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，其中极高比例的类群为该区域特有。本研究针对一个被推测存在隐秘分类多样性的被子植物物种复合体展开深入分析。我们聚焦于桔梗科（Campanulaceae）桔梗亚科（Campanuloideae）中一个得到充分支持的演化支——Roucela物种复合体（Roucela complex）内目前被认可的4个物种：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），旨在揭示该演化支内的隐秘分类多样性，并检验关于杂交与多倍化的相关假说。
基因组大小估算结果显示，在目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。尽管基因组数据能够清晰区分这两种细胞型，但我们未能观测到对应的形态学差异。
我们推测，分布于地中海东部的隐秘八倍体演化支的形成，源于一次异源多倍化事件，该事件保留了其中一个亲本的形态特征。研究结果表明，四倍体C. erinus与同为四倍体的C. creutzburgii为该八倍体类群的亲本谱系。
本研究结果凸显了靶向富集技术（target-enrichment approaches）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。