Did glacials and/or interglacials promote allopatric incipient speciation in East Asian temperate plants? Phylogeographic and coalescent analyses on refugial isolation and divergence in Dysosma versipellis

Molecular Phylogenetics and Evolution

Volumn 51, Issue 2, 2009, Pages 281-293

  Qiu, Ying Xiong ^a   Guan, Bi Cai ^a   Fu, Cheng Xin ^a   Comes, Hans Peter ^b  

^a BEIJING UNIVERSITY OF POSTS AND TELECOMMUNICATIONS   (China)

^b UNIVERSITY OF SALZBURG   (Austria)

Author keywords

China; Chloroplast DNA; Coalescent theory; Divergence population genetics; Dysosma versipellis; Isolation migration; Phylogeography; Quaternary

Indexed keywords

CHLOROPLAST DNA; PLANT DNA;

ARTICLE; BERBERIDACEAE; BIOLOGICAL MODEL; CHINA; CLIMATE; DNA SEQUENCE; ECOSYSTEM; GENETIC POLYMORPHISM; GENETICS; GEOGRAPHY; HAPLOTYPE; MOLECULAR EVOLUTION; PHYLOGENY; POPULATION DYNAMICS; POPULATION GENETICS; SPECIES DIFFERENTIATION;

BERBERIDACEAE; CHINA; CLIMATE; DNA, CHLOROPLAST; DNA, PLANT; ECOSYSTEM; EVOLUTION, MOLECULAR; GENETIC SPECIATION; GENETICS, POPULATION; GEOGRAPHY; HAPLOTYPES; MODELS, GENETIC; PHYLOGENY; POLYMORPHISM, GENETIC; POPULATION DYNAMICS; SEQUENCE ANALYSIS, DNA;

DYSOSMA VERSIPELLIS;

EID: 67349198064     PISSN: 10557903     EISSN: 10959513     Source Type: Journal    
DOI: 10.1016/j.ympev.2009.01.016     Document Type: Article

References (87)

1. Avise J.C. Phylogeography: The History and Formation of Species (2000), Harvard University Press, Cambridge, MA
2. Cao T.R., Qi C.J., Yu X.L., Long C.L., and Zhou J.R. Study on Fagus lucida forests in Badagong Mountains of Hunan and their flora. J. Central South Forestry Univ. 13 (1993) 8-16 (in Chinese with an English abstract)
3. Cheng Y.P., Hwang S.Y., and Lin T.P. Potential refugia in Taiwan revealed by the phylogeographical study of Castanopsis carlesii Hayata (Fagaceae). Mol. Ecol. 14 (2005) 2075-2085
4. Chiang Y.C., Hung K.H., Schaal B.A., Ge X.J., Hsu T.W., and Chiang T.Y. Contrasting phylogeographical patterns between mainland and island taxa of the Pinus luchensis complex. Mol. Ecol. 15 (2006) 765-779
5. Chung J.D., Lin T.P., Chen Y.L., Cheng Y.P., and Hwang S.Y. Phylogeographic study reveals the origin and evolutionary history of a Rhododendron species complex in Taiwan. Mol. Phylogenet. Evol. 42 (2007) 14-24
6. Clement M., Posada D., and Crandall K.A. tcs: a computer program to estimate gene genealogies. Mol. Ecol. 9 (2000) 1657-1660
7. Coyne J.A., and Orr H.A. Speciation (2004), Harvard University Press, Cambridge, MA
8. Delaunay B. Sur la sphère vide. Bull. Acad. Sci. USSR 7 (1934) 793-800
9. Demesure B., Sodzi N., and Petit R.J. A set of universal primers for amplification of polymorphic non-coding regions of mitochondrial and chloroplast DNA in plants. Mol. Ecol. 4 (1995) 129-131
10. Dolman G., and Moritz C. A multilocus perspective on refugial isolation and divergence in rainforest skinks (Carlia). Evolution 60 (2006) 573-582
11. Drummond C.S., and Hamilton M.B. Hierarchical components of genetic variation at a species boundary: population structure in two sympatric varieties of Lupinus microcarpus (Leguminosae). Mol. Ecol. 16 (2007) 753-769
12. Dubey B., Cosson J.F., Vohralík V., Kryštufek B., Diker E., and Vogel P. Molecular evidence of Pleistocene bidirectional faunal exchange between Europe and the Near East: the case of the bicoloured shrew (Crocidura leucodon, Soricidae). J. Evol. Biol. 7 (2007) 1799-1808
13. Excoffier L., Smouse P.E., and Quattro J.M. Analysis of molecular variance inferred from metric distances among DNA haplotypes: application to human mitochondrial DNA restriction data. Genetics 131 (1992) 479-491
14. Excoffier L., Laval G., and Schneider S. arlequin Ver. 3.0: an integrated software package for population genetics data analysis. Evol. Bioinformatics 1 (2005) 47-50
15. Fu Y.X. Statistical tests of neutrality of mutations against population growth, hitchhiking and background selection. Genetics 147 (1997) 915-925
16. Gao L.M., Möller M., Zhang X.M., Hollingsworth M.L., Liu J., Mill R.R., Gibby M., and Li D.Z. High variation and strong phylogeographic pattern among cpDNA haplotypes in Taxus wallichiana (Taxaceae) in China and North Vietnam. Mol. Ecol. 16 (2007) 4684-4698
17. Ge X.J., Chiang Y.C., Chou C.H., and Chiang T.Y. Nested clade analysis of Dunnia sinensis (Rubiaceae), a monotypic genus from China based on organelle DNA sequences. Conserv. Genet. 3 (2002) 351-362
18. Godbout J., Jaramillo-Correa J.P., Beaulieu J., and Bousquet J. A mitochondrial DNA minisatellite reveals the postglacial history of jack pine (Pinus banksiana), a broad-range North American conifer. Mol. Ecol. 14 (2005) 3497-3512
19. Gong W., Chen C., Dobes C., Fu C.X., and Koch M.A. Phylogeography of a living fossil: Pleistocene glaciations force Ginkgo biloba L. (Ginkgoaceae) into two refuge areas with limited subsequent postglacial expansion. Mol. Phylogenet. Evol. 48 (2008) 1094-1105
20. Graur D., and Li W.H. Fundamentals of Molecular Evolution (1999), Sinauer Associates, Sunderland, MA
21. Griswold C.K., and Baker A.J. Time to the most recent common ancestor and divergence times of populations of common chaffinches (Fringilla coelebs) in Europe and North Africa: insights into Pleistocene refugia and current levels of migration. Evolution 56 (2002) 143-153
22. Harpending H.C. Signature of ancient population growth in a low-resolution mitochondrial DNA mismatch distribution. Hum. Biol. 66 (1994) 591-600
23. Harrison S.P., Yu G., Takahara H., and Prentice I.C. Palaeovegetation: diversity of temperate plants in East Asia. Nature 413 (2001) 129-130
24. Hasegawa M., Kishino H., and Yano T. Dating the human-ape splitting by a molecular clock of mitochondrial DNA. J. Mol. Evol. 22 (1985) 160-174
25. Hey J., and Nielsen R. Multilocus methods for estimating population sizes, migration rates and divergence time, with applications to the divergence of Drosophila pseudoobscura and D. persimilis. Genetics 167 (2004) 747-760
26. Hey J., and Nielsen R. Integration within the Felsenstein equation for improved Markov chain Monte Carlo methods in population genetics. Proc. Natl. Acad. Sci. USA 104 (2007) 2785-2790
27. Huang S.F., Hwang S.Y., Wang J.C., and Lin T.P. Phylogeography of Trochodendron aralioides (Trochodendraceae) in Taiwan and its adjacent areas. J. Biogeogr. 31 (2004) 1251-1259
28. Huang S.S.F., Hwang S.Y., and Lin T.P. Spatial pattern of chloroplast DNA variation of Cyclobalanopsis glauca in Taiwan and East Asia. Mol. Ecol. 11 (2002) 2349-2358
29. Hudson R.R. Gene genealogies and the coalescent process. In: Futuyma D., and Antonovics J. (Eds). Oxford Surveys in Evolutionary Biology (1990), Oxford University Press, New York 1-44
30. Hwang S.Y., Lin T.P., Ma C.S., Lin C.L., Chung J.D., and Yang J.C. Postglacial population growth of Cunninghamia konishii (Cupressaceae) inferred from phylogeographical and mismatch analysis of chloroplast DNA variation. Mol. Ecol. 12 (2003) 2689-2695
31. Ingvarsson P.K., Ribstein S., and Taylor D.R. Molecular evolution of insertions and deletions in the chloroplast genome of Silene. Mol. Biol. Evol. 20 (2003) 1737-1740
32. Kumar S., Tamura K., and Nei M. mega 3: integrated software for molecular evolutionary genetics analysis and sequence alignment. Brief Bioinform. 5 (2004) 150-163
33. Loconte H. Berberidaceae. In: Kubitzki K., Rohwer J.G., and Bittrich V. (Eds). The Families and Genera of Vascular Plants. II. Flowering Plants: Dicotyledons, Magnoliid, Hamamelid and Caryophyllid Families (1993), Oxford University Press, New York 147-152
34. Li Z.C., and Wang W.Y. Ecological and biological characteristics of endangered medicinal plant Dysosma versipellis. J. Trop. Subtrop. Bot. 14 (2006) 190-195
35. Liu H., Xing Q., Ji Z., Xu L., and Tian Y. An outline of Quaternary development of Fagus forest in China: palynological and ecological perspectives. Flora 198 (2003) 249-259
36. Liu J.Q., Chen Z.D., and Lu A.M. Molecular evidence for the sister relationship of the eastern Asia-North American intercontinental species pair in the Podophyllum group (Berberidaceae). Bot. Bull. Acad. Sin. 43 (2002) 147-154
37. Liu K.B. Quaternary history of the temperate forests of China. Quatern. Sci. Rev. 7 (1988) 1-20
38. Ma S.B., and Hu Z.H. A contribution to the geographical distribution and phylogeny of Podophylloideae (Berberidaceae). Acta Bot. Yunnan. 19 (1997) 48-56
39. Manni, F., Guérard, E., 2004. barrier Version 2.2. Manual of the User. Population Genetics Team, Museum of Mankind (Musée de I'Homme), Paris (publication distributed by the authors).
40. Manni F., Guérard E., and Heyer E. Geographic patterns of (genetic, morphologic, linguistic) variation: how barriers can be detected using Monmonier's algorithm. Hum. Biol. 76 (2004) 173-190
41. Monmonier M.S. Maximum-difference barriers: an alternative numerical regionalization method. Geogr. Anal. 3 (1973) 245-261
42. Moritz C. Defining 'Evolutionarily Significant Units' for conservation. Trends Ecol. Evol. 9 (1994) 373-375
43. Müller K. seqstate - primer design and sequence statistics for phylogenetic DNA data sets. Appl. Bioinformatics 4 (2005) 65-69
44. Nei M., and Kumar S. Molecular Evolution and Phylogenetics (2000), Oxford University Press, New York
45. Nielsen R., and Wakeley J. Distinguishing migration from isolation: a Markov chain Monte Carlo approach. Genetics 158 (2001) 885-896
46. Peters J.L., Gretes W., and Omland K.E. Late Pleistocene divergence between eastern and western populations of wood ducks (Aix sponsa) inferred by the isolation with migration coalescent method. Mol. Ecol. 14 (2005) 3407-3418
47. Petit R.J., Duminil J., Fineschi S., Hampe A., Salvini D., and Vendramin G.G. Comparative organization of chloroplast, mitochondrial and nuclear diversity in plant populations. Mol. Ecol. 14 (2005) 689-701
48. Pons O., and Petit R.J. Measuring and testing genetic differentiation with ordered versus unordered alleles. Genetics 144 (1996) 1237-1245
49. Qian H., and Ricklefs R.E. Large-scale processes and the Asian bias in species diversity of temperate plants. Nature 407 (2000) 180-182
50. Qian H., and Ricklefs R.E. Diversity of temperate plants in East Asia - reply. Nature 413 (2001) 130
51. Qiu Y.X., Li J.H., Liu H.L., Chen Y.Y., and Fu C.X. Population structure and genetic diversity of Dysosma versipellis (Berberidaceae), a rare endemic from China. Biochem. Syst. Ecol. 34 (2006) 745-752
52. Qiu Y.X., Zhou X.W., Fu C.X., and Gilbert C.Y.S. A preliminary study of genetic variation in the endangered, Chinese endemic species Dysosma versipellis (Berberidaceae). Bot. Bull. Acad. Sin. 46 (2005) 61-69
53. Ren G., and Beug H.J. Mapping Holocene pollen data and vegetation of China. Quatern. Sci. Rev. 21 (2002) 1395-1422
54. Rogers A.R., and Harpending H. Population growth makes waves in the distribution of pairwise genetic differences. Mol. Biol. Evol. 9 (1992) 552-569
55. Rogers A.R. Genetic evidence for a Pleistocene population explosion. Evolution 49 (1995) 608-615
56. Rohlf F.J. ntsys-pc, Version 2.02: Numerical Taxonomy and Multivariate Analysis System (1997), Exeter Ltd., Setauket, New York
57. Rousset F. Genetic differentiation and estimation of gene flow from F-statistics under isolation by distance. Genetics 145 (1997) 1219-1228
58. Rozas J., and Rozas R. dnasp, Version 3: an integrated program for molecular population genetics and molecular evolution analysis. Bioinformatics 15 (1999) 174-175
59. Sang T., Crawford D.J., and Stuessy T.F. Chloroplast DNA phylogeny, reticulate evolution and biogeography of Paeonia (Paeoniaceae). Am. J. Bot. 84 (1997) 1120-1136
60. Schaal B.A., Hayworth D.A., Olsen K.M., Rauscher J.T., and Smith W.A. Phylogeographic studies in plants: problems and prospects. Mol. Ecol. 7 (1998) 465-474
61. Schneider S., and Excoffier L. Estimation of demographic parameters from the distribution of pairwise differences when the mutation rates vary among sites: application to human mitochondrial DNA. Genetics 152 (1999) 1079-1089
62. Schneider, S., Roessli, D., Excoffier, L., 2000. arlequin, Version 2.000: a Software for Population Genetic Data Analysis. Genetics and Biometry Laboratory, University of Geneva, Geneva, Switzerland.
63. Shi Y.F., Cui Z.J., and Li J.J. Reassessment of Quaternary glaciation problems in East China. Earth Sci. 2 (1987) 45-54
64. Smith C.I., and Farrell B.D. Phylogeography of the longhorn cactus beetle Moneilema appressum LeConte (Coleoptera: Cerabycidae): was the differentiation of the Madrean sky islands driven by Pleistocene climate changes?. Mol. Ecol. 14 (2005) 3049-3065
65. Städler T., Roselius K., and Stephan W. Genealogical footprints of speciation processes in wild tomatoes: demography and evidence for historical gene flow. Evolution 59 (2005) 1268-1279
66. Su Y.J., Wang T., Chen G.P., Sun Y.F., Jiang Y., Deng F., and Wang B.S. Postglacial population expansion of Dacrydium pectinatum (Podocarpaceae) in Hainan, southern China, based on cpDNA trnL-F noncoding sequence data. Front. Biol. China 1 (2006) 263-269
67. Su Y.J., Wang T., Zheng B., Jiang Y., Chen G.P., Ouyang P.Y., and Sun Y.F. Genetic differentiation of relictual populations of Alsophila spinulosa in southern China inferred from cpDNA trnL-F noncoding sequences. Mol. Phylogenet. Evol. 34 (2005) 323-333
68. Swofford D.L. paup*: Phylogenetic Analysis Using Parsimony (* and Other Methods), Version 4.0b10 (2002), Sinauer Associates, Sunderland, MA
69. Taberlet P., Ludovic G., Pautou G., and Bouvet J. Universal primers for amplification of three non-coding regions of chloroplast DNA. Plant Mol. Biol. 17 (1991) 1105-1109
70. Tamura K., and Nei M. Estimation of the number of nucleotide substitutions in the control region of mitochondrial DNA in humans and chimpanzees. Mol. Biol. Evol. 10 (1993) 512-526
71. Tang L.Y., Shen C.M., Kong Z.Z., Wang F.B., and Liu K.B. Pollen evidence of climate during the Last Glacial Maximum in eastern Tibetan plateau. J. Glaciol. Geocryol. 20 (1998) 133-140
72. Templeton A.R. Statistical phylogeography: methods of evaluating and minimizing inference errors. Mol. Ecol. 13 (2004) 789-809
73. Thompson J.D., Higgins D.G., and Gibon T.J. 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 (1994) 4673-4680
74. Wakeley J. Inferences about the structure and history of populations: coalescents and intraspecific phylogeography. In: Singh R.S., and Uyenoyama M.K. (Eds). The Evolution of Population Biology (2003), Cambridge University Press, Cambridge 193-215
75. Wang S., and Xie Y. China Species Red List (vol. 1 Red List) (2004), Higher Education Press, Beijing, China p. 324
76. Won Y.J., and Hey J. Divergence population genetics of chimpanzees. Mol. Biol. Evol. 22 (2005) 297-307
77. Wu M.J., Huang S.F., Huang T.C., and Lin T.P. Evolution of Euphrasia transmorrisonensis complex (Orobanchaceae) in alpine area of Taiwan. J. Biogeogr. 32 (2005) 1921-1929
78. Wu S.H., Hwang C.Y., Lin T.P., Chung J.D., Cheng Y.P., and Hwang S.Y. Contrasting phylogeographic patterns of two closely related species, Machilus thunbergii and Machilus kusanoi (Lauraceae), in Taiwan. J. Biogeogr. 33 (2006) 936-947
79. Xiang Q.Y., Soltis D.E., Soltis P.S., Manchester S.R., and Crawford D.J. Timing the eastern Asian-eastern north American floristic disjunction: molecular clock corroborates paleontological estimates. Mol. Phylogenet. Evol. 15 (2000) 462-472
80. Yi C.L., Cui Z.J., and Xiong H.G. Numerical periods of Quaternary glaciations in China. Quatern. Sci. 25 (2005) 609-619
81. Yi S., Saito Y., Zhao Q., and Wang P. Vegetation and climate changes in the Changjiang (Yangtze River) Delta during the past 13,000 years inferred from pollen records. Quatern. Sci. Rev. 22 (2003) 1501-1519
82. Ying T.S., Zhang Y.L., and Boufford D.E. The Endemic Genera of Seed Plants of China (1993), Science Press, Beijing
83. Zhang D.C., Shao J.Z., and Li D.L. A study on the karyotypes of Dysosma versipellis and D. pleiantha endemic to China. Guihaia 11 (1991) 58-62
84. Zhang Q., Chiang T.Y., George M., Liu J.Q., and Abbott R.J. Phylogeography of the Qinghai-Tibetan Plateau endemic Juniperus przewalskii (Cupressaceae) inferred from chloroplast DNA sequence variation. Mol. Ecol. 14 (2005) 3513-3524
85. Zhang Q., Liu Y., and Sodmergen. Examination of the cytoplasmic DNA in male reproductive cells to determine the potential for cytoplasmic inheritance in 295 angiosperm species. Plant Cell Physiol. 44 (2003) 941-951
86. Zhang R.Z. Relict distribution of land vertebrates and Quaternary glaciation in China. Acta Zool. Sin. 50 (2004) 841-851
87. Zheng Z. Vegetation and climate since the Late Pleistocene in southern China. J. Geosci. China 2 (2000) 7-20