Results
Field observations
A total of 3,670 P. ochraceus were counted in belt transects across five sites, with incidence of SSWS ranging from 5.2% to 10.0% (Table 1). In three of the sites (Boiler Bay, Yachats Bay, and Strawberry Hill), all surveyed sea stars showed either symptoms of lesions or arm loss, while at Tokatee Klootchman, 25% showed the more advanced symptom of grip loss. Fogarty Creek harbored sea stars with the most advanced stage of SSWS; all wasting individuals surveyed were disintegrating (Table 1). Metadata associated with the 410 individuals from which we collected tissue sample can be found on Table S1.
Sequencing and genotyping
Illumina sequencing yielded ~1.6 billion reads. After removing low quality reads 1.4 billion reads remained, with an average of 6.9 million reads per sample. A total of 259,407 RAD stacks passed sample and population filters, surveying a total of 9,526,221 bases (~2.3% of the 401.9 Mb genome) and with mean per-sample coverage of 38.1x. As mentioned above, 71,784 RAD stacks contained at least one polymorphic site, and a single random site was retained per stack in the full dataset (Table S2). Moreover, given our estimated LD block of 15 kb, this full SNP set allowed for an average of 2.5 SNPs sampled per block. This level of coverage suggests our data set may provide sufficient power to detect genomic regions associate with phenotypic differences, if these exist and have a strong genetic component (Lowry et al., 2017a, 2017b).