Scientific Publications
Unsorted homology within locus and species trees.
Systematic biology, 63, 988-92
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, whereas if they arose through speciation they are orthologs. If one of them was transferred from a contemporaneous species, we call them xenologs. 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. 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, such genome-wide data sets not only have unveiled extensive phylogenomic incongruence but have brought back to the spotlight the consideration of how ancestral polymorphisms sort within populations. Altogether, phylogenomic data make imperative the explicit distinction between organismal and gene histories.
Systematic biology, 63, 988-92
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