Estimation of Phylogenetic Inconsistencies in the Three Domains of Life

Discrepancies in phylogenetic trees of bacteria and archaea are often explained as lateral gene transfer events. However, such discrepancies may also be due to phylogenetic artifacts or orthology assignment problems. A first step that may help to resolve this dilemma is to estimate the extent of phylogenetic inconsistencies in trees of prokaryotes in comparison with those of higher eukaryotes, where no lateral gene transfer is expected. To test this, we used 21 proteomes each of eukaryotes (mainly opisthokonts), proteobacteria, and archaea that spanned equivalent levels of genetic divergence. In each domain of life, we defined a set of putative orthologous sequences using a phylogenetic-based orthology protocol and, as a reference topology, we used a tree constructed with concatenated genes of each domain. Our results show, for most of the tests performed, that the magnitude of topological inconsistencies with respect to the reference tree was very similar in the trees of proteobacteria and eukaryotes. When clade support was taken into account, prokaryotes showed some more inconsistencies, but then all values were very low. Discrepancies were only consistently higher in archaea but, as shown by simulation analysis, this is likely due to the particular tree of the archaeal species used here being more difficult to reconstruct, whereas the trees of proteobacteria and eukaryotes were of similar difficulty. Although these results are based on a relatively small number of genes, it seems that phylogenetic reconstruction problems, including orthology assignment problems, have a similar overall effect over prokaryotic and eukaryotic trees based on single genes. Consequently, lateral gene transfer between distant prokaryotic species may have been more rare than previously thought, which opens the way to obtain the tree of life of bacterial and archaeal species using genomic data and the concatenation of adequate genes, in the same way as it is usually done in eukaryotes.