Data from: 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-wide data sets not only have unveiled extensive
phylogenomic incongruence (Jeffroy, Brinkmann, et al. 2006; Salichos and
Rokas 2013) but have brought back to the spotlight the consideration of
how ancestral polymorphisms sort within populations (Edwards 2009).
Altogether, phylogenomic data makes imperative the explicit distinction
between organismal and gene histories.