The original definition of Phylogenomics by Eisen suggested that we use the phylogeny to understand the evolution of gene function. In this sense, phylogenomics is a kind of applied phylogenetics, using species relationships to reconstruct the evolution of genomic traits.
In plants, whole genome duplication (WGD) is common– all flowering plants descend from an ancestor that experienced one or more WGD events. Following these WGD events, plant lineages quickly return to functioning as diploid organisms, but multiple copies of some genes are retained.
In this context we are interested in using genomic techniques to ask the following questions:
- Are gene duplication events clustered on the phylogeny a result of whole genome duplication or several small-scale duplications?
- Is there a functional bias to which genes retain multiple copies following?
- Are gene duplications associated with a relaxation in purifying selection?