Unsorted homology within locus and species trees

The concept of homology lies at the root of evolutionary biology. Since the seminal work of Fitch (1970) three main categories of homology relationships have been defined at the molecular level: orthology, paralogy and xenology. In brief, if two gene copies arose by duplication they are paralogs, while if they arose via speciation they are orthologs. If one of them was transferred from a contemporaneous species, we call them xenologs (Fig. S1 in doi: ; see Gray and Fitch 1983; Fitch 2000). Indeed, these terms were coined under a phylogenetic framework in which species were represented by single individuals, and as such they have remained very much intact during the last four decades –although particular cases within these categories have received specific names (Mindell and Meyer 2001). However, advances in sequencing technology have changed the field, and it is now very common to collect data sets containing multiple gene loci and/or multiple individuals per species. In general, genome...