Data for "Evolutionary relationships between invasive Senecio madagascariensis (fireweed) and the Australian Senecio pinnatifolius complex, and their implications for biological control research"

DNA sequence supermatrices and phylogenetic trees underlying a paper submitted to Capitulum.\nLineage: To add to our understanding of the placement of taxa of relevance to fireweed biocontrol research, we generated new Sanger sequence data for 38 samples representing some taxa for which no data were previously available, species whose phylogenetic placement we wanted to confirm independently, and all taxonomic varieties of Senecio pinnatifolius except var. leucocarpus I. Thomps., which is presumed extinct. The targeted sequence regions and primers used were the same as in our previous study (Schmidt-Lebuhn & al., 2020), i.e., the nuclear ETS and ITS as well as chloroplast psbA-trnH and trnL regions, so that the new data could be added to the existing dataset. For the purposes of the results presented here, we focus on ribosomal data (ETS, ITS), because they provide stronger phylogenetic resolution and confidence than the chloroplast regions.\n\nDNA was extracted from herbarium specimens at CANB and NU. Laboratory work and sequencing was outsourced to the Australian Genome Research Facility. Contigs were produced using Geneious (www.geneious.com). We removed the sequences of Senecio pinnatifolius from the data matrices used in Schmidt-Lebuhn & al. (2020), because their varietal affiliation was not always known and may have been chimeric, and added the new sequences.\n\nETS and ITS sequences were concatenated using a custom Python script, and alignments were produced using MAFFT 7.453 (Katoh & Standley, 2013). A Maximum Likelihood phylogeny was inferred with IQ-TREE 2.1.2 (Minh & al., 2020), with both gene partitions under the substitution model GTR+F+I+G4 chosen by automatic model and partition testing, and 1,000 UltraFast Bootstrap (UFB) replicates as branch support values (Minh & al., 2013). Chloroplast psbA-trnH and trnL sequences were likewise concatenated and analysed with the same approach; model testing favoured K3Pu+F+G4 for psbA-trnH and TIM+F+G4 for trnL.

提交至《Capitulum》期刊的论文所依托的DNA序列超级矩阵与系统发育树。

分类群与研究背景：为加深对与火草（fireweed）生物防治研究相关分类群分类地位的理解，我们为38份样本生成了全新的桑格测序数据（Sanger sequence data）。这些样本涵盖三类分类群：此前无可用序列数据的分类群、需独立验证其系统发育位置的物种，以及除Leucocarpus I. Thomps.变种（据推测已灭绝）外的所有羽叶千里光（Senecio pinnatifolius）分类变种。本次研究所用的目标序列区域与引物，与我们此前的研究（Schmidt-Lebuhn等，2020）完全一致，即核基因组ETS（ETS）、ITS（ITS）以及叶绿体psbA-trnH和trnL区域，以便将新生成的数据整合至现有数据集。针对本文展示的研究结果，我们重点分析核糖体数据（ETS、ITS），因其相较于叶绿体区域序列，能够提供更强的系统发育分辨率与置信度。

DNA提取自CANB与NU馆藏的腊叶标本。实验操作与测序工作外包至澳大利亚基因组研究设施（Australian Genome Research Facility）。序列重叠群通过Geneious（Geneious，www.geneious.com）组装得到。我们从Schmidt-Lebuhn等（2020）所用的数据矩阵中移除了羽叶千里光（Senecio pinnatifolius）的原有序列，因这些序列的变种归属并不明确，且可能存在嵌合现象，随后加入了本次新生成的序列。

ETS与ITS序列通过自定义Python脚本进行拼接，序列比对则通过MAFFT 7.453（MAFFT 7.453，Katoh & Standley, 2013）完成。基于IQ-TREE 2.1.2（IQ-TREE 2.1.2，Minh等，2020）构建最大似然系统发育树：通过自动模型与分区测试，为两个基因分区均选择了GTR+F+I+G4替换模型，并以1000次超快速自举（UltraFast Bootstrap, UFB）重复抽样结果作为分支支持度（Minh等，2013）。叶绿体psbA-trnH与trnL序列同样采用上述方法进行拼接与分析；模型测试结果显示，psbA-trnH区域优选替换模型为K3Pu+F+G4，trnL区域则为TIM+F+G4。