Many recent studies have addressed the mechanisms operating during the early stages of speciation, but surprisingly few studies have tested theoretical predictions on the evolution of strong reproductive isolation (RI). To help address this gap, we first undertook a quantitative review of the hybrid zone literature for flowering plants in relation to reproductive barriers. Then, using Populus as an exemplary model group, we analysed genome-wide variation for phylogenetic tree topologies in both early- and late-stage speciation taxa to determine how these patterns may be related to the genomic architecture of RI. Our plant literature survey revealed variation in barrier complexity and an association between barrier number and introgressive gene flow. Focusing on Populus, our genome-wide analysis of tree topologies in speciating poplar taxa points to unusually complex genomic architectures of RI, consistent with earlier genome-wide association studies. These architectures appear to facilitate the ‘escape’ of introgressed genome segments from polygenic barriers even with strong RI, thus affecting their relationships with recombination rates. Placed within the context of the broader literature, our data illustrate how phylogenomic approaches hold great promise for addressing the evolution and temporary breakdown of RI during late stages of speciation.

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

许多最近的研究已经解决了物种形成早期阶段的运作机制，但令人惊讶的是，很少有研究测试关于强生殖隔离 (RI) 进化的理论预测。为了帮助解决这一差距，我们首先对开花植物与生殖障碍相关的杂交区文献进行了定量审查。然后，使用杨树作为示例模型组，我们分析了早期和晚期物种形成分类群中系统发育树拓扑的全基因组变异，以确定这些模式如何与 RI 的基因组结构相关。我们的植物文献调查揭示了屏障复杂性的变化以及屏障数量与基因渗入流之间的关联。专注于胡杨，我们对特定杨树分类群中树拓扑的全基因组分析指出了 RI 异常复杂的基因组结构，这与早期的全基因组关联研究一致。即使具有强 RI，这些结构似乎也有助于渗入基因组片段从多基因屏障中“逃逸”，从而影响它们与重组率的关系。放在更广泛的文献背景下，我们的数据说明了系统基因组学方法如何在物种形成的后期解决 RI 的进化和暂时崩溃方面大有希望。

这篇文章是主题问题“走向物种形成的完成：超越第一道障碍的生殖隔离的演变”的一部分。