Phylogeography of the mountain chickadee (Poecile gambeli): Diversification, introgression, and expansion in response to Quaternary climate change

Molecular Ecology

Volumn 16, Issue 5, 2007, Pages 1055-1068

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

^a UNIVERSITY OF NEVADA   (United States)

^b BLACK HILLS STATE UNIVERSITY   (United States)

Author keywords

Divergence times; Gene flow; Incomplete lineage sorting; Phylogeography; Poecile; Quaternary

Indexed keywords

MITOCHONDRIAL DNA;

ANIMAL; ANIMAL BEHAVIOR; ARTICLE; CANADA; CHEMISTRY; CLASSIFICATION; CLIMATE; DNA SEQUENCE; GENE FLOW; GENETIC VARIABILITY; GENETICS; GEOGRAPHY; PHYLOGENY; PHYSIOLOGY; SONGBIRD; UNITED STATES;

ANIMALS; CANADA; CLIMATE; DNA, MITOCHONDRIAL; GENE FLOW; GEOGRAPHY; HOMING BEHAVIOR; PASSERIFORMES; PHYLOGENY; SEQUENCE ANALYSIS, DNA; UNITED STATES; VARIATION (GENETICS);

AVES; PARUS GAMBELI; POECILE; POECILE GAMBELI;

EID: 33847018735     PISSN: 09621083     EISSN: 1365294X     Source Type: Journal    
DOI: 10.1111/j.1365-294X.2007.03199.x     Document Type: Article

References (86)

1. Anderson E (1948) Hybridization of the habitat. Evolution, 2, 1-9.
2. Anderson E (1949) Introgressive Hybridization. John Wiley and Sons, New York.
3. Anderson E (1953) Introgressive hybridization. Biological Review, 28, 280-307.
4. Arbogast BS (1999) Mitochondrial DNA phylogeography of the New World flying squirrels (Glaucomys): implications for Pleistocene biogeography. Journal of Mammalogy, 82, 142-155.
5. Arbogast BS, Kenagy GJ (2001) Comparative phylogeography as an integrative approach to historical biogeography. Journal of Biogeography, 28, 819-825.
6. Arbogast BS, Edwards SV, Wakeley J, Beerli P, Slowinski JB (2002) Estimating divergence times from molecular data on phylogenetic or population genetic timescales. Annual Review of Ecology and Systematics, 33, 707-740.
7. Avise JC (2000) Phylogeography: the History and Formation of Species. Harvard, Cambridge.
8. Avise JC (2004) Molecular Markers, Natural History, and Evolution, 2nd edn. Sinauer, Sunderland, Massachusetts.
9. Axelrod DI (1958) Evolution of the Madro-Tertiary geoflora. Botanical Review, 24, 433-509.
10. Axelrod DI (1979) Age and origin of Sonoran Desert vegetation. Occasional Papers of the California Academy of Science, 132, 1-74.
11. Bandel HJ, Forster P, Röhl A (1999) Median-joining networks for inferring intraspecific phylogenies. Molecular Biology and Evolution, 16, 37-48.
12. Barrowclough GF, Groth JG, Mertz LA, Gutierrez RJ (2004) Phylogeographic structure, gene flow and species status in blue grouse (Dendragapus obscurus). Molecular Ecology, 13, 1911-1922.
13. Beerli P (2002) MIGRATE: Documentation and Program, Part of LAMARCK, Version 1.5. http://evolution.genetics.washington.edi/ lamarc.html.
14. Beerli P, Felsenstein J (2001) Maximum likelihood estimation of a migration matrix and effective population sizes in n subpopulations by using a coalescent approach. Proceedings of the National Academy of Science, 98, 4563-4568.
15. Behle WH (1956) A systematic review of the mountain chickadee. Condor, 58, 51-70.
16. Bennett KJ (1998) Evolution and Ecology: the Pace of Life. Cambridge University Press.
17. Betancourt JL, VanDevender TR (1990) Martin Packrat Middens: the Last 40 000 Years of Biotic Change. University of Arizona Press, Tucson.
18. Brown JH (1978) The theroy of insular biogeography and the distribution of boreal birds and mammals. Great Basin Naturalist Memoirs, 2, 209-227.
19. Brunsfeld SJ, Sullivan J, Soltis DE, Soltis PS (2002) Comparative phylogeography of north-western North America: a synthesis. Integrating ecology and evolution in a spatial context. The 14th Special Symposium of the British Ecological Society. pp. 319-339. Royal Halloway College, University of London.
20. Burns KJ, Barhoum DN (2006) Population-level history of the wrentit (Chamaea fasciata): Implications for comparative phylogeography in the California Floristic Province. Molecular Phylogenetics and Evolution, 38, 117-129.
21. Calsbeek R, Thompson JN, Richardson JE (2003) Pattersn of molecular evolution and diversification in a biodiversity hotspot: the Californian Floristic Province. Molecular Ecology, 12, 1021-1029.
22. Carstens BC, Brunsfeld SJ, Demboski JR, Good JM, Sullivan J (2005) Investigating the evolutionary history of the Pacific northwest mesic forest ecosystem: hypothesis testing within a comparative phylogeographic framework. Evolution, 59, 1639-1652.
23. Cicero C (1996) Sibling Species of Titmice in the Parus Inornatus Complex (Aves: Paridae). University of California Press, Berkeley.
24. DeChaine EJ, 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.
25. Desjardins P, Morais R (1990) Sequence and gene organization of the chicken mitochondrial genome. Journal of Molecular Biology, 212, 599-634.
26. Drovetski SV, Zink RM, Rohwer S et al. (2004) Complex biogeographic history of a Holarctic passerine. Proceedings of the Royal Society of London, Series B, 21, 545-551.
27. Edwards SV, Beerli P (2000) Perspective: Gene divergence, population divergence, and the variance in coalescence time in phylogeographic studies. Evolution, 54, 1839-1854.
28. Ekman J (1989) Ecology of non-breeding social systems in Parus. Wilson Bulletin, 101, 263-288.
29. Emerson BC, Paradis E, Thebaud C (2001) Revealing the demographic histories of species using DNA sequences. Trends in Ecology and Evolution, 16, 707-716.
30. 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.
31. Felsenstein J (1985) Confidence limits on phylogenies: an approach using the bootstrap. Evolution, 39, 738-791.
32. Fu YX (1997) Statistical test of neutrality of mutations against population growth, hitchhiking and background selection. Genetics, 147, 915-925.
33. Gill FB, Mostrom A, Mack AL (1993) Speciation in North American chickadees: I. Patterns of mtDNA genetic divergence. Evolution, 47, 193-212.
34. Gill FB, Slikas B, Sheldon FH (2005) Phylogeny of titmice (Paridae): II. Species relationships based on sequences of the mitochondrial cytochrome-b gene. Auk, 122, 121-143.
35. Graham A (1999) Late Cretaceous and Cenozoic History of North American Vegetation. Oxford University Press, New York.
36. Hackett SJ (1996) Molecular phylogenetics and biogeography of tanagers in the genus Ramphocelus (Aves). Molecular Phylogenetics and Evolution, 5, 368-382.
37. Harding RM (1996) New Phylogenies: an introductory look at the coalescent. In: New Uses for New Phylogenies (eds Harvey PH, Brown AJL, Smith JM, Nee S), pp. 15-22. Oxford University Press, Oxford, UK.
38. 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.
39. Hewitt GM (1999) Post-glacial re-colonization of European biota. Biological Journal of the Linnaean Society, 68, 87-112.
40. Hewitt GM (2000) The genetic legacy of the Quaternary ice ages. Nature, 405, 907-913.
41. Hewitt GM (2004) Genetic consequences of climatic oscillations of the Quaternary. Philosophical Transactions of the Royal Society, London, 359, 183-195.
42. Hey J, Nielsen R (2004) Multilocus methods for estimating population sizes, migration rates, and divergence time, with applications to the divergence of Drosophila pseudoobscura and D. persimilis. Genetics, 167, 747-760.
43. Hillis DM, Bull JJ (1993) An empirical test of bootstrapping as a method for assessing confidence in phylogenetic analysis. Systematic Biology, 42, 182-192.
44. Hubbard JP (1973) Avian evolution in the aridlands of North America. Living Bird, 12, 155-196.
45. Hudson RR, 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.
46. Jobb G, von Haeseler A, Strimmer K (2004) TREEFINDER: a powerful graphical analysis environment for molecular phylogenetics. BMC Evolutionary Biology, 4, 18.
47. Johnson NK (1975) Controls of the number of birds species on the mountain islands of the Great Basin. Evolution, 29, 545-567.
48. Johnson NK (1978) Patterns of avian geography and speciation in the intermountain region. Great Basin Naturalist Memoirs, 2, 137-159.
49. Johnson KP, Sorenson MD (1998) Comparing molecular evolution in two mitochondrial protein coding genes (cytochrome b and ND2) in the dabbling ducks (tribe Anatini). Molecular Phylogenetics and Evolution, 10, 82-94.
50. Kimura M, Weiss GH (1964) The stepping stone model of population structure and the decrease of genetic correlation with distance. Genetics, 49, 561-576.
51. Kingery HE, Ghalambor CK (2001) Pygmy Nuthatch (Sitta pygmaea). In: The Birds of North America, No. 567 (eds Poole A, Gill F). The Birds of North America., Inc., Philadelphia, Pennsylvania.
52. Klicka J, Zink RM (1997) The importance of recent ice ages in speciation: a failed paradigm. Science, 277, 1666-1669.
53. Knowles LL, Maddison WP (2002) Statistical phylogeography. Molecular Ecology, 11, 2623-2635.
54. Lascoux M, Palme AE, Cheddadi R, Latta RG (2004) Impact of the Ice Ages on the genetic structure of trees and shrubs. Philosophical Transactions of the Royal Society, 359, 197-207.
55. Latta RG, Mitton JB (1999) Historical separation and present gene flow through a zone of secondary contact in ponderosa pine. Evolution, 53, 769-776.
56. Lessa EP, Cook JA, Patton JL (2003) Genetic footprints of demographic expansion in North America, but not Amazonia, during the late Quaternary. Proceedings of the National Academy of Sciences, USA, 100, 10331-10334.
57. Lovette IJ (2004) Mitochondrial dating and mixed support for the '2% rule' in birds. Auk, 121, 1-6.
58. MacArthur RH, Wilson EO (1963) An equilibrium theory of insular biogeography. Evolution, 17, 373-387.
59. Mantel N (1967) The detection of disease clustering and generalized regression approach. Cancer Research, 27, 209-220.
60. Matthysen E (1990) Nonbreeding social organization in Parus. Current Ornithology, 7, 209-244.
61. McCallum DA (1990) Variable cone crops, migration, and dynamics of a population of mountain chickadees (Parus gambeli). In: Population Biology of Passerine Birds: an Integrated Approach (eds Blondel J, Gosler A, Lebreton JD, McCleery R), pp. 103-116. Springer-Verlag, Berlin.
62. McCallum DA, Grundel R, Dahlsten DL (1999) Mountain chickadee (Poecile gambeli). In: The Birds of North America, No. 453 (eds Poole A, Gill F). The Birds of North America, Inc., Philadelphia, Pennsylvania.
63. Mengel R (1964) The probable history of species formation in some northern and wood warblers (Parulidae). Living Bird, 3, 9-43.
64. Mila B, Girman D, Kimura M, Smith TB (2000) Genetic evidence for the effect of a postglacial population expansion on the phylogeography of a North American songbird. Proceedings of the Royal Society, Series B, 267, 1-8.
65. Miller AH (1951) A comparison of the avifaunas of Santa Cruz and Santa Rosa islands, California. Condor, 53, 117-123.
66. Nei M (1987) Molecular Evolutionary Genetics. Columbia University Press, New York.
67. Nielsen R, Wakeley J (2001) Distinguishing migration from isolation: a Markov Chain Monte Carlo approach. Genetics, 158, 885-896.
68. Peters JL, Gretes W, Omland KE (2005) Late Pleistocene divergence between eastern and western populations of wood ducks (Aix sponsa) inferred by the 'isolation with migration' coalescent method. Molecular Ecology, 14, 3407-3418.
69. Posada D, Crandall KA (1998) MODELTEST: testing the model of DNA substitution. Bioinformatics, 14, 817-818.
70. Remington CL (1968) Suture zones of hybrid interaction between recently joined biotas. In: Evolutionary Biology (eds Dobzhansky T, Hecht MK, Steere WC), pp. 321-428. Plenum Press, New York.
71. Rozas J, Rozas R (1999) dnasp version 3: an integrated program for molecular population genetics and molecular evolution analysis. Bioinformatics, 15, 174-175.
72. Schneider S, Roessli D, Excoffier L (2000) ARLEQUIN (vers. 2.000): a software for population genetic data analysis. Genetics and Biometry Laboratory, University of Geneva, Switzerland.
73. Sgariglia EA, Burns KJ (2003) Phylogeography of the California Thrasher (Toxostoma redivivum) based on nested-clade analysis of mitochondrial-DNA variation. Auk, 120, 346-361.
74. Shapiro B, Rambaut A, Drummond AJ (2006) Choosing appropriate substitution models for the phylogenetic analysis of protein-coding sequences. Molecular Biology and Evolution, 23, 7-9.
75. Slatkin M, Hudson RR (1991) Pairwise comparisons in mitochondrial DNA sequences in stable and exponentially growing populations. Genetics, 129, 555-562.
76. Swofford DL (2001) 'PAUP*. Phylogenetic analysis using parsimony (*and other methods), version 4.0b4a.' Sinauer Associates, Sunderland, Massachusetts.
77. Tajima F (1989a) Statistical method for testing the neutral mutation hypothesis by DNA polymorphism. Genetics, 123, 585-595.
78. Tajima F (1989b) The effect of change in population size on DNA polymorphism. Genetics, 123, 597-601.
79. Williams D, Dunkerley D, DeDeckker P, Kershaw P, Chappell M (1998) Quaternary Environments. Arnold, London, UK.
80. Willis KJ, Whittaker RJ (2000) Paleoecology - The refugial debate. Science, 287, 1406-1407.
81. Zhang D, Hewitt GM (2003) Nuclear DNA analyses in genetic studies of populations: practice, problems and prospects. Molecular Ecology, 12, 563.
82. Zink RM (1994) The geography of mitochondrial DNA variation, population structure, hybridization, and species limits in the fox sparrow (Passerella iliaca). Evolution, 48, 96-111.
83. Zink RM (1997) Phylogeographic studies of North American birds. In: Avian Molecular Evolution and Systematics (ed. Mindell DP), pp. 301-324. Academic Press, San Diego, California.
84. Zink RM, Barrowclough GF, Atwood JL, Blackwell-Rago RC (2000) Genetics, taxonomy, and conservation of the threatened California gnatcatcher. Conservation Biology, 14, 1394-1405.
85. Zink RM, Kessen A, Line TV, Blackwell-Rago RC (2001) Comparative phylogeography of some aridland birds. Condor, 103, 1-10.
86. Zink RM, Pavlova A, Rohwer S, Drovetski SV (2006) Barn swallows before barns: range expansion and intercontinental colonization. Proceedings of the Royal Society of London, Series B, doi:10.1098/rspb.2005.3414.