Chloroplast DNA phylogeography of the Chinese endemic alpine quillwort Isoetes hypsophila hand.-mazz. (isoetaceae)

International Journal of Plant Sciences

Volumn 169, Issue 6, 2008, Pages 792-798

  Chen, Jin Ming ^a   Liu, Fan ^a   Gituru, Wahiti Robert ^b   Wang, Qing Feng ^a  

^a WUHAN UNIVERSITY   (China)

^b JOMO KENYATTA UNIVERSITY OF AGRICULTURE AND TECHNOLOGY   (Kenya)

Author keywords

Alpine quillwort; cpDNA trnL intron sequence; Isoetes hypsophila; Nested clade analysis; Phylogeography

Indexed keywords

CHLOROPLAST; CLADISTICS; DNA; ENDEMIC SPECIES; GENE FLOW; GENETIC DIFFERENTIATION; GENETIC VARIATION; PHYLOGEOGRAPHY; PLANT; SPATIAL DISTRIBUTION; SPECIES DIVERSITY;

ASIA; CHINA; EURASIA; FAR EAST; SICHUAN; YUNNAN;

ISOETACEAE; ISOETALES; ISOETES HYPSOPHILA;

EID: 47649125533     PISSN: 10585893     EISSN: None     Source Type: Journal    
DOI: 10.1086/588065     Document Type: Article

References (49)

1. Cannon HC, PS Manos 2003 Phylogeography of the Southeast Asian stone oaks (Lithocarpus). J Biogeogr 30:211-226.
2. Coleman M, K Hodges 1995 Evidence for Tibetan plateau uplift before 14 Myr ago from a new minimum age for east-west extension. Nature 374:49-52.
3. Excoffier L, P Smouse 1994 Using allele frequencies and geographic divisions to reconstruct gene genealogies within a species: molecular variance parsimony. Genetics 136:343-359.
4. Excoffier L, PE Smouse, JM Quattro 1992 Analysis of molecular variance inferred from metric distances among DNA haplotypes: application to human mitochondrial DNA restriction data. Genetics 131:479-491.
5. Felsenstein J 1985 Confidence limits on phylogenies: an approach using the bootstrap. Evolution 39:783-791.
6. Ferris C, RA King, R Vainola, GM Hewitt 1998 Chloroplast DNA recognizes three refugia sources of European oaks and suggests independent eastern and western immigrations to Finland. Heredity 80:584-593.
7. Fu CX, YX Qiu, HH Kong 2003 RAPD analysis for genetic diversity in Changium smyrnioides (Apiaceae), an endangered plant. Bot Bull Acad Sin 44:13-18.
8. Fu YX, WH Li 1993 Statistical tests of neutrality of mutations. Genetics 133:693-709.
9. Ge XJ, YC Chiang, CH Chou, TY Chiang 2002 Nested clade analysis of Dunnia sinensis (Rubiaceae), a monotypic genus from China based on organelle DNA sequences. Conserv Genet 3:351-362.
10. Hewitt GM 2000 The genetic legacy of the Quaternary ice ages. Nature 405:907-913.
11. _ 2004 Genetic consequence of climatic oscillations in the Quaternary. Philos Trans R Soc B 359:183-195.
12. Honjo M, S Ueno, Y Tsumura, I Washitani, R Ohsawa 2004 Phylogeographic study based on intraspecific sequence variation of chloroplast DNA for the conservation of genetic diversity in the Japanese endangered species Primula sieboldii. Biol Conserv 120:211-220.
13. Hooper EA, CH Haufler 1997 Genetic diversity and breeding system in a group of Neotropical epiphytic ferns (Pleopeltis; Polypodiaceae). Am J Bot 84:1664-1674.
14. Huang SF, SY Hwang, JC Wang, TP Lin 2004 Phylogeography of Trochodendron aralioides (Trochodendraceae) in Taiwan and its adjacent areas. J Biogeogr 31:1251-1259.
15. Ikeda H, H Setoguchi 2007 Phylogeography and refugia of the Japanese endemic alpine plant, Phyllodoce nipponica Makino (Ericaceae). J Biogeogr 34:169-176.
16. Kimura M 1980 A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. J Mol Evol 16:111-120.
17. Kumar S, K Tamura, M Nei 2004 MEGA 3: integrated software for molecular evolutionary genetics analysis and sequence alignment. Brief Bioinform 5:150-163.
18. Li JW, CH Haufler 1999 Genetic variation, breeding systems, and patterns of diversification in Hawaiian Polypodium (Polypodiaceae). Syst Bot 24:339-355.
19. Liu X, WR Gituru, QF Wang 2004 Distribution of basic diploid and polyploid species of Isoetes in East Asia. J Biogeogr 31:1239-1250.
20. Liu X, JY Wang, QF Wang 2005 Current status and conservation strategies for Isoetes in China: a case study for the conservation of threatened aquatic plants. Oryx 39:335-338.
21. Maki M, YJ Asada 1998 High genetic variability revealed by allozymic loci in the narrow endemic fern Polystichum otomasui (Dryopteridaceae). Heredity 80:604-610.
22. Nei M, F Tajima 1983 Maximum likelihood estimation of the number of nucleotide substitutions from restriction sites data. Genetics 105:207-217.
23. Petit RJ, I Aguinagalde, JL de Beaulieu, C Bittkau, S Brewer, R Cheddadi, R Ennos, et al 2003 Glacial refugia: hotspots but not melting pots of genetic diversity. Science 300:1563-1565.
24. Pigg KB 2001 Isoetalwan lycopsid evolution: from the Devonian to the present. Am Fern J 91:99-114.
25. Posada D, KA Crandall, AR Templeton 2000 GeoDis, a program for the cladistic nested analysis of the geographical distribution of genetic haplotypes. Mol Ecol 9:487-488.
26. Pryor KV, JE Young, FJ Rumsey, KJ Edwards, MW Bruford, HJ Rogers 2001 Diversity, genetics structure and evidence of outcrossing in British populations of the rock fern Adiantum capillus-veneris using microsatellites. Mol Ecol 10:1881-1894.
27. Ranker TA, CEC Gemmill, PG Trapp 2000 Microevolutionary patterns and processes of the native Hawaiian colonizing fern Odontosoria chinensis (Lindsaesceae). Evolution 54:829-839.
28. Rozas J, JC Sanchez-Delbarrio, X Messeguer, R Rozas 2003 DnaSP, DNA polymorphism analyses by the coalescent and other methods. Bioinformatics 19:2496-2497.
29. Rumsey FJ, SJ Russell, J Ji, M Gibby 1996 Genetic variation in the endangered filmy fern Trichomanes speciosum Willd. Pages 161-165 in JM Camus, M Gibby, RJ Johns, eds. Pteridology in perspective. Royal Botanic Gardens, London.
30. Schneider S, D Roessli, L Excoffier 2000 ARLEQUIN, version 2.000: a software for population genetics data analysis. Genetics and Biometry Laboratory, University of Geneva.
31. Schneller J, R Holderegger, F Guguerli, K Eichenberger, E Lutz 1998 Patterns of genetic variation detected by RAPDs suggests a single origin with subsequent mutations and long-distance dispersal in the apomictic fern Dryopteris remota (Dryopteridaceae). Am J Bot 85: 1038-1042.
32. Shi YF, JJ Li, BY Li 1998 Uplift and environmental changes of Qinghai-Tibetan Plateau in the Late Cenozoic. Guangdong Science and Technology Press, Guangzhou.
33. Small R, RJ Hickey 1997 Levels and patterns of genetic variation in Isoetes karstenii with observations on I. palmeri. Am Fern J 87:104-115.
34. Su YJ, T Wang, B Zheng, Y Jiang, GP Chen, PY Ouyang, YF Sun 2005a Genetic differentiation of relictual populations of Alsophila spinulosa in southern China inferred from cpDNA trnL-F noncoding sequences. Mol Phylogenet Evol 34:323-333.
35. Su YJ, T Wang, B Zheng, Y Jiang, PY Ouyang, GP Chen 2005b Genetic variation and phylogeographical patterns in Alsophila podophylla from Southern China based on cpDNA atpB-rbcL sequence data. Am Fern J 95:68-79.
36. Sun H 2002 Tethys retreat and Himalaya-Hengduanshan Mountains uplift and their significance on the origin and development of the Sino-Himalayan elements and alpine flora. Acta Bot Yunnan 24: 273-288.
37. Taberlet P, L Fumagalli, AG Wust-Saucy, JF Cosson 1998 Comparative phylogeography and postglacial colonization routes in Europe. Mol Ecol 7:453-464.
38. Taberlet P, L Gielly, G Pautou, J Bouvet 1991 Universal primers for amplification of three non-coding regions of chloroplast DNA. Plant Mol Biol 17:1105-1109.
39. Tajima F 1989 Statistical method for testing the neutral mutation hypothesis by DNA polymorphism. Genetics 123:585-595.
40. Taylor WC, RJ Hickey 1992 Habitat, evolution, and speciation in Isoetes. Ann Mo Bot Gard 79:613-622.
41. Templeton AR 2004 Statistical phylogeography: methods of evaluating and minimizing inference errors. Mol Ecol 13:789-809.
42. Templeton AR, E Routman, CA Philips 1995 Separating population structure from population history: a cladistic analysis of the geographical distribution of mitochondria DNA haplotypes in the tiger salamander, Ambystoma tigrinum. Genetics 140:767-782.
43. Templeton AR, CF Sing 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.
44. Thompson JD, TJ Gibson, F Plewniak, F Jeanmougin, DG Higgins 1997 The ClustalX windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res 24:4876-4882.
45. Trewick SA, M Morgan-Richards, SJ Russell, S Henderson, FJ Rumsey, I Pinter, A Barrett, M Gibby, JC Vogel 2002 Polyploidy, phylogeography, and Pleistocene refugia of the rockfern Asplenium ceterach: evidence from chloroplast DNA. Mol Ecol 11:2003-2012.
46. Trewick SA, GP Wallis, M Morgan-Richards 2000 Phylogeographical pattern correlates with Pliocene mountain building in the alpine scree weta (Orthoptera, Anostostomatidae). Mol Ecol 9:657-666.
47. Van Zanten BO 1978 Experimental studies of trans-oceanic longrange dispersal of moss spores in the Southern Hemisphere. J Hatton Bot Lab 44:455-482.
48. Yu YF 1999 A milestone of wild plant conservation in China. Plants 5:3-11.
49. Zhang DF, L Fengquan, B Jianmin 2000 Eco-environmental effects of the Qinghai-Tibet Plateau uplift during the Quaternary in China. Environ Geol 39:1352-1358.