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并确立物种界限是分类学的首要目标，但此类研究在概念与分析层面仍颇具挑战。本研究整合基因组与表型数据，采用一系列全面的基于溯祖（coalescent）的分析方法，针对一个近期发生进化辐射的蝗虫类群——二斑雏蝗（Chorthippus binotatus）类群——构建并评估了相互竞争的系统发育与物种界定假说；该类群包含2个物种与8个推定亚种。为厘清该复杂类群内的演化关系，我们首先评估了多种基因组数据处理流程衍生出的不同系统发育假说，并将基于遗传的推论与不同来源的表型信息进行了对比。其次，我们探究了基因座数量、人口统计学先验信息、表型性状的数量与类型，以及基于性别的性状变异，对构建不同物种界定假说的影响。得到最高支持度的拓扑结构与表型数据大体吻合，且显示存在两个对应于指名物种组的演化支：一支包含3个分辨率良好的支系，另一支则由4个支系形成的多歧分支与一个分化显著的姊妹类群组成。整合式物种界定分析表明，所用基因座的数量对所得推论影响甚微，但结果显示，随着表型性状数量的增加，分析效力得以提升，同时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也颇具价值。总体而言，本研究凸显了整合多源信息以检验相互竞争的系统发育假说、阐明处于早期分化阶段的物种复合体演化历史的重要性——此类复合体更易出现相互矛盾的推论。