When homology is applied to genes, at least two fundamentally different subclasses must be distinguished: paralogy, the relationship between genes that have originated by gene duplication; and orthology, which refers to genes that originated by speciation. Phylogenetic reconstructions of organisms created using information from the nucleotide sequences of genes require orthologous, rather than paralogous, genes, so the distinction between these two gene classes is important for practical reasons. More fascinating is the observation that orthologues and paralogues usually have very different evolutionary fates. Orthologues often take over the function of the precursor gene in the species of origin and thus tend to be conserved. In contrast, young paralogues have redundant functions, which is an evolutionarily unstable situation. Thus, in the long run — with a few exceptions — paralogues either diverge functionally, or all but one of the versions is lost.

Although the theoretical definition of orthology seems straightforward, the term is misused or misunderstood in many ways, particularly in developmental biology and genomics. An example is the romantic, but incorrect, idea that every gene in a species' genome has exactly one orthologue in the genome of another species. Genes can be lost during evolution, meaning that a given gene may or may not have surviving orthologues in other species. Moreover, gene duplications can follow a speciation event, generating orthologous 'clades' of paralogues.

Enjoying our latest content?
Log in or create an account to continue

  • Access the most recent journalism from Nature's award-winning team
  • Explore the latest features & opinion covering groundbreaking research
Access through your institution

or

Sign in or create an account
Continue with Google
Continue with ORCiD