Species-wide phylogeography of North American mule deer (Odocoileus hemionus): Cryptic glacial refugia and postglacial recolonization

Molecular Ecology

Volumn 18, Issue 8, 2009, Pages 1730-1745

  Latch, Emily K ^a   Heffelfinger, James R ^b   Fike, Jennifer A ^c   Rhodes Jr , Olin E ^c  

^a UNIVERSITY OF WISCONSIN MILWAUKEE   (United States)

^b ARIZONA GAME AND FISH DEPARTMENT   (United States)

^c PURDUE UNIVERSITY   (United States)

Author keywords

Alexander Archipelago; Black tailed deer; Cervidae; Haplogroup; Intraspecific; MtDNA

Indexed keywords

MITOCHONDRIAL DNA;

ANIMAL; ARTICLE; BIOLOGICAL MODEL; DEER; DNA SEQUENCE; GENETIC VARIABILITY; GENETICS; GEOGRAPHY; HAPLOTYPE; MOLECULAR EVOLUTION; NORTH AMERICA; PHYLOGENY; POPULATION GENETICS; SPECIES DIFFERENCE;

ANIMALS; DEER; DNA, MITOCHONDRIAL; EVOLUTION, MOLECULAR; GENETIC VARIATION; GENETICS, POPULATION; GEOGRAPHY; HAPLOTYPES; MODELS, GENETIC; NORTH AMERICA; PHYLOGENY; SEQUENCE ANALYSIS, DNA; SPECIES SPECIFICITY;

ANIMALIA; CERVIDAE; ODOCOILEUS HEMIONUS; ODOCOILEUS HEMIONUS COLUMBIANUS; UNGULATA;

EID: 63849202703     PISSN: 09621083     EISSN: 1365294X     Source Type: Journal    
DOI: 10.1111/j.1365-294X.2009.04153.x     Document Type: Article

References (88)

1. Akaike H (1974) A new look at the statistical model identification. IEEE Transactions on Automatic Control, 19, 716 723.
2. Anderson AE, Wallmo OC (1984) Odocoileus hemionus. Mammalian Species, 219, 1 9.
3. Avise JC, Walker D, Johns GC (1998) Speciation durations and Pleistocene effects on vertebrate phylogeography. Proceedings of the Royal Society B: Biological Sciences, 265, 1707 1712.
4. Bennett KD, Tzedakis PC, Willis KJ (1991) Quaternary refugia of north European trees. Journal of Biogeography, 18, 103 115.
5. Bernatchez L, Wilson CC (1998) Comparative phylogeography of Nearctic and Palearctic fishes. Molecular Ecology, 7, 431 452.
6. Bradley RD, Bryant FC, Bradley LC, Haynie ML, Baker RJ (2003) Implications of hybridization between white-tailed deer and mule deer. The Southwestern Naturalist, 48, 654 660.
7. Brunsfeld SJ, Sullivan J, Soltis DE, Soltis PS (2001) Comparative phylogeography of northwestern North America: a synthesis. In : Integrating Ecological and Evolutionary Processes in a Spatial Context (eds Silvertown J, Antonovics J pp. 319 339. Blackwell Science, Oxford, UK.
8. Cann RL, Stoneking M, Wilson AC (1987) Mitochondrial DNA and human evolution. Nature, 325, 31 36.
9. Carr SM, Hughes GA (1993) Direction of introgressive hybridization between species of North American deer (Odocoileus) as inferred from mitochondrial cytochrome-b sequences. Journal of Mammalogy, 74, 331 342.
10. Carr SM, Ballinger SW, Derr JN, Blankenship LH, Bickham JW (1986) Mitochondrial DNA analysis of hybridization between sympatric white-tailed deer and mule deer in west Texas. Proceedings of the National Academy of Sciences, USA, 48, 9576 9580.
11. Carrara PE, Ager TA, Baichtal JF, VanSistine DP (2003) Map of glacial limits and possible refugia in the southern Alexander Archipelago, Alaska, during the late Wisconsin glaciation. US Geological Survey Miscellaneous Field Studies Map MF-2424, US Geological Survey, Denver, Colorado.
12. Carrara PE, Ager TA, Baichtal JF (2007) Possible refugia in the Alexander Archipelago of southeastern Alaska during the late Wisconsin glaciation. Canadian Journal of Earth Sciences, 44, 229 244.
13. Cathey JC, Bickham JW, Patton JC (1998) Introgressive hybridization and nonconcordant evolutionary history of maternal and paternal lineages in North American deer. Evolution, 52, 1224 1229.
14. Catto NR, Liverman DGE, Bobrowsky PT, Rutter N (1996) Laurentide, Cordilleran, and Montane glaciation in the western Peace River - Grande prairie region, Alberta and British Columbia. Quaternary International, 32, 21 32.
15. Clement M, Posada D, Crandall KA (2000) tcs: a computer program to estimate gene genealogies. Molecular Ecology, 9, 1657 1660.
16. Clutton-Brock TH (1989) Mammalian mating systems. Proceedings of the Royal Society B: Biological Sciences, 236, 339 372.
17. Cook JA, Dawson NG, MacDonald SO (2006) Conservation of highly fragmented systems: the north temperate Alexander Archipelago. Biological Conservation, 133, 1 15.
18. Cowan IM (1936) Distribution and variation in deer (Genus Odocoileus) of the Pacific Coast region of North America. California Fish and Game, 22, 155 246.
19. Cowan IM (1956) What and where are the mule and black-tailed deer? In : The Deer of North America (ed. Taylor WP pp. 334 359. Stackpole Books, Harrisburg, Pennsylvania.
20. Crandall KA, Templeton AR (1993) Empirical tests of some predictions from coalescent theory with applications to intraspecific phylogeny reconstruction. Genetics, 134, 959 969.
21. Cronin MA (1991a) Mitochondrial and nuclear genetic relationships of deer (Odocoileus spp.) in western North America. Canadian Journal of Zoology, 69, 1270 1279.
22. Cronin MA (1991b) Mitochondrial DNA phylogeny of deer (Cervidae). Journal of Mammalogy, 72, 533 566.
23. Cronin MA (1992) Intraspecific variation in mitochondrial DNA of North American cervids. Journal of Mammalogy, 73, 70 82.
24. Cronin MA, Bleich VC (1995) Mitochondrial DNA variation among populations and subspecies of mule deer in California. California Fish and Game, 81, 45 54.
25. Cronin MA, Vyse ER, Cameron DG (1988) Genetic relationships between mule deer and white-tailed deer in Montana. Journal of Wildlife Management, 52, 320 328.
26. Cronin MA, Nelson ME, Pac DF (1991) Spatial heterogeneity of mitochondrial DNA and allozymes among populations of white-tailed deer and mule deer. Journal of Heredity, 82, 118 127.
27. Cronin MA, MacNeil MD, Patton JC (2005) Variation in mitochondrial DNA and microsatellite DNA in caribou (Rangifer tarandus) in North America. Journal of Mammalogy, 86, 495 505.
28. Cwynar LC, MacDonald GM (1987) Geographical variation of lodgepole pine in relation to population history. American Naturalist, 129, 463 469.
29. Dalen L, Nystrom V, Valdiosera C et al 2007) Ancient DNA reveals lack of postglacial habitat tracking in the Arctic fox. Proceedings of the National Academy of Sciences, USA, 104, 6726 6729.
30. Dixon CJ (2006) A means of estimating the completeness of haplotype sampling using the Stirling probability distribution. Molecular Ecology Notes, 6, 650 652.
31. Eldredge N (1989) Macroevolutionary Dynamics: Species, Niches and Adaptive Peaks. McGraw-Hill, New York.
32. Excoffier L, Ray N (2008) Surfing during population expansions promotes genetic revolutions and structuration. Trends in Ecology & Evolution, 23, 347 351.
33. Excoffier L, Laval G, Schneider S (2005) Arlequin version 3.0: an integrated software package for population genetics data analysis. Evolutionary Bioinformatics Online, 1, 47 50.
34. Flagstad O, Roed KH (2003) Refugial origins of reindeer (Rangifer tarandus L.) inferred from mitochondrial DNA sequences. Evolution, 57, 658 670.
35. Fu Y-X (1997) Statistical tests of neutrality of mutations against population growth, hitchhiking and background selection. Genetics, 147, 915 925.
36. Gavin TA, May B (1988) Taxonomic status and genetic purity of Columbian white-tailed deer. Journal of Wildlife Management, 52, 1 10.
37. Geist V (1987) On the evolution and adaptations of Alces. Swedish Wildlife Research Suppl. 1 11 23.
38. Gilbert C, Ropiquet A, Hassanin A (2006) Mitochondrial and nuclear phylogenies of Cervidae (Mammalia, Ruminantia). Systematics, morphology, and biogeography. Molecular Phylogenetics and Evolution, 40, 101 117.
39. Golden JL, Bain JF (2000) Phylogeographic patterns and high levels of chloroplast DNA diversity in four Packera (Asteraceae) species in southwestern Alberta. Evolution, 54, 1566 1579.
40. Gratton P, Konopinski MK, Sbordoni V (2008) Pleistocene evolutionary history of the Clouded Apollo (Parnassius mnemosyne): genetic signatures of climate cycles and a 'time-dependent' mitochondrial substitution rate. Molecular Ecology, 17, 4248 4262.
41. Heaton TH, Grady F (2003) The Late Wisconsin vertebrate history of Prince of Wales Island, southeast Alaska. In : Ice Age Cave Faunas of North America (eds Schubert BW, Mead JI, Graham RW pp. 17 53. Indiana University Press, Bloomington, Indiana.
42. Heaton TH, Talbot SL, Shields GF (1996) An Ice Age refugium for large mammals in the Alexander Archipelago, southeastern Alaska. Quaternary Research, 46, 186 192.
43. Heffelfinger JR (1999) Hybridization in large mammals. In : Conservation and Management of Large Mammals in North America (eds Krausman PR, Demarais S pp. 27 37. Stackpole Books, Harrisburg, Pennsylvania.
44. Hewitt GM (1993) Postglacial distribution and species substructures: lessons from pollen, insects, and hybrid zones. In : Evolutionary Patterns and Processes (eds Lees DR, Edwards D pp. 97 123. Academic Press, London.
45. Hewitt GM (1996) Some genetic consequences of ice ages, and their role in divergence and speciation. Biological Journal of the Linnean Society, 58, 247 276.
46. Hewitt GM (1999) Post-glacial re-colonization of European biota. Biological Journal of the Linnean Society, 68, 87 112.
47. Hewitt GM (2000) The genetic legacy of Quaternary ice ages. Nature, 405, 907 913.
48. Ho SY, Larson G (2006) Molecular clocks: when times are a-changin'. Trends in Genetics, 22, 79 83.
49. Hundertmark K, Shields GF, Udina IG et al 2002) Mitochondrial phylogeography of moose (Alces alces): Late Pleistocene divergence and population expansion. Molecular Phylogenetics and Evolution, 22, 375 387.
50. Hutton D (1972) Variation in skulls and antlers of wapiti. MS Thesis. University of Calgary, Alberta, Canada.
51. Ibrahim KM, Nichols RA, Hewitt GM (1996) Spatial patterns of genetic variation generated by different forms of dispersal during range expansion. Heredity, 77, 282 291.
52. Idaghdour Y, Broderick D, Korrida A, Chbel F (2004) Mitochondrial control region diversity of the houbara bustard Chlamydotis undulata complex and genetic structure along the Atlantic seaboard of North Africa. Molecular Ecology, 13, 43 54.
53. Klein DR, Meldgaard M, Fancy SG (1987) Factors determining leg length in Rangifer tarandus. Journal of Mammalogy, 68, 642 655.
54. Klopfstein S, Currat M, Excoffier L (2006) The fate of mutations surfing on the wave of a range expansion. Molecular Biology and Evolution, 23, 482 490.
55. Kurten B, Anderson E (1980) Pleistocene Mammals of North America. Columbia University Press, New York.
56. Latch EK, Amann RA, Jacobson JP, Rhodes OE (2008) Competing hypotheses for the etiology of cryptorchidism in Sitka black-tailed deer: an evaluation of evolutionary alternatives. Animal Conservation, 11, 234 246.
57. Leonard JA, Wayne RK, Cooper A (2000) Population genetics of Ice Age brown bears. Proceedings of the National Academy of Sciences, USA, 97, 1651 1654.
58. Liebers D, Helbig AJ (2002) Phylogeography and colonization history of lesser black-backed gulls (Larus fuscus) as revealed by mtDNA sequences. Journal of Evolutionary Biology, 15, 1021 1033.
59. Loehr J, Worley K, Grapputo A et al 2006) Evidence for cryptic glacial refugia from North American mountain sheep mitochondrial DNA. Journal of Evolutionary Biology, 19, 419 430.
60. Loveless MD, Hamrick JL (1984) Ecological determinants of genetic structure in plant populations. Annual Review of Ecology and Systematics, 15, 60 90.
61. Maddison DR, Maddison WP (2000) MacClade 4: Analysis of Phylogeny and Character Evolution, Version 4.06. Sinauer Associates, Sunderland, Massachusetts.
62. Meadows JRS, Cemal I, Karaca O, Gootwine E, Kijas JW (2007) Five ovine mitochondrial lineages identified from sheep breeds of the near east. Genetics, 175, 1371 1379.
63. Naderi S, Rezaei H, Taberlet P et al 2007) Large-scale mitochondrial DNA analysis of the domestic goat reveals six haplogroups with high diversity. PLoS One, 2, e1012.
64. Nei M, Maruyama T, Chakraborty R (1975) The bottleneck effect and genetic variability in populations. Evolution, 29, 1 10.
65. Nixon KC (1999) The Parsimony Ratchet, a new method for rapid parsimony analysis. Cladistics, 15, 407 414.
66. Pielou EC (1991) After the Ice Age: The Return of Life to Glaciated North America. University of Chicago Press, Chicago.
67. Polziehn RO, Strobeck C (2000) Phylogeny of wapiti, red deer, sika deer, and other North American cervids as determined from mitochondrial DNA. Molecular Phylogenetics and Evolution, 10, 249 258.
68. Posada D, Crandall KA (1998) ModelTest: testing the model of DNA substitution. Bioinformatics, 14, 817 818.
69. Raught RW (1967) White-tailed deer. In : New Mexico Wildlife Management (ed. Huey WS pp. 52 60. New Mexico Department of Game and Fish, Santa Fe, New Mexico.
70. Robinette WL, Hancock NV, Jones DA (1977) The Oak Creek mule deer herd in Utah. Utah Division of Wildlife Resources Publication 77-15.
71. Rogers AR, Harpending H (1992) Population growth makes waves in the distribution of pairwise genetic differences. Molecular Biology and Evolution, 9, 552 569.
72. Rozas J, Sanchez-De I, Barrio JC, Messeguer X, Rozas R (2003) DnaSP: DNA polymorphism analyses by the coalescent and other methods. Bioinformatics, 19, 2496 2497.
73. Schneider S, Excoffier L (1999) Estimation of demographic parameters from the distribution of pairwise differences when the mutation rates vary among sites: application to human mitochondrial DNA. Genetics, 152, 1079 1089.
74. Schonewald-Cox CM, Bayless JW, Schonewald J (1985) Cranial morphometry of Pacific coast elk (Cervus elaphus). Journal of Mammalogy, 66, 63 74.
75. Sikes DS, Lewis PO (2001) Beta software, version 1. PAUPRat: PAUP* implementation of the parsimony ratchet. Distributed by the authors at http://www.ucalgary.ca/∼dsikes/software2.htm. Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs, Connecticut.
76. Soltis DE, Gitzendanner MA, Strenge DD, Soltis PS (1997) Chloroplast DNA intraspecific phylogeography of plants from the Pacific Northwest of North America. Plant Systematics and Evolution, 206, 353 373.
77. Soltis DE, Soltis PS, Ranker TA, Ness BD (1989) Chloroplast DNA variation in a wild plant, Tolmiea menziesii. Genetics, 121, 819 826.
78. Steele CA, Storfer A (2006) Coalescent-based hypothesis testing supports multiple Pleistocene refugia in the Pacific Northwest for the Pacific giant salamander (Dicamptodon tenebrosus). Molecular Ecology, 15, 2477 2487.
79. Swofford DL (2003) paup*: Phylogenetic Analysis Using Parsimony (*and Other Methods), Version 4.0b10a. Sinauer Associates, Sunderland, Massachusetts.
80. Talavera G, Castresana J (2007) Improvement in phylogenies after removing divergent and ambiguously aligned blocks from protein sequence alignment. Systematic Biology, 56, 564 577.
81. Tavare S (1986) Some probabilistic and statistical problems in the analysis of DNA sequences. In : Some Mathematical Questions in Biology - DNA Sequence Analysis (ed. Miura RM pp. 57 86. American Mathematics Society, Providence, Rhode Island.
82. Templeton AR (1998) Nested clade analyses of phylogeographic data: testing hypotheses about gene flow and population history. Molecular Ecology, 7, 381 397.
83. Templeton AR, Crandall KA, Sing DF (1992) A cladistic analysis of phenotypic associations with haplotypes inferred from restriction endonuclease mapping and DNA sequence data. III. Cladogram estimation. Genetics, 132, 619 633.
84. Travis SE, Keim P (1995) Differentiating individuals and populations of mule deer using DNA. Journal of Wildlife Management, 59, 824 831.
85. Valdiosera CE, Garcia N, Anderung C et al 2007) Staying out in the cold: glacial refugia and mitochondrial DNA phylogeography in ancient European brown bears. Molecular Ecology, 16, 5140 5148.
86. Vigilant L, Pennington R, Harpending H, Kocher TD, Wilson AC (1989) Mitochondrial DNA sequences in single hairs from a southern African population. Proceedings of the National Academy of Sciences, USA, 86, 9350 9354.
87. Villesen P (2007) FaBox: an online toolbox for fasta sequences. Molecular Ecology Notes, 7, 965 968.
88. Williams D, Dunkerley D, DeDeckker P, Kershaw P, Chappell M (1998) Quaternary Environments. Arnold, London.