The advent of the genome era and the availability of a growing number of fully-sequenced genomes have changed the way in which biologists study the evolutionary relationships among groups of organisms. For instance, the use of phylogenetics in the context of whole genomes, a field known as phylogenomics 
, allows for the combination of evolutionary signals from various genes into a single tree. It has long been observed that phylogenetic trees built from different genes may provide conflicting topologies. Thus, the use of multiple gene approaches is a way to average out these discrepancies in order to provide a single topology that is expected to reflect the true evolutionary relationships more accurately. In recent years, the use of multi-gene approaches, and especially gene concatenation, is becoming the method of choice in most studies aiming to elucidate the evolutionary relationships among a group of species 
. Such approaches are, however, not free from criticism. For instance, it has been argued that they use the information derived from a small fraction of the genes in a genome and, therefore, cannot represent the actual diversity of evolutionary histories within a genome 
. Indeed, initial genome-wide phylogenetic studies have shown that the topological diversity encountered across a genome is high 
. Besides questioning the validity of species trees, these findings have raised doubts regarding the possible sources for the high topological variability and the implications for large-scale phylogenetic inferences such as the prediction of orthology relationships.
Here we address the question of whether species trees constructed with standard alignment concatenation approaches do fairly represent the topologies that can be found in gene phylogenies across a genome. Conversely, we test whether the topological information found across all genes in a genome can be used to identify conflicting nodes and provide alternative reliability values in species trees. We test these ideas by using molecular data from fungal genomes, the group of eukaryotic organisms that is best sampled in terms of fully sequenced genomes 
. Currently, more than 60 fungal species have been sequenced, including many human pathogens as well as other species of industrial or agricultural interest. This has facilitated that the evolutionary relationships among fungi have been addressed by means of phylogenomic methods, being gene concatenation the most widely used 
. To assess the extent of congruence between trees based on concatenated alignments and individual phylogenies, we compare the topology of phylogenies of genes encoded in the yeast genome with fungal species trees reconstructed from the concatenated alignments of widespread proteins present across different sets of fungal species. Our results show that, despite the large topological diversity of the yeast phylome, most nodes in the species tree do represent genome-wide supported evolutionary relationships. Some conflicting nodes, however, concentrate most of the topological variations found between gene and species trees. We propose to incorporate such information in the tree of life in the form of genome-wide levels of topological support, thereby identifying conflicting nodes. Finally, some of the possible causes for the existing topological diversity within a genome and its implications for orthology prediction are discussed.