Table 1. cont. Species Peltigera aphthosa (L.) Willd. Peziza phyllogena Cooke Peziza varia (Hedw.) Fr. Phacidiopycnis pyri (Fuckel) Weindlm. Phialocephala fortinii C.J.K. Wang & H.E. Wilcox Phyllactinia moricola (Henn.) Homma Piceomphale bulgarioides (Rabenh.) Svrcek Pleochaeta shiraiana (Henn.) Kimbr. & Korf Protomyces inouyei Henn. Rhytisma sp. Rutstroemia firma (Pers.) P. Karst. Saccharomyces cerevisiae Meyen ex E.C. Hansen Sarcoleotia sp. Sarea resinae (Fr.) Kuntze Schizosaccaromyces pombe Lindner Scleromitrula shiraiana (Henn.) S. Imai Sclerotinia sclerotiorum (Lib.) de Bary Sordaria fimicola (Roberge ex Desm) Ces. & De Not. Spathularia flavida Pers. Taphrina wiesneri (Rathay) Mix Trapelia placodioides Coppins & P. James Trichoglossum hirsutum (Pers.) Boud. Uncinula septata E.S. Salmon Vibrissea flavovirens (Pers.) Korf & J.R. Dixon Vibrissea truncorum (Alb. & Schwein.) Fr. Xylaria hypoxylon L. & Grev. Reproductive Morphology SSU-rDNA LSU-rDNA 5.8S rDNA AY424225 AY789327 AY789390 DQ470997 AY524846 AB033481 Z81388 AB120750 AY548295 AF356695 DQ471010 J01353 AY789298 AY641004 Z19578 AY789406 AY789346 AY545724 AY789356 AY548293 AF119500 AY789312 AB183530 AY789425 AY789401 AY544692 AF286759 AY789328 AY789391 DQ470949 AF269219 AB022401 Z81415 AB022403 EU056299 AF356696 DQ470963 J01355 AY789299 AY640965 Z19578 AY789407 AY789347 AY545728 AF433142 AY548292 AF274103 AY789313 AB183532 AY789426 AY789402 AF132333 AF158645 AY789329 AY789392 EU156058 AY347413 D84385 Z81441 D84380 DQ497617 AY465516 U21824 AY247400 AY789300 AY781237 Z19578 AY789408 AF455526 EU918704 AF433152 DQ497616 AF274081 AY789314 AB183533 AY789427 AY789403 AF163035 Information about unpublished sequences is available from the AFTOL website (http://aftol.org). doi:10.1371/journal.pone.0004246.t001 2. Phylogenetic analyses One data set was prepared based on sequences of 78 taxa from three nuclear genes, SSU rDNA, LSU rDNA and 5.8S rDNA. The LSU rDNA sequence of Rutstroemia bolaris was 527 bp shorter than in other taxa. No 5.8S rDNA data of Hemiphacidium longisporum were available. Sequences were aligned with ClustalX [21], then adjusted by eye in the data editor of PAUP* 4.0b [13]. Introns and short insertions were deleted, and ambiguously aligned positions were excluded from the data sets before performing the analyses. Alignments were deposited and are available at TreeBASE (accession number SN3978). A basidiomycete Cotylidia sp. was used to root the tree in the analyses. The data set was analyzed with PAUP* 4.0b and MrBayes 3.1.1 [14]. Gaps were treated as missing data. Parsimony analyses were performed using equal weighting of characters and transformations. Heuristic searches were per- formed with one thousand replicate searches, each with a random taxon addition sequence, MAXTREES set to autoincrease, and TBR branch swapping. Robustness of individual branches was estimated by maximum parsimony bootstrap proportions (BP), using 500 replicates, each consisting of a heuristic search with 50 random taxon addition sequences, MAXTREES set to auto- increase, and TBR branch swapping. Bayesian posterior proba- bilities were computed using the Metropolis-coupled Markov chain Monte Carlo method (MCMCMC) under the GTR+C+I model in MrBayes 3.1.1 by running four chains with 2,000,000 generations. Trees were sampled every 100 generations. Likeli- hoods converged to a stable value after ca. 500,000 generations in the wider-range analyses and after ca. 100,000 generations in the narrower-range analysis, and all trees prior to the convergence were discarded as the ‘‘burn-in’’ phase before computing a consensus tree in PAUP*. Bayesian posterior probabilities (PP) were obtained from the 50% majority rule consensus of the remaining trees, and clades with PP$0.95 were considered to be significantly supported. 2. Analysis of correlation between leaf-living ecology and reduced morphology To evaluate the correlation between leaf-living ecology and reduced apothecium morphology across ascomycetes, BayesTraits [15] was used. All sampled 19000 trees from the above Bayesian analyses were used as the input treefile for the program [22]. An additional two-character data set for the 78 taxa was prepared as the input file. The characters and their binary character states were: 1. Whether or not a species is a leaf-endophyte. Many ascomycetes can have a endophytic stage in their life cycle, so here we used a strict sense of leaf-living that included only PLoS ONE | www.plosone.org 5 January 2009 | Volume 4 | Issue 1 | e4246