Population genomic and morphological datasets from: An evolutionary mosaic challenges traditional monitoring of a foundation species in a coastal environment - the Baltic Fucus vesiculosus

Genetic diversity in foundation species is critical for ecosystem functions and resilience under environmental change but remains largely overlooked in environmental monitoring. In the Baltic Sea, a key species for monitoring is the brown seaweed Fucus vesiculosus, which forms sublittoral 3D habitats providing shelter and food for fish and invertebrates.  Ecological distribution models predict a significant loss of Baltic F. vesiculosus due to ocean warming unless populations can adapt. Genetic variation and recombination during sexual reproduction are essential for adaptation, but studies have revealed large-scale clonal reproduction within the Baltic Sea. We analyzed genome-wide SNP data from the east Atlantic, the "Transition zone", and the Baltic Sea, and found a mosaic of divergent lineages in the Baltic Sea contrasting an outside dominance of a few genetic groups. We determined that the previously described endemic species Fucus radicans is predominantly a large female clone of F. vesiculosus in its northern Baltic distribution. In two Estonian sites, however, individuals are sexual but reproductively isolated from Baltic F. vesiculosus, revealing a separate diverged lineage that predates the formation of the Baltic Sea. Monitoring Baltic Fucus without considering this genetic complexity will fail to prioritise populations with adaptive potential to new climate conditions. From our genomic data, we can extract informative and diagnostic genetic markers that differentiate major genetic entities. Such an SNP panel will provide a straightforward tool for spatial and temporal monitoring and informing management decisions and actions.