Mitogenomic Insights into the Tinfoil Barb Barbonymus schwanefeldii from Sumatra, Indonesia: Structural Features, Selective Pressure, Genetic Diversity, and Phylogenetic Placement.

Prior to this study, the mitogenomic characterization, genetic diversity, and phylogenetic placement of the Tinfoil Barb Barbonymus schwanefeldii remained largely unexplored, despite its notable ecological and economic importance. Hence, this study aimed to provide the first in-depth insight into the mitogenomic features of this species from its native range in Sumatra, Indonesia. The generated mitogenome is 16,578 bp in length and contains 37 genes along with a control region (CR). The genome also exhibited a 57.03% A + T bias and all protein-coding genes (PCGs) initiated with the ATG codon, except COI (GTG). The codon usage was dominated by arginine, leucine, and serine, whereas methionine and tryptophan were rare. The pairwise nonsynonymous-to-synonymous substitution ratios demonstrated strong purifying selection across all Barbonymus species. This pattern was further supported by complementary codon-based approaches, which showed that the 13 PCGs were predominantly subject to strong evolutionary constraints, with evidence of positive selection confined to a small number of sites in a limited subset of genes. Most transfer RNA genes of B. schwanefeldii maintained the canonical cloverleaf secondary structure, except tRNA-Ser1, which lacked the dihydrouridine stem. The comparative profiling of conserved sequence blocks within the CR among Barbonymus taxa highlighted variation in length and nucleotide composition, with tandem repeats exclusively detected in B. gonionotus. A mitogenome-wide assessment of B. schwanefeldii revealed considerable intra-specific genetic divergence (0%-3.932%) and notable haplotypic diversity across Southeast Asian islands and mainland populations. This population genetic structure likely reflects historical connectivity during the Pleistocene via ancient drainage systems of the Malacca Strait or North Sunda, followed by subsequent isolation after post-glacial eustatic sea-level rise. The phylogenetic inference robustly corroborated a sister-species relationship between B. schwanefeldii and Barbonymus altus within the clade 'Poropuntiinae'. Collectively, these findings elucidate the phylogeographic patterns and evolutionary history of this Southeast Asian endemic cyprinid fish within the Sundaland biodiversity hotspot.