Mitogenomic Insights of notopterids (Actinopterygii: Osteoglossomorpha) from Sundaland biodiversity hotspot: Transcontinental diversification and colonization before Last Glacial Maximum

Notopterid freshwater fishes are distributed across Africa and Asia, but their genomic diversity and evolutionary history, particularly within the Sundaland biodiversity hotspot, remain poorly understood. This study provides a novel mitochondrial genome of Chitala borneensis and six additional mitogenomes of Chitala lopis and Notopterus notopterus , obtained from type localities across the three major Sundaic Islands. A comprehensive investigation involving structural analysis, comparative genomics, and phylogenetic reconstruction was conducted to elucidate genomic diversity, evolutionary relationships, and divergence patterns. All three species displayed typical teleost mitogenomic architecture, with C. borneensis possessing the largest genome (16,943 bp). The mitogenomes exhibited an AT bias, with most protein-coding genes initiating translation with the ATG start codon and showing evidence of strong purifying selection. The phylogenetic analyses using Bayesian and Maximum-likelihood methods illustrated two major clades of notopterids separating Asian and African lineages during Mesozoic era. However, the Asian lineages Chitala and Notopterus diverged during the Cenozoic, with evolutionary processes continuing into the Miocene. A notable high mean genetic divergence (8.84%) among Chitala species suggested long-term evolutionary isolation, while deep intraspecific variation in N. notopterus (4.32%) indicated the presence of possible cryptic diversity in Sundaland. These mitogenomic findings support the hypothesis of transcontinental diversification in this Old-World teleost lineages and underscore the historical biogeographic significance of South and Southeast Asia. Specifically, the Sundaland region likely facilitated gene flow among the common ancestors of extant valid species via interconnected palaeodrainage systems prior to the Last Glacial Maximum, with this connectivity subsequently disrupted by post-glacial sea-level rise.