Data from: Speciation in the presence of gene flow: population genomics of closely related and diverging Eucalyptus species

Speciation is a complex process that is fundamental to the origins of biological diversity. While there has been considerable progress in our understanding of speciation, there are still many unanswered questions, especially regarding barriers to gene flow in diverging populations. Eucalyptus is an appropriate system for investigating speciation mechanisms since it comprises species that are rapidly evolving across heterogeneous environments. We examined patterns of genetic variation within and among six closely related Eucalyptus species in subgenus Eucalyptus section Eucalyptus in south-eastern Australia (commonly known as the ‘green ashes’). We used reduced representation genome sequencing to genotype samples from populations across altitudinal and latitudinal gradients. We found one species, Eucalyptus cunninghamii, to be highly genetically differentiated from the others, and a population of mallees from Mount Banks to be genetically distinct and therefore likely to be a new undescribed species. Only modest levels of differentiation were found between all other species in the study. There was population structure within some species (e.g. E. obstans) corresponding to geographical factors, indicating that vicariance may have played a role in the evolution of the group. Overall, we found that lineages within the green ashes are differentiated to varying extents, from strongly diverged to much earlier stages of the speciation continuum. Furthermore, our results suggest the green ashes represent a group where a range of mechanisms (e.g. reticulate evolution and vicariance) have been operating in concert. These findings not only offer insights into recent speciation mechanisms in Eucalyptus, but also other species complexes.

物种形成（speciation）是一项复杂的过程，亦是生物多样性起源的核心基础。尽管学界对物种形成的认知已取得长足进展，但仍有诸多悬而未决的问题，尤其是关于分化种群间的基因流障碍相关议题。桉树（Eucalyptus）是研究物种形成机制的理想模式系统，因其包含众多在异质环境中快速演化的物种。我们针对澳大利亚东南部隶属于桉亚属（subgenus Eucalyptus）桉组（section Eucalyptus）的6个近缘桉树物种开展研究，分析其种群内部及种群之间的遗传变异格局，该类群通常被俗称为"绿灰类群（green ashes）"。我们采用简化基因组测序（reduced representation genome sequencing）技术，对分布于海拔和纬度梯度上的种群样本进行基因分型。研究发现，坎宁安桉（Eucalyptus cunninghamii）与其余物种存在高度显著的遗传分化；此外，来自班克斯山（Mount Banks）的多茎桉（mallee）种群也呈现独特的遗传特征，推测其可能为一个尚未被正式描述的新物种。本研究中其余所有物种之间仅存在中等程度的遗传分化。部分物种（如澳斯特桉（E. obstans））的种群结构与其地理分布存在显著关联，这表明隔离分化（vicariance）可能在该类群的演化过程中发挥了作用。总体而言，绿灰类群内的演化支系存在不同程度的遗传分化，涵盖了从强烈分化到物种形成连续体（speciation continuum）早期阶段的全部谱系。此外，我们的研究结果表明，绿灰类群是一类同时受多种演化机制（如网状演化（reticulate evolution）与隔离分化）共同作用的类群。本研究发现不仅为桉树类群的近期物种形成机制提供了新的认知视角，也为其他物种复合群的相关研究提供了重要参考。