Data in support of Using target sequence capture to improve the phylogenetic resolution of a rapid radiation in New Zealand Veronica

Includes alignments and trees for the analysis found in Thomas et al. 2021, Using target sequence capture to improve the phylogenetic resolution of a rapid radiation in New Zealand Veronica; American Journal of Botany, Special Issue: Exploring Angiosperms353: a Universal Toolkit for Flowering Plant Phylogenomics. Alignments comprise subsets of Angiosperms353 genes given each filtering scheme (full, intersection, sortadate_BP, sortadate_TL) and gene type/subset (exons, introns, supercontigs), and for markers downloaded from GenBank, as explained in the Methods section of Thomas et al. 2021. Trees were included for each of these alignments from IQtree and Astral; SVDquartets tree was only estimated for the full set of supercontigs. Gene trees were generated with IQtree. Tree files are named differently than the final manuscript; refer to the number of genes specified in Fig 1 of Thomas et al, 2021 and specified in each filename to identify filtering scheme. Raw sequence reads are available on the Sequence Read Archive at http://www.ncbi.nlm.nih.gov/bioproject/715342.

本数据集包含用于Thomas等人2021年发表于《美国植物学杂志》（American Journal of Botany）特刊《探索Angiosperms353：被子植物系统发育组学通用工具包》的研究《利用靶标序列捕获技术提升新西兰婆婆纳属（Veronica）快速辐射类群的系统发育分辨率》分析所需的比对序列与系统发育树。比对序列涵盖按各类过滤策略（全数据集、交集集、sortadate_BP、sortadate_TL）及不同基因类型/子集（外显子、内含子、超级重叠群（supercontigs））筛选得到的Angiosperms353基因集（Angiosperms353）子集，同时包含从GenBank数据库下载的分子标记序列，相关细节详见Thomas等人2021年研究的方法部分。针对上述每一类比对序列，均提供了IQtree与Astral构建的系统发育树；仅针对全数据集的超级重叠群，估算了SVDquartets系统发育树。基因树均通过IQtree生成。树文件的命名方式与最终发表的手稿存在差异，请参考Thomas等人2021年图1中指定的基因数量，结合各文件名中的相关信息，即可确定其对应的过滤策略。原始序列读段可在序列读段存档（Sequence Read Archive）的以下链接获取：http://www.ncbi.nlm.nih.gov/bioproject/715342。