- About this Journal ·
- Abstracting and Indexing ·
- Advance Access ·
- Aims and Scope ·
- Annual Issues ·
- Article Processing Charges ·
- Articles in Press ·
- Author Guidelines ·
- Bibliographic Information ·
- Citations to this Journal ·
- Contact Information ·
- Editorial Board ·
- Editorial Workflow ·
- Free eTOC Alerts ·
- Publication Ethics ·
- Reviewers Acknowledgment ·
- Submit a Manuscript ·
- Subscription Information ·
- Table of Contents
BioMed Research International
Volume 2013 (2013), Article ID 170980, 14 pages
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.
- 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.
- C. K. Ng, Kings of the Rivers: Mahseer in Malaysia and the Region, Inter Sea Fishery (M), Kuala Lumpur, Malaysia, 2004.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- J. C. Avise, Molecular Markers, Natural History and Evolution, Chapman and Hall, New York, NY, USA, 1994.
- 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.
- D. L. Swofford, PAUP*: pylogenetic analysis using parsimony (* and other Methods), V 4. 0b10, Sinaeur Associates, Sunderland, Mass, USA, 2001.
- J. C. Avise, Phylogeography: The History and Formation of Species, Harvard University Press, Cambridge, Mass, USA, 2000.
- F. R. Inger and P. K. Chin, The Freshwater Fishes of North Borneo, Natural History Publications, Kota Kinabalu, Malaysia, 2002.
- M. Kottelat, A. J. Whitten, S. N. Kartikasari, and S. Wirjoatmodjo, Freshwater Fishes of Western Indonesia and Sulawesi, Periplus Edition, Singapore, 1993.
- A. K. M. Mohsin and M. A. Ambak, Freshwater Fishes of Peninsular Malaysia, Universiti Pertanian Malaysia Publication, Serdang, Malysia, 1983.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- D. Posada and K. A. Crandall, “MODELTEST: testing the model of DNA substitution,” Bioinformatics, vol. 14, no. 9, pp. 817–818, 1998.
- 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.
- 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.
- 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.
- J. Felsenstein, “Confidence limits on phylogenies: an approach using the bootstrap,” Evolution, vol. 7, pp. 1193–1204, 1985.
- F. Ronquist and J. P. Huelsenbeck, “MrBayes 3: bayesian phylogenetic inference under mixed models,” Bioinformatics, vol. 19, no. 12, pp. 1572–1574, 2003.
- 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.
- 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.
- J. Goudet, “FSTAT version 1.2: a computer program to calculate F-statistics,” Heredity, vol. 86, no. 6, pp. 485–486, 1995.
- 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.
- M. Raymond and F. Rousset, “GENEPOP: population genetic software for exact test ecumenicism,” Journal of Heredity, vol. 86, pp. 248–249, 1995.
- 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.
- S. Wright, Evolution and the Genetics of Populations. Vol 2, the theory of Gene Frequencies, University of Chicago Press, Chicago, Ill, USA, 1969.
- W. R. Rice, “Analysing tables of statistical tests,” Evolution, vol. 43, pp. 223–225, 1989.
- 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.
- M. Nei, “Estimation of average heterozygosity and genetic distance from a small number of individuals,” Genetics, vol. 89, no. 3, pp. 583–590, 1978.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- B. P. Keong, Morphological and genetic analysis of Tor tambroides [M.S. thesis], Universiti Putra Malaysia, Selangor, Malaysia, 2006.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.