Coalescent-based hypothesis testing supports multiple Pleistocene refugia in the Pacific Northwest for the Pacific giant salamander (Dicamptodon tenebrosus)

Molecular Ecology

Volumn 15, Issue 9, 2006, Pages 2477-2487

  Steele, Craig A ^a   Storfer, Andrew ^a  

^a WASHINGTON STATE UNIVERSITY   (United States)

Author keywords

Coalescence; Columbia River; Dicamptodon; Dispersal; Klamath Siskiyou; Phylogeography

Indexed keywords

AMPHIBIA; ANIMAL; ARTICLE; BIOLOGICAL MODEL; ENVIRONMENT; GENETICS; HAPLOTYPE; NORTH AMERICA; PHYLOGENY; PHYSIOLOGY; POPULATION DYNAMICS; TIME;

ANIMALS; ENVIRONMENT; HAPLOTYPES; MODELS, BIOLOGICAL; NORTH AMERICA; PHYLOGENY; POPULATION DYNAMICS; TIME FACTORS; URODELA;

DICAMPTODON TENEBROSUS; DICAMPTODONTIDAE; SALAMANDROIDEA;

EID: 33745884418     PISSN: 09621083     EISSN: 1365294X     Source Type: Journal    
DOI: 10.1111/j.1365-294X.2006.02950.x     Document Type: Article

References (59)

1. Avise JC (2000) Phylogeography: The History and Formation of Species. Harvard University Press, Cambridge, Massachusetts.
2. Avise JC, Walker D, Johns GC (1998) Speciation durations and Pleistocene effects on vertebrate phylogeography. Proceedings of the Royal Society of London. Series B, Biological Sciences, 265, 1707-1712.
3. Beerli P (2004) MIGRATE, version 2.0.6: Documentation and Program, Part of LAMARC. Available at http://evolution.genetics.washington.edu/lamarc.html.
4. Bickham JW, Wood CC, Patton JC (1995) Biogeographic implications of cytochrome b sequences and allozymes in sockeye (Oncorhynchus nerka). Journal of Heredity, 86, 140-144.
5. Brown JR, Beckenbach AT, Smith MJ (1992) Influence of Pleistocene glaciations and human interaction upon mitochondrial DNA diversity in white sturgeon (Acipenser transmontanus) populations. Canadian Journal of Fisheries and Aquatic Sciences, 49, 358-367.
6. Brunsfeld SJ, Sullivan J, Soltis DE, Soltis PS (2001) Comparative phylogeography of Northwestern North America: a synthesis. In: Integrating Ecology and Evolution in a Spatial Context (eds Silvertown J, Antonovics J), pp. 319-339. Blackwell Science, Oxford.
7. Byun SA, Koop BF, Reimchen TE (1997) North American black bear mtDNA phylogeography: implications for morphology and the Haida Gwaii glacial refugium controversy. Evolution, 51, 1647-1653.
8. Carstens BC, Brunsfeld SJ, Demboski JR, Good JD, Sullivan J (2005a) Investigating the evolutionary history of the Pacific Northwest mesic forest ecosystem: hypothesis testing within a comparative phylogeographic framework. Evolution, 59, 1639-1652.
9. Carstens BC, Degenhardt JD, Stevenson AL, Sullivan J (2005b) Accounting for coalescent stochasticity in testing phylogeographic hypotheses: modeling Pleistocene population structure in the Idaho giant salamander Dicamptodon aterrimus. Molecular Ecology, 14, 255-265.
10. Carstens BC, Stevenson AL, Degenhardt JD, Sullivan J (2004) Testing nested phylogenetic and phylogeographic hypotheses in the Plethodon vandykei species group. Systematic Biology, 53, 781-792.
11. Clement M, Posada D, Crandall K (2000) TCS: a computer program to estimate gene genealogies. Molecular Ecology, 9, 1657-1660.
12. Conroy CJ, Cook JA (2000) Phylogeography of a post-glacial colonizer: Microtus longicaudus (Rodentia: Muridae). Molecular Ecology, 9, 165-175.
13. Daugherty CH, Allendorf FW, Dunlap WW, Knudsen KL (1983) Systematic implications of geographic patterns of genetic variation in the genus Dicamptodon. Copeia, 1983, 679-691.
14. Demboski JR, Stone ED, Cook JA (1999) Further perspectives on the Haida Gwaii glacial refugium. Evolution, 53, 2008-2012.
15. Excoffier L, Smouse P, Quattro J (1992) Analysis of molecular variance inferred from metric distances among DNA haplotypes: application to human mitochondrial DNA restriction data. Genetics, 136, 343-359.
16. Good DA (1989) Hybridization and cryptic species in Dicamptodon (Caudata: Dicamptodontidae). Evolution, 43, 728-744.
17. Haas GR, McPhail JD (2001) The post-Wisconsinan glacial biogeography of bull trout (Salvelinus confluentus): a multivariate morphometric approach for conservation biology and management. Canadian Journal of fisheries and Aquatic Sciences, 58, 2189-2203.
18. Harpending RC (1994) Signature of ancient population growth in a low-resolution mitochondrial DNA mismatch distribution. Human Biology, 66, 591-600.
19. 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.
20. Hewitt GM (1999) Post-glacial re-colonization of European biota. Biological Journal of the Linnean Society, 68, 87-112.
21. Hewitt GM (2000) The genetic legacy of the Quaternary ice ages. Nature, 405, 907-913.
22. Huelsenbeck JP, Ronquist F (2001) MRBAYES: Bayesian inference of phylogenetic trees. Bioinformatics, 17, 754-755.
23. 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.
24. Janzen FJ, Krenz JG, Haselkorn TS, Brodie ED Jr, Brodie ED III (2002) Molecular phylogeography of common garter snakes (Thamnophis sirtalis) in western North America: implications for regional historical forces. Molecular Ecology, 11, 1739-1751.
25. Knowles LL, Maddison WP (2002) Statistical phylogeography. Molecular Ecology, 11, 2623-2635.
26. Kuchta SR, Tan AM (2005) Isolation by distance and post-glacial range expansion in the rough skinned newt, Taricha granulosa. Molecular Ecology, 14, 225-244.
27. Kuhner M, Yamato J, Felsenstein J (1998) Maximum likelihood estimation of population growth rates based on the coalescent. Genetics, 149, 429-434.
28. Maddison WP, Maddison DR (2004) MESQUITE, version 1.05: A Modular System for Evolutionary Analysis. Available at http://mesquiteproject.org.
29. McCusker MR, Parkinson E, Taylor EB (2000) Mitochondrial DNA variation in rainbow trout (Oncorhynchus mykiss) across its native range: testing biogeographical hypotheses and their relevance to conservation. Molecular Ecology, 9, 2089-2108.
30. Mead LS, Clayton DR, Nauman RS, Olsen DH, Pfrender ME (2005) Newly discovered populations of salamanders from Siskiyou County, California, represent a species distinct from Plethodon stormi. Herpetologica, 61, 158-177.
31. Miller MP, Haig SM, Wagner RS (2005) Conflicting patterns of genetic structure produced by nuclear and mitochondrial markers in the Oregon slender salamander (Batrachoseps wrighti): implications for conservation efforts and species management. Conservation Genetics, 6, 275-287.
32. Minin V, Abdo Z, Joyce P, Sullivan J (2003) Performance-based selection of likelihood models for phytogeny estimation. Systematic Biology, 52, 674-683.
33. Nielsen R, Wakeley J (2001) Distinguishing migration from isolation: a Markov chain Monte Carlo approach. Genetics, 158, 885-896.
34. Nielson M, Lohman K, Sullivan J (2001) Phylogeography of the tailed frog (Ascaphus truei): implications for the biogeography of the Pacific Northwest. Evolution, 55, 147-160.
35. Noss RF, Strittholt JR, Vance-Borland K, Carroll C, Frost P (1999) A conservation plan for the Klamath-Siskiyou ecoregion. Natural Areas Journal, 19, 392-411.
36. Nussbaum RA (1976) Geographic variation and systematics of salamanders of the genus Dicamptodon Strauch (Ambystomatidae). Miscellaneous Publications of the Museum of Zoology, University of Michigan, 149, 1-94.
37. Nussbaum RA, Brodie ED Jr, Storm RM (1983) Amphibians and Reptiles of the Pacific Northwest. University of Idaho Press, Moscow, Idaho.
38. Posada D, Crandall KA, Templeton AR (2000) GEODIS: a program for the nested cladistic analysis of the geographical distribution of genetic haplotypes. Molecular Ecology, 9, 487-488.
39. Rogers AR, Harpending H (1992) Population growth makes waves in the distribution of pairwise genetic differences. Molecular Biology and Evolution, 9, 552-569.
40. Ronquist F, Huelsenbeck JP (2003) MRBAYES 3: Bayesian phylogenetic inference under mixed models. Bioinformatics, 19, 1572-1574.
41. Sambrook J, Fritsch EF, Maniatis T (1989) Molecular Cloning: A Laboratory Manual, 2nd edn. Cold Spring Harbor Laboratory Press, New York.
42. Schneider S, Roessli D, Excoffier L (2000) ARLEQUIN, version 2.0: A software for population genetics data analysis. Genetics and Biometry Laboratory, Department of Anthropology, University of Geneva, Switzerland, http://anthro.unige.ch/arlequin.
43. Shaffer HB, McKnight ML (1996) The polytypic species revisited: genetic differentiation and molecular phylogenetics of the tiger salamander (Ambystoma tigrinum) (Amphibia: Caudata) complex. Evolution, 50, 417-433.
44. Slatkin M, Maddison WP (1989) A cladistic measure of gene flow inferred from phytogenies of alleles. Genetics, 123, 603-613.
45. 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.
46. Steele CA, Carstens BC, Storfer A, Sullivan J (2005) Testing hypotheses of speciation timing in Dicamptodon copei and Dicamptodon aterrimus (Caudata: Dicamptodontidae). Molecular Phylogenetics and Evolution, 36, 90-100.
47. Swofford DL (2002) PAUP*: Phylogenetic Analysis Using Parsimony (*and Other Methods), version 4. Sinauer Associates, Sunderland, Massachusetts.
48. Taylor EB, Pollard S, Louie D (1999) Mitochondrial DNA variation in bull trout (Salvelinus confluentus) from northwestern North America: implications for zoogeography and conservation. Molecular Ecology, 8, 1155-1170.
49. Templeton AR (2004) Statistical phylogeography: methods of evaluating and minimizing inference errors. Molecular Ecology, 4, 789-809.
50. Templeton AR, Sing CF (1993) A cladistic analysis of phenotypic associations with haplotypes inferred from restriction endonuclease mapping. IV. Nested analyses with cladogram uncertainty and recombination. Genetics, 134, 659-669.
51. Templeton AR, Boerwinkle E, Sing CF (1987) A cladistic analysis of phenotypic associations with haplotypes inferred from restriction endonuclease mapping. I. Basic theory and analysis of alcohol dehydrogenase activity in Drosophila. Genetics, 117, 343-351.
52. Templeton AR, Crandall KA, Sing CF (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.
53. Templeton AR, Routman E, Phillips CA (1995) Separating population structure from population history: a cladistic analysis of the geographical distribution of mitochondrial DNA haplotypes in the tiger salamander, Ambysoma tigrinum. Genetics, 140, 767-782.
54. Wagner RS, Miller MP, Crisafulli CM, Haig SM (2005) Geographic variation, genetic structure, and conservation unit designation in the Larch Mountain salamander (Plethodon larselli). Canadian Journal of Zoology, 83, 396-406.
55. Waitt RB Jr, Thorson RM (1983) The Cordilleran ice sheet in Washington, Idaho, and Montana. In: Late-Quaternary Environments of the United States, the Late Pleistocene (eds Wright HE Jr, Porter SC), pp. 53-70. University of Minnesota Press, Minneapolis, Minnesota.
56. Wake D (1997) Incipient species formation in salamanders of the Ensatina complex. Proceedings of the National Academy of Sciences, USA, 94, 7761-7767.
57. Watterson GA (1975) On the number of segregating sites in genetical models without recombination. Theoretical Population Biology, 7, 256-276.
58. Whittaker RH (1960) Vegetation of the Siskiyou Mountains, Oregon and California. Ecological Monographs, 30, 279-338.
59. Wilke T, Duncan N (2004) Phylogeographical patterns in the American Pacific Northwest: lessons from the arionid slug Prophysaon coeruleum. Molecular Ecology, 13, 2303-2315.