Data from: Enriching the ant tree of life: enhanced UCE bait set for genome-scale phylogenetics of ants and other Hymenoptera

1. Targeted enrichment of conserved genomic regions (e.g., ultraconserved elements or UCEs) has emerged as a promising tool for inferring evolutionary history in many organismal groups. Because the UCE approach is still relatively new, much remains to be learned about how best to identify UCE loci and design baits to enrich them.

2. We test an updated UCE identification and bait design workflow for the insect order Hymenoptera, with a particular focus on ants. The new strategy augments a previous bait design for Hymenoptera by (a) changing the parameters by which conserved genomic regions are identified and retained, and (b) increasing the number of genomes used for locus identification and bait design. We perform in vitro validation of the approach in ants by synthesizing an ant-specific bait set that targets UCE loci and a set of “legacy” phylogenetic markers. Using this bait set, we generate new data for 84 taxa (16/17 ant subfamilies) and extract loci from an additional 17 genome-enabled taxa. We then use these data to examine UCE capture success and phylogenetic performance across ants. We also test the workability of extracting legacy markers from enriched samples and combining the data with published data sets.

3. The updated bait design (hym-v2) contained a total of 2,590-targeted UCE loci for Hymenoptera, significantly increasing the number of loci relative to the original bait set (hym-v1; 1,510 loci). Across 38 genome-enabled Hymenoptera and 84 enriched samples, experiments demonstrated a high and unbiased capture success rate, with the mean locus enrichment rate being 2,214 loci per sample. Phylogenomic analyses of ants produced a robust tree that included strong support for previously uncertain relationships. Complementing the UCE results, we successfully enriched legacy markers, combined the data with published Sanger data sets, and generated a comprehensive ant phylogeny containing 1,060 terminals.

4. Overall, the new UCE bait design strategy resulted in an enhanced bait set for genome-scale phylogenetics in ants and likely all of Hymenoptera. Our in vitro tests demonstrate the utility of the updated design workflow, providing evidence that this approach could be applied to any organismal group with available genomic information.

1. 保守基因组区域的靶向富集（例如超保守元件（ultraconserved elements, UCEs））已成为推断众多生物类群演化历史的极具前景的技术手段。鉴于UCE方法仍属较新兴技术，目前仍有诸多问题有待厘清，例如如何最优地识别UCE位点以及设计捕获探针以实现其富集。
2. 本研究针对昆虫纲膜翅目（Hymenoptera）测试了一套更新后的UCE识别与捕获探针设计流程，并重点聚焦蚁类类群。该新策略对既往膜翅目捕获探针设计方案进行了两处优化：(a) 调整了保守基因组区域的识别与保留参数；(b) 增加了用于位点识别与探针设计的基因组数量。我们通过合成靶向UCE位点与一套“传统（legacy）”系统发育标记的蚂蚁特异性捕获探针组，在蚁类中开展了体外验证实验。利用该探针组，我们为84个分类群（覆盖16/17个蚁亚科）生成了新的测序数据，并从另外17个已完成基因组测序的分类群中提取了目标位点。随后，我们利用这些数据评估了UCE在蚁类中的捕获成功率与系统发育分析表现。此外，我们还测试了从富集样本中提取传统系统发育标记的可行性，并将这些数据与已发表数据集进行整合。
3. 更新后的捕获探针设计方案（hym-v2）共计覆盖2590个膜翅目靶向UCE位点，相较于原始探针组（hym-v1，1510个位点），位点数量得到了显著提升。针对38个已完成基因组测序的膜翅目类群与84个富集样本的实验结果显示，该方法的捕获成功率高且无偏倚，平均每个样本的位点富集率可达2214个。对蚁类开展的系统发育基因组学分析得到了一棵稳健的系统发育树，其对此前存在争议的类群间亲缘关系给出了强支持度。与UCE结果相辅相成的是，我们成功富集了传统系统发育标记，并将这些数据与已发表的桑格（Sanger）测序数据集进行整合，最终构建了包含1060个终端类群的全面蚁类系统发育树。
4. 综上，这套新型UCE捕获探针设计策略为蚁类乃至整个膜翅目类群的基因组规模系统发育学研究提供了一套更优异的捕获探针组。我们的体外验证实验证实了更新后设计流程的实用性，证明该方法可推广应用于任何具备可用基因组信息的生物类群。