Evidence of Adaptation in Structural Variants among Wild Populations of the purple sea urchin, Strongylocentrotus purpuratus

Structural variants (SVs) are important components of genetic architecture, expanding beyond traditionally used single nucleotide polymorphisms (SNPs). Though growing, our understanding of the evolutionary forces maintaining SVs in natural populations is limited. Inversions in particular can facilitate local adaptation in populations with high gene flow, including many marine species. The purple sea urchin (Strongylocentrotus purpuratus) spans a broad latitudinal range with diverse environmental conditions and is known for its high genetic diversity, making it an ideal system for studying inversion polymorphism, as well as being a crucial foundation species for marine ecosystems. We used low-coverage whole genome sequence data from 140 individuals from seven populations to identify structural variants using a range of methods including local PCA. We integrated Bayesian selection scans to test for local adaptation in putative inversions. We identified nine loci of interest as putative inversions, three of which overlap with areas of the genome associated with local adaptation scans. Additionally, we find functional enrichment within these regions associated with biomineralisation and development. Our results are the first instance of identifying putative inversions in the purple sea urchin and add to the genomic repertoire of model species. This study offers a valuable resource for future research and reinforces the growing evidence that chromosomal inversions represent a fundamental component of standing genetic variation in natural populations, with important implications for the study of local adaptation. Significance statementChromosomal inversions are an important part of the repertoire of standing genetic variation in wild populations and can facilitate adaptation despite strong gene flow. The purple sea urchin, a widely studied marine species, exhibits high gene flow, large population sizes, and extensive genetic diversity across diverse environmental conditions, making it an ideal model for evolutionary genomics. We identified nine putative inversions, three with signatures of selection, adding echinoderms to the growing list of phyla with putatively adaptive inversions. These findings provide new insights into structural variation in a highly dispersive marine species and highlight potential evolutionary mechanisms maintaining these polymorphisms.