  The haloarchaea are aerobic, heterotrophic, photophosphorylating prokaryotes,
whose supposed closest relatives and ancestors, the methanogens, are
CO2-reducing, anaerobic chemolithotrophs. Using two available haloarchaeal
genomes we firstly confirmed the methanogenic ancestry of the group and then
investigated those individual genes in the haloarchaea that differ in their
phylogenetic signal to this relationship. We found that almost half the genes,
about which we can make strong statements, have bacterial ancestry and are
likely a result of multiple horizontal transfer events. Futhermore their
functions specifically relate to the phenotypic changes required for a
chemolithotroph to become a heterotroph. If this phylogenetic relationship is
correct, it implies the development of the haloarchaeal phenotype was among the
most extreme changes in cellular physiology fuelled by horizontal gene
transfer.
