Abstract Determining the optimal targets of genomic subsampling for phylogenomics, phylogeography, and population genomics remains a challenge for evolutionary biologists. Of the available methods for subsampling the genome, hybrid enrichment (sequence capture) has become one of the primary means of data collection for systematics, due to the flexibility and cost efficiency of this approach. Despite the utility of this method, information is lacking as to what genomic targets are most appropriate for addressing questions at different evolutionary scales. In this study, first, we compare the benefits of target loci developed for deep- and shallow scales by comparing these loci at each of three taxonomic levels: within a genus (phylogenetics), within a species (phylogeography), and within a hybrid zone (population genomics). Specifically, we target evolutionarily conserved loci that are appropriate for deeper phylogenetic scales and more rapidly evolving loci that are informative for phylogeographic and population genomic scales. Second, we assess the efficacy of targeting multiple-locus sets for different taxonomic levels in the same hybrid enrichment reaction, an approach we term hierarchical hybrid enrichment. Third, we apply this approach to the North American chorus frog genus Pseudacris to answer key evolutionary questions across taxonomic and temporal scales. We demonstrate that in this system the type of genomic target that produces the most resolved gene trees differs depending on the taxonomic level, although the potential for error is substantially lower for the deep-scale loci at all levels. We successfully recover data for the two different locus sets with high efficiency. Using hierarchical data targeting deep and shallow levels: we 1) resolve the phylogeny of the genus Pseudacris and introduce a novel visual and hypothesis testing method that uses nodal heat maps to examine the robustness of branch support values to the removal of sites and loci; 2) estimate the phylogeographic history of Pseudacris feriarum, which reveals up to five independent invasions leading to sympatry with congener Pseudacris nigrita to form replicated reinforcement contact zones with ongoing gene flow into sympatry; and 3) quantify with high confidence the frequency of hybridization in one of these zones between P. feriarum and P. nigrita, which is lower than microsatellite-based estimates. We find that the hierarchical hybrid enrichment approach offers an efficient, multitiered data collection method for simultaneously addressing questions spanning multiple evolutionary scales. [Anchored hybrid enrichment; heat map; hybridization; phylogenetics; phylogeography; population genomics; reinforcement; reproductive character displacement.]

中文翻译：

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Hierarchical Hybrid Enrichment：跨进化尺度的多层基因组数据收集，适用于合唱青蛙（Pseudacris）

摘要 确定系统基因组学、系统地理学和种群基因组学的基因组子采样的最佳目标仍然是进化生物学家面临的挑战。在用于对基因组进行二次采样的可用方法中，由于该方法的灵活性和成本效益，杂交富集（序列捕获）已成为系统学数据收集的主要手段之一。尽管这种方法有用，但缺乏关于哪些基因组目标最适合解决不同进化尺度问题的信息。在这项研究中，首先，我们通过在三个分类学级别中的每个级别比较这些位点来比较为深层次和浅层次开发的目标位点的好处：属内（系统发育学）、物种内（系统地理学）和杂交区域内（群体基因组学）。具体来说，我们的目标是进化上保守的基因座，这些基因座适用于更深的系统发育尺度和更快速进化的基因座，这些基因座为系统地理学和种群基因组尺度提供信息。其次，我们评估了在同一混合富集反应中针对不同分类水平的多位点集的功效，我们将这种方法称为分层混合富集。第三，我们将这种方法应用于北美合唱蛙属 Pseudacris，以回答跨分类和时间尺度的关键进化问题。我们证明，在该系统中，产生解析度最高的基因树的基因组目标类型因分类级别而异，尽管所有级别的深尺度基因座的错误可能性都大大降低。我们成功地高效地恢复了两个不同轨迹集的数据。使用针对深层和浅层的分层数据：我们 1) 解析 Pseudacris 属的系统发育，并引入了一种新的视觉和假设检验方法，该方法使用节点热图来检查分支支持值对去除位点和位点的稳健性；2) 估计 Pseudacris feriarum 的系统地理学历史，它揭示了多达 5 次独立的入侵，导致与同类 Pseudacris nigrita 形成重复的强化接触区，并有持续的基因流入 sympatry；3) 以高可信度量化 P. feriarum 和 P. nigrita 之间这些区域之一的杂交频率，该频率低于基于微卫星的估计。我们发现分层混合浓缩方法提供了一种有效的、多层次的数据收集方法，可以同时解决跨越多个进化尺度的问题。[锚定杂交富集；热图；杂交；系统发育学；系统地理学；群体基因组学；加强; 生殖特征位移。]