Alignments & Data Sets


Sequence chromatogram of the ITS2 region of the holotype of Hebeloma affine A.H. Sm. from Michigan collected in 1956.

Alignments & Data Sets

Matheny, Hobbs, & Esteve-Raventos (2019) Genera of Inocybaceae: New skin for the old ceremony. In review.

    Data matrices, including tree files.

Matheny & Kudzma (2019) New species of Inocybe (Agaricales) from eastern North America. Journal of the Torrey Botanical Society, in press.

    Data matrices, including tree files.

Swenie, Baroni, & Matheny (2018) Six new species and reports of Hydnum (Cantharellales) from eastern North America. Mycokeys 42: 35-72.

    Data matrices including tree files.

Korotkin et al. (2018) Stable isotope analyses reveal previously unknown trophic mode diversity in the Hymenochaetales. American Journal of Botany 105: 1869-1887.

    Data matrices, including tree files.

Matheny et al. (2018) Revision of pyrophilous taxa of Pholiota described from North America reveals four species - P. brunnescens, P. castanea, P. highlandensis, and P. molesta. Mycologia, in press.

   Data matrices, including tree files

Matheny & Swenie (2018) The Inocybe geophylla group in North America: a revision of the lilac species surrounding I. lilacina. Mycologia 110: 618-634.

    Data matrices, including tree files

Matheny et al. (2017) New species of Auritella (Inocybaceae) from Cameroon, with a worlwide key to the known species. IMA Fungus 8: 305-316.

    Data matrices, including tree files

Matheny et al. (2017) The wild edible mushroom Pleurocollybia cibaria from Peru is a species of Gerhardtia in the Lyophyllaceae. Cryptogamie, Mycologie 38: 205-212.

    Data matrices, including tree file

Pradeep et al. (2016) New and noteworthy species of Inocybe (Agaricales) from tropical India. Mycological Progress 15: article 24.

    Data matrices, incluidng tree files

Kuo & Matheny (2015) Contemporary documentation of the rare eastern North American species  Inocybe insignis (Inocybaceae, Agaricales). MycoKeys 11: 23-31.

    Data matrix, including tree file

Lodge et al (2013) Molecular phylogeny, morphology, pigment chemistry and ecology in Hygrophoraceae (Agaricales). Fungal Diversity 64: 1-99.

    Data matrices, including tree files

Kropp, Matheny & Hutchison (2013) Inocybe section Rimosae in Utah: phylogenetic affinities and new species. Mycologia 105: 728-747.

    Data matrices, including tree files

Matheny, Norvell & Giles (2013) A common new species of Inocybe in the Pacific Northwest with a diagnostic PDAB reaction. Mycologia 105: 436-446.

    Data matrices, including tree files

Ryberg & Matheny (2012) Asynchronous origins of ectomycorrhizal clades of Agaricales. Proceedings of the Royal Society B 279: 2003-2011.

    Perl pipeline for use of nLSU-rRNA sequences with emerencia

    Data matrices

Baroni & Matheny (2011) A re-evaluation of gasteroid and cyphelloid species of Entolomataceae from eastern North America. Harvard Papers in Botany 16: 293-310.

   Alignments, tree files, and gene partition file

Ryberg & Matheny (2011) Incomplete taxon sampling and diversification in a large clade of mushroom-forming fungi. Evolution 65: 1862-1878.

    Alignments and consensus trees

Alvarado et al. (2010) Tubariomyces, a new genus of Inocybaceae from the Mediterranean region. Mycologia 102: 1389-1397.

    Nexus file, PHYLIP file, ML tree file with bootstraps, and gene partition file

Matheny & Pradeep (2010) Auritella foveata, a new species of Inocybaceae (Agricales) from tropical India. Kew Bulletin 67: 119-125.

    Nexus file, PHYLIP file, ML tree file with bootstraps, and gene partition file

Matheny et al. (2010) Craterellus fallax, an endemic Black Trumpet mushroom from eastern North America with a broad host range. Mycorrhiza 20: 569-575.

    Nexus file, ML and MP bootstrap results, and ML tre file

Matheny & Griffith (2010) Mycoparasitism between Squamanita paradoxa and Cystoderma amianthinum (Cystodermateae, Agaricales). Mycoscience 51: 456-461.

    Squamanita_rRNA_alignment [alignment file]

    Squamanita_bipartitions.Squamanita.txt [rRNA Agaricales tree file with ML bootstrap values]

    Cystodermateae_rRNA_alignment [alignment file]

    Cystodermateae_bipartions.Cystodermateae.text [rRNA Cystodermateae tree file with ML bootstrap values]

    Cystoderma_amianthinum_ITS_alignment [alignment file]

    Cystoderma_amianthinum_ITS_bipartitions.txt [ITS Cystoderma amianthinum tree file with ML bootstraps]

Kropp et al (2010) Phylogenetic taxonomy of the Inocybe splendens group and evolution of supersection “Marginatae”. Mycologia 102: 56-573.

    splendens_supermatrix_alignment [alignment file]

    splendens_character_evolution_matrix [file]

Matheny et al (2009) Out of the palaeotropics? Historical biogeography and diversification of the cosmopolitan mushroom family Inocybaceae. Journal of Biogeography 36: 577-592.

    After downloading the XML files in txt format, change the extension to .xml

    Inocybaceae XML file

    Primary calibration XML file

    Inocybaceae_supermatrix_alignment [alignment file]

    Inocybaceae_ancestral_area_analysis [file]

    primary_calibration_alignment [alignment file]