Genetic Diversity and Inter-Specific Phylogeny of Three Sympatric Cetacean Species (Stenella spp.) in Thai Territorial Waters Based on Mitochondrial and Nuclear DNA Markers

Three Stenella species, S. attenuata, S. coeruleoalba, and S. longirostris, are widely distributed throughout the Indo-Pacific region, but genetic information on each population remains scarce. This gap is particularly notable in Thai waters, where these species co-occur in overlapping oceanic habitats. In contrast, previous studies in the Atlantic have revealed moderate to high mitochondrial genetic diversity and signs of ongoing hybridization among Stenella species. These findings raise the question of whether similar genetic patterns exist in other regions. To address this, we investigated genetic diversity, population structure, potential hybridization, and historical demographic change among three Stenella dolphin species in Thai waters. We analyzed 113 stranded specimens using 20 microsatellite loci and partial mitochondrial DNA (mtDNA) control region sequences. Results revealed high genetic diversity across all species, with expected heterozygosity highest in S. attenuata (He = 0.689), followed by S. longirostris (He = 0.651), and then S. coeruleoalba (He = 0.607). By contrast, S. longirostris exhibits the highest mtDNA diversity (haplotype diversity (H) = 0.988, nucleotide diversity (π) = 0.0194), followed by S. coeruleoalba (H = 0.986, π = 0.0173), and S. attenuata (H = 0.768, π = 0.0125). No population structure was detected within individual species by Bayesian clustering methods. However, analysis of the combined dataset for all three species suggests the presence of three genetic clusters (K = 3), with evidence of admixture across species but no shared mtDNA haplotypes, indicative of male-mediated gene flow. Unique haplotypes were also found in all three species inhabiting Thai waters. Differing demographic histories likely reflect species-specific responses to past environmental changes and recent anthropogenic impacts. These findings provide critical genetic insights for monitoring and informing conservation strategies in Thailand and surrounding regions.