Phylogenetic analyses used for the re-identification of Penicillium and Talaromyces catalogued in South African culture collections

DNA sequence datasets, alignments and phylogenetic trees used in a publication to describe eight Penicillium and three Talaromyces species. Datasets were aligned in MAFFT v. 7.490 (Katoh & Standley 2013) with the G-INS-I option selected, with alignments manually trimmed, adjusted and concatenated in Geneious where needed. The most appropriate partition schemes and substitution models were selected based on Bayesian information criterion using a greedy strategy implemented in PartitionFinder v. 2.1 (Lanfear et al. 2017), allowing gene regions, introns, exons and codon positions to be independent datasets. Phylogenies were calculated using both Maximum Likelihood (ML) and Bayesian tree Inference (BI). ML was performed in IQtree v. 2.2.0 (Minh et al. 2020) with support in nodes calculated using a bootstrap analysis of 1000 replicates. BI was performed in MrBayes v. 3.2.7 (Ronquist et al. 2012), with three sets of four chains (1 cold and three heated) and was stopped at an average standard deviation for split frequencies of 0.01 using the "stoprule". Trees were visualised in TreeViewer v. 2.0.1 (https://treeviewer.org/) and edited in Affinity Publisher 2.0.3 (Serif (Europe), Nottingham, UK) for publication. ML tree topologies were used to present the results, with both bootstrap and posterior probability values shown for the supported branches. Alignments, Partitionfinder results and phylogenetic trees were uploaded.本数据集包含某篇已发表论文中用于描述8种青霉属 (Penicillium) 和3种篮状菌属 (Talaromyces) 物种的DNA序列数据集、序列比对文件及系统发育树。所有数据集均采用MAFFT v.7.490 (Katoh与Standley, 2013) 的G-INS-I比对模式进行序列比对，随后根据需要在Geneious软件中对序列比对结果进行手动修剪、调整与拼接。基于贝叶斯信息准则，采用PartitionFinder v.2.1 (Lanfear等, 2017) 内置的贪心算法筛选最优分区方案与替换模型，允许将基因区域、内含子、外显子及密码子位置设为独立数据集。系统发育树分别通过最大似然法 (Maximum Likelihood, ML) 与贝叶斯推断法 (Bayesian Inference, BI) 构建：最大似然分析在IQtree v.2.2.0 (Minh等, 2020) 中完成，节点支持度通过1000次重复的自举检验计算得到；贝叶斯推断分析在MrBayes v.3.2.7 (Ronquist等, 2012) 中完成，设置3组共4条马尔可夫链 (1条冷链与3条热链)，并通过"stoprule"参数将分析终止于分裂频率的平均标准差为0.01时。系统发育树使用TreeViewer v.2.0.1 (https://treeviewer.org/) 进行可视化，并在Affinity Publisher 2.0.3 (Serif (Europe), Nottingham, UK) 中进行编辑以符合出版格式要求。研究结果采用最大似然树拓扑结构进行展示，所有得到支持的分支均标注自举支持值与后验概率值。本研究的序列比对文件、PartitionFinder分析结果及系统发育树均已上传存档。