Data from: Integrative taxonomy recognizes evolutionary units despite widespread mitonuclear discordance: evidence from a rotifer cryptic species complex

Mitonuclear discordance across taxa is increasingly recognized as posing a major challenge to species delimitation based on DNA sequence data. Integrative taxonomy has been proposed as a promising framework to help address this problem. However, we still lack compelling empirical evidence scrutinizing the efficacy of integrative taxonomy in relation to, for instance, complex introgression scenarios involving many species. Here, we report remarkably widespread mitonuclear discordance between about 15 mitochondrial and four nuclear Brachionus calyciflorus groups identified using different species delimitation approaches. Using coalescent-, Bayesian admixture-, and allele sharing-based methods with DNA sequence or microsatellite data, we provide strong evidence in support of hybridization as a driver of the observed discordance. We then describe our combined molecular, morphological, and ecological approaches to resolving phylogenetic conflict and inferring species boundaries. Species delimitations based on the ITS1 and 28S nuclear DNA markers proved a more reliable predictor of morphological variation than delimitations using the mitochondrial COI gene. A short-term competition experiment further revealed systematic differences in the competitive ability between two of the nuclear-delimited species under six different growth conditions, independent of COI delimitations; hybrids were also observed. In light of these findings, we discuss the failure of the COI marker to estimate morphological stasis and morphological plasticity in the B. calyciflorus complex. By using B. calyciflorus as a representative case, we demonstrate the potential of integrative taxonomy to guide species delimitation in the presence of mitonuclear phylogenetic conflicts.

类群间的核质冲突（mitonuclear discordance）正日益被视为基于DNA序列数据开展物种界定所面临的重大挑战。整合分类学（Integrative taxonomy）已被提出作为解决这一难题的极具前景的研究框架。然而，目前我们仍缺乏令人信服的实证证据，用以检视整合分类学在应对诸如涉及多物种的复杂渐渗情景时的效能。在此，我们报道了褶皱臂尾轮虫（Brachionus calyciflorus）中，基于不同物种界定方法所识别的约15个线粒体类群与4个核基因类群之间存在极为普遍的核质冲突。我们采用基于溯祖分析、贝叶斯基因混合分析以及等位基因共享的方法，结合DNA序列或微卫星（microsatellite）数据，为杂交作用是引发此次观测到的核质冲突的驱动因素提供了强有力的证据。随后，我们阐述了用于解决系统发育冲突、推断物种边界的整合分子、形态学与生态学研究方法。相较于基于线粒体细胞色素氧化酶亚基I（COI）基因的物种界定结果，基于ITS1与28S核DNA标记的物种界定结果能更可靠地预测形态变异。一项短期竞争实验进一步揭示，在六种不同生长条件下，两个核基因界定的物种间存在竞争能力的系统性差异，且该差异与COI界定结果无关；实验中还观测到了杂交个体。结合上述研究结果，我们讨论了COI标记在褶皱臂尾轮虫物种复合体中无法准确评估形态停滞与形态可塑性的问题。以褶皱臂尾轮虫作为典型案例，我们证实了在存在核质系统发育冲突的情况下，整合分类学可有效指导物种界定工作。