Population structure and phylogeography of Aphyocypris kikuchii (Oshima) based on mitochondrial DNA variation

Journal of Fish Biology

Volumn 72, Issue 8, 2008, Pages 2011-2025

  Lin, H D ^a   Hsu, K C ^a,b   Shao, K T ^b   Chang, Y C ^c   Wang, J P ^a   Lin, C J ^a   Chiang, T Y ^a  

^a NATIONAL CHENG KUNG UNIVERSITY   (Taiwan)

^b BIODIVERSITY RESEARCH CENTER   (Taiwan)

^c TZU CHI UNIVERSITY   (Taiwan)

Author keywords

Demographic expansion; Freshwater fish; Geographical structuring; Most recent common ancestor; Taiwan; Vicariance

Indexed keywords

APHYOCYPRIS KIKUCHII; CYPRINIDAE;

EID: 44949167688     PISSN: 00221112     EISSN: 10958649     Source Type: Journal    
DOI: 10.1111/j.1095-8649.2008.01836.x     Document Type: Article

References (41)

1. Alves, M. J., Coelho, H., Collares-Pereira, M. J. Coelho, M. M 2001). Mitochondrial DNA variation in the highly endangered cyprinid fish Anaecypris hispanica: importance for conservation. Heredity 87, 463 473.
2. Avise, J. C., Neigel, J. E. Arnold, J 1984). Demographic influences on mitochondrial DNA lineage survivorship in animal populations. Journal of Molecular Evolution 20, 99 105.
3. Bermingham, E. Martin, A. P 1998). Comparative mtDNA phylogeography of neotropical freshwater fish: testing shared history to infer the evolutionary landscape of lower Central America. Molecular Ecology 7, 499 517.
4. Blin, N. Stafford, D. W 1976). A general method for isolation of high molecular weight DNA from eukaryotes. Nucleic Acids Research 3, 2303 2308.
5. Cheng, H. L., Huang, S. Lee, S. C 2005). Morphological and molecular variation in Rhinogobius rubromaculatus (Pisces: Gobiidae) in Taiwan. Zoological Studies 44, 119 129.
6. Crandall, K. A. Templeton, A. R 1993). Empirical tests of some predictions from coalescent theory with applications to intraspecific phylogeny reconstruction. Genetics 134, 959 969.
7. Excoffier, L. Smouse, P. E 1994). Using allele frequencies and geographic subdivision to reconstruct gene trees within a species: molecular variance parsimony. Genetics 136, 343 359.
8. Felsenstein, J 1985). Confidence limits on phylogenies: an approach using the bootstrap. Evolution 39, 783 791.
9. Gelas, K. D. Meester, L. D 2005). Phylogeography of Daphnia magna in Europe. Molecular Ecology 14, 753 764.
10. Grant, W. S. Bowen, B. W 1998). Shallow population histories in deep evolutionary lineages of marine fishes: insights from sardines and anchovies and lessons for conservation. Journal of Heredity 89, 415 426.
11. Han, C. C., Tew, K. S., Chen, I. S., Su, L. Y. Fang, L. S 2000). Environmental biology of an endemic cyprinid, Varicorhinus alticorpus, in a subtropical mountain stream of Taiwan. Environmental Biology of Fishes 59, 153 161.
12. Hasegawa, M., Kishino, H. Yano, T 1985). Dating of the human-ape splitting by a molecular clock of mitochondrial DNA. Journal of Molecular Evolution 21, 160 174.
13. Hillis, D. M. Bull, J. J 1993). An empirical test of bootstrapping as a method assessing confidence in phylogenetic analysis. Systematic Biology 42, 182 192.
14. Jukes, T. H. Cantor, C. R 1969). Evolution of protein molecules. In Mammalian Protein Metabolism (Munro, H. N., ed. pp. 31 132. New York : Academic Press.
15. Kumar, S., Tamura, K., Jakobsen, I. B. Nei, M 2001). MEGA2: Molecular Evolutionary Genetics Analysis software. Bioinformatics 17, 1244 1245.
16. Liao, T. Y., Lin, H. D., Tao, T. L. Tzeng, C. S 2005). The forgotten rare and endangered fishes in Taiwan. Quarterlies Journal of Research 50, 52 58 (in Chinese).
17. Lin, C. C 1966). An outline of Taiwan's quaternary geohistory with a special discussion of the relation between natural history and cultural history in Taiwan. Bulletin of the Department of Archaeology and Anthropology 23, 7 44.
18. Lundberg, J. G 1993). African-South American freshwater fish clades and continental drift, problems with a paradigm. In Biotic Relationships Between Africa and South America (Goldblatt, P., ed. pp. 156 198. New Haven : Yale University Press.
19. Meffe, G. K. Vrijenhoek, R. C 1988). Conservation genetics in the management of desert fishes. Conservation Biology 2, 157 169.
20. Moritz, C 1994). Defining 'Evolutionarily Significant Units' for conservation. Trends in Ecology & Evolution 9, 373 375.
21. Nei, M 1987). Molecular Evolutionary Genetics. New York : Columbia University Press.
22. Nei, M. Tajima, F 1983). Maximum likelihood estimation of the number of nucleotide substitutions from restriction sites data. Genetics 105, 207 217.
23. Page, B. M. Suppe, J 1981). The Pliocene lichi melange of Taiwan: its plate tectonic and olistostromal origin. American Journal of Science 281, 193 227.
24. Perdices, A., Cunha, C. Coelho, M. M 2004). Phylogenetic structure of Zacco platypus (Teleostei, Cyprinidae) populations on the upper and middle Chang Jiang (= Yangtze) drainage inferred from cytochrome b sequences. Molecular Phylogenetics and Evolution 31, 192 203.
25. Posada, D. Crandall, K. A 1998). MODELTEST: testing the model of DNA substitution. Bioinformatics 14, 817 818.
26. Rambaut, A. Drummond, A 2004). Tracer - MCMC Trace Analysis Tool. Oxford : Oxford University.
27. Riginos, C. Nachman, M. W 2001). Population subdivision in marine environments: the contributions of biogeography, geographical distance and discontinuous habitat to genetic differentiation in a blennioid fish, Axoclinus nigricaudus. Molecular Ecology 10, 1439 1453.
28. Rogers, A. R. Harpending, H 1992). Population growth makes waves in the distribution of pairwise genetic differences. Molecular Biology and Evolution 9, 552 569.
29. Rozas, J. Rozas, R 1999). DnaSP version 3.0: an integrated program for molecular population genetics and molecular evolution analysis. Bioinformatics 15, 174 175.
30. Salzburger, W., Brandstatter, A., Gilles, A., Parson, W., Hempel, M., Sturmbauer, C. Meyer, A 2003). Phylogeography of the vairone (Leuciscus souffia, Risso 1826) in Central Europe. Molecular Ecology 12, 2371 2386.
31. Slatkin, M. Hudson, R. R 1991). Pairwise comparisons of mitochondrial DNA sequences in stable and exponentially growing populations. Genetics 129, 555 562.
32. Slechtova, V., Bohlena, J., Freyhofb, J., Persatc, H. Delmastrod, G. B 2004). The Alps as barrier to dispersal in cold-adapted freshwater fishes? Phylogeographic history and taxonomic status of the bullhead in the Adriatic freshwater drainage. Molecular Phylogenetics and Evolution 33, 225 239.
33. Tajima, F 1989). Statistical method for testing the neutral mutation hypothesis by DNA polymorphism. Genetics 123, 585 595.
34. Templeton, A. R., Boerwinkle, E. Sing, C. F 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.
35. Thompson, J. D., Gibson, T. J., Plewniak, F., Jeanmougin, F. Higgins, D. G 1997). The Clustal X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Research 25, 4876 4882.
36. Tzeng, C. S 1986). Distribution of the freshwater fishes of Taiwan. Journal of Taiwan Museum 39, 127 146.
37. Wang, J. P., Hsu, K. C. Chiang, T. Y 2000). Mitochondrial DNA phylogeography of Acrossocheilus paradoxus (Cyprinidae) in Taiwan. Molecular Ecology 9, 1483 1494.
38. Wang, J. P., Lin, H. D., Huang, S., Pan, C. H., Chen, X. L. Chiang, T. Y 2004). Phylogeography of Varicorhinus barbatulus (Cyprinidae) in Taiwan based on nucleotide variation of mtDNA and allozymes. Molecular Phylogenetics and Evolution 31, 1143 1156.
39. Yu, H. S. Song, G. S 1994). Oblique convergence between trench-arc system and continent-implications for the formation of the submarine physiography off southern Taiwan. Acta Oceanographica Taiwanica 32, 45 53.
40. Drummond, A. J. Rambaut, A 2003). BEAST. Version 1.3. Oxford : Oxford University Press. Available at http://evolve.zoo.ox.ac.uk/beast/
41. Schneider, S., Roessli, J. D. Excoffier, L 2000). arlequin Version 2.000. A Software for Population Genetic Data Analysis. Genetics and Biometry Laboratory. Switzerland : University of Geneva. Available at http://anthro.unige.ch/arlequin.