Incomplete lineage sorting or secondary admixture: Disentangling historical divergence from recent gene flow in the Vinous-throated parrotbill (Paradoxornis webbianus)

Molecular Ecology

Volumn 21, Issue 24, 2012, Pages 6117-6133

  Qu, Yanhua ^a   Zhang, Ruiying ^a   Quan, Qing ^a   Song, Gang ^a   Li, Shou Hsien ^b   Lei, Fumin ^a  

^a INSTITUTE OF ZOOLOGY   (China)

^b NATIONAL TAIWAN NORMAL UNIVERSITY   (Taiwan)

Author keywords

coalescent simulations; East Asia; ecological niche model; multilocus analyses; Pleistocene glaciations

Indexed keywords

MICROSATELLITE DNA; MITOCHONDRIAL DNA;

ANIMAL; ARTICLE; CELL NUCLEUS; CLASSIFICATION; DNA SEQUENCE; GENE FLOW; GENETIC VARIABILITY; GENETICS; MOLECULAR EVOLUTION; MOLECULAR GENETICS; NUCLEOTIDE SEQUENCE; PHYLOGENY; POPULATION GENETICS; SONGBIRD; STATISTICAL MODEL;

ANIMALS; CELL NUCLEUS; DNA, MITOCHONDRIAL; EVOLUTION, MOLECULAR; GENE FLOW; GENETIC VARIATION; GENETICS, POPULATION; LIKELIHOOD FUNCTIONS; MICROSATELLITE REPEATS; MOLECULAR SEQUENCE DATA; PASSERIFORMES; PHYLOGENY; SEQUENCE ANALYSIS, DNA;

AVES; PARADOXORNIS WEBBIANUS;

EID: 84870885418     PISSN: 09621083     EISSN: 1365294X     Source Type: Journal    
DOI: 10.1111/mec.12080     Document Type: Article

References (92)

1. Akaike H, (1973) Information theory as an extension of the maximum likelihood principle. In: Second International Symposium on Information Theory (eds, Petrov BN, Csaki F,), pp. 267-281. Akademiai Kiado, Budapest, Hungary.
2. Avise JC, (2008) Phylogeography: retrospect and prospect. Journal of Biogeography, 36, 3-15.
3. Ballard JW, (2000) Comparative genome of mitochondrial DNA in Drosophila simulans. Journal of Molecular Evolution, 51, 64-75.
4. Ballard JW, Whitlock MC, (2004) The incomplete natural history of mitochondria. Molecular Ecology, 13, 729-744.
5. Ballard JW, Chernoff B, James AC, (2002) Divergence of mitochondrial DNA is not corroborated by nuclear DNA, morphology, or behavior in Drosophila simulans. Evolution, 56, 527-545.
6. Belkhir K, Borsa P, Chikhi L, Raufaste N, Bonhomme F, (2004) Genetix 4.05, Logiciel sous Windows pour la Génétique des Populations. Laboratoire Génome, Populations, Interactions, CNRS UMR 5171, Université de Montpellier, France.
7. Booth DB, Troost KG, Clague JJ, Waitt RB, (2004) The cordilleran ice sheet. In: The Quaternary Period in the United States (eds, Gillespie AR, Porter SC, Atwater BF,), pp. 17-44. Elsevier Press, Elsevier, Amsterdam.
8. Braconnot P, Otto-Bliesner B, Harrison S, et al,. (2007) Results of PMIP2 coupled simulations of the Mid-Holocene and Last Glacial Maximum†"Part 1: experiments and large-scale features. Climate of the Past, 3, 261-277.
9. Buckley TR, Cordeiro M, Marshall DC, Simon C, (2006) Differentiating between hypotheses of lineage sorting and introgression in New Zealand alpine cicadas (Maoricicada Dugdale). Systematic Biology, 55, 411-425.
10. Carstens BC, Knowles LL, (2007) Shifting distributions and speciation: species divergence during rapid climate change. Molecular Ecology, 16, 619-627.
11. Carstens B, Richards CL, (2007) Integrating coalescent and ecological niche modelling in comparative phylogeography. Evolution, 61, 1439-1454.
12. Chesser RK, Baker RJ, (1996) Effective sizes and dynamics of uniparentally and diparentally inherited genes. Genetics, 144, 1225-1236.
13. Clement M, Posada D, Crandall KA, (2000) TCS: A computer program to estimate gene genealogies. Molecular Ecology, 9, 1657-1659.
14. Cooper SJB, Harvey MS, Saint KM, Main BY, (2011) Deep phylogeographic structuring of population of the trapdoor spide Moggridgea tingle (Migidae) from southwestern Australia: evidence for long-term refugia within refugia. Molecular Ecology, 20, 3219-3236.
15. Crottini A, Galimberti A, Boto A, et al,. (2010) Toward a resolution of a taxonomic enigma: first genetic analyses of Paradoxornis webbianus and Paradoxornis alphonsianus (Aves: Paradoxornithidae) from China and Italy. Molecular Phylogenetics and Evolution, 57, 1312-1318.
16. Del Hoyo J, Elliott A, Christie DA, (2007) Handbook of the Birds of the World, Vol.12. Lynx Edicions, Barcelona, Spain.
17. Drummond AJ, Rambaut A, (2006) Beast V1.4 Bayesian Evolutionary Analysis Sampling Trees. Available at: http://beast.bio.ed.ac.uk/Main-Page.
18. Drummond AJ, Simon YWH, Phillips MJ, Rambaut A, (2006) Relaxed phylogenetics and dating with confidence. Plos Biology, 4, e88.
19. Edwards ME, Anderson PM, Brubaker LB, et al,. (2000) Pollen-based biomes for Beringia 18 000, 6000 and 0.14C yr BY. Journal of Biogeography, 27, 621-634.
20. Elias SA, (1996) The Ice Age History of National Parks in the Rocky Mountains. Smithsonian Institution Press, Washington, DC.
21. Excoffier L, Laval G, Schneider S, (2005) Arlequin ver. 3.0: An integrated software package for population genetics data analysis. Evolutionary Bioinformatics Online, 1, 47-50.
22. Felsenstein J, (1993) PHYLIP (Phylogeny Inference Package), Version 3.5. Distributed by the author. Department of Genetics, University of Washington, Seattle, Washington.
23. Fu YX, (1997) Statistical tests of neutrality of mutations against population growth, hitchhiking and background selection. Genetics, 147, 915-925.
24. Funk DJ, Omland KE, (2003) Species-level paraphyly and polyphyly: frequency, causes, and consequences, with insights from animal mitochondrial DNA. Annual Review of Ecology, Evolution and Systematics, 34, 397-423.
25. Goudet J, (1995) FSTAT version 1.2: a computer program to calculate F-statistics. Journal of Heredity, 86, 485-486.
26. Gow JL, Peichel CL, Taylor EB, (2006) Contrasting hybridization rates between sympatric three spine sticklebacks highlight the fragility of reproductive barriers between evolutionarily young species. Molecular Ecology, 15, 739-752.
27. Guindon S, Gascuel O, (2003) A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood. Systematic Biology, 52, 696-704.
28. 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.
29. Hewitt GM, (2000) The genetic legacy of the Quaternary ice ages. Nature, 405, 907-913.
30. 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.
31. 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.
32. Hewitt GM, (2004) Genetic consequences of climatic oscillations in the Quaternary. Philosophical Transactions of the Royal Society of London, Series B Biological Sciences, 359, 183-195.
33. 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.
34. Hoelzer GA, (1997) Inferring phylogenies from mtDNA variation: mitochondrial-genes trees versus nuclear-gene trees revisited. Evolution, 51, 622-626.
35. Holder MT, Anderson JA, Holloway AK, (2001) Difficulties in detecting hybridization. Systematic Biology, 50, 978-982.
36. Hudson RR, (1987) Estimating the recombination parameter of a finite population-model without selection. Genetics Research, 50, 245-250.
37. Hudson RR, (1990) Gene genealogies and the coalescent process. Oxford Surveys in Evolutionary Biology, 7, 1-44.
38. Huelsenbeck JP, Rannala B, (2004) Frequentist properties of Bayesian posterior probabilities of phylogenetic trees under simple and complex substitution models. System Biology, 53, 904-913.
39. Joly S, McLenachan PA, Lockhart PJ, (2009) A statistical approach for distinguishing hybridization and incomplete lineage sorting. The American Naturalist, 174, 2.
40. Kimball RT, Braun EL, Barker FK, et al,. (2009) A well-tested set of primers to amplify regions spread across the avian genome. Molecular Phylogenetics and Evolution, 50, 654-660.
41. Klicka J, Zink RM, (1997) The importance of recent ice ages in speciation: a failed paradigm. Science, 277, 1666-1669.
42. Knowles LL, (2000) Tests of Pleistocene speciation in montane grasshoppers (genus Melanoplus) from the sky islands of western North America. Evolution, 54, 1337-1348.
43. Knowles LL, (2001) Did the Pleistocene glaciations promote divergence? Tests of explicit refugial models in montane grasshoppers. Molecular Ecology, 10, 691-701.
44. Kuhner M, Yamato J, Felsenstein J, (1998) Maximum likelihood estimation of population growth rates based on the coalescent. Genetics, 149, 429-434.
45. Lee JW, Kim MS, Burke T, Hatchwell BJ, (2009a) Extrapair paternity in a flock-living passerine, the vinous-throated parrotbill Paradoxornis webbianus. Journal of Avian Biology, 40, 469-474.
46. Lee JW, Jang BS, Dawson DA, Burke T, Hatchwell BJ, (2009b) Fine-scale genetic structure and its consequence in breeding aggregations of a passerine bird. Molecular Ecology, 18, 2728-2739.
47. Lee JW, Simeoni M, Burke T, Hatchwell BJ, (2010a) The consequences of winter flock demography for genetic structure and inbreeding risk in vinous-throated parrotbills, Paradoxornis webbianus. Heredity, 104, 472-481.
48. Lee JW, Lee YK, Hatchwell BJ, (2010b) Natal dispersal and philopatry in a group-living but noncooperative passerine bird, the vinous-throated parrotbill. Animal Behaviour, 79, 1017-1023.
49. Li SH, Yeung CKL, Feinstein J, et al,. (2009) Sailing through the Late Pleistocene: unusual historical demography of an East Asian endemic, the Chinese Hwamei (Leucodioptron canorum canorum), during the last glacial Period. Molecular Ecology, 18, 622-633.
50. Li JW, Yeung CKL, Tsai PW, et al,. (2010) Rejecting strictly allopatric speciation on a continental island: prolonged postdivergence gene flow between Taiwan (Leucodioptron taewanus, Passeriformes Timaliidae) and Chinese (L. canorum canorum) hwameis. Molecular Ecology, 19, 494-507.
51. MacKinnon J, Phillipps K, He F, (2000) A Field Guide of the Birds of China. Oxford University Press, New York.
52. Maddison WP, Knowles LL, (2006) Inferring phylogeny despite incomplete lineage sorting. Systematic Biology, 55, 21-30.
53. Maddison WP, Maddison DR, (2008) Mesquite: A Modular System for Evolutionary Analysis, Version 2.5. Available at: http://mesquiteproject.org.
54. McDonald JH, Kreitman M, (1991) Adaptive protein evolution at the Adh locus in Drosophila. Nature, 351, 652-654.
55. Muir G, Schlötterer C, (2005) Evidence for shared ancestral polymorphism rather than recurrent gene flow at microsatellite loci differentiating two hybridizing oaks (Quercus spp.). Molecular Ecology, 14, 549-561.
56. van Oosterhout C, Hutchinson WF, Wilis DPM, Shipley P, (2004) Micro-checker: software for identifying and correcting genotyping errors in microsatellite data. Molecular Ecology Notes, 4, 535-538.
57. Otto-Bliesner BL, Marshall SJ, Overpeck JT, Miller GH, Hu A, CAPE Last Interglacial Project Members (2006) Simulating arctic climate warmth and ice field retreat in the last interglaciation. Science, 311, 1751-1753.
58. Phillips SJ, Anderson RP, Schapire RE, (2006) Maximum entropy modeling of species geographic distributions. Ecological Modeling, 190, 231-259.
59. Pielou EC, (1991) After the Ice Age: The Return of Life to Glaciated North America. University of Chicago Press, Chicago, Illinois.
60. Pierce KL, (2004) Pleistocene glaciations of the Rocky Mountains. In: The Quaternary Period in the United States (eds, Gillespie AR, Porter SC, Atwater BF,), pp. 63-76. Elsevier Press, Elsevier, Amsterdam.
61. Posada D, Crandall KA, (1998) Modeltest: Testing the model of DNA substitution. Bioinformatics, 14, 817-818.
62. Posada D, Crandall KA, (2001) Intraspecific gene genealogies: trees grafting into networks. Trends in Ecology and Evolution, 16, 37-45.
63. Primmer CR, Borge T, Lindell J, Satre GP, (2002) Single-nucleotide polymorphism characterization in species with limited available sequence information: high nucleotide diversity revealed in the avian genome. Molecular Ecology, 11, 603-612.
64. Pritchard JK, Stephens M, Donnelly P, (2000) Inference of population structure using multilocus genotype data. Genetics, 155, 945-959.
65. Qu YH, Ericson PGP, Lei FM, Li SH, (2005) Post-glacial colonization of the Qinghai-Tibetan plateau inferred from matrilineal genetic structure of the endemic red-necked snow finch, Pyrgilauda ruficollis. Molecular Ecology, 14, 1767-1781.
66. Qu YH, Lei FM, Zhang RY, Lu X, (2010) Comparative phylogeography of five avian species: implications for Pleistocene evolutionary history in the Qinghai-Tibetan plateau. Molecular Ecology, 19, 338-351.
67. Qu YH, Luo X, Zhang RY, Song G, Zou FS, Lei FM, (2011) Lineage diversification and historical demography of a montane bird Garrulax elliotiiâ€"implications for the Pleistocene evolutionary history of the eastern Himalayas. BMC Evolutionary Biology, 11, 174.
68. Rambaut A, (2008) FigTree v.1.1.2. Available at: http://tree.bio.ed.ac. uk/software/figtree/.
69. Rambaut A, Drummond AJ, (2005) Tracer V1.3. Available at: http://beast.bio.ed.ac.uk/tracer.
70. Redenbach Z, Taylor EB, (2002) Evidence for historical introgression along a contact zone between two species of charr (pisces: Salmonidae) in North-western North America. Evolution, 56, 1021-1035.
71. Rozas J, Sánchez-De I, Barrio JC, Messeguer X, Rozas R, (2009) DnaSP, DNA polymorphism analyses by the coalescent and other methods. Bioinformatics, 19, 2496-2497.
72. Saitou N, Nei M, (1987) The neighbor-joining methodâ€"a new method for reconstructing phylogenetic trees. Molecular Biology and Evolution, 4, 406-425.
73. Sang T, Zhong Y, (2000) Testing hybridization hypotheses based on incongruent gene trees. Systematic Biology, 49, 422-434.
74. Sefc KM, Payne RB, Sorenson MD, (2005) Genetic continuity of brood-parasitic indigobird species. Molecular Ecology, 14, 1407-1419.
75. Song G, Qu YH, Yin ZH, Li SH, Liu N, Lei FM, (2009) Phylogeography of the Alcippe morrisonia (Aves: Timaliidae): ling population history beyond late Pleistocene glaciations. BMC Evolutionary Biology, 9, 143.
76. Stephens M, Scheet P, (2005) Accounting for decay of linkage disequilibrium in haplotype inference and missing data imputation. The American Journal of Human Genetics, 76, 449-462.
77. Stephens M, Smith N, Donnelly P, (2001) A new statistical method for haplotype reconstruction from population data. American Journal of Human Genetics, 68, 978-989.
78. Tajima F, (1989) Statistical method for testing the neutral mutation hypothesis by DNA polymorphism. Genetics, 123, 3585-3595.
79. Tegelstrom H, (1987) Transfer of mitochondrial DNA from the northern red-backed vole (Clethnonomys rutilus) to the bank vole (C. ghreoh). Journal of Molecular Evolution, 24, 218-227.
80. Templeton AR, Crandall KA, Sing CF, (1992) A cladistic analysis of phenotypic associations with haplotypes inferred from restriction endonuclease mapping and DNA sequence data. III. Cladogram estimation. Genetics, 132, 619-633.
81. Walker D, Avise JC, (1998) Principles of phylogeography as illustrated by freshwater and terrestrial turtles in the southeastern United States. Annual Review of Ecology, Evolution, and Systematics, 29, 23-58.
82. Watterson GA, (1975) On the number of segregating sites in genetic models without recombination. Theoretical Population Biology, 7, 256-276.
83. Webb III, Shuman TB, Williams JW, (2004) Climatically forced vegetation dynamics in eastern North America during the late quaternary period. In: The Quaternary Period in the United States (eds, Gillespie AR, Porter SC, Atwater BF,), pp. 459-478. Elsevier Press, Elsevier, Amsterdam.
84. Weckstein JD, Zink RM, Blackwell-Rago RC, Nelson DA, (2001) Anomalous variation in mitochondrial genomes of White-crowned (Zonotrichia leucophrys) and Golden-crowned (Z. atricapilla) sparrows: pseudogenes, hybridization, or incomplete linage sorting? Auk, 118, 231-236.
85. Weir JT, Schluter D, (2008) Calibrating the avian molecular clock. Molecular Ecology, 17, 2321-2328.
86. Wendel JE, Doyle JJ, (1998) Phylogenetic incongruence: window into genome history and molecular evolution. In: Molecular Systematics of Plants, II: DNA Sequencing (eds, Soltis D, Soltis P, Doyle J,), pp. 265-296. Kluwer Academic Publishers, Boston, Massachusetts.
87. Willis SC, Nunes M, Montana CG, Farisa IP, Orti G, Lovejoy NR, (2010) The Casiquiare river acts a corridor between the Amazonas and Orinoco river basins: biogeographic analysis of the genus Cichla. Molecular Ecology, 19, 1014-2030.
88. Wilson PJ, Grewal S, Lawford ID, et al,. (2000) DNA profiles of the eastern Canadian wolf and the red wolf provide evidence for a common evolutionary history independent of the gray wolf. Canadian Journal of Zoology, 78, 2156-2166.
89. Won YJ, Hey J, (2005) Divergence population genetics of chimpanzees. Molecular Biology and Evolution, 22, 297-307.
90. Yeung CKL, Lin RC, Lei FM, et al,. (2011) Beyond a morphological paradox: complicated phylogentic relationship of the parrotbills (Paradoxornithidae, Aves). Molecular Phylogenetics and Evolution, 61, 192-202.
91. Zhang DX, Hewitt GM, (2003) Nuclear DNA analyses in genetic studies of populations: practice, problems and prospects. Molecular Ecology, 12, 563-584.
92. Zhang W, Cui Z, Li Y, (2006) Review of the timing and extent of glaciers during the last glacial cycle in the bordering mountains of Tibet and in East Asia. Quaternary International, 154-155, 32-43.