| Summary: | A global decline in seagrass populations has led to renewed calls for their conservation as important providers of biogenic and foraging habitat, shoreline stabilisation, and carbon storage. Eelgrass (Zostera marina) occupies the largest geographic range among seagrass species spanning a commensurately broad spectrum of environmental conditions. However, relatively little is known about their fine-scale genetic structure and broad-scale genomic signatures of environmental adaptation, and in Canada, eelgrass is considered a single phylogroup despite occurring across three oceans. We used a pooled whole-genome re-sequencing approach to characterise population structure, gene flow, and adaptation of 23 eelgrass populations ranging from the Northeast United States, to Atlantic, subarctic, and Pacific Canada. We identified over 500,000 SNPs, which when mapped to a chromosome-level genome assembly revealed six broad clades of eelgrass across the study area, with pairwise FST ranging from 0 among neighbouring populations to 0.54 between Pacific and Atlantic coasts. Genetic diversity was highest in the Pacific and lowest in the Arctic, consistent with colonisation of the Arctic and Atlantic oceans from the Pacific. Using redundancy analyses and two climate change projection scenarios, we found that subarctic populations are more vulnerable to climate change through genomic offset predictions. Conservation planning in Canada should ensure that representative populations from each identified clade are included within a national network so that latent genetic diversity is protected, and gene flow is maintained. Northern populations, in particular, may require stronger protective measures given their susceptibility to change climate.
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