Evidence for lateral gene transfer (LGT) contradicted earlier theories that bacteria evolve clonally, with daughters only inheriting genetic material from mothers. LGT is extensive and has played a major role in microbial evolution, and indeed genes may be transferred from phylogenetically quite distantly related organisms, making the construction of a meaningful phylogenetic tree difficult. In the August 8 Science, Vincent Daubin and colleagues of the University of Arizona argue, however, that too much weight is given to LGT in the phylogenetic analysis of bacteria, and by using a more conservative approach than the usual "reciprocal best hit" method to detect orthologous genes, they found that those available for phylogenetic reconstruction are consistent with a single tree (Science, 301:829-832, August 8, 2003).

Daubin et al. analyzed quartets of related sequenced genomes whose phylogenetic relationship is known based upon small subunit ribosomal RNA sequence. They inferred the number of genes...