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.物种形成是一类复杂的生物学过程，对生物多样性的起源具有根本性意义。尽管学界对物种形成的认知已取得长足进展，但仍存在诸多悬而未决的问题，尤其是关于分化种群间基因流障碍的相关议题。桉树（Eucalyptus）是研究物种形成机制的理想实验体系，因其类群在异质化环境中呈现快速演化的特征。我们针对澳大利亚东南部桉亚属桉组的6个近缘桉树物种（该类群俗称“绿灰桉”），分析了其种群内部及种群间的遗传变异模式。我们采用简化基因组测序（reduced representation genome sequencing）技术，对沿海拔与纬度梯度分布的种群样本进行基因分型。研究发现，坎宁安桉（Eucalyptus cunninghamii）与其余物种间存在极高的遗传分化；而采自班克斯山的多茎桉种群亦呈现显著遗传分化，因此大概率为一个尚未被正式描述的新物种。本研究中其余所有物种间仅存在中等程度的遗传分化。部分物种（如奥斯坦斯桉（E. obstans））内部存在与地理因素相关的种群遗传结构，这表明异域分化可能在该类群的演化中发挥了作用。整体而言，绿灰桉类群内的演化支系存在不同程度的分化，跨度覆盖从高度分化的类群直至物种形成连续体（speciation continuum）的早期阶段。此外，本研究结果表明，绿灰桉类群是一类受多种演化机制（如网状进化（reticulate evolution）与异域分化（vicariance））协同作用的类群。这些发现不仅为桉树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（species complexes）的相关研究提供了重要参考。