The Fungal Tree of Life: from Molecular Systematics to Genome-Scale Phylogenies

Abstract

The kingdom Fungi is one of the more diverse clades of eukaryotes in terrestrial ecosystems, where they provide numerous ecological services ranging from decomposition of organic matter and nutrient cycling to beneficial and antagonistic associations with plants and animals. The evolutionary relationships of the kingdom have represented some of the more recalcitrant problems in systematics and phylogenetics. The advent of molecular phylogenetics, and more recently phylogenomics, has greatly advanced our understanding of the patterns and processes associated with fungal evolution, however. In this article, we review the major phyla, subphyla, and classes of the kingdom Fungi and provide brief summaries of ecologies, morphologies, and exemplar taxa. We also provide examples of how molecular phylogenetics and evolutionary genomics have advanced our understanding of fungal evolution within each of the phyla and some of the major classes. In the current classification we recognize 8 phyla, 12 subphyla, and 46 classes within the kingdom. The ancestor of fungi is inferred to be zoosporic, and zoosporic fungi comprise three lineages that are paraphyletic to the remainder of fungi. Fungi historically classified as zygomycetes do not form a monophyletic group and are paraphyletic to Ascomycota and Basidiomycota. Ascomycota and Basidiomycota are each monophyletic and collectively form the subkingdom Dikarya.

Clarifying the Relationships between Microsporidia and Cryptomycota

“…Taxonomic circumscriptions of Rozellomycota and, particularly, Cryptomycota, vary significantly (see Berbee et al 2017; Spatafora et al 2017;Richards et al 2017; and examples cited throughout this study). Some authors include aphelids within Cryptomycota (e.g.…”

“…Rozella species are zoosporic biotrophic parasites of oomycetes, chytrids, and Blastocladiomycota (Spatafora et al. ). Increased attention has recently been given to a large diversity of lineages shown by phylogenetic analyses including environmental sequences to be related to Microsporidia, rozellids, and aphelids.…”

“…Microsporidia are known primarily as parasites of invertebrates and vertebrates (including humans), but are also known as endosymbionts of ciliates (Fokin 2012;Fokin et al 2008), and hyperparasites in protists: metchnikovellids are parasites of gregarines, protistan gut symbionts of many invertebrates, and Hyperspora aquatica is a hyperparasite of the paramyxid Marteilia cochillia, a serious pathogen of European cockles (Stentiford et al 2017). Rozella species are zoosporic biotrophic parasites of oomycetes, chytrids, and Blastocladiomycota (Spatafora et al 2017). Increased attention has recently been given to a large diversity of lineages shown by phylogenetic analyses including environmental sequences to be related to Microsporidia, rozellids, and aphelids.…”

The origin and evolution of mycorrhizal symbioses: from palaeomycology to phylogenomics

“…The origin of modern fungus–plant associations, or at least of the evolutionary potential for such relationships, was probably established in the last common ancestor of Mucoromycotina and Glomeromycotina (Spatafora et al ., ), but the extent to which this ancestor would resemble its modern relatives remains an open question. The ubiquity and importance of Glomeromycotina have been understood for some time, but the significance of the Mucoromycontina in mycorrhizal symbioses has only recently been established.…”

“…Mucoromycotina resemble Glomeromycotina in having aseptate hyphae, endosymbiotic bacteria and asexual reproduction by chlamydospores, but they differ principally in having a broader ecology (i.e. saprotrophs, endomycorrhizal and ectomycorrhizal species) and, for some species, the ability to grow in vitro and develop sexually (Spatafora et al ., , ). By contrast, Glomeromycotina are considered as asexual (however, this view has recently been challenged; Riley et al ., ) – and they are strict AM biotrophs on plants (or cyanobacteria; Schüßler, ).…”