Response to Comment on "A Green Algal Apicoplast Ancestor"

We suggested lateral transfer of split cox2a and cox2b genes from a chlorophyte algal ancestor to an apicomplexan ancestor (1). Waller et al. (2) oppose this interpretation based on a phylogeny implying close affiliation of apicomplexan cox2a and cox2b genes with ciliate cox2 homologues; a 900-bp insertion that separates the corresponding domains in ciliate mitochondrial cox2 genes; and low hydrophobicity values for ciliate mitochondrial COXII and apicomplexan COXIIA and COXIIB subunits. They suggest that mitochondrial cox2 genes were split and transferred to the nuclei of the apicomplexan and chlorophyte ancestors during independent events.