Environmental Drivers of Genetic Structure and Local Adaptation in a Marine Foundation Species

ABSTRACT Predicting how species will respond to global change requires understanding how environmental drivers shape both neutral and adaptive genetic variation across space. The kelp Eisenia arborea is a thermally tolerant foundation species spanning more than 3000 km of coastline and a broad latitudinal temperature gradient in the Northeast Pacific, yet how environmental and demographic processes influence genomic and population structure remain unclear. We used genome‐wide ddRAD sequencing to investigate patterns of genetic diversity, connectivity and local adaptation in E. arborea across two depths and ~2700 km of coastline. We detected strong genetic differentiation between northern (British Columbia, Canada) and southern (Baja California, Mexico) populations, indicating limited gene flow across the species' broad range. Southern populations also had the lowest genetic diversity and highest inbreeding, broadly consistent with expectations for populations occupying environmentally marginal portions of a species' range. However, the two southernmost populations (~200 km apart) were highly similar and well connected, whereas mid‐range sites were more differentiated, indicating that the geographic range edge population was not genetically isolated as is often hypothesised. Environmental association analyses identified SNPs correlated with both sea surface temperature and depth, revealing signals of local adaptation to broad climatic gradients and fine‐scale habitat variation. The combination of high inbreeding, restricted connectivity and local adaptation highlights both the vulnerability and potential conservation value of distinct genetic units, especially warm‐adapted southern populations, for maintaining the resilience of these Eisenia forests under ocean warming.