The Genomic Landscape of Divergence Across the Speciation Continuum in an Island-colonising Bird. Zosterops lateralis

Understanding the drivers of global diversity patterns requires knowledge of evolutionary dynamics that transform undifferentiated taxa into reproductively isolated species. A goal of genomic-era analyses is to compare the genomes of diverging forms, and from the distribution of their genomic differences – their genomic landscape of divergence – infer the evolutionary dynamics at play. However, empirical assessment of genomic landscape dynamics across a speciation continuum under varying evolutionary scenarios are few, limiting the ability to achieve this goal. Here we evaluate how divergence accumulates across the genomic landscape in a naturally replicated system that serves as a proxy for the speciation continuum – island colonisations by the silvereye (Zosterops lateralis). Using reduced representation sequencing of comparisons matched for divergence timeframe and gene flow scenario, we document how genomic patterns accumulate as divergence progresses and demonstrate the role of gene flow in slowing the pace of divergence. We found limited support for the idea that divergence accumulates around loci under divergent selection. While a small number of genomic islands were found in populations diverging with and without gene flow, in only one case were SNPs tightly associated with a genomic island, and nor did genomic islands widen with time. Furthermore, the transition from localised to genome-wide levels of divergence was captured with an individual-based simulation model that considered only neutral processes. Our results challenge the ubiquity of verbal models that explain the progression of genomic differences across the speciation continuum by invoking initial divergence at selected loci, and subsequent divergence at adjacent linked loci.