Abstract The limited genetic information on the Hard-lipped Barb, Osteochilus vittatus, presents challenges for systematics and conservation genetics, particularly in Sumatra, a key region within the Sundaland biodiversity hotspot. This study aimed to generate partial mitochondrial COI and complete mitogenomic data to elucidate genetic diversity, phylogenetic relationships, and lineage diversification. Analysis of the COI dataset revealed high intraspecific genetic distance (6.67%) and haplotypic diversity (n = 15), suggesting four distinct genetic clusters across Southeast Asia. The observed phylogeographic patterns supported the hypothesis that eustatic sea-level fluctuations during the last glacial period influenced the lineage diversification of O. vittatus in this region. Additionally, the identification of multiple Molecular Operational Taxonomic Units (MOTUs) and COI-based phylogenetic clustering indicated cryptic diversity within this cyprinid species. The newly sequenced mitogenomes of O. vittatus from Sumatra (16,632 bp and 16,626 bp) contained 37 genes and an AT-rich control region (CR). These mitogenomes displayed notable AT bias and comprised 14 intergenic spacer with six overlapping regions. Most PCGs initiated with the ATG start codon, except for COI, which utilized GTG. The ratio of nonsynonymous to synonymous substitutions suggested strong purifying selection across all PCGs, while relative synonymous codon usage analysis reflected a high preference for leucine and serine codons in Osteochilus species. The tandem repeat analysis within the CR demonstrated that O. vittatus and O. schlegelii shared a predominant repeat element, whereas O. pentalineatus exhibited two distinct repeat motifs. The mitogenome-based phylogenetic analysis clearly distinguished all Osteochilus species, offering valuable insights into their evolutionary relationships. Collectively, these findings provide a comprehensive molecular framework for illuminating the population genetics and genomic characteristics of O. vittatus, offering critical insights to inform freshwater fish conservation strategies and support sustainable management initiatives across Southeast Asia.
Aini et al. (Sun,) studied this question.