About this Journal Submit a Manuscript Table of Contents
BioMed Research International
Volume 2013 (2013), Article ID 170980, 14 pages
http://dx.doi.org/10.1155/2013/170980
Research Article

Genetic Structure and Preliminary Findings of Cryptic Diversity of the Malaysian Mahseer (Tor tambroides Valenciennes: Cyprinidae) Inferred from Mitochondrial DNA and Microsatellite Analyses

1Department of Aquaculture, Faculty of Agriculture, Institute of Biosciences, Universiti Putra Malaysia, 43400 Serdang, Selangor, Malaysia
2Department of Aquatic Science, Faculty of Resource Science and Technology, Universiti Malaysia Sarawak, 94300 Kota Samarahan, Sarawak, Malaysia

Received 18 July 2013; Accepted 29 September 2013

Academic Editor: Sankar Subramanian

Copyright © 2013 Yuzine Esa and Khairul Adha Abdul Rahim. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

Linked References

  1. B. A. Litis, S. Sungan, K. Jugang, M. Ibrahim, and H. A. Bin, Features of Indigenous Fish Species Having Potential for Aquaculture, Inland Fisheries Division, Department of Agriculture Publication, Kuching, Malaysia, 1997.
  2. C. K. Ng, Kings of the Rivers: Mahseer in Malaysia and the Region, Inter Sea Fishery (M), Kuala Lumpur, Malaysia, 2004.
  3. S. S. Siraj, Y. B. Esa, B. P. Keong, and S. K. Daud, “Genetic characterization of the two colour-types of Kelah,” Malaysia Applied Biology, vol. 36, pp. 23–29, 2007.
  4. Y. B. Esa, Molecular phylogenetics and population structure of two mahseer species (Tor tambroides and Tor douronensis Valenciennes: Cyprinidae) in Malaysia [Ph.D. thesis], Universiti Putra Malaysia, Selangor, Malaysia, 2009.
  5. Y. B. Esa, S. S. Siraj, S. K. Daud, J. J. R. Ryan, K. A. A. Rahim, and S. G. Tan, “Molecular systematics of mahseers (Cyprinidae) in Malaysia inferred from sequencing of a mitochondrial Cytochrome C Oxidase I (COI) gene,” Pertanika Journal of Tropical Agricultural Science, vol. 31, no. 2, pp. 263–269, 2008. View at Scopus
  6. T. T. T. Nguyen, B. Ingram, S. Sungan et al., “Mitochondrial DNA diversity of broodstock of two indigenous mahseer species, Tor tambroides and T. douronensis (Cyprinidae) cultured in Sarawak, Malaysia,” Aquaculture, vol. 253, no. 1–4, pp. 259–269, 2006. View at Publisher · View at Google Scholar · View at Scopus
  7. T. T. T. Nguyen, U. Na-Nakorn, S. Sukmanomon, and C. ZiMing, “A study on phylogeny and biogeography of mahseer species (Pisces: Cyprinidae) using sequences of three mitochondrial DNA gene regions,” Molecular Phylogenetics and Evolution, vol. 48, no. 3, pp. 1223–1231, 2008. View at Publisher · View at Google Scholar · View at Scopus
  8. Y. B. Esa, S. S. Siraj, S. K. Daud, K. A. A. Rahim, J. R. R. Japning, and S. G. Tan, “Mitochondrial DNA diversity of Tor Tambroides valenciennes (Cyprinidae) from five natural populations in Malaysia,” Zoological Studies, vol. 47, no. 3, pp. 360–367, 2008. View at Scopus
  9. J. J. Dodson, F. Colombani, and P. K. Ng, “Phylogeographic structure in mitochondrial DNA of a South-east Asian freshwater fish, Hemibagrus nemurus (Siluroidei: Bagridae) and Pleistocene sea-level changes on the Sunda shelf,” Molecular Ecology, vol. 4, no. 3, pp. 331–346, 1995. View at Scopus
  10. J. C. Avise, Molecular Markers, Natural History and Evolution, Chapman and Hall, New York, NY, USA, 1994.
  11. S. K. J. McConnell, D. O. F. Skibinski, and G. C. Mair, “Microsatellite markers from a commercially important South-east Asian cyprinid, the silver barb (Barbodes gonionotus Bleeker),” Molecular Ecology Notes, vol. 1, no. 3, pp. 135–136, 2001. View at Publisher · View at Google Scholar · View at Scopus
  12. D. L. Swofford, PAUP*: pylogenetic analysis using parsimony (* and other Methods), V 4. 0b10, Sinaeur Associates, Sunderland, Mass, USA, 2001.
  13. J. C. Avise, Phylogeography: The History and Formation of Species, Harvard University Press, Cambridge, Mass, USA, 2000.
  14. F. R. Inger and P. K. Chin, The Freshwater Fishes of North Borneo, Natural History Publications, Kota Kinabalu, Malaysia, 2002.
  15. M. Kottelat, A. J. Whitten, S. N. Kartikasari, and S. Wirjoatmodjo, Freshwater Fishes of Western Indonesia and Sulawesi, Periplus Edition, Singapore, 1993.
  16. A. K. M. Mohsin and M. A. Ambak, Freshwater Fishes of Peninsular Malaysia, Universiti Pertanian Malaysia Publication, Serdang, Malysia, 1983.
  17. P. M. Grewe, C. C. Krueger, C. F. Aquadro, E. Bermingham, H. L. Kincaid, and B. May, “Mitochondrial DNA variation among lake trout (Salvelinus namaycush) strains stocked into Lake Ontario,” Canadian Journal of Fisheries and Aquatic Sciences, vol. 50, no. 11, pp. 2397–2403, 1993. View at Scopus
  18. S. Palumbi, A. Martin, S. Romano, W. O. McMillan, L. Stice, and G. Grabowski, The Simple Fool’s Guide to PCR, Department of Zoology and Kewalo Marine Laboratory, University of Hawaii, Honolulu, Hawaii, 1991.
  19. T. Nguyen, M. Baranski, M. Rourke, and H. McPartlan, “Characterization of microsatellite DNA markers for a mahseer species, Tor tambroides (Cyprinidae) and cross-amplification in four congeners,” Molecular Ecology Notes, vol. 7, no. 1, pp. 109–112, 2007. View at Publisher · View at Google Scholar · View at Scopus
  20. Y. B. Esa, S. S. Siraj, K. A. A. Rahim et al., “Genetic characterization of two mahseer species (Tor douronensis and Tor tambroides) using microsatellite markers from other cyprinids,” Sains Malaysiana, vol. 40, no. 10, pp. 1087–1095, 2011. View at Scopus
  21. R. P. M. A. Crooijmans, V. A. F. Bierbooms, J. Komen, J. J. Van Der Poel, and M. A. M. Groenen, “Microsatellite markers in common carp (Cyprinus carpio L.),” Animal Genetics, vol. 28, no. 2, pp. 129–134, 1997. View at Scopus
  22. A. Chenuil, N. Galtier, and P. Berrebi, “A test of the hypothesis of an autopolyploid vs. allopolyploid origin for a tetraploid lineage: application to the genus Barbus (Cyprinidae),” Heredity, vol. 82, no. 4, pp. 373–380, 1999. View at Scopus
  23. M. A. Larkin, G. Blackshields, N. P. Brown et al., “Clustal W and Clustal X version 2.0,” Bioinformatics, vol. 23, no. 21, pp. 2947–2948, 2007. View at Publisher · View at Google Scholar · View at Scopus
  24. X. Xia and Z. Xie, “DAMBE: Software package for data analysis in molecular biology and evolution,” Journal of Heredity, vol. 92, no. 4, pp. 371–373, 2001. View at Scopus
  25. N. Saitou and M. Nei, “The neighbor-joining method: a new method for reconstructing phylogenetic trees,” Molecular biology and evolution, vol. 4, no. 4, pp. 406–425, 1987. View at Scopus
  26. D. Posada and K. A. Crandall, “MODELTEST: testing the model of DNA substitution,” Bioinformatics, vol. 14, no. 9, pp. 817–818, 1998. View at Scopus
  27. H. Akaike, “Information theory as an extension of the maximum-likelihood principle,” in Proceedings of the 2nd International Symposium on Information Theory, B. Petrov and F. Csake, Eds., pp. 267–281, Akademiai Kiado, Budapest, Hungary, 1973.
  28. K. Tamura, J. Dudley, M. Nei, and S. Kumar, “MEGA4: molecular evolutionary genetics analysis (MEGA) software version 4.0,” Molecular Biology and Evolution, vol. 24, no. 8, pp. 1596–1599, 2007. View at Publisher · View at Google Scholar · View at Scopus
  29. M. Kimura, “A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences,” Journal of Molecular Evolution, vol. 16, no. 2, pp. 111–120, 1980. View at Scopus
  30. J. Felsenstein, “Confidence limits on phylogenies: an approach using the bootstrap,” Evolution, vol. 7, pp. 1193–1204, 1985.
  31. F. Ronquist and J. P. Huelsenbeck, “MrBayes 3: bayesian phylogenetic inference under mixed models,” Bioinformatics, vol. 19, no. 12, pp. 1572–1574, 2003. View at Publisher · View at Google Scholar · View at Scopus
  32. C. Van Oosterhout, W. F. Hutchinson, D. P. M. Wills, and P. Shipley, “MICRO-CHECKER: software for identifying and correcting genotyping errors in microsatellite data,” Molecular Ecology Notes, vol. 4, no. 3, pp. 535–538, 2004. View at Publisher · View at Google Scholar · View at Scopus
  33. M. Nei, “Analysis of gene diversity in subdivided populations,” Proceedings of the National Academy of Sciences of the United States of America, vol. 70, no. 12, pp. 3321–3323, 1973. View at Scopus
  34. J. Goudet, “FSTAT version 1.2: a computer program to calculate F-statistics,” Heredity, vol. 86, no. 6, pp. 485–486, 1995.
  35. A. El Mousadik and R. J. Petit, “High level of genetic differentiation for allelic richness among populations of the argan tree [Argania spinosa (L.) Skeels] endemic to Morocco,” Theoretical and Applied Genetics, vol. 92, no. 7, pp. 832–839, 1996. View at Publisher · View at Google Scholar · View at Scopus
  36. M. Raymond and F. Rousset, “GENEPOP: population genetic software for exact test ecumenicism,” Journal of Heredity, vol. 86, pp. 248–249, 1995.
  37. B. S. Weir and C. C. Cockerham, “Estimating F-statistics for the analysis of population structure,” Evolution, vol. 38, no. 6, pp. 1358–1370, 1984. View at Scopus
  38. S. Wright, Evolution and the Genetics of Populations. Vol 2, the theory of Gene Frequencies, University of Chicago Press, Chicago, Ill, USA, 1969.
  39. W. R. Rice, “Analysing tables of statistical tests,” Evolution, vol. 43, pp. 223–225, 1989.
  40. L. Excoffier, G. Laval, and S. Schneider, “Arlequin ver. 3. 0: an integrated software package for population genetics data analysis,” Evolutionary Bioinformatics, vol. 1, pp. 47–50, 2005.
  41. M. Nei, “Estimation of average heterozygosity and genetic distance from a small number of individuals,” Genetics, vol. 89, no. 3, pp. 583–590, 1978. View at Scopus
  42. F. C. Yeh and T. H. B. Boyle, “Population genetic analysis of codominant and dominant markers and quantitative traits,” Journal of Botany, vol. 129, p. 157, 1997.
  43. S. Piry, A. Alapetite, J.-M. Cornuet, D. Paetkau, L. Baudouin, and A. Estoup, “GENECLASS2: a software for genetic assignment and first-generation migrant detection,” Journal of Heredity, vol. 95, no. 6, pp. 536–539, 2004. View at Publisher · View at Google Scholar · View at Scopus
  44. B. Rannala and J. L. Mountain, “Detecting immigration by using multilocus genotypes,” Proceedings of the National Academy of Sciences of the United States of America, vol. 94, no. 17, pp. 9197–9201, 1997. View at Publisher · View at Google Scholar · View at Scopus
  45. D. Paetkau, R. Slade, M. Burden, and A. Estoup, “Genetic assignment methods for the direct, real-time estimation of migration rate: a simulation-based exploration of accuracy and power,” Molecular Ecology, vol. 13, no. 1, pp. 55–65, 2004. View at Publisher · View at Google Scholar · View at Scopus
  46. J. K. Pritchard, M. Stephens, and P. Donnelly, “Inference of population structure using multilocus genotype data,” Genetics, vol. 155, no. 2, pp. 945–959, 2000. View at Scopus
  47. S. Piry, G. Luikart, and J.-M. Cornuet, “BOTTLENECK: a computer program for detecting recent reductions in the effective population size using allele frequency data,” Journal of Heredity, vol. 90, no. 4, pp. 502–503, 1999. View at Publisher · View at Google Scholar · View at Scopus
  48. J. M. Cornuet and G. Luikart, “Description and power analysis of two tests for detecting recent population bottlenecks from allele frequency data,” Genetics, vol. 144, no. 4, pp. 2001–2014, 1996. View at Scopus
  49. A. Di Rienzo, A. C. Peterson, J. C. Garza, A. M. Valdes, M. Slatkin, and N. B. Freimer, “Mutational processes of simple-sequence repeat loci in human populations,” Proceedings of the National Academy of Sciences of the United States of America, vol. 91, no. 8, pp. 3166–3170, 1994. View at Scopus
  50. C. Maudet, C. Miller, B. Bassano et al., “Microsatellite DNA and recent statistical methods in wildlife conservation management: applications in Alpine ibex [Capra ibex (ibex)],” Molecular Ecology, vol. 11, no. 3, pp. 421–436, 2002. View at Publisher · View at Google Scholar · View at Scopus
  51. G. Luikart, F. W. Allendorf, J.-M. Cornuet, and W. B. Sherwin, “Distortion of allele frequency distributions provides a test for recent population bottlenecks,” Journal of Heredity, vol. 89, no. 3, pp. 238–247, 1998. View at Publisher · View at Google Scholar · View at Scopus
  52. J. Briolay, N. Galtier, R. M. Brito, and Y. Bouvet, “Molecular phylogeny of cyprinidae inferred fromcytochrome bDNA Sequences,” Molecular Phylogenetics and Evolution, vol. 9, no. 1, pp. 100–108, 1998. View at Publisher · View at Google Scholar · View at Scopus
  53. J. A. DeWoody and J. C. Avise, “Microsatellite variation in marine, freshwater and anadromous fishes compared with other animals,” Journal of Fish Biology, vol. 56, no. 3, pp. 461–473, 2000. View at Publisher · View at Google Scholar · View at Scopus
  54. B. P. Keong, Morphological and genetic analysis of Tor tambroides [M.S. thesis], Universiti Putra Malaysia, Selangor, Malaysia, 2006.
  55. V. Mohindra, A. Ranjana, L. Khulbe, A. G. Ponniah, and K. K. Lal, “Microsatellite loci to assess genetic variation in Tor putitora,” Journal of Applied Ichthyology, vol. 20, no. 6, pp. 466–469, 2004. View at Publisher · View at Google Scholar · View at Scopus
  56. T. T. T. Nguyen, “Population structure in the highly fragmented range of Tor douronensis (Cyprinidae) in Sarawak, Malaysia revealed by microsatellite DNA markers,” Freshwater Biology, vol. 53, no. 5, pp. 924–934, 2008. View at Publisher · View at Google Scholar · View at Scopus
  57. R. M. Barroso, A. W. S. Hilsdorf, H. L. M. Moreira, P. H. Cabello, and Y. M. Traub-Cseko, “Genetic diversity of wild and cultured populations of Brycon opalinus (Cuvier, 1819) (Characiforme, Characidae, Bryconiae) using microsatellites,” Aquaculture, vol. 247, no. 1–4, pp. 51–65, 2005. View at Publisher · View at Google Scholar · View at Scopus
  58. V. Castric, L. Bernatchez, K. Belkhir, and F. Bonhomme, “Heterozygote deficiencies in small lacustrine populations of brook charr Salvelinus fontinalis Mitchill (Pisces, Salmonidae): a test of alternative hypotheses,” Heredity, vol. 89, no. 1, pp. 27–35, 2002. View at Publisher · View at Google Scholar · View at Scopus
  59. G. H. Yue, Y. Li, L. C. Lim, and L. Orban, “Monitoring the genetic diversity of three Asian arowana (Scleropages formosus) captive stocks using AFLP and microsatellites,” Aquaculture, vol. 237, no. 1–4, pp. 89–102, 2004. View at Publisher · View at Google Scholar · View at Scopus
  60. P. Angel, G. Mercedes, L. Philippe, M. Concepcion, and A. Jose, “Effects of fishing protection on the genetic structure of fish populations,” Biological Conservation, vol. 129, no. 2, pp. 244–255, 2006. View at Publisher · View at Google Scholar · View at Scopus
  61. M. O. Bergh and W. M. Getz, “Stability and harvesting of competing populations with genetic variation in life history strategy,” Genetics, vol. 113, pp. 939–965, 1989. View at Scopus
  62. R. G. Harrison, “Animal mitochondrial DNA as a genetic marker in population and evolutionary biology,” Trends in Ecology and Evolution, vol. 4, no. 1, pp. 6–11, 1989. View at Scopus
  63. C. Wang, X. Yu, and J. Tong, “Microsatellite diversity and population genetic structure of redfin culter (Culter erythropterus) in fragmented lakes of the Yangtze River,” Hydrobiologia, vol. 586, no. 1, pp. 321–329, 2007. View at Publisher · View at Google Scholar · View at Scopus
  64. J. F. Y. Brookfield, “A simple new method for estimating null allele frequency from heterozygote deficiency,” Molecular Ecology, vol. 5, no. 3, pp. 453–455, 1996. View at Scopus
  65. H. K. Voris, “Maps of pleistocene sea levels in Southeast Asia: shorelines, river systems and time durations,” Journal of Biogeography, vol. 27, no. 5, pp. 1153–1167, 2000. View at Publisher · View at Google Scholar · View at Scopus
  66. J. R. J. Ryan and Y. B. Esa, “Phylogenetic analysis of Hampala fishes (subfamily cyprininae) in Malaysia inferred from partial mitochondrial cytochrome b DNA sequences,” Zoological Science, vol. 23, no. 10, pp. 893–901, 2006. View at Publisher · View at Google Scholar · View at Scopus
  67. Y. B. Esa, J. M. Waters, and G. P. Wallis, “Introgressive hybridization between Galaxias depressiceps and Galaxias sp D (Teleostei: Galaxiidae) in Otago, New Zealand: secondary contact mediated by water races,” Conservation Genetics, vol. 1, no. 4, pp. 329–339, 2000. View at Scopus