Are Signature Proteins the Key to Evaluating Eukaryotic Phylogeny

Eukaryotic Signature Proteins (ESPs) are proteins that delineate the eukaryotes from the archaea and bacteria. They have no readily recognisable homologues in any prokaryotic genome, but their homologues are present in all main branches of eukaryotes. Since ESPs are conserved in all eukaryotes, they are considered to be ancient proteins with a slow rate of evolution. These properties make them theoretically good candidates to analyse the phylogenetic relationships of eukaryotic species. This study examines the possibilities of using ESPs as a special group of proteins in deep phylogenetic analysis. After concatenation of ESP sequences, a phylogenetic tree of 15 mammalian species, and another phylogenetic tree including many divergent eukaryotes was generated to examine how ESPs perform. The latter tree is the longest concatenated sequences to built tree for eukaryotes to date. ESP performed very well for the mammal phylogenetics. The deep eukaryotic tree included some deeply divergent branches but has also showed promising results.