Data from: Development and preliminary evaluation of a genome-wide single-nucleotide polymorphisms resource generated by RAD-seq for the small yellow croaker (Larimichthys polyactis)

Recent advances in high-throughput sequencing technologies have offered
the possibility to generate genome-wide sequence data to delineate
previously unidentified genetic structure, obtain more accurate estimates
of demographic parameters, and to evaluate potential adaptive divergence.
Here, we identified 27 556 single-nucleotide polymorphisms for the small
yellow croaker (Larimichthys polyactis) using restriction-site-associated
DNA (RAD) sequencing of 24 individuals from two populations. Significant
sources of genetic variation was identified, with an average nucleotide
diversity (π) of 0.00105 ± 0.000425 across individuals and long-term
effective population size was thus estimated to range between 26 172 and
261 716. According to the results, no differentiation between the two
populations was detected based on the SNP dataset of top quality score per
contig or neutral loci. However, the two analyzed populations were highly
differentiated based on SNP dataset of both top FST value per contig and
the outlier SNPs. Moreover, local adaptation was highlighted by an
FST-based outlier tests implemented in LOSITAN and a total of 538
potentially locally selected SNPs were identified. BLAST2GO annotation of
contigs containing the outlier SNPs yielded hits for 37 (66%) of 56
significant BLASTX matches. Candidate genes for local adaptation
constituted a wide array of biological functions, including cellular
response to oxidative stress, actin filament binding, ion transmembrane
transport and synapse assembly. The generated SNP resources in the present
study provided a valuable tool for future population genetics and genomics
studies of L. polyactis.