It is now the turn for printed versions! You can find our penultimate paper in the current version of Systematic Biology (November 2014) . Here we show how classical homology categories can fail to describe homology relationships when we consider the effect of incomplete lineage sorting (ILS). In order to comprehensively describe these situations we had to rely in a three-tree representation (gene, locus and species trees), which points out the importance of considering the different phylogenetic layers to fully understand how evolution works.
From a pragmatic point of view, we also demonstrate how these situations can easily mislead commonly used parsimony reconciliation approaches, pointing out the need of quickly adopting the newest methodologies.
Last but not least, we consequently proposed a revised terminology describing the different homology categories (and subcategories).
Diego Mallo, Leonardo De Oliveira Martins and David Posada (2014). Unsorted Homology within Locus and Species Trees. Systematic Biology, 63: 988-992, doi: 10.1093/sysbio/syu050