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.

物种形成是一种复杂的生物学过程，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，但仍存在诸多悬而未决的问题，尤其是针对分化种群间的基因流障碍相关议题。桉树属（Eucalyptus）是探究物种形成机制的理想研究体系，该属物种在异质性环境中呈现快速演化的特征。本研究针对澳大利亚东南部桉亚属桉组的6个近缘桉树物种（俗称“绿灰桉类群”），分析了其种群内及种群间的遗传变异模式。研究采用简化基因组测序（reduced representation genome sequencing）技术，对分布于海拔及纬度梯度上的种群样本开展基因分型工作。结果显示，坎宁安桉（Eucalyptus cunninghamii）与其余物种间存在极高的遗传分化；而来自班克斯山的玛利桉（mallees）种群同样呈现显著遗传分化，大概率为一个尚未被描述的新物种。本研究中其余物种间仅呈现中等程度的遗传分化。部分物种（如障碍桉Eucalyptus obstans）内部存在与地理因素相关的种群结构，暗示隔离分化可能在该类群的演化中发挥了作用。总体而言，绿灰桉类群内的演化支系呈现不同程度的遗传分化，跨度从强烈分化到物种形成连续体的早期阶段。此外，研究结果表明，绿灰桉类群是一类由多种演化机制（如网状进化（reticulate evolution）与隔离分化）协同发挥作用形成的类群。本研究发现不仅为桉树属近期的物种形成机制提供了全新认知，也为其他物种复合群的相关研究提供了重要参考。