Vagaries of the molecular clock

Abstract

The hypothesis of the molecular evolutionary clock asserts that informational macromolecules (i.e., proteins and nucleic acids) evolve at rates that are constant through time and for different lineages. The clock hypothesis has been extremely powerful for determining evolutionary events of the remote past for which the fossil and other evidence is lacking or insufficient. I review the evolution of two genes, Gpdh and Sod. In fruit flies, the encoded glycerol-3-phosphate dehydrogenase (GPDH) protein evolves at a rate of 1.1 x 10(-10) amino acid replacements per site per year when Drosophila species are compared that diverged within the last 55 million years (My), but a much faster rate of approximately 4.5 x 10(-10) replacements per site per year when comparisons are made between mammals ( approximately 70 My) or Dipteran families ( approximately 100 My), animal phyla ( approximately 650 My), or multicellular kingdoms ( approximately 1100 My). The rate of superoxide dismutase (SOD) evolution is very fast between Drosophila species (16.2 x 10(-10) replacements per site per year) and remains the same between mammals (17.2) or Dipteran families (15.9), but it becomes much slower between animal phyla (5.3) and still slower between the three kingdoms (3.3). If we assume a molecular clock and use the Drosophila rate for estimating the divergence of remote organisms, GPDH yields estimates of 2,500 My for the divergence between the animal phyla (occurred approximately 650 My) and 3,990 My for the divergence of the kingdoms (occurred approximately 1,100 My). At the other extreme, SOD yields divergence times of 211 My and 224 My for the animal phyla and the kingdoms, respectively. It remains unsettled how often proteins evolve in such erratic fashion as GPDH and SOD.

Figure 1

Phylogeny of the nine species listed in Table 1 (14). s.g., subgenus. The thicker branch between nodes 3 and 5 indicates an inferred acceleration in the evolution of GPDH. The time scale is based on data from refs. and –.

Figure 2

Rate of amino acid replacement in fruit flies for the enzymes GPDH (Left) and SOD (Right). Open circles represent comparisons between species of Drosophila with each other (or with Scaptodrosophila); gray circles, between species of Chymomyza and Drosophila; solid circles, between Ceratitis and all other species; bars represent standard errors. It is apparent that a single straight line cannot provide a reasonable fit for all GPDH points; the rates shown on the right are amino acid replacements in units of 10⁻¹⁰ per site per year. The SOD rates are 16.2 for the Drosophila subgenera, 17.8 for the comparisons with Chymomyza, and 15.9 for the comparisons with Ceratitis; the two Chymomyza points are slightly displaced right and upwards for clarity. The species of Drosophila include 18 in addition to those listed in Table 1.

Figure 3

Rate of nucleotide substitution (K2) in fruit flies for the genes Gpdh (Left) and Sod (Right). Symbols and other conventions are as in Fig. 2. The K2 units are nucleotide substitutions × 10⁻¹⁰ per site per year, estimated by Kimura’s (22) two-parameter method; the rates on the right are in the same units, although their intercepts have been drawn at 50 My for clarity. The three rates are fairly similar, so that all points could have been subsumed within the same regression line, except perhaps for the Sod Ceratitis comparisons.

Figure 4

Rate of nonsynonymous (K_a) versus synonymous (K_s) substitutions in Gpdh (Left) and Sod (Right), estimated according to Li (23). Symbols and other conventions are as in Figs. 2 and 3, except that the K_a scale is in units of substitutions × 10⁻⁹ per site per year. In the case of Gpdh the correlation between nonsynonymous (replacement) and synonymous substitutions for comparisons with either Chymomyza or Ceratitis is not homogeneous with the correlation for the comparisons between Drosophila species; for Sod the correlation is more nearly homogeneous, although the dispersion is high.

Figure 5

Global rates of amino acid replacement for GPDH. The points at the lower left are for comparisons between fruit flies (open circles) or between mammals (filled circle). The rates on the right are for replacements × 10⁻¹⁰ per site per year and correspond to the comparisons between Drosophila species (1.1), between species from different animal phyla (4.0), and between species from different kingdoms (4.2). All three rates have been calculated as linear regressions over time.

Figure 6

Global rates of amino acid replacement for SOD. Symbols and other conventions as for Fig. 5. In contrast with GPDH, the fastest rate of evolution (16.2) is for comparisons between Drosophila species, and the lowest rate (3.3) is for comparisons between kingdoms. The intermediate rate (5.3) is for comparisons between animal phyla.