Traditional methods alone often make it difficult to identify isolates to species level. Armillaria and Cylindrocladium are examples where new technologies could achieve this quickly and reliably. Rapid identification of pathogens is of great importance in their control, especially when dealing with quarantine organisms where detection of pathogens at early stages is critical.

Over the past decade the use of molecular techniques has provided new ways to study old questions about how ectomycorrhizal fungi interact with each other and their environment. In their simplest form, these methods enable researchers to identify vegetative stages of fungi that would be difficult, slow, or impossible to identify by morphological or culture-based methods. This has resulted in quantitative views of complex fungal communities, which in turn have revealed new and unexpected patterns in community structure. In addition, molecular methods have been used to identify individual genotypes of fungi. This information has provided insights into the way that particular species of ectomycorrhizal fungi spread in nature. In this article we will mention the basic techniques and briefly discuss some of the findings that have resulted. Advances in this field have recently been comprehensively reviewed for scientific audiences, and we refer readers that have a more technical interest or a need to access the current literature to these reviews (Dahlberg, 2001; Horton & Bruns, 2001).

The study of the evolutionary history of organisms by tracing them to common ancestors is known as phylogenetics. Over the last 20 years or so, the increasingly widespread availability of molecular data has seen the blossoming of methodologies for converting DNA information to evolutionary trees and networks. This article will attempt to give an overview of some of the methods that are available, covering data types, considerations for their use, and methods by which evolutionary ancestry can be reconstructed. Where relevant, the text will include examples of the use of these methodologies for the obligately biotrophic plasmodiophorids.

The paper outlines the impact of molecular biology on the identification and detection of fungi and fungus-like micro-organisms. We have tried to use as little jargon as possible but avoiding it completely is very difficult. The article is centred around the ‘pseudofungus’ Phytophthora and its closest relatives, because that is the micro-organism with which we have had most experience. Nevertheless, most of the approaches and techniques mentioned are applicable to any fungus or fungus-like organism and, in that broader sense, the article should be of interest to those with no special interest in or knowledge of Phytophthora.

This article reviews the current state of knowledge about the evolutionary history of lichenized ascomycetes within an integrated system of all ascomycetes. Substantial progress has been made since molecular techniques were applied to unravel evolutionary relationships. Molecular approaches detect how often the lichen symbiosis arose, test current classification concepts, and find the proper placement for species with uncertain relationships. Uncertainties in some evolutionary hypotheses still need to be resolved by studying further genes. The currently available phylogenetic trees show a number of convergent phenotypic developments in lichenized ascomycetes. The current classification of ascomycetes is reviewed in the light of recent molecular data.

Some fungi are found only in specific geographical regions. The human pathogen Paracoccidioides brasiliensis has only rarely been isolated in nature and incidences of infections are restricted to Central and Southern America. Most commonly infected individuals are not urban dwellers, but rather farmers and people living in mountainous areas. In addition, it is almost invariably males who are infected. The gender bias has been reported as between 10 - 20:1 males over females! A possible explanation for this astonishing and unique phenomenon is given below. P. brasiliensis is the causative agent of paracoccidioidomycosis, a human systemic mycosis for which the portal of entry of the fungus is via inhalation of air-borne propagules into the respiratory tract. After entering the host, the fungus converts spontaneously to its yeast form, a fundamental step for the successful establishment of the infection.