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Molecular phylogeny of Malaysian groupers inferred from mitochondrial (Cytochrome b) and nuclear (Tmo-4c4 and Rag-1) genes

Groupers are known as one of the important marine and estuarine fishes. They are widely distributed in tropical and subtropical open waters. Difficulty in netting them in wild has increased their demand in the market thus resulting in overexploitation of these fishes. The classification also difficu...

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Main Author: Nor Rahim, Nor Syakina
Format: Thesis
Language:English
Published: 2017
Online Access:http://psasir.upm.edu.my/id/eprint/70473/1/FP%202017%2045%20IR.pdf
http://psasir.upm.edu.my/id/eprint/70473/
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spelling my.upm.eprints.704732019-08-16T07:36:48Z http://psasir.upm.edu.my/id/eprint/70473/ Molecular phylogeny of Malaysian groupers inferred from mitochondrial (Cytochrome b) and nuclear (Tmo-4c4 and Rag-1) genes Nor Rahim, Nor Syakina Groupers are known as one of the important marine and estuarine fishes. They are widely distributed in tropical and subtropical open waters. Difficulty in netting them in wild has increased their demand in the market thus resulting in overexploitation of these fishes. The classification also difficult for most species from this family due to their homology characteristics which is most notably among closely related species which makes the conservation and management of these fishes ambiguous. This study aimed to elucidate the phylogenetic relationship of wild grouper in Peninsular Malaysia. Sample collection was done for nine sites which are from Terengganu (N=24), Kelantan (N=6), Perak (N=9), Pahang (N=10), Perlis (N=1), Perlis (N=1), Kedah (N=5), Selangor (N=26), Pahang (N=10), Malacca (N=3) and Johor (N=2) coastal areas. Samples were identified based on their morphological characteristics. Molecular phylogeny study was done inferred using Mitochondrial Cytochrome b (Cyt b), Nuclear Tmo-4c4 and Recombination activating gene-1 (Rag-1) genes and combined Mitochondrial and Nuclear genes. The results revealed a total 86 individuals belonging to 12 species representing three genera which are Epinephelus, Cephalopholis and Plectropomus. The phylogenetic trees were contructed for Neighbour-Joining (NJ), Maximum Parsimony (MP), Maximum Likelihood (ML), Minimum Evolution (ME), and Bayesian Inference (BI) which were implemented by Molecular Evolution Genetic Analysis 7.01 (MEGA) and MrBayes 3.2.1. One consistent result across all the analyses was the monophyletic status of the subfamily of Epinephelinae. It is revealed that genus Plectropomus sister to the rest genera. Genus Epinephelus was clustered into two clades which is constant for all analyses. The separation confidence level between cluster Epinephelus, Cephalopolis and Plectropomus were 100% respectively for BI analysis based on combined dataset. Molecular data revealed that combined dataset helps increases the phylogenetic resolution compared to single gene phylogeny where the dataset well resolved the deeper node within genus Epinephelus compared to single gene analyses. Nevertheless, several genetic relationships remain unresolved particularly among morphologically similar species, for instance between Epinephelus fario and E. longispinis and species with limited number of individuals which is E. coioides. This study have aids in giving baseline information regarding groupers particularly in Malaysia which related to the area of taxonomy, phylogeny and genetic diversity which are important for their appropriate sustainable management, for conservation as well as aquaculture purposes. 2017-05 Thesis NonPeerReviewed text en http://psasir.upm.edu.my/id/eprint/70473/1/FP%202017%2045%20IR.pdf Nor Rahim, Nor Syakina (2017) Molecular phylogeny of Malaysian groupers inferred from mitochondrial (Cytochrome b) and nuclear (Tmo-4c4 and Rag-1) genes. Masters thesis, Universiti Putra Malaysia.
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 Groupers are known as one of the important marine and estuarine fishes. They are widely distributed in tropical and subtropical open waters. Difficulty in netting them in wild has increased their demand in the market thus resulting in overexploitation of these fishes. The classification also difficult for most species from this family due to their homology characteristics which is most notably among closely related species which makes the conservation and management of these fishes ambiguous. This study aimed to elucidate the phylogenetic relationship of wild grouper in Peninsular Malaysia. Sample collection was done for nine sites which are from Terengganu (N=24), Kelantan (N=6), Perak (N=9), Pahang (N=10), Perlis (N=1), Perlis (N=1), Kedah (N=5), Selangor (N=26), Pahang (N=10), Malacca (N=3) and Johor (N=2) coastal areas. Samples were identified based on their morphological characteristics. Molecular phylogeny study was done inferred using Mitochondrial Cytochrome b (Cyt b), Nuclear Tmo-4c4 and Recombination activating gene-1 (Rag-1) genes and combined Mitochondrial and Nuclear genes. The results revealed a total 86 individuals belonging to 12 species representing three genera which are Epinephelus, Cephalopholis and Plectropomus. The phylogenetic trees were contructed for Neighbour-Joining (NJ), Maximum Parsimony (MP), Maximum Likelihood (ML), Minimum Evolution (ME), and Bayesian Inference (BI) which were implemented by Molecular Evolution Genetic Analysis 7.01 (MEGA) and MrBayes 3.2.1. One consistent result across all the analyses was the monophyletic status of the subfamily of Epinephelinae. It is revealed that genus Plectropomus sister to the rest genera. Genus Epinephelus was clustered into two clades which is constant for all analyses. The separation confidence level between cluster Epinephelus, Cephalopolis and Plectropomus were 100% respectively for BI analysis based on combined dataset. Molecular data revealed that combined dataset helps increases the phylogenetic resolution compared to single gene phylogeny where the dataset well resolved the deeper node within genus Epinephelus compared to single gene analyses. Nevertheless, several genetic relationships remain unresolved particularly among morphologically similar species, for instance between Epinephelus fario and E. longispinis and species with limited number of individuals which is E. coioides. This study have aids in giving baseline information regarding groupers particularly in Malaysia which related to the area of taxonomy, phylogeny and genetic diversity which are important for their appropriate sustainable management, for conservation as well as aquaculture purposes.
format Thesis
author Nor Rahim, Nor Syakina
spellingShingle Nor Rahim, Nor Syakina
Molecular phylogeny of Malaysian groupers inferred from mitochondrial (Cytochrome b) and nuclear (Tmo-4c4 and Rag-1) genes
author_facet Nor Rahim, Nor Syakina
author_sort Nor Rahim, Nor Syakina
title Molecular phylogeny of Malaysian groupers inferred from mitochondrial (Cytochrome b) and nuclear (Tmo-4c4 and Rag-1) genes
title_short Molecular phylogeny of Malaysian groupers inferred from mitochondrial (Cytochrome b) and nuclear (Tmo-4c4 and Rag-1) genes
title_full Molecular phylogeny of Malaysian groupers inferred from mitochondrial (Cytochrome b) and nuclear (Tmo-4c4 and Rag-1) genes
title_fullStr Molecular phylogeny of Malaysian groupers inferred from mitochondrial (Cytochrome b) and nuclear (Tmo-4c4 and Rag-1) genes
title_full_unstemmed Molecular phylogeny of Malaysian groupers inferred from mitochondrial (Cytochrome b) and nuclear (Tmo-4c4 and Rag-1) genes
title_sort molecular phylogeny of malaysian groupers inferred from mitochondrial (cytochrome b) and nuclear (tmo-4c4 and rag-1) genes
publishDate 2017
url http://psasir.upm.edu.my/id/eprint/70473/1/FP%202017%2045%20IR.pdf
http://psasir.upm.edu.my/id/eprint/70473/
_version_ 1643839708575301632
score 13.211869

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