Getting Started in Gene Orthology and Functional Analysis
Figure 2
Phylogeny-based ortholog group construction.
(a) On the upper left panel, a tree delineates the phylogenetic relationships among six species, A–F. Below the species tree, a phylogenetic tree is shown, which includes ten genes taken from the six species. The right panel shows the tree after reconciliation, which is the process of comparing the gene tree with the species tree to date evolutionary events like duplication and deletion. For the reconciled tree, the dashed thick lines represent the species tree as the same as the one on the upper left panel, and solid lines indicate the reconciled gene tree. Three duplication events are dated. Duplication D1 occurs after the speciation of species A and B. D2 occurs before speciation of C and D, and D3 occurs before CD and EF. According to current tree analysis algorithms, functional partition points will be at D2 and D3. (b) Gene duplication close to leaf nodes does not necessarily result in function divergence. The schematic shows the evolutionary history of the same gene, with the only difference that the tree includes five closely related species of B, instead of one, where duplication D1 occurs before speciation of the five B species. D1 is so recent that it is hard to estimate if there will be subfunctionalization/neofunctionalization. It might result in “in-paralogs” where duplicated genes in all five B species have the same function. D2 and D3 are duplications that happened a long time ago. If paralogs due to D2 and D3 are present in most descendant species, there is a higher chance for them to have diverged biological functions.