Amino acid sequence data from 57 different enzymes were used to determine the divergence times of the major biological groupings. Deuterostomes and protostomes split about 670 million years ago and plants, animals, and fungi last shared a common ancestor about a billion years ago. With regard to these protein sequences, plants are slightly more similar to animals than are the fungi. In contrast, phylogenetic analysis of the same sequences indicates that fungi and animals shared a common ancestor more recently than either did with plants, the greater difference resulting from the fungal lineage changing faster than the animal and plant lines over the last 965 million years. The major protist lineages have been changing at a somewhat faster rate than other eukaryotes and split off about 1230 million years ago. If the rate of change has been approximately constant, then prokaryotes and eukaryotes last shared a common ancestor about 2 billion years ago, archaebacterial sequences being measurably more similar to eukaryotic ones than are eubacterial ones.
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.In theory, past biological events can be reconstructed on the basis of present-day macromolecular sequences. Certainly, the assignment of organisms to various biological groups on the basis of ribosomal or protein sequences has been largely successful. Attaching absolute time scales to phylogenetic trees has proved more troublesome, however. As a case in point, we recently reported the results of an analysis of 531 amino acid sequences from 57 different sets of enzymes drawn from 15 different biological groups (1). We had aligned the 57 sets of sequences, determined how similar they were from group to group, and calculated evolutionary distances based on those similarities. The distance data were calibrated on the basis of divergence times drawn from the fossil record, and extrapolations were made to estimate the divergence times of more distantly related groups. The data were also used to compute an overall phylogeny for these same groups. The most provocative finding was that the divergence time between eukaryotes and eubacteria was, after various corrections, only slightly more than 2 billion years ago.The results were harshly criticized by others on a number of counts. Some felt that it was unreasonable to extrapolate so far backwards in time on the basis of, mostly, the vertebrate fossil record (G. Olsen, quoted in ref.2). Others felt that the distance value calculations did not take sufficient account of variations in the rate of change at different amino acid locations (3-5). Concern was also expressed that the data were corrupted by the presence of sequences imported during the endosymbiotic acquisition of organelles (4). A pervading thought in all the ...
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