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 collected 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=1,510) 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=2,749) 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 MYA) to very young (≤ 1 MYA) 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.要获取系统发育（phylogeny）的基因组学研究视角，需从全基因组范围内收集多个假定独立的基因座（locus）的数据。在昆虫类群中，此类数据的收集愈发常用转录组测序（transcriptome sequencing）方法，原因在于：目前具备高质量基因组序列的昆虫物种寥寥无几；全新基因组组装仍为研究瓶颈；基因组的转录区域是一个合理的精简靶向基因组子集；且从转录区域获取的数据，其组成与生物学家传统研究中使用的数据类型（如外显子（exon））高度相似。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，但绝大多数具有重要生物学意义的昆虫样本往往无法满足这一要求。近期研究表明，若保守基因组元件（conserved genomic element）存在于昆虫基因组中且可被获取，那么基于DNA的保守基因组元件靶向富集技术，可为跨昆虫类群收集系统发育组学数据提供另一条可行路径。本研究鉴定出昆虫纲膜翅目（Hymenoptera）共有的一套大型超保守元件（ultraconserved element, UCE）集合（共1510个）。我们通过计算机模拟分析（in silico analysis）证实，这些基因座可准确重构已完成基因组测序的膜翅目类群的系统发育关系；同时设计了一套用于富集此类基因座的RNA诱饵探针（共2749条），可供研究人员使用从多种来源提取的DNA模板开展实验。我们利用该UCE诱饵探针套装，从30个膜翅目类群中平均富集得到721个UCE基因座，并基于这些基因座重构了膜翅目类群间从极古老（≥2.2亿年）到极年轻（≤100万年）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研究膜翅目系统发育的研究不同，本研究发现蚁类与所有其余针尾亚目（aculeate）类群互为姊妹群，且该节点得到完全支持——尽管这一结果可能受到类群采样等因素的影响。我们将结合解析这个物种丰富度与多样性均位居前列的动物类群之一的演化历史这一目标，对本研究采用的方法与结果展开讨论。