The effect of gene duplication on homology

Genes related by gene duplication within an organism's evolutionary lineage are termed paralogues; genes related by speciation are orthologues. It is generally agreed that orthologous genes must be compared when using DNA sequences to reconstruct the evolutionary history of organisms. There is an important exception: information from paralogous genes can reveal the root position of a phylogenetic tree. The duplicated rDNA genes of arrow worms provide an example. Gene duplication is also relevant when comparing gene expression between taxa; for example, when trying to identify homologous roles of genes. When gene duplication occurred after lineage divergence, single orthologues no longer exist, and comparison is complicated. This is a particular problem when comparing roles of vertebrate and invertebrate genes. Amphioxus and ascidian genes can be useful in such situations, since they diverged before extensive gene duplication in the vertebrate lineage. Using Otx and Pax as examples, I show how examination of amphioxus or ascidian genes reveals patterns of gene divergence after duplication, assisting the identification of homologous gene functions. Given the problems of comparing duplicated genes between species, the time is ripe for the introduction of additional terminology to elaborate on the concepts of paralogy and orthology.