Sirenian genomes illuminate the evolution of fully aquatic species within the mammalian superorder Afrotheria. Dozens of sirenian species have existed in the past, but unlike cetaceans (about 90 extant species) and pinnipeds (about 30 extant species), sirenians are today far less diverse. There are four extant sirenian species: the dugong (Dugong dugon) of the family Dugongidae (included the Steller’s sea cow, Hydrodamalis gigas, that became extinct about 250 years ago) and manatees (family Trichechidae: the West Indian manatee, Trichechus manatus (includes the subspecies Florida manatee, T. m. latirostris, and Antillean manatee, T. m. manatus); the Amazonian manatee, T. inunguis; and the African manatee, T. senegalensis). The dugong and manatees have been found in distinct tropical and subtropical habitats since the middle Miocene (~12.2 Mya). The dugong originally dispersed into the Pacific from near Florida, and today inhabits the coastlines of the Indo-Pacific oceans, while the three species of manatee occupy the Atlantic Ocean and associated rivers.

The research generated a chromosome-level dugong (Dugong dugon) genome. And by comparing the assembly and other afrotherian genomes reveals possible molecular adaptations to aquatic life by sirenians, including a shift in daily activity patterns (circadian clock) and tolerance to a high-iodine plant diet mediated through changes in the iodide transporter NIS (SLC5A5) and its co-transporters. The genomes from nine Australian locations and the functionally extinct Okinawan population confirm and date a genetic break ~10.7 thousand years ago on the Australian east coast and provide evidence of an associated ecotype, and highlight the need for whole-genome resequencing data from dugong populations worldwide for conservation and genetic management. New insights into dugong diversity and demography were provided using population genomics analysis. It was concluded that while dugongs on the east and west coasts of Australia have comparable genetic diversity to other marine mammals of conservation concern, the size of most populations (as indicated by our resequencing of 99 individuals from the Queensland coast) may limit inbreeding.

Genes with unique evolutionary signals in sirenians.

In conclusion, this study reveals insights into sirenian biology and the transition of terrestrial mammals to an aquatic lifestyle and provides a basis for future genomic explorations. Future studies should interrogate whole-genome resequencing data from extant and extinct dugong populations worldwide—including modern, historical, and ancient samples. Such efforts promise to shed further light on dugong evolution and inform their conservation.