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.