**2.1 The fungal tree of life**

Fungi are poorly documented organisms and the phylogenetic relationships within the kingdom are not yet fully understood, but recent efforts have been shedding light on the evolutionary history of the *Fungi* (James et al., 2006, Hibbet et al., 2007). Traditionally, fungi were classified based on morphological, chemical, and anatomical characters mainly associated with spore-bearing structures (McLaughlin et al 2009). However, molecular approaches revealed the existence of repeated trait evolution and thus the prevalence of artificial groupings in these traditional classifications. Molecular data sets have permitted the development of a more natural classification and a better understanding of the fungal relationships.

In the last decades the mycological community has invested heavily in developing the field of fungal systematics. Two National Science Foundation (NSF) projects contributed to this endeavor: the Deep Hypha Research Coordination Network and the Assembling the Fungal Tree of Life project (AFTOL1). This funding allowed for the sharing of information across the mycological community and the generation of molecular data for seven loci from ~1500

recent concerted efforts to bring fungi to conservation debates, such as the newly created

Fig. 1. A simplified tree of life, showing the relationships between three eukaryotic groups: fungi and animals are sister groups, with plants as their next closest relative. Taken from the

Fungi are poorly documented organisms and the phylogenetic relationships within the kingdom are not yet fully understood, but recent efforts have been shedding light on the evolutionary history of the *Fungi* (James et al., 2006, Hibbet et al., 2007). Traditionally, fungi were classified based on morphological, chemical, and anatomical characters mainly associated with spore-bearing structures (McLaughlin et al 2009). However, molecular approaches revealed the existence of repeated trait evolution and thus the prevalence of artificial groupings in these traditional classifications. Molecular data sets have permitted the development of a more natural classification and a better understanding of the fungal

In the last decades the mycological community has invested heavily in developing the field of fungal systematics. Two National Science Foundation (NSF) projects contributed to this endeavor: the Deep Hypha Research Coordination Network and the Assembling the Fungal Tree of Life project (AFTOL1). This funding allowed for the sharing of information across the mycological community and the generation of molecular data for seven loci from ~1500

Society for the Conservation of Fungi.

tree of life web project (http://tolweb.org/tree/).

**2. Fungi** 

relationships.

**2.1 The fungal tree of life** 

species belonguing to all groups of fungi (McLaughlin et al 2009). The result was the most recent comprehensive classification of the fungal kingdom to date, based on well-supported monophyletic groups (Hibbet et al 2007, fig. 2). This fungal tree of life includes only true fungi, and does not consider non-fungal groups traditionally studied by mycologists, such as Oomycetes and slime molds. It does, however, include microsporidians (unicellular obligate endoparasitic organisms with highly reduced genomes and mithochondria (Peyretaillade et al., 2008)), several lineages of chytrids (flagelatted fungi) and zygomycetes, including the Glomeromycota (obligate symbionts of photoautotrophs that are suggested to have been crucial to the process of land colonization by plants (Pirozynski and Malloch, 1975)).

Around 98% of all described fungal species belong to the subkingdom *Dikarya* composed of *Basidiomycota* and *Ascomycota* (fig. 2). The former includes subphyla *Pucciniomycotina* (rusts, pathogens specialized in infecting plants), *Ustilagomycotina* (true smuts and some yeasts, mostly plant pathogens), and *Agaricomycotina* (including the vast majority of mushroomforming fungi). *Ascomycota*, is also comprised of three subphyla, *Taphrinomycotina* (yeast-like

Fig. 2. The fungal tree of life (adapted from Hibbett et al., 2007 and McLaughlin et al., 2009), showing the higher level clades and the unresolved basal polytomy. The terminations – mycota refer to phyla and –mycotina to subphyla; 'chytrids' and 'zygomycetes' are informal non-monophyletic groups.

Fungal Diversity – An Overview 215

Fig. 3 Examples of agaricoid and gasteroid fruit body morphologies. *Amanita muscaria* (upper left corner), *Armillaria* sp. (upper right corner) and *Macrolepiota* sp. (lower right corner) all agaricoid, showing exposed hymenium and *Astraeus hygrometricus* (lower left

overall fruit body morpohology has not been a stable character across fungal evolution. Soon after this dicovery came the realization that monophyletic groups contain multiple morphologies and that these morphologies appear scattered across clades (Hibbett and Thorn, 2001), indicating that certain fruit body forms evolved multiple times independently

This phenomenon of labile fruit body morphology is not exclusive to the basidiomycetes. Another interesting example comes from a well-preserved fossil ascomycete fruit body. This flask-shaped specimen was named *Paloepyrenomycites devonicus* and classified as a pyrenomycete (*Sordariomycetes*, within the subphylum *Pezizomycotina*; Taylor et al. 1995). However, this fruit body morphology is found in several other groups within the subphylum, making it difficult to rule out the possibility that this fossil belongs to a more basal *Ascomycota* lineage, such as *Taphrinomycotina* (typically members of this clade do not fruit, however some species have open aphotecial fruit bodies), or even an earlier extinct

corner with internal spores. Courtesy of J. Vicente.

(see Hibbett, 2007 for a review on the topic).

and some filamentous fungi), *Saccharomycotina* (the true yeasts), and *Pezizomycotina* (with most of the filamentous and fruit-body producing ascomycetes). There has also been extensive work to understand the arrangement taxa within these higher-level clades, a task complicated by the large numbers of fungal taxa described. As evidenced by fig. 2, the base of the tree is a large polytomy, indicating uncertatinty on the resolution of the earliest branching events.

The results of these iniciatives were a big step forward for mycological research. They provided not only a rigorous overview of the main fungal monophyletic groups, but also a framework for understanding and appreciating the evolution of fungi. Although much has been achieved, accurately reconstructing the fungal tree of life is not an easy task and much research effort must be still gathered in order to resolve the earliy branching history of this group in order to have a clear view on how different groups of fungi relate to each other. AFTOL2, an NSF funded sequel to AFTOL1, is ongoing and targetting the unresolved issues and hypotheses raised during the first phase of the project. These include resolving the basal fungal lineages, including the placement of *Microsporidia* and *Glomeromycota*, as well as resolving key lineages within the *Ascomycota* and *Basidiomycota* needed for understanding the evolution of fungal morphology and ecology (McLaughlin et al., 2009).

The availability of an accurate fungal tree of life allows for not only an appreciation of fungal diversity and evaluation of the fundamental differences across groups, but also an understanding of the evolutionary histories of different lineages that gave rise to the diversity of fungi we see today. For example, estimates point to the split between the *Ascomycota* and *Basidiomycota* having occured ~400 million years ago (Taylor and Berbee, 2006), revealing the ancient nature of the fungal phyla. Reconstructing the timing of such evolutionary events occur can be particularly interesting, allowing for comparisons with diversification patterns in other biological groups and ultimately a more thorough understanding of how life evolves.
