Genomic insights into the divergence and conservation of Sotalia dolphins

The transition from terrestrial to aquatic life is well documented in cetaceans, yet secondary transitions between marine and freshwater habitats remain poorly understood. The dolphin genus Sotalia provides an exceptional natural system for investigating this process, comprising two recently diverged species (~ 2 Ma) that occupy contrasting environments: the coastal Guiana dolphin ( Sotalia guianensis ) and the riverine tucuxi ( Sotalia fluviatilis ). We present the first chromosome-level genome assembly of S. guianensis and the first genome sequence of S. fluviatilis , providing comprehensive genomic resources for investigating their evolutionary divergence and supporting conservation efforts. Phylogenomic analyses indicate that the two species diverged during Plio-Pleistocene sea-level fluctuations. Demographic genomic analyses reveal low contemporary and historical genetic diversity and high homozygosity in coastal populations, highlighting conservation concerns. These genomic resources establish Sotalia as a valuable model system for investigating the genomic basis of early-stage ecological speciation associated with marine-to-freshwater transitions. They also provide a critical foundation for future evolutionary, ecological, and conservation genomic studies of these vulnerable dolphins.