Data from: Population and phylogenomic decomposition via genotyping-by-sequencing in Australian Pelargonium

Species delimitation has seen a paradigm shift as increasing accessibility of genomic-scale data enables separation of lineages with convergent morphological traits and the merging of recently diverged ecotypes that have distinguishing characteristics. We inferred the process of lineage formation among Australian species in the widespread and highly variable genus Pelargonium by combining phylo- and population-genomic analyses along with breeding system studies and character analysis. Phylogenomic analysis and population genetic clustering supported seven of the eight currently described species but provided little evidence for differences in genetic structure within the most widely distributed group, that containing P. australe. In contrast, morphometric analysis detected three deep lineages within Australian Pelargonium; with P. australe consisting of five previously unrecognised entities occupying separate geographic ranges. The genomic approach enabled elucidation of parallel evolution in some traits formerly used to delineate species, as well as identification of ecotypic morphological differentiation within recognised species. Highly variable morphology and trait convergence each contribute to the discordance between phylogenomic relationships and morphological taxonomy. Data suggest that genetic divergence among species within the Australian Pelargonium may result from allopatric speciation while morphological differentiation within and among species may be more strongly driven by environmental differences.

物种界定（species delimitation）领域已迎来范式转变：随着基因组规模数据的可及性持续提升，研究者得以区分具有趋同形态性状的演化支，并合并具备独特特征的新近分化生态型。本研究结合系统发育基因组学（phylogenomic）分析、种群基因组学（population-genomic）分析，辅以繁育系统研究与性状分析，对分布广泛且形态高度多变的天竺葵属（Pelargonium）澳大利亚类群的物种形成过程进行了推演。系统发育基因组学分析与种群遗传聚类结果支持了当前已描述的8个物种中的7个，但在分布最广泛的类群——即包含澳洲天竺葵（Pelargonium australe）的类群——内部，几乎未发现遗传结构存在差异的证据。与之相反，形态计量学分析在澳大利亚天竺葵属类群中检测到3个深层演化支；其中澳洲天竺葵（P. australe）包含5个此前未被识别的、分别占据独立地理分布区的类群单元。本研究采用的基因组学方法，不仅阐明了此前用于界定物种的部分性状存在平行演化现象，还识别出已认定物种内部的生态型形态分化。高度多变的形态性状与性状趋同现象，共同导致了系统发育基因组学关系与形态分类学结果之间的不一致性。研究数据表明，澳大利亚天竺葵属物种种间的遗传分化可能源于异域物种形成，而物种种内及种间的形态分化，则更强烈地受到环境差异的驱动。