title: A consistent phylogenetic backbone for the fungi.
abstract: The kingdom of fungi provides model organisms for biotechnology, cell biology, genetics, and life sciences in general. Only when their phylogenetic relationships are stably resolved, can individual results from fungal research be integrated into a holistic picture of biology. However, and despite recent progress, many deep relationships within the fungi remain unclear. Here, we present the first phylogenomic study of an entire eukaryotic kingdom that uses a consistency criterion to strengthen phylogenetic conclusions. We reason that branches (splits) recovered with independent data and different tree reconstruction methods are likely to reflect true evolutionary relationships. Two complementary phylogenomic data sets based on 99 fungal genomes and 109 fungal expressed sequence tag (EST) sets analyzed with four different tree reconstruction methods shed light from different angles on the fungal tree of life. Eleven additional data sets address specifically the phylogenetic position of Blastocladiomycota, Ustilaginomycotina, and Dothideomycetes, respectively. The combined evidence from the resulting trees supports the deep-level stability of the fungal groups toward a comprehensive natural system of the fungi. In addition, our analysis reveals methodologically interesting aspects. Enrichment for EST encoded data-a common practice in phylogenomic analyses-introduces a strong bias toward slowly evolving and functionally correlated genes. Consequently, the generalization of phylogenomic data sets as collections of randomly selected genes cannot be taken for granted. A thorough characterization of the data to assess possible influences on the tree reconstruction should therefore become a standard in phylogenomic analyses.
authors: Center for Integrative Bioinformatics Vienna, University of Vienna, Medical University of Vienna, University of Veterinary Medicine Vienna, Vienna, Austria. ingo.ebersberger@univie.ac.at
authors: Ingo
authors: I
authors: Ebersberger
authors: Ricardo
authors: R
authors: de Matos Simoes
authors: Anne
authors: A
authors: Kupczok
authors: Matthias
authors: M
authors: Gube
authors: Erika
authors: E
authors: Kothe
authors: Kerstin
authors: K
authors: Voigt
authors: Arndt
authors: A
authors: von Haeseler
mesh_terms: D001499:Bayes Theorem; D030541:Databases, Genetic; D019143:Evolution, Molecular; D020224:Expressed Sequence Tags; D005658:Fungi / Q000145:classification* / Q000235:genetics*; D016681:Genome, Fungal; D023281:Genomics; D008957:Models, Genetic; D010802:Phylogeny