS; COYOTES; DOGS; GENE FREQUENCY; GENETICS, POPULATION; GENOTYPE; HETEROZYGOTE; PHYLOGENY; POLYMORPHISM, SINGLE NUCLEOTIDE; SPECIES SPECIFICITY; WOLVES;

EID: 84937965736     PISSN: 00221503     EISSN: 14657333     Source Type: Journal    
DOI: 10.1093/jhered/esu075     Document Type: Article

References (62)

1. Alexander DH, Novembre J, Lange K. 2009. Fast model-based estimation of ancestry in unrelated individuals. Genome Res. 19:1655-1664.
2. Avise JC, Ball RM Jr. 1990. Principles of genealogical concordance in species concepts and biological taxonomy. Oxford Survey Evol Biol. 7:45-67.
3. Bardeleben C, Moore RL, Wayne RK. 2005. A molecular phylogeny of the Canidae based on six nuclear loci. Mol Phylogenet Evol. 37:815-831.
4. Brown SK, Pedersen NC, Jafarishorijeh S, Bannasch DL, Ahrens KD, Wu JT, Okon M, Sacks BN. 2011. Phylogenetic distinctiveness of Middle Eastern and Southeast Asian village dog Y chromosomes illuminates dog origins. PLoS One. 6:e28496.
5. Carmichael LE, Krizan J, Nagy JA, Fuglei E, Dumond M, Johnson D, Veitch A, Berteaux D, Strobeck C. 2007. Historical and ecological determinants of genetic structure in arctic canids. Mol Ecol. 16:3466-3483.
6. Carmichael LE, Krizan J, Nagy JA, Dumond M, Johnson D, Veitch A, Strobeck C. 2008. Northwest passages: conservation genetics of Arctic island wolves. Conserv Genetics. 9:879-892.
7. CBD. 2011. Petition to list the Alexander Archipelago wolf (Canis lupus ligoni) as threatened or endangered under the United States Endangered Species Act. Center for Biological Diversity and Greenpeace, Petitioner, August 10, 2011. http://www.biologicaldiversity.org/species/mammals/Alexander-Archipelago-wolf/pdfs/AA-Wolf-ESA-Petition-10-Aug-2011.pdf.
8. Chakraborty R, Fuerst PA, Nei M. 1980. Statistical Studies on Protein Polymorphism in Natural Populations. III. Distribution of Allele Frequencies and the Number of Alleles per Locus. Genetics. 94:1039-1063.
9. Chambers SM, Fain SR, Fazio B, Amaral M. 2012. An account of the taxonomy of North American wolves from morphological and genetic analyses. North American Fauna. 77:1-67.
10. Clark RL, Templeton AR, Sing CF. 1981. Studies of Enzyme Polymorphisms in the Kamuela Population of D. MERCATORUM. I. Estimation of the Level of Polymorphism. Genetics. 98:597-611.
11. Cook JA, Dawson NG, MacDonald SO. 2006. Conservation of highly fragmented systems: The north temperate Alexander Archipelago. Biol Conserv. 133:1-15.
12. Cronin MA. 2006. A Proposal to eliminate redundant terminology for intra-species groups. Wildl Soc Bull. 34:237-241.
13. Cronin MA, Mech LD. 2009. Problems with the claim of ecotype and taxon status of the wolf in the Great Lakes region. Mol Ecol. 18:4991-3.
14. Cronin MA, MacNeil MD, Vu N, Leesburg V, Blackburn H, Derr J. 2013. Genetic variation and differentiation of bison (Bison bison) subspecies and cattle (Bos taurus) breeds and subspecies. J Hered. 104:500-509.
15. Decker JE, Pires JC, Conant GC, McKay SD, Heaton MP, Chen K, Cooper A, Vilkki J, et al. 2009. Resolving the evolution of extant and extinct ruminants with high-throughput phylogenomics. Proc Natl Acad Sci USA. 106:18644-18649.
16. Decker JE, McKay SD, Rolf MM, Kim J, Alcalá AM, Sonstegard TS, Hanotte O, Götherström A, et al. 2014. Worldwide patterns of ancestry, divergence, and admixture in domesticated cattle. PLoS Genet. 10:e1004254.
17. Felsenstein J. 1982. How can we infer geography and history from gene frequencies? J Theor Biol. 96:9-20.
18. Felsenstein, J. 2004. PHYLIP (Phylogeny Inference Package) version 3.6. Seattle (WA): Department of Genome Sciences, University of Washington.
19. Forbes SH, Boyd DK. 1996. Genetic variation of naturally colonizing wolves in the central Rocky Mountains. Conserv Biol. 10:1082-1090.
20. Forbes SH, Boyd DK. 1997. Genetic structure and migration in native and reintroduced Rocky Mountain wolf populations. Conserv Biol. 11:1226-1234.
21. García-Moreno J, Matocq MD, Roy RS, 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.
22. Gray MM, Sutter NB, Ostrander EA, Wayne RK. 2010. IGF1 haplotyping supports a Middle Eastern Origin for small dogs. BMC Biol. 8:16.
23. Hailer F, Leonard JA. 2008. Hybridization among three native North American Canis species in a region of natural sympatry. PLoS One. 3:e333.
24. Hall, ER. 1981. The mammals of North America. 2nd ed. Vol. II. New York: Wiley.
25. Hedrick P W, Fredrickson RJ. 2008. Captive breeding and the reintroduction of Mexican and red wolves. Mol Ecol. 17:344-350.
26. Hedrick P W, Miller PS, Geffen E, Wayne R. 1997. Genetic evaluation of the three captive Mexican wolf lineages. Zoo Biology. 16:47-69.
27. Honeycutt RL. 2010. Unraveling the mysteries of dog evolution. BMC Biol. 8:20.
28. Kays R, Curtis A, Kirchman JJ. 2010. Rapid adaptive evolution of northeastern coyotes via hybridization with wolves. Biol Lett. 6:89-93.
29. Klein DR. 1965. Post glacial distribution patterns of mammals in the southern coastal regions of Alaska. Arctic. 10:7-10.
30. Knowles JC. 2010. Population genomics of North American grey wolves (Canis lupus). [Master's Thesis]. [Edmonton (AB)]: University of Alberta.
31. Kurtén B, Anderson E. 1980. Pleistocene mammals of North America. New York: Columbia University Press.
32. 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.
33. MacDonald SO, Cook JA. 2009. Recent mammals of Alaska. Fairbanks (AK): University of Alaska Press.
34. Malaney JL, Cook JA. 2013. Using biogeographical history to inform conservation: the case of Preble's meadow jumping mouse. Mol Ecol. 22:6000-6017.
35. Mayr E. 1982. The growth of biological thought. Cambridge (MA): Harvard University Press.
36. Monzón J, Kays R, Dykhuizen DE. 2014. Assessment of coyote-wolf-dog admixture using ancestry-informative diagnostic SNPs. Mol Ecol. 23:182-197.
37. Muñoz-Fuentes V, Darimont CT, Wayne RK, Paquet PC, Leonard JA. 2009. Ecological factors drive differentiation in wolves from British Columbia. J Biogeogr. 36:1516-1531.
38. Muñoz-Fuentes V, Darimont CT, Paquet PC, Leonard JA. 2010. The genetic legacy of extirpation and re-colonization in Vancouver Island Wolves. Conserv Genetics. 11:547-556.
39. Nowak RM. 1979. North American Quaternary Canis. Monograph of the Museum of Natural History University of Kansas. 6:1-154.
40. Nowak RM.1995. Another look at wolf taxonomy. In: Carbyn LN, Fritts SH, Seip DR, editors. Ecology and conservation of wolves in a changing world. Canadian Circumpolar Institute, Occasional Publication No. 35. p. 375-398.
41. Nowak RM. 2002. The original status of wolves in eastern North America. Southeastern Naturalist. 1:95-130.
42. Orloci L. 1978. Multivariate analysis in vegetation research. The Hague (The Netherlands): W. Junk.
43. Ramey RR, Liu H-P, Epps C W, Carpenter LM, Wehausen JD. 2005. Genetic relatedness of the Preble's meadow jumping mouse (Zapus hudsonius preblei) to nearby subspecies of Z. hudsonius as inferred from variation in cranial morphology, mitochondrial DNA and microsatellite DNA: implications for taxonomy and conservation. Anim Conserv. 8:329-346.
44. Rincon G, Tengvall K, Belanger JM, Lagoutte L, Medrano JF, André C, Thomas A, Lawley CT, Hansen ST, Lindblad-Toh K, Oberbauer AM. 2011. Comparison of buccal and blood-derived canine DNA, either native or whole genome amplified, for array-based genome-wide association studies. BMC Res Notes. 4:226.
45. Saitou N, Nei M. 1987. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol. 4:406-425.
46. Tamura K, Peterson D, Peterson N, Stecher G, Nei M, Kumar S. 2011. MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Mol Biol Evol. 28:2731-2739.
47. USFWS. 2014. 90 day finding on a petition to List the Alexander Archipelago Wolf as threatened or endangered. Federal Register 79:17993-17995. U.S. Fish and Wildlife Service. 31 March 2014.
48. Vaysse A, Ratnakumar A, Derrien T, Axelsson E, Rosengren Pielberg G, Sigurdsson S, Fall T, et al. 2011. Identification of genomic regions associated with phenotypic variation between dog breeds using selection mapping. PLoS Genet. 7:e1002316.
49. Vilà C, Savolainen P, Maldonado JE, Amorim IR, Rice JE, Honeycutt RL, Crandall KA, Lundeberg J, Wayne RK. 1997. Multiple and ancient origins of the domestic dog. Science. 276:1687-1689.
50. Vilà C, Amorim IR, Leonard JA, Posada D, Castroviejo J, Petrucci-Fonseca F, Crandall KA, Ellegren H, Wayne RK. 1999. Mitochondrial DNA phylogeography and population history of the grey wolf Canis lupus. Mol Ecol. 8:2089-2103.
51. vonholdt BM, Pollinger JP, Lohmueller KE, Han E, Parker HG, Quignon P, Degenhardt JD, Boyko AR, et al. 2010. Genome-wide SNP and haplotype analyses reveal a rich history underlying dog domestication. Nature. 464:898-903.
52. vonHoldt BM, Pollinger JP, Earl DA, Knowles JC, Boyko AR, Parker H, Geffen E, Pilot M, et al. 2011. A genome-wide perspective on the evolutionary history of enigmatic wolf-like canids. Genome Res. 21:1294-1305.
53. Wayne RK, Vilà C. 2003. Molecular genetic studies of wolves. In: Mech LD, Boitani L, editors. Wolves: behavior, ecology, and conservation. Chicago (IL): University of Chicago Press. p. 218-238.
54. Wayne RK, vonHoldt BM. 2012. Evolutionary genomics of dog domestication. Mamm Genome. 23:3-18.
55. Weckworth B V, Talbot S, Sage GK, Person DK, Cook J. 2005. A signal for independent coastal and continental histories among North American wolves. Mol Ecol. 14:917-931.
56. Weckworth B V, Talbot SL, Cook JA. 2010. Phylogeography of wolves (Canis lupus) in the Pacific Northwest. J Mammal. 91: 363-375.
57. Weckworth B V, Dawson NG, Talbot SL, Flamme MJ, Cook JA. 2011. Going coastal: shared evolutionary history between coastal British Columbia and Southeast Alaska wolves (Canis lupus). PLoS One. 6:e19582.
58. Weir BS, Cockerham CC. 1984. Estimating F-Statistics for the Analysis of Population Structure. Evolution. 38:1358-1370.
59. Wilson EO, Brown WL. 1953. The subspecies concept and its taxonomic applications. Syst Zool. 2:97-122.
60. Zachos RE, Apollonio M, Bärmann EV, Festa-Bianchet M, Göhlich U, Habel JC, Haring E, Kruckenhauser L, et al. 2013. Species inflation and taxonomic artefacts - A critical comment on recent trends in mammalian classification. Mamm Biol. 78:1-6.
61. Zink RM. 2004. The role of subspecies in obscuring avian biological diversity and misleading conservation policy. Proc Royal Soc Lond B. 271:561-564.
62. Zink RM, Groth JG, Vazquez-Miranda H, Barrowclough GF. 2013. Phylogeography of the California gnatcatcher (Polioptila californica) using multilocus DNA sequences and ecological niche modeling: Implications for conservation. The Auk. 130:449-458.