Phylogenetic relationships and population structure of Portunus pelagicus in the coastal waters of Malaysia inferred from mitochondrial DNA and microsatellites

The abundance of blue swimmer crabs, Portunus pelagicus throughout the Indo-West Pacific region makes it a valuable target species for fishery industry. The increasing demands of P. pelagicus have led to a growing interest on the broodstock selection of this particular crab species. This study exami...

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Main Author:	Chai, Chuan Jian
Format:	Thesis
Language:	English
Published:	2017
Subjects:	Blue crab Coastal ecology
Online Access:	http://psasir.upm.edu.my/id/eprint/70365/1/FP%202017%2028%20IR.pdf
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spelling	my-upm-ir.703652019-08-16T07:34:04Z Phylogenetic relationships and population structure of Portunus pelagicus in the coastal waters of Malaysia inferred from mitochondrial DNA and microsatellites 2017-07 Chai, Chuan Jian The abundance of blue swimmer crabs, Portunus pelagicus throughout the Indo-West Pacific region makes it a valuable target species for fishery industry. The increasing demands of P. pelagicus have led to a growing interest on the broodstock selection of this particular crab species. This study examined the phylogenetic relationships, demographic history and population structure of P. pelagicus through sequence analyses of mitochondrial cytochrome c oxidase I (COI) gene (600 bp) as well as fragment analyses of four pairs of microsatellite loci. A total of 109 crab samples were collected from five different populations throughout the coastal areas of Malaysia. These include Perak (Pantai Remis and Kuala Sepetang), Johor (Pendas), Negeri Sembilan (Port Dickson), Terengganu (Besut) and Sarawak (Bako). In total, 15 haplotypes were obtained with 13 unique haplotypes and two shared haplotypes. The phylogenetic analyses via the Neighbour Joining (NJ), Maximum Parsimony (MP) and Maximum Likelihood (ML) methods supported the monophyletic status between P. pelagicus and P. sanguinolentus with high bootstrap value (100%). All three phylogenetic trees revealed similar tree topologies with differences in the bootstrap values. The clustering of all P. pelagicus samples into a single clade suggested that this species possibly belonged to a single species. The genetic identity of P. pelagicus was further elucidated with low genetic distances among the haplotypes (0.2-1.7%) via mitochondrial analyses. Limited variations were found among the populations of P. pelagicus with high haplotype diversity and low nucleotide diversity detected within each population. No hybrid individual was discovered based on the genetic analyses of P. pelagicus from sympatric sampling locations. Low FST values obtained among these populations also clarified that these crabs were compatible for breeding programs. One interesting finding of this study was the sharing of haplotypes between samples from Sarawak and Peninsular Malaysia. This situation proclaimed that the rise of sea levels during the last Pleistocene did not result in isolation of P. pelagicus populations from Sarawak, thus, allowed the migration and gene flow between both continents. Another remarkable result was the significant levels of genetic differentiation deduced through comparisons of P. pelagicus from Terengganu and the other four populations. The occurrence might be explained with overexploitation in the fishery industries across the coastal areas of Terengganu and the limited number of crab samples (n=25) analysed. Microsatellite analyses on the other hand indicated low levels of genetic differentiation among the P. pelagicus populations. The average observed heterozygosity (HO=0.48) obtained was lower than the standard heterozygosity found in most marine populations (HO=0.79). The high FIS values (mean FIS=0.4756) and low FST values (mean FST=0.0413) also suggested the existence of inbreeding among different populations of P. pelagicus. When compared with the outcomes from microsatellite analyses, mitochondrial dataset tended to show higher sensibility in detection of genetic variations. In conclusion, the present study was able to provide knowledge on the phylogenetic relationships, demographic history and population structure of P. pelagicus in coastal areas of Malaysia. Nevertheless, in order to better unravel the degrees of genetic differentiation within and among the populations, larger scale studies with higher population size and types of genetic markers used need to be implemented. Blue crab Coastal ecology 2017-07 Thesis http://psasir.upm.edu.my/id/eprint/70365/ http://psasir.upm.edu.my/id/eprint/70365/1/FP%202017%2028%20IR.pdf text en public masters Universiti Putra Malaysia Blue crab Coastal ecology
institution	Universiti Putra Malaysia
collection	PSAS Institutional Repository
language	English
topic	Blue crab Coastal ecology
spellingShingle	Blue crab Coastal ecology Chai, Chuan Jian Phylogenetic relationships and population structure of Portunus pelagicus in the coastal waters of Malaysia inferred from mitochondrial DNA and microsatellites
description	The abundance of blue swimmer crabs, Portunus pelagicus throughout the Indo-West Pacific region makes it a valuable target species for fishery industry. The increasing demands of P. pelagicus have led to a growing interest on the broodstock selection of this particular crab species. This study examined the phylogenetic relationships, demographic history and population structure of P. pelagicus through sequence analyses of mitochondrial cytochrome c oxidase I (COI) gene (600 bp) as well as fragment analyses of four pairs of microsatellite loci. A total of 109 crab samples were collected from five different populations throughout the coastal areas of Malaysia. These include Perak (Pantai Remis and Kuala Sepetang), Johor (Pendas), Negeri Sembilan (Port Dickson), Terengganu (Besut) and Sarawak (Bako). In total, 15 haplotypes were obtained with 13 unique haplotypes and two shared haplotypes. The phylogenetic analyses via the Neighbour Joining (NJ), Maximum Parsimony (MP) and Maximum Likelihood (ML) methods supported the monophyletic status between P. pelagicus and P. sanguinolentus with high bootstrap value (100%). All three phylogenetic trees revealed similar tree topologies with differences in the bootstrap values. The clustering of all P. pelagicus samples into a single clade suggested that this species possibly belonged to a single species. The genetic identity of P. pelagicus was further elucidated with low genetic distances among the haplotypes (0.2-1.7%) via mitochondrial analyses. Limited variations were found among the populations of P. pelagicus with high haplotype diversity and low nucleotide diversity detected within each population. No hybrid individual was discovered based on the genetic analyses of P. pelagicus from sympatric sampling locations. Low FST values obtained among these populations also clarified that these crabs were compatible for breeding programs. One interesting finding of this study was the sharing of haplotypes between samples from Sarawak and Peninsular Malaysia. This situation proclaimed that the rise of sea levels during the last Pleistocene did not result in isolation of P. pelagicus populations from Sarawak, thus, allowed the migration and gene flow between both continents. Another remarkable result was the significant levels of genetic differentiation deduced through comparisons of P. pelagicus from Terengganu and the other four populations. The occurrence might be explained with overexploitation in the fishery industries across the coastal areas of Terengganu and the limited number of crab samples (n=25) analysed. Microsatellite analyses on the other hand indicated low levels of genetic differentiation among the P. pelagicus populations. The average observed heterozygosity (HO=0.48) obtained was lower than the standard heterozygosity found in most marine populations (HO=0.79). The high FIS values (mean FIS=0.4756) and low FST values (mean FST=0.0413) also suggested the existence of inbreeding among different populations of P. pelagicus. When compared with the outcomes from microsatellite analyses, mitochondrial dataset tended to show higher sensibility in detection of genetic variations. In conclusion, the present study was able to provide knowledge on the phylogenetic relationships, demographic history and population structure of P. pelagicus in coastal areas of Malaysia. Nevertheless, in order to better unravel the degrees of genetic differentiation within and among the populations, larger scale studies with higher population size and types of genetic markers used need to be implemented.
format	Thesis
qualification_level	Master's degree
author	Chai, Chuan Jian
author_facet	Chai, Chuan Jian
author_sort	Chai, Chuan Jian
title	Phylogenetic relationships and population structure of Portunus pelagicus in the coastal waters of Malaysia inferred from mitochondrial DNA and microsatellites
title_short	Phylogenetic relationships and population structure of Portunus pelagicus in the coastal waters of Malaysia inferred from mitochondrial DNA and microsatellites
title_full	Phylogenetic relationships and population structure of Portunus pelagicus in the coastal waters of Malaysia inferred from mitochondrial DNA and microsatellites
title_fullStr	Phylogenetic relationships and population structure of Portunus pelagicus in the coastal waters of Malaysia inferred from mitochondrial DNA and microsatellites
title_full_unstemmed	Phylogenetic relationships and population structure of Portunus pelagicus in the coastal waters of Malaysia inferred from mitochondrial DNA and microsatellites
title_sort	phylogenetic relationships and population structure of portunus pelagicus in the coastal waters of malaysia inferred from mitochondrial dna and microsatellites
granting_institution	Universiti Putra Malaysia
publishDate	2017
url	http://psasir.upm.edu.my/id/eprint/70365/1/FP%202017%2028%20IR.pdf
_version_	1747812822659629056

Phylogenetic relationships and population structure of Portunus pelagicus in the coastal waters of Malaysia inferred from mitochondrial DNA and microsatellites

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