Comparative phylogeography of five avian species: Implications for Pleistocene evolutionary history in the Qinghai-Tibetan plateau

Molecular Ecology

Volumn 19, Issue 2, 2010, Pages 338-351

  Qu, Y ^a   Lei, F ^a   Zhang, R ^a   Lu, X ^b  

^a INSTITUTE OF ZOOLOGY   (China)

^b WUHAN UNIVERSITY   (China)

Author keywords

Comparative phylogeography; Edge and platform species; Glaciation refugia; Postglacial expansion; Qinghai Tibetan plateau

Indexed keywords

MITOCHONDRIAL DNA;

ANIMAL; ARTICLE; BAYES THEOREM; BIOLOGICAL MODEL; CHINA; COMPARATIVE GENOMIC HYBRIDIZATION; DNA SEQUENCE; GENE FLOW; GENETIC POLYMORPHISM; GENETICS; GEOGRAPHY; MITOCHONDRIAL GENOME; MOLECULAR EVOLUTION; MONTE CARLO METHOD; PHYLOGENY; POPULATION DENSITY; POPULATION DYNAMICS; POPULATION GENETICS; PROBABILITY; SONGBIRD;

ANIMALS; BAYES THEOREM; CHINA; COMPARATIVE GENOMIC HYBRIDIZATION; DNA, MITOCHONDRIAL; EVOLUTION, MOLECULAR; GENE FLOW; GENETICS, POPULATION; GENOME, MITOCHONDRIAL; GEOGRAPHY; MARKOV CHAINS; MODELS, GENETIC; MONTE CARLO METHOD; PHYLOGENY; POLYMORPHISM, GENETIC; POPULATION DENSITY; POPULATION DYNAMICS; SEQUENCE ANALYSIS, DNA; SONGBIRDS;

AVES; CARDUELIS FLAVIROSTRIS; EREMOPHILA (ANGIOSPERM); EREMOPHILA ALPESTRIS; MONTIFRINGILLA ADAMSI; PHOENICURUS OCHRUROS; PYRGILAUDA;

EID: 73949149898     PISSN: 09621083     EISSN: 1365294X     Source Type: Journal    
DOI: 10.1111/j.1365-294X.2009.04445.x     Document Type: Article

References (68)

1. Avise JC (2008) Phylogeography: retrospect and prospect. Journal of Biogeography, 36, 3 15.
2. Beerli P (1997) Migrate 0.7: documentation and program, part of LAMARC. Available at: http://evolution.genetics.washington.
3. Beerli P, Felsenstein J (1999) Maximum-likelihood estimation of migration rates and effective population numbers in two populations using a coalescent approach. Genetics, 152, 763 773.
4. Beheregaray LB (2008) Twenty years of phylogeography: the state of the field and the challenges for the Southern hemisphere. Molecular Ecology, 17, 3754 3774.
5. Clement M, Posada D, Crandall KA (2000) TCS: a computer program to estimate gene genealogies. Molecular Ecology, 9, 1657 1659.
6. Cramp S, Perrins CM (1994) The Birds of the Western Palearctic. Oxford University Press, Oxford, New York, pp. 386.
7. Drovetski SV, Pearson SF, Rohwer S (2005) Streaked horned lark Eremophila alpestric strigata has distinct mitochondrial DNA. Conservation Genetics, 6, 875 883.
8. Drummond AJ, Rambaut A (2006) beast V1.4. Bayesian evolutionary analysis sampling trees. Available at: http://beast.bio.ac.uk.
9. Drummond AJ, Ho SYW, Phillips MJ, Rambaut A (2006) Relaxed phylogenetics and dating with confidence. Public Library of Science, Biology, 4, 0699 0710.
10. Edwards ME, Anderson PM, Brubaker LB et al. (2000) Pollen-based biomes for Beringia 18 000, 6000 and 014 C yr BP. Journal of Biogeography, 27, 521 554.
11. Elenga H, Peyron O, Bonnefille R et al. (2000) Pollen-based biome reconstructions for southern Europe and Africa 18 000 years ago. Journal of Biogeography, 27, 621 634.
12. Endler JA (1977) Geographic Variation, Speciation and Clines. Princeton University Press, Princeton, New Jersey.
13. 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.
14. Fu YX (1997) Statistical tests of neutrality of mutations against population growth, hitchhiking and background selection. Genetics, 147, 915 925.
15. Fu TS (1998) Fauna Sinica. Aves. Vol. 14, Passeriformes: Ploceidae, Fringillidae. Science Press, Beijing.
16. Fu YX, Li WH (1993) Statistical tests of neutrality of mutations. Genetics, 133, 693 709.
17. Gavrilets S (2003) Perspective: model of speciation: what have we learned in 40 years? Evolution, 57, 2197 2215.
18. Gebauer A, Kaiser M (1994) Biology and behavior of General Asiatic snow finches (Montifringilla) and mountain-steppe sparrows (Pyrgilauda). Journal of Ornithology, 135, 55 57.
19. Gillespie A, Molnar P (1995) Asynchronous maximum advances of mountain and continental glaciers. Reviews of Geophysics, 33, 311 365.
20. Hansen MM, Nielsen EE, Mensberg KLD (1997) The problem of sampling families rather than populations: relatedness among individuals in samples of juvenile brown trout Salmo trutta L. Molecular Ecology, 6, 469 474.
21. Hebert PDN, Stoeckle MY, Zemlak TS, Francis CM (2004) Identification of birds through DNA barcodes. PLoS Biology, 2, 1657 1663.
22. 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.
23. Hewitt GM (2000) The genetic legacy of the Quaternary ice ages. Nature, 405, 907 913.
24. 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.
25. Jensen JL, Bohonak AJ, Kelley ST (2005) Isolation by distance, web service. BMC Genetics, 6, 13. v.3.16. Available at: http://ibdws.sdsu.edu/.
26. Ke MH, Sun JZ (1992) Paleoclimate and paleoenvironment of the last glacial stage in Salawusu area of Inner Mongolia. Acta Botanica Sinica, 34, 717 719. (In Chinese with English abstract).
27. Kimura M, Weiss GH (1964) The stepping stone model of population structure and the decrease of genetic correlation with distance. Genetics, 49, 561 576.
28. Klicka J, Zink RM (1997) The importance of recent ice ages in speciation: a failed paradigm. Sciences, 277, 1666 1669.
29. Kong ZC, Liu LS, Du NQ (1981) Neogene-Quaternary PalynoXora from the Kunlun to Tangula range and the uplift of the Qinghai-Xizang Plateau. In : The Comprehensive Scientific Expedition to the Qinghai-Xizang Plateau, Study on the Period, Amplitude and Type of the Uplift of the Qinghai-Xizang Plateau (eds Academia Sinica pp. 78 89. Science Press, Beijing In Chinese)
30. Kuhner M, Yamato J, Felsenstein J (1998) Maximum likelihood estimation of population growth rates based on the coalescent. Genetics, 149, 429 434.
31. Lessa EP, Cook JA, Patton JL (2003) Genetic footprints of demographic expansion in North America, but not Amazonia, during the Late Quaternary. Proceeding of the National Academy of Sciences, USA, 100, 10331 10334.
32. Li JJ (1986) Glaciers of Tibet. Sciences press, Beijing.
33. Li JJ, Fang XM (1999) Uplift of the Qinghai-Tibetan plateau and environmental changes. Chinese Science Bulletin, 44, 2117 2124.
34. Li JJ, Fang XM, Ma HZ (1996) Geomorphological and environmental evolution in the upper reaches of Huanghe River during the late Cenozoic. Science in China Series D, 39, 380 390.
35. Liu J, Yu G, Chen X (2002) Paleoclimatic simulation of 21 ka for the Qinghai-Tibetan plateau and eastern Asia. Climatic Dynamics, 19, 575 583.
36. McAvaney BJ, Bourke W, Puri K (1978) A global spectral model for simulation of the general circulation. Journal of the Atmospheric Sciences, 35, 1557 1583.
37. McDonald JH, Kreitman M (1991) Adaptive protein evolution at the Adh locus in Drosophila. Nature, 351, 652 654.
38. Meng LH, Yang R, Abbott RJ, Miehe G, Hu TH, Liu JQ (2007) Mitochondrial and chloroplast phylogeography of Picea crassifolia Kom. (Pinaceae) in the Qinghai-Tibetan Plateau and adjacent highlands. Molecular Ecology, 16, 4128 4137.
39. Merila J, Bjorklund M, Baker AJ (1997) Historical demography and present day population structure of the greenfinch, Carduelis chloris, an analysis of mtDNA control region sequence. Evolution, 51, 946 956.
40. Nylander JAA (2002) mrmodeltest v.1.0. Program Distributed by the Author. Department of Systematic Zoology, Uppsala University, Uppsala 2002. Available at: http://www.ebc.uu.se/systzoo/staV/nylander.html.
41. Peterson GM (1993) Vegetation and climatic history of the western former Soviet Union. In : Global Climates Since the Last Glacial Maximum (eds Wright HE, Kutzbach JE pp. 169 193. University of Minnesota Press, Minneapolis.
42. Qu YH, Lei FM (2009) Comparative phylogeography of two endemic birds of the Qinghai-Tibetan plateau, white-rumped snow finch (Onychostruthus taczanowskii) and Hume's ground tit (Pseudopodoces humilis). Molecular Phylogenetics and Evolution, 51, 312 326.
43. 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.
44. Rambaut A, Drummond AJ (2005) Tracer V1.3. Available at: http://beast.bio.ed.ac.uk/tracer ].
45. Rising JD, Avise JC (1993) An application of genealogical concordance principles to the taxonomy and evolutionary history of the sharp-tailed sparrow (Ammodramus caudacutus). Auk, 110, 844 856.
46. Rozas J, Sánchez-De I, Barrio JC, Messeguer X, Rozas R (2003) DnaSP, DNA polymorphism analyses by the coalescent and other methods. Bioinformatics, 19, 2496 2497.
47. Sharma MC, Owen LA (1996) Quaternary glacial history of NW Garhwal, central Himalayas. Quaternary Sciences Reviews, 15, 335 365.
48. Shi YF (1996) Timing and height of Qinghai-Xizang plateau uplifting into the cryosphere and its impact on the surrounding areas. In : Study of Evolutionary Process, Environmental Change and Ecological System of Qinghai-Xizang (Tibet) Plateau (eds Expert committee of the Tibet project pp. 36 146. Science Press, Beijing (In Chinese).
49. Shi YF (2002) Characteristics of late Quaternary monsoonal glaciation on the Qinghai-Tibetan plateau and in East Asia. Quaternary International, 97-98, 79 91.
50. Shi YF, Zheng BX, Li SJ (1990) Last glaciation and maximum glaciation in Qinghai-Xizang (Tibet) plateau. Journal of Glaciology and Geocryology, 12, 1 15 In Chinese with English Abstract).
51. Simmonds I (1985) Analysis of the "spinning" of a global circulation model. Journal of Geophysical Research, 90, 5637 5660.
52. Soltis DE, Morris AB, McLachlan J, Manos PS, Soltis PS (2006) Comparative phylogeography of unglaciated eastern North America. Molecular Ecology, 15, 4261 4293.
53. Sorenson MD, Ast JC, Dimcheff DE, Yuri T, Mindell DP (1999) Primers for a PCR-based approach to mitochondrial genome sequencing in birds and other vertebrates. Molecular Phylogenetics and Evolution, 12, 105 114.
54. Takahara H, Sugita S, Harrison SP, Miyoshi N, Morita Y, Uchiyama T (2000) Pollen-based reconstruction of Japanese biomes at 0, 6000 and 18 000 14 °C yr BP. Journal of Biogeography, 27, 665 683.
55. Tarasov PE, Volkova VS, Webb T III. et al. (2000) Last Glacial Maximum biomes reconstructed from pollen and plant pacrofossil data from Northern Eurasia. Journal of Biogeography, 27, 609 620.
56. Thompson RS, Anderson KH (2000) Biomes of western North America at 18 000, 6000 and 14 °C yr BP reconstructed from pollen and packrat middlen data. Journal of Biogeography, 27, 555 584.
57. Voous KH (1962) Die Vogelwelt Europas und Ihre Verbreitung. Parey Verlag, Hamburg.
58. Watterson GA (1975) On the number of segregating sites in genetic models without recombination. Theoretical Population Biology, 7, 256 276.
59. Weir JT, Schluter D (2008) Calibrating the avian molecular clock. Molecular Ecology, 17, 2321 2328.
60. Williams JW, Webb T III., Richard PJH, Newby P (2000) Late quaternary biomes of Canada and the eastern United States. Journal of Biogeography, 27, 585 607.
61. Xue Y, Sellers PJ, Kinter JL, Shukla J (1991) A simplified biosphere model for global climate studies. Journal of Climate, 4, 345 364.
62. Yang SJ, Yin ZH, Ma XM, Lei FM (2006) Phylogeography of ground tit (Pseudopodoces humilis) based on mtDNA: evidence of past fragmentation on the Qinghai-Tibetan plateau. Molecular Phylogenetics and Evolution, 41, 257 265.
63. Yu G, Xue B, Wang SM, Liu J (2000) Lake records and the LGM climate in China. Chinese Sciences Bulletin, 50, 250 255.
64. Zhang D, Liu F, Bing J (2000) Eco-environmental effects of the Qinghai-Tibet plateau uplift during the Quaternary in China. Environmental Geology, 39, 1352 1358.
65. Zhang Q, Chiang TY, George M, Liu JQ, Abbott RJ (2005) Phylogeography of the Qinghai-Tibetan Plateau endemic Juniperus przewalskii (Cupressaceae) inferred from chloroplast DNA sequence variation. Molecular Ecology, 14, 3513 3524. (Pubitemid 43919953)
66. 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.
67. Zheng B, Xu Q, Shen Y (2002) The relationship between climate change and Quaternary glacial cycles on the Qinghai-Tibetan plateau: review and speculation. Quaternary International, 97-98, 93 101.
68. Zhou S, Wang X, Wang J, Xu L (2006) A preliminary study on timing of the oldest Pleistocene glaciation in Qinghai-Tibetan plateau. Quaternary International, 154-155, 44 51.