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

To evaluate the generic relationships of Bacidia fuscovirdis within Ramalinaceae we carried out BLASTn searches of the existing reference sequences of B. fuscoviridis in NCBI which recovered representatives of Biatora Ach., Lecania A.Massal. and Mycobilimbia 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 Bilimbia, Lecania and Mycobilimbia with Biatora 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 & Maddison 2017. We then added the available reference sequences of B. fuscoviridis (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.