Data from: Multiplexed shotgun genotyping resolves species relationships within the North American genus Penstemon

Premise of the study: Evolutionary radiations provide opportunities to examine large-scale patterns in diversification and character evolution, yet are often recalcitrant to phylogenetic resolution due to rapid speciation events. The plant genus Penstemon has been difficult to resolve using Sanger sequence-based markers, leading to the hypothesis that it represents a recent North American radiation. The present study demonstrates the utility of multiplexed shotgun genotyping (MSG), a style of Restriction site-associated DNA sequencing (RADseq), to infer phylogenetic relationships within a subset of species in this genus and provide insight into evolutionary patterns. Methods: We sampled genomic DNA, primarily from herbarium material, and subjected it to MSG library preparation and Illumina sequencing. The resultant sequencing reads were clustered into homologous loci, aligned, and concatenated into data matrices that differed according to clustering similarity and amount of missing data. We performed phylogenetic analyses on these matrices using maximum likelihood (RAxML) and a species tree approach (SVDquartets). Key results: MSG data provide a highly resolved estimate of species relationships within Penstemon. While most species relationships were highly supported, the position of certain taxa remains ambiguous, suggesting that increased taxonomic sampling or additional methodologies may be required. The data confirm that evolutionary shifts from hymenopteran- to hummingbird-adapted flowers have occurred independently many times. Conclusions: This study demonstrates that phylogenomic approaches yielding thousands of variable sites can greatly improve species-level resolution of recent and rapid radiations. Similar to other studies, we found that less conservative similarity and missing data thresholds resulted in more highly supported topologies.研究背景：演化辐射为探究物种多样化与性状演化的宏观格局提供了绝佳契机，但由于快速成种事件的影响，这类类群往往难以实现系统发育解析。钓钟柳属（Penstemon）曾因基于桑格测序的分子标记难以获得清晰的系统发育框架，由此催生了“该类群属于近期北美演化辐射”的假说。本研究验证了多重鸟枪基因分型（multiplexed shotgun genotyping, MSG）——一种限制性酶切位点相关DNA测序（Restriction site-associated DNA sequencing, RADseq）技术——在推断该属部分物种类群系统发育关系、解析其演化模式中的应用价值。 研究方法：本研究以标本馆馆藏标本为主要来源获取基因组DNA，对其开展多重鸟枪基因分型文库构建及Illumina测序。将所得测序读段聚类为同源基因座，经序列比对、拼接后得到根据聚类相似度和缺失数据量不同而存在差异的数据集矩阵。随后采用最大似然法（RAxML）以及物种树推断方法（SVDquartets）对这些数据集矩阵开展系统发育分析。 主要结果：多重鸟枪基因分型数据可实现钓钟柳属内物种类群关系的高解析度推断。尽管多数物种类群的系统发育关系得到了较高支持度，但部分类群的系统位置仍不明确，提示后续需扩大类群采样范围或采用更多研究方法。本研究的数据证实，该属植物从适应膜翅目传粉的花型向适应蜂鸟传粉的花型的演化转变已独立发生多次。 研究结论：本研究表明，可获取数千个变异位点的系统发育组学方法，可显著提升近期快速成种辐射类群的物种级系统发育解析度。与其他同类研究结果一致，本研究发现放宽聚类相似度与缺失数据的保守阈值，可得到支持度更高的系统发育拓扑结构。