Chapter 6 - Molecular Ecology

Abstract

Research on fungal diversity, ecology and evolution increasingly involves molecular methods. Using nucleic acid sequence data, otherwise undetectable fungi present in environmental samples can be identified and assigned phylogenetically. Diagnostic PCR can detect human and crop pathogens present at very low levels. The rapid rate at which new fungal taxa are being discovered in the environment by high-throughput sequencing and bioinformatics requires reassessment of traditional protocols for naming and classifying species. In ecological studies, sequence-based methods, alongside imaging and isotope-based analyses, can help to identify fungi with important roles in ecosystem processes including carbon and mineral cycling. The metagenome and metatranscriptome of a habitat provide information about all the fungal species present and their gene expression. Comparative genomics across a range of species reveals the gene evolution underlying niche adaptation. Molecular clock analyses of comparative genomic data suggest that mechanisms of lignocellulose decay evolved alongside angiosperm and gymnosperm plants.