Seascape genomics reveals shared spatial genetic structure in three co-occurring sea snakes

Marine species with broad distributions often exhibit complex patterns of genetic connectivity, shaped by historical and contemporary processes. Understanding these patterns is critical for conserving taxa threatened by ongoing and future environmental change. Here, we use reduced-representation and whole-genome sequencing to investigate population genetic patterns in three co-occurring sea snake species ( Hydrophis stokesii , Hydrophis major , and Aipysurus laevis ) across northern Australia and New Caledonia. Broadscale analyses revealed major genetic breaks across all species between: (1) Australia and New Caledonia, (2) northwestern and northeastern Australia, and (3) the offshore Timor Sea reefs and adjacent northwestern continental shelf of Australia. More subtle genetic differentiation was observed between Shark Bay in Western Australia and northern localities. All species showed relatively large effective population sizes and broadscale connectivity across ∼1,300 km of Australia’s northwestern continental shelf. This likely reflects substantial historical range expansion over late Quaternary timescales, which may have contributed to the observed genetic connectivity across the region. However, subtle patterns of isolation by distance emphasised the contribution of species-specific traits in shaping connectivity. The isolated offshore reef populations are genetically distinct and potentially threatened by environmental change. Disjunct populations in Shark Bay and the Timor Sea maintain similar levels of genetic diversity to the extensive continental shelf populations, while New Caledonian populations exhibit reduced diversity. Our results support the delineation of spatial units for sea snake conservation based on shared phylogeographic structure, while also finding important population- and species-specific differences in connectivity at finer spatial and temporal scales. Highlights Broadscale phylogeographic structure is shared by three species of sea snakes. Populations along ∼1,300 km of the NW Australian shelf show extensive genetic connectivity. Fine-scale patterns highlight the role of species traits in shaping connectivity. Conservation planning must consider both broadscale and species-specific processes.