Evolutionary History and Divergence Dating in Fungi Using Phylogenomics

The fungal kingdom exhibits vast diversity that has historically challenged the establishment of a stable evolutionary taxonomy. Despite recent advances in fossil calibration and the growing use of horizontal gene transfer events as dating constraints, numerous lineages remain classified as incertae sedis, and discrepancies persist among existing fungal phylogenies. This thesis presents a broad, time-calibrated fungal phylogeny by analysing a dataset of 1,301 taxa. The phylogenetic approach used 119 protein markers, identified using BUSCO and aligned with MUSCLE, to construct a large concatenated supermatrix. Phylogenetic reconstruction was performed using IQ-TREE and high-performance computing resources, enabling large-scale phylogenomic analysis. By integrating extensive taxon sampling with a multi-gene phylogenomic approach, this work provides a broad framework for examining deep evolutionary relationships and contributes to the systematic placement of ambiguous taxa. The results provide insight into the evolutionary history of Fungi and offer a useful basis for future research into their ecological roles and functional diversity.