Integrating coalescent and ecological niche modeling in comparative phylogeography

Evolution

Volumn 61, Issue 6, 2007, Pages 1439-1454

  Carstens, Bryan C ^a   Richards, Corinne L ^a  

^a UNIVERSITY OF MICHIGAN   (United States)

Author keywords

Coalescent modeling; Comparative phylogeography; Ecological niche modeling; Pleistocene; Statistical phylogeography

Indexed keywords

MITOCHONDRIAL DNA;

BIODIVERSITY; COALESCENCE; COMPARATIVE STUDY; DIVERGENCE; ECOLOGICAL MODELING; FOSSIL RECORD; GENETIC STRUCTURE; LAST GLACIAL MAXIMUM; NICHE; PHYLOGEOGRAPHY; PLEISTOCENE; RECONSTRUCTION; SPATIAL ANALYSIS; STATISTICAL ANALYSIS; STOCHASTICITY; VARIANCE ANALYSIS;

AMPHIBIA; ANIMAL; ARTICLE; ARVICOLINAE; BIOLOGICAL MODEL; CHEMISTRY; CLASSIFICATION; CLIMATE; ECOSYSTEM; FROGS AND TOADS; GENETICS; GEOGRAPHY; NORTH AMERICA; PHYLOGENY; PHYSIOLOGY; POPULATION DYNAMICS; STATISTICAL MODEL; WILLOW;

ANIMALS; ANURA; ARVICOLINAE; CLIMATE; DNA, MITOCHONDRIAL; ECOSYSTEM; GEOGRAPHY; LIKELIHOOD FUNCTIONS; MODELS, BIOLOGICAL; NORTH AMERICA; PHYLOGENY; POPULATION DYNAMICS; SALIX; URODELA;

AMPHIBIA; MICROTUS RICHARDSONI; MURIDAE; SALIX; SALIX ARBUSCULOIDES;

EID: 34249820530     PISSN: 00143820     EISSN: 15585646     Source Type: Journal    
DOI: 10.1111/j.1558-5646.2007.00117.x     Document Type: Article

References (90)

1. Anderson, R. P., A. T. Peterson, and M. Gómez-Laverde. 2002. Using niche-based GIS modeling to test geographic predictions of competitive exclusion and competitive release in South American pocket mice. Oikos 98 : 3 16.
2. Anderson, R. P., D. Lew, and A. T. Peterson. 2003. Evaluating predictive models of species' distributions: criteria for selecting optimal models. Ecol. Model. 162 : 211 232.
3. Arbogast, B. S., S. V. Edwards, J. Wakeley, P. Beerli, and J. B. Slowinski. 2002. Estimating divergence times from molecular data on phylogenetic and population genetic timescales. Annu. Rev. Ecol. Syst. 33 : 707 740.
4. Arbogast, B. S. and G. J. Kenagy. 2001. Comparative phylogeography as an integrative approach to historical biogeography. J. Biogeogr. 28 : 819 825.
5. Araújo, M. B., and A. Guisan. 2006. Five (or so) challenges for species distribution modeling. J. Biogeogr. 33 : 1677 1688.
6. Austin, M. P. 1985. Continuum concept, ordination methods and niche theory. Annu. Rev. Ecol. Syst. 16 : 39 61.
7. Avise, J. 2000. Phylogeography: the history and formation of species. Harvard Univ. Press, Cambridge, MA.
8. Bermingham, E. and C. Moritz. 1998. Comparative phylogeography: concepts and applications. Mol. Ecol. 7 : 367 369.
9. Bond, J. E., D. A. Beamer, T. Lamb, and M. Hedin. 2006. Combining genetic and geospatial analyses to infer population extinction in mygalomorph spiders endemic to the Los Angeles region. Anim. Conser. 9 : 145 157.
10. Booth, D. B., K. G. Troost, J. J. Clague, and R. B. Waitt. 2004. The Cordilleran Ice Sheet. Pp. 17 43 in : A. R. Gillespie, S. C. Porter, and B. F. Atwater, eds. The Quaternary period in the United States. Elsevier Press, New York.
11. Brunsfeld, S. J., J. Sullivan, D. E. Soltis, and P. S. Soltis. 2001. Comparative phylogeography of northwestern North America: a synthesis. Pp. 319 339 in J. Silvertown and J. Antonovics, eds. Integrating ecology and evolution in a spatial context. Blackwell Publishing, Williston, VT.
12. Brunsfeld, S. J. and J. Sullivan. 2005. A multi-compartmented glacial refugium in the northern Rocky Mountains: evidence from the phylogeography of Cardamine constancei (Brassicaceae). Conser. Genet. 6 : 895 904.
13. Brunsfeld, S. J., T. R. Miller, and B. C. Carstens. 2006. Insights into the biogeography of the Pacific Northwest of North America: evidence from the phylogeography of Salix melanopsis (Salicaceae). Syst. Bot. 32 : 129 139.
14. Carstens, B. C., and L. L. Knowles. 2007. Shifting distributions and speciation: genomic resolution of species divergence during rapid climate change. Mol. Ecol. 16 : 619 627.
15. Carstens, B. C., A. L. Stevenson, J. D. Degenhardt, and J. Sullivan. 2004. Testing nested phylogenetic and phylogeographic hypotheses in the Plethodon vandykei species group. Syst. Biol. 53 : 781 792.
16. Carstens, B. C., J. D. Degenhardt, A. L. Stevenson, and J. Sullivan. 2005a. Accounting for coalescent stochasticity in testing phylogeographic hypotheses: modelling Pleistocene population structure in the Idaho Giant Salamander Dicamptodon aterrimus. Mol. Ecol. 14 : 255 265.
17. Carstens, B. C., S. J. Brunsfeld, J. R. Demboski, J. D. Good, and J. Sullivan. 2005b. Investigating the evolutionary history of the Pacific Northwest mesic forest ecosystem: hypothesis testing within a comparative phylogeographic framework. Evolution 59 : 1639 1652.
18. Collins, W. D., et al. 2006. The community climate system model version 3 (CCSM3). J. Clim. 19 : 2122 2143.
19. Daugherty, C. H. 1979. Population ecology and genetics of Ascaphus truei: an examination of gene flow and natural selection. Ph. D. diss., University of Montana, Missoula, MT.
20. Daubenmire, R. 1952. Plant geography of Idaho. Pp. 1 17 in : R. J. Davis, ed. Flora of Idaho. Brigham Young University Press, Provo, UT.
21. Daubenmire, R. and J. B. Daubenmire. 1968. Forest vegetation of Eastern Washington and Northern Idaho. Tech. Bull. 60, Washington Agricultural Experiment Station, Washington State University, Pullman, WA.
22. Daubenmire, R. 1975. Floristic plant geography of eastern Washington and northern Idaho. Brigham Young University Press, Provo, UT.
23. Davis, M. B. and R. G. Shaw. 2001. Range shifts and adaptive responses to quaternary climate change. Science 292 : 673 679.
24. DeChaine, E. G., and A. P. Martin. 2005. Historical biogeography of two alpine butterflies in the Rocky Mountains: broad-scale concordance and local-scale discordance. J. Biogeogr. 32 : 1943 1956.
25. Delcourt, P. A. and H. R. Delcourt. 1993. Paleoclimates, paleovegetation, and paleofloras during the late Quaternary. Pp. 71 94 in Editorial Committee. Flora of North America, Vol. 1, 1st edn. Oxford Univ. Press, New York.
26. Detling, L. E. 1968. Historical background of the flora of the Pacific Northwest. Bull. No. 13, Mus. Nat. Hist., Univ. Oregon, Eugene, OR.
27. Dolman, G., and C. Moritz. 2006. A multilocus perspective on refugial isolation and divergence in rainforest skinks (Carlia). Evolution 60 : 573 582.
28. Edwards, S. V., and P. Beerli. 2000. Gene divergence, population divergence, and the variance in coalescence time in phylogeographic studies. Evolution 54 : 1839 1854.
29. English, J. M., and S. T. Johnston. 2004. The Laramide Orogeny: what were the driving forces? Int. Geol. Rev. 46 : 833 883.
30. Gaston, K. J. 1996. Species-range-size distributions: patterns, mechanisms, and implications. Trends Ecol. Evol. 11 : 197 201.
31. Gates, D. M. 1993. Climate change and its biological consequences. Sinauer and Associates Press, Sunderland, MA.
32. Gibbard, P. and T. Van Kolfschoten. 2004. The Pleistocene and Holocene epochs. Pp. 441 452 in F. M. Gradstein, J. G. Ogg, and A. G. Smith, eds. A geologic time scale. Cambridge Univ. Press, London.
33. Graham, A. 1993. History of the vegetation: cretaceous-tertiary. Pp. 57 70 in Flora of North America, Vol. I. Oxford Univ. Press, New York.
34. Graham, A. 1999. Late Cretaceous and Cenozoic History of North American Vegetation. Oxford Univ. Press, New York.
35. Graham, C. H., S. Ron, J. C. Santos, C. J. Schneider, and C. Moritz. 2004a. Integrating phylogenetics and environmental niche models to explore speciation mechanisms in Dendrobatic frogs. Evolution 58 : 1781 1793.
36. Graham, C. H., S. Ferrier, F. Huettman, C. Moritz, and A. T. Peterson. 2004b. New developments in museum-based informatics and applications in biodiversity analysis. Trends Ecol. Evol. 19 : 497 503
37. Hadly, E. A., M. H. Kohn, J. A. Leonard, and R. K. Wayne. 1998. A genetic record of population isolation in pocket gophers during Holocene climatic change. Proc. Natl. Acad. Sci. USA 95 : 6893 6896.
38. Hewitt, G. M. 1996. Some genetic consequences of the ice ages, and their role in divergence and speciation. Biol. J. Linn. Soc. 58 : 247 276.
39. Hijmans, R. J., S. E. Cameron, J. L. Parra, P. G. Jones, and A. Jarvis. 2005. Very high resolution interpolated climate surfaces for global land areas. Int. J. Climatol. 25 : 1965 1978.
40. Hudson, R. R. 1992. Gene trees, species trees and the segregation of ancestral alleles. Genetics 131 : 509 512.
41. Hudson, R. R., and J. A. Coyne. 2002. Mathematical consequences of the genealogical species concept. Evolution 56 : 1557 1565.
42. Hudson, R. R., and M. Turelli. 2003. Stochasticity overrules the three-times rule: genetic drift, genetic draft, and coalescence times for nuclear loci versus mitochondrial DNA. Evolution 57 : 182 190.
43. Hugall, A., C. Moritz, A. Moussalli, and J. Stanisic. 2002. Reconciling paleodistribution models and comparative phylogeography in the Wet Tropics rainforest land snail Arosophia bellendenkerensis (Brazier 1875). Proc. Natl. Acad. Sci. USA 99 : 6112 6117.
44. Kidd, D. M., and M. G. Ritchie. 2006. Phylogeographic information systems: putting the geography into phylogeography. J. Biogeogr. 33 : 1851 1865.
45. Kingman, J. F. C. 1982. The Coalescent. Stochastic process. Appl. 13 : 235 248.
46. Knowles, L. L. 2001. Did the Pleistocene glaciations promote divergence? Tests of explicit refugial models in montane grasshoppers. Mol. Ecol. 10 : 691 701.
47. Knowles, L. L., and W. P. Maddison. 2002. Statistical phylogeography. Mol. Ecol. 11 : 2623 2635.
48. Knowles, L. L. 2004. The burgeoning field of statistical phylogeography. J. Evol. Biol. 17 : 1 10.
49. Knowles, L. L., and B. C. Carstens. 2007. Inferring a population-divergence model for statistical phylogeographic tests in montane grasshoppers. Evolution, 61 : 477 493.
50. Kuhner, M. K., J. Yamato, P. Beerli, L. P. Smith, E. Rynes, E. Walkup, C. Li, J. Sloan, P. Colacurcio, and J. Felsenstein. 2005. LAMARC v. 2.0. at http://evolution.gs.washington.edu/lamarc.html
51. Lawton, J. H. 1993. Range, population abundance and conservation. Trends Ecol. Evol. 8 : 409 413.
52. Lessa, E. P., J. A. Cook, and J. L. Patton. 2003. Genetic footprints of demographic expansion in North America, but not Amazonia, during the Late Quaternary. Proc. Natl. Acad. Sci. USA 100 : 10331 10334.
53. Liu, C., P. M. Berry, P. D. Dawson, and R. G. Pearson. 2005. Selecting thresholds of occurrence in the prediction of species distributions. Ecography 28 : 385 393.
54. Losos, J. B., and R. E. Glor. 2003. Phylogenetic comparative methods and the geography of speciation. Trends Ecol. Evol. 18 : 220 227.
55. Lyons, S. K. 2003. A quantitative assessment of the range shifts of Pleistocene mammals. J. Mammal. 84 : 385 402.
56. Maddison, W. P., and D. R. Maddison. 2004. Mesquite: a modular system for evolutionary analysis. Version 1.01. Available at http://mesquiteproject.org
57. Martinez-Meyer, E., A. T. Peterson, and W. W. Hargrove. 2004. Ecological niches as stable distributional constraints on mammal species, with implications for Pleistocene extinctions and climate change projections for biodiversity. Glob. Ecol. Biogeogr. 13 : 305 314.
58. Mehringer, Jr., P. E. 1985. Late-Quaternary pollen record from the interior Pacific Northwest and northern Great Basin of the United States. Pp. 167 189 in V. M. Bryant and R. G. Holloway Jr., eds. Pollen records of Late-Quaternary North America Sediments. Amer. Assoc. Strat. Palyn. Found., Dallas, TX.
59. Minin, V., Z. Abdo, P. Joyce, and J. Sullivan. 2003. Performance-based selection of likelihood models for phylogeny estimation. Syst. Biol. 52 : 674 683.
60. Myers, P., B. L. Lundrigan, and R. Van de Kopple. 2005. Climate change and the distribution of Peromyscus in Michigan: is global warming already having an impact? Pp. 101 125 in E. A. Lacey and P. Myers, eds. Mammalian diversification: from chromosomes to phylogeography (A celebration of the career of James L. Patton). University of California Press, Berkeley, CA.
61. Nielsen, R., and J. Wakeley. 2001. Distinguishing migration from isolation: a Markov-chain Monte Carlo approach. Genetics 158 : 885 896.
62. Nielson, M. K., K. Lohman, and J. Sullivan J. 2001. Phylogeography of the tailed frog (Ascaphus truei): implications for the biogeography of the Pacific Northwest. Evolution 55 : 147 160.
63. Pauken, R. J., and D. E. Metter. 1971. Geographic representation of morphological variation among populations of Ascaphus truei Stejneger. Syst. Zool. 20 : 431 441.
64. Pamilo, P., and M. Nei. 1988. Relationships between gene trees and species trees. Mol. Biol. Evol. 5 : 568 583.
65. Peterson, A. T. 2001. Predicting species geographic distributions based on ecological niche modeling. Condor 103 : 599 605.
66. Peterson, A. T., and D. A. Vieglais. 2001. Predicting species invasions using ecological niche modeling: new approaches from bioinformatics attach a pressing problem. BioScience 51 : 363 371.
67. Peterson, A. T., E. Martinez-Meyer, and C. Gonzalez-Salazar. 2004. Reconstructing the Pleistocene geography of the Aphelocoma jays (Corvidae). Divers. Distr. 10 : 237 246.
68. Pielou, E. C. 1991. After the ice age: the return of life to glaciated North America. Univ. of Chicago Press, Chicago.
69. Phillips, S. J., R. P. Anderson, and R. E. Schapire. 2006. Maximum entropy modeling of species geographic distributions. Ecol. Model. 190 : 231 259.
70. Ree, R. H., B. R. Moore, C. O. Webb, and M. J. Donoghue. 2005. A likelihood framework for inferring the evolution of geographic range on phylogenetic trees. Evolution 59 : 2299 2311.
71. Remington, C. L. 1968. Suture-zones of hybrid interactions between recently-joined biotas. Pp. 321 428 in T. Dobzhansky, M. K. Hecht, and W. C. Steere, eds. Evolutionary biology. Appleton-Crofts, New York.
72. Richardson, B. A., S. J. Brunsfeld, and N. B. Klopfenstein. 2002. DNA from bird-dispersed seed and wind-disseminated pollen provides insights into postglacial colonization and population genetic structure of whitebark pine (Pinus albicaulis). Mol. Ecol. 11 : 215 227.
73. Rissler, L. J., R. J. Hijmans, C. H. Graham, C. Moritz, and D. B. Wake. 2006. Phylogeographic lineages and species comparisons in conservation analyses: a case study of the California herpetofauna. Am. Nat. 167 : 655 666.
74. Rosenberg, N. A. 2003. The shapes of neutral gene genealogies in two species: probabilities of monophyly, paraphyly, and polyphyly in a coalescent model. Evolution 57 : 1465 1477.
75. Ruegg, K. C., R. J. Hijmans, and C. Moritz. 2006. Climate change and the origin of migratory pathways in the Swainson's thrush, Catharus ustulatus. J. Biogeogr. 33 : 1172 1182.
76. Russell, A. L., R. A. Medellin, and G. F. McCracken. 2005. Genetic variation in the Mexican free-tail bat (Tadarida brasilliensis mexicana). Mol. Ecol. 14 : 2207 2222.
77. Schneider, C. J., M. Cunningham, and C. Moritz. 1998. Comparative phylogeography and the history of endemic vertebrates in the Wet Tropics rainforests of Australia. Mol. Ecol. 7 : 487 498.
78. Steele, C. A., B. C. Carstens, A. Storfer, and J. Sullivan. 2005. Testing hypotheses of speciation timing in Dicamptodon copei and Dicamptodon aterrimus (Caudata: Dicamptodontidae). Mol. Phylog. Evol. 36 : 90 100.
79. Steele, C. A., and A. Storfer. 2006. Coalescent-based hypothesis testing supports multiple Pleistocene refugia in the Pacific Northwest for the Pacific giant salamander (Dicamptodon tenebrosus). Mol. Ecol. 15 : 2477 2487.
80. Stigall, A. L., and B. S. Lieberman. 2006. Quantitative paleobiogeography: GIS, phylogenetic biogeographical analysis, and conservation insights. J. Biogeogr. In press.
81. Stockwell, D. R. B. and A. T. Peterson. 2002. Effects of sample size on accuracy of species distribution models. Ecol. Model. 148 : 1 13.
82. Sullivan, J., E. Arellano, and D. S. Rogers. 2000. Comparative phylogeography of Mesoamerican highland rodents: concerted versus independent response to past climatic fluctuations. Am. Nat. 155 : 755 768.
83. Swofford, D. L. 2002. Paup*. Phylogenetic Analysis Using Parsimony (and other methods). Version 4. Sinauer Assoc., Sunderland, MA.
84. Swenson, N. G. 2006. GIS-based niche models reveal unifying climatic mechanisms that maintain the location of avian hybrid zones in a North American suture zone. J. Evol. Biol. 19 : 717 725.
85. Swenson, N. G., and D. J. Howard. 2005. Clustering of contact zone, hybrid zones, and phylogeographic breaks in North America. Am. Nat. 166 : 581 591.
86. Takahata, N. 1989. Gene genealogy in three related populations: consistency probability between gene and population trees. Genetics 122 : 957 966.
87. Wakeley, J. 2003. Inferences about the structure and history of populations: coalescents and intraspecific phylogeography. Pp. 193 213 in R. Singh and M. Uyenoyama, eds. The Evolution of Population Biology. Cambridge Univ. Press, Cambridge, UK.
88. Weins, J. J. 2004. What is speciation and how should we study it? Am. Nat. 163 : 914 923.
89. Yesson, C., and A. Culham. 2006. Phyloclimatic modeling: combining phylogenetics and bioclimatic modeling. Syst. Biol. 55 : 785 802.
90. Zhang, D.-X. and G. M. Hewitt. 2003. Nuclear DNA analyses in genetic studies of populations: practice, problems and prospects. Mol. Ecol. 12 : 563 584.