Chloroplast DNA variation and phylogeography of Ligularia tongolensis (Asteraceae), a species endemic to the Hengduan Mountains region of China

Journal of Systematics and Evolution

Volumn 49, Issue 2, 2011, Pages 108-119

  Wang, Jin Feng ^a,b   Pan, Yue Zhi ^a   Gong, Xun ^a   Chiang, Yu Chung ^c   Kuroda, Chiaki ^d  

^a KUNMING INSTITUTE OF BOTANY   (China)

^b UNIVERSITY OF CHINESE ACADEMY OF SCIENCES   (China)

^c NATIONAL SUN YAT SEN UNIVERSITY   (Taiwan)

^d RIKKYO UNIVERSITY   (Japan)

Author keywords

Genetic variation; Ligularia tongolensis; Phylogeography; Quaternary glaciation

Indexed keywords

ASTERACEAE; LIGULARIA TONGOLENSIS;

EID: 79955979454     PISSN: 16744918     EISSN: 17596831     Source Type: Journal    
DOI: 10.1111/j.1759-6831.2011.00117.x     Document Type: Article

References (68)

1. Abbott RJ, Brochmann C. 2003. History and evolution of the arctic flora: In the footsteps of Eric Hultén. Molecular Ecology 12:299-313. (Pubitemid 36144711)
2. Abbott RJ, Smith LC, Milne RI, Crawford RMM, Wolff K, Balfour J. 2000. Molecular analysis of plant migration and refugia in the arctic. Science 289:1343-1346. (Pubitemid 30656049)
3. Abramson NI. 2007. Phylogeography: Results, issues and perspectives. Vogis Herald 11:307-331.
4. Anderson LL, Hu FS, Nelson DM, Petit RJ, Paige KN. 2006. Iceage endurance: DNA evidence of a white spruce refugium in Alaska. Proceedings of the National Academy of Sciences USA 103:12447-12450. (Pubitemid 44267279)
5. Banu S, Bhagwat RM, Kadoo NY, Lagu MD, Gupta VS. 2010. Understanding the genetic structure of Symplocos laurina Wall. populations using nuclear gene markers. Genetica 138:197-210.
6. Birky CW, Fuerst P, Maruyama T. 1989. Organelle gene diversity under migration, mutation, and drift: Equilibrium expectations, approach to equilibrium, effects of heteroplasmic cells, and comparison to nuclear genes. Genetics 121:613-627. (Pubitemid 19077114)
7. Chen SY, Wu GL, Zhang DJ, Gao QB, Duan YZ, Zhang FQ, Chen SL. 2008. Potential refugium on the Qinghai-Tibet Plateau revealed by the chloroplast DNA phylogeography of the alpine species Metagentiana striata (Gentianaceae). Botanical Journal of the Linnean Society 157:125-140.
8. Clement M, Posada D, Crandall KA. 2000. TCS: A computer program to estimate gene genealogies. Molecular Ecology 9:1657-1659.
9. Crandall KA, Templeton AR. 1993. Empirical tests of some predictions from coalescent theory with applications to intraspecific phylogeny reconstruction. Genetics 134:959-969. (Pubitemid 23193592)
10. Donnelly P, Tavaré S. 1986. The ages of alleles and a coalescent. Advances in Applied Probability 18:1-19.
11. Doyle JJ, Doyle JL. 1990. Isolation of plant DNA from fresh tissue. Focus 12:13-15.
12. Drummond AJ, Rambaut A. 2007. BEAST: Bayesian evolutionary analysis by sampling trees. BMC Evolutionary Biology 7:214-221.
13. Dupanloup I, Schneider S, Excoffier L. 2002. A simulated annealing approach to define the genetic structure of populations. Molecular Ecology 11:2571-2581. (Pubitemid 35436677)
14. Ennos RA. 1994. Estimating the relative rates of pollen and seed migration among plant populations. Heredity 72:250-259. (Pubitemid 2057321)
15. Excoffier L, Laval G, Schneider S. 2005. Arlequin (version 3.0): An integrated software package for population genetics data analysis. Evolutionary Bioinformatics Online 1:47-50.
16. Excoffier L, Smouse PE, Quattro JM. 1992. Analysis of molecular variance inferred from metric distances among DNA haplotypes: Application to human mitochondrial DNA restriction data. Genetics 131:479-491.
17. Fehlberg SD, Ranker TA. 2009. Evolutionary history and phylogeography of Encelia farinosa (Asteraceae) from the Sonoran, Mojave, and Peninsular Deserts. Molecular Phylogenetics and Evolution 50:326-335.
18. Fér T, Vašák P, Vojta J, Marhold K. 2007. Out of the Alps or Carpathians? Origin of central European populations of Rosa pendulina. Preslia 79:367-376. (Pubitemid 350253602)
19. Gao LM, Möller M, Zhang XM, Hollingsworth ML, Liu J, Mill RR, Gibby M, Li DZ. 2007. High variation and strong phylogeographic pattern among cpDNA haplotypes in Taxus wal - lichiana (Taxaceae) in China and North Vietnam. Molecular Ecology 16:4684-4698. (Pubitemid 350135216)
20. Grassi F, Minuto L, Casazza G, Labra M, Sala F. 2009. Haplotype richness in refugial areas: Phylogeographical structure of Saxifraga callosa. Journal of Plant Research 122:377-387.
21. Hao RM. 1997. On the areal-types of the Chinese endemic genera of seed plants. Acta Phytotaxonomica Sinica 35:500-510.
22. 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. (Pubitemid 38231471)
23. Jensen JL, Bohonak AJ, Kelley ST. 2005. Isolation by distance, web service. BMC Genetics 6:13. v. 3.16 Available from: http://ibdws.sdsu.edu/ i&tild;bdws/[Accessed 13 February 2011].
24. Li JJ, Fang XM, Pan BT, Zhao ZJ, Song YG. 2001. Late Cenozoic intensive uplift of Qinghai-Xizang Plateau and its impacts on environments in surrounding area. Quaternary Sciences 21:381-391.
25. Li XW. 1994. Two big biodiversity centers of Chinese endemic genera of seed plants and their characteristics in Yunnan Province. Acta Botanica Yunnanica 16:221-227.
26. Liu JQ, Wang YJ, Wang AL, Ohba H, Abbott RJ. 2006. Radiation and diversification within the Ligularia-Cremanthodium-Parasenecio complex (Asteraceae) triggered by uplift of the Qinghai-Tibetan Plateau. Molecular Phylogenetics and Evolution 38:31-49. (Pubitemid 41773272)
27. Liu SW. 1989. Compositae-Senecioneae. Flora Reipublicae Popularis Sinicae. Beijing: Science Press. 77(2).
28. Liu SW, Deng DS, Liu JQ. 1994. Origin, evolution and distribution of Ligularia Cass. (Compositae). Acta Phytotaxonomica Sinica 32:514-525.
29. Liu Z, Ren B, Wei F, Long Y, Hao Y, Li M. 2007. Phylogeography and population structure of the Yunnan snub-nosed monkey (Rhinopithecus bieti) inferred from mitochondrial control region DNA sequence analysis. Molecular Ecology 16:3334-3349. (Pubitemid 47221128)
30. Martinez P, Lopez C, Roldan M, Sabater B, Martin M. 1997. Plastid DNA of five ecotypes of Arabidopsis thaliana: Sequence of ndhG gene and maternal inheritance. Plant Science 123:113-122. (Pubitemid 27123115)
31. Myers N, Mittermeier R, Mittermeier C, Fonseca G, Kent J. 2000. Biodiversity hotspots for conversation priorities. Nature 403:853-858.
32. Ni J, Yu G, Harrison SP, Prentice IC. 2010. Palaeovegetation in China during the late Quaternary: Biome reconstructions based on a global scheme of plant functional types. Palaeogeography, Palaeoclimatology, Palaeoecology 289:44-61.
33. Pan YZ, Gong X, Yang ZY, Yin Q. 2004. Karyological studies on five species of the genus Ligularia (Compositae: Senecioneae). Acta Botanica Yunnanica 26:65-72.
34. Petit RJ, Aguinagalde I, de Beaulieu JL, Bittkau C, Brewer S, Cheddadi R, Ennos R, Fineschi S, Grivet D, Lascoux M. 2003. Glacial refugia: Hotspots but not melting pots of genetic diversity. Science 300:1563-1565. (Pubitemid 36682886)
35. Petit RJ, Hampe A, Cheddadi R. 2005. Climate changes and tree phylogeography in the Mediterranean. Taxon 54:877-885. (Pubitemid 43219437)
36. Petit RJ, Pineau E, Demesure B, Bacilieri R, Ducousso A, Kremer A. 1997. Chloroplast DNA footprints of postglacial recolonization by oaks. Proceedings of the National Academy of Sciences USA 94:9996-10001. (Pubitemid 27408179)
37. Pons O, Petit RJ. 1996. Measuring and testing genetic differentiation with ordered versus unordered alleles. Genetics 144:1237-1245. (Pubitemid 26378263)
38. Posada D, Crandall KA. 1998. Model Test: Testing the model of DNA substitution. Bioinformatics 14:817-818. (Pubitemid 28552116)
39. Rambaut A, Drummond AJ. 2009. Tracer vs. 1.5. MCMC trace analysis tool [online]. Available from http://tree.bio.ed.ac.uk/software/tracer/[Accessed 1 December 2009].
40. Rogers AR. 1995. Genetic evidence for a Pleistocene population explosion. Evolution 49:608-615.
41. Rogers AR, Harpending H. 1992. Population growth makes waves in the distribution of pairwise genetic differences. Molecular Biology and Evolution 9:552-569.
42. Rousset F. 1997. Genetic differentiation and estimation of gene flow from F-statistics under isolation by distance. Genetics 145:1219-1228. (Pubitemid 27149123)
43. Rozas J, Sanchez-Del Barrio JC, Messeguer X, Rozas R. 2003. DnaSP, DNA polymorphism analyses by the coalescent and other methods. Bioinformatics 19:2496-2497. (Pubitemid 38016658)
44. Schaal BA, Hayworth DA, Olsen KM, Rauscher JT, Smith WA. 1998. Phylogeographic studies in plants: Problems and prospects. Molecular Ecology 7:465-474. (Pubitemid 28226693)
45. Schneider S, Excoffier L. 1999. Estimation of past demographic parameters from the distribution of pairwise differences when the mutation rates vary among sites: Application to human mitochondrial DNA. Genetics 152:1079-1089. (Pubitemid 29330907)
46. Shaw J, Lickey EB, Schilling EE, Small RL. 2007. Comparison of whole chloroplast genome sequences to choose noncoding regions for phylogenetic studies in angiosperms: The tortoise and the hare III. American Journal of Botany 94:275-288. (Pubitemid 46955026)
47. Shi YF, Li J, Li B, Yao TD, Wang SM, Li SJ, Cui Z, Wang F, Pan B, Fang X. 1999. Uplift of the Qinghai-Xizang (Tibetan) plateau and east Asia environmental change during late Cenozoic. Acta Geographica Sinica 54:20-28.
48. Shi YF, Li JJ, Li BY. 1998. Uplift and environmental changes of Qinghai-Tibetan Plateau in the late Cenozoic. Guangzhou: Guangdong Science and Technology Press.
49. Soltis DE, Morris AB, McLachlan JS, Manos PS, Soltis PS. 2006. Comparative phylogeography of unglaciated eastern North America. Molecular Ecology 15:4261-4293. (Pubitemid 44749551)
50. Sun H. 2002. Tethys retreat and Himalayas-Hengduanshan Mountains uplift and their significance on the origin and development of the Sino-Himalayan elements and alpine flora. Acta Botanica Yunnanica 24:273-288.
51. Swofford DL. 2002. PAUP*: Phylogenetic analysis using parsimony (*and other methods), version 4.0 b10. Sunderland: Sinauer Associates.
52. Thompson JD, Gibson TJ, Plewniak F, Jeanmougin F, Higgins DG. 1997. The ClustalX windows interface: Flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Research 25:4876-4882. (Pubitemid 28022245)
53. Wang FY, Gong X, Hu CM, Hao G. 2008. Phylogeography of an alpine species Primula secundiflora inferred from the chloroplast DNA sequence variation. Journal of Systematics and Evolution 46:13-22.
54. Wang HS. 2000. The nature of China's flora and the relationships between its different elements. Acta Botanica Yunnanica 22:119-126.
55. Wang HW, Ge S. 2006. Phylogeography of the endangered Cathaya argyrophylla (Pinaceae) inferred from sequence variation of mitochondrial and nuclear DNA. Molecular Ecology 15:4109-4122. (Pubitemid 44607155)
56. Wang J, Raisbeck G, Xu X, Yiou F, Bai S. 2006. In situ cosmogenic 10Be dating of the Quaternary glaciations in the southern Shaluli Mountain on the Southeastern Tibetan Plateau. Science in China Series D: Earth Sciences 49:1291-1298. (Pubitemid 46152136)
57. Wang JF, Kuroda C, Gong X. 2007. Assessment of genetic variation and differentiation of Ligularia tongolensis (Compositae) detected by ISSR. Acta Botanica Yunnanica 29:537-542.
58. Wang LY, Abbott RJ, Zheng W, Chen P, Wang YJ, Liu JQ. 2009. History and evolution of alpine plants endemic to the Qinghai-Tibetan Plateau: Aconitum gymnandrum (Ranunculaceae). Molecular Ecology 18:709-721.
59. Whitlock MC, McCauley DE. 1999. Indirect measures of gene flow and migration: FST≠ 1/(4Nm+ 1). Heredity 82:117-125. (Pubitemid 29120325)
60. Wright S. 1978. Variability within and among natural populations. Chicago: University of Chicago Press.
61. Wu LL, Cui XK, Milne RI, Sun YS, Liu JQ. 2010. Multiple autopolyploidizations and range expansion of Allium przewalskianum Regel. (Alliaceae) in the Qinghai-Tibetan Plateau. Molecular Ecology 19:1691-1704.
62. Xu LB, Zhou SZ. 2009. Quaternary glaciations recorded by glacial and fluvial landforms in the Shaluli Mountains, southeastern Tibetan Plateau. Geomorphology 103:268-275.
63. Xu LB, Zhou SZ, Wang J. 2005. Pleistocene glaciations in the Shaluli Shan and the influences of southwest monsoon on the glaciations during the last glacial period. Quaternary Science 25:620-629.
64. Yamane K, Yano K, Kawahara T. 2006. Pattern and rate of indel evolution inferred from whole chloroplast intergenic regions in sugarcane, maize and rice. DNA Research 13:197-204. (Pubitemid 46026343)
65. Yang FS, Li YF, Ding X, Wang XQ. 2008. Extensive population expansion of Pedicularis longiflora (Orobanchaceae) on the Qinghai-Tibetan Plateau and its correlation with the Quaternary climate change. Molecular Ecology 17:5135-5145.
66. Yang SJ, Yin ZH, Ma XM, Lei FM. 2006. Phylogeography of ground tit (Pseudopodoces humilis) based on mtDNA: Evidence of past fragmentation on the Tibetan Plateau. Molecular Phylogenetics and Evolution 41:257-265.
67. Yuan QJ, Zhang ZY, Peng H, Ge S. 2008. Chloroplast phylogeography of Dipentodon (Dipentodontaceae) in southwest China and northern Vietnam. Molecular Ecology 17:1054-1065. (Pubitemid 351197361)
68. Zhou SZ, Xu LB, Cui JX, Zhang XW, Zhao JD. 2005. Geomorphologic evolution and environmental changes in the Shaluli Mountain region during the Quaternary. Chinese Science Bulletin 50:52-57.