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 phylogenomic 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 unrecognized 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 recognized 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（genomic-scale data）的可及性不断提升，研究人员得以区分具有趋同形态性状的演化支，并合并新近分化但具备独特区分特征的生态型。本研究结合系统发育基因组学（phylogenomic）与种群基因组学（population genomic）分析，辅以繁育系统（breeding system）研究与性状分析（character analysis），对分布广泛且形态高度多变的天竺葵属（Pelargonium）澳大利亚类群的支系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分析（population genetic clustering）结果支持了当前已描述的8个物种中的7个，但在包含澳大利亚天竺葵（P. australe）的分布最广类群内，几乎未检测到遗传结构差异的相关证据。与之相对，形态测量分析（morphometric analysis）在澳大利亚天竺葵属类群中识别出3个深度演化支；其中澳大利亚天竺葵（P. australe）包含5个此前未被认知的演化单元，各自占据独立的地理分布范围。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，同时也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，共同造成了系统发育基因组学关系与形态分类学之间的不一致。数据表明，澳大利亚天竺葵属内物种间的遗传分化可能源于异域物种形成（allopatric speciation），而物种内部及物种间的形态分化，则更可能受环境差异的强烈驱动。