title: Phylogenomic analyses predict sistergroup relationship of nucleariids and fungi and paraphyly of zygomycetes with significant support.
abstract: BACKGROUND
  Resolving the evolutionary relationships among Fungi remains challenging because of their highly variable evolutionary rates, and lack of a close phylogenetic outgroup. Nucleariida, an enigmatic group of amoeboids, have been proposed to emerge close to the fungal-metazoan divergence and might fulfill this role. Yet, published phylogenies with up to five genes are without compelling statistical support, and genome-level data should be used to resolve this question with confidence.
  
  
  RESULTS
  Our analyses with nuclear (118 proteins) and mitochondrial (13 proteins) data now robustly associate Nucleariida and Fungi as neighbors, an assemblage that we term 'Holomycota'. With Nucleariida as an outgroup, we revisit unresolved deep fungal relationships.
  
  
  CONCLUSIONS
  Our phylogenomic analysis provides significant support for the paraphyly of the traditional taxon Zygomycota, and contradicts a recent proposal to include Mortierella in a phylum Mucoromycotina. We further question the introduction of separate phyla for Glomeromycota and Blastocladiomycota, whose phylogenetic positions relative to other phyla remain unresolved even with genome-level datasets. Our results motivate broad sampling of additional genome sequences from these phyla.
authors: Robert Cedergren Centre, Département de biochimie, Université de Montréal, Montréal, Québec, Canada. yuliu2001ca@yahoo.ca
authors: Yu
authors: Y
authors: Liu
authors: Emma T
authors: ET
authors: Steenkamp
authors: Henner
authors: H
authors: Brinkmann
authors: Lise
authors: L
authors: Forget
authors: Hervé
authors: H
authors: Philippe
authors: B Franz
authors: BF
authors: Lang
mesh_terms: D004271:DNA, Fungal / Q000235:genetics; D004272:DNA, Mitochondrial / Q000235:genetics; D019143:Evolution, Molecular; D020224:Expressed Sequence Tags; D005658:Fungi / Q000145:classification / Q000235:genetics*; D015723:Gene Library; D016681:Genome, Fungal; D010802:Phylogeny; D017422:Sequence Analysis, DNA
chemical_list: D004271:DNA, Fungal; D004272:DNA, Mitochondrial