Data from: Divergent diapause life history timing drives both allochronic speciation and reticulate hybridization in an adaptive radiation of Rhagoletis flies

Divergent adaptation to new ecological opportunities can be an important
factor initiating speciation. However, as niches are filled during
adaptive radiations, trait divergence driving reproductive isolation
between sister taxa may also result in trait convergence with more
distantly related taxa, increasing the potential for reticulated gene flow
across the radiation. Here, we demonstrate such a scenario in a recent
adaptive radiation of Rhagoletis fruit flies, specialized on different
host plants. Throughout this radiation, shifts to novel hosts are
associated with changes in diapause life history timing, which act as
“magic traits” generating allochronic reproductive isolation and
facilitating speciation-with-gene-flow. Evidence from laboratory rearing
experiments measuring adult emergence timing and genome-wide
DNA-sequencing surveys supported allochronic speciation between
summer-fruiting Vaccinium spp.-infesting Rhagoletis mendax and its
hypothesized and undescribed sister taxon infesting fall-fruiting
sparkleberries. The sparkleberry fly and R. mendax were shown to be
genetically discrete sister taxa, exhibiting no detectable gene flow and
allochronically isolated by a two-month average difference in emergence
time corresponding with host availability. At sympatric sites across the
southern USA, the later fruiting phenology of sparkleberries overlaps with
that of flowering dogwood, the host of another more distantly related and
undescribed Rhagoletis taxon. Laboratory emergence data confirmed broadly
overlapping life history timing and genomic evidence supported on-going
gene flow between sparkleberry and flowering dogwood flies. Thus,
divergent phenological adaptation can drive the initiation of reproductive
isolation, while also enhancing genetic exchange across broader adaptive
radiations, potentially serving as a source of novel genotypic variation
and accentuating further diversification.