Molecular Phylogeny Reconstruction of Grouper (Serranidae: Epinephelinae) at Northern Part of Bird’s Head Seascape - Papua Inferred from COI Gene

Abstract

Grouper is one of the most economically important fishes with various morphological forms and characteristics, meaning it is often difficult to identify species and distinguish between life stages, sometimes leading to morphological misidentification. Therefore, identification using a molecular deoxyribose nucleic acid (DNA) approach was needed as an alternative means to identify closely related species. This study aims to determine the molecular phylogeny of grouper from the northern part of the Bird's Head Seascape of Papua. The DNA sequence of each cytochrome oxidase I (COI) gene was used to study the molecular relationship among closely related species of grouper. The results showed that there were 16 Epinephelinae that have been compared to a gene bank (National Centre for Biotechnology Information, NCBI) in the sequence length of 623 base pairs. The closest genetic distance was found between Cephalopholis miniata and Cephalopholis sexmaculata (0.036), while the furthest genetic distance was observed between Plectropomus laevis and Cephalopholis spiloparaea (0.247). This finding was further reinforced by the morphological characters of each species. This finding highlighted that five genera were represented as a monophyletic group (clade), i.e., Epinephelus, Cephalopholis, Plectropomus, Saloptia and Variola.

DNA Barcode Characterization of Chocolate Hind Grouper (Cephalopholis boenak) in Several Indonesia Waters with the New Sequences Record from Madura Island

“…A partial sequence of the CO1 gene are proved effective in determining species in the genus of Cephalopholis in Indonesia, with samples of C. boenak found in it (Fadli et al 2021;Limmon et al 2020;Tapilatu et al 2021). In line with the results of previous studies, the partial sequence of the CO1 gene has indicated a high degree of accuracy in determining C. boenak species in this study, even in general grouping samples based on geographic position.…”

“…Among the many species of groupers, specific DNA barcode to C. boenak has been limited in Indonesia, despite currently occupying an important position in the assessment of the genetic diversity of this species. The partial sequence of the CO1 gene is a DNA barcode that is widely selected to identify grouper in Indonesia waters, including the genus Cephalopholis (Fadli et al 2021;Limmon et al 2020;Razi et al 2021;Tapilatu et al 2021).…”

Genetic diversity analysis and phylogenetic reconstruction of groupers Epinephelus spp. from Madura Island, Indonesia based on partial sequence of CO1 gene

“…The validation results depicted that the 14 samples were grouped into 7 species, including: E. coioides, E. bleekeri, E. areolatus, E. heniochus, E. ongus, E. erythrurus and E. fasciatus. In accordance with the results of the sequence validation, the similarity of the sequences reported by Jefri et al (2015) was in the range of 99-100% and Tapilatu et al (2021) was in the range of 98-100%. All species of Epinephelus spp.…”

“…Thus, it is perceived that closer genetic distance equals to closer phylogenetic branching, indicating more similar morphology of Epinephelus spp., thereby generating misidentification. The conclusion regarding the suitability between the phylogenetic branching proximity and morphological similarities is in accordance with the study conducted by Tapilatu et al (2021). obtained from Madura Island, East Java Province, Indonesia Kamal et al (2019) explained that grouper from Peukan Bada waters had been misidentified due to its morphological ambiguity, thereby requiring the application of partial sequence of CO1 gene for authentication.…”

“…Meanwhile in Indonesia, the application of partial sequence of CO1 gene in several grouper species has generally been reported by Jefri et al (2015) at distant sampling points, in Lampung, Karimunjawa, Madura, Lombok, Tanakeke, Kendari, and Numfor. In addition, grouper sampling at more specific locations was also reported, some of which were in Aceh (Kamal et al 2019), Pangandaran West Java (Ariyanti and Farajallah 2019), and West Papua (Tapilatu et al 2021). Then to complement previous research, this study focuses on observing the genetic diversity and reconstructing the phylogenetic tree of various grouper types (Epinephelus spp.)…”