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

Volumn 157, Issue 1, 2008, Pages 125-140

  Chen, Shengyun ^a,b   Wu, Guili ^c   Zhang, Dejun ^a,b   Gao, Qingbo ^a,b   Duan, Yizhong ^a,b   Zhang, Faqi ^a,b   Chen, Shilong ^a  

^a NORTHWEST INSTITUTE OF PLATEAU BIOLOGY   (China)

^b UNIVERSITY OF CHINESE ACADEMY OF SCIENCES   (China)

^c LANZHOU UNIVERSITY   (China)

Author keywords

Hengduan Mountain; Qilianshan Mountains; trnS trnG

Indexed keywords

ALLOPATRY; ANCESTRY; ANGIOSPERM; CHLOROPLAST; DNA; GENE FLOW; GENETIC DIFFERENTIATION; GEOGRAPHICAL DISTRIBUTION; GLACIATION; PHYLOGEOGRAPHY; POPULATION GENETICS; QUATERNARY; RANGE EXPANSION; SPATIAL DISTRIBUTION;

ASIA; CHINA; EURASIA; FAR EAST; HENGDUAN MOUNTAINS; QINGHAI-XIZANG PLATEAU;

GENTIANACEAE; METAGENTIANA STRIATA;

EID: 43049138389     PISSN: 00244074     EISSN: 10958339     Source Type: Journal    
DOI: 10.1111/j.1095-8339.2008.00785.x     Document Type: Article

References (98)

1. Abbott RJ, Comes HP. 2004. Evolution in the Arctic: a phylogeographic analysis of the circumarctic plant, Saxifraga oppositifolia (purple saxifrage). New Phytologist 161 : 211 224.
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.
3. Afzal-Rafii Z, Dodd RS. 2007. Chloroplast DNA supports a hypothesis of glacial refugia over postglacial recolonization in disjunct populations of black pine (Pinus nigra) in western Europe. Molecular Ecology 16 : 723 736.
4. Alsos IG, Engelskjon T, Gielly L, Taberlet P, Brochmann C. 2005. Impact of ice ages on circumpolar molecular diversity: insights from an ecological key species. Molecular Ecology 14 : 2739 2753.
5. Avise JC. 2000. Phylogeography: the history and formation of species. Cambridge, MA : Harvard University Press.
6. Avise JC, Arnold J, Ball RM. 1987. Intraspecific phylogeography: the mitochondrial DNA bridge between population genetics and systematics. Annual Review of Ecology and Systematics 18 : 489 522.
7. Axelrod DI, Al-Shehbaz I, Raven PH. 1996. History of the modern flora of China. In : Zhang A, Wu SG, eds. Floristic characteristics and diversity of East Asian plants. Beijing : China Higher Education Press, 43 55.
8. Bartish IV, Kadereit JW, Comes HP. 2006. Late Quaternary history of Hippophae rhamnoides L. (Elaeagnaceae) inferred from chalcone synthase intron (Chsi) sequences and chloroplast DNA variation. Molecular Ecology 15 : 4065 4083.
9. Birky CM, 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.
10. Brochmann C, Gabrielsen TM, Nordal I, Landvik JY, Elven R. 2003. Glacial survival or tabula rasa? The history of North Atlantic biota revisited. Taxon 52 : 417.
11. Chase MW, Hills HH. 1991. Silica gel: an ideal material for field preservation of leaf samples for DNA studies. Taxon 40 : 215 220.
12. Chen S, Xia TAO, Wang Y, Liu J, Chen S. 2005. Molecular systematics and biogeography of Crawfurdia, Metagentiana and Tripterospermum (Gentianaceae) based on nuclear ribosomal and plastid DNA sequences. Annals of Botany 96 : 413 424.
13. Cheng Y-P, Hwang S-Y, Lin T-P. 2005. Potential refugia in Taiwan revealed by the phylogeographical study of Castanopsis carlesii Hayata (Fagaceae). Molecular Ecology 14 : 2075 2085.
14. Chiang TY, Chiang YC, Chen YJ, Chou CH, Havanond S, Hong TN, Huang S. 2001. Phylogeography of Kandelia candel in East Asiatic mangroves based on nucleotide variation of chloroplast and mitochondrial DNAs. Molecular Ecology 10 : 2697.
15. Clegg MT, Gaut BS, Learn GH, Morton RR. 1994. Rates and pattern of chloroplast DNA evolution. Proceedings of the National Academy of Sciences of the United States of America 91 : 6795 6801.
16. Crandall K. 1996. Multiple interspecies transmissions of human and simian T-cell leukemia/lymphoma virus type I sequences. Molecular Biology and Evolution 13 : 115 131.
17. Crespi EJ, Rissler LJ, Browne RA. 2003. Testing Pleistocene refugia theory: phylogeographical analysis of Desmognathus wrighti, a high-elevation salamander in the southern Appalachians. Molecular Ecology 12 : 969 984.
18. Dobes CH, Mitchell-Olds T, Koch MA. 2004. Extensive chloroplast haplotype variation indicates Pleistocene hybridization and radiation of North American Arabis drummondii, A. × divaricarpa, and A. holboellii (Brassicaceae). Molecular Ecology 13 : 349 370.
19. Doyle JJ, Doyle JL. 1987. A rapid DNA isolation procedure for small quantities of fresh leaf material. Phytochemical Bulletin 19 : 11 15.
20. Ennos RA. 1994. Estimating the relative rates of pollen and seed migration among plant populations. Heredity 72 : 250 259.
21. Excoffier L, Laval G, Schneider S. 2006. Arlequin 3.01: an integrated software package for population genetics data analysis. Berne : Institute of Zoology, University of Berne.
22. Excoffier L, Smouse PE. 1994. Using allele frequencies and geographic subdivision to reconstruct gene trees with a species: molecular variance parsimony. Genetics 136 : 343 359.
23. Excoffier LP, Smouse E, 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.
24. Felsenstein J. 1985. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 39 : 783 791.
25. Fitch WM. 1971. Toward defining the course of evolution: minimum change for a specific tree topology. Systematic Zoology 20 : 406 416.
26. Fu YX. 1997. Statistical tests of neutrality of mutations against population growth, hitchhiking and background selection. Genetics 147 : 915 925.
27. Fu YX, Li WH. 1993. Statistical tests of neutrality of mutations. Genetics 133 : 693 709.
28. Hamilton MB. 1999. Four primer pairs for the amplification of chloroplast intergenic regions with intraspecific variation. Molecular Ecology 8 : 521 523.
29. Hampe A, Arroyo J, Jordano P, Petit RJ. 2003. Rangewide phylogeography of a bird-dispersed Eurasian shrub: contrasting Mediterranean and temperate glacial refugia. Molecular Ecology 12 : 3415 3426.
30. Hewitt GM. 1993. Postglacial distribution and species substructure: lessons from pollen, insects and hybrid zones. In : Lees DR, Edwards D, eds. Evolutionary patterns and processes. London : Academic Press, 98 123.
31. Hewitt GM. 1996. Some genetic consequences of ice ages, and their role in divergence and speciation. Biological Journal of the Linnean Society 58 : 247 276.
32. Hewitt G. 2000. The genetic legacy of the Quaternary ice ages. Nature 405 : 907 913.
33. Hewitt GM. 2001. Speciation, hybrid zones and phylogeography - or seeing genes in space and time. Molecular Ecology 10 : 537 549.
34. Hewitt GM. 2004. Biodiversity: a climate for colonization. Heredity 92 : 1 2.
35. Ho TN, Chen SL, Liu SW. 2002. Metagentiana, a new genus of Gentianaceae. Botanical Bulletin of Academia Sinica 43 : 83 91.
36. Ho TN, Pringle JS. 1995. Gentianaceae. In : Wu ZY, Raven PH, eds. Flora of China. Beijing/St. Louis, MO : Science Press/Missouri Botanical Garden, 1 140.
37. Huairen Y, Xin X. 1985. The influence of Quaternary climate on Chinese loess and desert. In : Li T, ed. Contribution to the Quaternary glaciology and Quaternary geology. Beijing : Geological Publishing House, 126 134.
38. Huelsenbeck JP, Ronquist F. 2001. MrBayes: Bayesian inference of phylogeny. Bioinformatics 17 : 754 755.
39. Hwang S-Y, Lin T-P, Ma C-S, Lin C-L, Jeng-Der C, Yang J-C. 2003. Postglacial population growth of Cunninghamia konishii (Cupressaceae) inferred from phylogeographical and mismatch analysis of chloroplast DNA variation. Molecular Ecology 12 : 2689 2695.
40. Ikeda H, Senni KEI, Fujii N, Setoguchi H. 2006. Refugia of Potentilla matsumurae (Rosaceae) located at high mountains in the Japanese archipelago. Molecular Ecology 15 : 3731 3740.
41. Knowles LL, Futuyma DJ, Eanes WF, Rannala B. 1999. Insight into speciation from historical demography in the phytophagous beetle genus Ophraella. Evolution 53 : 1846 1856.
42. Koch MA, Kiefer C, Ehrich D, Vogel J, Brochmann C, Mummenhoff K. 2006. Three times out of Asia Minor: the phylogeography of Arabis alpina L. (Brassicaceae). Molecular Ecology 15 : 825 839.
43. Larget B, Simon DL. 1999. Markov chain Monte Carlo algorithms for the Bayesian analysis of phylogenetic trees. Molecular Biology and Evolution 16 : 750 759.
44. Lewis PO, Crawford DJ. 1995. Pleistocene refugium endemics exhibit greater allozymic diversity than widespread congeners in the genus Polygonella (Polygonaceae). American Journal of Botany 82 : 141 149.
45. Li WH. 1997. Molecular evolution. Sunderland, MA : Sinauer.
46. Lu SY, Hong KH, Liu SL, Cheng YP, Wu WL, Chiang TY. 2002. Genetic variation and population differentiation of Michelia formosana (Magnoliaceae) based on cpDNA variation and RAPD fingerprints: relevance to post-Pleistocene recolonization. Journal of Plant Research 115 : 203 216.
47. Maddison DR. 1991. The discovery and importance of multiple islands of most-parsimonious trees. Systematic Zoology 40 : 315 318.
48. Marjoram P, Donnelly P. 1994. Pairwise comparisons of mitochondrial DNA sequences in subdivided populations and implications for early human evolution. Genetics 136 : 673 683.
49. Marshall HD, Newton C, Ritland K. 2002. Chloroplast phylogeography and evolution of highly polymorphic microsatellites in lodgepole pine (Pinus contorta). Theoretical and Applied Genetics 104 : 367 378.
50. 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.
51. Meng LH, Yang R, Abbott RJ, Miehe G, Hu TH, Liu JQ. 2007. Mitochondrial and chloroplast phylogeography of Picea crassifolia Kom. (Pinaceae) in the Qinghai-Tibetan Plateau and adjacent highlands. Molecular Ecology 16 : 412.
52. Nei M. 1987. Molecular evolutionary genetics. New York : Columbia University Press.
53. Nie ZL, Wen J, Gu ZJ, Boufford DE, Sun H. 2005. Polyploidy in the flora of the Hengduan mountains hotspot, southwestern China. Annals of the Missouri Botanical Garden 92 : 275 306.
54. Petit RJ, Aguiagalde I, de Beaulieu JL, Bittkau C, Brewer S, Cheddadi R, Ennos R, Fineschi S, Grivet D, Lascoux M, Aparajita M, Müller-Starck G, Demesure-Musch B, Palmé A, Martín JP, Rendell S, Vendramin GG. 2003. Glacial refugia: hotspots but not melting pots of genetic diversity. Science 300 : 1563 1565.
55. Pinceel JAN, Jordaens K, Pfenninger M, Backeljau T. 2005. Rangewide phylogeography of a terrestrial slug in Europe: evidence for Alpine refugia and rapid colonization after the Pleistocene glaciations. Molecular Ecology 14 : 1133 1150.
56. Pons O, Petit RJ. 1996. Measuring and testing genetic differentiation with ordered versus unordered alleles. Genetics 144 : 1237 1245.
57. Posada D, Crandall KA. 1998. Modeltest: testing the model of DNA substitution. Bioinformatics 14 : 817 818.
58. Posada D, Crandall KA, Templeton AR. 2000. GEODIS: a program for the cladistic nested analysis of the geographical distribution of genetic haplotypes. Molecular Ecology 9 : 487 488.
59. Ren GY, Beug HJ. 2002. Mapping Holocene pollen data and vegetation of China. Quaternary Science Reviews 21 : 1395 1422.
60. Rogers AR, Harpending H. 1992. Population growth makes waves in the distribution of pairwise differences. Molecular Biology and Evolution 9 : 552 569.
61. Ronquist F, Huelsenbeck JP. 2003. MrBayes 3: Bayesian phylogenetic inference under mixed models. Bioinformatics 19 : 1572 1574.
62. Rozas J, De Sanchez I, Barrie JC, Messeguer X, Rozas R. 2003. DNASP: DNA polymorphism analyses by the coalescent and other methods. Bioinformatics 19 : 2496 2497.
63. Shi YF, Huang M, Yao T. 2000. Glaciers and their environments in China. Beijing : Science Press.
64. 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.
65. Shi YF, Zheng B, Li S, Ye B. 1995. Studies on altitude and climatic environment in the middle and east parts of Tibetan Plateau during Quaternary maximum glaciation. Journal of Glaciology and Geocryology 17 : 97 112.
66. Shi YF, Zheng B, Yao T. 1997. Glaciers and environments during the Last Glacial Maximum (LGM) on the Tibetan Plateau. Journal of Glaciology and Geocryology 19 : 97 113.
67. Stehlik I, Blattner FR, Holderegger R, Bachmann K. 2002. Nunatak survival of the high Alpine plant Eritrichium nanum (L.) Gaudin in the central Alps during the ice ages. Molecular Ecology 11 : 2027 2036.
68. Sun H, Li ZM. 2003. Qinghai-Tibet plateau uplift and its impact on Tethys flora. Advance in Earth Sciences 18 : 852 862.
69. Swofford DL. 2003. PAUP*: phylogenetic analysis using parsimony (*and other methods), version 4.0b10. Sunderland, MA : Sinauer Associates.
70. Taberlet P, Fumagalli L, Wust-Saucy A-G, Cosson J-F. 1998. Comparative phylogeography and postglacial colonization routes in Europe. Molecular Ecology 7 : 453 464.
71. Tajima F. 1989. Statistical method for testing the neutral mutation hypothesis by DNA polymorphism. Genetics 7 : 381 397.
72. Tang L, Shen C, Kong Z, Wang F, Liu K. 1998. Pollen evidence of climate during the last glacial maximum in eastern Tibetan Plateau. Journal of Glaciology and Geocryology 20 : 133 140.
73. Tao JR. 1992. The Tertiary vegetation and flora and floristic regions in China. Acta Phytotaxonomica Sinica 30 : 25 43.
74. Templeton AR. 1998. Nested clade analyses of phylogeographic data: testing hypotheses about gene flow and population history. Molecular Ecology 7 : 381 397.
75. Templeton AR. 2004. Statistical phylogeography: methods of evaluating and minimizing inference errors. Molecular Ecology 13 : 789 809.
76. Templeton AR, Boerwinkle E, Sing CF. 1987. A cladistic analysis of phenotypic associations with haplotypes inferred from restriction endonuclease mapping. I. Basic theory and an analysis of alcohol dehydrogenase activity in Drosophila. Genetics 117 : 343 351.
77. Templeton AR, Crandall KA, Sing CF. 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.
78. Templeton AR, Routman E, Phillips CA. 1995. Separating population structure from population history: a cladistic analysis of the geographical distribution of mitochondrial DNA haplotypes in the Tiger Salamander, Ambystoma tigrinurn. Genetics 140 : 767 778.
79. 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.
80. Wagner DB. 1992. Nuclear, chloroplast and mitochondrial DNA polymorphisms as biochemical markers in population genetic analysis of forest trees. New Forests 6 : 373 390.
81. Wang HS, Zhang YL. 1994. The biodiversity and characters of spermatophytic genera endemic to China. Acta Botanica Yunnanica 16 : 209 220.
82. Wang WT. 1992. On some distribution patterns and some migration routes found in the Eastern Asiatic region (cont'd). Acta Phytotaxonomica Sinica 30 : 97 117.
83. Watanabe K, Kajita T, Murata J. 2006. Chloroplast DNA variation and geographical structure of the Aristolochia kaempferi group (Aristolochiaceae). American Journal of Botany 93 : 442 453.
84. Weider LJ, Hobæk A. 2000. Phylogeography and arctic biodiversity: a review. Annales Zoologici Fennici 37 : 217 231.
85. Weir BS. 1996. Genetic data analysis II. Sunderland, MA : Sinauer Associates.
86. Widmer A, Baltisberger M. 1999. Extensive intraspecific chloroplast DNA (cpDNA) variation in the alpine Draba aizoides L. (Brassicaceae): haplotype relationships and population structure. Molecular Ecology 8 : 1405 1415.
87. Wu CY. 1979. The regionalization of Chinese flora. Acta Botanica Yunnanica 1 : 1 22.
88. Wu CY. 1980. The vegetation of China. Beijing : Science Press.
89. Wu CY. 1988. Hengduan mountain flora and her significance. Journal of Japanese Botany 63 : 297 311.
90. Wu CY, Wu SG. 1996. A proposal for a new floristic kingdom (realm) - the E. Asiatic kingdom, its delineation and characteristics. In : Zhang A, Wu SG, eds. Floristic characteristics and diversity of East Asian plants. Beijing : China Higher Education Press, 3 42.
91. Wu SG, Yang YP, Fei Y. 1995. On the flora of the alpine region in the Qinghai-Xizang (Tibet) Plateau. Acta Botanica Yunnanica 17 : 233 250.
92. Ying TS, Boufford DE, Zhang YL. 1993. The endemic genera of seed plants of China. Beijing : Science Press.
93. Zhang DF, Li FQ, Ben JM. 2000. Eco-environmental effects of the Qinghai-Tibet Plateau uplift during the Quaternary in China. Environmental Geology 39 : 1352 1358.
94. Zhang Q, Chiang TY, George M, Liu JQ, Abbott RJ. 2005. Phylogeography of the Qinghai-Tibetan Plateau endemic Juniperus przewalskii (Cupressaceae) inferred from chloroplast DNA sequence variation. Molecular Ecology 14 : 3513 3524.
95. Zhang RZ, Jin SK, Quan GQ, Li SH, Ye ZY, Wang PG, Zhang ML. 1997. Distribution of mammalian species in China. Beijing : China Forestry Publishing House.
96. Zhang XS. 1983. The Tibetan Plateau in relation to the vegetation of China. Annals of the Missouri Botanical Garden 70 : 564 570.
97. Zheng BX, Xu QQ, Shen YP. 2002. The relationship between climate change and Quaternary glacial cycles on the Qinghai-Tibetan Plateau: review and speculation. Quaternary International 97 : 93 101.
98. Zheng D. 1996. The system of physico-geographical regions of the Qinghai-Tibet (Xizang) Plateau. Science in China (Series D) 39 : 410 417.