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.

不同类群间的核质冲突（mitonuclear discordance）日益被学界认可为基于DNA序列数据开展物种界定的重大挑战。整合分类学（integrative taxonomy）已被提出为解决该问题的颇具前景的研究框架。然而，当前我们仍缺乏令人信服的实证证据，来检视整合分类学在涉及多物种的复杂渐渗（introgression）情境下的应用效能。
在此，我们报道了萼花臂尾轮虫（Brachionus calyciflorus）中，基于不同物种界定方法所鉴定出的约15个线粒体类群与4个核类群之间存在极为广泛的核质冲突。我们借助基于溯祖理论（coalescent）、贝叶斯聚类（Bayesian admixture）以及等位基因共享（allele sharing）的方法，结合DNA序列或微卫星（microsatellite）数据，为杂交事件是导致观测到的核质冲突的驱动因素提供了坚实的证据。
随后，我们阐述了结合分子、形态与生态学手段以解决系统发育冲突、推断物种边界的研究路径。对比基于线粒体COI（细胞色素c氧化酶亚基I）基因的物种界定结果，基于ITS1（内部转录间隔区1）与28S核DNA标记的物种界定，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，两个经核基因界定的物种在竞争能力上存在系统性差异，且该差异与基于COI的界定结果无关；实验中同时观测到了杂交个体。
基于上述发现，我们讨论了COI标记无法准确估算萼花臂尾轮虫复合类群中形态停滞与形态可塑性的问题。本研究以萼花臂尾轮虫为代表性案例，证实了在存在核质系统发育冲突的情境下，整合分类学可有效指导物种界定工作。