Phylogenetic Relationships of Epinephelus fuscoguttatus and Epinephelus hexagonatus Inferred from Mitochondrial Cytochrome b Gene Sequences using Bioinformatic Tools

Abstract

Abstract-Molecular markers can be identified via a DNA test regardless of the developmental stage, age, or environmental challenges experienced by the organism. The degree of conservation of sequence using the cytochrome b gene from mitochondrial DNA is sufficient to discriminate between closely related species. A partial DNA sequence of cytochrome b gene was used to investigate the molecular relationship between Epinephelus hexagonatus and Epinephelus fuscoguttatus. Polymerase Chain Reaction (PCR) and sequence analysis were used to determine the genetic variation in approximately 450-nucleotides region of the mitochondrial cytochrome b gene in 160 fresh tissue samples. Phylogenetic trees were constructed using bioinformatic tools with ME method, NJ method and MP method with bootstrapping using arithmetic average method. There are no differences or only small differences were detected between these two taxa. The results showed that Epinephelus fuscoguttatus clustered with Epinephelus hexagonatus, based on the phylogenetic trees Epinephelus hexagonatus and Epinephelus fuscoguttatus consistently clustered together with following the suggestion referring on their morphological data, that they may be closely related, or possibly placed within the same species.

Homogeneous Nature of Malaysian Marine Fish Epinephelus fuscoguttatus (Perciformes; Serranidae): Evidence Based on Molecular Markers, Morphology and Fourier Transform Infrared Analysis

“…The samples from Terengganu were clustered on the right side of the plot, and the samples from Sabah (Borneo) were clustered on the left, which indicates that the ATR-FTIR is able to separate samples based on location. The separation of individuals in the score scatter plot was in agreement with known locations of the fish and also supports the findings of a previous study [ 10 ]. However, the score scatter plot could not separate E. fuscoguttatus from E. hexagonatus , indicating that the samples should be in one group.…”

“…Phylogenetic inference by neighbor-joining and maximum-parsimony analysis revealed that E. fuscoguttatus and E. hexagonatus representing a similar taxon analysed either in COI, COIII or in 16S. This study also supported our previous phylogenetic relationships of E. fuscoguttatus and E. hexagonatus using cytochrome b mtDNA markers [ 10 ].…”

“…Previously, we reported a study identifying E. fuscoguttatus and E. hexagonatus using the Cyt b gene to construct phylogenetic tree. Based on the previous results, the phylogenetic tree of Maximum Parsimony (MP), Molecular Evolution (ME) and Neighbor-Joining (NJ) showed that the group cluster of the trees have a mix of individuals of those two different species [ 10 ]. In this study, we used the 16s rRNA, Cytochrome Oxidase Subunit I (COI) and III (COIII) genes as molecular markers to study the Malaysian marine fishes Epinephelus fuscoguttatus and Epinephelus hexagonatus .…”

Genetic Diversity and Phylogenetic Relationship in Four Channid Species Based on Sequence Variations in the Mitochondrial Cytochrome B Gene

“…This is because cytochrome b, contain slowly evolving sites which facilitate the investigation of species identification and their relationships [18]. Also, the cytochrome b markers are useful in aquaculture [8,18], evolutionary biology, genetic conservation, population genetics, molecular ecology and food safety [19,20,21]. Some of the important fish species studied by Cyt.…”

Molecular identification of stone loaches of Choman River system, Tigris Basin, based on the Cytochrome b gene with an overview of the Cobitoidea Superfamily

“…Molecular procedures have been applied in many studies for new species identification and it is clear that these methods have great potential in resolving identification and phylogenic relationship of cryptic species and could be highly effective in classification of confusing species (Teletchea, 2009). Cytochrome b gene (Cytb) is frequently utilized for fish identification and phylogenetic study (Song et al, 1998;Biswas et al, 2001;Farias et al, 2001;Perkins & Schall, 2002;Perdices et al, 2004;Baharum & Nurdalila, 2011).…”