title: A phylum-level phylogenetic classification of zygomycete fungi based on genome-scale data.
abstract: Zygomycete fungi were classified as a single phylum, Zygomycota, based on sexual reproduction by zygospores, frequent asexual reproduction by sporangia, absence of multicellular sporocarps, and production of coenocytic hyphae, all with some exceptions. Molecular phylogenies based on one or a few genes did not support the monophyly of the phylum, however, and the phylum was subsequently abandoned. Here we present phylogenetic analyses of a genome-scale data set for 46 taxa, including 25 zygomycetes and 192 proteins, and we demonstrate that zygomycetes comprise two major clades that form a paraphyletic grade. A formal phylogenetic classification is proposed herein and includes two phyla, six subphyla, four classes and 16 orders. On the basis of these results, the phyla Mucoromycota and Zoopagomycota are circumscribed. Zoopagomycota comprises Entomophtoromycotina, Kickxellomycotina and Zoopagomycotina; it constitutes the earliest diverging lineage of zygomycetes and contains species that are primarily parasites and pathogens of small animals (e.g. amoeba, insects, etc.) and other fungi, i.e. mycoparasites. Mucoromycota comprises Glomeromycotina, Mortierellomycotina, and Mucoromycotina and is sister to Dikarya. It is the more derived clade of zygomycetes and mainly consists of mycorrhizal fungi, root endophytes, and decomposers of plant material. Evolution of trophic modes, morphology, and analysis of genome-scale data are discussed.
authors.affiliation: Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon 97331 spatafoj@oregonstate.edu.
authors.forename: Joseph W
authors.initials: JW
authors.lastname: Spatafora
authors.affiliation: Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon 97331.
authors.forename: Ying
authors.initials: Y
authors.lastname: Chang
authors.affiliation: Department of Plant Pathology, University of Florida, Gainesville, Florida 32611.
authors.forename: Gerald L
authors.initials: GL
authors.lastname: Benny
authors.affiliation: Department of Plant Pathology, University of Florida, Gainesville, Florida 32611.
authors.forename: Katy
authors.initials: K
authors.lastname: Lazarus
authors.affiliation: Department of Plant Pathology, University of Florida, Gainesville, Florida 32611.
authors.forename: Matthew E
authors.initials: ME
authors.lastname: Smith
authors.affiliation: Department of Botany, University of British Columbia, Vancouver, British Columbia, V6T 1Z4 Canada.
authors.forename: Mary L
authors.initials: ML
authors.lastname: Berbee
authors.affiliation: Department of Plant, Soil, and Microbial Sciences, Michigan State University, East Lansing, Michigan 48824.
authors.forename: Gregory
authors.initials: G
authors.lastname: Bonito
authors.affiliation: Department of Biology, University of Ottawa, Ottawa, Ontario, K1N 6N5 Canada.
authors.forename: Nicolas
authors.initials: N
authors.lastname: Corradi
authors.affiliation: US Department of Energy (DOE) Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, California 94598.
authors.forename: Igor
authors.initials: I
authors.lastname: Grigoriev
authors.affiliation: L.F. Lambert Spawn Co., Coatesville, Pennsylvania 19320.
authors.forename: Andrii
authors.initials: A
authors.lastname: Gryganskyi
authors.affiliation: Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, Michigan 48103.
authors.forename: Timothy Y
authors.initials: TY
authors.lastname: James
authors.affiliation: Mycotoxin Prevention and Applied Microbiology Research Unit, NCAUR-ARS-USDA, 1815 N. University Street, Peoria, Illinois 61604.
authors.forename: Kerry
authors.initials: K
authors.lastname: O'Donnell
authors.affiliation: School of Life Sciences, Arizona State University, Tempe, Arizona 85287.
authors.forename: Robert W
authors.initials: RW
authors.lastname: Roberson
authors.affiliation: Department of Ecology and Evolutionary Biology, and Natural History Museum and Biodiversity Research Center, University of Kansas, Lawrence, Kansas 66045.
authors.forename: Thomas N
authors.initials: TN
authors.lastname: Taylor
authors.affiliation: Biology Department, Box 90338, Duke University, Durham, North Carolina 27708.
authors.forename: Jessie
authors.initials: J
authors.lastname: Uehling
authors.affiliation: Biology Department, Box 90338, Duke University, Durham, North Carolina 27708.
authors.forename: Rytas
authors.initials: R
authors.lastname: Vilgalys
authors.affiliation: Department of Biological Sciences, Boise State University, Boise, Idaho 83725.
authors.forename: Merlin M
authors.initials: MM
authors.lastname: White
authors.affiliation: Department of Plant Pathology & Microbiology and Institute for Integrative Genome Biology, University of California-Riverside, Riverside, California 92521.
authors.forename: Jason E
authors.initials: JE
authors.lastname: Stajich
mesh_terms: D005658:Fungi / Q000145:classification* / Q000235:genetics*; D016681:Genome, Fungal; D010802:Phylogeny
keywords: Entomophthoromycotina; Glomeromycotina; Kickellomycotina; Mortierellomycotina; Mucoromycota; Mucoromycotina; Zoopagomycota Zoopagomycotina; fungi; paraphyly; systematics