Phylogenomics Illuminates the Evolution of the Apicomplexan Phylum
We have developed two new methods for the inference of species trees from genome and EST sequence databases utilising protein domains. The methods we have developed are computationally feasible given modest computing resources. These methods are able to reconstruct deep phyogenies and are ideally suited to inferring species trees for organisms with unannotated genomes and from the results of new sequencing technologies. Application of these methods to the genomes of Apicomplexan parasites has suggested a new model of Plasmodium evolution in which parasites that initially infected mammalian hosts were the subject of a species switch from early primates to reptiles and birds.