Comparing divergence in quantitative traits and neutral molecular markers, such as Q_ST–F_ST comparisons, provides a means to distinguish between natural selection and genetic drift as causes of population differentiation in complex polygenic traits. Onithochiton neglectus (Rochebrune, 1881) is a morphologically variable chiton endemic to New Zealand, with populations distributed over a broad latitudinal environmental gradient. In this species, the morphological variants cluster into two geographically separated shell shape groups, and the phenotypic variation in shell shape has been hypothesised to be adaptive. Here, we assessed this hypothesis by comparing neutral genomic differentiation between populations (F_ST) with an index of phenotypic differentiation (P_ST). We used 7,562 putatively neutral single nucleotide polymorphisms (SNPs) across 15 populations and three clades of O. neglectus throughout New Zealand to infer F_ST. P_ST was calculated from 18 shell shape traits and gave highly variable estimates across populations, clades and shape groups. By systematically comparing P_ST with F_ST, we identified evidence of local adaptation in a number of the O. neglectus shell shape traits. This supports the hypothesis that shell shape could be an adaptive trait, potentially correlated with the ability to live and raft in kelp holdfasts.

Information on methods of collection and processing can be found in the associated publication.