Significance of pre-Quaternary climate change for montane species diversity: Insights from Asian salamanders (Salamandridae: Pachytriton)

Molecular Phylogenetics and Evolution

Volumn 66, Issue 1, 2013, Pages 380-390

  Wu, Yunke ^a   Wang, Yuezhao ^b   Jiang, Ke ^c   Hanken, James ^a  

^a HARVARD UNIVERSITY   (United States)

^b CHENGDU INSTITUTE OF BIOLOGY   (China)

^c KUNMING INSTITUTE OF ZOOLOGY   (China)

Author keywords

Amphibians; East Asian summer monsoon; Pliocene warming; Range expansion; Temperature buffer zone model

Indexed keywords

MITOCHONDRIAL DNA;

ANIMAL; ARTICLE; BAYES THEOREM; BIODIVERSITY; BIOLOGICAL MODEL; CELL NUCLEUS; CHINA; CLASSIFICATION; CLIMATE CHANGE; DNA SEQUENCE; ENVIRONMENT; GENETICS; MOLECULAR EVOLUTION; PHYLOGENY; POPULATION DYNAMICS; STATISTICAL MODEL; URODELA;

ANIMALS; BAYES THEOREM; BIODIVERSITY; CELL NUCLEUS; CHINA; CLIMATE CHANGE; DNA, MITOCHONDRIAL; ENVIRONMENT; EVOLUTION, MOLECULAR; LIKELIHOOD FUNCTIONS; MODELS, GENETIC; PHYLOGENY; POPULATION DYNAMICS; SEQUENCE ANALYSIS, DNA; URODELA;

AMPHIBIA; PACHYTRITON; SALAMANDRIDAE; SALAMANDROIDEA;

EID: 84870251376     PISSN: 10557903     EISSN: 10959513     Source Type: Journal    
DOI: 10.1016/j.ympev.2012.10.011     Document Type: Article

References (92)

1. An Z., Kutzbach J.E., Prell W.L., Porter S.C. Evolution of Asian monsoons and phased uplift of the Himalayan Tibetan plateau since Late Miocene times. Nature 2001, 411:62-66.
2. An Z., Zhang P., Wang E., Wang S., Qiang X., Li L., Song Y., Chang H., Liu X., Zhou W., Liu W., Cao J., Li X., She J., Liu Y., Ai L. Changes of the monsoon-arid environment in China and growth of the Tibetan Plateau since the Miocene. Quat. Sci. 2006, 26:678-693.
3. Barraclough T.G., Vogler A.P. Detecting the geographical pattern of speciation from species-level phylogenies. Am. Nat. 2000, 155:419-434.
4. Bermingham E., Moritz C. Comparative phylogeography: concepts and applications. Mol. Ecol. 1998, 7:367-369.
5. Bernardo J., Spotila J.R. Physiological constraints on organismal response to global warming: mechanistic insights from clinally varying populations and implications for assessing endangerment. Biol. Lett. 2006, 2:135-139.
6. Bouckaert R.R. DensiTree: making sense of sets of phylogenetic trees. Bioinformatics 2010, 26:1372-1373.
7. Bouton N., Witte F., van Alphen J.J.M., Schenk A., Seehausen O. Local adaptations in populations of rock-dwelling haplochromines (Pisces: Cichlidae) from southern Lake Victoria. Proc. Roy. Soc. B: Biol. Sci. 1999, 266:355-360.
8. Buckley L.B., Jetz W. Environmental and historical constraints on global patterns of amphibian richness. Proc. Roy. Soc. B: Biol. Sci. 2007, 274:1167-1173.
9. Cerling T.E., Harris J.M., MacFadden B.J., Leakey M.G., Quade J., Eisenmann V., Ehleringer J.R. Global vegetation change through the Miocene/Pliocene boundary. Nature 1997, 389:153-158.
10. Clemens S.C., Murray D.W., Prell W.L. Nonstationary phase of the Plio-Pleistocene Asian monsoon. Science 1996, 274:943-948.
11. Cosford J., Qing H., Eglington B., Mattey D., Yuan D., Zhang M., Cheng H. East Asian monsoon variability since the Mid-Holocene recorded in a high-resolution, absolute-dated aragonite speleothem from eastern China. Earth Planet. Sci. Lett. 2008, 275:296-307.
12. Crawford A.J. Huge populations and old species of Costa Rican and Panamanian dirt frogs inferred from mitochondrial and nuclear gene sequences. Mol. Ecol. 2003, 12:2525-2540.
13. Cusimano N., Renner S.S. Slowdowns in diversification rates from real phylogenies may not be real. Syst. Biol. 2010, 59:458-464.
14. Dasmahapatra K.K., Lamas G., Simpson F., Mallet J. The anatomy of a 'suture zone' in Amazonian butterflies: a coalescent-based test for vicariant geographic divergence and speciation. Mol. Ecol. 2010, 19:4283-4301.
15. Drummond A.J., Ho S.Y.W., Phillips M.J., Rambaut A. Relaxed phylogenetics and dating with confidence. Plos Biol. 2006, 4:e88.
16. Drummond A.J., Rambaut A. BEAST: Bayesian evolutionary analysis by sampling trees. BMC Evol. Biol. 2007, 7:214.
17. Edwards S.V., Beerli P. Perspective: gene divergence, population divergence, and the variance in coalescence time in phylogeographic studies. Evolution 2000, 54:1839-1854.
18. Espregueira Themudo G., Babik W., Arntzen J.W. A combination of techniques proves useful in the development of nuclear markers in the newt genus Triturus. Mol. Ecol. Notes 2009, 9:1060-1162.
19. Fei L., Hu S., Ye C., Huang Y. Fauna Sinica. Amphibia 2006, vol. 1. Science Press, Beijing.
20. Fu Y.X., Li W.H. Statistical tests of neutrality of mutations. Genetics 1993, 133:693-709.
21. Gao L.M., Moeller M., Zhang X.M., Hollingsworth M.L., Liu J., Mill R.R., Gibby M., Li D.Z. High variation and strong phylogeographic pattern among cpDNA haplotypes in Taxus wallichiana (Taxaceae) in China and North Vietnam. Mol. Ecol. 2007, 16:4684-4698.
22. Gifford M.E., Kozak K.H. Islands in the sky or squeezed at the top? Ecological causes of elevational range limits in montane salamanders. Ecography 2012, 35:193-203.
23. Guo F. Meso-Cenozoic Nanhua (South China) orogenic belt: subaerial tridirectional orogeny. Acta Geol. Sin. 1998, 72:22-33.
24. Hansen J., Sato M., Ruedy R., Lo K., Lea D.W., Medina-Elizade M. Global temperature change. Proc. Natl. Acad. Sci. USA 2006, 103:14288-14293.
25. Harris N. The elevation history of the Tibetan Plateau and its implications for the Asian monsoon. Palaeogeogr. Palaeocl. 2006, 241:4-15.
26. Harrison T.M., Copeland P., Kidd W.S.F., Yin A. Raising Tibet. Science 1992, 255:1663-1670.
27. Harvey P.H., Rambaut A. Phylogenetic extinction rates and comparative methodology. Proc. Roy. Soc. B: Biol. Sci. 1998, 265:1691-1696.
28. Heled J., Drummond A.J. Bayesian inference of population size history from multiple loci. BMC Evol. Biol. 2008, 8:289.
29. Heled J., Drummond A.J. Bayesian inference of species trees from multilocus data. Mol. Biol. Evol. 2010, 27:570-580.
30. Hewitt G. The genetic legacy of the Quaternary ice ages. Nature 2000, 405:907-913.
31. Hijmans R.J., Cameron S.E., Parra J.L., Jones P.G., Jarvis A. Very high resolution interpolated climate surfaces for global land areas. Int. J. Climatol. 2005, 25:1965-1978.
32. Ho S.Y.W., Shapiro B. Skyline-plot methods for estimating demographic history from nucleotide sequences. Mol. Ecol. Resour. 2011, 11:423-434.
33. Huang S., He S., Peng Z., Zhao K., Zhao E. Molecular phylogeography of endangered sharp-snouted pitviper (Deinagkistrodon acutus; Reptilia, Viperidae) in Mainland China. Mol. Phylogenet. Evol. 2007, 44:942-952.
34. Huelsenbeck J.P., Ronquist F. MRBAYES: Bayesian inference of phylogenetic trees. Bioinformatics 2001, 17:754-755.
35. IPCC, 2007. Climate Change 2007: The physical science basis. contribution of working Group I to the fourth assessment: Report of the intergovernmental panel on climate change. In: Solomon, S., Qin, D., Manning, M., Chen, Z., Marquis, M., Averyt, K.B., Tignor M., Miller H.L. (Eds.), Report of the Intergovernmental Panel on Climate Change. Cambridge University Press, Cambridge and New York.
36. Jia G.D., Peng P.A., Zhao Q.H., Jian Z.M. Changes in terrestrial ecosystem since 30 Ma in East Asia: stable isotope evidence from black carbon in the South China Sea. Geology 2003, 31:1093-1096.
37. Kozak K.H., Graham C.H., Wiens J.J. Integrating GIS-based environmental data into evolutionary biology. Trends Ecol. Evol. 2008, 23:141-148.
38. Kozak K.H., Weisrock D.W., Larson A. Rapid lineage accumulation in a non-adaptive radiation: phylogenetic analysis of diversification rates in eastern North American woodland salamanders (Plethodontidae: Plethodon). Proc. Roy. Soc. B: Biol. Sci. 2006, 273:539-546.
39. Li J., Shu Q., Zhou S., Zhao Z., Zhang J. Review and prospects of Quaternary glaciation research in China. J. Glaciol. Geocryol. 2004, 26:235-243.
40. Li S., Yeung C.K.L., Feinstein J., Han L., Manh Hung L., Wang C., Ding P. 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. 2009, 18:622-633.
41. Librado P., Rozas J. DnaSP v5: a software for comprehensive analysis of DNA polymorphism data. Bioinformatics 2009, 25:1451-1452.
42. Lo Presti R.M., Oberprieler C. Evolutionary history, biogeography and eco-climatological differentiation of the genus Anthemis L. (Compositae, Anthemideae) in the circum-Mediterranean area. J. Biogeogr. 2009, 36:1313-1332.
43. Mayr E. Animal Species and Evolution 1963, Harvard University Press, Cambridge, MA.
44. Milanovich J.R., Peterman W.E., Nibbelink N.P., Maerz J.C. Projected loss of a salamander diversity hotspot as a consequence of projected global climate change. Plos ONE 2010, 5:10.
45. Miralles A., Carranza S. Systematics and biogeography of the neotropical genus Mabuya, with special emphasis on the Amazonian skink Mabuya nigropunctata (Reptilia, Scincidae). Mol. Phylogenet. Evol. 2010, 54:857-869.
46. Moyle R.G., Filardi C.E., Smith C.E., Diamond J. Explosive Pleistocene diversification and hemispheric expansion of a great speciator. Proc. Natl. Acad. Sci. USA 2009, 106:1863-1868.
47. Mueller R.L. Evolutionary rates, divergence dates, and the performance of mitochondrial genes in Bayesian phylogenetic analysis. Syst. Biol. 2006, 55:289-300.
48. Murphy R.W., Fu J.Z., Upton D.E., De Lema T., Zhao E.M. Genetic variability among endangered Chinese giant salamanders, Andrias davidianus. Mol. Ecol. 2000, 9:1539-1547.
49. Nishikawa K., Jiang J., Matsui M. Two new species of Pachytriton from Anhui and Guangxi, China (Amphibia: Urodela: Salamandridae). Curr. Herpetol. 2011, 30:15-31.
50. Nogués-Bravo D. Predicting the past distribution of species climatic niches. Global Ecol. Biogeogr. 2009, 18:521-553.
51. Novacek M.J. 100 million years of land vertebrate evolution: the Cretaceous-Early Tertiary transition. Ann. Mol. Bot. Gard. 1999, 86:230-258.
52. Nylander, J.A.A., 2004. MrModeltest v2. Program Distributed by the Author. Evolutionary Biology Centre, Uppsala University. (accessed 20.06.12). http://www.abc.se/.
53. Özeti N., Wake D.B. The morphology and evolution of the tongue and associated structures in salamanders and newts (Family Salamandridae). Copeia 1969, 1969:91-123.
54. Pamilo P., Nei M. Relationships between gene trees and species trees. Mol. Biol. Evol. 1988, 5:568-583.
55. Patel S., Weckstein J.D., Patane J.S.L., Bates J.M., Aleixo A. Temporal and spatial diversification of Pteroglossus aracaris (AVES: Ramphastidae) in the neotropics: constant rate of diversification does not support an increase in radiation during the Pleistocene. Mol. Phylogenet. Evol. 2011, 58:105-115.
56. Pounds J.A., Bustamante M.R., Coloma L.A., Consuegra J.A., Fogden M.P.L., Foster P.N., La Marca E., Masters K.L., Merino-Viteri A., Puschendorf R., Ron S.R., Sanchez-Azofeifa G.A., Still C.J., Young B.E. Widespread amphibian extinctions from epidemic disease driven by global warming. Nature 2006, 439:161-167.
57. Pybus O.G., Harvey P.H. Testing macro-evolutionary models using incomplete molecular phylogenies. Proc. Roy. Soc. B: Biol. Sci. 2000, 267:2267-2272.
58. Pybus O.G., Rambaut A., Harvey P.H. An integrated framework for the inference of viral population history from reconstructed genealogies. Genetics 2000, 155:1429-1437.
59. Qian H., Ricklefs R.E. Large-scale processes and the Asian bias in species diversity of temperate plants. Nature 2000, 407:180-182.
60. Qiang X., Yang X. Onset and end of the first rainy season in south China. Chin. J. Geophys. 2008, 51:1333-1345.
61. Rambaut, A., 1995. Se-Al: Sequence Alignment Program. Oxford University, Oxford, U.K. (accessed 20.06.12). http://tree.bio.ed.ac.uk/software/seal/.
62. Rambaut, A., Drummond, A.J., 2007. Tracer v1.4. (accessed 20.06.12). http://beast.bio.ed.ac.uk/Tracer.
63. Ravelo A.C., Andreasen D.H., Lyle M., Lyle A.O., Wara M.W. Regional climate shifts caused by gradual global cooling in the Pliocene epoch. Nature 2004, 429:263-267.
64. Roelants K., Gower D.J., Wilkinson M., Loader S.P., Biju S.D., Guillaume K., Moriau L., Bossuyt F. Global patterns of diversification in the history of modern amphibians. Proc. Natl. Acad. Sci. USA 2007, 104:887-892.
65. Rovito S.M., Parra-Olea G., Vasquez-Almazan C.R., Papenfuss T.J., Wake D.B. Dramatic declines in neotropical salamander populations are an important part of the global amphibian crisis. Proc. Natl. Acad. Sci. USA 2009, 106:3231-3236.
66. Salzmann U., Haywood A.M., Lunt D.J. The past is a guide to the future? Comparing Middle Pliocene vegetation with predicted biome distributions for the twenty-first century. Philos. Trans. Roy. Soc. A 2009, 367:189-204.
67. Salzmann U., Williams M., Haywood A.M., Johnson A.L.A., Kender S., Zalasiewicz J. Climate and environment of a Pliocene warm world. Palaeogeogr. Palaeocl. 2011, 309:1-8.
68. Schalk C.M., Luhring T.M. Vagility of aquatic salamanders: implications for wetland connectivity. J. Herpetol. 2010, 44:104-109.
69. Shen Y., Shen D., Mo X. A new species of salamander Pachytriton archospotus from Hunan Province, China (Amphibia, Salamandridae). Acta Zool. Sin. 2008, 54:645-652.
70. Shepard D.B., Burbrink F.T. Lineage diversification and historical demography of a sky island salamander, Plethodon ouachitae, from the Interior Highlands. Mol. Ecol. 2008, 17:5315-5335.
71. Song G., Qu Y., Yin Z., Li S., Liu N., Lei F. Phylogeography of the Alcippe morrisonia (Aves: Timaliidae): long population history beyond late Pleistocene glaciations. BMC Evol. Biol. 2009, 9:143.
72. Stamatakis A. RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models. Bioinformatics 2006, 22:2688-2690.
73. Stuart S.N., Chanson J.S., Cox N.A., Young B.E., Rodrigues A.S.L., Fischman D.L., Waller R.W. Status and trends of amphibian declines and extinctions worldwide. Science 2004, 306:1783-1786.
74. Tajima F. The effect of change in population size on DNA polymorphism. Genetics 1989, 105:437-460.
75. Titus T.A., Larson A. A molecular phylogenetic perspective on the evolutionary radiation of the salamander family Salamandridae. Syst. Biol. 1995, 44:125-151.
76. Utescher T., Bruch A.A., Micheels A., Mosbrugger V., Popova S. Cenozoic climate gradients in Eurasia-a palaeo-perspective on future climate change?. Palaeogeogr. Palaeocl. 2011, 304:351-358.
77. Van Bocxlaer I., Loader S.P., Roelants K., Biju S.D., Menegon M., Bossuyt F. Gradual adaptation toward a range-expansion phenotype initiated the global radiation of toads. Science 2010, 327:679-682.
78. Vieites D.R., Min M.-S., Wake D.B. Rapid diversification and dispersal during periods of global warming by plethodontid salamanders. Proc. Natl. Acad. Sci. USA 2007, 104:19903-19907.
79. Vieites D.R., Nieto-Roman S., Wake D.B. Reconstruction of the climate envelopes of salamanders and their evolution through time. Proc. Natl. Acad. Sci. USA 2009, 106:19715-19722.
80. Wake D.B. What salamanders have taught us about evolution. Annu. Rev. Ecol. Evol. Syst. 2009, 40:333-352.
81. Wake D.B. Facing extinction in real time. Science 2012, 335:1052-1053.
82. Wake D.B., Vredenburg V.T. Are we in the midst of the sixth mass extinction? A view from the world of amphibians. Proc. Natl. Acad. Sci. USA 2008, 105:11466-11473.
83. Weisrock D.W., Macey J.R., Ugurtas I.H., Larson A., Papenfuss T.J. Molecular phylogenetics and historical biogeography among salamandrids of the "true" salamander clade: rapid branching of numerous highly divergent lineages in Mertensiella luschani associated with the rise of Anatolia. Mol. Phylogenet. Evol. 2001, 18:434-448.
84. Wu Y., Wang Y., Jiang K., Chen X., Hanken J. Homoplastic evolution of external coloration in Asian stout newts (Pachytriton) inferred from molecular phylogeny. Zool. Scr. 2010, 39:9-22.
85. Wu Y., Wang Y., Hanken J. Comparative osteology of the genus Pachytriton (Caudata: Salamandridae) from southeastern China. Asian Herpetol. Res. 2012, 3:83-102.
86. Wu Y., Wang Y., Hanken J. New species of Pachytriton (Caudata: Salamandridae) from the Nanling Mountain Range, southeastern China. Zootaxa 2012, 3388:1-16.
87. Xu J., Zou P., Wen C., Li S. Ecological observation on Pachytriton labiatus in Nanling nature reserve of north Guangdong. J. Shaoguan Univ. 2002, 23:83-86.
88. Zachos J., Pagani M., Sloan L., Thomas E., Billups K. Trends, rhythms, and aberrations in global climate 65 Ma to present. Science 2001, 292:686-693.
89. Zhang H., Yan J., Zhang G., Zhou K. Phylogeography and demographic history of Chinese black-spotted frog populations (Pelophylax nigromaculata): evidence for independent refugia expansion and secondary contact. BMC Evol. Biol. 2008, 8:21.
90. Zhang P., Papenfuss T.J., Wake M.H., Qu L., Wake D.B. Phylogeny and biogeography of the family Salamandridae (Amphibia: Caudata) inferred from complete mitochondrial genomes. Mol. Phylogenet. Evol. 2008, 49:586-597.
91. Zhao X., Zeng L., Zeng J., Lei Y. Ecological study on Pachytriton labiatus in Yunshan Forest Park. J. Shaoyang Coll. 1994, 7:147-149.
92. Zheng Y., Fu J., Li S. Toward understanding the distribution of Laurasian frogs: a test of Savage's biogeographical hypothesis using the genus Bombina. Mol. Phylogenet. Evol. 2009, 52:70-83.