Data from: Target enrichment of ultraconserved elements from arthropods provides a genomic perspective on relationships among Hymenoptera

Gaining a genomic perspective on phylogeny requires the collection of data from many putatively independent loci across the genome. Among insects, an increasingly common approach to collecting this class of data involves transcriptome sequencing, because few insects have high-quality genome sequences available; assembling new genomes remains a limiting factor; the transcribed portion of the genome is a reasonable, reduced subset of the genome to target; and the data collected from transcribed portions of the genome are similar in composition to the types of data with which biologists have traditionally worked (e.g. exons). However, molecular techniques requiring RNA as a template, including transcriptome sequencing, are limited to using very high-quality source materials, which are often unavailable from a large proportion of biologically important insect samples. Recent research suggests that DNA-based target enrichment of conserved genomic elements offers another path to collecting phylogenomic data across insect taxa, provided that conserved elements are present in and can be collected from insect genomes. Here, we identify a large set (n = 1510) of ultraconserved elements (UCEs) shared among the insect order Hymenoptera. We used in silico analyses to show that these loci accurately reconstruct relationships among genome-enabled hymenoptera, and we designed a set of RNA baits (n = 2749) for enriching these loci that researchers can use with DNA templates extracted from a variety of sources. We used our UCE bait set to enrich an average of 721 UCE loci from 30 hymenopteran taxa, and we used these UCE loci to reconstruct phylogenetic relationships spanning very old (≥220 Ma) to very young (≤1 Ma) divergences among hymenopteran lineages. In contrast to a recent study addressing hymenopteran phylogeny using transcriptome data, we found ants to be sister to all remaining aculeate lineages with complete support, although this result could be explained by factors such as taxon sampling. We discuss this approach and our results in the context of elucidating the evolutionary history of one of the most diverse and speciose animal orders.若要从基因组层面解析系统发育关系，需采集基因组内多个假定独立的基因座的数据。在昆虫研究领域，采集这类数据的常用手段为转录组测序（transcriptome sequencing），原因在于：目前仅有少量昆虫拥有高质量基因组序列，全新基因组组装仍为研究瓶颈；基因组的转录区域是兼具合理性与简化性的靶向基因组子集；且从转录区域获取的数据，与生物学家传统研究中常用的数据类型（如外显子）组成相似。然而，以RNA为模板的分子技术（包括转录组测序）仅能使用极高质量的实验材料，但多数具有重要生物学意义的昆虫样本往往无法满足该要求。近期研究表明，若昆虫基因组中存在保守基因组元件且可被成功获取，基于DNA的保守元件靶向富集技术可为昆虫类群的系统发育组学数据采集提供全新路径。本研究鉴定出膜翅目（Hymenoptera）昆虫共有的一套大型超保守元件（ultraconserved elements, UCEs）集合，共计1510个（n=1510）。通过计算机模拟分析，我们证实这些基因座可准确重建具备基因组数据的膜翅目类群间的演化关系；同时设计了一套用于富集这些基因座的RNA诱饵探针（RNA baits）集合，共计2749条（n=2749），研究人员可将其与从多种来源提取的DNA模板配合使用。我们利用该UCE诱饵探针集，从30个膜翅目类群中平均富集得到721个UCE基因座，并借助这些基因座重建了膜翅目类群间从极古老（≥220百万年）到极年轻（≤1百万年）的分化事件对应的系统发育关系。与近期一项利用转录组数据解析膜翅目系统发育的研究不同，我们的结果显示蚁类为所有其余针尾亚目类群的姊妹群，且得到完全支持——尽管该结果可能受类群采样等因素影响。我们结合解析这一物种最为多样、类群最为丰富的动物目级类群之一的演化历史这一背景，对本研究的方法与结果进行了讨论。