Genomic Insights and Matrilineal Evolution Reveal Potential Dispersal Patterns of Chitala Species (Osteoglossomorpha: Notopteridae) in the Sundaland Biodiversity Hotspot

The family Notopteridae is distributed across Africa and Asia and plays an important role in ecological functioning, local economies, and conservation initiatives. However, mitogenomic data for notopterids from the Sundaland hotspot remain scarce, limiting comprehensive understanding of their genetic architecture and matrilineal evolutionary history. To address this knowledge gap, the present study reports the first complete mitochondrial genome of Chitala borneensis and re‐sequences the mitogenome of Chitala lopis , two sympatric species endemic to Sundaland. Both Chitala mitogenomes exhibit the canonical teleost mitochondrial organization, comprising 37 genes and an AT‐rich control region, with C. borneensis (16,943 bp) representing the longest mitogenome reported within the genus to date. The codon usage analyses revealed a bias toward arginine, leucine, and serine, while nonsynonymous‐to‐synonymous substitution rate estimates indicated that most protein‐coding genes are evolving under purifying selection. The phylogenetic analyses recovered well‐supported African and Asian notopterid clades, with C. borneensis resolved as the sister lineage to C. lopis . Nevertheless, mitogenomic‐ and COI‐based phylogenetic frameworks inferred using Bayesian inference and maximum‐likelihood approaches supported multiple hypotheses regarding the systematic positions of mainland and island Chitala species in Southeast Asia. The divergence time estimates were congruent with historical biogeographic reconstructions, suggesting that Miocene tectonic events played a major role in the diversification of Chitala from other Asian notopterids. Furthermore, paleodrainage reorganization during the Last Glacial Maximum appears to have been critical in shaping the contemporary population structure of Chitala across the insular landscapes of this region. Collectively, this study provides new insights into the matrilineal evolutionary history of African and Asian notopterids, with particular emphasis on Sundaic Chitala species. The findings underscore the need for expanded taxon sampling and additional molecular data to improve population monitoring, inform conservation genetics, and ensure the long‐term persistence of these freshwater fishes within this biodiversity hotspot.