Genealogy and demographic history of a widespread amphibian throughout indochina

Journal of Heredity

Volumn 104, Issue 1, 2013, Pages 72-85

  Blair, Christopher ^a,b   Davy, Christina M ^a,b   Ngo, Andre ^a,b   Orlov, Nikolai L ^c   Shi, Hai Tao ^d   Lu, Shun Qing ^e   Gao, Lan ^f   Rao, Ding Qi ^g   Murphy, Robert W ^a,b,d,g  

^a UNIVERSITY OF TORONTO   (Canada)

^b DEPARTMENT OF NATURAL HISTORY   (Canada)

^c ZOOLOGICAL INSTITUTE   (Russian Federation)

^d HAINAN NORMAL UNIVERSITY   (China)

^e HUANGSHAN UNIVERSITY   (China)

^f LANZHOU UNIVERSITY   (China)

^g KUNMING INSTITUTE OF ZOOLOGY   (China)

Author keywords

Climatic shift; Cryptic species; Demographic expansion; Phylogeography; Polypedates leucomystax; Red River; Rhacophoridae; Tibetan Plateau; Vietnam; Whipping frogs

Indexed keywords

CYTOCHROME B; MITOCHONDRIAL DNA;

AMPHIBIA; ANURA; ARTICLE; CLADOGENESIS; CLIMATE; GENEALOGY; GENETIC ISOLATION BY DISTANCE; GENETIC VARIABILITY; GEOGRAPHIC DISTRIBUTION; GEOLOGY; HUMAN; MIOCENE; MOLECULAR CLOCK; NONHUMAN; NUCLEOTIDE SEQUENCE; NULL HYPOTHESIS; PLEISTOCENE; POLYPEDATES LEUCOMYSTAX; POPULATION GENETICS; PRIORITY JOURNAL; SOUTHEAST ASIA; UNINDEXED SEQUENCE;

ANIMALS; ANURA; ASIA, SOUTHEASTERN; BASE SEQUENCE; BAYES THEOREM; BIOLOGICAL EVOLUTION; CLIMATE; COMPUTATIONAL BIOLOGY; DEMOGRAPHY; DNA PRIMERS; DNA, MITOCHONDRIAL; GENETIC VARIATION; GENETICS, POPULATION; GEOGRAPHY; MODELS, GENETIC; MOLECULAR SEQUENCE DATA; PHYLOGENY; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS, DNA;

AMPHIBIA; ANURA; HOMO SAPIENS; HYLIDAE; POLYPEDATES LEUCOMYSTAX; RHACOPHORIDAE;

EID: 84871883170     PISSN: 00221503     EISSN: 14657333     Source Type: Journal    
DOI: 10.1093/jhered/ess079     Document Type: Article

References (83)

1. Abramowski U, Bergau A, Seebach D, Zech R, Glaser B, Sosin P, Kubik PW, Zech W. 2006. Pleistocene glaciations of central Asia: results from 10Be surface exposure ages of erratic boulders from the Pamir (Tajikistan) and the Alay-Turkestan Range (Kyrgyzstan). Quat Sci Rev. 25: 1080-1096.
2. Bain RH, Lathrop A, Murphy RW, Orlov NL, Ho CT, 2003. Cryptic species of a cascade frog from Southeast Asia: taxonomic revisions and descriptions of six new species. Am Mus Novit. 3417: 1-60.
3. Becerra JX. 2005. Timing the origin and expansion of the Mexican tropical dry forest. Proc Natl Acad Sci USA. 102: 10919-10923.
4. Bennett KD. 2004. Continuing the debate on the role of Quaternary environmental change for macroevolution. Philos Trans R Soc Lond B Biol Sci. 359: 295-303.
5. Benton MJ, Ayala FJ. 2003. Dating the tree of life. Science. 300: 1698-1700.
6. Brown RM, Linkem CW, Siler CD, Sukumaran J, Esselstyn JA, Diesmos AC, Iskandar DT, Bickford D, Evans BJ, McGuire JA, et al. 2010. Phylogeography and historical demography of Polypedates leucomystax in the islands of Indonesia and the Philippines: evidence for recent human-mediated range expansion? Mol Phylogenet Evol. 57: 598-619.
7. Bryson RW, Murphy RW, Lathrop A, Lazcano-Villareal D. 2011. Evolutionary drivers of phylogeographic diversity in the highlands of Mexico: a case study of the Crotalus triseriatus species group of montane rattlesnakes. J Biogeogr. 38: 697-710.
8. Che J, Zhou WW, Hu JS, Yan F, Papenfuss TJ, Wake DB, Zhang YP. 2010. Spiny frogs (Paini) illuminate the history of the Himalayan region and Southeast Asia. Proc Natl Acad Sci USA. 107: 13765-13770.
9. Christy MT, Savidge JA, Rodda GH. 2007. Multiple pathways for invasion of anurans on a Pacific island. Divers Distrib. 13: 598-607.
10. Diesmos A, Alcala A, Brown R, Afuang L, Gee G, Sukumaran J, Yaakob N, Tzi Ming L, Chuaynkern Y, Thirakhupt K, et al. 2004. Polypedates leucomystax. In: IUCN 2010. IUCN Red List of Threatened Species. Version 2010.4. Cambridge (UK): IUCN. [cited 2011 January 23]. Available from: http://www.iucnredlist.org.
11. Ding L, Gan XN, He SP, Zhao EM. 2011. A phylogeographic, demographic and historical analysis of the short-tailed pit viper (Gloydius brevicaudus): evidence for early divergence and late expansion during the Pleistocene. Mol Ecol. 20: 1905-1922.
12. Drummond AJ, Ho SY, Phillips MJ, Rambaut A. 2006. Relaxed phylogenetics and dating with confidence. PLoS Biol. 4: e88.
13. Drummond AJ, Rambaut A. 2007. BEAST: Bayesian evolutionary analysis by sampling trees. BMC Evol Biol. 7: 214-221.
14. Drummond AJ, Rambaut A, Shapiro B, Pybus OG. 2005. Bayesian coalescent inference of past population dynamics from molecular sequences. Mol Biol Evol. 22: 1185-1192.
15. Dupanloup I, Schneider S, Excoffier L. 2002. A simulated annealing approach to define the genetic structure of populations. Mol Ecol. 11: 2571-2581.
16. Excoffier L, Laval G, Schneider S. 2005. Arlequin (version 3.0): an integrated software package for population genetics data analysis. Evol Bioinform Online. 1: 47-50.
17. Frost D. Amphibian Species of the World (ASW) [Internet]. 2011 - v5.5. New York: American Museum of Natural History. [cited 2011 January 31]. Available from: http://research.amnh.org/vz/herpetology/amphibia/
18. Fu YX. 1997. Statistical tests of neutrality of mutations against population growth, hitchhiking and background selection. Genetics. 147: 915-925.
19. Haffer J. 1969. Speciation in amazonian forest birds. Science. 165: 131-137.
20. Hall R. 1998. The plate tectonics of Cenozoic SE Asia and the distribution of land and sea. In: Hall R, Holloway JD, editors. Biogeography and geological evolution of SE Asia. Leiden (Netherlands): Backhuys. p. 99-131.
21. Hall TA. 1999. BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucleic Acids Symp Ser. 41: 95-98.
22. Harpending HC. 1994. Signature of ancient population growth in a low-resolution mitochondrial DNA mismatch distribution. Hum Biol. 66: 591-600.
23. Heaney LR. 1991. A synopsis of climatic and vegetational change in Southeast Asia. Clim Change. 19: 53-61.
24. Hewitt G. 2000. The genetic legacy of the Quaternary ice ages. Nature. 405: 907-913.
25. Hoffman EA, Blouin MS. 2004. Evolutionary history of the northern leopard frog: reconstruction of phylogeny, phylogeography, and historical changes in population demography from mitochondrial DNA. Evolution. 58: 145-159.
26. Huang S, He S, Peng Z, Zhao K, Zhao E. 2007. Molecular phylogeography of endangered sharp-snouted pitviper (Deinagkistrodon acutus; Reptilia, Viperidae) in Mainland China. Mol Phylogenet Evol. 44: 942-952.
27. Huang Z, Zhang W, Jiang L. 2005. The characteristics of quaternary climate fluctuation in the tropics of China. Geogr Geo-Inform Sci. 21: 65-70.
28. Huelsenbeck JP, Ronquist F. 2001. MRBAYES: Bayesian inference of phylogenetic trees. Bioinformatics. 17: 754-755.
29. Inger RF, Tan LF. 1996. Checklist of the frogs of Borneo. Raffles B Zool. 44: 551-574.
30. Jensen JL, Bohonak AJ, Kelley ST. 2005. Isolation by distance, web service. BMC Genet. 6: 13. doi: 10.1186/1471-2156-6-13
31. Kuraishi M, Mastui M, Ota H. 2009. Estimation of the origin of Polypedates leucomystax (Amphibia: Anura: Rhacophoridae) introduced to the Ryuku Archipelago, Japan. Pacific Sci. 63: 317-325.
32. Li JT, Che J, Murphy RW, Zhao H, Zhao EM, Rao DQ, Zhang YP. 2009a. New insights to the molecular phylogenetics and generic assessment in the Rhacophoridae (Amphibia: Anura) based on five nuclear and three mitochondrial genes, with comments on the evolution of reproduction. Mol Phylogenet Evol. 53: 509-522.
33. Li SH, Yeung CK, Feinstein J, Han L, Le MH, Wang CX, Ding P. 2009b. Sailing through the Late Pleistocene: unusual historical demography of an East Asian endemic, the Chinese Hwamei (Leucodioptron canorum canorum), during the last glacial period. Mol Ecol. 18: 622-633.
34. Librado P, Rozas J. 2009. DnaSP v5: a software for comprehensive analysis of DNA polymorphism data. Bioinformatics. 25: 1451-1452.
35. Liu CC. 1950. Amphibians of western China. Fieldiana Zool Membr. 2: 1-400.
36. Maeda N, Matsui M. 1999. Frogs and toads of Japan. Revised ed. Tokyo: Bun-khi Sogo Shuppan Co.
37. Mantel N. 1967. The detection of disease cluste and a generalized regression approach. Cancer Res. 27: 209-220.
38. Manthey U, Grossmann W. 1997. Amphibien and reptilien Südostasiens. Münster (Germany): Natur und Tier Verlag.
39. Mao XG, Zhu GJ, Zhang S, Rossiter SJ. 2010. Pleistocene climatic cycling drives intra-specific diversification in the intermediate horseshoe bat (Rhinolophus affinis) in Southern China. Mol Ecol. 19: 2754-2769.
40. Matsui M, Seto T, Utsunomiya T. 1986. Acoustic and karyotypic evidence for specific separation of Polypedates megacephalus from P. leucomystax. J Herpetol. 20: 483-489.
41. Murphy RW, Aguirre-León G. 2002. The non-avian reptiles: origins and evolution. In: Case TJ, Cody ML, Ezcurra E, editors. A new island biogeography of the Sea of Cortés. Oxford: Oxford University Press. p. 181-220.
42. Narins PM, Feng AS, Yong HS, Christensen-Dalsgaard J. 1998. Morphological, behavioral, and genetic divergence of sympatric morphotypes of the treefrog Polypedates leucomystax in peninsular Malaysia. Herpetologica. 54: 129-142.
43. Noonan BP, Gaucher P. 2005. Phylogeography and demography of Guianan harlequin toads (Atelopus): diversification within a refuge. Mol Ecol. 14: 3017-3031.
44. Nylander JAA. 2004. MrModeltest v2. Uppsala (Sweden): Evolutionary Biology Centre, Uppsala University.
45. Orlov NL, Lathrop A, Murphy RW, Cue HT. 2001. Frogs of the family Rhacophoridae (Anura: Amphibia) in the northern Hoang Lien Mountains (Mount Fan Si Pan, Sa Pa District, Lao Cai Province), Vietnam. Russ J Herpetol. 8: 17-44.
46. Outlaw DC, Voelker G. 2008. Pliocene climatic change in insular Southeast Asia as an engine of diversification in Ficedula flycatchers. J Biogeogr. 35: 739-752.
47. Pope CH. 1931. Notes on the amphibians from Fukien, Hainan, and other parts of China. Bull Amer Mus Nat Hist. 61: 397-611.
48. Pybus OG, Harvey PH. 2000. Testing macro-evolutionary models using incomplete molecular phylogenies. Proc Biol Sci. 267: 2267-2272.
49. Rabosky DL. 2006a. LASER: a maximum likelihood toolkit for detecting temporal shifts in diversification rates from molecular phylogenies. Evol Bioinform Online. 2: 273-276.
50. Rabosky DL. 2006b. Likelihood methods for detecting temporal shifts in diversification rates. Evolution. 60: 1152-1164.
51. Rambaut A, Drummond AJ. 2007. Tracer v1.4. Available from: http://beast.bio.ed.ac.uk/Tracer
52. Ramos-Onsins SE, Rozas J, 2002. Statistical properties of new neutrality tests against population growth. Mol Biol Evol. 19: 2092-2100.
53. Reisz RR, Müller J. 2004. Molecular timescales and the fossil record: a paleontological perspective. Trends Genet. 20: 237-241.
54. Riyanto A, Mumpun I, McGuire JA. 2011. Morphometry of striped tree frogs, Polypedates leucomystax (Gravenhorst, 1829) from Indonesia with description of a new species. Russ J Herpetol. 18: 29-35.
55. Rogers AR, Harpending H. 1992. Population growth makes waves in the distribution of pairwise genetic differences. Mol Biol Evol. 9: 552-569.
56. Rousset F. 1997. Genetic differentiation and estimation of gene flow from F-statistics under isolation by distance. Genetics. 145: 1219-1228.
57. Sheridan JA, Bickford D, Su KFD, Meier R. 2010. An examination of call and genetic variation in three wide-ranging Southeast Asian anuran species. Raffles B Zool. 58: 197-207.
58. Shi H, Zhong H, Peng Y, Dong YL, Qi XB, Zhang F, Liu LF, Tan SJ, Ma RZ, Xiao CJ, et al. 2008. Y chromosome evidence of earliest modern human settlement in East Asia and multiple origins of Tibetan and Japanese populations. BMC Biol. 6: 45.
59. Silvestro D, Michalak I. 2011. raxmlGUI: a graphical front-end for RAxML.Org Divers Evol. doi: 10.1007/s13127-011-0056-0
60. Smouse PE, Long JC, Sokal RR. 1986. Multiple regression and correlation extensions of the Mantel test of matrix correspondence. Syst Biol. 35: 627-632.
61. Song G, Qu Y, Yin Z, Li S, Liu N, Lei F. 2009. Phylogeography of the Alcippe morrisonia (Aves: Timaliidae): long population history beyond late Pleistocene glaciations. BMC Evol Biol. 9: 143.
62. Stamatakis A. 2006. RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models. Bioinformatics. 22: 2688-2690.
63. Stamatakis A, Hoover P, Rougemont J. 2008. A rapid bootstrap algorithm for the RAxML Web servers. Syst Biol. 57: 758-771.
64. Stanyon R, Sazzini M, Luiselli D. 2009. Timing the first human migration into eastern Asia. J Biol. 8: 18.
65. Stuart BL, Inger RF, Voris HK. 2006. High level of cryptic species diversity revealed by sympatric lineages of Southeast Asian forest frogs. Biol Lett. 2: 470-474.
66. Tajima F. 1989. Statistical method for testing the neutral mutation hypothesis by DNA polymorphism. Genetics. 123: 585-595.
67. Tamura K, Peterson D, Peterson N, Stecher G, Nei M, Kumar S. 2011. MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Mol Biol Evol. 28: 2731-2739.
68. Thompson JD, Higgins DG, Gibson TJ. 1994. CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res. 22: 4673-4680.
69. Trépanier TL, Lathrop A, Murphy RW. 1999. Rhacophorus leucomystax in Vietnam with an acoustic analysis of advertisement and release calls. Asiat Herpetol Res. 8: 102-106.
70. Verstappen HT. 1997. The effect of climatic change on Southeast Asian geomorphology. J Quat Sci. 12: 413-418.
71. Voris HK. 2000. Maps of Pleistocene sea levels in Southeast Asia: shorelines, river systems and time durations. J Biogeogr. 27: 1153-1167.
72. Welch JJ, Bromham L. 2005. Molecular dating when rates vary. Trends Ecol Evol. 20: 320-327.
73. Wiles GJ. 2000. Recent records of reptiles and amphibians accidentally transported to Guam, Mariana Islands. Micronesica. 32: 285-287.
74. Williams MAJ. 1975. Late Pleistocene tropical aridity synchronous in both hemispheres? Nature. 253: 617-618.
75. Wright S. 1943. Isolation by Distance. Genetics. 28: 114-138.
76. Wynn A, Heyer WR. 2001. Do geographically widespread species of tropical amphibians exist? An estimate of genetic relatedness within the Neotropical frog Leptodactylus fuscus (Schneider 1799). (Anura Leptodactylidae). Trop Zool. 14: 255-285.
77. Zachos J, Pagani M, Sloan L, Thomas E, Billups K. 2001. Trends, rhythms, and aberrations in global climate 65 Ma to present. Science. 292: 686-693.
78. Zhang DR, Chen MY, Murphy RW, Che J, Pang JF, Hu JS, Luo J, Wu SJ, Ye H, Zhang YP. 2010. Genealogy and palaeodrainage basins in Yunnan Province: phylogeography of the Yunnan spiny frog, Nanorana yunnanensis (Dicroglossidae). Mol Ecol. 19: 3406-3420.
79. Zhang H, Yan J, Zhang G, Zhou K. 2008. Phylogeography and demographic history of Chinese black-spotted frog populations (Pelophylax nigromaculata): evidence for independent refugia expansion and secondary contact. BMC Evol Biol. 8: 21.
80. Zhang Y, Shi L. 1993. Phylogeny of rhesus monkeys (Macaca mulatta) as revealed by mitochondrial DNA restriction enzyme analysis. Int J Primatol. 14: 587-605.
81. Zhao H, Wang L, Yuan J. 2007. Origin and time of Qiongzhou Strait. Mar Geol Quat Geol. 27: 33-40.
82. Zhisheng A, Kutzbach JE, Prell WL, Porter SC. 2001. Evolution of Asian monsoons and phased uplift of the Himalaya-Tibetan plateau since Late Miocene times. Nature. 411: 62-66.
83. Zink RM, Klicka J, Barber BR. 2004. The tempo of avian diversification during the Quaternary. Philos Trans R Soc Lond, B, Biol Sci. 359: 215-9.