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Open Access Highly Accessed Research article

Phylogenomic analyses predict sistergroup relationship of nucleariids and Fungi and paraphyly of zygomycetes with significant support

Yu Liu13, Emma T Steenkamp2, Henner Brinkmann1, Lise Forget1, Hervé Philippe1 and B Franz Lang1*

Author Affiliations

1 Robert Cedergren Centre, Département de biochimie, Université de Montréal, Montréal, Québec, Canada

2 Department of Microbiology and Plant Pathology, Forestry and Agricultural Biotechnology Institute, University of Pretoria, Pretoria, South Africa

3 Present address: Donnelly Centre for Cellular and Bio-molecular Research, Department of Molecular Genetics, University of Toronto, 160 College Street, Toronto, ON, M5S 3E1, Canada

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BMC Evolutionary Biology 2009, 9:272  doi:10.1186/1471-2148-9-272

Published: 25 November 2009



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.


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.


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.