Sequencing data for: Chronosequence of invasion reveals minimal losses of population genomic diversity, niche expansion, and trait divergence in the polyploid, leafy spurge

Sampling and sequencing In 2019, we collected leaf tissue from six individuals in each of 14 populations distributed evenly across Minnesota (hereafter: population samples). In addition, we collected tissue from one individual in each of 157 populations distributed relatively evenly across Minnesota, eastern South Dakota, eastern North Dakota, and western Wisconsin (hereafter: landscape samples). We sampled tissue from individuals that were at least five meters apart to minimize collecting from the same genet and placed tissues immediately in silica for preservation until DNA extraction. We extracted DNA using QIAGEN DNeasy Plant Mini Kits (QIAGEN Inc.). Dual-indexed GBS (genotyping-by-sequencing) libraries were created using the BamHI + NsiI enzyme combination. All libraries were pooled and sequenced on an Illumina NovaSeq System (Illumina Inc., San Diego, CA, USA) with 1x100-bp sequencing. Once sequenced, the reads were demultiplexed and balanced with a mean quality score ≥ Q30 for all libraries. We filtered low-quality bases using Trimmomatic (Bolger et al. 2014) and used Stacks v.2.5.9 (Rochette et al. 2019) to build loci de novo (i.e., without aligning reads to a reference genome). Overall, we obtained 510 million reads across the 241 samples (599,386 – 3,376,078 of raw reads per individual). Mean read depth per locus ranged from 14x to 26x.

采样与测序：2019年，我们从均匀分布于明尼苏达州的14个种群中各采集6个个体的叶片组织，以下简称种群样本（population samples）。此外，我们从相对均匀分布于明尼苏达州、南达科他州东部、北达科他州东部以及威斯康星州西部的157个种群中各采集1个个体的组织，以下简称景观样本（landscape samples）。为避免采集同一基株的个体，我们采样时确保个体间间距至少为5米，并将采集的组织立即置于硅胶中保存，直至DNA提取环节。我们使用QIAGEN DNeasy植物微量提取试剂盒（QIAGEN公司）完成DNA提取。采用BamHI与NsiI酶组合构建双索引测序分型（genotyping-by-sequencing, GBS）文库。将所有文库混合后，在美国加利福尼亚州圣地亚哥的Illumina公司Illumina NovaSeq测序系统上进行1×100 bp单端测序。测序完成后，对下机reads进行解多重索引与质量平衡处理，确保所有文库的平均质量得分不低于Q30。我们使用Trimmomatic（Bolger等人，2014）过滤低质量碱基，并采用Stacks v.2.5.9（Rochette等人，2019）进行从头位点构建（即不将reads比对至参考基因组）。总体而言，我们对241个样本共获得5.10亿条reads，单个个体的原始reads数介于599,386至3,376,078之间；每个位点的平均测序深度为14×至26×。