Data from: Widespread selection and gene flow shape the genomic landscape during a radiation of monkeyflowers

Speciation genomic studies aim to interpret patterns of genome-wide
variation in light of the processes that give rise to new species.
However, interpreting the genomic ‘landscape’ of speciation is difficult,
because many evolutionary processes can impact levels of variation.
Facilitated by the first chromosome-level assembly for the group, we use
whole-genome sequencing and simulations to shed light on the processes
that have shaped the genomic landscape during a radiation of
monkeyflowers. After inferring the phylogenetic relationships among the
nine taxa in this radiation, we show that highly similar diversity (π) and
differentiation (FST) landscapes have emerged across the group. Variation
in these landscapes was strongly predicted by the local density of
functional elements and the recombination rate, suggesting that the
landscapes have been shaped by widespread natural selection. Using the
varying divergence times between pairs of taxa, we show that the
correlations between FST and genome features arose almost immediately
after a population split and have become stronger over time. Simulations
of genomic landscape evolution suggest that background selection (i.e.,
selection against deleterious mutations) alone is too subtle to generate
the observed patterns, but scenarios that involve positive selection and
genetic incompatibilities are plausible alternative explanations. Finally,
tests for introgression among these taxa reveal widespread evidence of
heterogeneous selection against gene flow during this radiation. Combined
with previous evidence for adaptation in this system, we conclude that the
correlation in FST among these taxa informs us about the processes
contributing to adaptation and speciation during a rapid radiation.