Fungal phylogeny reconstructed using heterogeneous models reveals new placement of Microsporidia

Abstract

AbstractFungi have significant impacts on global ecosystems, playing roles in organic matter decomposition, as disease agents, as well as having both positive and negative economic effects. Fungal evolutionary history remains partly unresolved with the presence on manyincertae sedisclades, lacking a robust placement on the fungal phylogenetic tree. Some of the more problematic groups whose placement remains unclear are the intracellular parasitesMicrosporidiaand Cryptomycota, both of whom have accelerated rates of nucleotide substitution and reduced genomes, which makes the resolution of these groups hard. In this project we used tree and data heterogeneous models, that can account for different substitution rates between different protein families as well as different parts of the phylogenetic tree, to reconstruct the phylogeny. We recovered a well-supported topology for much of the fungal phylogeny as well as a robust placement for bothMicrosporidiaand Cryptomycota, the former being rooted deeply within the fungi and the latter a placement on a sister branch to the fungi.