Data from: Transitions between phases of genomic differentiation during stick-insect speciation

Speciation can involve a transition from a few genetic loci that are resistant to gene flow to genome-wide differentiation. However, only limited data exist concerning this transition and the factors promoting it. Here, we study phases of speciation using data from >100 populations of 11 species of Timema stick insects. Consistent with early phases of genic speciation, adaptive colour-pattern loci reside in localized genetic regions of accentuated differentiation between populations experiencing gene flow. Transitions to genome-wide differentiation are also observed with gene flow, in association with differentiation in polygenic chemical traits affecting mate choice. Thus, intermediate phases of speciation are associated with genome-wide differentiation and mate choice, but not growth of a few genomic islands. We also find a gap in genomic differentiation between sympatric taxa that still exchange genes and those that do not, highlighting the association between differentiation and complete reproductive isolation. Our results suggest that substantial progress towards speciation may involve the alignment of multi-faceted aspects of differentiation.物种形成（Speciation）可涉及从少数抗基因流（gene flow）的基因座（genetic loci）向全基因组分化（genome-wide differentiation）的过渡过程。然而，目前针对该过渡过程及其促进因子的相关研究数据仍较为有限。本研究依托11个物种、共计100余个种群的Timema竹节虫（Timema stick insects）数据，对物种形成的不同阶段进行了系统探究。与基因物种形成（genic speciation）的早期阶段特征一致，适应性体色图案基因座（adaptive colour-pattern loci）坐落于存在基因流的种群间分化程度加剧的局部遗传区域之中。在存在基因流的类群中，我们同样观测到向全基因组分化的过渡现象，该现象与影响配偶选择（mate choice）的多基因化学性状（polygenic chemical traits）的分化密切相关。据此可知，物种形成的中间阶段与全基因组分化及配偶选择存在关联，而非依赖少数基因组岛（genomic islands）的扩张。我们还发现，仍存在基因交流的同域类群（sympatric taxa）与不再发生基因交流的同域类群之间，存在显著的基因组分化差异，这进一步凸显了基因组分化与完全生殖隔离（reproductive isolation）之间的紧密关联。本研究结果表明，物种形成进程中的实质性进展，或许涉及多维度分化特征的协同整合。