The phylogeography and population demographics of selected freshwater fishes in Taiwan

Zoological Studies

Volumn 45, Issue 3, 2006, Pages 285-297

  Tzeng, Chyng Shyan ^a   Lin, Yeong Shin ^a,b   Lin, Si Min ^a,c   Wang, Tzi Yuan ^a,d   Wang, Feng Yung ^a  

^a NATIONAL TSING HUA UNIVERSITY   (Taiwan)

^b NATIONAL CHIAO TUNG UNIVERSITY   (Taiwan)

^c CHINESE CULTURE UNIVERSITY   (Taiwan)

^d GENOMICS RESEARCH CENTER   (Taiwan)

Author keywords

Biogeography; Conservation; Evolution; Mitochondrial control region; Mutation rate

Indexed keywords

CALLOGOBIUS ATRATUS; MACROPODUS OPERCULARIS; ONCORHYNCHUS; ONCORHYNCHUS MASOU; ORYZIAS; ORYZIAS LATIPES; PISCES; RHINOGOBIUS GIURINUS;

EID: 33749666857     PISSN: 10215506     EISSN: 1810522X     Source Type: Journal    
DOI: None     Document Type: Article

References (56)

1. Arbogast BS, JB Slowinski. 1998. Pleistocene speciation and the mitochondrial DNA clock. Science 282: 1955a.
2. Arbogast BS, SV Edwards, J Wakeley, P Beerli, JB Slowinski. 2002. Estimating divergence times from molecular data on phylogenetic and population genetic timescales. Annu. Rev. Ecol. Syst. 33: 707-740.
3. Bagley MJ, GAE Gall. 1998. Mitochondrial and nuclear DNA sequence variability among populations of rainbow trout (Oncorhynchus mykiss). Mol. Ecol. 7: 945-961.
4. Balakrishnan CN, SL Monfort, A Gaur, L Singh, MD Sorenson. 2003. Phylogeography and conservation genetics of Eld's deer (Cervus eldi). Mol. Ecol. 12: 1-10.
5. Bonnin I, B Colas, C Bacles, AC Holl, F Hendoux, B Destine, F Viard. 2002. Population structure of an endangered species living in contrasted habitats: Parnassia palustris (Saxifragaceae). Mol. Ecol. 11: 979-990.
6. Chen IS. 1994. The systematic studies of Rhinogobius brunneus complex from Taiwan. Master thesis, National Sun Yat-Sen University, Kaohsiung. (in Chinese with English abstract)
7. Chen IS, CH Hsu, CF Hui, KT Shao, PJ Miller, LS Fang. 1998. Sequence length and variation in the mitochondrial control region of two freshwater gobiid fishes belonging to Rhinogobius (Teleostei: Gobioidei). J. Fish Biol. 53: 179-191.
8. Cox AJ, PD Hebert. 2001. Colonization, extinction, and phylogeographic patterning in a freshwater crustacean. Mol. Ecol. 10: 371-386.
9. Donaldson KA, RR Jr Wilson. 1999. Amphi-panamic geminates of snook (Perciformes: Centropomidae) provide a calibration of the divergence rate in the mitochondrial DNA control region of fishes. Mol. Phylogenet. Evol. 13: 208-213.
10. Emery KO, H Nino, B Sullivan. 1971. Post-Pleistocene levels of the East China Sea. In KK Turekian, ed. The Late Cenozoic Glacial Ages. New Haven, CT: Yale University Press, pp. 381-390.
11. Felsenstein J. 1985. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 39: 783-791.
12. Frankham R. 1999. Quantitative genetics in conservation biology. Genet. Res. 74: 237-244.
13. Fu YX. 1997. Statistical tests of neutrality of mutations against population growth, hitchhiking and background selection. Genetics 147: 915-925.
14. Fu YX, WH Li. 1993. Statistical tests of neutrality of mutations. Genetics 133: 693-709.
15. Hsu B, WL Wang, TQ Lee, SR Song. 2005. Based on the fossil diatom records reconstruct the paleoclimate changes from Yilan during the last 45 kyrs. Abstract of 2005 Annual Join Symposium of Animal Behavior and Ecology, Society of Stream and Society of Biology, Taiwan, pp. 34.
16. Huang CY, PM Liew, M Zhao, Z An, TC Chang, CM Kuo, MT Chen, CH Wang, LF Zheng. 1997. Deep sea and lake sediment records of the Southeast Asian paleomonsoons in the last 25,000 kyrs. Earth Planet. Sc. Lett. 146: 59-72.
17. Huang CY, PB Yuan, SR Song, CW Lin, C Wang, MT Chen, CT Shyu, B Karp. 1995. Tectonics of short-lived intra-arc basins in arc-continent collisionterrane of the Costal Range, eastern Taiwan. Tectonics 14: 19-38.
18. Innis MA, DH Gelfand, JJ Sninsky, TJ White. 1989. PCR protocols: a guide to methods and applications. San Diego, CA: Academic Press.
19. Kimura M. 1969. The rate of molecular evolution considered from the standpoint of population genetics. Proc. Natl. Acad. Sci. USA 63: 1181-1188.
20. Kocher TD, KL Carleton. 1997. Base substitution in fish mitochondrial DNA: Patterns and rates. In TD Kocher, CA Stepien, eds. Molecular systematics of fishes. San Diego, CA: Academic Press. pp. 13-24.
21. Kocher TD, WK Thomas, A Meyer, SV Edwards, S Pääbo, FX Villablanca, AC Wilson. 1989. Dynamics of mitochondrial DNA evolution in animals: amplification and sequencing with conserved primers. Proc. Natl. Acad. Sci. USA 86: 6196-6200.
22. Kumar S, K Tamura, M Nei. 1993. MEGA: Molecular Evolutionary Genetics Analysis, version 1.02. University Park, PA: Pennsylvania State Univ.
23. Liew PM. 1994. Palynological study of Quaternary lake deposits in Yuan-Shan Ilan. NSC82-0202-M002-113. Taipei, Taiwan: National Science Council, (in Chinese with English abstract)
24. Lin SM. 1995. Characterization of Medaka fish (Oryzias latipes) mtDNA D-loop. Master's thesis, National Tsing Hua Univ., Hsinchu, Taiwan, (in Chinese with English abstract)
25. Lin SM, YS Lin, CF Huang, CS Tzeng. 1999. The phylogenetic study on the endangered ricefish (Oryzias latipes) from Taiwan. Acta Zool. Taiwanica 10: 75.
26. Lin YS, YP Poh, CS Tzeng. 2001. A phylogeny of freshwater eels inferred from mitochondrial genes. Mol. Phylogenet. Evol. 20: 252-261.
27. McKay SJ, RH Devlin, MJ Smith. 1996. Phylogeny of Pacific salmon and trout based on growth hormone type 2 and mitochondrial NADH dehydrogenase subunit 3 DNA sequences. Can. J. Fish. Aquat. Sci. 53: 1165-1176.
28. Miller LM, AR Kapuscinski. 1997. Historical analysis of genetic variation reveals low effective population size in a northern pike (Esox lucius) population. Genetics 147: 1249-1258.
29. Numachi K, T Kobayashi, KH Chang, YS Lin. 1990. Genetic identification and differentiation of the Formosan land-locked salmon, Oncorhynchus masou formosanus, by restriction analysis of mitochondrial DNA. Bull. Inst. Zool. Acad. Sinica 29: 61-72.
30. O'Brien SJ. 1994. A role for molecular genetics in biological conservation. Proc. Natl. Acad. Sci. USA 91: 5748-5755.
31. Oohara I, K Sawano, T Okazaki. 1997. Mitochondrial DNA sequence analysis of the masu salmon - phylogeny in the genus Oncorhynchus. Mol. Phylogenet. Evol. 7: 71-78.
32. Oshima M. 1919. Contribution to the study of the freshwater fishes of the island of Formosa. Ann. Carn. Mus. 12:169-328.
33. Pestano J, RP Brown, F Rodriguez, A Moreno. 2000. Mitochondrial DNA control region diversity in the endangered blue chaffinch, Fringilla teydea. Mol. Ecol. 9: 1421-1425.
34. Poh YP. 2001. The study of the influence by the process of Taiwan island formation to the population genetics structure of freshwater fishes in Taiwan. Master thesis, National Tsing Hua Univ., Hsinchu, Taiwan. (in Chinese with English abstract)
35. Rogers AR, H Harpending. 1992. Population growth makes waves in the distribution of pairwise genetic differences. Mol. Biol. Evol. 9: 552-569.
36. Rozas J, R Rozas. 1999. DnaSP version 3: an integrated program for molecular population genetics and molecular evolution analysis. Bioinformatics 15: 174-175.
37. Saitou N, M Nei. 1987. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol. Biol. Evol. 4: 406-425.
38. Schneider S, D Roessli, L Excoffier. 2000. Arlequin: a software for population genetics data analysis. Ver 2.000. Geneva: Genetics and Biometry Lab, Department of Anthropology, University of Geneva.
39. Shedlock AM, JD Parker, DA Crispin, TW Pietsch, GC Burmer. 1992. Evolution of the salmonid mitochondrial control region. Mol. Phylogenet. Evol. 1: 179-192.
40. Slatkin M, RR Hudson. 1991. Pairwise comparisons of mitochondrial DNA sequences in stable and exponential growing populations. Genetics 129: 555-562.
41. Taira A, H Tokuyama, W Soh. 1989. Accretion tectonics and evolution of Japan. In Z Ben-Avraham, ed. The evolution of the Pacific Ocean margins. Oxford, UK: Clarendon Press, pp. 100-123.
42. Tajima F. 1989. Statistical method for testing the neutral mutation hypothesis by DNA polymorphism. Genetics 123: 585-595.
43. Tamura K, M Nei. 1993. Estimation of the number of nucleotide substitutions in the control region of mitochondrial DNA in humans and chimpanzees. Mol. Biol. Evol. 10: 512-526.
44. Templeton AR, RJ Robertson, J Brisson, J Strasburg. 2001. Disrupting evolutionary processes: the effect of habitat fragmentation on collared lizards in the Missouri Ozarks. Proc. Natl. Acad. Sci. USA 98: 5426-5432.
45. Teng LS. 1990. Geotectonic evolution of Late Cenozoic arc-continent collision in Taiwan. Tectonophysics 183: 57-76.
46. Thompson J, D Higgins, T Gibson. 1994. 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: 4673-4690.
47. Tzeng CS. 1986. Distribution of the freshwater fishes of Taiwan. J. Taiwan. Mus. 39: 127-146.
48. Tzeng CS, CH Yang. 2003. Population monitoring and ecological investigation of Formosan landlocked salmon Oncorhynchus masou formosanus (VI). Miaoli, Taiwan: Shei-Pa National Park. (in Chinese with English abstract)
49. Uphyrkina O, D Miquelle, H Quigley, C Driscoll, SJ O'Brien. 2002. Conservation genetics of the Far Eastern leopard (Panthera pardus orientalis). J. Hered. 93: 303-311.
50. Wang HY, MP Tsai, MJ Yu, SC Lee. 1999. Influence of glaciation on divergence patterns of the endemic minnow, Zacco pachycaphalus, in Taiwan. Mol. Ecol. 8: 1879-1888.
51. Wang JP, KC Hsu, TY Chiang. 2000. Mitochondrial DNA phylogeography of Acrossocheilus paradoxus (Cyprinidae) in Taiwan. Mol. Ecol. 9: 1483-1494.
52. Watanabe M, YL Lin. 1985. Revision of the salmonid fish in Taiwan. Bull. Biogeogr. Soc. Jpn. 40: 75-84.
53. Watterson GA. 1975. On the number of segregation sites in genetical models without recombination. Theor. Popul. Biol. 7: 256-276.
54. Yang Z 1994. Maximum likelihood phylogenetic estimation from DNA sequences with variable rates over sites: approximate methods. J. Mol. Evol. 39: 306-314.
55. Yasue Y. 1982. The specificity of Formosan landlocked salmon of Tachia River in Taiwan. In E Kimura, ed. Special on freshwater fishes; Oncorhynchus masou et O. rhodurus. Japan: Society of Freshwater Fishes Protection, pp. 143-147. (in Japanese)
56. Zawko G, SL Krauss, KW Dixon, K Sivasithamparam. 2001. Conservation genetics of the rare and endangered Leucopogon obtectus (Ericaceae). Mol. Ecol. 10: 2389-2396.