Genome-wide sequencing of clonal seagrass reveals high heterozygosity and low genetic structure in the Western Mediterranean

<title>Abstract</title> <p>Posidonia oceanica is a keystone Mediterranean seagrass whose clonality, episodic sexual recruitment, and slow growth constrain adaptation to environmental change. We generated whole-genome resequencing data for 24 individuals from the Balearic Islands and nearby western Mediterranean localities and analyzed ~25 million variants (1.30 million SNPs after linkage disequilibrium pruning) to characterize genome-wide diversity, relatedness, and structure. SNP density and nucleotide diversity (π ≈ 0.00011 in 50-kb windows) were broadly uniform across chromosomes and highly concordant, indicating no strong sweep-like signatures at the sampled scale. Tajima's D was frequently positive (often &gt;2), and inbreeding coefficients were negative for most samples, revealing excess heterozygosity consistent with divergent haplotypes within long-lived clones. Kinship estimates showed that many genotypes were second- to third-degree relatives despite wide geographic separation, including one first-degree pair (CHA2-MAL4), suggesting historical dispersal followed by long-term clonal persistence. Spatial ancestry inference favored a one-ancestry-cluster solution (K = 1), although models with K = 2-3 revealed a subtle east-west gradient and a distinct Alborán component; a maximum-likelihood tree recovered an eastern clade sister to the remaining samples and a monophyletic Alborán subclade within western lineages. Together, these results show that Balearic P. oceanica meadows combine exceptional clonal longevity with high genome-wide heterozygosity and occupy a central position within a weak but detectable west-to-east cline. These findings highlight how clonality and rare sex can maintain standing genetic variation over millennial timescales despite limited contemporary gene flow.</p>