Variation in lateral plating in stickleback fish represents a classical example of rapid and parallel adaptation in morphology. The underlying genetic architecture involves polymorphism at the ectodysplasin-A (EDA) gene. However, lateral plate number is influenced by additional loci that remain poorly characterized. Here we search for such loci by performing genome-wide differentiation mapping based on pooled whole-genome sequence data from a European stickleback population variable in the extent of lateral plating, while tightly controlling for the phenotypic effect of EDA. This suggests a new candidate locus, the EDA receptor (EDAR) gene, for which additional support is obtained by individual-level targeted Sanger sequencing and by comparing allele frequencies among natural populations. Overall, our study illustrates the power of pooled whole-genome sequencing for searching phenotypically relevant loci and opens opportunities for exploring the population genetics and ecological significance of a new candidate locus for stickleback armor evolution.

These data were generated to investigate candidate genes for the reduction in the lateral plates of stickleback fish (Gasterosteus acculeatus). These consist mainly of pool whole-genome single nucleotide polymorphism (SNP) data.
Individuals were pooled, by plating phenotype, controlling for EDA genotype and lateral plate phenotype, and all raw whole-genome read data has been deposited in the NCBI SRA library (see file SRA_Accession_Info.xlsx for specif codes). Phenotypic data to access lateral plate number for the focus population (a stream from Constance Lake) is also provided. See methods section in DOI: 10.1093/g3journal/jkac077 for further details.

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