Phylogeographic incongruence of codistributed amphibian species based on small differences in geographic distribution

Molecular Phylogenetics and Evolution

Volumn 43, Issue 2, 2007, Pages 468-479

  Steele, Craig A ^a   Storfer, Andrew ^a  

^a WASHINGTON STATE UNIVERSITY   (United States)

Author keywords

AU test; Bayesian hypothesis testing; Biogeography; Columbia River; Comparative phylogeography; Dicamptodon; Pacific Northwest parametric bootstrap; Plethodon; SH test

Indexed keywords

MITOCHONDRIAL DNA;

AMPHIBIA; ANIMAL; ARTICLE; BAYES THEOREM; CANADA; CLASSIFICATION; ECOSYSTEM; GENETICS; PHYLOGENY; UNITED STATES;

ANIMALS; BAYES THEOREM; BRITISH COLUMBIA; DNA, MITOCHONDRIAL; ECOSYSTEM; PHYLOGENY; URODELA; WASHINGTON;

AMPHIBIA; CRYPTOBRANCHIDAE; DICAMPTODON; DICAMPTODON COPEI; PLETHODON; PLETHODON VANDYKEI; SALAMANDROIDEA;

EID: 34247631069     PISSN: 10557903     EISSN: 10959513     Source Type: Journal    
DOI: 10.1016/j.ympev.2006.10.010     Document Type: Article

References (78)

1. Argobast B.S., and Kenagy G.J. Comparative phylogeography as an integrative approach to historical biogeography. J. Biogeog. 28 (2001) 819-825
2. Avise J.C. Molecular population structure and the biogeographic history of a regional fauna: a case history with lessons for conservation biology. Oikos 63 (1992) 62-76
3. Avise J.C. Toward a regional conservation genetics perspective: phylogeography of faunas in the southeastern United States. In: Avise J.C., and Hamrick J.L. (Eds). Conservation Genetics: Case Histories from Nature (1996), Chapman and Hall, New York, NY 431-470
4. Avise J.C. Phylogeography: The History and Formation of Species (2000), Harvard University Press, Cambridge, MA
5. Baker R.G. Holocene vegetational history of the western United States. In: Wright Jr. H.E. (Ed). Late Quaternary environments of the United States vol. 2 (1983), University of Minnesota Press, Minneapolis, MN 109-127
6. Barnosky, C.W., 1981. A record of late Quaternary vegetation from Davis Lake, southern Puget Lowland, Washington: Quatern. Res. 16, 221-239.
7. Barnosky C.W., Anderson P.M., and Bartlein P.J. The northwestern U.S. during deglaciation; vegetational history and paleoclimatic implications. In: Ruddiman W.F., and Wright H.E. (Eds). North America and Adjacent Oceans during the last Deglaciation (1987), Geological Society of North America, Boulder, CO 289-321
8. Bermingham E., and Moritz C. Comparative phylogeography: concepts and applications. Mol. Ecol. 7 (1998) 367-369
9. Bickham J.W., Wood C.C., and Patton J.C. Biogeographic implications of cytochrome b sequences and allozymes in sockeye (Oncorhynchus nerka). J. Hered. 86 (1995) 140-144
10. Bowen B.W., and Avise J.C. The genetic structure of Atlantic and Gulf of Mexico populations of sea bass, menhaden, and sturgeon: the influence of zoogeographic factors and life history patterns. Mar. Biol. 107 (1990) 371-381
11. Brodie Jr. E.D. Western salamanders of the genus Plethodon: systematics and geographic variation. Herpetologica 26 (1970) 468-516
12. Brown J.R., Beckenbach A.T., and Smith M.J. Influence of Pleistocene glaciations and human interaction upon mitochondrial DNA diversity in white sturgeon (Acipenser transmontanus) populations. Can. J. Fish. Aquat. Sci. 49 (1992) 358-367
13. Brunsfeld S.J., Sullivan J., Soltis D.E., and Soltis P.S. Comparative phylogeography of northwestern North America: a synthesis. In: Silvertown J., and Antonovics J. (Eds). Integrating Ecology and Evolution in a Spatial Context (2001), Blackwell Publishing, Williston, VT 319-339
14. Buckley T.R. Model misspecification and probabilistic tests of topology: evidence from empirical data sets. Syst. Biol. 51 (2002) 509-523
15. Carstens B.C., Stevenson A.L., Degenhardt J.D., and Sullivan J. Testing nested phylogenetic and phylogeographic hypotheses in the Plethodon vandykei species group. Syst. Biol. 53 (2004) 781-792
16. Carstens B.C., Brunsfeld S.J., Demboski J.R., Good J.D., and Sullivan J. Investigating the evolutionary history of the Pacific Northwest mesic forest ecosystem: hypothesis testing within a comparative phylogeographic framework. Evolution 59 (2005) 1639-1652
17. Carstens B.C., Degenhardt J.D., Stevenson A.L., and Sullivan J. Accounting for coalescent stochasticity in testing phylogeographic hypotheses: modeling Pleistocene population structure in the Idaho giant salamander Dicamptodon aterrimus. Mol. Ecol. 14 (2005) 255-265
18. Clement M., Posada D., and Crandall K. TCS: a computer program to estimate gene genealogies. Mol. Ecol. 9 (2000) 1657-1660
19. Crandell D. The glacial history of western Washington and Oregon. In: Wright Jr. H.E., and Frey D.G. (Eds). The Quaternary of the United States (1965), Princeton University Press, Princeton, NJ 341-353
20. Crisci J.V., Katinas L., and Posadas P. Historical Biogeography: An Introduction (2003), Harvard University Press, Cambridge
21. Cunningham C.W., and Collins T. Developing model systems for molecular biogeography: Vicariance and interchange in marine invertebrates. In: DeSalle R., Schierwater B., and Wagner G. (Eds). Molecular Ecology and Evolution: Approaches and Applications (1994), Birkhauser Verlag, Basel, Switzerland 405-433
22. Donoghue M.J., and Moore B.R. Toward an integrative historical biogeography. Integr. Comp. Biol. 43 (2003) 261-270
23. Donovan M.F., Semlitsch R.D., and Routman E.J. Biogeography of the southeastern United States: a comparison of salamander phylogeographic studies. Evolution 54 (2000) 1449-1456
24. Easterbrook D.J. Quaternary geology of the Pacific Northwest. In: Mahaney W.C. (Ed). Quaternary Stratigraphy of North America (1976), Dowden, Hutchinson and Ross, Stroudsburg, PA 441-462
25. Goldman N.J. Statistical tests of models of DNA substitution. J. Mol. Evol. 36 (1993) 182-198
26. Goldman N., Anderson J.P., and Rodrigo A.G. Likelihood-based tests of topologies in phylogenetics. Syst. Biol. 49 (2000) 652-670
27. Good D.A., and Wake D.B. Geographic variation and speciation in the torrent salamanders of the genus Rhyacotriton (Caudata: Rhyacotritonidae). University of California Publications in Zoology 126 (1992) 1-91
28. Haas G.R., and McPhail J.D. The post-Wisconsinan glacial biogeography of bull trout (Salvelinus confluentus): a multivariate morphometric approach for conservation biology and management. Can. J. Fish. Aquat. Sci. 58 (2001) 2189-2203
29. Hewitt G.M. Post-glacial recolonisation of European biota. Biol. J. Linn. Soc. 58 (1999) 87-112
30. Howard J.H., Seeb L.W., and Wallace R. Genetic-variation and population divergence in the Plethodon vandykei species group (Caudata, Plethodontidae). Herpetologica 49 (1993) 238-247
31. Huelsenbeck J.P., and Bull J.J. A likelihood ratio test to detect conflicting phylogenetic signal. Syst. Biol. 45 (1996) 92-98
32. Huelsenbeck J.P., and Ronquist F. MRBAYES: Bayesian inference of phylogenetic trees. Bioinformatics 17 (2001) 754-755
33. Huelsenbeck J.P., Hillis D.M., and Jones R. Parametric bootstrapping in molecular phylogenetics: applications and performance. In: Ferraris J.D., and Palumbi S.R. (Eds). Molecular Zoology: Advances, Strategies, and Protocols (1996), Wiley-Liss, NEWyork 19-45
34. Huelsenbeck J.P., Lagret B., Miller R.E., and Ronquist F. Potential applications and pitfalls of Bayesian inference of phylogeny. Syst. Biol. 51 (2002) 673-688
35. Kishino H., and Hasegawa M. Evaluation of the maximum-likelihood estimate of the evolutionary tree topologies from DNA sequence data, and the branching order in Hominoidea. J. Mol. Evol. 29 (1989) 170-179
36. Knowles L.L., and Maddison W.P. Statistical phylogeography. Mol. Ecol. 11 (2002) 2623-2635
37. Lomolino M.V., Riddle B.R., and Brown J.H. Biogeography. Third ed. (2006), Sinauer Associates, Sunderland, MA
38. Mason-Gamer R.J., and Kellogg E.A. Testing for phylogenetic conflict among molecular data sets in the tribe Triticeae (Gramineae). Syst. Biol. 45 (1996) 524-545
39. McCusker M.R., Parkinson E., and Taylor E.B. Mitochondrial DNA variation in rainbow trout (Oncorhynchus mykiss) across its native range: testing biogeographical hypotheses and their relevance to conservation. Mol. Ecol. 9 (2000) 2089-2108
40. Michaux J.R., Libois R., and Filippucci M.G. So close and so different: comparative phylogeography of two small mammal species, the yellow-necked fieldmouse (Apodemus flavicollis) and the woodmouse (Apodemus sylvaticus) in the western Palearctic region. Heredity 94 (2005) 52-63
41. Miller M.P., Haig S.M., and Wagner R.S. 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. Conserv. Genet. 6 (2005) 275-287
42. Minin V., Abdo Z., Joyce P., and Sullivan J. Performance-based selection of likelihood models for phylogeny estimation. Syst. Biol. 52 (2003) 674-683
43. Nelson G. Historical biogeography: an alternative formalization. Syst. Zool. 23 (1974) 555-558
44. Nelson G., and Platnick N. Systematics and Biogeography: Cladistics and Vicariance (1981), Columbia University Press, New York, NY
45. Nielson M.K., Lohman K., and Sullivan J. Phylogeography of the tailed frog (Ascaphus truei): implications for biogeography of the Pacific Northwest. Evolution 55 (2001) 147-160
46. Nussbaum, R.A., 1976. Geographic variation and systematics of salamanders of the genus Dicamptodon Strauch (Ambystomatidae). Miscellaneous Publications No. 149, Museum of Zoology, University of Michigan, Ann Arbor, MI.
47. Nussbaum R.A., Brodie Jr. E.D., and Storm R.M. Amphibians and Reptiles of the Pacific Northwest (1983), University of Idaho Press, Moscow, ID
48. Petranka J.W. Salamanders of the United States and Canada (1998), Smithsonian Institution Press, Washington DC
49. Posada D., Crandall K.A., and Templeton A.R. GeoDis: a program for the nested cladistic analysis of the geographical distribution of genetic haplotypes. Mol. Ecol. 9 (2000) 487-488
50. Rambaut A.E., and Grassly N.C. SEQ-GEN: an application for the Monte Carlo simulation of DNA sequence evolution along phylogenetic trees. Comp. Appl. Biosci. 13 (1997) 235-238
51. Riddle B.R., Hafner D.J., Alexander L.F., and Jaeger J.R. Cryptic vicariance in the historical assembly of a Baja California peninsular desert biota. Proc. Natl. Acad. Sci. USA 97 (2000) 14438-14443
52. Rocha L.A., Robertson D.R., Roman J., and Bowen B.W. Ecological speciation in tropical reef fishes. Proc. R. Soc. Lond. B 272 (2005) 573-579
53. Ronquist F., and Huelsenbeck J.P. MrBayes 3: Bayesian phylogenetic inference under mixed models. Bioinformatics 19 (2003) 1572-1574
54. Rosen D.E. Vicariant patterns and historical explanations in biogeography. Syst. Zool. 27 (1978) 159-188
55. Sambrook J., Fritsch E.F., and Maniatis T. Molecular Cloning: A Laboratory Manual. Second Ed. (1989), Cold Spring Harbor Laboratory Press, NeWYork
56. Schneider C.J., Cunningham M., and Moritz C. Comparative phylogeography and the history of endemic vertebrates in the wet tropics rainforests of Australia. Mol. Ecol. 7 (1998) 487-498
57. Shaffer H.B., and McKnight M.L. The polytypic species revisited: genetic differentiation and molecular phylogenetics of the tiger salamander (Ambystoma tigrinum) (Amphibia: Caudata) complex. Evolution 50 (1996) 417-433
58. Shimodaira H. An approximately unbiased test of phylogenetic tree selection. Syst. Biol. 51 (2002) 492-508
59. Shimodaira H., and Hasegawa M. Multiple comparisons of log-likelihoods with applications to phylogenetic inference. Mol. Biol. Evol. 16 (1999) 1114-1116
60. Shimodaira H., and Hasegawa M. CONSEL: for assessing the confidence of phylogenetic tree selection. Bioinformatics 17 (2001) 1246-1247
61. Soltis D.E., Gitzendanner M.A., Strenge D.D., and Soltis P.E. Chloroplast DNA intraspecific phylogeography of plants from the Pacific Northwest of North America. Plant Syst. Evol. 206 (1997) 353-373
62. Steele C.A., and Storfer A. Coalescent-based hypothesis testing supports multiple Pleistocene refugia in the Pacific Northwest for the Pacific giant salamander (Dicamptodon tenebrosus). Mol. Ecol. 15 (2006) 2477-2487
63. Steele C.A., Carstens B.C., Storfer A., and Sullivan J. Testing hypotheses of speciation timing in Dicamptodon copei and Dicamptodon aterrimus (Caudata: Dicamptodontidae). Mol. Phylogenet. Evol. 36 (2005) 90-100
64. Sullivan J., Arellano E., and Rogers D.S. Comparative phylogeography of mesoamerican highland rodents: concerted versus independent responses to past climatic fluctuations. Am. Nat. 155 (2000) 755-768
65. Swofford, D.L., 2002. PAUP*. Phylogenetic Analysis Using Parsimony (*and other methods). Ver. 4. Sinauer Associates, Sunderland, MA.
66. Taberlet P., Fumagalli L., Wust-Saucy A.G., and Cosson J.F. Comparative phylogeography and postglacial colonization routes in Europe. Mol. Ecol. 7 (1998) 453-464
67. Taylor E.B., Pollard S., and Louie D. Mitochondrial DNA variation in bull trout (Salvelinus confluentus) from northwestern North America: implications for zoogeography and conservation. Mol. Ecol. 8 (1999) 1155-1170
68. Templeton A.R. Statistical phylogeography: methods of evaluating and minimizing inference errors. Mol. Ecol. 4 (2004) 789-809
69. Templeton A.R., and Sing C.F. A cladistic analysis of phenotypic associations with haplotypes inferred from restriction endonuclease mapping. IV. Nested analyses with cladogram uncertainty and recombination. Genetics 134 (1993) 659-669
70. Templeton A.R., Boerwinkle E., and Sing C.F. 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 (1987) 343-351
71. Templeton A.R., Crandall K.A., and Sing C.F. A cladistic analysis of phenotypic associations with haplotypes inferred from restriction endonuclease mapping and DNA sequence data. III. cladogram estimation. Genetics 132 (1992) 619-633
72. Templeton A.R., Routman E., and Phillips C.A. 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 (1995) 767-782
73. van Veller M.G., Zandee P.M., and Kornet D.J. Two requirements for obtaining valid common patterns under different assumptions in vicariance biogeography. Cladistics 15 (1999) 393-406
74. Wagner R.S., Miller M.P., Crisafulli C.M., and Haig S.M. Geographic variation, genetic structure, and conservation unit designation in the Larch Mountain salamander (Plethodon larselli). Can. J. Zool. 83 (2005) 396-406
75. Wilson A.G., and Larsen J.H. Morphometric analysis of salamanders of the Plethodon vandykei species group. Am. Midl. Nat. 141 (1999) 266-276
76. Wilson Jr. A.G., Larsen Jr. J.H., and McAllister K.R. Distribution of Van Dyke's salamander (Plethodon vandykei Van Denburgh). Am. Midl. Nat. 134 (1995) 288-393
77. Zink R.M. Comparative phylogeography in North American birds. Evolution 50 (1996) 308-317
78. Zink R.M. Methods in comparative phylogeography, and their application to studying evolution in the North American aridlands. Integr. Comp. Biol. 42 (2002) 953-959