Faheema Kalsoom Khan: The Origin and Diversification of Ectomycorrhizal Fungi

Abstract

Ectomycorrhiza (ECM) is a symbiotic relationship between fungi and plants, which is essential for many woody plants. ECM fungi have evolved independently multiple times in several lineages from saprotrophic ancestors. However, the origin and diversification processes of ECM lineages are still not well understood. In Paper I, we addressed whether ECM lineages evolved independently or if reversals to saprotrophy occurred. These hypotheses were tested using model-based methods and a phylogeny based on 2 174 ECM taxa. We concluded that our inferences about ECM evolution are affected by whether a rate shift in different time periods or ECM clades is allowed, and that reversals to saprotrophy are probably rare. In Paper II, I investigated whether the ECM-linked genomic changes occurred abruptly at the transition to the ECM lifestyle or were part of a trend before or after the transition in ECM lineages. I compared 26 genomes from ECM species in Inocybaceae with six saprotrophic outgroups. The findings suggest that the molecular changes, important for transition to the ECM lifestyle, occur in proximity to the origin of this lifestyle in Inocybaceae. In Paper III, I explored whether genomic diversity in ECM lineages is shaped by independent transitions or due to diversification within each lineage. I compiled a phylogenetically diverse dataset of 75 genomes, representing eight ECM lineages. The findings show that while genomic diversity from lineage-level additions quickly saturates for all enzyme groups investigated, species-level additions continue to contribute new diversity beyond the limits of our dataset. In Paper IV, we tested the mutual exclusivity of psilocybin and muscarine in Inocybaceae species by screening 21 samples. I also explored the origin and evolution of genes involved in psilocybin production in these species using 24 genomes. We detected both psilocybin and muscarine, for the first time, in a single species of Inocybaceae and also concluded that the psilocybin gene cluster has evolved through convergent evolution, with two possible origins of the gene cluster within the family. Overall, this thesis contributes to improving our understanding of ECM fungal evolution and highlights how traits that appear alike can emerge through distinct evolutionary processes.