During the course of evolution genes undergo both fusion and fission by which 
ORFs are joined or separated. These processes can amend gene function and 
represent an important factor in the evolution of protein interaction networks. 
Gene fusions have been suggested to be useful characters for identifying 
evolutionary relationships because they constitute synapomorphies or cladistic 
characters. To investigate the fidelity of gene-fusion characters, we developed 
an approach for identifying differentially distributed gene fusions among 
whole-genome datasets: fdfBLAST. Applying this tool to the Fungi, we identified 
63 gene fusions present in two or more genomes. Using a combination of 
phylogenetic and comparative genomic analyses, we then investigated the 
evolution of these genes across 115 fungal genomes, testing each gene fusion for 
evidence of homoplasy, including gene fission, convergence, and horizontal gene 
transfer. These analyses demonstrated 110 gene-fission events. We then 
identified a minimum of three mechanisms that drive gene fission: separation, 
degeneration, and duplication. These data suggest that gene fission plays an 
important and hitherto underestimated role in gene evolution. Gene fusions 
therefore are highly labile characters, and their use for polarizing 
evolutionary relationships, without reference to gene and species phylogenies, 
is limited. Accounting for these considerable sources of homoplasy, we 
identified fusion characters that provide support for multiple nodes in the 
phylogeny of the Fungi, including relationships within the deeply derived 
flagellum-forming fungi (i.e., the chytrids).