The effect of divergent and parallel selection on the genomic landscape of divergence

While the role of selection in divergence along the speciation continuum is theoretically well
understood, defining specific signatures of selection in the genomic landscape of divergence
is empirically challenging. Modelling approaches can provide insight into the potential role of
selection on the emergence of a heterogenous genomic landscape of divergence. Here, we
extend and apply an individual-based approach that simulates the phenotypic and genotypic
distributions of two populations under a variety of selection regimes, genotype-phenotype
maps, modes of migration, and genotype-environment interactions. We show that genomic islands of high differentiation and genomic valleys of similarity may respectively form under
divergent and parallel selection between populations. For both types of between-population
selection, negative and positive frequency-dependent selection within populations generated
genomic islands of higher magnitude and genomic valleys of similarity, respectively.
Divergence rates decreased under strong dominance with divergent selection, as well as in
models including genotype-environment interactions under parallel selection. For both
divergent and parallel selection models, divergence rate was higher under an intermittent
migration regime between populations, in contrast to a constant level of migration across
generations, despite an equal number of total migrants. We highlight that interpreting a
particular evolutionary history from an observed genomic pattern must be done cautiously, as
similar patterns may be obtained from different combinations of evolutionary processes.
Modelling approaches such as ours provide an opportunity to narrow the potential routes that
generate the genomic patterns of specific evolutionary histories.