Lateral Gene Transfer, Genome Surveys and the Phylogeny of Prokaryotes.
Doolittle argued that to construct phylogenies, an organism should be regarded as either less or more than the sum of its genes (1). The argument is based on the observation that gene phylogenies are rarely consistent with one another because, among others, of lateral gene transfer (LGT). Creating phylogenies from sequence data in which an organism is described exactly as the sum of its genes is not, however, the only approach (2). Rather than creating phylogenies based on sequence identity for separate genes, this alternative creates a distance-based phylogeny at the genome level by comparing the fraction of genes shared between genomes (2). The resulting phylogeny (Fig. 1) of completely sequenced genomes (for an overview, see http://www.tigr.org/tdb/tdb.html) is remarkably similar to the phylogenies that are based on 16S ribosomal RNA (3). Not only is the trichotomy between Eukarya, Bacteria, and Archaea present, but within each of these taxa the clusters generally recognized as being monophyletic and for which multiple genomes are available, all have high bootstrap values (the Proteobacteria and their branching order, the Spirochaetales, the low (G+C) Gram-positive bacteria, and the Euryarchaeota). This method does not resolve the major branchings of the Bacteria, but neither do the phylogenies based on sequences that do not show LGT resolve this part of Bacterial phylogeny with a high degree of confidence.