Spatial Genetic Structuring and Divergence in Labeo rohita Across South Asian Rivers: Insights for Conservation Management

Understanding how large river networks shape genetic variation is critical for conserving freshwater biodiversity in the regions under ecological and socio-economic pressures. In South Asia, the rohu carp Labeo rohita is one of the most popular freshwater fish. Yet, the diversity of its population structure across rivers of different countries remains poorly understood. Here, we integrate mitochondrial cytb sequences of L. rohita originating from Bangladeshi rivers with those from Indian rivers to assess genetic diversity, spatial structure, and divergence across eight rivers. Analyses of 308 individuals revealed two divergent genetic clusters: one comprising eastern rivers (Ganga, Padma, Jamuna, Halda) and the other including western and northern rivers (Satluj, Rapti, Mahanadi, Brahmaputra). Despite its location in India, the Ganga population clustered with Bangladeshi rivers, consistent with historical hydrological connectivity, while the Satluj population showed the highest genetic divergence, likely reflecting long-term isolation in the Indus basin. The Ganga population also exhibited notably low haplotype and nucleotide diversity, suggesting genetic erosion due to decades of unregulated hatchery stocking. Bayesian clustering, AMOVA, and pairwise FST analyses confirmed strong spatial structuring (FST = 0.203, p < 0.001), and isolation-by-distance patterns indicated a relationship between distance and gene flow. A median-joining haplotype network revealed a star-like topology, suggestive of recent demographic expansion. Phylogenetic reconstruction supported recognition of eastern and western lineages as distinct management units. These findings highlight the need for basin-specific broodstock management, genetic monitoring, and international conservation strategies to sustain genetic diversity in this economically important freshwater species.