Comparison of target-capture and restriction-site associated DNA sequencing for phylogenomics: a test in cardinalid tanagers (Aves, genus: Piranga)

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 datasets. 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 datasets 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 my – 6 my), contains eleven recognized species, and lacks a resolved phylogeny. We compared two species tree methods for the RAD-seq data and six species tree ...限制性位点相关DNA测序（Restriction-site associated DNA sequencing, RAD-seq）与特定基因组区域（如超保守元件（ultraconserved elements, UCEs））的靶向捕获技术，正逐渐成为基于简化基因组数据集开展系统发育基因组学研究的两种主流方法。这两种方法的设计初衷适配不同的进化时间尺度：RAD-seq旨在解决群体基因组学层面的科学问题，而UCEs则用于深度系统发育学研究。目前，尚未在同一分类类群中充分比较这两种数据集在不同分类学层级下构建系统发育树的效能。此外，非信息性基因树对靶向捕获数据的物种树分析造成的影响，也尚未得到探索。本研究利用RAD-seq与UCE数据，对裸鼻雀属（Piranga）的系统发育关系进行推断。该类群的分化时间跨度为0.5百万年至6百万年，包含11个已确认物种，且至今尚未拥有解析度完善的系统发育树。本研究针对RAD-seq数据比较了两种物种树分析方法，并针对UCE数据采用了六种物种树……