Data from: Using targeted enrichment of nuclear genes to increase phylogenetic resolution in the neotropical rain forest genus Inga (Leguminosae: Mimosoideae)

Evolutionary radiations are prominent and pervasive across many plant lineages in diverse geographical and ecological settings; in neotropical rainforests there is growing evidence suggesting that a significant fraction of species richness is the result of recent radiations. Understanding the evolutionary trajectories and mechanisms underlying these radiations demands much greater phylogenetic resolution than is currently available for these groups. The neotropical tree genus Inga (Leguminosae) is a good example, with ~300 extant species and a crown age of 2-10 MY, yet over 6kb of plastid and nuclear DNA sequence data gives only poor phylogenetic resolution among species. Here we explore the use of larger-scale nuclear gene data obtained though targeted enrichment to increase phylogenetic resolution within Inga. Transcriptome data from three Inga species were used to select 264 nuclear loci for targeted enrichment and sequencing. Following quality control to remove probable paralogs from these sequence data, the final dataset comprised 259,313 bases from 194 loci for 24 accessions representing 22 Inga species and an outgroup (Zygia). Bayesian phylogenies reconstructed using either all loci concatenated or a subset of 60 loci in a gene-tree/species-tree approach yielded highly resolved phylogenies. We used coalescent approaches to show that the same targeted enrichment data also have significant power to discriminate among alternative within-species population histories in the widespread species I. umbellifera. In either application, targeted enrichment simplifies the informatics challenge of identifying orthologous loci associated with de novo genome sequencing. We conclude that targeted enrichment provides the large volumes of phylogenetically-informative sequence data required to resolve relationships within recent plant species radiations, both at the species level and for within-species phylogeographic studies.进化辐射在多种地理与生态环境下的众多植物类群中广泛存在且特征显著；在新热带界雨林中，越来越多的证据表明，相当一部分物种丰富度源自近期的进化辐射事件。解析此类进化辐射的演化轨迹与内在机制，需要比现有类群更高分辨率的系统发育数据。新热带界乔木属印加树属（Inga，豆科Leguminosae）便是典型代表：该属现存约300个物种，冠群起源时间为200万至1000万年，但基于6千碱基对以上的质体与核DNA序列数据，其物种种间系统发育分辨率仍较差。本研究探讨通过靶向富集技术获取大规模核基因数据，以提升印加树属内的系统发育分辨率。研究人员基于3个印加树物种的转录组数据，筛选出264个核基因座用于靶向富集与测序。经质控剔除序列数据中可能存在的旁系同源基因后，最终数据集包含194个基因座的259313个碱基位点，覆盖代表22个印加树物种的24份种质材料，以及1个外类群（合爪榄属Zygia）。采用所有基因座串联法，或是基于60个基因座子集的基因树-物种树方法构建贝叶斯系统发育树，均得到了分辨率极高的系统发育拓扑结构。本研究通过溯祖分析方法证实，同一套靶向富集数据还具备较强的区分能力，可解析广布物种伞形印加树（I. umbellifera）内不同的种群演化历史。无论应用于物种间还是物种内的系统发育研究，靶向富集技术均简化了与从头基因组测序相关的直系同源基因座识别的生物信息学难题。综上，靶向富集技术可获取足够量的系统发育信息序列数据，能够解析近期植物物种辐射演化类群的种间关系，同时也适用于物种内的系统地理学研究。