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 and how host-related selection on diapause timing associates with genome-wide differentiation during ecological speciation by comparing ancestral hawthorn and newly formed apple-infesting host races of Rhagoletis pomonella to their sibling species Rhagoletis mendax that attacks blueberries. The associations of 57 857 single nucleotide polymorphisms in a diapause genome-wide-association study (GWAS) on the hawthorn race strongly predicted the direction and magnitude of genomic divergence among the three fly populations at a field site in Fennville, MI, USA. 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 GWAS on R. mendax revealed compensatory changes 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.

This article is part of the theme issue ‘Towards the completion of speciation: the evolution of reproductive isolation beyond the first barriers'.

评估进化可预测性的研究通常侧重于种群内的短期适应或谱系之间变化的可重复性。物种形成研究中缺少的一个考虑因素是确定自然选择是否可预测地将种群内的遗传变异转化为物种之间的差异。在这里，我们通过比较祖先山楂和新形成的苹果侵染宿主品种Rhagoletis pomonella与其同胞物种Rhagoletis mendax来测试滞育时间的宿主相关选择是否以及如何与生态物种形成过程中的全基因组分化相关攻击蓝莓。在一项关于山楂树种的滞育全基因组关联研究 (GWAS) 中，57 857 个单核苷酸多态性的关联强烈预测了美国密歇根州芬维尔野外现场三个果蝇种群之间基因组差异的方向和大小。与山楂相比，苹果品种和R. mendax显示出与苹果和蓝莓较早结果期相关的三个染色体上推定倒位频率的平行变化。对R. mendax 的滞育 GWAS揭示了整个基因组的补偿性变化，解释了蓝莓的早期羽化，但不是苹果蝇。因此，尽管不完全，但在整个生态物种形成连续体的滞育基因组学中存在一定程度的可预测性。雷戈莱蒂斯。这个结果的一般性放在其他类似系统的上下文中。

本文是主题问题“走向物种形成的完成：超越第一道障碍的生殖隔离的进化”的一部分。