Determining divergence times with a protein clock: update and reevaluation

Abstract

A recent study of the divergence times of the major groups of organisms as gauged by amino acid sequence comparison has been expanded and the data have been reanalyzed with a distance measure that corrects for both constraints on amino acid interchange and variation in substitution 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 archaebacteria with eukaryotes. Instead, they are either outliers or mixed in with eubacterial orthologs. The simplest resolution of the problem is to postulate that many of these sequences were carried into eukaryotes by early eubacterial endosymbionts about 2 billion years ago, only very shortly after or even coincident with the divergence of eukaryotes and archaebacteria. The strong resemblances of these same enzymes among the major eubacterial groups suggest that the cyanobacteria and Gram-positive and Gram-negative eubacteria also diverged at about this same time, whereas the much greater differences between archaebacterial and eubacterial sequences indicate these two groups may have diverged between 3 and 4 billion years ago.

Figure 1

Evolutionary distances calculated according to Grishin (9) plotted against divergence times from the vertebrate fossil record. Error bars are standard deviations.

Figure 2

Phylogenetic trees of major groups of eukaryotes based on mean intergroup distances; the eubacteria were used as outlier for obtaining the topology of other groups. (A) Based on 11 fully represented enzyme sets. (B) Based on average intergroup distances for all enzyme sets. In both cases the plant divergence was taken to be 1200 Mya.

Figure 3

(A) Phylogeny of eukaryotes, archaebacteria, and principal eubacterial groups as determined with six of the eight enzyme sets in which the archaebacteria are nearest neighbors with eukaryotes (group A in Table 1; two of the enzyme sets were not included because sequences were not available for all bacterial groups). (B) Phylogeny of the same groups determined with 16 of the 17 enzymes sets in which the archaebacteria are outliers (group B in Table 1; in the case of lactate dehydrogenase, sequences were not available for all bacterial groups). Average sequence resemblances (% identical) are shown at key divergence points.