Analysis of multilocus DNA reveals hybridization in a contact zone between Empidonax flycatchers

Journal of Avian Biology

Volumn 40, Issue 6, 2009, Pages 614-624

  Rush, Andrew C ^a   Cannings, Richard J ^b   Irwin, Darren E ^c  

^a UNIVERSITY OF CALIFORNIA   (United States)

^b RR1 ^*  (Canada)

^c UNIVERSITY OF BRITISH COLUMBIA   (Canada)

Author keywords

[No Author keywords available]

Indexed keywords

ALLOPATRY; CLADISTICS; CONTACT ZONE; DNA; GENETIC ANALYSIS; GENETIC MARKER; HYBRIDIZATION; MOLECULAR ANALYSIS; PASSERINE; PHENOTYPE;

ALBERTA; BRITISH COLUMBIA; CANADA;

AVES; EMPIDONAX; EMPIDONAX DIFFICILIS; EMPIDONAX OCCIDENTALIS;

EID: 72249097671     PISSN: 09088857     EISSN: 1600048X     Source Type: Journal    
DOI: 10.1111/j.1600-048X.2009.04681.x     Document Type: Article

References (75)

1. Ainsley, D. T. J. 1992. Vocalizations and nesting behaviour of the Pacific-slope flycatcher, Empidonax difficilis MSc thesis. Univ. of Victoria, Canada.
2. American Ornithologists' Union. 1989. Thirty-seventh supplement to the American Ornithologists' Union check-list of North American birds Auk 106 : 532 538.
3. Avise, J. C. 2004. Molecular markers, natural history, and evolution. Sinauer Ass, Sunderland.
4. Ballard, J. W. Whitlock, M. C. 2004. The incomplete natural history of mitochondrial DNA Mol. Ecol. 13 : 729 744.
5. Barrowclough, G. F. 1980. Genetic and phenotypic differentiation in a wood warbler (genus Dendroica) hybrid zone Auk 97 : 655 668.
6. Barton, N. H. Gale, K. S. 1993. Genetic analysis of hybrid zones Harrison, R. G. Hybrid zones and the evolutionary process. Oxford Univ. Press, New York 13 45.
7. Barton, N. H. Hewitt, G. M. 1981. Hybrid zones and speciation Atchley, W. R. Woodruff, D. S. Evolution and speciation: essays in honor of M. J. D. White. Cambridge Univ. Press 109 145.
8. Barton, N. H. Hewitt, G.M. 1985. Analysis of hybrid zones Ann. Rev. Ecol. Syst. 16 : 113 148.
9. Barton, N. H. Hewitt, G. M. 1989. Adaptation, speciation and hybrid zones Nature 341 : 497 503.
10. Bensch, S. Åkesson, M. 2005. Ten years of AFLP in ecology and evolution: why so few animals? Mol. Ecol. 14 : 2899 2914.
11. Bowie, R. C. K., Fjeldså, J., Hackett, S. J. Crowe, T. M. 2004. Molecular evolution in space and through time: mtDNA phylogeography of the olive sunbird (Nectarina olivacea/obscura) throughout continental Africa Mol. Phyl. Evol. 33 : 56 74.
12. Campbell, R. W., Dawe, N., McTaggart-Cowan, I., Cooper, J., Kaiser, G., McNall, M. Smith, G. 1997. The birds of British Columbia. UBC Press, Vancouver.
13. Campbell, D., Duchesne, P. Bernatchez, L. 2003. AFLP utility for population assignment studies: analytical investigation and empirical comparison with microsatellites Mol. Ecol. 12 : 1979 1991.
14. Cicero, C. 2004. Barriers to sympatry between avian sibling species (Paridae: Baeolophus) in tenuous secondary contact Evolution 58 : 1573 1587.
15. Cicero, C. Johnson, N. K. 1998. Molecular phylogeny and ecological diversification in a clade of New World songbirds (genus Vireo) Mol. Ecol. 7 : 1359 1370.
16. Clement, M., Posada, D. Crandall, K. A. 2000. TCS: a computer program to estimate gene genealogies Mol. Ecol. 9 : 1657 1659.
17. Corander, J. Marttinen, P. 2006. Bayesian identification of admixture events using multilocus molecular markers Mol. Ecol. 15 : 2833 2843.
18. Corander, J., Marttinen, P., Siren, J. Tang, J. 2008. Enhanced Bayesian modeling in BAPS software for learning genetic structures of populations BMC Informatics. 9 : 539.
19. Coyne, J. A. Orr, H. A. 2004. Speciation. Sinauer Ass., Inc, Sunderland.
20. Drovetski, S. V., Zink, R. M., Rohwer, S., Fadeev, I. V., Nesterov, E. V., Karagodin, I., Koblik, E. A. Red'kin, Y. A. 2004. Complex biogeographic history of a Holarctic passerine Proc. R. Soc. B 271 : 545 551.
21. Edwards, S. V., Kingan, S. B., Calkins, J. D., Balakrishnan, C. N., Jennings, W. B., Swanson, W. J. Sorenson, M. D. 2005. Speciation in birds: genes, geography, and sexual selection Proc. Natl. Acad. Sci. U S A 102 : 6550 6557.
22. Endler, J. A. 1977. Geographic variation, speciation, and clines. Princeton Univ. Press, New Jersey.
23. Excoffier, L., Laval, G. Schneider, S. 2005. Arlequin ver. 3.0: An integrated software package for population genetics data analysis Evol. Bioinform. Online 1 : 47 50.
24. Falush, D., Stephens, M. Pritchard, J. K. 2007. Inference of population structure using multilocus genotype data: dominant markers and null alleles Mol. Ecol. Not. 7 : 574 578.
25. Fu, Y. X. 1997. Statistical tests of neutrality of mutations against population growth, hitchhiking and background selection Genetics 133 : 693 709.
26. García-Moreno, J. 2004. Is there a universal mtDNA clock for birds? J. Avian Biol. 35 : 465 468.
27. Good, J. M., Hird, S., Reid, N., Demboski, J. R., Steppan, S. J., Martin-Nims, T. R. Sullivan, J. 2008. Ancient hybridization and mitochondrial capture between two species of chipmunks Mol. Ecol. 17 : 1313 1327.
28. Hackett, S. J. 1996. Molecular phylogenetics and biogeography of tanagers in the genus Ramphocelus (Aves) Mol. Phyl. Evol. 5 : 368 382.
29. Harrison, R.G. 1993. Hybrid zones and the evolutionary process. Oxford Univ. Press, New York.
30. Hubbard, J. P. 1969. The relationships and evolution of the Dendroica coronata complex Auk 86 : 393 432.
31. Irwin, D. E. 2002. Phylogeographic breaks without geographic barriers to gene flow Evolution 56 : 2383 2394.
32. Irwin, D. E., Alström, P., Olsson, U. Benowitz-Fredericks, Z. M. 2001a. Cryptic species in the genus Phylloscopus (Old World leaf warblers) Ibis 143 : 233 247.
33. Irwin, D. E., Bensch, S., Irwin, J. H. Price, T. D. 2005. Speciation by distance in a ring species Science 307 : 414 416.
34. Irwin, D. E., Bensch, S. Price, T. D. 2001. Speciation in a ring Nature 409 : 333 337.
35. Johnson, N. 1963. Biosystematics of sibling species of flycatchers in the Empidonax hammondii-oberholseri-wrightii complex. Univ. of California Press, Berkeley.
36. Johnson, N. 1980. Character evolution and evolution of sibling species in the Empidonax difficilis-flavescens complex (Aves: Tyrannidae). Univ. of California Press, Berkeley.
37. Johnson, N. K. 1994. Old-school taxonomy versus modern biosystematics: species-level decision in Stelgidopteryx and Empidonax Auk 111 : 773 780.
38. Johnson, N. Cicero, C. 2002. The role of ecologic diversification in sibling speciation of Empidonax flycatchers (Tyrannidae): multigene evidence from mtDNA Mol. Ecol. 11 : 2065 2081.
39. Johnson, N. K. Marten, J. A. 1988. Evolutionary genetics of flycatchers. II. Differentiation in the Empidonax difficilis complex Auk 105 : 177 191.
40. Kroodsma, D. 1984. Song of the alder flycatcher (Empidonax alnorum) and the willow flycatcher (Empidonax trailli) are innate Auk 101 : 13 24.
41. Kroodsma, D. 1985. Development and use of two song forms by the eastern phoebe Wilson Bull. 97 : 21 29.
42. Kroodsma, D. E., Albano, D. J., Houlihan, P. W. Wells, J. A. 1995. Song development by black-capped chickadees (Parus atricapillus) and Carolina chickadees (P. carolinensis) Auk 112 : 29 43.
43. Kulba, B. McGillivray, W. 2000. The distribution and habitat preferences of the "western flycatcher" in Alberta [WWW document, 365kb]. URL http://www.pma.edmonton.ab.ca/vpub/wefl/index.htm.
44. LI-COR Biosciences. 2003. Applications manual: model 4300 DNA analyzer. LI-COR Biosci., Lincoln.
45. Lovette, I. J. 2004. Mitochondrial dating and mixed-support for the "2% rule in birds" Auk 121 : 1 6.
46. Lowther, P. E. 2000. Pacific-slope flycatcher (Empidonax difficilis) and Cordilleran flycatcher (Empidonax occidentalis) Poole, A. Gill, F. The birds of North America, no. 556. The birds of North America, Inc., Philadelphia.
47. Maddison, D. R. Maddison, W. P. 2003. MacClade 4: Analysis of phylogeny and character evolution. Version 4.06. Sinauer Ass., Sunderland.
48. Marshall, D. B., Hunter, M. G. Contreras, A. L. 2003. Birds of Oregon. Oregon State Univ. Press, Corvallis.
49. Mayr, E. 1942. Systematics and the origin of species. Columbia Univ. Press, New York.
50. McCarthy, E. M. 2006. Handbook of avian hybrids of the world. Oxford Univ. Press.
51. McDonald, J. H. Kreitman, M. 1991. Adaptive protein evolution at the Adh locus in Drosophila Nature. 354 : 114 116.
52. Miller, A. 1956. Ecologic factors that accelerate formation of races and species of terrestrial vertebrates Evolution. 10 : 262 277.
53. Moore, W.S. 1977. An evaluation of narrow hybrid zones in vertebrates Q. Rev. Biol. 52 : 263 277.
54. Moore, W. S. Price, J. T. 1993. Nature of selection in the northern flicker hybrid zone and its implications for speciation theory Harrison, R.G. Hybrid zones and the evolutionary process. Oxford Univ. Press 196 225.
55. Newton, I. 2003. The speciation and biogeography of birds. Academic Press, London.
56. Parish, R., Coupé, R. Lloyd, D. 1996. Plants of southern interior British Columbia and the inland northwest. Lone Pine Publ., Vancouver.
57. Patton, J. L. Smith, M. F. 1994. Paraphyly, polyphyly, and the nature of species boundaries in pocket gophers (genus Thomomys) Syst. Biol. 43 : 11 26.
58. Price, T. 2008. Speciation in birds. Roberts and Co. Publ., Colorado.
59. Pritchard, J. K., Stephens, M. Donnelly, P. 2000. Inference of population structure using multilocus genotype data Genetics 155 : 945 959.
60. Pyle, P. 1997. Identification guide to North American birds. Slate Creek Press, California.
61. R Development Core Team. 2006. R: a language and environment for statistical computing. R Found. for Stat. Comp, Vienna, Austria http://www.R-project.org.
62. Rising, J. D. 1996. The stability of the oriole hybrid zone in western Kansas Condor 98 : 658 663.
63. Rozas, J., Sánchez-DelBarrio, J. C., Messeguer, X. Rozas, R. 2003. DnaSP, DNA polymorphism analyses by the coalescent and other methods Bioinform. 19 : 2496 2497.
64. Rohwer, S., Bermingham, E. Wood, C. 2001. Plumage and mitochondrial DNA haplotype variation across a moving hybrid zone Evolution 55 : 405 422.
65. Ruegg, K. 2007. Genetic, morphological, and ecological characterization of a hybrid zone that spans a migratory divide Evolution 62 : 452 466.
66. Seutin, G., White, B. N. Boag, P. T. 1991. Preservation of avian blood and tissue samples for DNA analyses Can. J. Zool. 69 : 82 90.
67. Stein, R. C. 1963. Isolating mechanisms between populations of Traill's flycatchers Proc. Am. Phil. Soc. 107 : 21 50.
68. Toews, D. P. L. Irwin., D. E. 2008. Cryptic speciation in a Holarctic passerine revealed by genetic and bioacoustic analyses Mol. Ecol. 17 : 2691 2705.
69. Vallender, R., Robertson, R. J., Friesen, V. L. Lovette, I. J. 2007. Complex hybridization dynamics between golden-winged and blue-winged warblers (Vermivora chrysoptera and Vermivora pinus) revealed by AFLP, microsatellite, intron and mtDNA markers Mol. Ecol. 16 : 2017 2029.
70. Vos, P., Hogers, R., Bleeker, M., Reijans, M., van de Lee, T., Hornes, M., Frijters, A., Pot, J., Peleman, J., Kuiper, M. Zabeau, M. 1995. AFLP: A new technique for DNA fingerprinting Nucl. Acids Res. 23 : 4405 4414.
71. Wahl, T. R., Tweit, B. Mlodinow, S. G. Birds of Washington. Oregon State Univ. Press, Corvallis 2005 Schneider, C.J. 1998. Taxonomy of the Plethodontid salamander genus Ensatina Herpetologica 54 : 279 298.
72. Wang, Z., Baker, A. J., Hill, G. E. Edwards, S. V. 2003. Reconciling actual and inferred population histories in the house finch (Carpodacus mexicanus) by AFLP analysis Evolution 57 : 2852 2864.
73. Weir, J. T. Schluter, D. 2004. Ice sheets promote speciation in boreal birds Proc. R. Soc. B 271 : 1881 1887.
74. Weir, J. T. Schluter, D. 2008. Calibrating the avian molecular clock Mol. Ecol. 17 : 2321 2328.
75. Zink, R. M. Barrowclough, G. F. 2008. Mitochondrial DNA under siege in avian phylogeography Mol. Ecol. 17 : 2107 2121.