Chloroplast phylogeography of Dipentodon (Dipentodontaceae) in southwest China and northern Vietnam

Molecular Ecology

Volumn 17, Issue 4, 2008, Pages 1054-1065

  Yuan, Qing Jun ^a,d   Zhang, Zhi Yong ^b,c   Peng, Hua ^a   Ge, Song ^c  

^a KUNMING INSTITUTE OF BOTANY   (China)

^b JIANGXI AGRICULTURAL UNIVERSITY   (China)

^c INSTITUTE OF BOTANY   (China)

^d UNIVERSITY OF CHINESE ACADEMY OF SCIENCES   (China)

Author keywords

Chloroplast DNA; Dipentodon Dunn; Phylogeography; Tibetan Plateau

Indexed keywords

CHLOROPLAST DNA;

ANGIOSPERM; ARTICLE; CHINA; CLASSIFICATION; DNA SEQUENCE; GENETIC VARIABILITY; GENETICS; GEOGRAPHY; HAPLOTYPE; MOLECULAR GENETICS; NUCLEOTIDE SEQUENCE; PHYLOGENY; SEQUENCE ALIGNMENT; VIET NAM;

ANGIOSPERMS; BASE SEQUENCE; CHINA; DNA, CHLOROPLAST; GEOGRAPHY; HAPLOTYPES; MOLECULAR SEQUENCE DATA; PHYLOGENY; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS, DNA; VARIATION (GENETICS); VIETNAM;

DIPENTODON; DIPENTODON SINICUS; DIPENTODONTACEAE;

EID: 38849182234     PISSN: 09621083     EISSN: 1365294X     Source Type: Journal    
DOI: 10.1111/j.1365-294X.2007.03628.x     Document Type: Article

References (57)

1. Avise JC (2000) Phylogeography: The History and Formation of Species. Harvard University Press, Cambridge, Massachusetts; London, England.
2. Avise JC (2004) Molecular Markers, Natural History, and Evolution, 2nd edn. Sinauer & Associates, Sunderland, Massachusetts.
3. Axelrod DI, Al-Shehbaz I, Raven PH (1996) History of the modern flora of China. In : Floristic Characteristics and Diversity of East Asian Plants (eds Zhang A, Wu S pp. 43 55. Springer, New York.
4. Barton NH, Charlesworth B (1984) Genetic revolutions, founder effects, and speciation. Annual Review of Ecology and Systematics, 15, 133 164.
5. Caicedo AL, Schaal BA (2004) Population structure and phylogeography of Solanum pimpinellifolium inferred from a nuclear gene. Molecular Ecology, 13, 1871 1882.
6. Cheng J, Liu X, Gao Z, Tang D, Yue J (2001) Effect of the Tibetan Plateau uplifting on the geological environment of the Yunnan Plateau. Geoscience, 15, 290 296.
7. Chiang TY (2000) Lineage sorting accounting for the disassociation between chloroplast and mitochondrial lineages in oaks of southern France. Genome, 43, 1090 1094.
8. Chiang TY, Schaal BA (1999) Phylogeography of North American populations of the moss species Hylocomium splendens based on the nucleotide sequence of internal transcribed spacer 2 of nuclear ribosomal DNA. Molecular Ecology, 8, 1037 1042.
9. Chiang YC, Hung KH, Schaal BA, Ge XJ, Hsu TW, Chiang TY (2006) Contrasting phylogeographical patterns between mainland and island taxa of the Pinus luchuensis complex. Molecular Ecology, 15, 765 779.
10. Clement M, Posada D, Crandall KA (2000) tcs: a computer program to estimate gene genealogies. Molecular Ecology, 9, 1657 1659.
11. Crandall KA, Templeton AR (1993) Empirical tests of some predictions from coalescent theory with applications to intraspecific phylogeny reconstruction. Genetics, 134, 959 969.
12. Doyle JJ, Doyle JL (1987) A rapid DNA isolation procedure for small quantities of fresh leaf tissue. Phytochemical Bulletin, 19, 11 15.
13. Doyle JJ, Gaut BS (2000) Evolution of genes and taxa: a primer. Plant Molecular Biology, 42, 1 23.
14. Ge X-J, Zhang L-B, Yuan Y-M, Hao G, Chiang T-Y (2005) Strong genetic differentiation of the East-Himalayan Megacodon stylophorus (Gentianaceae) detected by inter-simple sequence repeats (ISSR). Biodiversity and Conservation, 14, 849 861.
15. Graur D, Li WH (1999) Fundamentals of Molecular Evolution. Sinauer & Associates, Sunderland, Massachusetts.
16. Guo X, He S, Zhang Y (2005) Phylogeny and biogeography of Chinese sisorid catfishes re-examined using mitochondrial cytochrome b and 16S rRNA gene sequences. Molecular Phylogenetics and Evolution, 35, 344 362.
17. Hamilton MB (1999) Four primer pairs for the amplification of chloroplast intergenic regions with intraspecific variation. Molecular Ecology, 8, 521 522.
18. Hamrick JL, Godt MJW, Sherman-Broyles SL (1992) Factors influencing levels of genetic diversity in woody plant species. New Forests, 6, 95 124.
19. Hewitt GM (2000) The genetic legacy of the Quaternary ice ages. Nature, 405, 907 913.
20. Hewitt GM (2001) Speciation, hybrid zones and phylogeography - or seeing genes in space and time. Molecular Ecology, 10, 537 549.
21. 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.
22. Huang JC, Wang WK, Peng CI, Chiang TY (2005) Phylogeography and conservation genetics of Hygrophila pogonocalyx (Acanthaceae) based on atpB-rbcL noncoding spacer cpDNA. Journal of Plant Research, 118, 1 11.
23. Huang S, Chiang YC, Schaal BA, Chou CH, Chiang TY (2001) Organelle DNA phylogeography of Cycas taitungensis, a relict species in Taiwan. Molecular Ecology, 10, 2669 2681.
24. Hudson RR (1990) Gene genealogies and the coalescent process. In : Oxford Surveys in Evolutionary Biology (eds Futuyma D, Antonovics J pp. 1 44. Oxford University Press, Oxford, UK.
25. Hutchison DW, Templeton AR (1999) Correlation of pairwise genetic and geographic distance measures: inferring the relative influences of gene flow and drift on the distribution of genetic variability. Evolution, 53, 1898 1914.
26. Jensen JL, Bohonak AJ, Kelley ST (2005) Isolation by distance, web service. BMC Genetics 6: 13 v. 3.11 http://ibdws.sdsu.edu/.
27. Kuchta SR, Meyer D (2001) A genealogical view of geographical variation. Molecular Ecology, 10, 2569 2576.
28. Kumar S, Tamura K, Nei M (2004) mega 3: integrated software for molecular evolutionary genetics analysis and sequence alignment. Briefings in Bioinformatics, 5, 150 163.
29. Li W-H (1997) Molecular Evolution. Sinauer & Associates, Sunderland, Massachusetts.
30. Liu JS, Cheng JR (1991) On the systematic position of genus Dipentodon Dunn. Journal of Wuhan Botanical Research, 9, 29 39.
31. Liu JQ, Wang YJ, Wang AL, Hideaki O, 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.
32. Luo J, Yang D, Suzuki H et al 2004) Molecular phylogeny and biogeography of Oriental voles: genus Eothenomys (Muridae, Mammalia). Molecular Phylogenetics and Evolution, 33, 349 362.
33. Myers N, Mittermeier RA, Mittermeier CG, da Fonseca GAB, Kent J (2000) Biodiversity hotspots for conservation priorities. Nature, 403, 853 858.
34. Nei M, Kumar S (2000) Molecular Evolution and Phylogenetics. Oxford University Press, New York.
35. Newton AC, Allnutt AR, Gillies ACM, Lowe AJ, Ennos RA (1999) Molecular phylogeography, intraspecific variation and the conservation of tree species. Trends in Ecology and Evolution, 14, 140 145.
36. Peng Y-L, Chen D, Gong X, Zhong Y, Shi S-H (2003) Phylogenetic position of Dipentodon sinicus: evidence from DNA sequences of chloroplast rbcL, nuclear ribosomal 18S, and mitochondria matR genes. Botanical Bulletin of Academia Sinica, 44, 217 222.
37. Petit RJ, Aguinagalde I, de Beaulieu J-L et al 2003) Glacial refugia: hotspots but not melting pots of genetic diversity. Science, 300, 1563 1565.
38. Petit RJ, Duminil J, Fineschi S, Hampe A, Salvini D, Vendramin GG (2005) Comparative organization of chloroplast, mitochondrial and nuclear diversity in plant populations. Molecular Ecology, 14, 689 701.
39. Pons O, Petit RJ (1996) Measuring and testing genetic differentiation with ordered versus unordered alleles. Genetics, 144, 1237 1245.
40. 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.
41. Rieseberg LH, Church SA, Morjan CL (2003) Integration of populations and differentiation of species. New Phytologist, 161, 59 69.
42. Rozas J, Sanchez-De I, Barrio JC, Messeguer X, Rozas R (2003) dnasp, DNA polymorphism analyses by the coalescent and other methods. Bioinformatics, 19, 2496 2497.
43. Sang T, Crawford DJ, Stuessy TF (1997) Chloroplast DNA phylogeny, reticulate evolution, and biogeography of Paeonia (Paeoniaceae). American Journal of Botany, 84, 1120 1136.
44. Schaal BA, Hayworth DA, Olsen KM, Rauscher JT, Smith W (1998) Phylogeography studies in plants: problems and prospects. Molecular Ecology, 7, 465 474.
45. Su B, Wang YX, Lan H, Wang W, Zhang Y (1999) Phylogenetic study of complete cytochrome b genes in musk deer (genus Moschus) using museum samples. Molecular Phylogenetics and Evolution, 12, 241 249.
46. Sun HL, Zheng D (1998) Formation, Evolution and Development of Qinghai-Xizang (Tibetan) Plateau. Guangdong Science & Technology Press, Guangzhou, China.
47. Templeton AR (2004) Statistical phylogeography: methods of evaluating and minimizing inference errors. Molecular Ecology, 13, 789 809.
48. Templeton AR, Sing CF (1993) A cladistic analysis of phenotypic associations with haplotypes inferred from restriction endonuclease mapping. IV. Nested analyses with cladogram uncertainty and recombination. Genetics, 134, 659 669.
49. 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.
50. 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.
51. Thompson JDTJ, Gibson PF, Jeanmougin F, Higgins DG (1997) The windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Research, 24, 4876 4882.
52. Thorne RF (1999) Eastern Asia as a living museum for Archaic Angiosperms and other seed plants. Taiwania, 44, 413 422.
53. Wang S, Xie Y (2004) China Species Red List Vol. 1: Red List. Higher Education Press, Beijing, China.
54. Wendel JF, Doyle JJ (1998) Phylogenetic incongruence: window into genomes history and molecular evolution. In : Molecular Systematics of Plants II: DNA Sequencing (eds Soltis DE, Soltis PS, Doyle J), pp. 265 296. Kluwer Academic, Dordrecht, The Netherlands.
55. Wilson EO (1992) The Diversity of Life. Harvard University Press, Cambridge, Massachusetts.
56. 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.
57. Zheng D (1996) The system of physico-geographical regions of the Qinghai-Tibet (Xizang) Plateau. Science in China (Series D), 39, 410 417.