The genomic landscape of divergence across the speciation continuum in island-colonising silvereyes (Zosterops lateralis)

A goal of the genomic era is to infer the evolutionary dynamics at play during the process of speciation by analysing the genomic landscape of divergence. However, empirical assessments of genomic landscapes under varying evolutionary scenarios are few, limiting the ability to achieve this goal. Here we combine RAD-sequencing and individual-based simulations to evaluate the genomic landscape in the silvereye (Zosterops lateralis). Using comparisons matched for divergence timeframe and gene flow context, we document how genomic patterns accumulate along the speciation continuum. In contrast to previous predictions, our results provide limited support for the idea that divergence accumulates around loci under divergent selection or that genomic islands widen with time. While a small number of genomic islands were found in populations diverging with and without gene flow, in few cases were SNPs putatively under selection tightly associated with genomic islands. Furthermore, we modelled the transition from localised to genome-wide levels of divergence using individual-based simulations that considered only neutral processes. Our results challenge the ubiquity of existing verbal models that explain the accumulation of genomic differences across the speciation continuum and instead support the idea that divergence both within and outside of genomic islands is important during the speciation process. DATA ACCESSION NUMBERSResequencing data from this study have been submitted to the National Center for Biotechnology Information (NCBI; https://www.ncbi.nlm.nih.gov) under accession number PRJNA489169.