Data from: Resolving relationships among the megadiverse butterflies and moths with a novel pipeline for Anchored Phylogenomics

The advent of next-generation sequencing technology has allowed for the collection of large portions of the genome for phylogenetic analysis. Hybrid enrichment and transcriptomics are two techniques that leverage next-generation sequencing and have shown much promise. However, methods for processing hybrid enrichment data are still limited. We developed a pipeline for anchored hybrid enrichment (AHE) read assembly, orthology determination, contamination screening, and data processing for sequences flanking the target “probe” region. We apply this approach to study the phylogeny of butterflies and moths (Lepidoptera), a megadiverse group of more than 157,000 described species with poorly understood deep-level phylogenetic relationships. We introduce a new, 855 locus anchored hybrid enrichment kit for Lepidoptera phylogenetics and compare resulting trees to those from transcriptomes. The enrichment kit was designed from existing genomes, transcriptomes and expressed sequence tag (EST) data and was used to capture sequence data from 54 species from 23 lepidopteran families. Phylogenies estimated from AHE data were largely congruent with trees generated from transcriptomes, with strong support for relationships at all but the deepest taxonomic levels. We combine AHE and transcriptomic data to generate a new Lepidoptera phylogeny, representing 76 exemplar species in 42 families. The tree provides robust support for many relationships, including those among the seven butterfly families. The addition of AHE data to an existing transcriptomic dataset lowers node support along the Lepidoptera backbone, but firmly places taxa with AHE data on the phylogeny. To examine the efficacy of AHE at different taxonomic levels, phylogenetic analyses were also conducted on a sister group representing a more recent divergence, the Saturniidae and Sphingidae. These analyses utilized sequences from the probe region and data flanking it, nearly doubled the size of the dataset; all resulting trees were well supported. We hope that our data processing pipeline, hybrid enrichment gene set, and approach of combining AHE data with transcriptomes will be useful for the broader systematics community.下一代测序（next-generation sequencing, NGS）技术的问世，使得科研人员能够获取基因组大片段区域用于系统发育分析。杂交富集（hybrid enrichment）与转录组学（transcriptomics）是两种依托下一代测序技术的研究手段，已展现出可观的应用前景。然而当前针对杂交富集数据的处理方法仍较为有限。我们开发了一套针对锚定杂交富集（anchored hybrid enrichment, AHE）的分析流程，可实现测序读段组装、直系同源基因判定、污染筛查，以及靶标“探针”区域侧翼序列的数据处理工作。我们将该流程应用于鳞翅目（Lepidoptera，涵盖蝶类与蛾类）的系统发育研究——鳞翅目是一个物种多样性极高的类群，已描述物种超过15.7万种，但其深层系统发育关系仍未被充分阐明。我们研发了一款包含855个基因座的锚定杂交富集试剂盒，用于鳞翅目系统发育研究，并将其产出的系统发育树与转录组数据构建的系统发育树进行了对比。该富集试剂盒基于已公开的基因组、转录组及表达序列标签（expressed sequence tag, EST）数据设计，成功从23个鳞翅目科的54个物种中捕获到目标序列数据。基于AHE数据构建的系统发育树与转录组数据构建的系统发育树整体一致性较高，除最深级的分类阶元外，其余所有类群关系均得到了较强的支持度。我们整合AHE与转录组数据，构建了新的鳞翅目系统发育树，涵盖了42个科的76个代表物种。该系统发育树对诸多类群关系提供了高可信度的支持，包括7个蝴蝶科之间的演化关系。在已有的转录组数据集中补充AHE数据后，鳞翅目系统发育主干节点的支持度有所下降，但成功将带有AHE数据的类群稳定锚定在了系统发育树上。为验证AHE在不同分类阶元下的应用效能，我们还对一个分化时间较近的姊妹类群——天蚕蛾科（Saturniidae）与天蛾科（Sphingidae）开展了系统发育分析。本次分析使用了探针区域及其侧翼序列的数据，使数据集规模几乎翻倍，最终构建的所有系统发育树均得到了良好的支持度。我们期望本研究开发的数据处理流程、杂交富集基因套装以及AHE与转录组数据整合的分析方法，能够为更广范围的系统学研究社区提供助力。