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Phylogenetic analysis and population genetics study of Plotosus canius (Siluriformes, Plotosidae) from Malaysian coastal waters

Plotosus canius (Hamilton, 1822) is a significant marine species in Malaysia from nutritional and commercial perspectives. Despite numerous fundamental research on biological characteristics of P. canius, there are various concerns on the level of population differentiation, genomic structure, and t...

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Main Authors: Samani, Nima Khalili, Esa, Yuzine, Nurul Amin, Sanker Mohammad, Mohd Ikhsan, Natrah Fatin
Format: Article
Language:English
Published: PeerJ 2015
Online Access:http://psasir.upm.edu.my/id/eprint/45841/1/PLOTOSUS.pdf
http://psasir.upm.edu.my/id/eprint/45841/
https://peerj.com/preprints/1640/
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spelling my.upm.eprints.458412021-05-05T23:33:31Z http://psasir.upm.edu.my/id/eprint/45841/ Phylogenetic analysis and population genetics study of Plotosus canius (Siluriformes, Plotosidae) from Malaysian coastal waters Samani, Nima Khalili Esa, Yuzine Nurul Amin, Sanker Mohammad Mohd Ikhsan, Natrah Fatin Plotosus canius (Hamilton, 1822) is a significant marine species in Malaysia from nutritional and commercial perspectives. Despite numerous fundamental research on biological characteristics of P. canius, there are various concerns on the level of population differentiation, genomic structure, and the level of genetic variability among their populations due to deficiency of genetic-based studies. Deficiency on basic contexts such as stock identification, phylogenetic relationship and population genetic structure would negatively impact their sustainable conservation. Hence, this study was conducted to characterize the genetic structure of P. canius for the first time through the application of mitochondrial Cytochrome Oxidase I (COI) gene, cross amplification of Tandanus tandanus microsatellites, and a total of 117 collected specimens across five selected populations of Malaysia. The experimental results of the mitochondrial analysis revealed that the haplotype diversity and nucleotide diversity varied from 0.395–0.771 and 0.033–0.65 respectively. Moreover, the statistical analysis of microsatellites addressed a considerable heterozygote insufficiency in all populations, with average observed heterozygosity (Ho) value of 0.2168, which was lower than the standard heterozygosity in marine populations (Ho = 0.79). This alongside the high Fis values estimation, high pairwise differentiation among populations and low within population variations are supposed to be associated with small sample size, and inbreeding system. Besides, the significant finding of this study was the sharing of common haplotype KR086940, which reflects a historical genetic connectivity between Peninsular Malaysia and Borneo populations due to the geological history of Southeast Asia during Pleistocene era. Demographic analyses showed that all populations were in an equilibrium state with no significant evidence of population expansion. To put it briefly, the current study has managed to provide an initial genomic database toward understanding of the genetic characterization, phylogenetic, molecular diversification and population structure in P. canius, and should be necessary highlighted for appropriate management and conservation of species. Further studies must be carried out involving more geographical and sampling sites, larger population size per site, and utilization of species specific microsatellites loci. PeerJ 2015 Article PeerReviewed text en http://psasir.upm.edu.my/id/eprint/45841/1/PLOTOSUS.pdf Samani, Nima Khalili and Esa, Yuzine and Nurul Amin, Sanker Mohammad and Mohd Ikhsan, Natrah Fatin (2015) Phylogenetic analysis and population genetics study of Plotosus canius (Siluriformes, Plotosidae) from Malaysian coastal waters. PeerJ, 4. art. no. e1930. pp. 1-32. ISSN 2167-8359 https://peerj.com/preprints/1640/ 10.7287/peerj.preprints.1640v3
institution Universiti Putra Malaysia
building UPM Library
collection Institutional Repository
continent Asia
country Malaysia
content_provider Universiti Putra Malaysia
content_source UPM Institutional Repository
url_provider http://psasir.upm.edu.my/
language English
description Plotosus canius (Hamilton, 1822) is a significant marine species in Malaysia from nutritional and commercial perspectives. Despite numerous fundamental research on biological characteristics of P. canius, there are various concerns on the level of population differentiation, genomic structure, and the level of genetic variability among their populations due to deficiency of genetic-based studies. Deficiency on basic contexts such as stock identification, phylogenetic relationship and population genetic structure would negatively impact their sustainable conservation. Hence, this study was conducted to characterize the genetic structure of P. canius for the first time through the application of mitochondrial Cytochrome Oxidase I (COI) gene, cross amplification of Tandanus tandanus microsatellites, and a total of 117 collected specimens across five selected populations of Malaysia. The experimental results of the mitochondrial analysis revealed that the haplotype diversity and nucleotide diversity varied from 0.395–0.771 and 0.033–0.65 respectively. Moreover, the statistical analysis of microsatellites addressed a considerable heterozygote insufficiency in all populations, with average observed heterozygosity (Ho) value of 0.2168, which was lower than the standard heterozygosity in marine populations (Ho = 0.79). This alongside the high Fis values estimation, high pairwise differentiation among populations and low within population variations are supposed to be associated with small sample size, and inbreeding system. Besides, the significant finding of this study was the sharing of common haplotype KR086940, which reflects a historical genetic connectivity between Peninsular Malaysia and Borneo populations due to the geological history of Southeast Asia during Pleistocene era. Demographic analyses showed that all populations were in an equilibrium state with no significant evidence of population expansion. To put it briefly, the current study has managed to provide an initial genomic database toward understanding of the genetic characterization, phylogenetic, molecular diversification and population structure in P. canius, and should be necessary highlighted for appropriate management and conservation of species. Further studies must be carried out involving more geographical and sampling sites, larger population size per site, and utilization of species specific microsatellites loci.
format Article
author Samani, Nima Khalili
Esa, Yuzine
Nurul Amin, Sanker Mohammad
Mohd Ikhsan, Natrah Fatin
spellingShingle Samani, Nima Khalili
Esa, Yuzine
Nurul Amin, Sanker Mohammad
Mohd Ikhsan, Natrah Fatin
Phylogenetic analysis and population genetics study of Plotosus canius (Siluriformes, Plotosidae) from Malaysian coastal waters
author_facet Samani, Nima Khalili
Esa, Yuzine
Nurul Amin, Sanker Mohammad
Mohd Ikhsan, Natrah Fatin
author_sort Samani, Nima Khalili
title Phylogenetic analysis and population genetics study of Plotosus canius (Siluriformes, Plotosidae) from Malaysian coastal waters
title_short Phylogenetic analysis and population genetics study of Plotosus canius (Siluriformes, Plotosidae) from Malaysian coastal waters
title_full Phylogenetic analysis and population genetics study of Plotosus canius (Siluriformes, Plotosidae) from Malaysian coastal waters
title_fullStr Phylogenetic analysis and population genetics study of Plotosus canius (Siluriformes, Plotosidae) from Malaysian coastal waters
title_full_unstemmed Phylogenetic analysis and population genetics study of Plotosus canius (Siluriformes, Plotosidae) from Malaysian coastal waters
title_sort phylogenetic analysis and population genetics study of plotosus canius (siluriformes, plotosidae) from malaysian coastal waters
publisher PeerJ
publishDate 2015
url http://psasir.upm.edu.my/id/eprint/45841/1/PLOTOSUS.pdf
http://psasir.upm.edu.my/id/eprint/45841/
https://peerj.com/preprints/1640/
_version_ 1699238809542066176
score 13.211869

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