Population Genomics Informs Resilience and Vulnerability of Habitat‐Building Coralline Algae

Maerl beds, formed by free-living coralline red algae, are biodiversity-rich and carbon-storing habitats of high conservation value but remain understudied at the genomic level. Here, we present the first draft genomes and population genomic analyses for two dominant maerl-forming species in the north-east Atlantic, <i>Phymatolithon calcareum</i> and <i>Lithothamnion corallioides</i>. Using maerl samples genotyped at over 15,000 single nucleotide polymorphisms (SNPs) across England, Wales and additional European sites, we assessed clonal diversity, population structure and potential adaptation to environmental gradients. <i>P. calcareum</i> generally showed moderate clonal diversity, though extreme clonality driven by a single genet (multi-locus lineage) was detected at certain sites. In comparison, <i>L. corallioides</i> displayed high clonal diversity, with most maerl samples representing distinct genets, although local dominance of a single genet was occasionally observed. Contrasting clonal dynamics have important implications for resilience, as populations dominated by a few clones may be more sensitive to environmental change. Population structure analyses in both species revealed strong genetic differentiation between sites, consistent with limited dispersal, while genomic associations identified candidate SNPs linked to climate in <i>P. calcareum</i>, albeit explaining only a small proportion of the observed genetic variation. Genomic offset analyses suggested that certain populations may require greater shifts in allele frequencies to avoid being maladapted to mid-century climate scenarios. Together, these findings highlight both genetically diverse and potentially vulnerable maerl populations, some of which fall within existing marine protected areas. Integrating genomic insights with ecological monitoring will help inform conservation and restoration strategies for these irreplaceable, high natural capital value habitats.