Data from: Deciphering the origin of mito-nuclear discordance in two sibling caddisfly species

An increasing number of phylogenetic studies have reported discordances among nuclear and mitochondrial markers. These discrepancies are highly relevant to widely used biodiversity assessment approaches, such as DNA barcoding, that rely almost exclusively on mitochondrial markers. Although the theoretical causes of mito-nuclear discordances are well understood, it is often extremely challenging to determine the principal underlying factor in a given study system. In this study, we uncovered significant mito-nuclear discordances in a pair of sibling caddisfly species. Application of genome sequencing, ddRAD, and DNA barcoding revealed ongoing hybridization, as well as historical hybridization in Pleistocene refugia, leading us to identify introgression as the ultimate cause of the observed discordance pattern. Our novel genomic data, the discovery of a European-wide hybrid zone, and the availability of established techniques for laboratory breeding make this species pair an ideal model system for studying species boundaries with ongoing gene flow.

越来越多的系统发育研究报道了核基因标记与线粒体基因标记之间的不一致性。这类不一致性与当前广泛使用的、几乎完全依赖线粒体标记的生物多样性评估方法（如DNA条形码（DNA barcoding））密切相关。尽管核-线粒体不一致性（mito-nuclear discordances）的理论成因已得到充分阐明，但在特定研究体系中确定其核心驱动因素往往极具挑战。本研究中，我们在一对姊妹石蛾物种中发现了显著的核-线粒体不一致性。通过基因组测序、ddRAD测序（ddRAD）及DNA条形码技术的应用，我们发现该类群正发生持续杂交，同时在更新世避难所中也曾存在历史杂交事件，由此确定基因渐渗（introgression）是本研究中观察到的不一致性模式的根本成因。本研究产生的新型基因组数据、欧洲范围内杂交带的发现，以及成熟的实验室繁育技术储备，使得这对姊妹物种成为研究存在持续基因流的物种边界问题的理想模型体系。