Mort Mark E, Crawford Daniel J, Kelly John K, Santos-Guerra Arnoldo, Menezes de Sequeira Miguel, Moura Mónica, Caujapé-Castells Juli
Department of Ecology and Evolutionary Biology, and Biodiversity Institute; University of Kansas, 1200 Sunnyside Ave, Lawrence, Kansas 66045 USA.
Department of Ecology and Evolutionary Biology, 1200 Sunnyside Ave, Lawrence, Kansas 66045 USA.
Am J Bot. 2015 Apr;102(4):634-41. doi: 10.3732/ajb.1400551. Epub 2015 Apr 10.
Endemic plants on oceanic islands have long served as model systems for studying patterns and processes of evolution. However, phylogenetic studies of island plants frequently illustrate a decoupling of molecular divergence and ecological/morphological diversity, resulting in phylogenies lacking the resolution required to interpret patterns of evolution in a phylogenetic context. The current study uses the primarily Macaronesian flowering plant genus Tolpis to illustrate the utility of multiplexed shotgun genotyping (MSG) for resolving relationships at relatively deep (among archipelagos) and very shallow (within archipelagos) nodes in this small, yet diverse insular plant lineage that had not been resolved with other molecular markers.
Genomic libraries for 27 accessions of Macaronesian Tolpis were generated for genotyping individuals using MSG, a form of reduced-representation sequencing, similar to restriction-site-associated DNA markers (RADseq). The resulting data files were processed using the program pyRAD, which clusters MSG loci within and between samples. Phylogenetic analyses of the aligned data matrix were conducted using RAxML.
Analysis of MSG data recovered a highly resolved phylogeny with generally strong support, including the first robust inference of relationships within the highly diverse Canary Island clade of Tolpis.
The current study illustrates the utility of MSG data for resolving relationships in lineages that have undergone recent, rapid diversification resulting in extensive ecological and morphological diversity. We suggest that a similar approach may prove generally useful for other rapid plant radiations where resolving phylogeny has been difficult.
海洋岛屿上的特有植物长期以来一直是研究进化模式和过程的模型系统。然而，对岛屿植物的系统发育研究经常表明分子分歧与生态/形态多样性之间存在脱钩现象，导致系统发育缺乏在系统发育背景下解释进化模式所需的分辨率。当前的研究使用主要分布于马卡罗尼西亚的开花植物属托尔皮斯（Tolpis）来阐明多重鸟枪法基因分型（MSG）在解决这个小型但多样的岛屿植物谱系中相对较深（群岛间）和非常浅（群岛内）节点的关系方面的效用，而这些关系此前用其他分子标记尚未得到解决。
为马卡罗尼西亚托尔皮斯的27个样本构建基因组文库，使用MSG（一种简化代表性测序形式，类似于限制性位点关联DNA标记（RADseq））对个体进行基因分型。使用pyRAD程序处理所得数据文件，该程序对样本内部和样本之间的MSG位点进行聚类。使用RAxML对排列好的数据矩阵进行系统发育分析。
对MSG数据的分析得到了一个分辨率很高且支持度普遍很强的系统发育树，包括对托尔皮斯高度多样化的加那利群岛分支内关系的首次有力推断。
当前研究阐明了MSG数据在解决经历了近期快速多样化并导致广泛生态和形态多样性的谱系中的关系方面的效用。我们认为，类似的方法可能对解决系统发育一直很困难的其他快速植物辐射普遍有用。
