Balancing selection and microhabitat heterogeneity enhance resilience of a mussel Septifer virgatus to heat stress

Double digest restriction site-associated DNA sequencing (ddRADseq) was performed to identify SNPs in a total of 64 extracted DNA samples (21 collected in April, 23 collected in August and 20 collected in December) (Peterson et al., 2012). Sequencing libraries were prepared using the EcoRI and MspI restriction enzymes (New England Biolabs, MA, USA) and a protocol adapted from McDaniel Laboratory in University of Florida (https://mcdaniellab.biology.ufl.edu/data/). Libraries were sequenced on an Illumina NovaSeq as 150 bp paired-end reads in Berry Genomics Corporation (Beijing, China). The raw reads were quality filtered and demultiplexed using process_radtags.pl included in the STACKS 1.19 packages (Catchen et al., 2013).