An evolutionary perspective on synonymous codon usage in unicellular organisms

Summary Observed patterns of synonymous codon usage are explained in terms of the joint effects of mutation, selection, and random drift. Examination of the codon usage in 165Escherichia coli genes reveals a consistent trend of increasing bias with increasing gene expression level. Selection on codon usage appears to be unidirectional, so that the pattern seen in lowly expressed genes is best explained in terms of an absence of strong selection. A measure of directional synonymous-codon usage bias, the Codon Adaptation Index, has been developed. In enterobacteria, rates of synonymous substitution are seen to vary greatly among genes, and genes with a high codon bias evolve more slowly. A theoretical study shows that the patterns of extreme codon bias observed for someE. coli (and yeast) genes can be generated by rather small selective differences. The relative plausibilities of various theoretical models for explaining nonrandom codon usage are discussed.Presented at the FEBS Symposium on Genome Organization and Evolution, held in Crete, Greece, September 1–5, 1986     

PERSPECTIVE: SPONTANEOUS DELETERIOUS MUTATION

Mildly deleterious mutation has been invoked as a leading explanation for a diverse array of observations in evolutionary genetics and molecular evolution and is thought to be a significant risk of extinction for small populations. However, much of the empirical evidence for the deleterious-mutation process derives from studies of Drosophila melanogaster, some of which have been called into question. We review a broad array of data that collectively support the hypothesis that deleterious mutations arise in flies at rate of about one per individual per generation, with the average mutation decreasing fitness by about only 2% in the heterozygous state. Empirical evidence from microbes, plants, and several other animal species provide further support for the idea that most mutations have only mildly deleterious effects on fitness, and several other species appear to have genomic mutation rates that are of the order of magnitude observed in Drosophila. However, there is mounting evidence that some organisms have genomic deleterious mutation rates that are substantially lower than one per individual per generation. These lower rates may be at least partially reconciled with the Drosophila data by taking into consideration the number of germline cell divisions per generation. To fully resolve the existing controversy over the properties of spontaneous mutations, a number of issues need to be clarified. These include the form of the distribution of mutational effects and the extent to which this is modified by the environmental and genetic background and the contribution of basic biological features such as generation length and genome size to interspecific differences in the genomic mutation rate. Once such information is available, it should be possible to make a refined statement about the long-term impact of mutation on the genetic integrity of human populations subject to relaxed selection resulting from modern medical procedures.     

Low Diversity and Divergence in the fil1 Gene Family of Antirrhinum (Scrophulariaceae)

Detailed nucleotide diversity studies revealed that the fil1 gene of Antirrhinum, which has been reported to be single copy, is a member of a gene family composed of at least five genes. In four Antirrhinum majus populations with different mating systems and one A. graniticum population, diversity within populations is very low. Divergence among Antirrhinum species and between Antirrhinum and Digitalis is also low. For three of these genes we also obtained sequences from a more divergent member of the Scrophulariaceae, Verbascum nigrum. Compared with Antirrhinum, little divergence is again observed. These results, together with similar data obtained previously for five cycloidea genes, suggest either that these gene families (or the Antirrhinum genome) are unusually constrained or that there is a low rate of substitution in these lineages. Using a sample of 52 genes, based on two measures of codon usage (ENC and GC3 content), we show that cyc and fil1 are among the least biased Antirrhinum genes, so that their low diversity is not due to extreme codon bias. Received: 20 June 2000 / Accepted: 25 October 2000     

A simple procedure for joint estimation of the long‐term rates of sexuality and mutation in predominantly clonal populations,for use with dominant molecular markers

In highly clonal populations, mutation can contribute to the rate of apparent sexuality. To remove this bias, a method is presented that jointly estimates the rates of sexuality (Ns) and mutation (Nµ) for populations, based upon levels of single‐locus vs. multilocus clonal identity. This effectively haploid model assumes equilibrium, and can be used with dominant molecular data and in conjunction with organisms of various ploidies. Simulations indicate that while equilibrium can take thousands of generations to attain, and afterwards have a large evolutionary variance, the method gives approximate estimates of Ns.     

Molecular evolution of bacteriophages: Discrete patterns of codon usage in T4 genes are related to the time of gene expression

Summary Patterns of codon usage in certain coliphages are adapted to expression inEscherichia coli. Bacteriophage T4 may be an exception to test the rule, as it produces eight tRNAs with specificities that are otherwise rare inE. coli. A database of all known T4 DNA sequences has been compiled, comprising 174 genes and a total of 115 kb (approximately 70% of the T4 genome). Codon usage has been examined in all T4 genes; some of these are known to be expressed before, and some after, the production of phage tRNAs. The results show two different patterns of codon usage: by comparison with the early genes, the late genes exhibit a shift in preference toward those codons recognized by the phage-encoded tRNAs. The T4 tRNAs translate A-ending codons, and it is possible that the phage acquired the tRNA genes because the mutation bias of the T4 DNA polymerase forces the T4 genome toward A+T-richness.Presented at the NATO Advanced Workshop on Genome Organization and Evolution, held in Spetses, Greece, September 1990     

Neutral Evolution of Synonymous Base Composition in the Brassicaceae

The GC content of synonymous sites is elevated in genes from both Brassica oleraceae and Arabidopsis lyrata compared with Arabidopsis thaliana. However, this shift in base composition is independent of gene expression level, and there is no evidence for a similar difference in the frequency of codons preferred by translational selection. The results suggest that composition evolution is caused by a change in mutation bias or biased gene conversion, rather than by a reduction in the efficacy of natural selection in selfing Arabidopsis. [Reviewing Editor: Dr. Magrus Nordborg]     

Codon evolution is governed by linear formulas

When nucleotide (G, C, T and A) contents were plotted against each nucleotide, their relationships were clearly expressed by a linear formula, y = αx + β in the coding and non-coding regions. This linear relationship was obtained from the complete single-stranded DNA. Similarly, nucleotide contents at all three codon positions were expressed by linear regression lines based on the content of each nucleotide. In addition, 64 codon usages were also expressed by linear formulas against nucleotide content. Thus, the nucleotide content not only in coding sequence but also in non-coding sequence can be expressed by a linear formula, y = αx + β, in 145 organisms (112 bacteria, 15 archaea and 18 eukaryotes). Based on these results, the ratio of C/T, G/T, C/A or G/A one can essentially estimate all four nucleotide contents in the complete single-stranded DNA, and the determination of any ratio of two kinds of nucleotides can essentially estimate four nucleotide contents, nucleotide contents at the three different codon positions and codon distributions at 64 codons in the coding region. The maximum and minimum values of G content were ∼0.35 and ∼0.15, respectively, among various organisms examined. Codon evolution occurs according to linear formulas between these two values. Electronic supplementary material The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

The effect of population bottlenecks on mutation rate evolution in asexual populations

In the absence of recombination, a mutator allele can spread through a population by hitchhiking with beneficial mutations that appear in its genetic background. Theoretical studies over the past decade have shown that the survival and fixation probability of beneficial mutations can be severely reduced by population size bottlenecks. Here, we use computational modelling and evolution experiments with the yeast S. cerevisiae to examine whether population bottlenecks can affect mutator dynamics in adapting asexual populations. In simulation, we show that population bottlenecks can inhibit mutator hitchhiking with beneficial mutations and are most effective at lower beneficial mutation supply rates. We then subjected experimental populations of yeast propagated at the same effective population size to three different bottleneck regimes and observed that the speed of mutator hitchhiking was significantly slower at smaller bottlenecks, consistent with our theoretical expectations. Our results, thus, suggest that bottlenecks can be an important factor in mutation rate evolution and can in certain circumstances act to stabilize or, at least, delay the progressive elevation of mutation rates in asexual populations. Additionally, our findings provide the first experimental support for the theoretically postulated effect of population bottlenecks on beneficial mutations and demonstrate the usefulness of studying mutator frequency dynamics for understanding the underlying dynamics of fitness‐affecting mutations.     

Migration promotes mutator alleles in subdivided populations

Mutator alleles that elevate the genomic mutation rate may invade nonrecombining populations by hitchhiking with beneficial mutations. Mutators have been repeatedly observed to take over adapting laboratory populations and have been found at high frequencies in both microbial pathogen and cancer populations in nature. Recently, we have shown that mutators are only favored by selection in sufficiently large populations and transition to being disfavored as population size decreases. This population size‐dependent sign inversion in selective effect suggests that population structure may also be an important determinant of mutation rate evolution. Although large populations may favor mutators, subdividing such populations into sufficiently small subpopulations (demes) might effectively inhibit them. On the other hand, migration between small demes that otherwise inhibit hitchhiking may promote mutator fixation in the whole metapopulation. Here, we use stochastic, agent‐based simulations and evolution experiments with the yeast Saccharomyces cerevisiae to show that mutators can, indeed, be favored by selection in subdivided metapopulations composed of small demes connected by sufficient migration. In fact, we show that population structure plays a previously unsuspected role in promoting mutator success in subdivided metapopulations when migration is rare.     

Horizontal gene transfer contributes to the wide distribution and evolution of type II restriction-modification systems

Restriction modification (RM) systems serve to protect bacteria against bacteriophages. They comprise a restriction endonuclease activity that specifically cleaves DNA and a corresponding methyltransferase activity that specifically methylates the DNA, thereby protecting it from cleavage. Such systems are very common in bacteria. To find out whether the widespread distribution of RM systems is due to horizontal gene transfer, we have compared the codon usages of 29 type II RM systems with the average codon usage of their respective bacterial hosts. Pronounced deviations in codon usage were found in six cases:EcoRI,EcoRV,KpnI,SinI,SmaI, andTthHB81. They are interpreted as evidence for horizontal gene transfer in these cases. As the methodology is expected to detect only one-fourth to one-third of all horizontal gene transfer events, this result implies that horizontal gene transfer had a considerable influence on the distribution and evolution of RM systems. In all of these six cases the codon usage deviations of the restriction enzyme genes are much more pronounced than those of the methyltransferase genes. This result suggests that in these cases horizontal gene transfer had occurred sequentially with the gene for the methyltransferase being first acquired by the cell. This can be explained by the fact that an active restriction endonuclease is highly toxic in cells whose DNA is not protected from cleavage by a corresponding methyltransferase.     

Are codon usage patterns in unicellular organisms determined by selection-mutation balance?

Strongly biased codon usage is common in unicellular organisms, particularly in highly expressed genes. The bias is most simply explained as a balance between selection and mutation, with selection favouring those codons which are more efficiently translated. In a review Ikemura (1985) has proposed four rules for predicting which codons will be preferred, based on the properties of the transfer RNAs responsible for translating messenger RNA into protein. In this paper codon usage in E. coli and yeast is re-examined using the recent compilation of Maruyama et al. (1986). The codon adaptation index of Sharp and Li (1986a) is used as a measure of gene expression to investigate the importance of this factor. It is found that Ikemura's rules successfully predict preferred codons for yeast, but that two of them work less well for E. coli, and it is suggested that some of the apparent bias in weakly expressed genes of E. coli may be due to contextual effects on mutation rates.     

Fitness decline in spontaneous mutation accumulation lines of Caenorhabditis elegans with varying effective population sizes

The rate and fitness effects of new mutations have been investigated by mutation accumulation (MA) experiments in which organisms are maintained at a constant minimal population size to facilitate the accumulation of mutations with minimal efficacy of selection. We evolved 35 MA lines of Caenorhabditis elegans in parallel for 409 generations at three population sizes (N = 1, 10, and 100), representing the first spontaneous long-term MA experiment at varying population sizes with corresponding differences in the efficacy of selection. Productivity and survivorship in the N = 1 lines declined by 44% and 12%, respectively. The average effects of deleterious mutations in N = 1 lines are estimated to be 16.4% for productivity and 11.8% for survivorship. Larger populations (N = 10 and 100) did not suffer a significant decline in fitness traits despite a lengthy and sustained regime of consecutive bottlenecks exceeding 400 generations. Together, these results suggest that fitness decline in very small populations is dominated by mutations with large deleterious effects. It is possible that the MA lines at larger population sizes contain a load of cryptic deleterious mutations of small to moderate effects that would be revealed in more challenging environments.     

The effect of the reproductive system on mutation load

J. B. S. Haldane (Amer. Nat. 71, 337–349, 1937) argued that, in equilibrium populations, the effect of deleterious mutation on average fitness depends primarily on the mutation rate and is independent of the severity of the mutations. Specifically, the equilibrium population fitness is e^−μH, where μ_H is the haploid genomic mutation rate. Here we extend Haldane's result to a variety of reproductive systems. Using an analysis based on the frequency of classes of individuals with a specified number of mutations, we show that Haldane's principle holds exactly for haploid sex, haploid apomixis, and facultative haploid sex. In the cases of diploid automixis with terminal fusion, diploid automixis with central fusion, and diploid selfing, Haldane's principle holds exactly for recessive mutations and approximately for mutations with some heterozygous effect. In the cases of K-ploid apomixis, diploid endomitosis, and haplodiploidy, we show that Haldane's principle holds exactly for recessive lethal mutations. In addition we extend Haldane's result to various mixtures of the above-mentioned reproductive systems. In the case of diploid out-crossing sexuals, we do not obtain an exact analytic result, but present arguments and computer simulations which show that Haldane's result extends to this case as well in the limit as the number of loci becomes large. Although diverse reproductive systems are equally fit at equilibrium, different reproductive systems harbor vastly different numbers of recessive genes at equilibrium and we provide estimates of these numbers. These different numbers of mutations may create transient selective pressures on individuals with reproductive systems different from that of the equilibrium population.     

Using stage‐based system dynamics modeling for demographic management of captive populations

Management of captive populations relies on a complex synthesis of genetic and demographic analyses to guide populations toward sustainability. Demographic analyses of captive populations currently utilize age‐based matrix projections to predict a population's trajectory. An alternate approach is to use a stage‐based, system dynamics model for captive systems. Such models can more easily incorporate complex captive systems in which population dynamics are dependent on a combination of management and a species' biology. By linking these two areas, population managers can gain a more accurate understanding of how management decisions impact captive populations and which aspects of a species' demography should be of special concern in the future. We present a general stage‐based system dynamics model that has been developed for use with captive populations. The utility of the model is then illustrated by applying it to three captive bear populations: spectacled bears (Tremarctos ornatus), sloth bears (Melursus ursinus), and sun bears (Helarctos malayanus). Zoo Biol 22:45–64, 2003. © 2003 Wiley‐Liss, Inc.     

Genetic loads under fitness‐dependent mutation rates

Abstract Although much theory depends on the genome‐wide rate of deleterious mutations, good estimates of the mutation rate are scarce and remain controversial. Furthermore, mutation rate may not be constant, and a recent study suggests that mutation rates are higher in mildly stressful environments. If mutation rate is a function of condition, then individuals carrying more mutations will tend to be in worse condition and therefore produce more mutations. Here I examine the mean fitnesses of sexual and asexual populations evolving under such condition‐dependent mutation rates. The equilibrium mean fitness of a sexual population depends on the shape of the curve relating fitness to mutation rate. If mutation rate declines synergistically with increasing condition the mean fitness will be much lower than if mutation rate declines at a diminishing rate. In contrast, asexual populations are less affected by condition‐dependent mutation rates. The equilibrium mean fitness of an asexual population only depends on the mutation rate of the individuals in the least loaded class. Because such individuals have high fitness and therefore a low mutation rate, asexual populations experience less genetic load than sexual populations, thus increasing the twofold cost of sex.     

High mutation rate of TPE repeats: a microsatellite in the putative transposase of the hobo element in Drosophila melanogaster

The hobo transposable element contains a polymorphic microsatellite sequence located in its coding region, the TPE repeats. Previous surveys of natural populations of Drosophila melanogaster have detected at least seven different hobo transposons. These natural populations are geographically structured with regard to TPE polymorphism, and a scenario has been proposed for the invasion process. Natural populations have recently been completely invaded by hobo elements with three TPE repeats. New elements then appeared by mutation, triggering a new stage of invasion by other elements. Since TPE polymorphism appeared over a short period of time, we focused on estimating the mutation rate of these TPE repeats. We used transgenic lines harboring three TPE and/or five TPE hobo elements that had been evolving for at least 16 generations to search for a new TPE repeat polymorphism. We detected three mutants, with four, seven, and eight TPE repeats, respectively. The estimated mutation rate of the TPE repeats is therefore higher than that of neutral microsatellites in D. melanogaster (4.2 x 10-4 versus 6.5 x 10-6). The role of the transposition mechanism and the particular structure of the TPE repeats of the hobo element in this increase in the mutation rate are discussed.     

Reduced Selection for Codon Usage Bias in <Emphasis Type="Italic">Drosophila miranda</Emphasis>

Biased codon usage in many species results from a balance among mutation, weak selection, and genetic drift. Here I show that selection to maintain biased codon usage is reduced in Drosophila miranda relative to its ancestor. Analyses of mutation patterns in noncoding DNA suggest that the extent of this reduction cannot be explained by changes in mutation bias or by biased gene conversion. Low levels of variability in D. miranda relative to its sibling species, D. pseudoobscura, suggest that it has a much smaller effective population size. Reduced codon usage bias in D. miranda may thus result from the reduced efficacy of selection against newly arising mutations to unpreferred codons. [Reviewing Editor: Dr. Richard Kliman]     

A study on population genetic structure of Oryza meyeriana (Zoll. et Mor. ex Steud.) Baill. from Yunnan and its in situ conservation significance

In order to determine genetic diversity ofOryza meyeriana (Zoll. et Mor. ex Steud.) Baill., 12 enzyme systems encoded by 17 loci were electrophoretically analyzed in 164 individuals of seven populations from Simao Prefecture, Yunnan Province, China. In comparison with those seed plants with the same life history and breeding systems, as well as the other species in the genusOryza, the species shows rather low levels of genetic diversity (A = 1.1,P = 8.0 %, Ho = 0.004 and He = 0.015) within populations and high genetic differentiation among populations. F_st was up to 0. 649, suggesting that 64. 9% of total genetic variability exists among populations. Considering high genetic differentiation among populations from a limited geographic region, most of the populations of the species are worth being protected, and therefore, great natural protection regions should theoretically be established in which a great deal of populations should be involved for developingin situ conservation management. Meanwhile, some priory localities forin situ conservation ofO. meyerzana in Yunnan Province, were proposed. Project supported by the Grant of the President of the Chinese Academy of Sciences.     

Synonymous Nucleotide Divergence and Saturation: Effects of Site-Specific Variations in Codon Bias and Mutation Rates

The synonymous divergence between Escherichia coli and Salmonella typhimurium is explained in a model where there is a large variation between mutation rates at different nucleotide sites in the genome. The model is based on the experimental observation that spontaneous mutation rates can vary over several orders of magnitude at different sites in a gene. Such site-specific variation must be taken into account when studying synonymous divergence and will result in an apparent saturation below the level expected from an assumption of uniform rates. Recently, it has been suggested that codon preference in enterobacteria has a very large site-specific variation and that the synonymous divergence between different species, e.g., E. coli and Salmonella, is saturated. In the present communication it is shown that when site-specific variation in mutation rates is introduced, there is no need to invoke assumptions of saturation and a large variability in codon preference. The same rate variation will also bring average mutation rates as estimated from synonymous sequence divergence into numerical agreement with experimental values. Received: 10 July 1998 / Accepted: 20 August 1998