Speciation in the White-breasted Nuthatch (Sitta carolinensis): A multilocus perspective

Molecular Ecology

Volumn 21, Issue 4, 2012, Pages 907-920

  Walstrom, V Woody ^a   Klicka, John ^b   Spellman, Garth M ^a  

^a BLACK HILLS STATE UNIVERSITY   (United States)

^b UNIVERSITY OF NEVADA   (United States)

Author keywords

coalescent analysis; multilocus; Sitta carolinensis; speciation; species tree

Indexed keywords

MITOCHONDRIAL DNA;

ANIMAL; CELL NUCLEUS; CLASSIFICATION; DNA SEQUENCE; ECOSYSTEM; GENE FLOW; GENETICS; MOLECULAR GENETICS; NORTH AMERICA; NUCLEOTIDE SEQUENCE; PHYLOGEOGRAPHY; PRINCIPAL COMPONENT ANALYSIS; REPRODUCTIVE ISOLATION; REVIEW; SONGBIRD; SPECIES DIFFERENTIATION;

ANIMALS; CELL NUCLEUS; DNA, MITOCHONDRIAL; ECOSYSTEM; GENE FLOW; GENETIC SPECIATION; MOLECULAR SEQUENCE DATA; NORTH AMERICA; PASSERIFORMES; PHYLOGEOGRAPHY; PRINCIPAL COMPONENT ANALYSIS; REPRODUCTIVE ISOLATION; SEQUENCE ANALYSIS, DNA;

SITTA CAROLINENSIS;

EID: 84856284011     PISSN: 09621083     EISSN: 1365294X     Source Type: Journal    
DOI: 10.1111/j.1365-294X.2011.05384.x     Document Type: Review

References (67)

1. Akaike H, (1973) Information theory as an extension of the maximum likelihood principle. In: Second International Symposium on Information Theory (eds, Petrov BN, and, Csaki F,), pp. 267-281. Akademiai Kiado, Budapest.
2. Alderfer J, (2006) National Geographic Complete Birds of North America. National Geographic, Washington, DC.
3. American Ornithologists' Union (1957) Check-list of North American Birds, 5th edn. Am. Ornithol. Union, Washington, DC.
4. Avise JC, (2000) Phylogeography: The History and Formation of Species. Harvard University Press, Cambridge, Massachusetts/London.
5. Avise JC, Wollenberg K, (1997) Phylogenetics and the origin of species. Proceedings of the National Academy of Sciences of the United States of America, 94, 7748-7755. (Pubitemid 27343721)
6. Backström N, Fagerberg S, Ellegren H, (2008) Genomics of natural bird populations: a gene-based set of reference markers evenly spread across the avian genome. Molecular Ecology., 17, 964-980. (Pubitemid 351197356)
7. Barrowclough GF, Groth JG, Mertz LA, Gutiérrez RJ, (2004) Phylogeographic structure, gene flow and species status in blue grouse (Dendragapus obscurus). Molecular Ecology, 13, 1911-1922. (Pubitemid 38847595)
8. Bhagabati NK, Brown JL, Bowen BS, (2004) Geographic variation in Mexican jays (Aphelocoma ultramarina): local differentiation, polyphyly or hybridization? Molecular Ecology, 13, 2721-2734. (Pubitemid 39151629)
9. Bulgin NL, Gibbs HL, Vickery P, et al., (2003) Ancestral polymorphisms in genetic markers obscure detection of evolutionarily distinct populations in the endangered Florida grasshopper sparrow (Ammodramus savannarum floridanus). Molecular Ecology, 12, 831-844. (Pubitemid 36530682)
10. Carling MD, Brumfield RT, (2008) Haldane's rule in an avian system: using cline theory and divergence population genetics to test for differential introgression of mitochondrial, autosomal, and sexlinked loci across the Passerina bunting hybrid zone. Evolution International Journal of Organic Evolution, 62, 2600-2615.
11. Carstens BC, Reid N, Stoute HN, (2009) An information theoretical approach to phylogeography. Molecular Ecology, 18, 4270-4282.
12. Cummings MP, Neel MC, Shaw KL, (2008) A genealogical approach to quantifying lineage divergence. Evolution, 62, 2411-2422.
13. Eckert AJ, Carstens BC, (2008) Does gene flow destroy phylogenetic signal? The performance of three methods for estimating species phylogenies in the presence of gene flow. Molecular Phylogenetics & Evolution, 49, 832-842.
14. Edwards SV, Beerli P, (2000) Perspective: gene divergence, population divergence, and the variance in coalescence time in phylogeographic studies. Evolution, 54, 1839-1854. (Pubitemid 32113816)
15. Edwards S, Bensch S, (2009) Looking forwards or looking backwards in avian phylogeography? A comment on Zink and Barrowclough 2008. Molecular Ecology, 18, 2930-2933.
16. Graham A, (1999) Late Cretaceous and Cenozoic History of North American Vegetation. Oxford University Press, New York.
17. Grubb Jr. TC, Pravosudov VV,. (2008). Whitebreasted nuthatch (Sitta carolinensis). In: The Birds of North America, No. 054 (eds, Poole A, and, Gil F,), The Academy of Natural Sciences, Philadelphia, PA, and the American Ornithologists' Union, Washington, District of Columbia.
18. Guindon S, Gascuel O, (2003) A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood. Systematic Biology, 52, 696-704. (Pubitemid 37365050)
19. Harrap S, Quinn D, (1996) Tits, Nuthatches and Treecreepers. Christopher Helm, pp. 150-155. Princeton University Press; Princeton, NJ.
20. Hasegawa M, Kishino H, Yano TA, (1985) Dating of the human-ape splitting by a molecular clock of mitochondrial DNA. Journal of Molecular Evolution, 21, 160-174. (Pubitemid 16227864)
21. Heled J, Drummond AJ, (2010) Bayesian inference of species trees from multilocus data. Molecular Biology and Evoution, 27, 570-580.
22. Hey J, Nielsen R, (2007) Integration within the Felsenstein equation for improved Markov chain Monte Carlo methods in population genetics. Proceedings of the National Academy of Sciences of the United States of America, 104, 2785-2790. (Pubitemid 46327957)
23. Hickerson MJ, Carstens BC, Cavender-Bares J, et al. (2010) Phylogeography's past, present, and future: 10 years after Avise, 2000. Molecular Phylogenetics and Evolution, 54, 291-301.
24. Hijmans RJ, Cameron SE, Parra JL, Jones PG, Jarvis A, (2005) Very high resolution interpolated climate surfaces for global land areas. International Journal of Climatology, 25, 1965-1978. (Pubitemid 43013915)
25. Holder K, Montgomerie R, Friesen VL, (1999) A test of the glacial refugium hypothesis using patterns of mitochondrial and nuclear DNA sequence variation in rock ptarmigan (Lagopus mutus). Evolution, 53, 1936-1950. (Pubitemid 30044824)
26. Jennings WB, Edwards SV, (2005) Speciational history of Australian grass finches (Poephila) inferred from 30 gene trees. Evolution, 59, 2033-2047. (Pubitemid 41384386)
27. Johannesson K, (2010) Are we analyzing speciation without prejudice? Annals of the New York Academy of Sciences, 1206, 1.
28. Klicka J, Zink RM, (1997) The importance of recent ice ages in speciation: a failed paradigm. Science, 277, 1666-1669. (Pubitemid 27446229)
29. Klicka J, Spellman GM, Winker K, Chua V, Smith BT, (2011) A phylogeographic and population genetic analysis of a widespread, sedentary North American bird: the Hairy Woodpecker (Picoides villosus). Auk, 128, 346-362.
30. Knowles LL, Carstens BC, (2007) Delimiting species without monophyletic gene trees. Systematic Biology, 56, 887-895. (Pubitemid 350129639)
31. Kubatko LS, Degnan JH, (2007) Inconsistency of phylogenetic estimates from concatenated data under coalescence. Systematic Biology., 56, 17-24.
32. 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.
33. Librado P, Rozas J, (2009) DnaSP v5. A software for comprehensive analysis of DNA polymorphism data. Bioinformatics, 25, 1451-1452.
34. Lovette IJ, (2004) Mitochondrial dating and mixed support for the '2% rule' in birds. Auk, 121, 1-6. (Pubitemid 38215551)
35. Maddison W, (1997) Gene trees in species trees. Systematic Biology, 46, 523-536.
36. Manthey JD, Klicka J, Spellman GM, (2011a) Cryptic diversity in a widespread North American songbird: phylogeography of the brown creeper (Certhia americana). Molecular Phylogenetics and Evolution, 58, 502-512.
37. Manthey JD, Klicka J, Spellman GM, (2011b) Isolation-driven divergence: speciation in a widespread North American songbird (Aves: Certhiidae). Molecular Ecology, doi
38. Mayr E, (1963) Animal Species and Evolution. Belknap Press, Cambridge, MA.
39. McCormack JE, Zellmer AJ, Knowles LL, (2010) Does niche divergence accompany allopatric divergence in aphelocoma jays as predicted under ecological speciation?: insights from tests with niche models. Evolution, 64, 1231-1244.
40. Milá B, Smith TB, Wayne RK, (2006) Postglacial population expansion drives the evolution of long-distance migration in a songbird. Evolution, 60, 2403-2409. (Pubitemid 44925479)
41. Milne I, Lindner D, Bayer M, et al. (2009) TOPALi v2: a rich graphical interface for evolutionary analyses of multiple alignments on HPC clusters and multi-core desktops. Bioinformatics Applications Note, 25, 126-127.
42. Ödeen A, Björklund M, (2003) Dynamics in the evolution of sexual traits: losses and gains, radiation and convergence in yellow wagtails (Motacilla flava). Molecular Ecology, 12, 2113-2130. (Pubitemid 36922325)
43. Paschou P, Ziv E, Burchard EG, et al. (2007) PCA-correlated SNPs for structure identification in worldwide human populations. PLoS Genetics, 3, 1672-1686. (Pubitemid 47510260)
44. Peakall R, Smouse PE, (2006) GENALEX 6 genetic analysis in Excel. Population genetic software for teaching and research. Molecular Ecology Notes, 6, 288-295. (Pubitemid 43373825)
45. Phillips AR, (1986) The Known birds of North and Middle America Part 1. Hirundinadae to Mimidae; Cethiidae. Denver Museum of Natural History, Denver.
46. Phillips SJ, Anderson RP, Schapire RE, (2006) Maximum entropy modeling of species geographic distributions. Ecological Modeling, 190, 231-259. (Pubitemid 41680650)
47. Pitra C, Lieckfeldt D, Alonso JC, (2000) Population subdivision in Europe's great bustard inferred from mitochondrial and nuclear DNA sequence variation. Molecular Ecology, 9, 1165-1170. (Pubitemid 30613163)
48. Prichard JK, Stephens M, Donnelly PJ, (2000) Inference of population structure using multilocus genotype data. Genetics, 155, 945-959. (Pubitemid 30397141)
49. Rambaut A, Drummond AJ, (2007a) BEAUTi v1.4. Available at: (last accessed 10 Oct. 2010).
50. Rambaut A, Drummond AJ, (2007b) Tracer v1.4. Available at: (last accessed 10 Oct. 2010).
51. Rambaut A, Drummond AJ, (2008) TreeAnnotator v1.4.8. Available at: (last accessed 10 Oct. 2010).
52. Ruegg K, (2008) Genetic, morphological, and ecological characterization of a hybrid zone that spans a migratory divide. Evolution, 62, 452-466. (Pubitemid 351294549)
53. Ruegg KC, Smith TB, (2002) Not as the crow flies: a historical explanation for circuitous migration in Swainson's thrush (Catharus ustulatus). Proceedings of the Royal Society of London. Series B: Biological Sciences, 269, 1375-1381. (Pubitemid 34753671)
54. Schoener TW, (1968) Anolis lizards of Bimini: resource partitioning in a complex fauna. Ecology, 49, 704-726.
55. Sibley DA, (2000) Sibley Guide to Birds/National Audubon Society Sibley Guide to Birds. Alfred A. Knopf, New York.
56. Smit AFA, Hubley R, Green P, (19962004) RepeatMasker Open-3.0. Available at: (last accessed 01 April 2010).
57. Smith BT, Klicka J, (2010) The profound influence of the Late Pliocene Panamanian uplift on the exchange, diversification, and distribution of New World birds. Ecography, 33, 333-342.
58. Spellman GM, Klicka J, (2006) Testing hypotheses of Pleistocene population history using coalescent simulations: phylogeography of the pygmy nuthatch (Sitta pygmaea). Proceedings of the Royal Society B: Biological Sciences, 273, 3057-3063. (Pubitemid 46622446)
59. Spellman GM, Klicka J, (2007) Phylogeography of the White-breasted Nuthatch (Sitta carolinensis): diversification in North American pine and oak woodlands. Molecular Ecology, 16, 1729-1740. (Pubitemid 46525389)
60. Spellman GM, Riddle B, Klicka J, (2007) Phylogeography of the Mountain Chickadee (Poecile gambeli): diversification, introgression, and expansion in response to Quaternary climate change. Molecular Ecology, 16, 1055-1068.
61. Stephens M, Smith NJ, Donnelly P, (2001) A new statistical method for haplotype reconstruction from population data. American Journal of Human Genetics, 68, 978-989. (Pubitemid 32289743)
62. Warren DL, Glor RE, Turelli M, (2008) Environmental niche equivalency versus conservatism: quantitative approaches to niche evolution. Evolution, 62, 2868-2883.
63. Weir JT, Schulter D, (2004) Ice sheets promote speciation in boreal birds. Proceedings of the Royal Society B: Biological Sciences, 271, 1881-1887.
64. Wright S, (1931) Evolution in Mendelian populations. Genetics, 16, 97-159.
65. 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. (Pubitemid 2113195)
66. Zink RM, Slowinski JB, (1995) Evidence from molecular systematics for decreased avian diversification in the Pleistocene Epoch. Proceedings of the National Academy of Sciences of the United States of America, 92, 5832-5835.
67. Zink RM, Barrowclough GF, (2008) Mitochondrial DNA under siege in avian phylogeography. Molecular Ecology, 17, 2107-2121. (Pubitemid 351562803)