Phylogeography and demographic history of Chinese black-spotted frog populations (Pelophylax nigromaculata): Evidence for independent refugia expansion and secondary contact

BMC Evolutionary Biology

Volumn 8, Issue 1, 2008, Pages

  Zhang, Hua ^a   Yan, Jie ^a   Zhang, Guoqiang ^a   Zhou, Kaiya ^a  

^a NANJING NORMAL UNIVERSITY   (China)

Author keywords

[No Author keywords available]

Indexed keywords

NUCLEOTIDE; CYTOCHROME B; MITOCHONDRIAL DNA;

ARTICLE; BLACK SPOTTED FROG; CHINA; DEMOGRAPHY; EVOLUTION; FROG; GENE FLOW; GENETIC LINKAGE; GENETIC VARIABILITY; GLACIAL PERIOD; HAPLOTYPE; INTER SIMPLE SEQUENCE REPEAT; INTROGRESSION; MITOCHONDRION; NONHUMAN; NUCLEOTIDE SEQUENCE; PARSIMONY ANALYSIS; PELOPHYLAX NIGROMACULATA; PHYLOGENY; PLEISTOCENE; POLYMERASE CHAIN REACTION; POPULATION; SEQUENCE ANALYSIS; ANIMAL; GENE; GENETICS; GEOGRAPHY; MOLECULAR EVOLUTION; RESTRICTION FRAGMENT LENGTH POLYMORPHISM;

ANURA; MYA; RANA NIGROMACULATA; VERTEBRATA;

ANIMALS; CHINA; CYTOCHROMES B; DEMOGRAPHY; DNA, MITOCHONDRIAL; EVOLUTION, MOLECULAR; GEOGRAPHY; HAPLOTYPES; NESTED GENES; PHYLOGENY; POLYMERASE CHAIN REACTION; POLYMORPHISM, RESTRICTION FRAGMENT LENGTH; RANIDAE; VARIATION (GENETICS);

EID: 40449108635     PISSN: None     EISSN: 14712148     Source Type: Journal    
DOI: 10.1186/1471-2148-8-21     Document Type: Article

References (61)

1. Some genetic consequences of ice ages, and their role in divergence and speciation. GM Hewitt, Biol J Linn Soc 1996 58 247 276
2. The genetic legacy of the Quaternary ice ages. G Hewitt, Nature 2000 405 6789 907 913 10.1038/35016000 10879524
3. Speciation durations and Pleistocene effects on vertebrate phylogeography. JC Avise D Walker GC Johns, Proc Biol Sci 1998 265 1407 1707 1712 9787467 10.1098/rspb.1998.0492
4. Pleistocene phylogeographic effects on avian populations and the speciation process. JC Avise D Walker, Proc Bio Sci 1998/05/07 1998 265 1395 457 463 10.1098/rspb.1998.0317
5. The tempo of avian diversification: a comment on Johnson and Cicero. RM Zink J Klicka, Evolution 2006/04/14 2006 60 2 411 412 16610332
6. The tempo of avian diversification: Reply. C Cicero NK Johnson, Evolution 2006 60 2 413 414
7. Glacial cycles and the tempo of avian speciation. IJ Lovette, Trends Ecol Evol 2006/05/17 2005 20 2 57 59 10.1016/j.tree.2004.11.011 16701342
8. Zoogeography of China. RZ Zhang, Beijing, Science Press 1999
9. Geological events and mammalian distribution in China. RZ Zhang, Acta Zoologica Sinica 2002 48 2 141 153
10. Geography of Asia. DS Liu ZG Li, Beijing, Commercial Press 1996
11. Key to Chinese Amphibia. L Fei CY Ye YZ Huang, Chongqing, Chongqing Branch, Science and Technology Literature Publishing House 1990
12. Evolutionary relationships among Chinese ranid frogs inferred from mitochondrial DNA sequences of 12S rRNA gene. JP Jiang KY Zhou, Acta Zoologica Sinica 2001 47 1 38 44
13. Phylogenetic relationships among Chinese ranids: inferred from sequence data set of 12S and 16S rDNA. JP Jiang KY Zhou, Herpe J 2005 15 1 1 8
14. The amphibian tree of life. DR Frost T Grant J Faivovich RH Bain A Haas CFB Haddad RO De Sá A Channing M Wilkinson SC Donnellan CJ Raxworthy JA Campbell BL Blotto P Moler RC Drewes RA Nussbaum JD Lynch DM Green WC Wheeler, Bulletin of the AMNH 2006 297 1 370
15. Phylogeny of Raninae (Anura: Ranidae) inferred from mitochondrial and nuclear sequences. J Che J Pang H Zhao GF Wu EM Zhao YP Zhang, Mol Phylogenet Evol 2007 43 1 1 13 10.1016/j.ympev.2006.11.032 17300963
16. Mitochondrial DNA diversity and preliminary biogeographic inference of the evolutionary history of the black-spotted pond frog Rana nigromaculata populations in China. YH Yang DX Zhang YM Li JY J., Acta Zoologica Sinica 2004 50 2 193 201
17. Population genetic structure of Pelophylax nigromaculata in Chinese mainland, based on mtDNA control region sequences. XF Zhang KY Zhou Q Chang, Acta Genetica Sinica 2004 31 11 1232 1240 15651675
18. Nested clade analyses of phylogeographic data: testing hypotheses about gene flow and population history. AR Templeton, Mol Ecol 1998 7 4 381 397 10.1046/j.1365-294x.1998.00308.x 9627999
19. Population growth makes waves in the distribution of pairwise genetic differences. AR Rogers H Harpending, Mol Biol Evol 1992 9 3 552 569 1316531
20. Phylogeography: The History and Formation of Species. JC Avise, Cambridge, Harvard University Press 2000
21. Sequence variation and structural conservation in the D-loop region and flanking genes of mitochondrial DNA from Japanese pond frogs. M Sumida H Kaneda Y Kato Y Kanamori H Yonekawa M Nishioka, Genes Genet Syst 2000 75 2 79 92 10.1266/ggs.75.79 10925786
22. Asynchronous maximum advances of mountain and continental glaciers. A Gillespie P Molnar, Rev Geophys 1995 33 3 311 364 10.1029/95RG00995
23. High degree of population subdivision in a widespread amphibian. JU Palo DS Schmeller A Laurila CR Primmer SL Kuzmin J Merila, Mol Ecol 2004 13 9 2631 2644 10.1111/j.1365-294X.2004.02269.x 15315676
24. Phylogeography of the canyon treefrog, Hyla arenicolor (Cope) based on mitochondrial DNA sequence data. PH Barber, Mol Ecol 1999 8 4 547 562 10.1046/j.1365-294x.1999.00593.x 10327656
25. Genetic consequences of Pleistocene glaciations for the tundra vole (Microtus oeconomus) in Beringia. KE Galbreath JA Cook, Mol Ecol 2004 13 1 135 148 10.1046/j.1365-294X.2004.02026.x 14653795
26. Discordant temporal and geographic patterns in maternal lineages of eastern north American frogs, Rana catesbeiana (Ranidae) and Pseudacris crucifer (Hylidae). JD Austin SC Lougheed PT Boag, Mol Phylogenet Evol 2004 32 3 799 816 10.1016/j.ympev.2004.03.006 15288057
27. Phylogeography of the tailed frog (Ascaphus truei): Implications for the biogeography of the Pacific Northwest. M Nielson K Lohman J Sullivan, Evolution 2001 55 1 147 160 11263735
28. Geography of the Vegetation in Northeast China. YL Zhou, Beijing, Science Press 1997
29. On the complex of the Stegodon-Ailuropoda-Fauna of Southern China and the chronological position of Gigantopithecus blacki v. Koenigswald. HD Kahlke, Vertebrate Palastatica 1961 5 2 83 108
30. On the dispersal events of Mammuthus during the late Late Pleistocene. CZ Jin QQ Xu JJ Zheng, Vertebrate Palastatica 1998 36 1 47 53
31. Relict distribution of land vertebrates and Quaternary glaciation in China. RZ Zhang, Acta Zoologica Sinica 2004 50 5 841 851
32. Review and prospects of Quaternary glaciation research in China. JJ Li Q Shu SZ Zhou ZJ Zhao JM Zhang, J Glaciol Geocryol 2004 26 3 235 243
33. The research of the geographic distribution of the rare and endangered plants in Sichuan and their characteristics of flora. J Zeng YC Liu, Journal of Chongqing Teachers College 1995 12 4 39 47
34. Geochemical Evidence for Quaternary Sea-level Changes. RL Edwards KB Cutler H Cheng CD Gallup, Treatise on Geochemistry 2003 6 343 364
35. Deglacial sea-level record from Tahiti corals and the timing of global meltwater discharge. E Bard B Hamelin M Arnold L Montaggioni G Cabioch G Faure F Rougerie, Nature 1996 382 6588 241 244 10.1038/382241a0
36. Island biogeography of the Japanese terrestrial mammal assemblages: an example of a relict fauna. V Millien-Parra JJ Jaeger, J Biogeography 1999 26 5 959 972 10.1046/j.1365-2699.1999.00346.x
37. Main Palaeoclimatic events in the Quaternary. JQ Liu YY Ni GQ Chu, Quatern Sci 2001 21 3 239 248
38. Discussion about the glacier extent and advance/retreat asynchrony during the last glaciation. ZJ Cui W Zhang, J Glaciol Geocryol 2003 25 5 510 516
39. Suture-zones of hybrid interaction between recently joined biotas. CL Remington, Evol Biol 1968 2 321 428
40. Mitochondrial DNA phylogeography of the polytypic North American rat snake (Elaphe obsoleta): A critique of the subspecies concept. FT Burbrink R Lawson JB Slowinski, Evolution 2000 54 6 2107 2118 11209786
41. Historical isolation, range expansion, and secondary contact of two highly divergent mitochondrial lineages in spotted salamanders (Ambystoma maculatum). KR Zamudio WK Savage, Evolution 2003 57 7 1631 1652 12940367
42. Hybridization between multiple fence lizard lineages in an ecotone: locally discordant variation in mitochondrial DNA, chromosomes, and morphology. AD Leaché CJ Cole, Mol Ecol 2007 16 5 1035 1054 10.1111/j.1365-294X.2006. 03194.x 17305859
43. Complete nucleotide sequence and gene rearrangement of the mitochondrial genome of the Japanese pond frog Rana nigromaculata. M Sumida Y Kanamori H Kaneda Y Kato M Nishioka M Hasegawa H Yonekawa, Genes Genet Syst 2001 76 5 311 325 10.1266/ggs.76.311 11817647
44. The CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. JD Thompson TJ Gibson F Plewniak F Jeanmougin DG Higgins, Nucleic Acids Res 1997 25 24 4876 4882 9396791 10.1093/nar/25.24.4876
45. PAUP* - Phylogenetic Analysis Using Parsimony (* and Other Methods. Beta version 4.0b10). DL Swofford, Sunderland, Sinauer Associates.
46. MODELTEST: testing the model of DNA substitution. D Posada KA Crandall, Bioinformatics 1998 14 9 817 818 10.1093/bioinformatics/14.9.817 9918953
47. Confidence limits on phylogenetics: an approach using the bootstrap. J Felsenstein, Evolution 1985 39 783 791 10.2307/2408678
48. Statistical tests of neutrality of mutations. YX Fu WH Li, Genetics 1993 133 3 693 709 8454210
49. Statistical method for testing the neutral mutation hypothesis by DNA polymorphism. F Tajima, Genetics 1989 123 3 585 595 2513255
50. DnaSP version 3: an integrated program for molecular population genetics and molecular evolution analysis. J Rozas R Rozas, Bioinformatics 1999 15 2 174 175 10.1093/bioinformatics/15.2.174 10089204
51. The neutral theory of molecular evolution. M Kimura, Cambridge, Massachusetts, Cambridge University Press 1983
52. A cladistic analysis of phenotypic associations with haplotypes inferred from restriction endonuclease mapping and DNA sequence data. III. Cladogram estimation. AR Templeton KA Crandall CF Sing, Genetics 1992 132 2 619 633 1385266
53. TCS: a computer program to estimate gene genealogies. M Clement D Posada KA Crandall, Mol Ecol 2000 9 10 1657 1659 10.1046/j.1365-294x.2000.01020.x 11050560
54. GeoDis: a program for the cladistic nested analysis of the geographical distribution of genetic haplotypes. D Posada KA Crandall AR Templeton, Mol Ecol 2000 9 4 487 488 10.1046/j.1365-294x.2000.00887.x 10736051
55. Statistical phylogeography: methods of evaluating and minimizing inference errors. AR Templeton, Mol Ecol 2004 13 4 789 809 10.1046/j.1365-294X. 2003.02041.x 15012756
56. ARLEQUIN ver. 2.000 A Software for Population Genetic Data Analysis. S Schnerider D Roessli L Excoffier, Geneva, Genetics and Biometry Laboratory, University of Geneva 2000
57. The effect of change in population size on DNA polymorphism. F Tajima, Genetics 1989 123 3 597 601 2599369
58. Statistical tests of neutrality of mutations against population growth, hitchhiking and background selection. YX Fu, Genetics 1997 147 2 915 925 9335623
59. Distinguishing migration from isolation: A Markov chain Monte Carlo approach. R Nielsen J Wakeley, Genetics 2001 158 2 885 896 11404349
60. POPGENE, the user friendly shareware for population genetic analysis. FC Yeh RC Yang T Boyle, Edmonton, Canada, Molecular Biology and Biotechnology Center, University of Alberta 1999
61. NTSYS-pc, Numerical Taxonomy and Multivariate Analysis System, version 2.1. FJ Rohlf, Setauket, New York, Exeter Software 2000