Data from: Can the genomics of ecological speciation be predicted across the divergence continuum from host races to species? A case study in Rhagoletis

Studies assessing the predictability of evolution typically focus on
short-term adaptation within populations or the repeatability of change
among lineages. A missing consideration in speciation research is to
determine whether natural selection predictably transforms standing
genetic variation within populations into differences between species.
Here, we test whether host-related selection on diapause timing
anticipates genome-wide differentiation during ecological speciation by
comparing ancestral hawthorn and newly formed apple-infesting host races
of Rhagoletis pomonella to their sibling species R. mendax that attacks
blueberries. The responses of 57,857 single nucleotide polymorphisms in a
diapause study on the hawthorn race strongly predicted the direction and
magnitude of genomic divergence among the three flies at a field site in
Fennville, Michigan, USA. As anticipated, the apple race and R. mendax
show parallel changes in the frequencies of putative inversions on three
chromosomes associated with the earlier fruiting times of apples and
blueberries compared to hawthorns. A diapause experiment on R. mendax
revealed compensatory mutations throughout the genome accounting for the
earlier eclosion of blueberry, but not apple flies. Thus, a degree of
predictability, although not complete, exists in the genomics of diapause
across the ecological speciation continuum in Rhagoletis. The generality
of this result is placed in the context of other similar systems.