Analysis of Amplified Fragment Length Polymorphisms (AFLP) in a sample population of Epichloë and Neotyphodium was conducted
to evaluate the usefulness of this technique in estimating phylogenetic relationships among these fungi. A total of 963 unique
restriction fragments were identified with 13 selective primer combinations. Neighbour-joining and parsimony analysis produced
phylogenetic trees with high bootstrap support. All Epichloë festucae isolates were monophyletic, and clades of E. festucae were
identified that correspond to the host species from which they were isolated. These groups may indicate the importance of
coevolution in the development of the fine fescue-E. festucae symbiosis. The grouping of E. festucae isolates from hard fescue and
Chewings fescue into one clade conflicts with the current taxonomy of these host grasses. Sequencing of ribosomal DNA spacer
regions ITS1 and ITS2 was conducted for comparisons to the phylogenetic relationships estimated by AFLP. Using the maximum
likelihood test, a significant difference was detected between AFLP and rDNA trees due to discrepancies in the association of
anamorphs (Neotyphodium) and teleomorphs (Epichloë). This discrepancy may be due to some mechanism of genetic recombination,
such as hybridization or parasexual recombination, that occurs in Neotyphodium populations. It is concluded that AFLP markers are
useful for producing meaningful phylogenies among a diverse group of fungi and for identifying groups of closely related
individuals that are genetically and biologically similar. Further investigation is needed to determine how AFLP markers change over
short periods of time in populations and over evolutionary time.