Evolution of proteins and proteomes: a phylogenetics approach

The study of evolutionary relationships among protein sequences was one of the first applications of bioinformatics. Since then, and accompanying the wealth of biological data produced by genome sequencing and other high-throughput techniques, the use of bioinformatics in general and phylogenetics in particular has been gaining ground in the study of protein and proteome evolution. Nowadays, the use of phylogenetics is instrumental not only to infer the evolutionary relationships among species and their genome sequences, but also to reconstruct ancestral states of proteins and proteomes and hence trace the paths followed by evolution. Here I survey recent progress in the elucidation of mechanisms of protein and proteome evolution in which phylogenetics has played a determinant role.