**3.1 Documenting fungal diversity**

Fungi are cryptic and hyperdiverse organisms that assemble in complex and dynamic communities. For the most part, fungi grow as a network of thin filaments on the substrate (soil, wood, insect guts, living plant parts, etc.) making them difficult to detect. Species that produce spore-bearing structures can be easier to discover, although fruiting periods can be short and fructifications ephemeral. Some species can be cultured *in vitro*, however the vast majority are not amenable to culturing, often leaving mycologists with little to work with experimentally.

Traditionally, taxonomists have been responsible for undertaking the task of uncovering new fungi. Morphological, anatomical, and sometimes chemical characters are the basis for the description of fungal species. Interestingly for new species of fungi to be formally

lineage (Taylor & Berbee, 2006). These doubts make the placement of this fossil into the

Some fungi live in symbiotic associations with photosynthetic partners, obtaining carbohydrates from their symbionts and providing water, nutrients, or protection in return. The two most remarkable types of symbioses involving fungi are lichens and mycorrhizal associations. In lichens fungi associate with green algae or cyanobacteria (or both) to form a vegetative structure called thallus. Lichens are remarkably successful, colonizing all kinds of habitats and regions (Nash, 1996). Lutzoni et al. (2000) used a phylogenetic framework to study the evolution of lichenization in the *Ascomycota* (including most of the lichenized fungi) and found that this life-style arouse early in the evolutionary history of the phylum and that it has been easier for lineages to loose the ability to be lichenized than it is to become lichens. These results led them to conclude that many non-lichenized *Ascomycota* lineages (including important well-known fungi such as *Penicillium* and *Aspergillus*)

Mycorrhizal associations are symbioses involving fungi and plant roots. The mycorrhizal condition is the natural state for most plants under most ecological conditions. Mycorrhizas (the structure constituted by the root and the fungus) are the main organs of nutrient uptake in land plants (Smith & Read, 2008). The evolution of mycorrhizal associations had a tremendous impact on terrestrial ecosystems and is thought to have facilitated the initial colonization of land by plants (Pirozynski & Malloch, 1975). Ectomycorrhizal (ECM) fungi are one of the major groups of mycorrhizal fungi. They are mainly basidiomycetes and associate with about 30 plant families, including oaks, pines, poplars, and dipterocarps (Smith & Read, 2008). A broad phylogenetic analysis of mycorrhizal and free-living mushroom-forming fungi (*Homobasidiomycetes*, within *Agaricomycotina*) revealed that the ancestor of this group was free-living, and that ectomycorrhizal symbioses were lost and gained a number of times within the clade (Hibbett et al., 2001). This means that ectomycorrhizal fungal symbionts have evolved repeatedly from decomposer percursors and that there have been several reversals to this latter stage, with half of all Homobasiomycetes potentially deriving from ectomycorrhizal ancestors. Such findings suggest that although ECM symbioses are widespread and play relevant ecological roles in

Fungi are cryptic and hyperdiverse organisms that assemble in complex and dynamic communities. For the most part, fungi grow as a network of thin filaments on the substrate (soil, wood, insect guts, living plant parts, etc.) making them difficult to detect. Species that produce spore-bearing structures can be easier to discover, although fruiting periods can be short and fructifications ephemeral. Some species can be cultured *in vitro*, however the vast majority are not amenable to culturing, often leaving mycologists with little to work with

Traditionally, taxonomists have been responsible for undertaking the task of uncovering new fungi. Morphological, anatomical, and sometimes chemical characters are the basis for the description of fungal species. Interestingly for new species of fungi to be formally

*Ascomycota* phylogeny difficult and impair its use for calibrating phylogenetic trees.

**2.2.2 The evolution of fungal symbioses** 

descend from lichenized ancestors.

nature, they are an evolutionary unstable mutualism.

**3. Fungal diversity** 

experimentally.

**3.1 Documenting fungal diversity** 

accepted, a Latin diagnosis is still required, as recommended by the International Code of Botanical Nomenclature (McNeil et al., 2006), the code followed by mycologists to name fungi. Describing new species also requires the deposition of voucher specimens in official collections.
