Data from: Genomic evidence that resource-based trade-offs limit host-range expansion in a seed beetle

Trade-offs have often been invoked to explain the evolution of ecological specialization. Phytophagous insects have been especially well studied, but there has been little evidence that resource-based trade-offs contribute to the evolution of host specialization in this group. Here, we combine experimental evolution and partial genome resequencing of replicate seed beetle selection lines to test the trade-off hypothesis and measure the repeatability of evolution. Bayesian estimates of selection coefficients suggest that rapid adaptation to a poor host (lentil) was mediated by standing genetic variation at multiple genetic loci and involved many of the same variants in replicate lines. Sublines that were then switched back to the ancestral host (mung bean) showed a more gradual and variable (less repeatable) loss of adaptation to lentil. We were able to obtain estimates of variance effective population sizes from genome-wide differences in allele frequencies within and between lines. These estimates were relatively large, which suggests that the contribution of genetic drift to the loss of adaptation following reversion was small. Instead, we find that some alleles that were favored on lentil were selected against during reversion on mung bean, consistent with the genetic trade-off hypothesis.

生态特化的演化常被用以权衡效应机制加以解释。植食性昆虫（phytophagous insects）是该领域研究最为充分的类群，但目前鲜有证据表明基于资源的权衡效应参与推动了该类群宿主特化的演化。本研究结合实验进化（experimental evolution）技术与重复豆象选择品系的部分基因组重测序（partial genome resequencing），对该权衡假说进行验证，并量化演化过程的可重复性。贝叶斯选择系数（selection coefficients）估计结果显示，对劣质宿主（兵豆）的快速适应性演化由多个基因座上的现存遗传变异（standing genetic variation）所介导，且各重复品系中涉及了大量共有的变异位点。随后被转回祖先宿主（绿豆）的亚品系，其对兵豆适应性的丧失过程更为缓慢且异质性更强（可重复性更低）。我们通过品系内与品系间等位基因频率（allele frequencies）的全基因组差异，获得了方差有效种群大小（variance effective population sizes）的估计值；该估计值相对较大，表明遗传漂变（genetic drift）在宿主转回后适应性丧失过程中的贡献占比极小。与之相反，我们发现部分在兵豆上受到正向选择的等位基因，在转回绿豆的选择压力下受到了负向选择，这与遗传权衡假说的预测相符。