Phylogenetics and Phylogenomics of the Fungal Tree of Life

Abstract

Phylogenetic trees, once restricted to studies on systematics, are now used throughout all disciplines of fungal biology and provide the evolutionary context for a broad suite of studies that include understanding the evolution of major life forms, description of complex biotic communities, and predictive experimental biology. This is especially true in the genomic era, where a rapid convergence of phylogenetics and genomics is occurring and is resulting in the emerging field of phylogenomics. This chapter provides a review of (i) the current status of fungal phylogenetics based on multigene phylogenies, (ii) current evolutionary hypotheses on the evolutionary relationships of organisms that are classified in the Kingdom Fungi, and (iii) the use of genome-scale sampling to infer evolutionary relationships of the fungi. The goal of the Deep Hypha Research Coordination Network was to accelerate the collection of multigene sequence data across the Fungal Tree of Life. By the Fungal Tree of Life, we explicitly refer to the monophyletic Kingdom Fungi (Fungi) and all of its subgroups. One of the more elusive areas of research in fungal phylogenetics has been the calibration of the Fungal Tree of Life to geologic time. Here we focus on the use of genome-scale data sets in phylogenetic analyses. Multigene analyses have had a major impact on phylogenetic studies of the Fungi, resulting in our most thorough understanding of evolutionary relationships of the Kingdom to date.