Taxon-specific or universal? Using target capture to study the evolutionary history of a rapid radiation

Target capture emerged as an important tool for phylogenetics and population genetics in non-model taxa. Whereas developing taxon-specific capture probes requires sustained efforts, available universal kits may have a lower power to reconstruct relationships at shallow phylogenetic scales and within rapidly radiating clades. We present here a newly-developed target capture set for Bromeliaceae, a large and ecologically-diverse plant family with highly variable diversification rates. The set targets 1,776 coding regions, including genes putatively involved in key innovations, with the aim to empower testing of a wide range of evolutionary hypotheses. We compare the relative power of this taxon-specific set, Bromeliad1776, to the universal Angiosperms353 kit. The taxon-specific set results in higher enrichment success across the entire family, however, the overall performance of both kits to reconstruct phylogenetic trees is relatively comparable, highlighting the vast potential of univer..., The bait set was designed using whole-genome sequences and gene models from Ananas comosus v.3 (Ming et al., 2015). Random protein coding genes were selected based on genetic diversity parameters, total exonic size, individual exon size and copy-number variation. We then added genes associated with key innovative traits in Bromeliaceae, either genes previously annotated in A. comosus or when annotate in other species, using BLAST to find the A. comosus genes with the highest match scores. Genes underpinning innovative traits were included in the bait design, regardless of criteria used for random proteing coding genes, like size and duplication rate. We included markers previously used for phylogenomic inference in Bromeliaceae and genes orthologous to those in the Angiosperms353 bait set. An additional round of filtering was performed by the manufacturer of the final bait set, Arbor Biosciences (Ann Arbor, MI, 167 USA), where multi-copy genes with sequences that are more than 95% ident..., List of bait sequences in fasta format of the Bromeliad1776 target capture kit including all 57,445 baits of 80bp., # Taxon-specific or universal? Using target capture to study the evolutionary history of a rapid radiation

## Description of the data and file structure

* Baits-80-40-Pass_Client_filtering_GC_Under_70.fas.clust-75-95.fasta - FASTA sequences for bait probes. Baits are 80bp with x2 (40bp) overlap and designed as described in the manuscript: [10.1111/1755-0998.13523](https://doi.org/10.1111%2F1755-0998.13523), further information in the github repository:
* supporting_information_Table1.csv - Genes included in the Bromeliad1776 bait design, with identifiers as annotated in *Ananas comosus* genome v.3 (Ming et al., 2015). The table includes details about exon composition, copy number and putatively associated pathways. See legend in file supporting_information_Table1_legend.csv.
* supporting_information_Table1_legend.csv - Legend for table S1.
* supporting_information_Table2.csv - Categories of pathways and traits used to choose genes of interest for the Bromeliad1776 bait set,...

目标捕获技术现已成为非模式类群系统发育学与群体遗传学研究的重要工具。尽管开发类群专属捕获探针需要持续投入大量工作，但现有的通用试剂盒在重建浅系统发育尺度以及快速辐射类群内的演化关系时，效能往往较低。本研究针对凤梨科（Bromeliaceae）——一个物种丰富、生态多样且分化速率差异极大的植物科——开发了一套全新的目标捕获试剂盒。该试剂盒靶向1776个编码区，其中包含推测参与关键创新性状的基因，旨在助力验证各类演化假说。本研究将该类群专属试剂盒Bromeliad1776与通用的被子植物353（Angiosperms353）试剂盒的效能进行了对比。结果显示，在凤梨科全类群范围内，专属试剂盒的富集成功率更高；但二者在系统发育树重建方面的整体表现较为相近，凸显了通用试剂盒的巨大应用潜力——（原文截断）。该诱饵试剂盒的设计基于菠萝（*Ananas comosus*）v3版本的全基因组序列与基因模型（Ming等，2015）。研究人员首先依据遗传多样性参数、外显子总长度、单外显子长度以及拷贝数变异筛选随机编码蛋白基因；随后，针对凤梨科关键创新性状相关的基因——包括此前已在菠萝基因组中注释的基因，或通过BLAST比对在其他物种中注释后找到的高匹配度菠萝同源基因——进行了补充添加。对于关键创新性状相关的基因，无论其是否符合随机编码基因的筛选标准（如基因长度、复制速率），均被纳入诱饵设计流程。此外，研究团队还纳入了此前用于凤梨科系统发育组学推断的分子标记，以及与被子植物353试剂盒中基因同源的序列。最终试剂盒由制造商Arbor Biosciences（美国密歇根州安阿伯市，167号）完成了额外一轮过滤，移除了序列相似度超过95%的多拷贝基因——（原文截断）。Bromeliad1776目标捕获试剂盒的FASTA格式诱饵序列列表，包含全部57445条长度为80bp的诱饵序列。# 类群专属还是通用？利用目标捕获技术研究快速辐射类群的演化历史

## 数据与文件结构说明
* Baits-80-40-Pass_Client_filtering_GC_Under_70.fas.clust-75-95.fasta：诱饵探针的FASTA序列文件。该文件中的诱饵序列长度为80bp，存在2倍（40bp）的重叠区域，设计方法详见论文：[10.1111/1755-0998.13523](https://doi.org/10.1111%2F1755-0998.13523)，更多信息可查阅GitHub仓库：
* supporting_information_Table1.csv：Bromeliad1776诱饵设计中纳入的基因列表，基因标识符基于菠萝基因组v3版本的注释（Ming等，2015）。该表格包含外显子组成、拷贝数以及推测关联通路的详细信息，相关说明详见文件supporting_information_Table1_legend.csv。
* supporting_information_Table1_legend.csv：附表S1的注释说明文档。
* supporting_information_Table2.csv：用于筛选Bromeliad1776试剂盒目标基因的通路与性状类别列表……