Cytochrome b gene reveals panmixia among Japanese Threadfin Bream, Nemipterus japonicus (Bloch, 1791) populations along the coasts of Peninsular Malaysia and provides evidence of a cryptic species

References

• Abu Talib A, Mohammad Isa M, Mohamad Saupi I, Sharum Y. (2003). Status of demersal fishery resources of Malaysia. In: Silvestre G, Garces L, Stobutzki I, Ahmed M, Valmonte-Santos RA, Luna C, Lachica-Aliño L, et al., editors. Assessment, management and future directions for coastal fisheries in Asian Countries. Malaysia: World Fish Center Conference Proceedings. p 83–136
   Google Scholar
• Avise JC, Arnold J, Ball RM. (1987). Intraspecific phylogeography: The mitochondrial DNA bridge between population genetics and systematics. Annu Rev Ecol Evol Syst 18:489–522
   Web of Science ®Google Scholar
• Avise JC. (1998). Phylogeography. Cambridge, MA: Harvard University Press
   Google Scholar
• Bailey KM. (1997). Structural dynamics and ecology of flatfish populations. J Sea Res 37:269–80
   Web of Science ®Google Scholar
• Bandelt HJ, Forster P, Sykes BC, Richards MB. (1995). Mitochondrial portraits of human populations using median networks. Genetics 141:743–53
   PubMed Web of Science ®Google Scholar
• Begg GA, Friedland KD, Pearce JB. (1999). Stock Identification – Its role in stock assessment and fisheries management: An overview. Fish Res 43:1–8
   Web of Science ®Google Scholar
• Bowen BW, Bass AL, Rocha LA, Grant WS, Robertson DR. (2001). Phylogeography of the trumpetfishes (Aulostomus): Ring species complex on a global scale. Evolution 55:1029–39
   PubMed Web of Science ®Google Scholar
• Butcher JG. (2004). The closing of the Frontier: A History of marine fisheries of Southeast Asia c. 1850–2000. Singapore: Institute of Southeast Asian Studies (ISEAS)
   Google Scholar
• Chee SY. (2009). Population genetics of the Malaysian blood cockle (Anadara granosa) using RAPD-PCR and partial mtDNA sequencing methods. [Msc Thesis]. Malaysia: University Sains Malaysia
   Google Scholar
• Chen SP, Liu T, Li ZF, Gao TX. (2008). Genetic population structuring and demographic history of red spotted grouper (Epinephelus akaara) in South and East China Sea. Afr J Biotechnol 7:3554–62
   Google Scholar
• Chen XL, Chiang TY, Lin HD, Zheng HS, Shao KT, Zhang Q, Hsu KC. (2007). Mitochondrial DNA phylogeography of (Glyptothorax fokiensis) and (Glyptothorax hainanensis) in Asia. J Fish Biol Supplement A 75–93
   Google Scholar
• Department of Fisheries. (2011). Annual Fisheries Statistics 2011. Malaysia: Department of Fisheries, Ministry of Agriculture. [Online] Available at: http://www.dof.gov.my/html/themes/moa_dof/documents/1.Penulisan.pdf (Accessed 25 February 2013).
   Google Scholar
• Esa YB, Japning JRR, Rahim KA, Siraj SS, Daud S K, Tan SG, Sungan S. (2012). Phylogenetic relationships among several freshwater fishes (Family: Cyprinidae) in Malaysia inferred from partial sequencing of the cytochrome b mitochondrial DNA (mtDNA) gene. Pertanika J Trop Agric Sci 35:307–18
   Google Scholar
• Excoffier L, Laval G, Schneider S. (2007). Arlequin (version 3.11): An integrated software package for population genetics data analysis. Evol Bioinform Online 1:47–50
   PubMed Web of Science ®Google Scholar
• Fauvelot C, Bernardi G, Planes S. (2003). Reduction in the mitochondrial DNA diversity of coral reef fish provides evidence of population bottlenecks resulting from Holocene sea-level change. Evolution 57:1571–83
   PubMed Web of Science ®Google Scholar
• Fisheries Research Institute. (2007). Fisheries Research Institute Trawl Survey Data 2005, 2004, 1997, 1992, 1990. Malaysia: Fisheries Research Institute
   Google Scholar
• Felsenstein J. (1985). Confidence-limits on phylogenies – An approach using the bootstrap. Evolution 39:783–91
   PubMed Web of Science ®Google Scholar
• Fu YX. (1997). Statistical tests of neutrality of mutations against population growth, hitchhiking and background selection. Genetics 147:915–25
   PubMed Web of Science ®Google Scholar
• Garcia SM, Grainger RJR. (2005). Gloom and doom? The future of marine capture fisheries. Phil Trans Royal Soc B 360:21–46
   PubMed Web of Science ®Google Scholar
• Google. (2010). Google Earth (Version 5.1.3535.3218). [Online] Available at: http://www.google.com/earth/index.html (Accessed 5 May 2011).
   Google Scholar
• Grant WS, Bowen BW. (1998). Shallow population histories in deep evolutionary lineages of marine fishes: Insights from sardines and anchovies and lessons for conservation. J Heredity 89:416–26
   Google Scholar
• Great Britain Hydrographic Office. (1958). Malacca Strait pilot. 4th ed. UK: Hydrographic Department, Admiralty. In: Alfaro ME, Karns DR, H. Voris HK, Abernat E, Sellins SL. (2004). Phylogeny of Cerberus (Serpentes: Homalopsinae) and phylogeography of (Cerberus rynchops): diversification of a coastal marine snake in Southeast Asia. J Biogeogr 3:1277–92
   Google Scholar
• Han ZQ, Gao TX, Yanagimoto T, Sakura Y. (2008). Deep phylogeographic break among white croaker Pennahia argentata (Sciaenidae, Perciformes) populations in North-western Pacific. Fish Sci 74:770–80
   Web of Science ®Google Scholar
• Hamzah BA. (1988). Malaysia's Exclusive Economic Zone: A study in legal aspects. Petaling Jaya (Malaysia): Pelanduk Publication
   Google Scholar
• Hellberg ME. (2009). Gene flow and isolation among populations of marine animals. Annu Rev Ecol Evol Syst 40:291–310
   Web of Science ®Google Scholar
• Hewitt GM. (2000). The genetic legacy of the Quaternary ice ages. Nature 405:907–13
   PubMed Web of Science ®Google Scholar
• Hillis DM, Mable BK, Larson A, Davis SK, Zimmer EA. (1996). Nucleic Acids IV: Sequencing and cloning. In: Hillis DM, Moritz C, Mable BK, editors. Molecular systematics. 2nd ed. Sunderland (MA): Sinauer Associates. p 321–78
   Google Scholar
• Hoarau G, Piquet AMT, van der Veer HW, Rijnsdorp AD, Stam WT, Olsen JL. (2004). Population structure of plaice (Pleuronectes platessa L.) in northern Europe: A comparison of resolving power between microsatellites and mitochondrial DNA data. J Sea Res 51:183–90
   Web of Science ®Google Scholar
• Hsu KC, Shih NT, Ni IH, Shao KT. (2009). Speciation and population structure of three Trichiurus species based on mitochondrial DNA. Zool Studies 48:835–49
   Google Scholar
• Johannesson K, Smolarz K, Grahn M, Andre C. (2011). The future of Baltic Sea populations: Local extinction or evolutionary rescue? AMBIO 40:179–90
   PubMed Web of Science ®Google Scholar
• Joshi KK. (2010). Population dynamics of (Nemipterus japonicas) (Bloch) in the trawling grounds off Cochin. Indian J Fish 57:7–12
   Web of Science ®Google Scholar
• Kocher TD, Thomas WK, Meyer A, Edwards SV, Paabo S, Villablanca FX, Wilson AC. (1989). Dynamics of mitochondrial DNA evolution in animals: Amplification and sequencing with conserved primers. Proc Natl Acad Sci 86:6196–200
   PubMed Web of Science ®Google Scholar
• Larmuseau MHD, Vancampenhout K, Raeymaekers JAM, Van Houdt JKJ, Volchaert FAM. (2010). Differential modes of selection on the rhodopsin gene in coastal Baltic and North Sea populations of the sand goby, (Pomatoschistus minutes). Mol Ecol 19:2256–68
   PubMed Web of Science ®Google Scholar
• Lecomte F, Grant WS, Dodson JJ, Rodriguez-Sanchez R, Bowen BW. (2004). Living with uncertainty: Genetic imprints of climate shrifts in East Pacific anchovy (Engraulis mordax) and sardine (Sardinops sagax). Mol Ecol 13:2169–82
   PubMed Web of Science ®Google Scholar
• Li CH, Li TW, Song LS, Su XR. (2003). RAPD analysis on intraspecies differentiation of Tegillarca granosa populations to the south and north of Fujian province. Zool Res 24:362–6. (In Chinese with English abstract)
   Google Scholar
• Liu JX, Gao TX, Yokogawa K, Zhang YP. (2006). Differential population structuring and demographic history of two closely related fish species, Japanese sea bass (Lateolabrax japonicus) and spotted sea bass (Lateolabrax maculatus) in Northwestern Pacific. Mol Phylogenet Evol 39:799–811
   PubMed Web of Science ®Google Scholar
• Magoulas A. (2005). Mitochondrial DNA. In: Cadrin SX, Friedland KD, Waldman JR, editors. Stock identification methods – Applications in fishery science. San Diego: Elsevier. p 311–30
   Google Scholar
• Mahyam MI, Abu-Talib A, Mansor MI. (2001). Population parameters of dominant finfish and cephalopod species caught in the offshore areas of Malaysia. In: Mohd-Taupek MN, Mansor MI, editors. Fisheries resources survey in the exclusive economic zone of Malaysia 1997–1999: Biology and environmental conditions, supplementary volume. Malaysia: Department of Fisheries . p 17–50
   Google Scholar
• Maruyama T, Birky CW. (1991). Effects of periodic selection on gene diversity in organelle genome and other systems with recombination. Genetics 127:449–51
   PubMed Web of Science ®Google Scholar
• Maruyama T, Fuerst PA. (1984). Population bottlenecks and non-equilibrium models in population genetics. I. Allele numbers when populations evolve from zero variability. Genetics 108:745–63
   PubMed Web of Science ®Google Scholar
• Maruyama T, Fuerst PA. (1985). Population bottlenecks and non-equilibrium models in population genetics. II. Number of Alleles in a Small Population that was formed by a Recent Bottleneck. Genetics 111:675–89
   PubMed Web of Science ®Google Scholar
• Meyer A. (1993). Evolution of mitochondrial DNA in fishes. In: Hochachka PW, Mommsen TP, editors. Biochemistry and molecular biology of fishes. Vol. 2. Amstredam: Elsevier Publishers. p 1–38
   Google Scholar
• Miller MP. (1997). Tools for population genetic analyses (TFPGA) 1.3: A Windows program for the analysis of allozyme and molecular population genetic data. Distributed by the author
   Google Scholar
• Mohd Taupek MN, Ibrahim I. (1996). Status of the demersal fishery on the east coast of Peninsular Malaysia. Prosiding Persidangan Penyelidikan Perikanan 1996. Malaysia: Department of Fisheries Malaysia
   Google Scholar
• Myers N, Mittermeier RA, Mittermeier CG, da Fonseca GAB, Kent J. (2000). Biodiversity hotspots for conservation priorities. Nature 403:853–8
   PubMed Web of Science ®Google Scholar
• Myers RA, Worm B. (2003). Rapid worldwide depletion of predatory fish communities. Nature 423:280–3
   PubMed Web of Science ®Google Scholar
• Nei M. (1987). Molecular evolutionary genetics. New York: Columbia University Press
   Google Scholar
• Pan BP, Song LS, Pu WJ, Sun JS. (2005). Studies on genetic diversity and differentiation between two allopatric populations of Cyclina sinensis. Acta Hydrobiol Sin 29:372–8 (In Chinese with English abstract)
   Google Scholar
• Pauly D, Watson R, Alder J. (2005). Global trends in world fisheries: Impacts on marine ecosystems and food security. Phil Trans R Soc B 360:5–12
   PubMed Web of Science ®Google Scholar
• Planes S, Doherty PJ, Bernardi G. (2001). Strong genetic divergence among populations of a marine fish with limited dispersal, Acanthochromis polyacanthus, within the great barrier reef and the coral sea. Evolution 55:2263–73
   PubMed Web of Science ®Google Scholar
• Perdices A, Sayanda D, Coelho MM. (2005). Mitochondrial diversity of Opsariichthys bidens (Teleostei, Cyprinidae) in three Chinese drainages. Mol Phylogenet Evol 37:920–7
   PubMed Web of Science ®Google Scholar
• Perez-Losada M, Nolte MJ, Crandall KA, Shaw PA. (2007). Testing hypotheses of population structuring in the Northeast Atlantic Ocean and Mediterranean Sea using the common cuttlefish (Sepia officinalis). Mol Ecol 16:2667–79
   PubMed Web of Science ®Google Scholar
• Rivera MAJ, Kelly CD, Roderick GK. (2004). Subtle population genetic structure in the Hawaiian grouper, Epinephelus quernus (Serranidae) as revealed by mitochondrial DNA analysis. Biol J Linnean Soc 81:449–68
   Web of Science ®Google Scholar
• Rogers AR, Harpending H. (1992). Population growth makes waves in the distribution of pairwise genetic difference. Mol Biol Evol 9:552–69
   PubMed Web of Science ®Google Scholar
• Roldán MI, Perrotta RG, Cortey M, Pla C. (2000). Molecular and morphologic approaches to discrimination of variability patterns in Chub mackerel (Scomber japonicas). J Exp Mar Biol Ecol 253:63–74
   PubMed Web of Science ®Google Scholar
• Rozas J, Sanchez-DelBarrio JC, Messeguer X, Rozas R. (2003). DnaSP, DNA polymorphism analyses by the coalescent and other methods. Bioinformatics 19:2496–7
   PubMed Web of Science ®Google Scholar
• Russell BC. (1990). FAO species catalogue, vol 12. Nemipterid fishes of the world. (Threadfin breams, whiptail breams, monocle breams, dwarf monocle breams, and coral breams), Family Nemipteridae. An annotated and illustrated catalogue of nemipterid species known to date. FAO Fisheries Synopsis No. 125. Rome: FAO. p 149 (VIII plates)
   Google Scholar
• Shaw PW, Arkhipkin AI, Al-Khairulla H. (2004). Genetic structuring of Patagonian toothfish populations in Southwest Atlantic Ocean: The effect of the Antarctic Polar Front and deep-water trough as barriers to genetic exchange. Mol Ecol 13:3293–303
   PubMed Web of Science ®Google Scholar
• Siti Azizah MN, Abu Talib A, Mohd Ghows MA, Samsudin B. (2008). A preliminary genetic investigation of Rastrelliger kanagurta Based on RAPD and Mitochondrial ND2 Gene. Wetland Sci 6:518–25
   Google Scholar
• Slatkin M, Hudson RR. (1991). Pairwise comparison of mitochondrial DNA sequences in stable exponentially growing populations. Genetics 129:555–62
   PubMed Web of Science ®Google Scholar
• Smith WD, Bizzarro JJ, Richards VP, Nielsen J, M’arquez-Far’ıas F, Shivji MS. (2009). Morphometric convergence and molecular divergence:the taxonomic status and evolutionary history of (Gymnura crebripunctata) and (Gymnura marmorata) in the eastern Pacific Ocean. J Fish Biol 75:761–83
   PubMed Web of Science ®Google Scholar
• Suzuki N, Uchikawa K, Yamada H, Chow S. (2005). Genetic divergence and identification of two controversial Lanternfishes (Actinopterygii: Myctophidae: Diaphus) based on mitochondrial cytochrome b sequences and PCR-RFLP Analysis. Species Divers 10:289–99
   Google Scholar
• Syed-Abdullah SAK, Mansor MI, Kamariah I. (2002). Population structure of some commercially important fishes in coastal fisheries of the East Coast of Peninsular Malaysia. In: Mansor MI, editor. Thirteenth Trawl Survey of the Coastal Waters off the East Coast of Peninsular Malaysia (April–June 2001). Malaysia: Department of Fisheries. p 138
   Google Scholar
• Szovenyi P, Hock Z, Schneller JJ, Toth Z. (2007). Multilocus dataset reveals demographic histories of two peat mosses in Europe. BMC Evol Biol 7:144
   PubMed Web of Science ®Google Scholar
• Tajima F. (1989). Statistical Method for Testing the Neutral Mutation Hypothesis by DNA Polymorphism. Genetics 123:585–95
   PubMed Web of Science ®Google Scholar
• Tamura K, Dudley J, Nei M, Kumar S. (2007). MEGA4: Molecular Evolutionary Genetics Analysis (MEGA) software version 4.0. Mol Biol Evol 24:1596–9
   PubMed Web of Science ®Google Scholar
• Valles-Jimenez R, Cruz P, Perez-Enriquez R. (2004). Population genetic structure of Pacific white shrimp (Litopenaeus vannamei) from Mexico to Panama: Microsatellie DNA varation. Mar Biotechnol 6:475–84
   PubMed Web of Science ®Google Scholar
• Vergara J, Mercedes Azpelicueta MDL, Garcia G. (2008). Phylogeography of the Neotropical catfish Pimelodus albicans (Siluriformes: Pimelodidae) from Rio de la Plata basin, South America, and conservation remarks. Neotrop Ichthyol 61:75–85
   Web of Science ®Google Scholar
• Zardoya R, Castilho R, Grande C, Favre-Krey L, Caetano S, Marcato S, Krey G, Patarnello T. (2004). Differential population structuring of two closely related fish species, the mackerel (Scomber scombrus) and the chub mackerel (Scomber japonicus) in the Mediterranean Sea. Mol Ecol 13:1785–98
   PubMed Web of Science ®Google Scholar
• Zhang D, Hewitt G. (1996). Nuclear integrations: Challenges for mitochondrial DNA markers. Trends Ecol Evol 11:247–51
   PubMed Web of Science ®Google Scholar