Figure 3

Phylogenetic tree comparing the small putative group IC1 introns in the rRNA small subunit gene of species of Phialophora ( Ph .), Arthonia and Porpidia with other group I introns found in the nuclear rRNA gene locus. The tree presented is the single most parsimonious tree (determined using PAUP [21]), based on 115 nucleotide positions (only P1, P9, and the intron portion of P10 were used for the analyses). Gaps were counted as a fifth base. Bootstrap values (based on 1000 replications) greater than 50% are shown for the supported branches. The tree has 748 steps, with a consistency index of 0.5040. When gaps were considered as "missing data", 12 most parsimonious trees resulted, with 495 steps and a CI of 0.5515. While the branching pattern differed among the 12 trees, the small putative introns always formed a monophyletic clade. Triangles indicate clades that are summarized for simplicity, as indicated as follows: Clade A, subgroup IC1 introns from Ascolacicola austriaca, Cryptendoxyla hypophloia, and Leucostoma personii; Clade B, subgroup IC1 introns from Gaeumannomyces graminis, Hypocrea pallida, Mycoarachis inversa, and Nectria aureofulva; Clade C, subgroup IC1 introns from Apioplagiostoma aceriferum, Cephalotheca sulfurea, Cordycepioideus bisporus, and Gnomoniella tubiformis; Clade D, subgroup IC1 introns from Ahtiana sphaerosporella, Arctocetraria nigricascens, Arctoparmelia centrifuga, Asahinea chrysantha, Cavernularia lophyrea, Cetraria ericetorum, Cetraria islandica (3 isolates), Cetraria nigricans, Cladonia arbuscula, Melanelia hepatizon, Melanelixia fulginosa, Myelochroa metarevuluta, Nephromopsis ahtii, Nephromopsis komarovii, Nephromopsis laureri, Nephromopsis stracheyi, Parmelia cochleata, Parmelia fertilis, Parmelia saxatilis, Parmelia squarrosa, Parmelia sulfata, Pseudophebe pubescens, Tuckermanella coralligera, Tuckermanella orbata, Tuckermanella playyphylla, Vulcipida pinasrti and Vulcipida viridis. Accession numbers for the Phialophora sequences are provided in Table 1, while those for the other sequences are listed in reference [13]. Lengths of the introns are indicated within the parentheses, as are the physical positions in the rRNA genes. All locations are in the rRNA SSU gene, relative to the E. coli rRNA SSU gene, except where noted (i.e., 2449 LSU is in the rRNA LSU gene). Dashed box indicates the clade that includes all of the small putative group I introns compared in this study.