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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
Online Access:http://psasir.upm.edu.my/id/eprint/30913/1/FS%202012%206R.pdf
http://psasir.upm.edu.my/id/eprint/30913/
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spelling my.upm.eprints.309132015-02-05T06:51:15Z http://psasir.upm.edu.my/id/eprint/30913/ Molecular phylogenetics of selected Clarias spp. inferred from mitochondrial DNA and nuclear genes 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. 2012-05 Thesis NonPeerReviewed application/pdf en http://psasir.upm.edu.my/id/eprint/30913/1/FS%202012%206R.pdf Othman, Nor Hasnita (2012) Molecular phylogenetics of selected Clarias spp. inferred from mitochondrial DNA and nuclear 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 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
author Othman, Nor Hasnita
spellingShingle Othman, Nor Hasnita
Molecular phylogenetics of selected Clarias spp. inferred from mitochondrial DNA and nuclear genes
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
publishDate 2012
url http://psasir.upm.edu.my/id/eprint/30913/1/FS%202012%206R.pdf
http://psasir.upm.edu.my/id/eprint/30913/
_version_ 1643830203026243584
score 13.211869

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