Phylogenetic classification and the universal tree

From comparative analyses of the nucleotide sequences of genes encoding rib osomal RNAs and several proteins, molecular phylogeneticists have construct ed a "universal tree of life," taking it as the basis for a "natural" hiera rchical classification of all living things. Although confidence in some of the tree's early branches has recently been shaken, new approaches could s till resolve many methodological uncertainties. More challenging is evidenc e that most archaeal and bacterial genomes (and the inferred ancestral euka ryotic nuclear genome) contain genes from multiple sources. If "chimerism" or "lateral gene transfer" cannot be dismissed as trivial in extent: or lim ited to special categories of genes, then no hierarchical universal classif ication can be taken as natural. Molecular phylogeneticists will have faile d to find the "true tree," not because their methods are inadequate or beca use they have chosen the wrong genes, but because the history of Life canno t properly be represented as a tree. However, taxonomies based on molecular sequences will remain indispensable, and understanding of the evolutionary process will ultimately be enriched, not impoverished.