Publications and alignments used in publications of AFTOL

• Lutzoni et al. 2004. American Journal of Botany 91(10): 1446-1480

Alignments:


• RPB2
• Mitochondrial Small Subunit rDNA
• Nuclear Large Subunit rDNA
• Nuclear Small Subunit rDNA

• Matheny et al. (2006) Resolving the phylogenetic position of the Wallemiomycetes: an enigmatic major lineage of Basidiomycota. Can. J. Bot. 84: 1794-1805

Alignments:


• Wallemia, 91 taxa; rpb1, rpb2, tef1, 18S, 25S, and 5.8S rRNA
• Wallemia, 182 taxa; 18S, 25S, and 5.8S rRNA

• Matheny et al. (2007) Contributions of rpb2 and tef1 to the phylogeny of mushrooms and allies (Basidiomycota, Fungi). Mol. Phylogenet. Evol. 43

Alignments:


• Basidiomycota, 132 taxa, RPB2, amino acids
• Basidiomycota, 132 taxa, RPB2, nucleotides
• Basidiomycota, 138 taxa, EF1alpha, amino acids
• Basidiomycota, 140 taxa, EF1alpha, nucleotides
• Basidiomycota, 146 taxa, nuc5.8s, nucLSU, nucSSU, RPB2, EF11alpha, amino acids
• Basidiomycota, 146 taxa, nuc5.8s, nucLSU, nucSSU, RPB2, EF11alpha, nucleotiodes

• James et al. (2006) Reconstructing the early evolution of the fungi using a six gene phylogeny. Nature 443: 818-822

Alignments:


• Combined data set, 214 taxa, excluded characters removed, amino acids
• Combined data set, 214 taxa, nucleotides
• Combined data set, 214 taxa, excluded characters removed, nucleotides
• Combined data set, 214 taxa, excluded characters and 3rd positions removed, nucleotides
• EF1alpha, 185 taxa, nucleotides
• 5.8s, 199 taxa, nucleotides
• nucLSU, 206 taxa, nucelotides
• nucSSU, 211 taxa, nucelotides
• RPB1, 187 taxa, nucleotides
• RPB2, 199 taxa, nucleotides
• Nonmolecular character states, 214 taxa

• Miadlikowska et al. (2006) New insights into classification and evolution of the Lecanoromycetes (Pezizomycotina, Ascomycota) from phylogenetic analyses of three ribosomal RNA- and two protein-coding genes. Mycologia (pub. not yet available)

Alignments:


• Combined data set with mitssu, nucssu, nuclsu, rpb1 rpb2

• Matheny et al. (2006). Major clades of Agaricales: a multilocus phylogenetic overview. Mycologia 98: 982-995

Alignments:


• Agaricales, combined data set, 25S, 18S, 5.8S, 282 taxa
• Agaricales, combined data set, rpb1 A-C, rpb1-intron2, rpb2 5-7, 25S, 18S, and 5.8S rRNA, 250 taxa

• Schoch et al (subm., PDF not yet available) A phylum wide phylogeny of the Ascomycota to address phylogenetic informativeness, ancestral character reconstruction and define novel lineages

Alignments:


• full alignment