Deep origins, distinct adaptations, and species-level status indicated for a glacial relict seal.

Isolated populations of postglacial relicts are known from many regions and are typically found on mountains for terrestrial species and in lakes for aquatic species. Among the few aquatic mammalian relicts, the Saimaa ringed seal (Pusa hispida saimensis) has been landlocked in Lake Saimaa, Finland, for the last 10,000 y. Saimaa ringed seals show genetic, behavioral, and morphological differences from the other ringed seal subspecies, but the extent these differences stem from the end of the last glacial period remains unclear. Here, we demonstrate with comprehensive sampling and state-of-the-art genomic methods that the Saimaa ringed seals are much older than the lake they inhabit, having formed a separate evolutionary branch for at least 60,000 y. This deep evolutionary origin of the Saimaa ringed seals is further underscored by anatomical differences, including our ecomorphological analyses revealing adaptively distinct features in their dentition and tongue. Overall, glacial relicts may harbor a richer selection of evolutionary history than might be expected from their recent isolation history alone.