Department of Plant Sciences, University of Cambridge, Cambridge CB2 3EA, UK.
Departamento de Biología (Botánica), Facultad de Ciencias, Universidad Autónoma de Madrid, 28049 Madrid, Spain.
Syst Biol. 2018 Mar 1;67(2):250-268. doi: 10.1093/sysbio/syx062.
Disentangling species boundaries and phylogenetic relationships within recent evolutionary radiations is a challenge due to the poor morphological differentiation and low genetic divergence between species, frequently accompanied by phenotypic convergence, interspecific gene flow and incomplete lineage sorting. Here we employed a genotyping-by-sequencing (GBS) approach, in combination with morphometric analyses, to investigate a small western Mediterranean clade in the flowering plant genus Linaria that radiated in the Quaternary. After confirming the morphological and genetic distinctness of eight species, we evaluated the relative performances of concatenation and coalescent methods to resolve phylogenetic relationships. Specifically, we focused on assessing the robustness of both approaches to variations in the parameter used to estimate sequence homology (clustering threshold). Concatenation analyses suffered from strong systematic bias, as revealed by the high statistical support for multiple alternative topologies depending on clustering threshold values. By contrast, topologies produced by two coalescent-based methods (NJ${\mathrm{st}}$, SVDquartets) were robust to variations in the clustering threshold. Reticulate evolution may partly explain incongruences between NJ${\mathrm{st}}$, SVDquartets and concatenated trees. Integration of morphometric and coalescent-based phylogenetic results revealed (i) extensive morphological divergence associated with recent splits between geographically close or sympatric sister species and (ii) morphological convergence in geographically disjunct species. These patterns are particularly true for floral traits related to pollinator specialization, including nectar spur length, tube width and corolla color, suggesting pollinator-driven diversification. Given its relatively simple and inexpensive implementation, GBS is a promising technique for the phylogenetic and systematic study of recent radiations, but care must be taken to evaluate the robustness of results to variation of data assembly parameters.
在最近的进化辐射中，由于物种之间形态差异小、遗传分化低，常伴随着表型趋同、种间基因流和不完全谱系分选，因此厘清物种界限和系统发育关系是一个挑战。在这里，我们采用了基于测序的基因分型（GBS）方法，结合形态计量学分析，研究了开花植物属林菀（Linaria）中一个在第四纪辐射的小的西地中海分支。在确认了 8 个物种的形态和遗传独特性之后，我们评估了连锁和合并方法在解决系统发育关系方面的相对表现。具体来说，我们重点评估了这两种方法对用于估计序列同源性（聚类阈值）的参数变化的稳健性。连锁分析受到强烈的系统偏差的影响，这表现为依赖聚类阈值值的多个替代拓扑结构的统计支持很高。相比之下，两种基于合并的方法（NJ${\mathrm{st}}$、SVDquartets）产生的拓扑结构对聚类阈值的变化具有稳健性。网状进化可能部分解释了 NJ${\mathrm{st}}$、SVDquartets 和连锁树之间的不匹配。形态计量学和基于合并的系统发育结果的整合揭示了（i）与地理上接近或同域的姐妹种之间最近的分裂相关的广泛形态分歧，以及（ii）地理上离散物种之间的形态趋同。这些模式尤其适用于与传粉者专业化相关的花部特征，包括蜜腺距长度、管宽和花冠颜色，表明传粉者驱动的多样化。鉴于其相对简单和廉价的实现方式，GBS 是研究近期辐射的系统发育和系统学的一种很有前途的技术，但必须注意评估结果对数据组装参数变化的稳健性。
