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      Genetic diversity and population structure of Terapon jarbua (Forskål, 1775) (Teleostei, Terapontidae) in Malaysian waters

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          Abstract

          Abstract

          A background study is important for the conservation and stock management of a species. Terapon jarbua is a coastal Indo-Pacific species, sourced for human consumption. This study examined 134 samples from the central west and east coasts of Peninsular (West) Malaysia and East Malaysia. A 1446-bp concatenated dataset of mtDNA COI and Cyt b sequences was used in this study and 83 haplotypes were identified, of which 79 are unique haplotypes and four are shared haplotypes. Populations of T. jarbua in Malaysia are genetically heterogenous as shown by the high level of haplotype diversity ranging from 0.9167–0.9952, low nucleotide diversity ranging from 0.0288–0.3434, and high F ST values (within population genetic variation). Population genetic structuring is not distinct as shown by the shared haplotypes between geographic populations and mixtures of haplotypes from different populations within the same genetic cluster. The gene flow patterns and population structuring observed among these regions are likely attributed to geographical distance, past historical events, allopatric speciation, dispersal ability and water currents. For instance, the mixture of haplotypes revealed an extraordinary migration ability of T. jarbua (>1200 km) via ancient river connectivity. The negative overall value of the neutrality test and a non-significant mismatch distribution are consistent with demographic expansion(s) in the past. The median-joining network concurred with the maximum likelihood haplotype tree with three major clades resolved. The scarcity of information on this species is an obstacle for future management and conservation purposes. Hence, this study aims to contribute information on the population structure, genetic diversity, and historical demography of T. jarbua in Malaysia.

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          Most cited references 40

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          DnaSP, DNA polymorphism analyses by the coalescent and other methods.

          DnaSP is a software package for the analysis of DNA polymorphism data. Present version introduces several new modules and features which, among other options allow: (1) handling big data sets (approximately 5 Mb per sequence); (2) conducting a large number of coalescent-based tests by Monte Carlo computer simulations; (3) extensive analyses of the genetic differentiation and gene flow among populations; (4) analysing the evolutionary pattern of preferred and unpreferred codons; (5) generating graphical outputs for an easy visualization of results. The software package, including complete documentation and examples, is freely available to academic users from: http://www.ub.es/dnasp
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            Maps of Pleistocene sea levels in Southeast Asia: shorelines, river systems and time durations

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              Signature of ancient population growth in a low-resolution mitochondrial DNA mismatch distribution.

              A mismatch distribution is a tabulation of the number of pairwise differences among all DNA sequences in a sample. In a population that has been stationary for a long time these distributions from nonrecombinant DNA sequences become ragged and erratic, whereas a population that has been growing generates mismatch distributions that are smooth and have a peak. The position of the peak reflects the time of the population growth. The signature of an ancient population expansion is apparent even in the low-resolution mtDNA typings described by Merriwether et al. (1991). The smoothness of the mismatch distribution, an indicator of population expansion, is hardly affected by population structure, whereas mean sequence divergence increases in a pooled sample from highly isolated subpopulations.
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                Author and article information

                Contributors
                Journal
                Zookeys
                Zookeys
                2
                urn:lsid:arphahub.com:pub:45048D35-BB1D-5CE8-9668-537E44BD4C7E
                urn:lsid:zoobank.org:pub:91BD42D4-90F1-4B45-9350-EEF175B1727A
                ZooKeys
                Pensoft Publishers
                1313-2989
                1313-2970
                2020
                12 February 2020
                : 911
                : 139-160
                Affiliations
                [1 ] Institute of Ocean and Earth Sciences, University of Malaya, Kuala Lumpur 50603, Malaysia University of Malaya Kuala Lumpur Malaysia
                [2 ] Institute for Advanced Studies, University of Malaya, Kuala Lumpur 50603, Malaysia Third Institute of Oceanography, Ministry of Natural Resources Xiamen China
                [3 ] Third Institute of Oceanography, Ministry of Natural Resources, Xiamen 361005, China National Sun Yat-sen University Kaohsiung Taiwan
                [4 ] Department of Oceanography, National Sun Yat-sen University, Kaohsiung 80424, Taiwan Ministry of Natural Resources Xiamen China
                [5 ] Fujian Provincial Station for Field Observation and Research of Island and Coastal Zone in Zhangzhou, Xiamen 361005, China Station for Field Observation and Research of Island and Coastal Zone Xiamen China
                [6 ] Fujian Provincial Key Laboratory of Marine Ecological Conservation and Restoration, Xiamen 361005, China Key Laboratory of Marine Ecological Conservation and Restoration Xiamen China
                [7 ] Endangered Marine Species Research Unit, Borneo Marine Research Institute, Universiti Malaysia Sabah, Kota Kinabalu 88400, Sabah, Malaysia Universiti Malaysia Sabah Kota Kinabalu Malaysia
                [8 ] Department of Fisheries Sabah, Kota Kinabalu 88624, Sabah, Malaysia Department of Fisheries Sabah Kota Kinabalu Malaysia
                [9 ] Fisheries Research Institute, Sarawak, Department of Fisheries Malaysia, Kuching 93744, Sarawak, Malaysia Department of Fisheries Malaysia Kuching Malaysia
                Author notes
                Corresponding author: Kar-Hoe Loh ( khloh@ 123456um.edu.my )

                Academic editor: Nina Bogutskaya

                Article
                39222
                10.3897/zookeys.911.39222
                7031388
                Shyama Sundari Devi Chanthran, Phaik-Eem Lim, Yuan Li, Te-Yu Liao, Sze-Wan Poong, Jianguo Du, Muhammad Ali Syed Hussein, Ahemad Sade, Richard Rumpet, Kar-Hoe Loh

                This is an open access article distributed under the terms of the Creative Commons Attribution License (CC BY 4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.

                Categories
                Research Article
                Animalia
                Chordata
                Pisces
                Terapontidae
                Vertebrata
                Genetics
                Molecular Genetics
                Population Genetics
                Asia
                Far East
                Malaysia

                Animal science & Zoology

                coi, crescent perch, cyt b, historical demography, ikan mengkerong, pleistocene

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