Eugene V. Koonin, “Darwinian evolution in the light of genomics,” Nucleic Acids Research 2009, 1-24.
The overall pattern of life’s history, he argues, may be a Forest, not a single Tree of Life [TOL]:
Evolutionary genomics effectively demolished the straightforward concept of the TOL by revealing the dynamic, reticulated character of evolution where HGT, genome fusion, and interaction between genomes of cellular life forms and diverse selfish genetic elements take the central stage. In this dynamic worldview, each genome is a palimpsest, a diverse collection of genes with different evolutionary fates and widely varying likelihoods of being lost, transferred, or duplicated. So the TOL becomes a network, or perhaps, most appropriately, the Forest of Life that consists of trees, bushes, thickets of lianas, and of course, numerous dead trunks and branches. Whether the TOL can be salvaged as central trend in the evolution of multiple conserved genes or this concept should be squarely abandoned for the Forest of Life image remains an open question. (p. 17)
Nonetheless, Koonin stands by “common ancestry,” but attenuates its meaning: “the very concept of a distinct LUCA [Last Universal Common Ancestor] becomes ambiguous, and it might be more appropriate to speak of LUCAS, the Last Universal Common Ancestral State” (p. 9). Molecular discontinuities among major groups probably indicate multiple independent originations of key systems:
Regardless of which scenario is preferred, the lack of conservation of central cellular systems among the domains of life indicates that the early stages of cell evolution involved radical changes which are hardly compatible with uniformitarianism. (p. 9)
Nucleic Acids Research has made this paper open access, so go check it out.