Data from: A test of genomic modularity among life-history adaptations promoting speciation with gene flow

Speciation with gene flow may require adaptive divergence of multiple
traits to generate strong ecologically based reproductive isolation.
Extensive negative pleiotropy or physical linkage of genes in the wrong
phase affecting these diverging traits may therefore hinder speciation,
while genetic independence or “modularity” among phenotypic traits may
reduce constraints and facilitate divergence. Here, we test whether the
genetics underlying two components of diapause life history, initial
diapause intensity and diapause termination timing, constrain
differentiation between sympatric hawthorn and apple-infesting host races
of the fly Rhagoletis pomonella through analysis of 10,256 SNPs measured
via genotyping-by-sequencing (GBS). Loci genetically associated with
diapause termination timing were mainly observed for SNPs mapping to
chromosomes 1–3 in the genome, most notably for SNPs displaying higher
levels of linkage disequilibrium (LD), likely due to inversions. In
contrast, selection on initial diapause intensity affected loci on all
five major chromosomes of the genome, specifically those showing low
levels of LD. This lack of overlap in genetically associated loci suggests
that the two diapause phenotypes are largely modular. On chromosome 2,
however, intermediate level LD loci and a subgroup of high LD loci
displayed significant negative relationships between initial diapause
intensity and diapause termination time. These gene regions on chromosome
2 therefore affected both traits, while most regions were largely
independent. Moreover, loci associated with both measured traits also
tended to exhibit highly divergent allele frequencies between the host
races. Thus, the presence of nonoverlapping genetic modules likely
facilitates simultaneous, adaptive divergence for the measured
life-history components.