DETERMINING DIVERGENCE TIMES WITH A PROTEIN CLOCK - UPDATE AND REEVALUATION

A recent study of the divergence times of the major groups of organism s as gauged by amino acid sequence comparison has been expanded and th e data have been reanalyzed with a distance measure that corrects for both constraints on amino acid interchange and variation in substituti on rate at different sites. Beyond that, the availability of complete genome sequences for several eubacteria and an archaebacterium has had a great impact on the interpretation of certain aspects of the data. Thus, the majority of the archaebacterial sequences are not consistent with currently accepted views of the Tree of Life which cluster the a rchaebacteria with eukaryotes. Instead, they are either outliers or mi xed in with eubacterial orthologs. The simplest resolution of the prob lem is to postulate that many of these sequences were carried into euk aryotes by early eubacterial endosymbionts about 2 billion years ago, only very shortly after or even coincident with the divergence of euka ryotes and archaebacteria. The strong resemblances of these same enzym es among the major eubacterial groups suggest that the cyanobacteria a nd Gram-positive and Gram-negative eubacteria also diverged at about t his same time, whereas the much greater differences between archaebact erial and eubacterial sequences indicate these two groups may have div erged between 3 and 4 billion years ago.