Phylogeographic and demographic effects of Pleistocene climatic fluctuations in a montane salamander, Plethodon fourchensis

Molecular Ecology

Volumn 18, Issue 10, 2009, Pages 2243-2262

  Shepard, Donald B ^a,b   Burbrink, Frank T ^b  

^a UNIVERSITY OF OKLAHOMA   (United States)

^b CITY UNIVERSITY OF NEW YORK   (United States)

Author keywords

Biogeography; Climate change; Niche modelling; Ouachita Mountains; Sky islands; Statistical phylogeography

Indexed keywords

AMPHIBIA; ANIMAL; ARTICLE; BIOLOGICAL MODEL; CLIMATE; COMPUTER SIMULATION; DNA SEQUENCE; ECOSYSTEM; GENE FLOW; GENETICS; GEOGRAPHY; MOLECULAR EVOLUTION; PHYLOGENY; POPULATION DYNAMICS; POPULATION GENETICS;

ANIMALS; CLIMATE; COMPUTER SIMULATION; ECOSYSTEM; EVOLUTION, MOLECULAR; GENE FLOW; GENETICS, POPULATION; GEOGRAPHY; MODELS, GENETIC; PHYLOGENY; POPULATION DYNAMICS; SEQUENCE ANALYSIS, DNA; URODELA;

PLETHODON FOURCHENSIS; SALAMANDROIDEA;

EID: 65549134678     PISSN: 09621083     EISSN: 1365294X     Source Type: Journal    
DOI: 10.1111/j.1365-294X.2009.04164.x     Document Type: Article

References (107)

1. Anthony CB (2005) Plethodon fourchensis Duncan and Highton, 1979. Fourche mountain salamander. In : Amphibian Declines: The Conservation Status of United States Species (ed. Lannoo M). University of California Press, Berkeley, California.
2. Anthony CD, Wicknick JA, Jaeger RG (1997) Social interactions in two sympatric salamanders: effectiveness of a highly aggressive strategy. Behaviour, 134, 71 88. (Pubitemid 127029988)
3. Arbogast BS, Kenagy BS (2001) Comparative phylogeography as an integrative approach to historical biogeography. Journal of Biogeography, 28, 819 825. (Pubitemid 33072918)
4. Avise JC (2000) Phylogeography: The History and Formation of Species. Harvard University Press, Cambridge, Massachusetts.
5. Beerli P (2008) Migrate-N, Version 2.4. http://popgen.scs.fsu.edu/ Migrate-n.html.
6. Bennett KD (1990) Milankovitch cycles and their effects on species and ecological and evolutionary time. Paleobiology, 16, 11 21. (Pubitemid 20416617)
7. Bertorelle G, Slatkin M (1995) The number of segregating sites in expanding human populations, with implications for estimates of demographic parameters. Molecular Biology and Evolution, 12, 887 892.
8. Blair AP, Lindsay HL Jr. (1965) Color pattern variation and distribution of two large Plethodon salamanders endemic to the Ouachita Mountains of Oklahoma and Arkansas. Copeia, 1965, 331 335.
9. Carstens BC, Knowles LL (2007) Shifting distributions and speciation: Species divergence during rapid climate change. Molecular Ecology, 16, 619 627. (Pubitemid 46161083)
10. Carstens BC, Richards CL (2007) Integrating coalescent and ecological niche modelling in comparative phylogeography. Evolution, 61, 1439 1454. (Pubitemid 46848830)
11. Carstens BC, Stevenson AL, Degenhardt JD, Sullivan J (2004b) Testing nested phylogenetic and phylogeographic hypotheses in the Plethodon vandykei species group. Systematic Biology, 53, 781 792. (Pubitemid 39568278)
12. Carstens BC, Sullivan J, Davalos LM, Larsen PA, Pedersen SC (2004a) Exploring population genetic structure in three species of Lesser Antillean bats. Molecular Ecology, 13, 2557 2566. (Pubitemid 39151615)
13. Carstens BC, Brunsfeld SJ, Demboski JR, Good JM, 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. (Pubitemid 41266770)
14. Carstens BC, Degenhardt JD, Stevenson AL, Sullivan J (2005b) Accounting for coalescent stochasticity in testing phylogeographical hypotheses: modelling Pleistocene population structure in the Idaho giant salamander Dicamptodon aterrimus. Molecular Ecology, 14, 255 265. (Pubitemid 40141492)
15. Clark JM (1985) Fossil plethodontid salamanders from the latest Miocene of California. Journal of Herpetology, 19, 41 47. (Pubitemid 18286405)
16. Clark PU, Alley RB, Pollard D (1999) Northern Hemisphere ice-sheet influences on global climate change. Science, 286, 1104 1111. (Pubitemid 129515797)
17. 2. Quaternary Science Reviews, 25, 3150 3184. (Pubitemid 46209385)
18. Costa GC, Wolfe CA, Shepard DB, Caldwell JP, Vitt LJ (2008) Detecting the influence of climatic variables on species' distributions: a test using GIS niche-based models along a steep longitudinal environmental gradient. Journal of Biogeography, 35, 637 646.
19. Crespi EJ, Rissler LJ, Browne RA (2003) Testing Pleistocene refugia theory: phylogeographical analysis of Desmognathus wrighti, a high-elevation salamander in the southern Appalachians. Molecular Ecology, 12, 969 984. (Pubitemid 36524290)
20. Davis MB (1983) Quaternary history of deciduous forests of eastern North America and Europe. Annals of the Missouri Botanical Garden, 70, 550 563.
21. DeChaine EG, Martin AP (2004) Historic cycles of fragmentation and expansion in Parnassius smintheus (Papilionidae) inferred using mitochondrial DNA. Evolution, 58, 113 127. (Pubitemid 38355642)
22. DeChaine EG, Martin AP (2005) Historical biogeography of two alpine butterflies in the Rocky Mountains: broad-scale concordance and local-scale discordance. Journal of Biogeography, 32, 1943 1956. (Pubitemid 43934549)
23. DeChaine EG, Martin AP (2006) Using coalescent simulations to test the impact of Quaternary climate cycles on divergence in an alpine plant-insect association. Evolution, 60, 1004 1013.
24. Denniston RF, Gonzalez LA, Semken HA et al 1999) Integrating stalagmite, vertebrate, and pollen sequences to investigate Holocene vegetation and climate change in the southern Midwestern United States. Quaternary Research, 52, 381 387. (Pubitemid 30061755)
25. Drummond AJ, Rambaut A (2007) beast: Bayesian evolutionary analysis by sampling trees. BMC Evolutionary Biology, 7, 214.
26. Drummond AJ, Rambaut A, Shapiro B, Pybus OG (2005) Bayesian coalescent inference of past population dynamics from molecular sequences. Molecular Biology and Evolution, 22, 1185 1192. (Pubitemid 40577756)
27. Drummond AJ, Ho SYW, Phillips MJ, Rambaut A (2006) Relaxed phylogenetics and dating with confidence. Public Library of Science, Biology, 4, e88.
28. Duncan R, Highton R (1979) Genetic relationships of the eastern large Plethodon of the Ouachita Mountains. Copeia, 1979, 95 110.
29. Edwards SV, Beerli P (2000) Gene divergence, population divergence, and the variance in coalescence time in phylogeographic studies. Evolution, 54, 1839 1854. (Pubitemid 32113816)
30. Excoffier L, Schneider S (1999) Why hunter-gatherer populations do not show signs of Pleistocene demographic expansions. Proceedings of the National Academy of Sciences, USA, 96, 10597 10602. (Pubitemid 29442189)
31. Excoffier L, Smouse PE, Quattro JM (1992) Analysis of molecular variance inferred from metric distances among DNA restriction data. Genetics, 131, 479 491.
32. Feldman CR, Spicer GS (2006) Comparative phylogeography of woodland reptiles in California: repeated patterns of cladogenesis and population expansion. Molecular Ecology, 15, 2201 2222. (Pubitemid 43876461)
33. Felsenstein J (1985) Confidence limits on phylogenies: an approach using the bootstrap. Evolution, 39, 783 791.
34. Felsenstein J (1992) Estimating effective population size from samples of sequences: inefficiency of pairwise and segregating sites as compared to phylogenetic estimates. Genetical Research, 59, 139 147.
35. Felsenstein J (2004) Inferring Phylogenies. Sinauer Associates, Sunderland, Massachusetts.
36. Foti TL, Bukenhofer GA (1998) A description of the sections and subsections of the Interior Highlands of Arkansas and Oklahoma. Journal of the Arkansas Academy of Science, 52, 53 62.
37. Foti TL, Glenn SM (1991) The Ouachita Mountain landscape at the time of settlement. In : Proceedings of the Conference on Restoration of Old Growth Forests in the Interior Highlands of Arkansas and Oklahoma, September 19-20, 1990, Morrilton, AR (ed. Henderson D, Hedrick LD). USDA Forest Service, Ouachita National Forest and Winrock International Institute for Agricultural Development, Hot Springs, Arkansas.
38. Fu XY (1997) Statistical tests of neutrality of mutations against population growth, hitchhiking, and background selection. Genetics, 147, 915 925. (Pubitemid 27418596)
39. Gelman A, Carlin JB, Stern HS, Rubin DB (1995) Bayesian Data Analysis. Chapman & Hall, London.
40. Genecodes (2000) Sequencher 4.1. GeneCodes Corporation, Ann Arbor, Michigan.
41. Greller AM (1988) Deciduous forest. In : North American Terrestrial Vegetation (ed. Barbour MG, Billings WD). Cambridge University Press, Cambridge.
42. Hairston NG (1951) Interspecies competition and its probable influence upon the vertical distribution of Appalachian salamanders of the genus Plethodon. Ecology, 32, 266 274.
43. 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. (Pubitemid 26389802)
44. Hewitt GM (2000) The genetic legacy of the Quaternary ice ages. Nature, 405, 907 913. (Pubitemid 30435039)
45. Hewitt GM (2004) Genetic consequences of climatic oscillations in the Quaternary. Philosophical Transactions of the Royal Society B: Biological Sciences, 359, 183 195. (Pubitemid 38231471)
46. Hickerson MJ, Cunningham CW (2005) Contrasting Quaternary histories in an ecologically divergent sister pair of low-dispersing intertidal fish (Xiphister) revealed by multilocus DNA analysis. Evolution, 59, 344 360. (Pubitemid 40356048)
47. Highton R (1995) Speciation in eastern North American salamanders of the genus Plethodon. Annual Review of Ecology and Systematics, 26, 579 600. (Pubitemid 3019639)
48. Hijmans RJ, Cameron SE, Parra JL, Jones PG, Jarvis A (2005) Very high resolution interpolated climate surfaces for global land areas. International Journal of Climatology, 25, 1965 1978. (Pubitemid 43013915)
49. Hillis DM, Bull JJ (1993) An empirical test of bootstrapping as a method of assessing confidence in phylogenetic analysis. Systematic Biology, 42, 182 192. (Pubitemid 23958220)
50. Huelsenbeck JP, Ronquist F (2001) MrBayes: Bayesian inference of phylogenetic trees. Bioinformatics, 17, 754 755. (Pubitemid 32851390)
51. Jackson ST, Webb RS, Anderson KH et al 2000) Vegetation and environment in eastern North America during the last glacial maximum. Quaternary Science Reviews, 19, 489 508. (Pubitemid 30170287)
52. Jaeger RG (1971) Moisture as a factor influencing the distribution of two species of terrestrial salamanders. Oecologia, 6, 191 207.
53. Jansson R, Dynesius M (2002) The fate of clades in a world of recurrent climatic change: Milankovitch oscillations and evolution. Annual Review of Ecology and Systematics, 33, 741 777. (Pubitemid 36035156)
54. Jesus FF, Wilkins JF, Solferini VN, Wakeley J (2006) Expected coalescent times and segregating sites in a model of glacial cycles. Genetics and Molecular Research, 5, 466 474. (Pubitemid 44379903)
55. Jockusch EL, Wake DB (2002) Falling apart and merging: diversification of slender salamanders (Plethodontidae: Batrachoseps) in the American West. Biological Journal of the Linnean Society, 76, 361 391.
56. Kass RE, Raftery AE (1995) Bayes factors and model uncertainty. Journal of the American Statistical Association, 90, 773 795.
57. Keogh JS, Webb JK, Shine R (2007) Spatial genetic analysis and long-term mark-recapture data demonstrate male-biased dispersal in a snake. Biology Letters, 3, 33 35.
58. King JE (1973) Late Pleistocene palynology and biogeography of the western Missouri Ozarks. Ecological Monographs, 43, 539 565.
59. Knowles LL (2000) Tests of Pleistocene speciation in montane grasshoppers (genus Melanoplus) from the sky islands of western North America. Evolution, 54, 1337 1348.
60. Knowles LL (2001) Did the Pleistocene glaciations promote divergence? Tests of explicit refugial models in montane grasshoppers. Molecular Ecology, 10, 691 701. (Pubitemid 32406354)
61. Knowles LL, Maddison WP (2002) Statistical phylogeography. Molecular Ecology, 11, 2623 2635. (Pubitemid 35436682)
62. Kozak KH, Wiens JJ (2006) Does niche conservatism promote speciation? A case study in North American salamanders. Evolution, 60, 2604 2621. (Pubitemid 46220868)
63. Kozak KH, Weisrock DW, Larson A (2006a) Rapid lineage accumulation in a non-adaptive radiation: phylogenetic analysis of diversification rates in eastern North American woodland salamanders (Plethodontidae: Plethodon). Proceedings of the Royal Society B: Biological Sciences, 273, 539 546. (Pubitemid 46768057)
64. Kozak KH, Blaine RA, Larson A (2006b) Gene lineages and eastern North American paleodrainage basins: phylogeography and speciation in salamanders of the Eurycea bislineata species complex. Molecular Ecology, 15, 191 207.
65. Kozak KH, Graham CH, Wiens JJ (2008) Integrating GIS-based environmental data into evolutionary biology. Trends in Ecology & Evolution, 23, 141 148.
66. Lapointe FJ, Rissler LJ (2005) Congruence, consensus, and the comparative phylogeography of codistributed species in California. American Naturalist, 166, 290 299. (Pubitemid 41076651)
67. Lisiecki LE, Raymo M (2007) Plio-Pleistocene climate evolution: trends and transitions in glacial cycle dynamics. Quaternary Science Reviews, 26, 56 69. (Pubitemid 46037944)
68. Maddison WP (1997) Gene trees in species trees. Systematic Biology, 46, 523 536. (Pubitemid 127138566)
69. Maddison WP, Maddison DR (2008) Mesquite: A Modular System for Evolutionary Analysis. Version 2.5. http://mesquiteproject.org.
70. Maddison WP, McMahon M (2000) Divergence and reticulation among montane populations of a jumping spider (Habronattus pugillis Griswold). Systematic Biology, 49, 400 421.
71. Mahoney MJ (2004) Molecular systematics and phylogeography of the Plethodon elongatus species group: combining phylogenetic and population genetic methods to investigate species history. Molecular Ecology, 13, 149 166. (Pubitemid 38106481)
72. Marjoram P, Donnelly P (1994) Pairwise comparisons of mitochondrial DNA sequences in subdivided populations and implications for early human evolution. Genetics, 136, 673 683. (Pubitemid 24045485)
73. Martínez-Solano I, Jockusch EL, Wake DB (2007) Extreme population subdivision throughout a continuous range: phylogeography of Batrachoseps attenuatus (Caudata: Plethodontidae) in western North America. Molecular Ecology, 16, 4335 4355. (Pubitemid 47511226)
74. Masta SE (2000) Phylogeography of the jumping spider Habronattus pugillis (Araneae: Salticidae): recent vicariance of sky island populations? Evolution, 54, 1699 1711.
75. Newton MA, Raftery AE (1994) Approximate Bayesian inference with the weighted likelihood bootstrap. Journal of the Royal Statistical Society B, 56, 3 48.
76. Petranka JW (1998) Salamanders of the United States and Canada. Smithsonian Institution Press, Washington, D.C.
77. Phillips SJ, Anderson RP, Schapire RE (2006) Maximum entropy modelling of species geographic distributions. Ecological Modelling, 190, 231 259. (Pubitemid 41680650)
78. Pope CH, Pope SH (1951) A study of the salamander Plethodon ouachitae and the description of an allied form. Bulletin of the Chicago Academy of Sciences, 9, 129 151.
79. Pybus OG, Rambaut A, Harvey PH (2000) An integrated framework for the inference of viral population history from reconstructed genelogies. Genetics, 155, 1429 1437. (Pubitemid 30463449)
80. Rambaut A, Drummond AJ (2007) Tracer version 1.4. http://beast.bio.edsac. uk/Tracer.
81. Ramos-Osins SE, Rozas J (2002) Statistical properties of new neutrality tests against population growth. Molecular Biology and Evolution, 19, 2092 2100. (Pubitemid 35440445)
82. Ray N, Currat M, Excoffier L (2003) Intra-deme molecular diversity in spatially expanding populations. Molecular Biology and Evolution, 20, 76 86. (Pubitemid 36077902)
83. Raymo M (1997) The timing of major climate terminations. Paleoceanography, 12, 577 585. (Pubitemid 127618036)
84. Richards CL, Carstens BC, Knowles LL (2007) Distribution modelling and statistical phylogeography: an integrative framework for generating and testing alternative biogeographical hypotheses. Journal of Biogeography, 34, 1833 1845. (Pubitemid 47610616)
85. Rogers AR, Harpending H (1992) Population growth makes waves in the distribution of pairwise genetic differences. Molecular Biology and Evolution, 9, 552 569.
86. Rogers AR, Fraley AE, Bamshad MJ, Watkins WS, Jorde LB (1996) Mitochondrial mismatch analysis is insensitive to the mutational process. Molecular Biology and Evolution, 13, 895 902. (Pubitemid 26284905)
87. Ronquist F, Huelsenbeck JP (2003) MrBayes 3: Bayesian phylogenetic inference under mixed models. Bioinformatics, 19, 1572 1574. (Pubitemid 37038874)
88. Rozas J, Sánchez-De I, Barrio JC, Messeguer X, Rozas R (2003) DnaSP, DNA polymorphism analyses by the coalescent and other methods. Bioinformatics, 19, 2496 2497. (Pubitemid 38016658)
89. Shepard DB, Burbrink FT (2008) Lineage diversification and historical demography of a sky island salamander, Plethodon ouachitae, from the Interior Highlands. Molecular Ecology, 17, 5315 5335.
90. Smith CI, Farrell BD (2005) Phylogeography of the longhorn cactus beetle Moneilema appressum LeConte (Coleoptera: Cerambycidae): was the differentiation of the Madrean sky islands driven by Pleistocene climate changes? Molecular Ecology, 14, 3049 3065. (Pubitemid 43919347)
91. Soltis DE, Morris AB, McLachlan JS, Manos PS, Soltis PS (2006) Comparative phylogeography of unglaciated eastern North America. Molecular Ecology, 15, 4261 4293.
92. Spotila JR (1972) Temperature and water in the ecology of lungless salamanders. Ecological Monographs, 42, 95 125.
93. Stamatakis A (2006) RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models. Bioinformatics, 22, 2688 2690. (Pubitemid 44642609)
94. Stamatakis A, Ludwig T, Meier H (2005) RAxML-III: a fast program for maximum likelihood-based inference of large phylogenetic trees. Bioinformatics, 21, 456 463. (Pubitemid 40310232)
95. Stamatakis A, Hoover P, Rougemont J (2008) A rapid bootstrap algorithm for the RAxML web servers. Systematic Biology, 57, 758 771.
96. Sullivan J, Arellano E, Rogers DS (2000) Comparative phylogeography of Mesoamerican highland rodents: concerted versus independent responses to past climatic fluctuations. American Naturalist, 155, 755 768. (Pubitemid 30390832)
97. Tajima F (1989) Statistical method for testing the neutral mutation hypothesis by DNA polymorphism. Genetics, 123, 585 595. (Pubitemid 19274682)
98. Tihen JA, Wake DB (1981) Vertebrae of plethodontid salamanders from the Lower Miocene of Montana. Journal of Herpetology, 15, 35 40.
99. Trauth SE, Wilhide JD (1999) Status of three plethodontid salamanders (genus Plethodon) from the Ouachita National Forest of southwestern Arkansas. Journal of the Arkansas Academy of Science, 53, 125 137.
100. Wakeley J (2000) The effects of subdivision on the genetic divergence of populations and species. Evolution, 54, 1092 1101.
101. Webb T, Bartlein PJ (1992) Global changes during the last 3 million years: climatic controls and biotic responses. Annual Review of Ecology and Systematics, 23, 141 173. (Pubitemid 24412256)
102. Weisrock DW, Larson A (2006) Testing hypotheses of speciation in the Plethodon jordani species complex with allozymes and mitochondrial DNA sequences. Biological Journal of the Linnean Society, 89, 25 51. (Pubitemid 44243749)
103. Weisrock DW, Kozak KH, Larson A (2005) Phylogeographic analysis of mitochondrial gene flow and introgression in the salamander, Plethodon shermani. Molecular Ecology, 14, 1457 1472. (Pubitemid 40554801)
104. Wiens JJ (2004) Speciation and ecology revisited: phylogenetic niche conservatism and the origin of species. Evolution, 58, 193 197. (Pubitemid 38355649)
105. Wiens JJ, Graham CH (2005) Niche conservatism: integrating evolution, ecology, and conservation biology. Annual Review of Ecology, Evolution, and Systematics, 36, 519 539. (Pubitemid 43068869)
106. Wiens JJ, Engstrom TN, Chippendale PT (2006) Rapid diversification, incomplete isolation, and the 'speciation clock' in North American salamanders (Genus: Plethodon): testing the hybrid swarm hypothesis of rapid radiation. Evolution, 60, 2585 2603. (Pubitemid 46220867)
107. Zink RM (1996) Comparative phylogeography in North American birds. Evolution, 50, 308 317. (Pubitemid 3035470)