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Determining divergence times with protein clocks.

ported was a divergence time for prokaryotes and eukaryotes of only slightly more than two billion years ago. In line with this result, the average resemblance of these enzymes between Bacteria (a.k.a. eubacteria) and Eukarya (a.k.a. eukaryotes) was 37% identity. The recency of this divergence time was criticized by others on several grounds, particularly with regard to the way we converted sequence-based distances into evolutionary time. We had used a modified Poisson relationship and applied a post-hoc correction factor. The distance data were themselves calibrated on the basis of divergence times drawn from the fossil record and mostly involved sequences from vertebrate animals. The study has now been expanded and the data reanalyzed with a distance measure that corrects for both constraints on amino acid interchange and variation in substitution rate at different sites (2). The validity of the method was checked by an in-depth simulation study (3). Beyond that, the number of enzyme sets compared was increased to 64 and the total number of sequences used was 823 (4). Interestingly, the average sequence resemblance between Bacteria and Eukarya held steady at 37% identity. The study was greatly enriched by the availability of complete genome sequences for several eubacteria and an archaebacterium. The latter not only expanded the data set but also had a great impact on the interpretation of certain aspects of the data. As it happens, the majority of the