Data from: Embracing discordance: Phylogenomic analyses provide evidence for allopolyploidy leading to cryptic diversity in a Mediterranean (Campanula) (Campanulaceae) clade

The Mediterranean Basin harbors a remarkable amount of biodiversity, a high proportion of which is endemic to this region. Here we present an in-depth study of an angiosperm species complex, in which cryptic taxonomic diversity has been hypothesized. Specifically, we focus on four currently recognized species in the Roucela complex, a well-supported clade in the Campanulaceae/Campanuloideae: (Campanula creutzburgii), (C. drabifolia), (C. erinus), and (C. simulans). This study takes a phylogenomic approach, utilizing near-complete plastomes and 130 nuclear loci, to uncover cryptic diversity and test hypotheses regarding hybridization and polyploidy within this clade. Genome size estimates recovered tetraploid and octoploid lineages within the currently recognized, widespread species (C. erinus), showing an east-west geographic pattern. Though genomic data clearly differentiate these two cytotypes, we failed to discern morphological differences. The formation of a cryptic octoploid lineage, distributed across the eastern Mediterranean, is hypothesized to be the result of an allopolyploid event in which one parental morphology is retained. The tetraploid (C. erinus) and (C. creutzburgii) (also a tetraploid) are implicated as parental lineages. Our results highlight the utility of target-enrichment approaches for obtaining genomic datasets for thorough assessments of species diversity and the importance of carefully considering gene-tree discordance within such datasets.

地中海盆地拥有极为丰富的生物多样性，其中极高比例的物种为该区域特有。本研究针对一个被子植物（angiosperm）物种复合体展开深入分析，该类群曾被推测存在隐蔽的分类学多样性。具体而言，本研究聚焦于Roucela复合体中的4个当前已被认可的物种——该复合体是桔梗科（Campanulaceae）桔梗亚科（Campanuloideae）中一个支持度极高的演化支，涉及类群包括Campanula creutzburgii、C. drabifolia、C. erinus及C. simulans。本研究采用系统发育基因组学方法，利用近乎完整的质体基因组（plastomes）与130个核基因座（nuclear loci），以揭示该演化支内的隐蔽多样性，并验证关于杂交与多倍化的相关假说。基因组大小估算结果显示，在当前被广泛认可的广布物种C. erinus中存在四倍体与八倍体演化支，且呈现出东-西向的地理分布格局。尽管基因组数据可明确区分这两种细胞型（cytotypes），但研究团队未能观测到二者的形态学差异。分布于东地中海的隐蔽八倍体演化支的形成，被推测为一次异源多倍化事件的产物，该事件保留了其中一个亲本的形态特征。四倍体的C. erinus与同样为四倍体的C. creutzburgii被认定为该异源多倍化事件的亲本演化支。本研究结果凸显了靶向富集技术在获取基因组数据集以全面评估物种多样性方面的应用价值，同时也强调了在这类数据集中审慎考量基因树冲突（gene-tree discordance）的重要性。