Investigating niche and lineage diversification in widely distributed taxa: Phylogeography and ecological niche modeling of the Peromyscus maniculatus species group

Ecography

Volumn 35, Issue 1, 2012, Pages 54-64

  Kalkvik, Håkon M ^a   Stout, I Jack ^a   Doonan, Terry J ^b   Parkinson, Christopher L ^a  

^a UNIVERSITY OF CENTRAL FLORIDA   (United States)

^b FISH AND WILDLIFE RESEARCH INSTITUTE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ALGORITHM; CLADISTICS; CONSERVATION MANAGEMENT; DIVERGENCE; ECOLOGICAL MODELING; ENTROPY; FUNCTIONAL MORPHOLOGY; GENETIC ANALYSIS; MULTIVARIATE ANALYSIS; NICHE; NUMERICAL MODEL; PHYLOGEOGRAPHY; POPULATION DISTRIBUTION; RODENT; TAXONOMY;

UNITED STATES;

PEROMYSCUS; PEROMYSCUS MANICULATUS; PEROMYSCUS POLIONOTUS;

EID: 84860395764     PISSN: 09067590     EISSN: 16000587     Source Type: Journal    
DOI: 10.1111/j.1600-0587.2011.06994.x     Document Type: Article

References (67)

1. Avise J. C. 2000. Phylogeography: the history and formation of species. - Harvard Univ. Press.
2. Avise J. C. et al. 1983. Mitochondrial DNA differentiation during the speciation process in Peromyscus. Mol. Biol. Evol. 1: 38-56.
3. Avise J. C. et al. 1987. Intraspecific phylogeography: the mitochondrial DNA bridge between population genetics and systematics. Annu. Rev. Ecol. Syst. 18: 489-522.
4. Blair W. F. 1950. Ecological factors in speciation of Peromyscus. Evolution 4: 253-275.
5. Bradley R. D. et al. 2000. Taxonomic status of Peromyscus boylii sacarensis: inference from DNA sequences of the mitochondrial cytochrome-B gene. J. Mammal. 81: 875-884.
6. Brandley M. C. et al. 2005. Partitioned Bayesian analyses, partition choice, and the phylogenetic relationships of scincid lizards. Syst. Biol. 54: 373-390.
7. Brito P. and Edwards S. 2009. Multilocus phylogeography and phylogenetics using sequence-based markers. Genetica 135: 439-455.
8. Carleton M. D. 1989. Systematics and evolution. - In: Kirkland G. L. and Layne J. N. (eds), Advances in the study of Peromyscus (Rodentia). Texas Tech Univ. Press, pp. 7-142.
9. Clement M. et al. 2000. TCS: a computer program to estimate gene genealogies. Mol. Ecol. 9: 1657-1659.
10. Degner J. et al. 2007. Population genetics and conservation of the threatened southeastern beach mouse (Peromyscus polionotus niveiventris): subspecies and evolutionary units. Conserv. Genet. 8: 1441-1452.
11. Dormann C. F. et al. 2010. Evolution of climate niches in European mammals? Biol. Lett. 6: 229-232.
12. Dragoo J. W. et al. 2006. Phylogeography of the deer mouse (Peromyscus maniculatus) provides a predictive framework for research on hantaviruses. J. Gen. Virol. 87: 1997-2003.
13. Elith J. 2002. Quantitative methods for modeling species habitat: comparative performance and an application to Australian plants. - In: Ferson S. and Burgman M. (eds), Quantitative methods for conservation biology. Springer, pp. 39-58.
14. Elith J. and Leathwick J. R. 2009. Species distribution models: ecological explanation and prediction across space and time. Annu. Rev. Ecol. Evol. Syst. 40: 677-697.
15. Elith J. et al. 2006. Novel methods improve prediction of species' distributions from occurrence data. Ecography 29: 129-151.
16. Elith J. et al. 2011. A statistical explanation of MaxEnt for ecologists. Divers. Distrib. 17: 43-57.
17. Evans M. E. K. et al. 2009. Climate, niche evolution, and diversification of the "bird-cage" evening primroses (Oenothera, sections Anogra and Kleinia). Am. Nat. 173: 225-240.
18. Fields Development Team 2006. fields: tools for spatial data.
19. Fontanella F. M. et al. 2008. Phylogeography of Diadophis punctatus: extensive lineage diversity and repeated patterns of historical demography in a trans-continental snake. Mol. Phylogenet. Evol. 46: 1049-1070.
20. Gering E. J. et al. 2009. Molecular evolution of cytochrome b in high- and low-altitude deer mice (genus Peromyscus). Heredity 102: 226-235.
21. Graham C. H. et al. 2004. Integrating phylogenetics and environmental niche models to explore speciation mechanisms in Dendrobatid frogs. Evolution 58: 1781-1793.
22. Guisan A. et al. 2007. Sensitivity of predictive species distribution models to change in grain size. Divers. Distrib. 13: 332-340.
23. Hall E. R. 1981. The mammals of North America. - Wiley.
24. Hernandez P. A. et al. 2006. The effect of sample size and species characteristics on performance of different species distribution modeling methods. Ecography 29: 773-785.
25. Herron M. D. et al. 2004. Sciurid phylogeny and the paraphyly of Holarctic ground squirrels (Spermophilus). Mol. Phylogenet. Evol. 31: 1015-1030.
26. Hickerson M. J. et al. 2010. Phylogeography's past, present, and future: 10 years after. Mol. Phylogenet. Evol. 54: 291-301.
27. Hijmans R. J. et al. 2005. Very high resolution interpolated climate surfaces for global land areas. Int. J. Climatol. 25: 1965-1978.
28. Hoffman E. A. and Blouin M. S. 2004. Evolutionary history of the northern leopard frog: reconstruction of phylogeny, phylogeography, and historical changes in population demography from mitochondrial DNA. Evolution 58: 145-159.
29. Hooper E. T. 1942. An effect on the Peromyscus maniculatus rassenkreis of land utilization in Michigan. J. Mammal. 23: 193-196.
30. Huelsenbeck J. P. and Ronquist F. 2001. MrBayes: Bayesian inference of phylogenetic trees. Bioinformatics 17: 754-755.
31. Hutchinson G. E. 1978. An introduction to population ecology. - Yale Univ. Press.
32. Jakob S. S. et al. 2009. Phylogeographic analyses and paleodistribution modeling indicate Pleistocene in situ survival of Hordeum species (Poaceae) in southern Patagonia without genetic or spatial restriction. Mol. Biol. Evol. 26: 907-923.
33. Kozak K. H. and Wiens J. J. 2006. Does niche conservatism promote speciation? A case study in North American salamanders. Evolution 60: 2604-2621.
34. Kozak K. H. et al. 2008. Integrating GIS-based environmental data into evolutionary biology. Trends Ecol. Evol. 23: 141-148.
35. Lansman R. A. et al. 1983. Extensive genetic variation in mitochondrial DNA's among geographic populations of the deer mouse, Peromyscus maniculatus. Evolution 37: 1-16.
36. Lord J. et al. 1995. Seed size and phylogeny in six temperate floras: constraints, niche conservatism, and adaptation. Am. Nat. 146: 349-364.
37. Losos J. B. 2008. Phylogenetic niche conservatism, phylogenetic signal and the relationship between phylogenetic relatedness and ecological similarity among species. Ecol. Lett. 11: 995-1003.
38. Losos J. B. et al. 2003. Niche lability in the evolution of a Caribbean lizard community. Nature 424: 542-545.
39. MacMillen R. E. and Garland Jr T. 1989. Adaptive physiology. - In: Kirkland G. L. and Layne J. N. (eds), Advances in the study of Peromyscus (Rodentia). Texas Tech Univ. Press, pp. 143-168.
40. Martins F. et al. 2009. Phylogeography of the common vampire bat (Desmodus rotundus): marked population structure, Neotropical Pleistocene vicariance and incongruence between nuclear and mtDNA markers. BMC Evol. Biol. 9: 294.
41. McNyset K. M. 2009. Ecological niche conservatism in North American freshwater fishes. Biol. J. Linn. Soc. 96: 282-295.
42. Nicholas K. B. et al. 1997. GeneDoc: analysis and visualization of genetic variation. EMBnet.news 4: 14.
43. Nylander J. A. A. 2004. MrModeltest v2.
44. Oksanen J. 2009. Vegan: R functions for vegetation ecologists.
45. Osgood W. H. 1909. Revision of the mice of the American genus Peromyscus. N. Am. Fauna 28: 1-285.
46. Peterson A. T. 2001. Predicting species' geographic distributions based on ecological niche modeling. Condor 103: 599-605.
47. Peterson A. T. et al. 1999. Conservatism of ecological niches in evolutionary time. Science 285: 1265-1267.
48. Phillips S. J. and Dudík M. 2008. Modeling of species distributions with Maxent: new extensions and a comprehensive evaluation. Ecography 31: 161-175.
49. Phillips S. J. et al. 2006. Maximum entropy modeling of species geographic distributions. Ecol. Model. 190: 231-259.
50. Pyron R. A. and Burbrink F. T. 2009. Lineage diversification in a widespread species: roles for niche divergence and conservatism in the common kingsnake, Lampropeltis getula. Mol. Ecol. 18: 3443-3457.
51. Rambaut A. and Drummond A. J. 2007. Tracer v1.4.
52. Rissler L. J. and Apodaca J. J. 2007. Adding more ecology into species delimitation: ecological niche models and phylogeography help define cryptic species in the black salamander (Aneides flavipunctatus). Syst. Biol. 56: 924-942.
53. Rowe K. C. et al. 2004. Surviving the ice: northern refugia and postglacial colonization. Proc. Natl Acad. Sci. USA 101: 10355-10359.
54. Schoener T. W. 1968. The anolis lizards of Bimini: resource partitioning in a complex fauna. Ecology 49: 704-726.
55. Stamatakis A. et al. 2008. A rapid bootstrap algorithm for the RAxML web servers. Syst. Biol. 57: 758-771.
56. Swets J. A. 1988. Measuring the accuracy of diagnostic systems. Science 240: 1285-1293.
57. Taberlet P. et al. 1998. Comparative phylogeography and postglacial colonization routes in Europe. Mol. Ecol. 7: 453-464.
58. Tamura K. et al. 2007. MEGA4: molecular evolutionary genetics analysis (MEGA) software version 4.0. Mol. Biol. Evol. 24: 1596-1599.
59. Tannenbaum M. and Pivorun E. 1984. Differences in daily torpor patterns among three southeastern species Peromyscus. J. Comp. Physiol. B 154: 233-236.
60. Van Zant J. L. and Wooten M. C. 2007. Old mice, young islands and competing biogeographical hypotheses. Mol. Ecol. 16: 5070-5083.
61. Warren D. L. et al. 2008. Environmental niche equivalency versus conservatism: quantitative approaches to niche evolution. Evolution 62: 2868-2883.
62. Webb C. O. et al. 2002. Phylogenies and community ecology. Annu. Rev. Ecol. Syst. 33: 475-505.
63. Wecker S. C. 1963. The role of early experience in habitat selection by the prairie deer mouse, Peromyscus maniculatus bairdi. Ecol. Monogr. 33: 307-325.
64. Wiens J. J. and Penkrot T. A. 2002. Delimiting species using DNA and morphological variation and discordant species limits in spiny lizards (Sceloporus). Syst. Biol. 51: 69-91.
65. Wiens J. J. and Graham C. H. 2005. Niche conservatism: integrating evolution, ecology, and conservation biology. Annu. Rev. Ecol. Evol. Syst. 36: 519-539.
66. Wisz M. S. et al. 2008. Effects of sample size on the performance of species distribution models. Divers. Distrib. 14: 763-773.
67. Zheng X. et al. 2003. Historical demography and genetic structure of sister species: deermice (Peromyscus) in the North American temperate rain forest. Mol. Ecol. 12: 711-724.