Multilocus phylogeography of a Holarctic duck: Colonization of North America from Eurasia by gadwall (Anas strepera)

Evolution

Volumn 62, Issue 6, 2008, Pages 1469-1483

  Peters, Jeffrey L ^a,d   Zhuravlev, Yuri N ^b   Fefelov, Igor ^c   Humphries, Elizabeth M ^a,e   Omland, Kevin E ^c  

^a UNIVERSITY OF MARYLAND BALTIMORE COUNTY   (United States)

^b INSTITUTE OF BIOLOGY AND SOIL SCIENCE   (Russian Federation)

^c IRKUTSK STATE UNIVERSITY   (Russian Federation)

^d UNIVERSITY OF ALASKA FAIRBANKS   (United States)

^e UNIVERSITY OF ALASKA MUSEUM   (United States)

Author keywords

Anatidae; Coalescent theory; Founder effect; Multiple loci; Nuclear introns; Selection

Indexed keywords

MITOCHONDRIAL DNA; PRIMER DNA;

ALLELE; COLONIZATION; DIVERGENCE; GENE FLOW; GENETIC DIFFERENTIATION; MITOCHONDRIAL DNA; NATURAL SELECTION; PHYLOGEOGRAPHY; PLEISTOCENE; WADER;

ANIMAL; ARTICLE; BIOLOGICAL MODEL; COMPARATIVE STUDY; DEMOGRAPHY; DNA SEQUENCE; DUCK; EUROPE; GENETIC VARIABILITY; GENETICS; GEOGRAPHY; HAPLOTYPE; MOLECULAR GENETICS; NORTH AMERICA; NUCLEOTIDE SEQUENCE; PHYLOGENY; POPULATION GENETICS; SPECIES DIFFERENCE;

ANIMALS; BASE SEQUENCE; DEMOGRAPHY; DNA PRIMERS; DNA, MITOCHONDRIAL; DUCKS; EUROPE; GENETICS, POPULATION; GEOGRAPHY; HAPLOTYPES; MODELS, GENETIC; MOLECULAR SEQUENCE DATA; NORTH AMERICA; PHYLOGENY; SEQUENCE ANALYSIS, DNA; SPECIES SPECIFICITY; VARIATION (GENETICS);

EURASIA; NORTH AMERICA;

ANAS; ANAS STREPERA; ANATIDAE; AVES;

EID: 44449119051     PISSN: 00143820     EISSN: 15585646     Source Type: Journal    
DOI: 10.1111/j.1558-5646.2008.00372.x     Document Type: Article

References (93)

1. Arnold, T. W., and R. G. Clark. 1996. Survival and philopatry of female dabbling ducks in southcentral Saskatchewan. J. Wildl. Manage. 60 : 560 568.
2. Ballard, J. W. O., and M. C. Whitlock. 2004. The incomplete natural history of mitochondria. Mol. Ecol. 13 : 729 744.
3. Bamshad, M., and S. P. Wooding. 2003. Signatures of natural selection in the human genome. Nat. Rev. Genet. 4 : 99 111.
4. Bandelt, H.-J., P. Forster, and A. Röhl. 1999. Median-joining networks for inferring intraspecific phylogenies. Mol. Biol. Evol. 16 : 37 48.
5. Bazin, E., S. Glemin, and N. Galtier. 2006. Population size does not influence mitochondrial genetic diversity in animals. Science 312 : 570 572.
6. Beaumont, M. A., and R. A. Nichols. 1996. Evaluating loci for use in genetic analysis of population structure. Proc. R. Soc. Lond. B 263 : 1619 1626.
7. Bensch, S., D. E. Irwin, J. H. Irwin, L. Kvist, and S. åkesson. 2006. Conflicting patterns of mitochondrial and nuclear DNA diversity in Phylloscopus warblers. Mol. Ecol. 15 : 161 171.
8. Buehler, D. M., and A. J. Baker. 2005. Population divergence times and historical demography in red knots and dunlins. Condor 107 : 497 513.
9. Cook, L. G., and M. D. Crisp. 2005. Directional asymmetry of long-distance dispersal and colonization could mislead reconstructions of biogeography. J. Biogeogr. 32 : 741 754.
10. Cowie, R. H., and B. S. Holland. 2006. Dispersal is fundamental to biogeography and the evolution of biodiversity on oceanic islands. J. Biogeogr. 33 : 193 198.
11. Dawson, A. G. 1992. Ice age earth: late quaternary geology and climate. Routledge Press, London.
12. del Hoyo, J., A. Elliott, and J. Sargatal. 1992-2007. Handbook of birds of the world (12 volumes). Lynx Editions, Barcelona, Spain.
13. de Queiroz, A. 2005. The resurrection of oceanic dispersal in historical biogeography. Trends Ecol. Evol. 20 : 68 73.
14. Donnelly, P., and S. Tavaré. 1995. Coalescents and genealogical structure under neutrality. Annu. Rev. Genet. 29 : 401 421.
15. Donoghue, M. J., and S. A. Smith. 2004. Patterns in the assembly of temperate forests around the Northern Hemisphere. Philos. Trans. R. Soc. B 359 : 1633 1644.
16. Drummond, A. J., and A. Rambaut. 2006. BEAST v1.4. Available from http://beast.bio.ed.ac.uk/
17. Drummond, A. J., G. K. Nicholls, A. G. Rodrigo, and W. Solomon. 2002. Estimating mutation parameters, population history and genealogy simultaneously from temporally spaced sequence data. Genetics 161 : 1307 1320.
18. Edwards, S. V., and P. Beerli. 2000. Perspective: gene divergence, population divergence, and the variance in coalescence time in phylogeographic studies. Evolution 54 : 1839 1854.
19. Ellegren, H., and A. K. Fridolfsson. 1997. Male-driven evolution of DNA sequences in birds. Nat. Genet. 17 : 182 184.
20. Excoffier, L., P. E. Smouse, and J. M. Quattro. 1992. Analysis of molecular variance inferred from metric distances among DNA haplotypes: application to human mitochondrial DNA restriction data. Genetics 131 : 479 491.
21. Excoffier, L., G. Laval, and S. Schneider. 2005. Arlequin (version 3.0): an integrated software package for population genetics data analysis. Evol. Bioinformatics Online 1 : 47 50.
22. Felsenstein, J. 2004. Inferring phylogenies. Sinauer Associates, Inc. Sunderland, MA.
23. Galtier, N., F. Depaulis, and N. H. Barton. 2000. Detecting bottlenecks and selective sweeps from DNA sequence polymorphism. Genetics 155 : 981 987.
24. Hare, M. P. 2001. Prospects for nuclear gene phylogeography. Trends Ecol. Evol. 16 : 700 706.
25. Hewitt, G. M. 1996. Some genetic consequences of ice ages, and their role in divergence and speciation. Biol. J. Linn. Soc. 58 : 247 276.
26. Hewitt, G. M. 2004. Biodiversity: a climate for colonization. Heredity 92 : 1 2.
27. Hey, J. 2004. HKA - A computer program for tests of natural selection. Available at http://lifesci.rutgers.edu/∼heylab.
28. Hey, J. 2005. On the number of New World founders: a population genetic portrait of the peopling of the Americas. PLoS Biol. 3 : e193.
29. Hey, J., and R. Nielsen. 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.
30. Hey, J., Y. J. Won, A. Sivasundar, R. Nielsen, and J. A. Markert. 2004. Using nuclear haplotypes with microsatellites to study gene flow between recently separated Cichlid species. Mol. Ecol. 13 : 909 919.
31. Ho, S. Y. W., M. J. Phillips, A. Cooper, and A. J. Drummond. 2005. Time dependency of molecular rate estimates and systematic overestimation of recent divergence times. Mol. Biol. Evol. 22 : 1561 1568.
32. Holder, K., R. Montgomerie, and V. L. Friesen. 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.
33. Hudson, R. R., and M. Turelli. 2003. Stochasticity overrules the "three-times rule": genetic drift, genetic draft, and coalescence times for nuclear loci versus mitochondrial DNA. Evolution 57 : 182 190.
34. Hudson, R. R., M. Kreitman, and M. Aguadé. 1987. A test of neutral molecular evolution based on nucleotide data. Genetics 116 : 153 159.
35. Humphries, C. J., and L. R. Parenti. 1999. Cladistic Biogeography. 2nd edn Interpreting Patterns of Plant and Animal Distributions. Oxford University Press, Oxford.
36. Ibrahim, K. M., R. A. Nichols, and G. M. Hewitt. 1996. Spatial patterns of genetic variation generated by different forms of dispersal during range expansion. Heredity 77 : 282 291.
37. International Chicken Genome Sequencing Consortium. 2004. Sequence and comparative analysis of the chicken genome provide unique perspectives on vertebrate evolution. Nature 432 : 695 716.
38. Johnson, K. P., and M. D. Sorenson. 1999. Phylogeny and biogeography of dabbling ducks (genus: Anas): a comparison of molecular and morphological evidence. Auk 116 : 792 805.
39. Kharitonov, S. P. 2002. Migration and some population parameters of the gadwall Anas strepera in Europe and Asia. Pp. 123 140. in G. A. Noskov, A. Czajkowki, and K. P. Fertikova, eds. Study of the status and trends of migratory bird populations in Russia, 4th issue. OMPO Special Publication, St. Petersburg.
40. Kimura, M. 1968. Evolutionary rate at the molecular level. Nature 217 : 624 626.
41. Kimura, M. 1969. The number of heterozygous nucleotide sites maintained in a finite population due to steady flux of mutations. Genetics 61 : 893 903.
42. Knowles, L. L. 2004. The burgeoning field of statistical phylogeography. J. Evol. Biol. 17 : 1 10.
43. Knowles, L. L., and W. P. Maddison. 2002. Statistical phylogeography. Mol. Ecol. 11 : 2623 1235.
44. Kondo, B., J. L. Peters, B. Rosensteel, and K. E. Omland. 2008. Coalescent analyses of multiple loci support a new route to speciation in birds. Evolution in press.
45. Kulikova, I. V., Y. N. Zhuravlev, and K. G. McCracken. 2004. Asymmetric hybridization and sex-biased gene flow between Eastern spot-billed ducks (Anas zonorhyncha) and mallards (A. platyrhynchos) in the Russian Far East. Auk 121 : 930 949.
46. Kulikova, I. V., S. V. Drovetski, D. D. Gibson, R. J. Harrigan, S. Rohwer, M. D. Sorenson, K. Winker, Y. N. Zhuravlev, and K. G. McCracken. 2005. Phylogeography of the mallard (Anas platyrhynchos): hybridization, dispersal, and lineage sorting contribute to complex geographic structure. Auk 122 : 949 965.
47. Liebers, D., P. de Knijff, and A. J. Helbig. 2004. The herring gull complex is not a ring species. Proc. R. Soc. Lond. B 271 : 893 901.
48. Lokemoen, J. T., H. F. Duebbert, and D. E. Sharp. 1990. Homing and reproductive habits of mallards, gadwalls, and blue-winged teal. Wildl. Monogr. 106.
49. Maak, S., K. Neumann, G. von Lengerken, and R. Gattermann. 2000. First seven microsatellites developed for the Peking duck (Anas platyrhynchos). Anim. Genet. 31 : 233.
50. Maddison, W. P., and L. L. Knowles. 2006. Inferring phylogeny despite incomplete lineage sorting. Syst. Biol. 55 : 21 30.
51. Maynard-Smith, J., and J. Haigh. 1974. The hitch-hiking effect of a favourable gene. Genet. Res. 23 : 23 35.
52. Mayr, E. 1942. Systematics and the origin of species. Harvard Univ. Press, Cambridge, MA.
53. Mayr, E. 1970. Populations, species and evolution: an abridgement of animal species and evolution. Harvard Univ. Press, Cambridge.
54. McCracken, K. G., W. P. Johnson, and F. H. Sheldon. 2001. Molecular population genetics, phylogeography, and conservation biology of the mottled duck (Anas fulvigula). Conserv. Genet. 2 : 87 102.
55. McGlone, M. S. 2005. Goodbye Gondwana. J. Biogeogr. 32 : 739 740.
56. Muñoz-Fuentes, V., A. J. Green, J. J. Negro, and M. D. Sorenson. 2005. Population structure and loss of genetic diversity in the endangered white-headed duck, Oxyura leucocephala. Conserv. Genet. 6 : 999 1015.
57. Muñoz-Fuentes, V., A. J. Green, M. D. Sorenson, J. J. Negro, and C. Vilà. 2006. The ruddy duck Oxyura jamaicensis in Europe: natural colonization or human introduction? Mol. Ecol. 15 : 1441 1453.
58. Nei, M., and N. Takahata. 1993. Effective population size, genetic diversity, and coalescence time in subdivided populations. J. Mol. Evol. 37 : 240 244.
59. Omland, K. E., J. M. Baker, and J. L. Peters. 2006. Genetic signatures of intermediate divergence: population history of Old and New World Holarctic ravens (Corvus corax). Mol. Ecol. 15 : 795 808.
60. Palmer, R. S. 1976. Handbook of North American Birds. Vol. 2: Waterfowl. Yale Univ. Press New Haven, CT.
61. Paxinos, E. E., H. F. James, S. L. Olson, M. D. Sorenson, J. Jackson, and R. C. Fleischer. 2002. mtDNA from fossils reveals a radiation of Hawaiian geese recently derived from the Canada goose (Branta canadensis). Proc. Natl. Acad. Sci. USA 99 : 1399 1404.
62. Pearce, J. M., S. L. Talbot, B. J. Pierson, M. R. Petersen, K. T. Scribner, D. L. Dickson, and A. Mosbech. 2004. Lack of spatial genetic structure among nesting and wintering king eiders. Condor 106 : 229 240.
63. Pearce, J. M., S. L. Talbot, M. R. Petersen, and J. R. Rearick. 2005. Limited genetic differentiation among breeding, molting, and wintering groups of the threatened Steller's eiders: the role of historic and contemporary factors. Conserv. Genet. 6 : 743 757.
64. Pereira, S. L., and A. J. Baker. 2006. A mitogenomic timescale for birds detects variable phylogenetic rates of molecular evolution and refutes the standard molecular clock. Mol. Biol. Evol. 23 : 1731 1740.
65. Peters, J. L., and K. E. Omland. 2007. Population structure and mitochondrial polyphyly in North American gadwalls (Anas strepera). Auk 124 : 444 462.
66. Peters, J. L., W. Gretes, and K. E. Omland. 2005a. Late Pleistocene divergence between eastern and western populations of wood ducks (Aix sponsa) inferred by the 'isolation with migration' coalescent method. Mol. Ecol. 14 : 3407 3418.
67. Peters, J. L., K. G. McCracken, Y. N. Zhuravlev, Y. Lu, R. E. Wilson, K. P. Johnson, and K. E. Omland. 2005b. Phylogenetics of wigeons and allies (Anatidae: Anas): the importance of sampling multiple loci and multiple individuals. Mol. Phylogenet. Evol. 35 : 209 224.
68. Peters, J. L., Y. N. Zhuravlev, I. Fefelov, A. Logie, and K. E. Omland. 2007. Nuclear loci and coalescent methods support ancient hybridization as cause of mitochondrial paraphyly between gadwall and falcated duck (Anas spp.). Evolution 61 : 1992 2006.
69. Pielou, E. C. 1991. After the ice age: the return of life to glaciated North America. University of Chicago Press Chicago, Illinois.
70. Rausch, R. L. 1994. Transberingian dispersal of cestodes in mammals. Int. J. Parasitol. 24 : 1203 1212.
71. Rosenberg, N. A., and M. Nordborg. 2002. Genealogical trees, coalescent theory and the analysis of genetic polymorphisms. Nat. Rev. Genet. 3 : 380 390.
72. Rozas, J., and R. Rozas. 1999. DnaSP version 3: an integrated program for molecular population genetics and molecular evolution analysis. Bioinformatics 15 : 174 175.
73. Sæther, B.-E., R. Lande, S. Engen, H. Weimerskirch, M. Lillegård, R. Altwegg, P. H. Becker, T. Bregnballe, J. E. Brommer, R. H. McCleery, et al. 2005. Generation time and temporal scaling of bird population dynamics. Nature 436 : 99 102.
74. Seutin, G., L. M. Ratcliffe, and P. T. Boag. 1995. Mitochondrial DNA homogeneity in the phenotypically diverse redpoll finch complex (Aves: Carduelinae: Carduelis flammea-hornemanni). Evolution 49 : 962 973.
75. Simpson, G. G. 1940. Mammals and land bridges. J. Wash. Acad. Sci. 30 : 137 163.
76. Slatkin, M., and L. Excoffier. 1996. Testing for linkage disequilibrium in genotypic data using the Expectation-Maximization algorithm. Heredity 76 : 377 383.
77. Sorenson, M. D., and R. C. Fleischer. 1996. Multiple independent transpositions of mitochondrial DNA control region sequences to the nucleus. Proc. Natl. Acad. Sci. USA 93 : 15239 15243.
78. Sorenson, M. D., J. C. Ast, D. E. Dimcheff, T. Yuri, and D. P. Mindell. 1999. Primers for a PCR-based approach to mitochondrial genome sequencing in birds and other vertebrates. Mol. Phylogenet. Evol. 12 : 105 114.
79. Stephens, M., and P. Donnelly. 2003. A comparison of Bayesian methods for haplotype reconstruction from population genotype data. Am. J. Hum. Genet. 73 : 1162 1169.
80. Stephens, M., N. J. Smith, and P. Donnelly. 2001. A new statistical method for haplotype reconstruction from population data. Am. J. Hum. Genet. 68 : 978 989.
81. Storz, J. F., B. A. Payseur, and M. W. Nachman. 2004. Genome scans of DNA variability in humans reveal evidence for selective sweeps outside of Africa. Mol. Biol. Evol. 21 : 1800 1811.
82. Suarez, A. V., and N. D. Tsutsui. 2008. The evolutionary consequences of biological invasions. Mol. Ecol. 17 : 351 360.
83. Szymczak, M. R., and E. A. Rexstad. 1991. Harvest distribution and survival of a Gadwall population. J. Wildl. Manage. 55 : 592 600.
84. U. S. Fish and Wildlife Service. 2005. 2005 Pacific Flyway Databook. U.S. Department of the Interior, Division of Migratory Bird Management, Portland, Oregon U.S.A. U.S. Fish and Wildlife Service.
85. U. S. Fish and Wildlife Service. 2007. Waterfowl population status, 2007. U.S. Department of the Interior, Washington, D.C. U.S.A.
86. Waltari, E., E. P. Hoberg, E. P. Lessa, and J. A. Cook. 2007. Eastward ho: phylogeographical perspectives on colonization of hosts and parasites across the Beringian nexus. J. Biogeogr. 34 : 561 574.
87. Wares, J. P., and C. W. Cunningham. 2001. Phylogeography and historical ecology of the North Atlantic intertidal. Evolution 55 : 2455 2469.
88. Wenink, P. W., A. J. Baker, and M. G. J. Tilanus. 1994. Mitochondrial control-region sequences in two shorebird species, the turnstone and the dunlin, and their utility in population genetic studies. Mol. Biol. Evol. 11 : 22 31.
89. Wetlands International. 2006. Waterbird Population Estimates - Fourth Edition. Wetlands International, Wageningen, The Netherlands
90. Wooding, S., and A. Rogers. 2002. The matrix coalescent and an application to human single-nucleotide polymorphisms. Genetics 161 : 1641 1650.
91. Yoder, A. D., and M. D. Nowak. 2006. Has vicariance or dispersal been the predominant biogeographic force in Madagascar? Only time will tell. Ann. Rev. Ecol. Evol. Syst. 37 : 405 431.
92. Zink, R. M., S. Rohwer, A. V. Andreev, and D. L. Dittmann. 1995. Trans-Beringia comparisons of mitochondrial DNA differentiation in birds. Condor 97 : 639 649.
93. Zhang, D.-X., and G. M. Hewitt. 2003. Nuclear DNA analyses in genetic studies of populations: practice, problems and prospects. Mol. Ecol. 12 : 563 584.