An information-theoretical approach to phylogeography

Molecular Ecology

Volumn 18, Issue 20, 2009, Pages 4270-4282

  Carstens, Bryan C ^a   Stoute, Holly N ^a   Reid, Noah M ^a  

^a LOUISIANA STATE UNIVERSITY   (United States)

Author keywords

Coalescent; Hypothesis testing; Information theory; Phylogeography

Indexed keywords

AMPHIBIA; ANIMAL; ARTICLE; BIOLOGICAL MODEL; COMPUTER SIMULATION; GENE FLOW; GENETICS; GEOGRAPHY; MOLECULAR EVOLUTION; PHYLOGENY; POPULATION GENETICS;

ANIMALS; COMPUTER SIMULATION; EVOLUTION, MOLECULAR; GENE FLOW; GENETICS, POPULATION; GEOGRAPHY; MODELS, GENETIC; PHYLOGENY; URODELA;

PLETHODON IDAHOENSIS;

EID: 70349849562     PISSN: 09621083     EISSN: 1365294X     Source Type: Journal    
DOI: 10.1111/j.1365-294X.2009.04327.x     Document Type: Article

References (65)

1. Akaike H (1973) Information theory as an extension of the maximum likelihood principle. In : Second International Symposium on Information Theory (eds Petrov BN, Csaki F pp. 267 281. Akademiai Kiado, Budapest.
2. Anderson DR (2008) Model Based Inference in the Life Sciences. Springer, New York.
3. Arbogast BS, Edwards SV, Wakeley J, Beerli P, Slowinski J (2002) Estimating divergence times from molecular data on phylogenetic and population genetic timescales. Annual Review of Ecology and Systematics, 33, 707 740.
4. Avise JC, Arnold J, Ball RM et al. (1987) Intraspecific phylogeography: the mitochondrial DNA bridge between population genetics and systematics. Annual Reviews of Ecology, Evolution, and Systematics, 18, 489 522.
5. Brumfield RT, Liu L, Lum DE, Edwards SV (2008) Comparison of species tree methods for reconstructing the phylogeny of Bearded Manakins (Aves: Pipridae, Manacus) from multilocus sequences data. Systematic Biology, 57, 719 731.
6. Brunhoff C, Galbreath E, Federov VB, Cook JA, Jaarola M (2003) Holarctic phylogeography of the root vole (Microtus oeconomus): implications for late Quaternary biogeography of high latitudes. Molecular Ecology, 12, 957 968.
7. Burnham KP, Anderson DR (1998) Model Selection and Multimodel Inference: A Practical Information-Theoretic Approach. Springer, New York.
8. Burnham KP, Anderson DR (2002) Model Selection and Multimodel inference: A practical Information-Theoretic Approach. Springer, New York.
9. Carling MD, Brumfield RT (2007) Gene sampling strategies for multi-locus population estimates of genetic diversity. PLoS ONE, e160, 1 6.
10. Carling MD, Brumfield RT (2008) Integrating phylogenetic and population genetic analyses of multiple loci to test species divergence hypotheses in Passerina buntings. Genetics, 178, 363 377.
11. Carstens BC, Knowles LL (2007) Shifting distributions and speciation: species divergence during rapid climate change. Molecular Ecology, 16, 619 627.
12. Carstens BC, Richards CL (2007) Integrating coalescent and ecological niche modeling in comparative phylogeography. Evolution, 61, 1439 1454.
13. Carstens BC, Stevenson AL, Degenhardt JD, Sullivan J (2004a) Testing nested phylogenetic and phylogeographic hypotheses in the Plethodon vandykei species group. Systematic Biology, 53, 781 792.
14. Carstens BC, Degenhardt JD, Stevenson AL, Sullivan J (2005a) Accounting for coalescent stochasticity in testing phylogeographical hypotheses: modelling Pleistocene population structure in the Idaho giant salamander Dicamptodon aterrimus. Molecular Ecology, 14, 255 265.
15. Carstens BC, Brunsfeld SJ, Demboski JR, Good JM, Sullivan J (2005b) Investigating the evolutionary history of the Pacific Northwest mesic forest ecosystem: hypothesis testing within a comparative phylogeographic framework. Evolution, 59, 1639 1652.
16. Carstens BC, Bankhead A III., Joyce P, Sullivan J (2005c) Testing population genetic structure using parametric bootstrapping. Genetica, 124, 71 75.
17. Chamberlin TC (1890) The method of multiple working hypotheses. Journal of Geology, 5, 937.
18. Cleland CA (2001) Historical science, experimental science, and the scientific method. Geology, 29, 987 990.
19. Cognato AI, Harlin AD, Fisher ML (2003) Genetic structure among Pinyon Pine Beetle populations (Scolytinae: Ips confusus). Environmental Entomology, 32, 1262 1270.
20. Cruzan MB, Templeton AR (2000) Paleoecology and coalescence: phylogeographic analysis of hypotheses from the fossil record. Trends in Ecology and Evolution, 15, 491 496.
21. Darwin C (1859) On the Origin of Species. A Facsimile of the First Edition. Harvard University Press, Cambridge, MA.
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.
23. Edwards SV, Beerli P (2000) Perspective: gene divergence, population divergence, and the variance in coalescent time in phylogeographic studies. Evolution, 54, 1839 1854.
24. Fitzpatrick BM, Placyk JS Jr., Niemiller ML, Casper GS, Burghardt GM (2008) Distinctiveness in the face of gene flow: hybridization between specialist and generalist gartersnakes. Molecular Ecology, 17, 4107 4117.
25. Geraldes A, Carneiro M, Delibes-Mateos M et al. (2008) Reduced introgression of the Y chromosome between subspecies of the European rabbit (Oryctolagus cuniculus) in the Iberian peninsula. Molecular Ecology, 17, 4489 4499.
26. Good JM, Hird S, Reid N et al. (2008) Ancient hybridization and mitochondrial capture between two species of chipmunks. Molecular Ecology, 17, 1313 1327.
27. Hammer MF, Blackmer F, Garrigan D, Nachman MW, Wilder JA (2003) Human population structure and its effects on sampling Y chromosome sequence variation. Genetics, 164, 1495 1509.
28. Hey J, Machaho CA (2003) The study of structured populations - new hope for a difficult and divided science. Nature Reviews Genetics, 4, 535 543.
29. Hey J, Nielsen R (2007) Integration within the Felsenstein equation or improved Markov chain Monte Carlo methods in population genetics. Proceedings of the National Academy of Sciences, USA, 104, 2785 2790.
30. 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.
31. Hillis DM, Dixon MT (1991) Ribosomal DNA: molecular evolution and phylogenetic inference. Quarterly Review of Biology, 66, 411 453.
32. Hird S, Sullivan J (2009) Assessment of gene flow across a hybrid zone in red-tailed chipmunks (Tamias ruficaudis). Molecular Ecology, 18, 3097 3109
33. Hudson RR (2002) Generating samples under a Wright-Fisher neutral model of genetic variation. Bioinformatics, 18, 337 338.
34. Hudson RR, Turelli M (2003) Stochasticity overrules the "three-times rule": genetic drift, genetic draft, and coalescent times for nuclear loci versus mitochondrial DNA. Evolution, 57, 182 190.
35. Johnson JB, Omland KE (2004) Model selection in ecology and evolution. Trends in Ecology and Evolution, 19, 101 108.
36. Knowles LL (2001) Did the Pleistocene glaciations promote divergence? Tests of explicit refugial models in montane grasshoppers. Molecular Ecology, 10, 691 701.
37. Knowles LL (2004) The burgeoning field of statistical phylogeography. Journal of Evolutionary Biology, 17, 1 10.
38. Knowles LL, Maddison DR (2002) Statistical phylogeography. Molecular Ecology, 11, 2623 2635.
39. Kotlik P, Markova S, Choleva L et al. (2008) Divergence with gene flow between Ponto-Caspian refugia in an anadromous cyprinid Rutilus frissi revealed by multiple gene phylogeography. Molecular Ecology, 17, 1076 1088.
40. Kuhner MK (2006) lamarc 2.0: maximum likelihood and Bayesian estimation of population parameters. Bioinformatics, 22, 768 770.
41. Kuhner MK, Yamato J, Felsenstein J (1995) Estimating effective population size and mutation rate from sequence data using Metropolis-Hasting sampling. Genetics, 140, 1421 1430.
42. Kullback S (1959) Information Theory and Statistics. John Wiley, New York.
43. Kullback S, Leibler RA (1951) On information and sufficiency. Annals of Mathematical Statistics, 22, 79 86.
44. Lee JY, Edwards SV (2008) Divergence across Australia's Carpentarian Barrier: statistical phylogeography of the Red-backed Fairy Wren (Malurus melanocephalus). Evolution, 62, 3117 3134.
45. Mayr E (1942) Systematics and the Origin of the Species. Columbia University Press, New York, NY.
46. McCormack JE, Bowen BS, Smith TB (2008) Integrating paleoecology and genetics of bird populations in two sky island archipelagos. BMC Biology, 6, 1 12.
47. Nickerson RS (1998) Confirmation bias: a ubiquitous phenomenon in many guises. Review of General Psychology, 2, 175 220.
48. Nielsen R, Beaumont MA (2009) Statistical inferences in phylogeography. Molecular Ecology, 18, 1034 1047.
49. Nielsen R, Wakeley J (2001) Distinguishing migration from isolation: a Markov chain monte carlo approach. Genetics, 158, 885 896.
50. Niemiller ML, Fitzpatrick BM, Miller BT (2008) Recent divergence with gene flow in Tennessee cave salamanders (Plethodontidae: Gyrinophilus) inferred from gene genealogies. Molecular Ecology, 17, 2258 2275.
51. Nikula R, Stelkov P, Valnola R (2007) Diversity and trans-Arctic invasion history of mitochondrial lienages in the North Atlantic Macoma balthica complex (Bivalvia: Tellinidae). Evolution, 61, 928 941.
52. Pritchard JK, Stephens M, Donnelly P (2000) Inference of population structure using multilocus genotype data. Genetics, 155, 945 959.
53. Rambaut A, Grassly NC (1997) seq-gen: an application for the Monte Carlo simulation of DNA sequence evolution along phylogenetic trees. Computational Applications to Biosciences, 13, 235 238. (Pubitemid 27249927)
54. Richards CL, Carstens BC, Knowles LL (2007) Distribution modelling and statistical phylogeography: an integrative framework for generating and testing alternative biogeographic hypotheses. Journal of Biogeography, 34, 1833 1845.
55. Rozas J, Rozas R (1999) DnaSP version 3: an integrated program for molecular population genetics and molecular evolution analysis. Bioinformatics, 15, 174 175.
56. Smouse P (1998) To tree or not to tree. Molecular Ecology, 7, 399 412.
57. Sokal RR, Rohlf FJ (1994) Biometry: The Principles and Practices of Statistics in Biological Research, 3rd edn. W. H. Freeman, New York.
58. Stephens M, Smith NJ, Donnelly P (2001) A new statistical method for haplotype reconstruction from population data. Genetics, 68, 978 989.
59. Sullivan J, Joyce P (2005) Model selection in phylogenetics. Annual Reviews of Ecology, Evolution, and Systematics, 36, 445 466.
60. Sullivan J, Arellano E, Rogers DS (2000) Comparative phylogeography of Mesoamerican highland rodents: concerted versus independent response to past climatic fluctuations. The American Naturalist, 155, 755 768.
61. Szovenyi P, Terracciano S, Ricca M, Giordano S, Shaw AJ (2008) Recent divergence, intercontinental dispersal and shared polymorphism are shaping the genetic structure of amphi-Atlantic peatmoss populations. Molecular Ecology, 17, 5364 5377.
62. Tajima F (1989) The effect of change in population size on DNA polymorphism. Genetics, 105, 437 460.
63. Tribsch A, Schonswetter P (2003) Patterns of endemism and comparative phylogeography confirm palaeoenvironmental evidence for Pleistocene refugia in the Eastern Alps. Taxon, 52, 477 497.
64. Wallace AR (1858) On the tendency of varieties to depart indefinitely from the original type. Journal of the Proceedings of the Linnean Society: Zoology, 3, 53 62.
65. Wiens JJ, Engstrom TN, Chippindale 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.