Ancient horizontal gene transfer

Ancient horizontal gene transfer (HGT) is the transfer of genes between the three domains of life: the Archaea, the Bacteria and the eukaryotes. Ancient HGT seems to have been a main force in organism evolution because examples of gene transfers exist for many combinations of species of Archaea, Bacteria and eukaryotes. The extent of HGT and the mechanisms surrounding it are still open to debate because there are no broadly occurring extant examples of inter-domain gene transfers. To many researchers, ancient HGT has seriously challenged the concept of the universal tree of life. Methods for detecting HGT include phylogenetic analysis, nucleotide composition analysis, analysis of gene distributions and homology analysis. Phylogenetic analysis remains the best method for establishing the occurrence of ancient HGT, although there are caveats about the methodology and the limited availability of sequence data from evolutionarily pivotal groups. Homology analysis of HGT, based on the comparisons of BLAST scores, can lead to overestimates or incorrect assignment of HGT events. Phylogenetic analyses based on whole-genome data generally support the basic tenets of the universal tree of life. The monophyly of the three domains of life is supported by proteins that show a closer evolutionary relationship between the Archaea and the eukaryotes. Eukaryotic genes that are similar to their bacterial counterparts might have evolved as a consequence of endosymbiotic events that evidently led to the evolution of organelles, such as mitochondria and plastids. However, many genes involved in mitochondrial or chloroplast maintenance did not evolve from putative bacterial endosymbionts (α-proteobacteria and cyanobacteria, respectively). New genomic data, in particular from protists that have secondarily lost their mitochondria, will show the extent of ancient HGT.