Can Single Protein and Protein Family Phylogenies be Resolved Better?

Single gene or protein sequences have been used in protein biology and molecular biology studies to make inferences about the dynamics of evolution of their structure and function. In addition, single gene or protein phylogenies are required input in statistical tests for natural selection or in the determination of sites in proteins that are coevolving. Gene phylogenies using members of a multigene family (the globin genes are a classic example) are important too, because they can decipher the relationships of the members of the overall gene family and can address potential neofunctionalization phenomena [13]. While the issue of how single gene and single proteins contribute to the overall phylogeny of a group of organisms is an important and copiously addressed topic [4-7], the focus here is on the use of gene and protein sequences in single gene studies.