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The Correlation Between Synonymous and Nonsynonymous Substitutions in Drosophila: Mutation, Selection or Relaxed Constraints?
Josep M. Comerona and Martin Kreitmanaa Department of Ecology and Evolution, University of Chicago, Chicago, Illinois 60637
Corresponding author: Josep M. Comeron, Department of Ecology and Evolution, University of Chicago, 1101 E. 57th St., Chicago, IL 60637., jcomeron{at}midway.uchicago.edu (E-mail).
| ABSTRACT |
|---|
Codon usage bias, the preferential use of particular codons within each codon family, is characteristic of synonymous base composition in many species, including Drosophila, yeast, and many bacteria. Preferential usage of particular codons in these species is maintained by natural selection acting largely at the level of translation. In Drosophila, as in bacteria, the rate of synonymous substitution per site is negatively correlated with the degree of codon usage bias, indicating stronger selection on codon usage in genes with high codon bias than in genes with low codon bias. Surprisingly, in these organisms, as well as in mammals, the rate of synonymous substitution is also positively correlated with the rate of nonsynonymous substitution. To investigate this correlation, we carried out a phylogenetic analysis of substitutions in 22 genes between two species of Drosophila, Drosophila pseudoobscura and D. subobscura, in codons that differ by one replacement and one synonymous change. We provide evidence for a relative excess of double substitutions in the same species lineage that cannot be explained by the simultaneous mutation of two adjacent bases. The synonymous changes in these codons also cannot be explained by a shift to a more preferred codon following a replacement substitution. We, therefore, interpret the excess of double codon substitutions within a lineage as being the result of relaxed constraints on both kinds of substitutions in particular codons.
THE rate of synonymous evolution (Ks) in Drosophila genes is correlated with the base composition at synonymous sites and is negatively correlated with the degree of synonymous codon usage bias (![]()
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In Drosophila, bacteria, and also mammals, the rate of nonsynonymous substitution (Ka) is also positively correlated with the rate of synonymous substitution (Ks) (![]()
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The basis of the correlation between Ks and Ka in Drosophila and prokaryotes is largely unexplored. In Drosophila, ![]()
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No attempt has been made to test hypotheses to explain the correlation between Ks and Ka in Drosophila. We test these hypotheses by investigating the evolution of codons with single synonymous and single nonsynonymous substitutions between D. pseudoobscura and D. subobscura.
| MATERIALS AND METHODS |
|---|
The genes and accession numbers used in this study are as follows: Adh (X78384, X62181, M15545), Adhr (X78384, Y00602, M55545), A/A-T/sesB (S43651, AF025798, AF025799), Aprt (M18432, L06281, AF025800), Arr2/ArrB (M32141, X54084), Bcd (X07870, X55735, X78058), Cp15 (X02497, X53423; ![]()
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(X03121, L19536, L19535), Sxl (M23636, X98370), Tpi (X57576/S70377, AF025814, AF025815), Ubx (X05723/24/25/27, X05179), Uro (X51940, X57113/S94076, AF025816), Xdh/ry (Y00307/308, M33977, Y08237), y (X04427, Y13909), and zen (X68347, X78058). Antp and hsp82 genes were not used in this study because for these genes the interspecific comparison is only possible for less than half of the entire coding sequence. Also, ATPsyn-ß and Vha14 genes were not used in the analyses because they exhibit significant variation in the synonymous substitution rate (P < 0.01) between lineages (![]()
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Computer simulations:
We generated pseudorandom coding regions of 250 codons with a G + C content of 0.70 at third positions of codons. We assumed both selection coefficients on synonymous (ss) and nonsynonymous (sa) mutations to be constant within a gene and to follow a normal distribution of mean and variance of 1.1 and 0.35, and 4.4 and 1.4, respectively, among genes. We used the means Ss = -1.1 and Sa = -4.4 because they predict averages for Ks of 0.824 and for Ka of 0.082, very close to the observed averages between D. melanogaster and the obscura species, D. subobscura and D. pseudoobscura, assuming Kn = 1.5. The number of synonymous and nonsynonymous substitutions was obtained from a Poisson distribution with mean the product of the value K, predicted by s following ![]()
| RESULTS |
|---|
As expected, we observed a significant positive correlation between Ks and Ka between D. melanogaster and the obscura group species (D. pseudoobscura and D. subobscura) for the 35 genes under analysis (r = 0.452, P = 0.006; Table 1 and Figure 1). This correlation is also detected when those codons with three substitutions are not taken into account (r = 0.437, P = 0.008). In Drosophila, one or two codons are preferred in each codon family (![]()
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Two other hypotheses have been proposed to explain this correlation: (ii) an excess of double mutation at adjacent sites, i.e., doublet mutations (![]()
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Doublet mutations do not appear to be the main cause of the correlation between Ks and Ka in these genes. According to the doublet mutation hypothesis ii, almost half (47.8%) of adjacent mutations, involving one synonymous and one nonsynonymous mutation, are expected to be in the third position of a codon and in the first position of the next codon because most, but not all (95.4%), substitutions at the first position of a codon are nonsynonymous, and 59.8% of substitutions at the third position are synonymous (substitutions at the second position are always nonsynonymous). Thus, under this hypothesis, Ks1 and Ka1 (see MATERIALS AND METHODS) should be positively correlated (![]()
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Hypotheses i and iiia, adaptive synonymous substitutions and covarying constraints on particular codons, make distinguishable predictions about the independent occurrence of double mutations in the same codon. Under the covarying constraints hypothesis, independent occurrences of synonymous and replacement substitutions are expected to accumulate in more weakly constrained codons. In contrast, the adaptive substitution hypothesis predicts nonindependence of substitutions. To distinguish between these two predictions, we have carried out a phylogenetic analysis of substitutions in those doubly substituted codons. If synonymous and nonsynonymous substitutions in the same codon are independent events, then they will be expected to have occurred at equal frequency as single mutations in each lineage leading to D. pseudoobscura and D. subobscura and as double mutations in the same species lineage. The adaptive hypothesis, otherwise, predicts an excess occurrence of the two substitutions in the same species lineage.
We first identified all codons with one synonymous and one nonsynonymous substitution when comparing D. subobscura and D. pseudoobscura sequences. We then used D. melanogaster sequences for the 22 genes whose sequences are available in the three species (![]()
2 = 10.31, P = 0.0013). Also, 48.1% of these codons show nonadjacent substitutions (first and third position), which is very close to the expected 47.8% (see above). Synonymous and nonsynonymous substitutions in the same codon are not independent occurrences, and they cannot be explained by doublet, and adjacent, mutations or by correlated selective constraints on particular codons. Only the adaptive substitution hypothesis is compatible with the data.
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To investigate the possible selective mechanism driving the nonindependent occurrence of synonymous and nonsynonymous substitutions, we considered a further prediction of the adaptive substitution hypothesis. Under any equilibrium model of codon bias maintained by selection, the expected rates of fixation of preferred and unpreferred mutations must be equal, while mutation pressure favors the appearance of unpreferred codons. In contrast, under the adaptive substitution hypothesis for doubly substituted codons, preferred substitutions are expected to exceed unpreferred substitutions. This relative excess of preferred substitutions is expected because the fixation of a nonsynonymous substitution (either by selection or drift) that generates an unpreferred codon will lead to positive selection for a subsequent synonymous substitution to the new preferred codon for that amino acid. The selection mechanism underlying adaptive synonymous substitution is not critical to this argument: selection may be to enhance either translational efficiency or accuracy. The important point is that the consequence of this selection will be to increase the substitution rate of preferred substitutions compared to unpreferred substitutions in the codons that have both synonymous and nonsynonymous substitutions occurring in the same lineage.
The data do not support this prediction. Under the assumption that a nonsynonymous substitution preceded a synonymous substitution, 65% of the inferred ancestral codons are preferred (for the 20 out of the 27 codons that conform to this assumption), while this percentage becomes 40 and 30% for the intermediate and doubly substituted codons, respectively. Thus, there is no evidence of selection for either a preferred synonymous substitution following a nonsynonymous substitution, or equilibrium between preferred and unpreferred codons. A G-test of independence among the number of preferred and unpreferred codons of the ancestral and doubly substituted codons reveals a smaller ratio of preferred to unpreferred codons in this latter group (G = 4.837, P = 0.0279 with the Williams correction). The expected frequency of preferred and unpreferred codons on the basis of random mutation can be estimated from the inferred ancestral codons and a mutational bias toward an A + T to G + C ratio of 60/40. The frequency of preferred codons consequence of both the first nonsynonymous substitution and the subsequent synonymous substitution in the same codon can be explained by random fixation of both the nonsynonymous (
2 = 0.695, P = 0.404) and the synonymous (
2 = 1.377, P = 0.241) mutations. By the same argument it is also possible to reject the converse of this adaptive hypothesis for doubly mutated codons, in which the initial occurrence of an unpreferred synonymous substitution established positive selection for an amino acid replacement that would be a more preferred codon (see below). From this analysis, and the preceding ones, we conclude that the data do not support any of the three hypotheses as explanations for the observed correlation between synonymous and replacement rates among genes. An additional alternative hypothesis to explain the data will be considered below.
| DISCUSSION |
|---|
Synonymous and replacement substitutions in the same codon:
Our interest in studying codons differing by both a synonymous and an amino acid replacement substitution was motivated by the knowledge that synonymous and amino acid replacement substitution rates are positively correlated in Drosophila genes. The detection of an excess of codons with both a synonymous and a nonsynonymous substitution, not explained by adjacent mutations, confirms that natural selection is acting at the codon, post-transcriptional, level in Drosophila. Thus, codon selection can give rise to coupled synonymous and nonsynonymous substitutions in the same codon. This result does not, however, rule out selection also acting on synonymous sites at the level of mRNA to maintain functional secondary structures (![]()
The analysis of doubly substituted codons between D. psedoobscura and D. subobscura, using D. melanogaster as an outgroup species, in a relatively large number of genes (22), allowed us to test several hypotheses. The discovery of a greater than expected number of these codons with both substitutions occurring in the same species lineage provides evidence for the nonindependence of replacement and synonymous substitutions in these codons. This nonindependence allowed us to reject the hypothesis of differential constraints among codons, predicted by the translational accuracy model.
The nonindependence of replacement and synonymous substitutions in doubly substituted codons is unlikely to be an artifact of the procedure used to assign changes to each lineage. The possible misassignment of a substitution to the wrong lineage, which might have occurred if the same mutational change had also occurred in the D. melanogaster lineage, or if a codon had multiple substitutions at the same nucleotide position, would be expected to obscure rather than enhance the nonrandom pattern of substitution we observed. This finding is also not likely to be due to unequal substitution rates in the D. pseudoobscura and the D. subobscura lineages, because these rates are very similar (![]()
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We therefore considered models of selection acting within the context of individual codons, i.e., codon selection. One attractive possibility is the idea that selection drives synonymous substitutions to a new preferred codon following the substitution of an amino acid replacement substitution to an unpreferred codon. Alternatively, one might also consider the reverse process, an adaptive substitution of an amino acid replacement substitution to a new preferred codon following a synonymous substitution to an unpreferred codon. Unfortunately, the evidence does not support either of these adaptive explanations: The majority of synonymous (or replacement) substitutions in these doubly substituted codons were to unpreferred rather than preferred codons. Thus, the second substitution, whichever it is, is not likely to be the result of positive codon selection.
An ad hoc explanation for the observed patterns of change in doubly substituted codons can be invoked by assuming a lineage-specific relaxation of selective constraints on particular amino acids within a protein. This relaxed selection at the amino acid level will allow for an increase in the amino acid replacement substitution rate, as well as for an increase in the synonymous substitution rate. The latter is expected to occur because translational accuracy will also be relaxed in these codons. Under this scenario, the first substitution is likely to be a synonymous change to a less preferred codon. The inferred ancestral codons are 68% preferred (for the 25 codons that conform to this assumption) whereas the intermediate codons, after the synonymous substitution, are 24% preferred. The clear increment of unpreferred codons can be explained by mutation on the basis of the expected frequency of preferred and unpreferred codons (see previous section;
2 = 0.802, P = 0.37). The increased occurrence of the second, nonsynonymous, substitution would not require the action of positive selection but only the relaxation of selective constraints on amino acid substitutions in this codon (
2 = 0.153, P = 0.696, based on the observed number of preferred codons and the expected frequency due to mutation). Such an explanation differs from the already rejected differential constraints hypothesis only in the additional requirement that selective constraints on individual codons change over time within a species lineage. This scenario is reminiscent of one aspect of Fitch's covarion model of protein evolution (![]()
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Our analysis indicates, therefore, that only a covarion-like model can explain the observed excess of doubly substituted codons on single-species lineages. Can the covarion-like model also account for the correlation between Ks and Ka observed in Drosophila data (Figure 1)? And if so, does it provide a more plausible explanation for this correlation than does a noncovarion model? To investigate these questions, we first explored the expected relationship between Ks and Ka when selection coefficients for synonymous (ss) and replacement (sa) mutations are completely correlated, and selection is constant for all sites (i.e., a noncovarion substitution model). Following ![]()

where Kn is the fixation probability of neutral mutations and S = 4 Ne s. Figure 2 shows that for linearly related selection coefficients for the two types of mutations, Ks and Ka are positively related, and that the relationship is a strongly nonlinear one. In fact, a similar trend can be observed in the data comparing synonymous and replacement changes between D. melanogaster and D. subobscura or D. pseudoobscura (Figure 1). We have also investigated by simulation the correlation between Ks and Ka for this same model, but when the selection coefficients on synonymous and replacement mutations are not completely correlated. As indicated in Table 5, a correlation between Ks and Ka in the range observed for Drosophila requires a very strong correlation between ss and sa, approaching a value of 1.
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Table 5 also gives the results of simulations for a covarion-like model, and Figure 3 shows the data generated for one of the conditions examined. Under this model a fraction, fc, of amino acid substitutions generates another amino acid substitution as well as a synonymous substitution. As shown in the table, the covarion-like model predicts moderately strong correlations between Ks and Ka for more permissive conditions of the relationship between ss and sa than the alternative model. This covarion-like model is therefore at least a viable explanation for the observed correlation between Ks and Ka seen in Drosophila data.
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This analysis of the covarion-like model, together with the detected excess of codons with doubly substituted codons in the same species lineage (and with a tendency toward unpreferred codons), support a covarion hypothesis of shifting selective constraints over time on individual amino acids. We propose that selection at the level of translational accuracy couples synonymous and nonsynonymous substitutions in codons with relaxed constraints.
| ACKNOWLEDGMENTS |
|---|
We are grateful to P. Andolfatto, M. Antezana, C. Bergman, A. Llopart, E. Stahl, C. Toomajian, and M. Przeworski for helpful discussions and/or comments on the manuscript. We also thank J. Hey and one anonymous reviewer for valuable comments that substantially improved the manuscript. J.M.C. is funded by a Postdoctoral Fellowship from Ministerio de Educación y Ciencia, Spain. This work was supported by a National Institutes of Health grant GM-39355 to M.K.
Manuscript received January 22, 1998; Accepted for publication July 9, 1998.
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