GBS data for admixture and experimental evolution in Callosobruchus maculatus

Admixture is common in nature, and can serve as a crucial source of adaptive potential through the generation of novel genotype combinations and phenotypes. Conversely, the presence of hybrid incompatibilities can decrease the fitness of hybrids. Due to the pervasiveness of admixture in nature and its potential role in facilitating adaptation, understanding how admixture affects the rate and repeatability of evolution is important for furthering our understanding of evolutionary dynamics. However, few studies have assessed how patterns of evolutionary parallelism in admixed lineages are affected by the presence of strong ecological pressure. In this experiment, we assessed patterns of evolution and parallelism across admixed and non-admixed cowpea seed beetles (Callosobruchus maculatus) during adaptation to a novel, stressful host: lentil. Specifically, we asked (1) whether admixture facilitates adaptation to lentil, (2) whether parallelism was higher in admixed or non-admixed lineages, and (3) to what degree parallelism in admixed lineages was associated with selection on globally adaptive alleles versus epistatic effects and hybrid incompatibilities. We extracted DNA from 19-20 beetle specimens each from 78 unique lineage x replicate x host x generation combinations, for a total of 1536 individuals. Using a GBS approach, we sequenced DNA from three time points during our experiment: generation 1 (F1; pre-adaptation), generation 7 (F7; early adaptation), and generation 20 (F20; late adaptation). From the F1 generation, we sequenced only purebred parental cowpea lineages (BF, BZ, and CA) from replicate 1.