The utility of AFLPs for supporting mitochondrial DNA phylogeographical analyses in the Taiwanese bamboo viper, Trimeresurus stejnegeri

Journal of Evolutionary Biology

Volumn 17, Issue 1, 2004, Pages 100-107

  Creer, S ^a   Thorpe, R S ^a   Malhotra, A ^a   Chou, W H ^b   Stenson, A G ^a  

^a BANGOR UNIVERSITY   (United Kingdom)

^b NATIONAL MUSEUM OF NATURAL SCIENCE   (Taiwan)

Author keywords

AFLP; Mitochondrial DNA; Phylogeography; Taiwan; Trimeresurus stejnegeri

Indexed keywords

MITOCHONDRIAL DNA; PRIMER DNA;

EVOLUTION; MITOCHONDRIAL DNA; PHYLOGEOGRAPHY; SNAKE;

ANALYSIS OF VARIANCE; ANIMAL; ARTICLE; BAYES THEOREM; CLUSTER ANALYSIS; COMPARATIVE STUDY; GENETICS; GEOGRAPHY; HAPLOTYPE; MOLECULAR EVOLUTION; PHYLOGENY; POLYACRYLAMIDE GEL ELECTROPHORESIS; POPULATION GENETICS; RESTRICTION FRAGMENT LENGTH POLYMORPHISM; SNAKE; TAIWAN;

ANALYSIS OF VARIANCE; ANIMALS; BAYES THEOREM; CLUSTER ANALYSIS; DNA PRIMERS; DNA, MITOCHONDRIAL; ELECTROPHORESIS, POLYACRYLAMIDE GEL; EVOLUTION, MOLECULAR; GENETICS, POPULATION; GEOGRAPHY; HAPLOTYPES; PHYLOGENY; POLYMORPHISM, RESTRICTION FRAGMENT LENGTH; TAIWAN; TRIMERESURUS;

ASIA; EURASIA; FAR EAST; TAIWAN;

AMPHIBIA; ANIMALIA; REPTILIA; SERPENTES; TRIMERESURUS; TRIMERESURUS STEJNEGERI; VERTEBRATA;

EID: 0842265971     PISSN: 1010061X     EISSN: None     Source Type: Journal    
DOI: 10.1046/j.1420-9101.2003.00642.x     Document Type: Article

References (54)

1. Albertson, R.C., Markert, J.A., Danley, P.D. & Kocher, T.D. 1999. Phylogeny of a rapidly evolving clade: the cichlid fishes of Lake Malawi, East Africa. Proc.Natl. Acad. Sci. U. S. A. 96: 5107-5110.
2. Avise, J.C. 1989. Gene trees and organismal histories: a phylogenetic approach to population biology. Evolution 43: 1192-1208.
3. Avise, J.C. 1994. Molecular Markers, Natural History and Evolution. Chapman and Hall, New York.
4. Avise, J.C. 1998. The history and purview of phylogeography: a personal reflection. Mol. Ecol. 7: 371-379.
5. Avise, J.C., Arnold, J., Ball, R.M., Bermingham, E., Lamb, T., Neigel, J.E., Reeb, C.A. & Saunders, N.C. 1987. Intraspecific phylogeography: the mitochondrial DNA bridge between population genetics and systematics. Ann. Rev. Ecol. Syst. 18: 489-522.
6. Brooks, D.R., Mayden, R.L., McLennan, D.A. 1992. Phylogeny and biodiversity: conserving our evolutionary legacy. TREE 7: 55-59.
7. Cockerham, C.C. 1969. Variance of gene frequencies. Evolution 23: 72-84.
8. Congiu, L., Dupanloup, I., Patarnello, T., Fontana, F., Rossi, R., Arlatis, G. & Zane, L. 2001. Identification of interspecific hybrids by amplified fragment length polymorphism: the case of sturgeon. Mol. Ecol. 10: 2355-2359.
9. Couper, A. 1983. The Times Atlas of the Oceans. Mandadaui, Verona.
10. Creer, S., Malhotra, A., Thorpe, R.S. & Chou, W.-H. 2001. Multiple causation of phylogeographical pattern as revealed by nested clade analysis of the bamboo viper (Trimeresurus stejnegeri) within Taiwan. Mol. Ecol. 10: 1967-1981.
11. Da Silva, M.N.F. & Patton, J.L. 1998. Molecular phylogeography and the evolution and conservation of Amazonian mammals. Mol. Ecol. 7: 475-486.
12. Dowling, T.E., Moritz, C., Palmer, J.D., & Rieseberg, L.M. 1996. Nucleic acids III: Analysis of fragments and restriction sites. In: Molecular Systematics, 2nd edn (D.M. Hillis, B.K. Mable, C. Moritz eds), pp. 249-320. Sinauer Associates, Inc. Sunderland, Massachusetts, USA.
13. Excoffier, L., Smouse, P.E. & Quattro, J.M. 1992. Analysis of molecular variance inferred from metric distances among DNA haplotypes: application to human mitochondrial DNA restriction data. Genetics 131: 479-491.
14. Felsenstein, J. 1985. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 39: 783-791.
15. García, J., Maekawa, K., Miura, T. & Matsumoto, T. 2002. Population structure and genetic diversity in insular populations of Nasutitermes takasagoensis (Isoptera: Termitidae) analyzed by AFLP markers. Zool. Sci. 19: 1141-1146.
16. Gaudeul, M., Taberlet, P. & Till-Bottraud, I. 2000. Genetic diversity in an endangered alpine plant, Eryngium alpinum L. (Apiaceae), inferred from amplified fragment length polymorphism markers. Mol. Ecol. 9: 1625-1637.
17. Giannasi, N., Thorpe, R.S. & Malhotra, A. 2001. The use of amplified fragment length polymorphism (AFLP) in determining species trees at fine taxonomic levels: Analysis of a medically important snake, Trimeresurus albolabris. Mol. Ecol. 10: 419-426.
18. Holsinger, K.E. & Lewis, P.O. 2002. Hickory: A Package for Analysis of Population Genetic Data v0.6. Department of Ecology and Evolutionary Biology, U-3043, University of Connecticut, Storrs, CT 06269-3043.
19. Holsinger, K.E., Lewis, E.O. & Dey, D.K. 2002. A Bayesian approach to inferring population structure from dominant markers. Mol. Ecol. 11: 1157-1164.
20. Hsu, V. (1990). Seismicity and tectonics of a Continent-Island arc collision zone at the island of Taiwan. J. Geophys. Res. 95 B4: 4725-4734.
21. Huang, J. 1984. Change of sea-level since the late Pleistocene in China. In: The Evolution of the East Asian Environment (R.O. Whyte ed.), pp. 309-319. Center of Asian Studies, University of Hong Kong.
22. de Knijff, P., Denkers, F., Swelm, N.D.V., Kuiper, M., on behalf of the port of Rotterdam Gull Study Group 2001. Genetic affinities within the herring gull Larus argentatus assemblage revealed by AFLP genotyping. J. Mol. Evol. 52: 85-93.
23. Larson, S.R., Cartier, E., McCracken, C.L. & Dwyer, D. 2001. Mode of reproduction and amplified fragment length polymorphism variation in purple needlegrass (Nassella pulchra): utilisation of natural germplasm sources. Mol. Ecol. 10: 1165-1177.
24. Liebers, D., Heibig, A.J. & de Kniff, P. 2001. Genetic differentiation and phylogeography of gulls in the Larus cachinnans-fuscus group (Aves-Charadriiformes). Mol. Ecol. 10: 2447-2462.
25. Liu, D. & Ding, M. 1984. The characteristics and evolution of the paleoenvironment of China since the late Tertiary. In: The Evolution of the East Asian Environment (R.O. Whyte ed.) pp. 11-40. Center of Asian Studies, University of Hong Kong.
26. Martin, A.P. & Palumbi, S.R. 1993. Body size, metabolic rate, generation time, and the molecular clock. Proc. Natl. Acad. Sci. U. S. A. 90: 4087-4091.
27. Mock, K.E., Theimer, T.C., Rhodes, O.E. Jr., Greenberg, D.L. & Keim, P. 2002. Genetic variation across the historical range of the wild turkey (Meleagris gallopevo). Mol. Ecol. 11: 643-657.
28. Moritz, C. 1995. Uses of molecular phylogenies for conservation. Phil. Trans. Roy. Soc. Lond. B 349: 113-118.
29. Moritz, C. & Faith, D.P. 1998. Comparative phylogeography and the identification of genetically divergent areas for conservation. Mol. Ecol. 7: 419-429.
30. Mueller, U.G. & Wolfenbarger, L.L. 1999. AFLP genotyping and fingerprinting. TREE 14: 389-394.
31. Nijman, I.J., Otsen, M., Verkaar, E.L.C., Ruijter, C. de, Hanekamp, E., Ochieng, J.W., Shamshad, S., Rege, J.E.O., Hanotte, O., Barwegen, M.W., Sulawati, T. & Lenstra, J.A. 2003. Hybridisation of banteng (Bos javanicus) and zebu (Bos indicus) revealed by mitochondrial DNA, satellite DNA, AFLP and microsatellites. Heredity 90:10-16.
32. O'Hanlon, P.C., Peakall, R. & Briese, D.T. (1999). Amplified fragment length polymorphism (AFLP) reveals introgression in weedy Onopordum thistles: hybridization and invasion. Mol. Ecol. 8: 1239-1246.
33. Ogden, R. & Thorpe, R.S. 2002. The usefulness of AFLP markers for taxon discrimination across graduated fine evolutionary levels in Caribbean Anolis lizards. Mol. Ecol. 11: 437-445.
34. Ota, H. 1997. Historical biogeographical implications in the variation and diversity of amphibians and reptiles in Taiwan. In: Proceedings of the Symposium on the Phylogeny, Biogeography and Conservation of Fauna and Flora of East Asian Region (K.-Y. Lue & T.H. Chen eds), pp. 75-86. National Science Council, ROC, Taipei.
35. Page, R.D.M. & Holmes, E.C. 1998. Molecular Evolution. A Phylogenetic Approach. Blackwell Science.
36. Parsons, Y.M. & Shaw, K.L. 2001. Species boundaries and genetic diversity among Hawaiian crickets of the genus Laupala identified using amplified fragment length polymorphism. Mol. Ecol. 10: 1765-1772.
37. Posada, D. & Crandall, K.A. 1998. MODELTEST: testing the model of DNA substitution. Bioinformatics 14: 817-818.
38. Rand, D.M. 1994. Thermal habit, metabolic rate and the evolution of mitochondrial DNA. TREE 9: 125-131.
39. Redecker, D., Szaro, T.M., Bowman, R.J. & Bruns, T.D. 2001. Small genets of Lactarius xanthogalactus, Russula cremoicolor and Amanita francheti in late-stage ectomycorrhizal successions. Mol. Ecol. 10: 1025-1034.
40. Salvato, P., Battisti, A., Concato, S., Masutti, L., Paternello, T. & Zane, L. 2002. Genetic differentiation in the winter pine processionary moth (Thaumetopera pityocampa - wilkinsoni complex), inferred by AFLP and mitochondrial DNA markers. Mol. Ecol. 11: 2435-2444.
41. Sambrook, J., Fritsch, E.F. & Maniatis, T. 1989. Molecular Cloning. A Laboratory Manual, 2nd edn. Cold Spring Harbor Laboratory Press.
42. Schneider, S., Kueffer, J.-M., Roessli, D., & Excoffier, L. 1997. Arlequin ver. 1.1: A Software for Population Genetic Data Analysis. Genetics and Biometry Laboratory, University of Geneva, Switzerland.
43. Sharbel, T.F., Haubold, B. & Mitchell-Olds, T. 2000. Genetic isolation by distance in Arabidopsis thaliana: biogeography and postglacial colonisation of Europe. Mol. Ecol. 9: 2109-2118.
44. Sokal, R.R. & Rohlf, F.J. 1995. Biometry, Third edn. W.H. Freeman and Co., NY.
45. Teo, L.L., Kiew, R., Set, O., Lee, S.K. & Gan, Y.Y. 2002. Hybrid status of kuwini, Mangifera odorata Griff. (Anacardiaceae) verified by amplified fragment length polymorphism. Mol. Ecol. 11: 1465-1469.
46. Toda, M., Nishida, M., Matsui, M., Wu, G.-F. & Ota, H. 1997. Allozyme variation among east asian populations of the Indian Rice Frog, Rana limnocharis (Amphibia: Anura). Biochem. Syst. Ecol 25: 143-159.
47. Toda, M., Nishida, M., Matsui, M., Lue, K.-Y. & Ota, H. 1998. Genetic variation in the Indian rice frog, Rana limnocharis (Amphibia: Anura), in Taiwan, as revealed by allozyme data. Herpetologica 54: 73-82.
48. Vos, P., Hogers, R., Blecker, M., Reijans, M., Lee, T.V., Hornes, M., Frijters, A., Pot, J., Peleman, J., Kuiper, M. & Zabeau, M. 1995. AFLP: a new technique for DNA fingerprinting. Nucl. Acids Res. 23: 4407-4414.
49. Wüster, W., Salomão, M.D.G., Quijada-Mascareñas, J.A., Thorpe, R.S. & BBBSP 2002. Origins and evolution of the South American pitviper fauna: evidence from mitochondrial DNA sequence analysis. In: Biology of the Vipers (G. Schuett, M. Höggren, M. Douglas, H. Greene eds), pp. 111-128. Eagle Mountain Publishing.
50. Yan, G., Romero-Severson, J., Walton, M., Chadee, D.D. & Severson, D.W. 1999. Population genetics of the yellow fever mosquito in Trinidad: comparisons of amplified fragment length polymorphism (AFLP) and restriction fragment length polymorphism (RFLP) markers. Mol. Ecol. 8: 951-964.
51. Yang, Y.-J., Lin, Y.-S., Wu, J.L. & Hui, C.F. 1994. Mitochondrial DNA and population structure of the Taipei treefrog Rhacophorous taipeianus in Taiwan. Mol. Ecol. 3: 219-228.
52. Yu, H.-T. 1995. Patterns of diversification and genetic population structure of small mammalsin Taiwan. Biol. J. Linn. Soc 55:69-89.
53. Zamudio, K.R. & Greene, H.W. 1997. Phylogeography of the bushmaster (Lachesis muta: Viperidae): implications for neotropical biogeography, systematics and conservation. Biol. J. Linn. Soc 62: 421-442.
54. Zawko, G., Krauss, S.L., Dixon, K.W. & Sivasithamparam, K. 2001. Conservation genetics of the rare and endangered Leucopogon obtectus (Ericaceae). Mol. Ecol. 10: 2389-2396.