Data from: Integrating genomic and phenotypic data to evaluate alternative phylogenetic and species delimitation hypotheses in a recent evolutionary radiation of grasshoppers

Although resolving phylogenetic relationships and establishing species limits is a primary goal of systematics, these tasks remain challenging at both conceptual and analytical levels. Here, we integrated genomic and phenotypic data and employed a comprehensive suite of coalescent-based analyses to develop and evaluate competing phylogenetic and species delimitation hypotheses in a recent evolutionary radiation of grasshoppers (Chorthippus binotatus group) composed of two species and eight putative subspecies. To resolve the evolutionary relationships within this complex, we first evaluated alternative phylogenetic hypotheses arising from multiple schemes of genomic data processing and contrasted genetic-based inferences with different sources of phenotypic information. Second, we examined the importance of number of loci, demographic priors, number and kind of phenotypic characters, and sex-based trait variation for developing alternative species delimitation hypotheses. The best-supported topology was largely compatible with phenotypic data and showed the presence of two clades corresponding to the nominative species groups, one including three well-resolved lineages and the other comprising a four-lineage polytomy and a well-differentiated sister taxon. Integrative species delimitation analyses indicated that the number of employed loci had little impact on the obtained inferences but revealed the higher power provided by an increasing number of phenotypic characters and the usefulness of assessing their phylogenetic information-content and differences between sexes in among-taxa trait variation. Overall, our study highlights the importance of integrating multiple sources of information to test competing phylogenetic hypotheses and elucidate the evolutionary history of species complexes representing early-stages of divergence where conflicting inferences are more prone to appear.

尽管厘清系统发育关系、界定物种边界是系统分类学（systematics）的核心研究目标之一，但此类工作在概念与分析层面仍存在诸多挑战。本研究整合基因组与表型数据，采用一系列基于溯祖理论（coalescent theory）的综合分析方法，针对由2个物种、8个推定亚种构成的近期演化辐射蚱蜢类群——双斑戟纹蝗类群（Chorthippus binotatus group）——构建并评估了相互竞争的系统发育与物种界定假说。为厘清该物种复合体内部的演化关系，我们首先评估了由多种基因组数据处理流程衍生出的不同系统发育假说，并将基于遗传数据的推断结果与不同来源的表型信息进行对比。其次，我们探究了基因座数量、种群历史先验（demographic priors）、表型性状的数量与类型，以及性别依赖的性状变异，在构建不同物种界定假说过程中的重要性。支持度最高的系统发育拓扑结构与表型数据整体契合，且显示存在两个对应于指名物种群的演化支：其一包含3个解析度优异的演化支系，其二则由一个含4个支系的多歧支（polytomy）与一个分化显著的姊妹类群（sister taxon）组成。整合式物种界定（integrative species delimitation）分析结果显示，所用基因座的数量对所得推断结果影响甚微，但表明随着表型性状数量增加，分析效力会相应提升；同时证实了评估其系统发育信息含量，以及类群间性状变异中的性别差异，具备重要应用价值。总体而言，本研究强调了整合多源信息的重要性，以此检验相互竞争的系统发育假说，并阐明处于早期分化阶段的物种复合体的演化历史——此类复合体更易出现相互矛盾的遗传推断结果。