Abstract
AbstractFungi are abundant in the biosphere. They have fascinated mankind as far as written history goes and have considerably influenced our culture. In biotechnology, cell biology, genetics, and life sciences in general fungi constitute relevant model organisms. Once the phylogenetic relationships of fungi are stably resolved individual results from fungal research can be combined into a holistic picture of biology. However, and despite recent progress, the backbone of the fungal phylogeny is not yet fully resolved. Especially the early evolutionary history of fungi and the order or below-order relationships within the ascomycetes remain uncertain. Here we present the first phylogenomic study for a eukaryotic kingdom that merges all publicly available fungal genomes and expressed sequence tags (EST) to build a data set comprising 128 genes and 146 taxa. The resulting tree provides a stable phylogenetic backbone for the fungi. Moreover, we present the first formal supertree based on 161 fungal taxa and 128 gene trees. The combined evidences from the trees support the deep-level stability of the fungal groups towards a comprehensive natural system of the fungi. They indicate that the classification of the fungi, especially their alliance with the Microsporidia, requires careful revision. Our analysis is also an inventory of present day sequence information for the fungi. It provides insights into which phylogenenetic conclusions can and which cannot be drawn from the current data and may serve as a guide to direct further sequencing initiatives. Together with a comprehensive animal phylogeny, we provide the second of three pillars to understand the evolution of the multicellular eukaryotic kingdoms, fungi, metazoa, and plants, in the past 1.6 billion years.
Highlights
Molecular data have proven useful to complement, and sometimes overrule, morphological evidences in attempts to re-classify the fungi[3]
expressed sequence tags (EST) data were proven useful for phylogenetic studies[7, 17, 18]
We computed a supertree based on 128 gene trees (Supplementary Fig. 2)
Summary
All available (as of July 2008) Expressed Sequence Tags (ESTs) from fungi and annotated gene sets from all fungal genome sequences were downloaded from the public databases (Supplementary Table 1). Phylogenetic trees were computed from the concatenated alignments (supermatrix) with RaXML27 and with PhyloBayes[28]. Gene trees were computed from the individual alignments with RaXML and were used for Matrix Representation with Parsimony supertree reconstruction[29, 30]. The backbone of the phylogeny as inferred from two supermatrix approaches (maximum likelihood, Bayesian) and a supertree approach. Denotes different branching pattern, n.a. denotes clades that are represented by a single taxon in the supermatrix approaches. The deep-level maximum likelihood phylogeny of the fungi. S. et al A higher-level phylogenetic classification of the Fungi. Y. et al A molecular phylogeny of the flagellated fungi (Chytridiomycota) and description of a new phylum (Blastocladiomycota). RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models.
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