A consistent phylogenetic backbone for the fungi Journal Article

Author(s): Ebersberger, Ingo; de Matos Simoes, Ricardo; Kupczok, Anne; Gube, Matthias; Kothe, Erika; Voigt, Kerstin; von Haeseler, Arndt
Article Title: A consistent phylogenetic backbone for the fungi
Affiliation IST Austria
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.
Keywords: consistency; dothideomycetes; ests; fungi; opisthokonts; phylogenomics; selection bias
Journal Title: Molecular Biology and Evolution
Volume: 29
Issue 5
ISSN: 0737-4038
Publisher: OUP  
Date Published: 2012-05-01
Start Page: 1319
End Page: 1334
Copyright Statement: CC BY-NC 3.0
Sponsor: This work was supported by the Wiener Wissenschafts-, Forschungs- und Technologie Fonds (WWTF) and from the DFG priority program SPP 1174 Deep Metazoan Phylogeny (grant HA 1628/9-2 to A.v.H.).
DOI: 10.1093/molbev/msr285
Open access: yes (OA journal)