Mayr Versus Woese: Akaryotes and Eukaryotes
In 1998, on the brink of a great public effort that by now has delivered the sequences of thousands of genomes and has annotated these genomes by translating tens of thousands of 3D protein domain structures from their coding sequences, Ernst Mayr and Carl Woese engaged in a debate. At issue were the virtues of phenotypic contra genotypic approaches to phylogeny and taxonomy. Though not conclusive, this confrontation in retrospect illustrates the defects of both their perspectives and simultaneously illuminates the strengths of the approach to phylogenetic systematics that was favored by Willi Hennig. Hennig’s cladism lends itself well to a rigorous exploitation of genome sequence data in which both the genotypic and phenotypic modes replace the technically questionable gene tree approach to deep phylogeny championed by Woese. Diverse phylogenomic data now suggest that though Mayr’s phenetic arguments were incomplete, his division of organisms into two major taxonomic groups, the akaryotes (formerly the prokaryotes) and eukaryotes, is probably correct. Thus, in a phylogeny based on genome repertoires of protein domains, the universal common ancestor of the three superkingdoms descends in two primary lineages, Akaryote and Eukaryote.
We are indebted to Siv Andersson, Otto Berg, Dan Dykhuizen, Måns Ehrenberg, Julian Gough, Diarmaid Hughes, Bruce Levin, Michael Levitt, Mikael Oliveberg, David Penny, Antonis Rokas, Anders Tunlid, Richard Villems, and Irmgard Winkler for essential criticism and help in preparing this paper.
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