Since the time of Darwin, science has accepted the principle that species decended from an ever more limited number of common ancestors, back to a single common ancestor. This all inclusive hierarchy has formed the basis for phylogenic classification. Modern phylogenetics is conducted at the molecular level using nucleotide (DNA and RNA) and amino acid (protein) sequencing. To an extent, a hierarchical tree of life has been derived using molecular phylogenetics (Woese, PNAS, 87 4576, 1990). More recently, Doolittle, in a review (Doolittle, Science, Vol 284, p. 2124, 1999) has discussed evidence that most archaeal and bacterial genomes, and by inference the ancestral eukaryote genome, contain genes from multiple sources. Such lateral gene transfer, if extensive, would deny the hypothesis of a single universal tree. If so, the so-called tree of life would comprise multiple, superimposed trees.

Doolittle WF. Phylogenetic classification and the universal tree. Science. 1999 Nov 19;286(5444):1443 [PubMed]