Restriction-site associated DNA sequencing (RAD-seq) and target capture of specific genomic regions, such as ultraconserved elements (UCEs), are emerging as two of the most popular methods for phylogenomics using reduced-representation genomic data sets. These two methods were designed to target different evolutionary timescales: RAD-seq was designed for population-genomic level questions and UCEs for deeper phylogenetics. The utility of both data sets to infer phylogenies across a variety of taxonomic levels has not been adequately compared within the same taxonomic system. Additionally, the effects of uninformative gene trees on species tree analyses (for target capture data) have not been explored. Here, we utilize RAD-seq and UCE data to infer a phylogeny of the bird genus Piranga The group has a range of divergence dates (0.5-6 myr), contains 11 recognized species, and lacks a resolved phylogeny. We compared two species tree methods for the RAD-seq data and six species tree methods for the UCE data. Additionally, in the UCE data, we analyzed a complete matrix as well as data sets with only highly informative loci. A complete matrix of 189 UCE loci with 10 or more parsimony informative (PI) sites, and an approximately 80% complete matrix of 1128 PI single-nucleotide polymorphisms (SNPs) (from RAD-seq) yield the same fully resolved phylogeny of Piranga We inferred non-monophyletic relationships of Piranga lutea individuals, with all other a priori species identified as monophyletic. Finally, we found that species tree analyses that included predominantly uninformative gene trees provided strong support for different topologies, with consistent phylogenetic results when limiting species tree analyses to highly informative loci or only using less informative loci with concatenation or methods meant for SNPs alone.

中文翻译：

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系统基因组学中目标捕获和限制位点相关 DNA 测序的比较：红雀唐纳雀（鸟纲，属：Piranga）的测试


限制性位点相关 DNA 测序 (RAD-seq) 和特定基因组区域（例如超保守元件 (UCE)）的目标捕获正在成为使用简化代表性基因组数据集进行系统发育组学的两种最流行的方法。这两种方法旨在针对不同的进化时间尺度：RAD-seq 设计用于群体基因组水平问题，UCE 设计用于更深入的系统发育。尚未在同一分类系统内充分比较这两个数据集在推断不同分类水平的系统发育方面的效用。此外，尚未探讨无信息基因树对物种树分析（针对目标捕获数据）的影响。在这里，我们利用 RAD-seq 和 UCE 数据来推断 Piranga 鸟类的系统发育。该群体具有一系列分歧日期（0.5-6 myr），包含 11 个已识别的物种，并且缺乏已解决的系统发育。我们比较了 RAD-seq 数据的两种物种树方法和 UCE 数据的六种物种树方法。此外，在 UCE 数据中，我们分析了完整的矩阵以及仅包含信息丰富的基因座的数据集。具有 10 个或更多简约信息 (PI) 位点的 189 个 UCE 位点的完整矩阵，以及 1128 个 PI 单核苷酸多态性 (SNP)（来自 RAD-seq）的约 80% 完整矩阵，产生与 Piranga We 相同的完全解析的系统发育推断 Piranga utea 个体的非单系关系，与所有其他先验物种被确定为单系。 最后，我们发现，主要包括无信息基因树的物种树分析为不同的拓扑提供了强有力的支持，当将物种树分析限制为信息丰富的基因座或仅使用信息较少的基因座与串联或仅用于 SNP 的方法时，具有一致的系统发育结果。