Testing hypotheses of Pleistocene population history using coalescent simulations: Phylogeography of the pygmy nuthatch (Sitta pygmaea)

Proceedings of the Royal Society B: Biological Sciences

Volumn 273, Issue 1605, 2006, Pages 3057-3063

  Spellman, Garth M ^a,b   Klicka, John ^a  

^a UNIVERSITY OF NEVADA   (United States)

^b BLACK HILLS STATE UNIVERSITY   (United States)

Author keywords

Coalescent simulations; Ponderosa pine (Pinus ponderosa); Pygmy nuthatch (Sitta pygmaea); Site specific mutation rate ( ); Theta ( )

Indexed keywords

REDUCED NICOTINAMIDE ADENINE DINUCLEOTIDE;

COALESCENCE; CONIFEROUS TREE; HABITAT SELECTION; PALEOECOLOGY; PHYLOGEOGRAPHY; PLEISTOCENE; POPULATION SIZE; SONGBIRD;

ANIMAL TISSUE; ARTICLE; CONTROLLED STUDY; ENZYME SUBUNIT; MITOCHONDRION; NONHUMAN; NORTH AMERICA; PHYLOGENY; PHYLOGEOGRAPHY; PINE; PLEISTOCENE; PRIORITY JOURNAL; SIMULATION; SONGBIRD; ANIMAL; BIOLOGICAL MODEL; CLASSIFICATION; COMPUTER SIMULATION; ECOSYSTEM; GENETICS; GEOGRAPHY; MEXICO; PONDEROSA PINE; POPULATION DYNAMICS; UNITED STATES;

ARIZONA; CALIFORNIA; NEW MEXICO; NORTH AMERICA; SIERRA NEVADA [CALIFORNIA]; UNITED STATES;

PINUS PONDEROSA; SITTA PYGMAEA;

ANIMALS; COMPUTER SIMULATION; ECOSYSTEM; GEOGRAPHY; MEXICO; MODELS, BIOLOGICAL; PASSERIFORMES; PHYLOGENY; PINUS PONDEROSA; POPULATION DYNAMICS; UNITED STATES;

EID: 39049190992     PISSN: 09628452     EISSN: 14712970     Source Type: Journal    
DOI: 10.1098/rspb.2006.3682     Document Type: Article

References (40)

1. Arbogast, B. S., Drovetslei, S. V., Curry, R. L., Boag, P., Grant, P., Grant, R., Seutin, G. & Anderson, D. J. 2006 Origin and diversification of Galápagos mockingbirds. Evolution 60, 370-382.
2. Avise, J. C. 2000 Phylogeography: the history and formation of species. Cambridge, MA: Harvard University Press.
3. Bandelt, H. J., Forster, P. & Röhl, A. 1999 Median-joining networks for inferring intraspecific phylogenies. Mol. Biol. Evol. 16, 37-48.
4. Beerli, P. 2002 MIGRATE: documentation and program, Part of LAMARCK Version 1.5. http://evolution.genetics.washington.edi/lamarc.html.
5. Betancourt, J. L. & VanDevender, T. R. 1990 Martin packrat middens: the last 40,000 years of biotic change. Tucson, AZ: University of Arizona Press.
6. Carstens, B. C., Stevenson, A. L., Degenhardt, J. D. & Sullivan, J. 2004 Testing nested phylogenetic and phylogeographic hypotheses in the Plethodon vandykei species group. Syst. Biol. 53, 781-793. (doi:10.1080/10635150490522296)
7. Carstens, B. C., Degenhardt, J. D., Stevenson, A. L. & Sullivan, J. 2005a Accounting for coalescent stochasticity in testing phylogeographic hypotheses: modeling Pleistocene population structure in the Idaho giant salamander Dicamptodon aterrimus. Mol. Ecol. 14, 255-265. (doi:10.1111/j.1365-294X.2004.02404.x)
8. Carstens, B. C., Brunsfeld, S. J., Demboski, J. R., Good, J. M. & 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. (doi:10.1554/04-661.1)
9. Charlesworth, B., Charlesworth, D. & Barton, N. H. 2003 The effects of genetic and geographic structure on neutral variation. Ann. Rev. Ecol. Syst. 34, 99-125. (doi:10.1146/annurev.ecolsys.34.011802.132359)
10. Critchfield, W. B. & Elbert Jr, L. L. 1966 Geographic distribution of the pines of the world. U.S. Department of Agriculture, Miscellaneous Publication 991, Washington, DC.
11. Desjardins, P. & Morais, R. 1990 Sequence and gene organization of the chicken mitochondrial genome. J. Mol. Biol. 212, 599-634. (doi:10.1016/0022-2836(90)90225-B)
12. Drummond, A. J., Rambaut, A., Shapiro, B. & Pybus, O. G. 2005 Bayesian coalescent inference of past population dynamics from molecular sequences. Mol. Biol. Evol. 22, 1185-1192. (doi:10.1093/molbev/ msi103)
13. Edwards, S. V. & Beerli, P. 2000 Perspective: gene divergence, population divergence, and the variance in coalescence time in phylogeographic studies. Evolution 54, 1839-1854. (doi:10.1554/0014-3820(2000) 054[1839: PGDPDA]2.0.CO;2)
14. Emerson, B. C., Paradis, E. & Thebaud, C. 2001 Revealing the demographic histories of species using DNA sequences. Trends Ecol. Evol. 16, 707-716. (doi:10.1016/S0169-5347(01)02305-9)
15. Excoffier, L., Smouse, P. & Quattro, J. 1992 Analysis of molecular variance inferred from metric distances among DNA haplotypes: application to human mitochondrial restriction data. Genetics 131, 479-491.
16. Felsenstein, J. 1985 Confidence limits on phylogenies: an approach using the bootstrap. Evolution 39, 738-791. (doi:10.2307/2408678)
17. Fu, Y. X. 1997 Statistical test of neutrality of mutations against population growth, hitchhiking and background selection. Genetics 147, 915-925.
18. Graham, A. 1999 Cretaceous and Cenozoic history of North American vegetation. New York, NY: Oxford University Press.
19. Hackett, S. J. 1996 Molecular phylogenetics and biogeography of tanagers in the genus Ramphocelus (Aves). Mol. Phylogenet. Evol. 5, 368-382. (doi:10.1006/mpev.1996.0032)
20. Harding, R. M. 1996 New phylogenies: an introductory look at the coalescent. In New uses for new phylogenies (ed. P. H. Harvey, A. J. L. Brown, J. M. Smith & S. Nee), pp. 15-22. Oxford, UK: Oxford University Press.
21. Hewitt, G. M. 1996 Some genetic consequences of ice ages, and their role in divergence and speciation. Biol. J. Linn. Soc. 58, 247-276. (doi:10.1006/bijl.1996.0035)
22. Hewitt, G. M. 2000 The genetic legacy of the Quaternary ice ages. Nature 405, 907-913. (doi:10.1038/35016000)
23. Hudson, R. R. & Turrelli, M. 2003 Stochasticity overrules the 'three-times rule': genetic drift, genetic draft, and coalescent times for nuclear loci versus mitochondrial data. Evolution 57, 182-190. (doi:10.1554/0014-3820(2003)057[0182:SOTTTR]2.0.CO;2)
24. Jennings, W. B. & Edwards, S. V. 2005 Speciational history of Australian grass finches (Poephila) inferred from thirty gene trees. Evolution 59, 2033-2047. (doi:10.1554/05-280.1)
25. Johnson, K. P. & Sorenson, M. D. 1998 Comparing molecular evolution in two mitochondrial protein coding genes (cytochrome b and ND2) in the dabbling ducks (Tribe Anatini). Mol. Phylogenet. Evol. 10, 82-94. (doi:10.1006/mpev.1997.0481)
26. Kingery, H. E. & Ghalambor, C. K. 2001 Pygmy nuthatch (Sitta pygmaea). In The birds of North America, no. 567 (ed. A. Poole & F. Gill). Philadelphia, PA: The Birds of North America, Inc.
27. Knowles, L. L. 2001 Did the Pleistocene glaciations promote speciation? Test of explicit refugial models in montane grasshoppers. Mol. Ecol. 10, 691-701. (doi:10.1046/ j.1365-294x.2001.01206.x)
28. Knowles, L. L. & Maddison, W. P. 2002 Statistical phylogeography. Mol. Ecol. 11, 2623-2635. (doi:10.1046/j.1365-294X.2002.01637.x)
29. Lande, R., Engen, S. & Sæther, B. E. 2003 Stochastic population dynamics in ecology and conservation. Oxford, UK: Oxford University Press.
30. Latta, R. G. & Mitton, J. B. 1999 Historical separation and present gene flow through a zone of secondary contact in ponderosa pine. Evolution 53, 769-776. (doi:10.2307/2640717)
31. Maddison, W. P. & Maddison, D. R. 2005 MESQUITE: a modular system of evolutionary analysis, version 1.05. http://mesquiteproject.org/ mesquite1.05/mesquite/mesquite.html
32. Mila, B., Girman, D., Kimura, M. & Smith, T. B. 2000 Genetic evidence for the effect of a postglacial population expansion on the phylogeography of a North American songbird. Proc. R. Soc. B 267, 1-8. (doi:10.1098/rspb.2000.0958)
33. Norris, R. A. 1958 Comparative biosystematics and life history of the nuthatches Sitta pygmaea and Sitta pusilla. Berkely, CA: University of California Press.
34. Posada, D. & Crandall, K. A. 1998 Modeltest: testing the model of DNA substitution. Bioinformatics 14, 817-818. (doi:10.1093/ bioinformatics/14.9.817)
35. Rozas, J. & Rozas, R. 1999 DnaSP version 3: an integrated program for molecular population genetics and molecular evolution analysis. Bioinformatics 15, 174-175. (doi:10.1093/bioinformatics/15.2.174)
36. Schneider, S., Roessli D. & Excoffier L. 2000 Arlequin (vers. 2.000): a software for population genetic data analysis. Switzerland: Genetics and Biometry Laboratory, University of Geneva.
37. Slatkin, M. & Maddison, W. P. 1989 A cladistic measure of gene flow inferred from phylogenies of alleles. Genetics 123, 603-613.
38. Tajima, F. 1989a Statistical method for testing the neutral mutation hypothesis by DNA polymorphism. Genetics 123, 585-595.
39. Tajima, F. 19896 The effect of change in population size on DNA polymorphism. Genetics 123, 597-601.
40. Zink, R. M. 1997 Phylogeographic studies of North American birds. In Avian molecular evolution and systematics (ed. D. P. Mindell), pp. 301-324. San Diego, CA: Academic Press.