Sains Malaysiana 46(12)(2017): 2393–2416

http://dx.doi.org/10.17576/jsm-2017-4612-16

 

Intra- and Inter-specific Variation of Four Acetes Species (Crustacea: Decapoda: Sergestidae) Sampled along the West Coast of Peninsular Malaysia

(Variasi Intra- dan antara-Spesies Empat Spesies Acetes (Crustacea: Decapoda: Sergestidae)  disampel Sepanjang Pantai Barat Semenanjung Malaysia)

 

BOON YEE WONG1, TARANJEET KAUR AWTAR SINGH2, GIDEON KHOO2

 & HAN KIAT ALAN ONG3*

 

1Faculty of Engineering and Science, Universiti Tunku Abdul Rahman, Jalan Genting Klang, Setapak

53300 Kuala Lumpur, Federal Territory, Malaysia

 

2Faculty of Science, Universiti Tunku Abdul Rahman, Jalan Universiti, Bandar Barat, 31900 Kampar, Perak Darul Ridzuan, Malaysia

 

3Department of Pre-clinical Sciences, Faculty of Medicine and Health Sciences, Universiti Tunku Abdul Rahman, Jalan Sungai Long, Bandar Sungai Long, Cheras, 43000 Kajang,

Selangor Darul Ehsan, Malaysia

 

Received: 5 November 2016/Accepted: 31 May 2017

 

ABSTRACT

 

The intra- and inter-specific variation of Acetes shrimps were evaluated based on samples collected from in-shore catches and off-shore trawling around the west coast of Peninsular Malaysia. Species captured were identified as Acetes indicus, A. serrulatus, A. japonicus and A. sibogae. A region of the mitochondrial cytochrome c oxidase subunit I (COI) gene comprising 552 base pairs (bp) was amplified from 159 Acetes specimens. The sequence alignment analysis generated phylogenetic trees which depicted the four major clades that were consistent with the species identified morphologically. These four species varied considerably for haplotype and nucleotide diversity, with A. indicus and A. serrulatus showing different demographic histories. Furthermore, the observation of two clades in the A. indicus and A. sibogae lineages, with relatively high levels of intraspecific divergence, suggests that cryptic diversity is possibly present in these two taxa. This study has contributed to the knowledge of the distribution patterns and molecular phylogenetics of four Acetes spp. in the Straits of Malacca.

 

Keywords: Acetes; COI gene; cryptic species; Peninsular Malaysia; phylogenetic analysis

 

ABSTRAK

 

Variasi intra- dan antara spesies Acetes dinilai berdasarkan sampel yang dikumpulkan daripada tangkapan di pantai dan tunda di luar pesisir pantai di sekitar pantai barat Semenanjung Malaysia. Spesies yang ditangkap dikenal pasti sebagai Acetes indicus, A. serrulatus, A. japonicus dan A. sibogae. Suatu kawasan gen sitokrom c oksidase mitokondria subunit I (COI) yang terdiri daripada 552 pasangan bes (bp) telah teramplifikasi daripada 159 spesimen Acetes. Analisis penjajaran jujukan menghasilkan pokok filogenetik yang menggambarkan empat klad utama adalah tekal dengan spesies yang telah dikenal pasti secara morfologi. Empat spesies ini sangat berbeza daripada segi kepelbagaian haplotip dan nukleotid dengan A. indicus dan A. serrulatus menunjukkan sejarah demografi yang berbeza. Tambahan pula, pemerhatian titisan dalam dua klad A. indicus dan A. sibogae, dengan tahap perbezaan intraspesies yang agak tinggi, menunjukkan bahawa kepelbagaian krip mungkin ada dalam dua taksa ini. Kajian ini telah menyumbang kepada pengetahuan tentang pola taburan dan molekul filogenetik empat Acetes spp. di Selat Melaka.

 

Kata kunci: Acetes; analisis filogenetik; gen COI; Semenanjung Malaysia; spesies kriptik

REFERENCES

 

Allendorf, F.W. & Luikart, G. 2006. Conservation and the Genetics of Populations. Oxford: Blackwell Publishing, MA.

Altschul, S.F., Gish, W., Miller, W., Myers, E.W. & Lipman, D.J. 1990. Basic local alignment search tool. Journal of Molecular Biology 215(3): 403-410.

Amani, A.A., Arshad, A., Amin, S.M.N. & Aziz, N.A.A. 2011a. Catch composition of a set bag net used for Acetes trapping in the estuarine waters of Kedah, Peninsular Malaysia. Journal of Fisheries and Aquatic Science 6(3): 279-284.

Amani, A.A., Amin, S.M.N., Arshad, A. & Rahman, M.A. 2011b. Population dynamics of sergestid shrimps Acetes japonicus in the estuary of Tanjung Dawai, Kedah, Malaysia. Journal of Fisheries and Aquatic Science 6(7): 751-760.

Amani, A.A., Amin, S.M.N. & Arshad, A. 2011c. Stomach contents of sergestid shrimp Acetes japonicus from the estuary of Tanjung Dawai, Peninsular Malaysia. Journal of Fisheries and Aquatic Science 6(7): 771-779.

Amin, S.M.N., Arshad, A., Siraj, S.S. & Bujang, J.S. 2011. Update on the species composition and distribution of sergestide shrimps (Acetes spp.) in Malaysian waters. Journal of Fisheries and Aquatic Science 6(7): 761-770.

Amin, S.M.N., Arshad, A., Siraj, S.S. & Japar, S.B. 2010. Reproductive seasonality and maturation of the sergestid shrimp, Acetes japonicus (Decapoda: Sergestidae) in coastal waters of Malacca, Peninsular Malaysia. African Journal of Biotechnology 9(45): 7747-7752.

Amin, S.M.N., Arshad, A., Bujang, J.S. & Siraj, S.S. 2009a. Age structure, growth, mortality and yield-per-recruit of sergestid shrmp, Acetes indicus (Decapoda: Sergestidae) from the coastal waters of Malacca, Peninsular Malaysia. Journal of Applied Sciences 9(5): 801-814.

Amin, S.M.N., Arshad, A., Bujang, J.S., Siraj, S.S. & Goddard, S. 2009b. Reproductive biology of the sergestid shrimp Acetes indicus (Decapoda: Sergestidae) in coastal waters of Malacca, Peninsular Malaysia. Zoological Studies 48(6): 753-760.

Amin, S.M.N., Arshad, A., Siraj, S.S. & Japar, S.B. 2009c. Population structure, growth, mortality and yield per recruit of sergestid shrimp, Acetes japonicus (Decapoda: Sergestidae) from the coastal waters of Malacca, Peninsular Malaysia. Indian Journal of Marine Science 38(1): 57-68.

Amin, S.M.N., Arshad, A., Siraj, S.S. & Bujang, J.S. 2009d. Population structure, growth and length - weight relationship of sergestid shrimps (Acetes spp.) from the coastal waters of Malacca, Peninsular Malaysia. Sains Malaysiana 38(2): 159-169.

Amin, S.M.N., Arshad, A., Zainal, Z., Idris, M.H., Siraj, S.S. & Japar, S.B. 2008. First distribution records of Acetes intermedius (Decapoda: Sergestidae) from the coastal waters of Bintulu, Sarawak: Population structure, length-weight and length-length relationship. Journal of Sustainability Science and Management 3(1): 74-83.

Aris-Brosou, S. & Excoffier, L. 1996. The impact of population expansion and mutation rate heterogeneity on DNA sequence polymorphism. Molecular Biology and Evolution 13(3): 494-504.

Arshad, A., Amin, S.M.N., Nuradiella, Y.L.Z., Cob, Z.C., Ara, R. & Aziz, D. 2012. Population characteristics of Acetes japonicus from the Kedah coastal waters of Peninsular Malaysia. Journal of Fisheries and Aquatic Science 7(2): 162-172.

Arshad, A., Amin, S.M.N., Yu, G.T., Oh, S.Y., Bujang, J.S. & Ghaffar, M.A. 2008. Population characteristics, length-weight and length-length relationships of Acetes vulgaris (Decapoda: Sergestidae) in the coastal waters of Pontian, Johor, Peninsular Malaysia. Journal of Biological Sciences 8(8): 1298-1303.

Arshad, A., Amin, S.M.N., Siraj, S.S. & Japar, S.B. 2007. New distribution records of sergestid shrimp, Acetes intermedius (Decapoda: Sergestidae) from Peninsular Malaysia with notes on its population characteristics. Journal of Biological Sciences 7(8): 1305-1313.

Avise, J., Neigel, J. & Arnold, J. 1984. Demographic influences on mitochondrial DNA lineage survivorship in animal populations. Journal of Molecular Evolution 20(2): 99-105.

Baldwin, J.D., Bass, A.L., Bowen, B.W. & Clark, W.H. 1998. Molecular phylogeny and biogeography of the marine shrimp Penaeus. Molecular Phylogenetics and Evolution 10(3): 399-407.

Bensasson, D., Zhang, D.X., Hartl, D.L. & Hewitt, G.M. 2001. Mitochondrial pseudogenes: Evolution’s misplaced witnesses. Trends in Ecology and Evolution 16(6): 314-321.

Bickford, D., Lohman, D.J., Sodhi, N.S., Ng, P.K.L., Meier, R., Winker, K., Ingram, K.K. & Das, I. 2007. Cryptic species as a window on diversity and conservation. Trends in Ecology & Evolution 22(3): 148-155.

Black, M.B., Halanych, K.M., Maas, P.A.Y., Hoeh, W.R., Hashimoto, J., Desbruyères, D., Lutz, R.A. & Vrijenhoek, R.C. 1997. Molecular systematics of vestimentiferan tubeworms from hydrothermal vents and cold-water seeps. Marine Biology 130(2): 141-149.

Black. A.R. & Dodson, S.I. 2003. Ethanol: A better preservation technique for Daphnia. Limnology and Oceanography: Methods 1: 45-50.

Bucklin, A. 2009. CMarz sample collection protocol. Census of Marine Zooplankton. CMarz Barcoding Association. (http://www.cmarz.org/barcode/protocols/barcode_CMarZ_ Sample_Protocol_jan06.html)

Camin, J. & Sokal, R. 1965. A method for deducing branching sequences in phylogeny. Evolution 19(3): 311-326.

Carvalho, G.R. & Hauser, L. 1994. Molecular genetics and the stock concept in fisheries. Reviews in Fish Biology and Fisheries 4(3): 326-350.

Chan, T.Y. 1998. Shrimps and prawns. In FAO Species Identification Guide for Fishery Purposes. The Living Marine Resource of the Western Central Pacific, Vol. 2. Cephalopds, Crustaceans, Holothurians and Sharks, edited by Carpenter, K.E. & Niem, V.H. Rome: FAO.

Chen, C.A., Ablan, M.C.A., Mcmanus, J.W., Bell, J.D., Tuan, V.S., Cabanban, A.S. & Shao, K.T. 2004. Population structure and genetic variability of six bar wrasse (Thallasoma hardwicki) in Northern South China Sea revealed by mitochondrial control region sequences. Marine Biotechnology 6(4): 312- 326.

Chen, H., Strand, M., Norenburg, J.L., Sun, S., Kajihara, H., Chernyshev, A.V., Maslakova, S.A. & Sundberg, P. 2010. Statistical parsimony networks and species assemblages in cephalotrichid nemerteans (nemertea). PLoS ONE 5(9): e12885.

Chu, K.H., Tong, J. & Chan, T.Y. 1999. Mitochondrial cytochrome oxidase I sequence divergence in some Chinese species of Charybdis (Crustacea: Decapoda: Portunidae). Biochemical Systematics and Ecology 27(5): 461-468.

Clement, M., Posada, D. & Crandall, K.A. 2000. TCS: A computer program to estimate gene genealogies. Molecular Ecology 9(10): 1657-1659.

Cook, B.D., Baker, A.M., Page, T.J., Grant, S.C., Fawcett, J.H., Hurwood, D.A. & Hughes, J.M. 2006. Biogeographic history of an Australian freshwater shrimp, Paratya australiensis (Atyidae): The role life history transition in phylogeographic diversification. Molecular Ecology 15: 1083-1093.

Costa, F.O., deWaard, J.R., Boutillier, J., Ratnasingham, S., Dooh, R.T., Hajibabaei, M. & Hebert, P.D. 2007. Biological identifications through DNA barcodes: The case of the Crustacea. Canadian Journal of Fisheries and Aquatic Sciences 64(2): 272-295.

Daeman, E., Cross, T., Ollevier, F. & Volckaert, F.A.M. 2001. Analysis of the genetic structure of European eel (Anguilla anguilla) using microsattelite DNA and mtDNA markers. Marine Biology 139(4): 755-764.

Deshmukh, V.D. 1991. Utilisation of paste shrimp Acetes: A review. Marine Fisheries Information Service Technical Extension Series 110: 7-8.

Díaz-Viloria, N., Sánchez-Velasco, L. & Perez-Enriquez, R. 2005. Inhibition of DNA amplification in marine fish larvae preserved in formalin. Journal of Plankton Research 27(8): 787-792.

DiStefano, R.J., Roell, M.J., Wagner, B.A. & Decoske, J.J. 1994. Relative performances of four preservatives on fish and crayfish. Transactions of the American Fisheries Society 123: 817-823.

DOF. 2013. Annual Fisheries Statistics. Kuala Lumpur: Department of Fisheries Malaysia, Ministry of Agriculture.

Excoffier, L. & Lischer, H.E.L. 2010. Arlequin suite ver 3.5: A new series of programs to perform population genetics analyses under Linux and Windows. Molecular Ecology Resources 10(3): 546-567.

Excoffier, L., Smouse, P.E. & Quattro, J.M. 1992. Analysis of molecular variance inferred from metric distances among DNA haplotypes: Application to human mitochondrial DNA restriction data. Genetics 131(2): 479-491.

Felsenstein, J. 1985. Confidence limits on phylogenies: An approach using the bootstrap. Evolution 39(4): 783-791.

Felsenstein, J. 1981. Evolutionary trees from DNA sequences: A maximum likelihood approach. Journal of Molecular Evolution 17(6): 368-376.

Fernandez-Leborans, G., Hanamura, Y., Siow, R. & Chee, P.E. 2009. Intersite epibiosis characterization on dominant mangrove crustacean species from Malaysia. Contributions to Zoology 78(1): 9-23.

Folmer, O., Black, M., Hoeh, W., Lutz, R. & Vrijenhoek, R. 1994. DNA primers for amplification of mitochondrial cytochrome c oxidase subunit I from diverse metazoan invertebrates. Molecular Marine Biology and Biotechnology 3(5): 294-299.

Frankham, R., Ballou, J.D. & Briscoe, D.A. 2002. Introduction to Conservation Genetics. Cambridge: Cambridge University Press.

Fu, Y.X. 1997. Statistical tests of neutrality against population growth, hitchhiking and background selection. Genetics 147: 915-925.

García-Machado, E., Robainas, A., Espinosa, G., Oliva, M., Páez, J., Verdecia, N. & Monnerot, M. 2001. Allozyme and mitochondrial DNA variation in Cuban populations of the shrimp Farfantepenaeus notialis (Crustacea: Decapoda). Marine Biology 138(4): 701-707.

Gascuel, O. 1997. BIONJ: An improved version of the NJ algorithm based on a simple model of sequence data. Molecular Biology and Evolution 14(7): 685-695.

Geyh, M.A., Steif, H. & Kudrass, H.R. 1979. Sea-level changes during the late Pleistocene and Holocene in the Strait of Malacca. Nature 278(5703): 441-443.

Grant, W.S. & Bowen, B.W. 1998. Shallow population in deep evolutionary lineages of marine fishes: Insights from sardines and anchovies and lessons for conservation. Journal of Heredity 89(5): 415-426.

Guindon, S., Lethiec, F., Duroux, P. & Gascuel, O. 2005. PHYML Online - a web server for fast maximum likelihood-based phylogenetic inference. Nucleic Acids Research 33(Suppl 2): W557-W559.

Hanamura, Y., Siow, R. & Chee, P.E. 2007. Abundance and spatio temporal distributions of hyper benthic crustaceans in the Merbok and Matang mangroves estuaries, Malaysia. In Sustainable Production Systems of Aquatic Animals in Brackish Mangrove Areas (2005), edited by Nakamura K. Japan International Research Center for Agriculture Sciences (JIRCAS).

Hanebuth, T., Stattegger, K. & Grootes, P.M. 2000. Rapid flooding of the Sunda Shelf: A late-glacial sea-level record. Science 288(5468): 1033-1035.

Harpending, H.C. 1994. Signature of ancient population growth in a low-resolution mitochondrial DNA mismatch distribution. Human Biology 66(4): 591-600.

Harrison, M.K. & Crespi, B.J. 1999. Phylogenetics of cancer crabs (Crustacea: Decapoda: Brachyura). Molecular Phylogenetics and Evolution 12(2): 186-199.

Hart, M.W. & Sunday, J. 2007. Things fall apart: Biological species form unconnected parsimony networks. Biology Letters 3(5): 509-512.

Hebert, P.D.N., Cywinska, A., Ball, S.L. & deWaard, J.R. 2003. Biological identifications through DNA barcodes. Proceedings of the Royal Society London B 270(1512): 313-321.

Holthuis, L.B. 1980. FAO Species Catalogue Vol. 1. Shrimps and Prawns of the World: An Annotated Catalogue of Species of Interest to Fisheries. Rome: FAO Fisheries Synopsis. 125(1): 62-67.

Hualkasin, W., Sirimontaporn, P., Chotigeat, W., Querci, J. & Phongdara, A. 2003. Molecular phylogenetic analysis of white prawns species and the existence of two clades in


Penaeus merguiensis. Journal of Experimental Marine Biology and Ecology 296(1): 1-11.

Hudson, R.R. 1990. Gene genealogies and the coalescent process. Oxford Surveys in Evolutionary Biology 7: 1-44.

Huelsenbeck, J.P. & Ronquist, F. 2001. MRBAYES: Bayesian inference of phylogenetic trees. Bioinformatics 17(8): 754- 755.

Hurvich, C.M. & Tsai, C.L. 1989. Regression and time series model selection in small samples. Biometrika 76(2): 297-307.

Jarvis, J.P., Luedeman, J.K. & Shier, D.R. 1983. Comments on computing the similarity of binary trees. Journal of Theoretical Biology 100(3): 427-433.

Job, S., Buu, D. & Vincent, A. 2006. Growth and survival of the tiger tail seahorse, Hippocampus comes. Journal of the World Aquaculture Society 37(3): 322-327.

Jorde, L.B., Watkins, W.S. & Bamshad, M.J. 2001. Population genomics: A bridge from evolutionary history to genetic medicine. Human Molecular Genetics 10(20): 2199-2207.

Khamnamtong, B., Klinbunga, S. & Menasveta, P. 2009. Genetic diversity and geographic differentiation of the giant tiger shrimp (Penaeus monodon) in Thailand analyzed by mitochondrial COI sequences. Biochemical Genetics 47(1- 2): 42-55.

Kimura, M. 1980. A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. Journal of Molecular Evolution 16(2): 111-120.

Knowlton, N. 1986. Cryptic and sibling species among the decapod crustacea. Journal of Crustacean Biology 6(3): 356-363.

Kong, X.Y., Li, Y.L., Shi, W. & Kong, J. 2010. Genetic variation and evolutionary demography of Fenneropenaeus chinensis populations, as revealed by the analysis of mitochondrial control region sequences. Genetics and Molecular Biology 33(2): 379-389.

Lai, J.C.Y., Ng, P.K.L. & Davie, P.J.F. 2010. A revision of the Portunus pelagicus (Linnaeus, 1758) species complex (Crustacea: Brachyura: Portunidae), with the recognition of four species. The Raffles Bulletin of Zoology 58(2): 199-237.

Li, Y.L., Kong, X.Y., Yu, Z.N., Kong, J., Ma, S. & Chen, L.M. 2009. Genetic diversity and historical demography of Chinese shrimp Fenneropenaeus chinensis in Yellow Sea and Bohai Sea based on mitochondrial DNA analysis. African Journal of Biotechnology 8(7): 1193-1202.

Librado, P. & Rozas, J. 2009. DnaSP v5: A software for comprehensive analysis of DNA polymorphism data. Bioinformatics 25(11): 1451-1452.

Liu, S.Y., Kokita, T. & Dai, C.F. 2008. Population genetic structure of the neon damselfish (Pomacentrus coelestis) in the northwestern Pacific Ocean. Marine Biology 154(4): 745-753.

Longhurst, A.R. 1970. Crustacean resources. In The Fish Resources of the Oceans, edited by Gulland, J.A. FAO Fisheries Technical Paper No. 97. Rome: FAO. pp. 252-305.

Machordom, A. & Macpherson, E. 2004. Rapid radiation and cryptic speciation in squat lobsters of the genus Munida (Crustacea, Decapoda) and related genera in the South West Pacific: Molecular and morphological evidence. Molecular Phylogenetics and Evolution 33(2): 259-279.

Macpherson, E. & Machordom, A. 2001. Phylogenetic relationships of species of Raymunida (Decapoda: Glatheidae) based on morphology and mitochondrial cytochrome oxidase sequences, with the recognition of four new species. Journal of Crustacean Biology 21(3): 696-714.

Maggio, T., Lo Brutto, S., Cannas, R., Deiana, A.M. & Arculeo, M. 2009. Environmental features of deep-sea habitats linked to the genetic population structure of a crustacean species in the Mediterranean Sea. Marine Ecology 30(3): 354-365.

Maggioni, R., Rogers, A.D., Maclean, N. & D’Incao, F. 2001. Molecular phylogeny of western atlantic Farfantepenaeus and Litopenaeus shrimp based on mitochondrial 16S partial sequences. Molecular Phylogenetics and Evolution 18(1): 66-73.

Mantel, N. 1967. The detection of disease clustering and a generalised regression approach. Cancer Research 27: 209-220.

Mathews, L.M., Schubart, C.D., Neigel, J.E. & Felder, D.L. 2002. Genetic, ecological, and behavioural divergence between two sibling snapping shrimp species (Crustacea: Decapoda: Alpheus). Molecular Ecology 11(8): 1427-1437.

Meyran, J.C., Monnerot, M. & Taberlet, P. 1997. Taxonmic status and phylogenetic relationships of some species of the genus Gammarus (Crustacea, Amphipoda) deduced from mitochondrial DNA sequence. Molecular Phylogenetics and Evolution 8(1): 1-10.

Nei, M. 1987. Molecular Evolutionary Genetics. New York: Columbia University Press.

Oh, S.Y., Arshad, A., Japar, S.B., Nor Azwady, A.A. & Amin, S.M.N. 2011. Diet composition of sergestid shrimp Acetes serrulatus from the coastal waters of Kukup, Johor, Malaysia. Journal of Fisheries and Aquatic Science 6(7): 809-815.

Oh, S.Y., Arshad, A., Pang, S.P. & Amin, S.N. 2010. Catch composition of estuarine set bag net fishery in the coastal area of Pontian, Johor, Peninsular Malaysia. Journal of Biological Sciences 10(3): 247-250.

Omori, M. 1978. Zooplankton fisheries of the world: a review. Marine Biology 48(3): 199-205.

Omori, M. 1975. The Systematics, Biogeography, and Fishery of Epipelagic Shrimps of the Genus Acetes (Crustacea, Decapoda, Sergestidae). Tokyo, Japan: Ocean Research Institute, University of Tokyo.

Page, R.D.M. 1996. Tree view: An application to display phylogenetic trees on personal computers. Computer Applications in the Biosciences 12(4): 357-358.

Pathansali, D. 1966. Acetes (Sergestidae) from Malay Peninsula. Bulletin of the National Museum Singapore 33(8): 59-63.

Pellerito, R., Arculeo, M. & Bonhomme, F. 2009. Recent expansion of Northeast Atlantic and Mediterranean populations of Melicertus (Penaeus) kerathurus (Crustacea: Decapoda). Fisheries Science 75(5): 1089-1095.

Pfeiler, E., Hurtado, L.A., Knowles, L.L., Torre-Cosío, J., Bourillón-Moreno, L., Márquez-Farías, J.F. & Montemayor- Lpoez, G. 2005. Population genetics of the swimming crab Callinectes bellicosus (Brachyura: Portunidae) from the eastern Pacific Ocean. Marine Biology 146(3): 559-569.

Pfenninger, M. & Schwenk, K. 2007. Cryptic animal species are homogenously distributed among taxa and biogeographical regions. BMC Evolutionary Biology 7: 121-126.

Pillians, B., Chappell, J. & Naish, T.R. 1998. A review of the Milankovitch climatic beat: Template for Plio-Pleistocene sea-level changes and sequence statigraphy. Sedimentary Geology 122(1-4): 5-21.

Posada, D. 2009. Selection of models of DNA evolution with jModelTest. In Bioinformatic Analysis of DNA Sequences, edited by Posada, D. New Jersey: Human Press. pp. 93-112.

Posada, D. 2008. jModelTest: Phylogenetic model averaging. Molecular Biology and Evolution 25(7): 1253-1256.

Quan, J., Zhuang, Z., Deng, J., Dai, J. & Zhang, Y.P. 2004. Phylogenetic relationships of 12 Penaeoidea shrimp species deduced from mitochondrial DNA sequences. Biochemical Genetics 42(9): 331-345.

Ramos-Onsins, S.E. & Rozas, J. 2002. Statistical properties of new neutrality tests against population growth. Molecular Biology and Evolution 19(12): 2092-2100.

Rand, D.M. 1996. Neutrality tests of molecular markers and connection between DNA polymorphism, demography, and conservation biology. Conservation Biology 10(2): 665-671.

Rogers, A.R. 1995. Genetic evidence for a Pleistocene population explosion. Evolution 49(4): 608-615.

Rogers, A.R. & Harpending, H.C. 1992. Population growth makes waves in the distribution of pairwise genetic differences. Molecular Biology and Evolution 9: 552-569.

Roldán, M.I., Heras, S., Patellani, R. & Maltagliati, F. 2009. Analysis of genetic structure of red shrimp Aristeus antennatus from the Western Mediterranean employing two mitochondrial regions. Genetica 136(1): 1-4.

Ronquist, F. & Huelsenbeck, J.P. 2003. MrBayes 3: Bayesian phylogenetic inference under mixed models. Bioinformatics 19(12): 1572-1574.

Saiki, R., Gelfand, D., Stoffel, S., Scharf, S., Higuchi, R., Horn, G.T., Mullis, K.B. & Erlich, H.A. 1988. Primer-directed enzymatic amplification of DNA with a thermostable DNA polymerase. Science 239(4839): 487-491.

Saitou, N. & Nei, M. 1987. The neighbor-joining method: A new method for reconstructing phylogenetic trees. Molecular Biology and Evolution 4(4): 406-425.

Schneider, S. & Excoffier, L. 1999. Estimation of past demographic parameters from the distribution of pairwise differences when mutation rates vary among sites: Application to human mitochondrial DNA. Genetics 152(3): 1079-1089.

Slatkin, M. & Hudson, R.R. 1991. Pairwise comparison of mitochondrial DNA sequences in stable and exponentially growing populations. Genetics 129(2): 555-562.

Song, H., Buhay, J.E., Whiting, M.F. & Crandall, K.A. 2008. Many species in one: DNA barcoding overestimates the number of species when nuclear mitochondrial pseudogenes are coamplified. Proceedings of the National Academy of Sciences of the United States of America 105(36): 13486- 13491.

Stockley, B., Menezes, G., Pinho, M.R. & Rogers, A.D. 2005. Genetic population structure in the black-spot sea bream (Pagellus bogaraveo Brűnnich, 1768) from the NE Atlantic. Marine Biology 146(4): 793-804.

Sugiura, N. 1978. Further analysts of the data by Akaike’s information criterion and the finite corrections. Communications in Statistics, Theory and Methods A7(1): 13-26.

Swofford, D. 2002. PAUP*. Phylogenetic Analysis using Parsimony (*and other methods). Version 4. Massachusetts: Sinauer Associates.

Tajima, F. 1989. Statistical method for testing the neutral mutation hypothesis by DNA polymorphism. Genetics 123: 585-595.

Tamura, K., Dudley, J., Nei, M. & Kumar, S. 2007. MEGA4: Molecular Evolutionary Genetics Analysis (MEGA) Software Version 4.0. Molecular Biology and Evolution 24(8): 1596- 1599.

Templeton, A.R., Crandall, K.A. & Sing, C.F. 1992. A cladistic analysis of phenotypic associations with haplotypes inferred from restriction endonuclease mapping and DNA sequence data. III. Cladogram estimation. Genetics 132(2): 619-633.

Thorpe, J.P., Solé-Cava, A.M. & Watts, P.C. 2000. Exploited marine invertebrates: Genetics and fisheries. Hydrobiologia 420(1): 165-184.

Tong, J.G., Chan, T.Y. & Chu, K.H. 2000. A preliminary phylogenetic analysis of Metapenaeopsis (Decapoda: Penaeidae) based on mitochondrial DNA sequences of selected species from the Indo-West Pacific. Journal of Crustacean Biology 20(3): 541-549.

Trontelj, P., Machino, Y. & Sket, B. 2005. Phylogenetic and phylogeographic relationships in the crayfish genus Austropotamobius inferred from mitochondrial COI gene sequences. Molecular Phylogenetics and Evolution 34(1): 212-226.

Tsoi, K.H., Chan, T.Y. & Chu, K.H. 2007. Molecular population structure of the kuruma shrimp Penaeus japonicus species complex in western Pacific. Marine Biology 150(6): 1345- 1364.

Tsoi, K.H., Wang, Z.Y. & Chu, K.H. 2005. Genetic divergence between two morphologically similar varieties of the kuruma shrimp Penaeus japonicus. Marine Biology 147(2): 367-379.

Voris, H.K. 2000. Maps of Pleistocene sea levels in Southeast Asia: Shorelines, river systems and time durations. Journal of Biogeography 27: 1153-1167.

Ward, R.D. 2000. Genetics in fisheries management. Hydrobiologia 420(1): 191-201.

Ward, R.D. & Grewe, P.M. 1994. Appraisal of molecular genetic techniques in fisheries. Reviews in Fish Biology and Fisheries 4(3): 300-325.

Weir, B.S. & Cockerham, C. 1984. Estimating F - statistics for the analysis of population structure. Evolution 38(6): 1358-1370.

Williams, S.T. & Knowlton, N. 2001. Mitochondrial pseudogenes are pervasive and often insidious in the snapping shrimp genus Alpheus. Molecular Biology and Evolution 18(8): 1484-1493.

Williams, S.T., Jara, J., Gomez, E. & Knowlton, N. 2002. The marine Indo-West Pacific break: Contrasting the resolving power of mitochondrial and nuclear genes. Integrative and Comparative Biology 42(5): 941-952.

Williams, S.T., Knowlton, N., Weigt, L.A. & Jara, J.A. 2001. Evidence for three major clades within the snapping shrimp genus Alpheus inferred from nuclear and mitochondrial gene sequence data. Molecular Phylogenetics and Evolution 20(3): 375-389.

Wong, B.Y. 2013. Genetic diversity and morphometric characterization of Acetes (Decapoda: Sergestidae) collected from the west coast of Peninsular Malaysia. Master of Science dissertation, Universiti Tunku Abdul Rahman, Malaysia (Unpublished). (http://eprints.utar.edu.my/802/).

Wong, B.Y., Ong, H.K.A. & Khoo, G. 2015. Length-weight relationships of Acetes spp. sampled along the west coast of Peninsular Malaysia. Sains Malaysiana 44(3): 379-386.

Xiao, Y. & Greenwood, J.G. 1993. The biology of Acetes (Crustacea: Sergestidae). In Oceanography and Marine Biology: An Annual Review, Vol. 31, edited by Ansell, A.D., Gibson, R.N. & Barnes, M. London: UCL Press.

Zhang, D.X. & Hewitt, G.M. 1996. Nuclear integrations: Challenges for mitochondrial DNA markers. Trends in Ecology and Evolution 11(6): 247-251.

Zitari-Chatti, R., Chatti, N., Fulgione, D., Caiazza, I., Aprea, G., Elouaer, A., Said, K. & Capriglione, T. 2009. Mitochondrial DNA variation in the caramote prawn Penaeus (Melicertus) kerathurus across a transition zone in the Mediterranean Sea. Genetica 136(3): 439-447.

 

 

*Corresponding author; email: onghk@utar.edu.my

 

 

 

 

previous