Bacidia fuscoviridis, another overlooked sorediate crustose lichen widely distributed in temperate eastern North America

To evaluate the generic relationships of <em>Bacidia fuscovirdis </em>within Ramalinaceae we carried out BLASTn searches of the existing reference sequences of <em>B. fuscoviridis</em> in NCBI which recovered representatives of <em>Biatora </em>Ach., <em>Lecania </em>A.Massal. and <em>Mycobilimbia</em> Rhem, as the closest hits for ITS and the lone sequence of rpb2. Based on these results we used the published phylogeny of Ramalinaceae from Kistenich et al. (2018) as a guide and constructed a multi-locus dataset that mirrored their sampling of the clade containing <em>Bilimbia</em>, <em>Lecania</em> and <em>Mycobilimbia</em> with <em>Biatora</em> as an outgroup. We downloaded the mtSSU, ITS, nucLSU and RPB2 sequences used by those authors (see Table 1) and manually aligned each dataset in Mesquite 3.31 (Maddison &amp; Maddison 2017. We then added the available reference sequences of<em> B. fuscoviridis </em>(three ITS sequences, one rpb2 sequence) to the relevant alignment, manually adjusted them, and defined all ambiguously aligned regions and gap-rich terminal regions in an exclusion set. The excluded regions were then manually deleted, terminal gaps transformed to missing data, and uncertainties and polymorphisms transformed to missing data. The alignments were then concatenated in Mesquite and exported a single PHYLIP file. The concatenated alignment was partitioned and RAxML v8.2x (Stamatakis 2006) was used to infer a maximum likelihood (ML) topology and bootstrapping was performed with 500 pseudoreplicates and implementing the model GTRGAMMA across all partitions. The results were visualized in FigTree 1.4.3 (Rambaut 2016). This data deposit includes the underlying files for the phylogeny presented in the published study (Curtis et al., Journal of the Torrey Botanical Society). It includes a translation table for GenBank accessions and terminal names used in the dataset, individual alignments for ITS, mtSSU, nucLSU and rpb2 all in NEXUS format, concatenated alignment in NEXUS and PHYLIP format as well as partitions file for RAxML, and the final tree figure presented in the publication.为评估暗绿芽衣（<em>Bacidia fuscovirdis</em>）在扁枝衣科（Ramalinaceae）中的系统发育亲缘关系，我们针对美国国家生物技术信息中心（NCBI）数据库中已有的<em>B. fuscoviridis</em>参考序列开展核苷酸局部比对搜索工具（BLASTn）搜索，获得的近缘比对结果涵盖拜阿拉衣属（<em>Biatora</em>）Ach.、蜡盘衣属（<em>Lecania</em>）A.Massal.以及粘盘衣属（<em>Mycobilimbia</em>）Rhem的代表序列，对应内转录间隔区（Internal Transcribed Spacer，ITS）区段与唯一的RNA聚合酶II第二亚基（RNA polymerase II subunit 2，rpb2）序列。基于上述结果，我们以Kistenich等人2018年发表的扁枝衣科系统发育研究作为参照框架，构建了多基因座数据集，该数据集复刻了其针对包含<em>Bilimbia</em>、<em>Lecania</em>与<em>Mycobilimbia</em>的演化支的采样策略，并以<em>Biatora</em>作为外类群。我们下载了该研究中使用的线粒体小亚基核糖体RNA（mitochondrial small subunit ribosomal RNA，mtSSU）、ITS、核大亚基核糖体RNA（nuclear large subunit ribosomal RNA，nucLSU）及RPB2序列（详见表1），并在Mesquite 3.31软件（Maddison与Maddison 2017）中对各数据集进行手动比对。随后，我们将已公开的<em>B. fuscoviridis</em>参考序列（3条ITS序列、1条rpb2序列）添加至对应比对文件中，再次进行手动调整，并将所有比对存疑区域与富含缺失位点的末端区域纳入排除集。随后手动删除上述被排除的区域，将末端空位转换为缺失数据，并将比对不确定区域与多态性位点统一转换为缺失数据。我们在Mesquite中完成序列拼接，导出单份PHYLIP格式的拼接比对文件。对拼接后的比对文件进行分区处理，随后使用RAxML v8.2x（Stamatakis 2006）构建最大似然（maximum likelihood, ML）拓扑结构，同时开展包含500次重复抽样的自展检验，并为所有分区指定GTRGAMMA替换模型。最终结果通过FigTree 1.4.3（Rambaut 2016）进行可视化。本数据集包含发表于《Torrey植物学会期刊》的Curtis等人研究中所呈现的系统发育分析原始文件，包括：基因银行（GenBank）登录号与数据集终端分类单元名称的转换对照表、NEXUS格式的ITS、mtSSU、nucLSU及rpb2单基因比对文件、NEXUS与PHYLIP格式的拼接比对文件、适配RAxML的分区文件，以及论文中呈现的最终系统发育树插图。