Medina, Edgar M. and Jones, Gary W. and Fitzpatrick, David A. (2011) Reconstructing the Fungal Tree of Life Using Phylogenomics and a Preliminary Investigation of the Distribution of Yeast Prion-Like Proteins in the Fungal Kingdom. Journal of Molecular Evolution, 73 (3-4). pp. 116-133. ISSN 0022-2844

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Abstract

We have used three independent phylogenomic approaches (concatenated alignments, single-, and multi-gene supertrees) to reconstruct the fungal tree of life (FTOL) using publicly available fungal genomes. This is the first time multi-gene families have been used in fungal supertree reconstruction and permits us to use up to 66% of the 1,001,217 genes in our fungal database. Our analyses show that different phylogenomic datasets derived from varying clustering criteria and alignment orientation do not have a major effect on phylogenomic supertree reconstruction. Overall the resultant phylogenomic trees are relatively congruent with one another and successfully recover the major fungal phyla, subphyla and classes. We find that where incongruences do occur, the inferences are usually poorly supported. Within the Ascomycota phylum, our phylogenies reconstruct monophyletic Saccharomycotina and Pezizomycotina subphyla clades and infer a sister group relationship between these to the exclusion of the Taphrinomycotina. Within the Pezizomycotina subphylum, all three phylogenies infer a sister group relationship between the Leotiomycetes and Sordariomycetes classes. However, there is conflict regarding the relationships with the Dothideomycetes and Eurotiomycetes classes. Within the Basidiomycota phylum, supertrees derived from single- and multi-gene families infer a sister group relationship between the Pucciniomycotina and Agaricomycotina subphyla while the concatenated phylogeny infers a poorly supported relationship between the Agaricomycotina and Ustilagomycotina. The reconstruction of a robust FTOL is important for future fungal comparative analyses. We illustrate this point by performing a preliminary investigation into the phyletic distribution of yeast prion-like proteins in the fungal kingdom.

Item Type:	Article
Keywords:	Fungal tree of life; Fungal phylogeny; Supertree; Supermatrix; Markovian clustering; Fungal prions;
Academic Unit:	Faculty of Science and Engineering > Biology
Item ID:	7459
Identification Number:	https://doi.org/10.1007/s00239-011-9461-4
Depositing User:	David Fitzpatrick
Date Deposited:	22 Sep 2016 15:24
Journal or Publication Title:	Journal of Molecular Evolution
Publisher:	Springer Verlag
Refereed:	Yes
Funders:	Health Research Board (HRB)
URI:	http://link.springer.com
Use Licence:	This item is available under a Creative Commons Attribution Non Commercial Share Alike Licence (CC BY-NC-SA). Details of this licence are available here

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