Table 2.
Number of taxa, loci, and characters included in each data set. Sources of reference sequences for each analysis are cited. ML phylogenetic placements of the two unknown groups of pycnidia-producing fungi are reported with bootstrap support (BS).
| Analyses | Data set | Source of data set | No. of taxa | No. of loci | No. of char. | Phylogenetic placement |
|---|---|---|---|---|---|---|
| “Dark” group | ||||||
| Analysis 1 (Fig. S1) | Fungi | James et al. (2006) | 219 | 6 | 8 482 | Arthoniomycetes + Dothideomycetes clade (BS = 80 %); Dothideomycetes (BS = 64 %); sister to Trypethelium (BS = 39 %) |
| Analysis 2 (Fig. S2) | Pezizomycotina | Carbone et al. (unpubl. data) | 986 | 6 | 7 269 | Arthoniomycetes + Dothideomycetes clade (BS = 58 %); Dothideomycetes (BS = 36 %); sister to Trypetheliales (BS = 37 %) |
| Analysis 2A | Pezizomycotina | Carbone et al. (unpubl. data) | 983 | 61 | 7 269 | Dothideomycetes (BS = 30 %); Botryosphaeriaceae (BS = 56 %) |
| Analysis 2B | Pezizomycotina | Carbone et al. (unpubl. data) | 986 | 62 | 7 269 | Dothideomycetes (BS = 40 %); related to Kirschsteiniotheliaceae and part of Phaeotrichiaceae (BS = 32 %) |
| Analysis 3 (Fig. 1, Table S3) | Dothideomycetes + Arthoniomycetes | Carbone et al. (unpubl. data) and Schoch & Grube (2015) | 236 | 7 | 7 072 | Dothideomycetes (BS = 68 %); sister to Trypetheliales (BS = 86 %) |
| Analysis 4 (Fig. S3, Table S3) | Dothideomycetes + Arthoniomycetes + additional Trypetheliales | Carbone et al. (unpubl. data) and Nelsen et al., 2009, Nelsen et al., 2011 | 260 | 7 | 7 072 | Dothideomycetes (BS = 75 %); sister to Trypetheliales (BS = 49 %) |
| Analysis 5 (Fig. S4) | Trypetheliales | Nelsen et al. (2014) and Ertz et al. (2015) | 95 | 2 | 1 011 | Outside of Trypetheliales |
| “Green” group: | ||||||
| Analysis 1 (Fig. S1) | Fungi | James et al. (2006) | 219 | 6 | 8 482 | Lecanoromycetes, Ostropomycetidae, Ostropales (BS = 80 %) |
| Analysis 6 (Fig. S5) | Lecanoromycetes | Miadlikowska et al. (2014) | 1 319 | 5 | 7 433 | Ostropales (BS = 21 %); sister to Cyanodermella viridula (BS = 100 %) |
| Analysis 7 (Fig. 3) | Ostropomycetidae | Resl et al. (2015) | 207 | 8 | 6 665 | Ostropales (BS = 76 %); Stictidaceae (BS = 43 %); sister to Cyanodermella viridula (BS = 100 %) |
1
“dark” group is represented by the ribosomal RNA loci only (ITS, nrLSU, and nrSSU).
2
“dark” group is represented by the protein-coding loci only (RPB1, RPB2 and EF-1α).