Mitogenomic Insights into the Hampala Barb (Hampala macrolepidota) from Sumatra, Indonesia: Characterization, Phylogenetic Placement, and Genetic Diversity

Despite its ecological and economic importance, <i>Hampala macrolepidota</i> (Cyprinidae: Smiliogastrinae) remains taxonomically debated, having undergone historical reclassifications across multiple taxonomic ranks. These challenges highlight the urgent need for integrative genomic analyses to resolve its phylogeny and assess genome-wide diversity, establishing a baseline for effective management and conservation. In this study, the newly assembled mitogenome of <i>H. macrolepidota</i> from within its native range in Lake Dibawah, West Sumatra, Indonesia, was sequenced. The mitogenome spanned 17,104 bp, encoded 37 genes and a control region, and exhibited a nucleotide composition biased toward adenine and thymine. The protein-coding genes (PCGs) predominantly utilized ATG as the initiation codon and showed a higher proportion of hydrophobic compared to hydrophilic amino acids. The nonsynonymous (Ka) and synonymous (Ks) substitution ratios were below '1', which indicates negative selection on most of the PCGs within <i>Hampala</i> and other Smiliogastrinae species. Mitogenome-wide analysis revealed overall high intraspecific genetic diversity (≥2.7%) in the native Indonesian population compared to mainland populations in Southeast Asia. The Bayesian and maximum-likelihood phylogenetic analyses elucidated matrilineal evolutionary relationships within the subfamily Smiliogastrinae, with the <i>Hampala</i> species forming a monophyletic cluster. The present mitogenome-based phylogenetic topologies also supported the taxonomic placement of several species in the revised classification, which previously were classified under the genera <i>Puntius</i> and <i>Barbus</i>, respectively. Additionally, the investigation of partial mitochondrial <i>COI</i> and <i>Cytb</i> genes further elucidated the population genetic structure of <i>H. macrolepidota</i> across Southeast and East Asia. The observed genetic divergence (0-4.2% in <i>COI</i> and 0-4.5% in <i>Cytb</i>), together with well-resolved phylogenetic clustering and the presence of both shared and distinct haplotypes among Indonesian samples, provides strong evidence for long-term population isolation and local adaptation. These patterns are most plausibly driven by historical hydrological dynamics, paleo-drainage connectivity, and persistent geographic barriers that have structured population divergence over time. In addition, this study emphasizes the need to generate mitogenomes of seven additional <i>Hampala</i> species from Southeast Asia to better understand their evolutionary patterns. Further, broader sampling of wild <i>H. macrolepidota</i> populations across their biogeographical range will be essential to strengthen understanding of their genetic diversity and guide effective conservation strategies.