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Genetic parallelism underlying repeated bill divergence in Island Scrub-Jays (Aphelocoma insularis) increases at higher genetic levels of organization

Cheek, Rebecca1; Hohenlohe, Paul2; Sillett, Scott3; Morrison, Scott4; Funk, Chris1; Ghalambor, Cameron5

Published Nov 25, 2025 on Dryad. https://doi.org/10.5061/dryad.hx3ffbgpf

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Abstract

Whether the same genes underlie parallel adaptive trait evolution remains an open question in biology. The degree of parallelism is expected to increase at higher hierarchical levels due to the hierarchical nature of the genetic basis of traits (i.e., single nucleotide polymorphisms (SNPs) to genes to pathways to phenotype), 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, USA. We analyzed 66,503 SNPs generated using restriction site-associated DNA sequencing (RADseq) 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 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 convergent evolution depends on the genetic level of organization being analyzed.