Gene fusion and fission events are key mechanisms in the evolution of gene 
architecture, whose effects are visible in protein architecture when they occur 
in coding sequences. Until now, the detection of fusion and fission events has 
been performed at the level of protein sequences with a post facto removal of 
supernumerary links due to paralogy, and often did not include looking for 
events defined only in single genomes. We propose a method for the detection of 
these events, defined on groups of paralogs to compensate for the gene 
redundancy of eukaryotic genomes, and apply it to the proteomes of 12 fungal 
species. We collected an inventory of 1,680 elementary fusion and fission 
events. In half the cases, both composite and element genes are found in the 
same species. Per-species counts of events correlate with the species genome 
size, suggesting a random mechanism of occurrence. Some biological functions of 
the genes involved in fusion and fission events are slightly over- or 
under-represented. As already noted in previous studies, the genes involved in 
an event tend to belong to the same functional category. We inferred the 
position of each event in the evolution tree of the 12 fungal species. The event 
localization counts for all the segments of the tree provide a metric that 
depicts the "recombinational" phylogeny among fungi. A possible interpretation 
of this metric as distance in adaptation space is proposed.