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（Mediterranean Basin）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所特有。本研究针对一个被子植物（angiosperm）物种复合体展开深入分析，该复合体被推测存在隐蔽分类多样性。具体而言，我们聚焦于鲁塞拉复合体（Roucela complex）中目前已被正式认可的4个物种——该类群是桔梗科-桔梗亚科（Campanulaceae/Campanuloideae）中一个得到充分支持的演化支，分别为：克氏风铃草（Campanula creutzburgii）、C. drabifolia、C. erinus以及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（plastome）数据与130个核基因座（nuclear loci），以揭示该演化支内的隐蔽分类多样性，并检验关于杂交（hybridization）与多倍化（polyploidy）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（tetraploid）与八倍体（octoploid）两个谱系，二者呈现东西向地理分布格局。尽管基因组数据能够清晰区分这两种细胞型（cytotype），但我们未能在形态上发现二者的差异。分布于地中海东部的隐蔽八倍体谱系的形成，被推测为一次异源多倍化（allopolyploidy）事件的结果，该事件保留了其中一个亲本的形态特征；研究表明，四倍体C. erinus与同为四倍体的克氏风铃草为该异源多倍化事件的亲本谱系。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。