DNA Barcoding, Phylogenetic Analysis, and Haplotype Characteristic of Mungkus Fish (Genus Sicyopterus) Existing in Eight Main Rivers in Bengkulu Province, Indonesia

Abstract

Mungkus fish is a culturally and economically important fish in Bengkulu. However, the accurate species name of the existing Mungkus fish in Bengkulu province remains unclear. Our research aimed to accurately identify the species of Mungkus fish by using a molecular approach. The DNA Barcoding method, using the Cytochrome c oxidase subunit 1 (COI) gene sequence, was employed for species identification and phylogenetic analysis. The DNA of 12 fin tissue samples, chosen from eight main rivers, was extracted using the Phenol-Chloroform method. The target DNA was amplified using the paired primers Fish-BCL and Fish-BCH before sequencing. The sequence data were then analyzed by using bioinformatic tools. This study successfully identifies three species of Mungkus fish in Bengkulu (Sicyopterus lagochepalus, Sicyopterus squamossissimus, and Sicyopterus cynocephalus), with similarity to GenBank data> 99.00%. ASAP analysis supports the species delimitation, which clustered into three species. Bayesian Inference phylogenetic analysis clearly resolved all samples into three distinct clades. The analysis also unveiled clear haplotype divergence among Sicyopterus species, indicating both shared and species-specific genetic lineages. Close genetic affinity was observed among S. lagocephalus populations from Bengkulu, Maluku, and the Philippines, whereas S. cynocephalus showed regional differentiation from Gorontalo populations. These findings provide taxonomic clarity that is fundamental for future sustainable management and conservation planning of Mungkus fisheries in Bengkulu Province.