Journal of Phylogenetics & Evolutionary Biology

It is generally believed that since the traits and characteristics exhibited by most organisms are a result of their genetic composition, then all gene trees must be the same as the containing species tree. While both trees appear to present dissimilar results or topologies, even between closely related species, the question most phylogeneticists have been asking is what could be responsible for the lack of congruence between them. Past and recent studies have shown that gene duplication, horizontal transfer and incomplete lineage and/or deep coalescence are factors that play a major role in topological disparity. All these factors can be linked to the fluid nature of genes. To address this issue, phylogeneticists have resorted to building models that can account for gene duplication, horizontal transfer, and incomplete lineage sorting. However, as good as some of these models are, results have shown that the discord between gene and species trees cannot be fully accounted for. In this paper, we describe the factors responsible for species/gene trees disparity and some of the different model approaches that have been proposed to solve them.