Genetic parallelism underlying repeated bill divergence in the island scrub-jay ( <i>Aphelocoma insularis</i> ) increases at higher genetic levels of organization

Whether the same genes underlie parallel adaptive trait evolution remains an open question in biology. The degree of genetic parallelism is expected to increase at higher genetic hierarchical levels (i.e., single nucleotide polymorphisms [SNPs] to genes to pathways to phenotype) due to the hierarchical nature of the genetic basis of traits, which genomic approaches can help elucidate. Previous research shows a large degree of variation in the extent to which phenotypic parallelism shares the same genetic mechanisms in nature. Here, we analyzed the degree of genetic parallelism underlying repeated divergence in bill morphology of island scrub-jays (Aphelocoma insularis), across three naturally replicated pine-oak ecotones on Santa Cruz Island, California, US. We analyzed 66,503 SNPs generated using restriction site-associated DNA sequencing in 161 island scrub-jays to identify candidate SNPs associated with environmental variation and divergence in bill morphology. We then examined signatures of parallelism in genomic regions containing candidate SNPs and the associated genetic pathways. We found little evidence for parallelism at the SNP or gene level, but substantial parallelism at the pathway level. Our results support the view that the degree of genetic parallelism underlying repeated phenotypes depends on the genetic level of organization being analyzed.