The sequencing of complete genomes of archaea,
bacteria, and eukaryotes has clearly “shaken the tree of
life” (Pennisi, 1998). The concept that organelles in
eukaryotes arose from endosymbiotic capture (Margulis,
1970) actually represents a large scale gene transfer event.
rRNA phylogeny had endorsed a tree that included a
primordial progenitor that gave rise to bacteria, and then
later a second branch which diverged into eucarya and
archaea. However, new evidence suggests that both
bacterial and archeal genes are showing up in eukaryotes
(Pennisi, 1998). Additionally, archaea have many
eukaryotic traits (Doolittle and Logsdon, 1998). It now
appears that early organisms stole genes from branch to
branch, either from food or swapping genes with neighbors.
Thus, it is difficult to make sense of phylogenies because
of all the gene swapping, and different phylogenies are
obtained depending on what genes are examined. For
example, the archaea look fairly homogeneous in terms of
16S rRNA phylogenies, but the CTP synthetase gene
spread archaea amongst all other organisms evaluated
(Penninsi, 1998). The spirochaete Treponema palladium
contains two Archeal ATPases.