Practical Aspects of Sequence-Based Species Delimitation in Fungi

Proper taxonomic assignment can provide a better understanding of the relationships among different fungal species, their interactions with other organisms, and their evolution over time. This, in turn, can provide insight into ecosystem functioning and lead to better management decisions. In recent years, the development of a plethora of molecular tools for fungal identification has spurred a number of studies on species delimitation using sequence-based methods. However, no single method has been shown to be effective in all circumstances, rather a combination of several criteria has been proposed for species delimitation. This chapter aims to provide a brief guide to conducting an integrative sequence-based species delimitation analysis in fungi, from data collection to discussion of results. The methods presented here are used in several taxonomy studies of fungi, although the main protocol steps can be broadly applied to other organisms such as animals and plants. Although species discovery using the DNA-based methods described here should be integrated with other approaches, the use of such molecular methods for species delimitation represents the first step of critical importance in delineating new taxonomic entities in the highly diverse fungal kingdom.