Molecular phylogenetics of selected Clarias spp. inferred from mitochondrial DNA and nuclear genes

Clarias spp., belonging to the family Clariidae, are among the important fishes in aquaculture and fisheries in Malaysia. A total of 37 samples were collected from five different geographic locations in Malaysia, namely Pahang, Kelantan, Perak, Selangor and Sarawak. In the present study, the phyloge...

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Main Author:	Othman, Nor Hasnita
Format:	Thesis
Language:	English
Published:	2012
Subjects:	Fish - Phylogeny Clarias Mitochondrial DNA
Online Access:	http://psasir.upm.edu.my/id/eprint/30913/1/FS%202012%206R.pdf
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spelling	my-upm-ir.309132015-02-05T06:51:15Z Molecular phylogenetics of selected Clarias spp. inferred from mitochondrial DNA and nuclear genes 2012-05 Othman, Nor Hasnita Clarias spp., belonging to the family Clariidae, are among the important fishes in aquaculture and fisheries in Malaysia. A total of 37 samples were collected from five different geographic locations in Malaysia, namely Pahang, Kelantan, Perak, Selangor and Sarawak. In the present study, the phylogenetic levels of four species of catfish were assessed using sequences of the cytochrome b (Cyb b), cytochrome oxidase subunit 1 (CO1) and a large subunit of 16s rRNA (16s rRNA) mitochondrial DNA, as well as a nuclear gene, the Recombination Activating Genes 2 (RAG2). The methods used to infer the phylogeny of this genus were neighbour joining, maximum parsimony, maximum likelihood and Bayesian analyses using MEGA4, PAUP and Mr. Bayes softwares. Thirty seven sequences of C. batrachus, C. macrocephlaus, C. nieuhofii and C. gariepinus were obtained and they were aligned together with outgroups of Pangasianodon gigas and Ictalurus punctatus from GeneBank. The results showed a monophyletic group of Asian Clarias and they are different from African catfish, C. gariepinus. These results were supported with significant bootstrap values. Approximately, 552bp were sequenced from 73 individuals of C. batrachus. There were high levels of within population but low level of interpopulation variabilities among the five populations of C. batrachus in Malaysia. Haplotype diversity and nucleotide diversity ranged from 0.0000 to 0.8333 and from 0.0000 to 0.0112, respectively. Twelve haplotypes were detected amongst the five C. batrachus populations. The results indicated that the haplotype diversity observed in Kelantan was the highest (0.8333), while the Sarawak population had the lowest (0.0000). Based on NJ and ML phylogenetic trees, the five populations of C. batrachus were divided into two clades, namely Clade I and Clade II. Clade I was further divided into subclades a and b. Hap1 and Hap2 are the common haplotypes found in three populations (Perak, Pahang and Johor) and these haplotypes were considered as the ancestral haplotypes for Clade I. However, Hap7 (Sarawak population) was also clustered together in Clade I. This may be due to the gene flow that occurred among islands of Sumatera, Borneo and Southeast Asia during the exposed Sunda Shelf in the Pleistocene Epoch. Clade II consisted of Hap8 to Hap12 which belonged to the Kelantan population. All populations of C. batrachus in this study were monophyletic to each other with Kelantan population being the most diverse. The low level of haplotype diversity in Sarawak population could be due to small samples used (n=4), past bottleneck events or the presence of physical barriers for gene flow among the populations, thus Sarawak populations have their own unique haplotypes. The genetic structure of C. batrachus agrees with previous study whereby the changes in sea level during the Pleistocene Epoch had little influence in shaping the biodiversity of Sunda Shelf. In order to validate the monophyletic status of Asian Clarias, more species and samples should be included in future studies. Fish - Phylogeny Clarias Mitochondrial DNA 2012-05 Thesis http://psasir.upm.edu.my/id/eprint/30913/ http://psasir.upm.edu.my/id/eprint/30913/1/FS%202012%206R.pdf application/pdf en public masters Universiti Putra Malaysia Fish - Phylogeny Clarias Mitochondrial DNA Faculty of Science
institution	Universiti Putra Malaysia
collection	PSAS Institutional Repository
language	English
topic	Fish - Phylogeny Clarias Mitochondrial DNA
spellingShingle	Fish - Phylogeny Clarias Mitochondrial DNA Othman, Nor Hasnita Molecular phylogenetics of selected Clarias spp. inferred from mitochondrial DNA and nuclear genes
description	Clarias spp., belonging to the family Clariidae, are among the important fishes in aquaculture and fisheries in Malaysia. A total of 37 samples were collected from five different geographic locations in Malaysia, namely Pahang, Kelantan, Perak, Selangor and Sarawak. In the present study, the phylogenetic levels of four species of catfish were assessed using sequences of the cytochrome b (Cyb b), cytochrome oxidase subunit 1 (CO1) and a large subunit of 16s rRNA (16s rRNA) mitochondrial DNA, as well as a nuclear gene, the Recombination Activating Genes 2 (RAG2). The methods used to infer the phylogeny of this genus were neighbour joining, maximum parsimony, maximum likelihood and Bayesian analyses using MEGA4, PAUP and Mr. Bayes softwares. Thirty seven sequences of C. batrachus, C. macrocephlaus, C. nieuhofii and C. gariepinus were obtained and they were aligned together with outgroups of Pangasianodon gigas and Ictalurus punctatus from GeneBank. The results showed a monophyletic group of Asian Clarias and they are different from African catfish, C. gariepinus. These results were supported with significant bootstrap values. Approximately, 552bp were sequenced from 73 individuals of C. batrachus. There were high levels of within population but low level of interpopulation variabilities among the five populations of C. batrachus in Malaysia. Haplotype diversity and nucleotide diversity ranged from 0.0000 to 0.8333 and from 0.0000 to 0.0112, respectively. Twelve haplotypes were detected amongst the five C. batrachus populations. The results indicated that the haplotype diversity observed in Kelantan was the highest (0.8333), while the Sarawak population had the lowest (0.0000). Based on NJ and ML phylogenetic trees, the five populations of C. batrachus were divided into two clades, namely Clade I and Clade II. Clade I was further divided into subclades a and b. Hap1 and Hap2 are the common haplotypes found in three populations (Perak, Pahang and Johor) and these haplotypes were considered as the ancestral haplotypes for Clade I. However, Hap7 (Sarawak population) was also clustered together in Clade I. This may be due to the gene flow that occurred among islands of Sumatera, Borneo and Southeast Asia during the exposed Sunda Shelf in the Pleistocene Epoch. Clade II consisted of Hap8 to Hap12 which belonged to the Kelantan population. All populations of C. batrachus in this study were monophyletic to each other with Kelantan population being the most diverse. The low level of haplotype diversity in Sarawak population could be due to small samples used (n=4), past bottleneck events or the presence of physical barriers for gene flow among the populations, thus Sarawak populations have their own unique haplotypes. The genetic structure of C. batrachus agrees with previous study whereby the changes in sea level during the Pleistocene Epoch had little influence in shaping the biodiversity of Sunda Shelf. In order to validate the monophyletic status of Asian Clarias, more species and samples should be included in future studies.
format	Thesis
qualification_level	Master's degree
author	Othman, Nor Hasnita
author_facet	Othman, Nor Hasnita
author_sort	Othman, Nor Hasnita
title	Molecular phylogenetics of selected Clarias spp. inferred from mitochondrial DNA and nuclear genes
title_short	Molecular phylogenetics of selected Clarias spp. inferred from mitochondrial DNA and nuclear genes
title_full	Molecular phylogenetics of selected Clarias spp. inferred from mitochondrial DNA and nuclear genes
title_fullStr	Molecular phylogenetics of selected Clarias spp. inferred from mitochondrial DNA and nuclear genes
title_full_unstemmed	Molecular phylogenetics of selected Clarias spp. inferred from mitochondrial DNA and nuclear genes
title_sort	molecular phylogenetics of selected clarias spp. inferred from mitochondrial dna and nuclear genes
granting_institution	Universiti Putra Malaysia
granting_department	Faculty of Science
publishDate	2012
url	http://psasir.upm.edu.my/id/eprint/30913/1/FS%202012%206R.pdf
_version_	1747811604913717248

Molecular phylogenetics of selected Clarias spp. inferred from mitochondrial DNA and nuclear genes

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