Complex topographic configuration in the hengduan mountains shaped the phylogeographic structure of chinese white-bellied rats

Journal of Zoology

Volumn 284, Issue 3, 2011, Pages 215-223

  Chen, W ^a,b   Li, Y ^a   Liu, Y ^c   Liu, S ^c   Yue, B ^a  

^a SICHUAN UNIVERSITY   (China)

^b Guangxi Natural History Museum   (China)

^c Academy of Forestry   (China)

Author keywords

Hengduan mountains; Niviventer confucianus; Phylogeography; Pleistocene glaciations

Indexed keywords

CLADISTICS; COMPLEX TERRAIN; DIVERGENCE; GLACIATION; MOUNTAIN REGION; PHYLOGEOGRAPHY; PLEISTOCENE; REFUGIUM; RODENT; TOPOGRAPHIC EFFECT;

CHINA; HENGDUAN MOUNTAINS;

NIVIVENTER CONFUCIANUS; RATTUS;

EID: 79959566824     PISSN: 09528369     EISSN: 14697998     Source Type: Journal    
DOI: 10.1111/j.1469-7998.2011.00797.x     Document Type: Article

References (53)

1. Bekken, D., Schepartz, L.A., Miller-antonio, S., Hou, Y. & Huang, W. (2004). Taxonomic abundance at Panxian Dadong, a middle. Pleistocene Cave in South China. Asian Perspect. 43, 333-359.
2. Chan, H.T. (2004). Geographic variation of Niviventer coxingi in body size and mitochondrial D-loop region. Master thesis, National Chungshan University, Kaohsiung.
3. Chen, W.C., Liu, S.Y., Liu, Y., Chen, S.D., Peng, H.Y., Yue, B.S. & Zhang, X.Y. (2010). The phylogeography of large white-bellied rat (Niviventer excelsior) implicate the influence patterns of Pleistocene glaciations in the Hengduan Mountains. Zool. Sci. 27, 487-493.
4. Cheng, J., Cao, B., Tian, M. & Li, L. (1995). A new record Pleistocene mammalia fauna from Zhoukoudian. Earth Sci. J. China Univ. Geosci. 20, 497-504.
5. Ci, H.X. & Lin, G.H. (2009). Population history of the plateau pika endemic to the Qinghai-Tibetan Plateau based on mtDNA sequence data. J. Zool. 279, 396-403.
6. Clement, M., Posada, D. & Crandall, K.A. (2000). tcs: a computer program to estimate gene genealogies. Mol. Ecol. 9, 1657-1659.
7. Drummond, A.J., Ho, S.Y.W., Phillips, M.J. & Rambaut, A. (2006). Relaxed phylogenetics and dating with confidence. PLoS Biol. 4, e88.
8. Drummond, A.J., Nicholls, G.K., Rodrigo, A.G. & Solomon, W. (2002). Estimating mutation parameters, population history and genealogy simultaneously from temporally spaced sequence data. Genetics 161, 1307-1320.
9. Drummond, A.J. & Rambaut, A. (2007). BEAST: Bayesian evolutionary analysis by sampling trees. BMC Evol. Biol. 7, 214.
10. Excoffier, L., Laval, G. & Schneider, S. (2005). Arlequin Ver.3.0: an integrated software package for population genetics data analysis. Evol. Bioinform. Online 1, 47-50.
11. Felsenstein, J. (1985). Confidence limits on phylogenies: an approach using the bootstrap. Evolution 39, 783-791.
12. Felsenstein, J. (1988). Phylogenies from molecular sequences: inference and reliability. Annu. Rev. Genet. 22, 521-565.
13. Felsenstein, J. (1993). Phylogeny inference package (PHYLIP). Version 3.5. Seattle: University of Washington.
14. Fu, J. & Zeng, X. (2008). How many species are in the genus Batrachuperus? A phylogeographical analysis of the stream salamanders (family Hynobiidae) from southwestern China. Mol. Ecol. 17, 1469-1488.
15. Fu, Y.X. (1997). Statistical tests of neutrality of mutations against population growth, hitchhiking and background selection. Genetics 147, 915-925.
16. Harpending, H.C. (1994). Signature of ancient population growth in a low-resolution mitochondrial DNA mismatch distribution. Hum. Biol. 66, 591-600.
17. Harrison, T.M., Copeland, P., Kidd, W.S.F. & Yin, A. (1992). Raising Tibet. Science 255, 1663-1670.
18. Hsu, F.H., Lin, F.J. & Lin, Y.S. (2000). Phylogeographic variation in mitochondrial DNA of Formosan white-bellied rat Niviventer culturatus. Zool. Stud. 39, 38-46.
19. Huang, F.S., Song, Z.S., Jiang, S.Q. & Wang, B.H. (2006). Biodiversity and environment frangibility in Southeast Tibet, China. Southwest China J. Agric. Sci. 19, 35-39.
20. Irwin, D.M., Kocher, T.D. & Wilson, A.C. (1991). Evolution of the cytochrome b gene of mammals. J. Mol. Evol. 32, 128-144.
21. Jing, M.D., Yu, H.T., Wu, S.H., Wang, W. & Zheng, X.G. (2007). Phylogenetic relationships in genus Niviventer (Rodentia: Muridae) in China inferred from complete mitochondrial cytochrome b gene. Mol. phylogenet. Evol. 44, 521-529.
22. Lehmkuhl, F. & Haselein, F. (2000). Quaternary palaeoenvironmental change on the Tibetan Plateau and adjacent areas (Western China and Western Mongolia). Quat. Int. 65/66, 121-145.
23. Li, J.J. & Fang, X.M. (1999). Uplift of the Tibetan Plateau and environmental changes. Chin. Sci. Bull. 44, 2217-2224.
24. Li, P.P., Lu, Y.Y., Li, J.L., Zhao, H., Hou, M. & Zhang, M.W. (2005). Herpetological surveys of Xizang Autonomous Region 1. From Lhasa to Zayüand Mêdog 62K. Sichuan J. Zool. 24, 245-249.
25. Meng, L.H., Yang, R., Abbott, R.J., Miehe, G., Hu, T.H. & Liu, J.Q. (2007). Mitochondrial and chloroplast phylogeography of Picea crassifolia Kom. (Pinaceae) in the Qinghai-Tibetan Plateau and adjacent highlands. Mol. Ecol. 16, 4128-4137.
26. Musser, G.G. (1981). Results of the Archbold Expeditions No.105. Notes on systematics of Indo-Malayan murid rodents and descriptions of new genera and species from Ceylon, Sulawesi and the Philippines. Bull. Am. Mus. Nat. Hist. 168, 236-256.
27. Musser, G.G. & Carleton, M.D. (1993). Muridae: Arvicolinae. In Mammal species of the world. A taxonomic and geographic reference: 632-635. Wilson, D.E. & Reeder, D.A.M. (Eds). Washington, DC: Smithsonian Institution Libraries and the National Science Foundation.
28. Niu, Y.D., Wei, F.W., Li, M., Liu, X.M. & Feng, Z.J. (2004). Phylogeny of pikas (Lagomorpha, Ochotona) inferred from mitochondrial cytochrome b sequences. Folia. Zool. 53, 141-155.
29. Paillard, D. (1998). The timing of Pleistocene glaciations from a simple multiple-state climate model. Nature 391, 378-381.
30. Posada, D. & Buckley, T. (2004). Model selection and model averaging in phylogenetics: advantages of Akaike information criterion and Bayesian approaches over likelihood ratio tests. Syst. Biol. 53, 793-808.
31. Posada, D. & Crandall, K.A. (1998). Modeltest: testing the model of DNA substitution. Bioinformatics 14, 817-818.
32. Posada, D. & Crandall, K.A. (2001). Intraspecific gene genealogies: trees grafting into networks. Trends Ecol. Evol. 16, 37-45.
33. Qu, Y.H., Ericson, P.G.P., Lei, F.M. & Li, S.H. (2005). Post-glacial colonization of the Tibetan plateau inferred from matrilineal genetic structure of the endemic red-necked snow finch, Pyrgilauda ruficollis. Mol. Ecol. 14, 1767-1781.
34. Qu, Y.H. & Lei, F.M. (2009). Comparative phylogeography of two endemic birds of the Tibetan plateau, the white-rumped snow finch (Onychostruthus taczanowskii) and the Hume's ground tit (Pseudopodoces humilis). Mol. Phylogenet. Evol. 51, 312-326.
35. Rambaut, A. & Drummond, A.J. (2007). Tracer v1.4, Available at
36. Rogers, A.R. & Harpending, H. (1992). Population-growth makes waves in the distribution of pairwise genetic-differences. Mol. Biol. Evol. 9, 552-569.
37. Rozas, J., Sánchez-DelBarrio, J.C., Messeguer, X. & Rozas, R. (2003). DnaSP, DNA polymorphism analyses by the coalescent and other methods. Bioinformatics 19, 2496-2497.
38. Sambrook, E., Fritsch, F. & Maniatis, T. (1989). Molecular cloning: a laboratory manual. Cold Spring Harbour: Cold Spring Harbour Laboratory Press.
39. Schepartz, L.A., Bakken, D.A., Miller-antonio, S., Paraso, C.K. & Karkanas, P. (2003). Faunal approaches to site formation processes at Panxian Dadong. In Current research in Chinese Pleistocene Archaeology: 99-110. Shen, C. & Keates, S.C. (Eds). Oxford: Archaeopress.
40. Shi, Y., Li, J. & Li, B. (1998). Uplift and environmental changes of Qinghai-Xizang (Tibetan) Plateau in the Late Cenozoic. Guangdong: Guangdong Science and Technology Press (in Chinese).
41. Su, Z., Shi, Y.F. & Zheng, B.X. (2002). Quaternary Glacial remains on the Gongga Mountain and the division of Glacial period. Adv. Earth Sci. 17, 639-646.
42. Sun, X.L. & Zheng, D. (1998). Formation, evolution and development of Qinghai-Xizang (Tibetan) plateau. Guangdong: Guangdong Science and Technology Press (in Chinese).
43. *. Sunderland: Sinauer Associates.
44. Tajima, F. (1989). Statistical methods to test for nucleotide mutation hypothesis by DNA polymorphism. Genetics 123, 585-595.
45. Tamura, K., Dudley, J., Nei, M. & Kumar, S. (2007). MEGA4: Molecular Evolutionary Genetics Analysis (MEGA) software version 4.0. Mol. Biol. Evol. 24, 1596-1599.
46. Templeton, A.R., Crandall, K.A. & Sing, C.F. (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.
47. Thompson, J.D., Gibson, T.J., Plewniak, F., Jeanmougin, F. & Higgins, D.G. (1997). The ClustalX windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res. 25, 4876-4882.
48. Wu, Y.Q., Cui, Z.J., Liu, G.N., Ge, D.K., Yin, J.R., Xu, Q.H. & Pang, Q.Q. (2001). Quanternary geomorphological evolution of the Kunlun Pass areas and uplift of the Qinghai-Xizang (Tibet) Plateau. Geomorphology 36, 203-216.
49. Xu, L.B., Zhou, S.Z., Cui, J.X., Wang, J. & David, M. (2004). Dating of the Pleistocene glaciations around the Daocheng ice cap. J. Glaciol. Geocryol. 26, 528-532.
50. Yang, S.J., Lei, F.M., Qu, Y.H. & Yin, Z.H. (2005). Intraspecific phylogeography of the white-rumped snowfinch (Onychostruthus taczanowskii) endemic to the Tibetan Plateau based on mtDNA sequences. J. Zool. 268, 187-192.
51. Yang, S.J., Yin, Z.H., Ma, X.M. & Lei, F.M. (2006). Phylogeography of ground tit (Pseudopodoces humilis) based on mtDNA: evidence of past fragmentation on the Tibetan Plateau. Mol. Phylogenet. Evol. 41, 257-265.
52. Yuan, S.L., Lin, L.L. & Oshida, T. (2006). Phylogeography of the mole-shrew (Anourosorex yamashinai) in Taiwan: implications of interglacial refugia in a high-elevation small mammal. Mol. Ecol. 15, 2119-2130.
53. Zhao, S., Dai, Q. & Fu, J. (2009). Do rivers function as genetic barriers for the plateau wood frog at high elevations? J. Zool. 279, 270-276.