Mutational Deterministic Hypothesis Research Articles

Sex and recombination purge the genome of deleterious alleles: An Individual Based Modeling Approach

The prevalence of sexual reproduction in most animal species despite its considerable costs such as useless males, energy spent on mating, the cost of meiosis and genome dilution remains a puzzle in evolutionary theory. One prominent single factor attempt to solve this persistent puzzle is the claim that sexual reproduction is instrumental in eliminating deleterious alleles from the species genome by the mechanism of recombination. There are three major versions of the deleterious allele hypothesis: First, the mutational deterministic hypothesis (MDH), which rests on the assumption of negative epistasis, predicts that recombination will help to purge the species genome of deleterious alleles by breaking apart linkages between these alleles. The assumption is that the joint negative effects of linked deleterious alleles is sometimes greater than the effects of the alleles considered separately. Second, there is the hypothesis that sexual reproduction speeds up purifying (negative) selection, which purges the genome of deleterious alleles. Alleles that are less deleterious than the wild type are naturally selected. These alleles, attained via recombination, are sometimes ‘leaky’ mutations giving rise to reduced functionality of attendant proteins. This hypothesis does not necessarily rest on the assumption of negative epistasis, which some argue is relatively rare in nature (Kouyos, Silander and Bonhoeffer (2012)) and which arguably could be seen as a virtue of the purifying selection hypothesis vs. the MDH. Third, Muller's ratchet hypothesis predicts that recombination will help to prevent the buildup of deleterious mutations by the mechanism of recombination. In this study, we focus primarily on testing the purifying selection hypothesis. We performed an individual-based model computer simulation using the program EcoSim to test this hypothesis. The experimental runs for sexual reproduction, asexual reproduction and facultative reproduction involved introducing a deleterious allele into the genome, which exacts an intermediate-level energy penalty on individuals. It was found that whereas on average, deleteriousness consistently declined over 18,000 time-steps due to recombination in sexual reproduction, deleteriousness did not decline for asexual and facultative runs. These results corroborate the hypothesis that recombination due to sexual reproduction helps to eliminate deleterious alleles from the genome through the selection of reduced function mutations.

Current hypotheses for the evolution of sex and recombination

The evolution of sex is one of the most important and controversial problems in evolutionary biology. Although sex is almost universal in higher animals and plants, its inherent costs have made its maintenance difficult to explain. The most famous of these is the twofold cost of males, which can greatly reduce the fecundity of a sexual population, compared to a population of asexual females. Over the past century, multiple hypotheses, along with experimental evidence to support these, have been put forward to explain widespread costly sex. In this review, we outline some of the most prominent theories, along with the experimental and observational evidence supporting these. Historically, there have been 4 classes of theories: the ability of sex to fix multiple novel advantageous mutants (Fisher-Muller hypothesis); sex as a mechanism to stop the build-up of deleterious mutations in finite populations (Muller's ratchet); recombination creating novel genotypes that can resist infection by parasites (Red Queen hypothesis); and the ability of sex to purge bad genomes if deleterious mutations act synergistically (mutational deterministic hypothesis). Current theoretical and experimental evidence seems to favor the hypothesis that sex breaks down selection interference between new mutants, or it acts as a mechanism to shuffle genotypes in order to repel parasitic invasion. However, there is still a need to collect more data from natural populations and experimental studies, which can be used to test different hypotheses.

Sequence diversity and potential recombination events in the coat protein gene of Apple stem pitting virus

The variability of the Apple stem pitting virus (ASPV) coat protein (CP) gene was investigated. The CP gene of ten virus isolates from apple and pear trees was sequenced. Comparison of all sequenced virus isolates revealed high diversity of the CP gene (70.7–93.5% at the nucleotide level and 77.8–98.7% at the amino acid level). Additionally, one or two deletions in the N-terminal part of the coat protein gene of the studied virus isolates were identified. The ratio of nonsynonymous to synonymous polymorphic sites indicated that purifying selection has acted to eliminate deleterious mutations in coding sites. Moreover, the evidences for recombination in analyzed sequences were provided. It is likely that recombination, along with selection, enhances the speed of elimination of deleterious mutations in ASPV, following the mutational deterministic hypothesis of Kondrashov.

Genetic Architecture and the Evolution of Sex

Theoretical investigations of the advantages of sex have tended to treat the genetic architecture of organisms as static and have not considered that genetic architecture might coevolve with reproductive mode. As a result, some potential advantages of sex may have been missed. Using a gene network model, we recently showed that recombination imposes selection for robustness to mutation and that negative epistasis can evolve as a by-product of this selection. These results motivated a detailed exploration of the mutational deterministic hypothesis, a hypothesis in which the advantage of sex depends critically on epistasis. We found that sexual populations do evolve higher mean fitness and lower genetic load than asexual populations at equilibrium, and, under moderate stabilizing selection and large population size, these equilibrium sexual populations resist invasion by asexuals. However, we found no evidence that these long- and short-term advantages to sex were explained by the negative epistasis that evolved in our experiments. The long-term advantage of sex was that sexual populations evolved a lower deleterious mutation rate, but this property was not sufficient to account for the ability of sexual populations to resist invasion by asexuals. The ability to resist asexual invasion was acquired simultaneously with an increase in recombinational robustness that minimized the cost of sex. These observations provide the first direct evidence that sexual reproduction does indeed select for conditions that favor its own maintenance. Furthermore, our results highlight the importance of considering a dynamic view of the genetic architecture to understand the evolution of sex and recombination.

Quasispecies theory for horizontal gene transfer and recombination

We introduce a generalization of the parallel, or Crow-Kimura, and Eigen models of molecular evolution to represent the exchange of genetic information between individuals in a population. We study the effect of different schemes of genetic recombination on the steady-state mean fitness and distribution of individuals in the population, through an analytic field theoretic mapping. We investigate both horizontal gene transfer from a population and recombination between pairs of individuals. Somewhat surprisingly, these nonlinear generalizations of quasispecies theory to modern biology are analytically solvable. For two-parent recombination, we find two selected phases, one of which is spectrally rigid. We present exact analytical formulas for the equilibrium mean fitness of the population, in terms of a maximum principle, which are generally applicable to any permutation invariant replication rate function. For smooth fitness landscapes, we show that when positive epistatic interactions are present, recombination or horizontal gene transfer introduces a mild load against selection. Conversely, if the fitness landscape exhibits negative epistasis, horizontal gene transfer or recombination introduces an advantage by enhancing selection towards the fittest genotypes. These results prove that the mutational deterministic hypothesis holds for quasispecies models. For the discontinuous single sharp peak fitness landscape, we show that horizontal gene transfer has no effect on the fitness, while recombination decreases the fitness, for both the parallel and the Eigen models. We present numerical and analytical results as well as phase diagrams for the different cases.

Evolution Can Favor Antagonistic Epistasis

The accumulation of deleterious mutations plays a major role in evolution, and key to this are the interactions between their fitness effects, known as epistasis. Whether mutations tend to interact synergistically (with multiple mutations being more deleterious than would be expected from their individual fitness effects) or antagonistically is important for a variety of evolutionary questions, particularly the evolution of sex. Unfortunately, the experimental evidence on the prevalence and strength of epistasis is mixed and inconclusive. Here we study theoretically whether synergistic or antagonistic epistasis is likely to be favored by evolution and by how much. We find that in the presence of recombination, evolution favors less synergistic or more antagonistic epistasis whenever mutations that change the epistasis in this direction are possible. This is because evolution favors increased buffering against the effects of deleterious mutations. This suggests that we should not expect synergistic epistasis to be widespread in nature and hence that the mutational deterministic hypothesis for the advantage of sex may not apply widely.

Sexual reproduction selects for robustness and negative epistasis in artificial gene networks

The mutational deterministic hypothesis for the origin and maintenance of sexual reproduction posits that sex enhances the ability of natural selection to purge deleterious mutations after recombination brings them together into single genomes. This explanation requires negative epistasis, a type of genetic interaction where mutations are more harmful in combination than expected from their separate effects. The conceptual appeal of the mutational deterministic hypothesis has been offset by our inability to identify the mechanistic and evolutionary bases of negative epistasis. Here we show that negative epistasis can evolve as a consequence of sexual reproduction itself. Using an artificial gene network model, we find that recombination between gene networks imposes selection for genetic robustness, and that negative epistasis evolves as a by-product of this selection. Our results suggest that sexual reproduction selects for conditions that favour its own maintenance, a case of evolution forging its own path.

Rates of deleterious mutation and the evolution of sex in Caenorhabditis.

A variety of models propose that the accumulation of deleterious mutations plays an important role in the evolution of breeding systems. These models make predictions regarding the relative rates of protein evolution and deleterious mutation in taxa with contrasting modes of reproduction. Here we compare available coding sequences from one obligately outcrossing and two primarily selfing species of Caenorhabditis to explore the potential for mutational models to explain the evolution of breeding system in this clade. If deleterious mutations interact synergistically, the mutational deterministic hypothesis predicts that a high genomic deleterious mutation rate (U) will offset the reproductive disadvantage of outcrossing relative to asexual or selfing reproduction. Therefore, C. elegans and C. briggsae (both largely selfing) should both exhibit lower rates of deleterious mutation than the obligately outcrossing relative C. remanei. Using a comparative approach, we estimate U to be equivalent (and < 1) among all three related species. Stochastic mutational models, Muller's ratchet and Hill-Robertson interference, are expected to cause reductions in the effective population size in species that rarely outcross, thereby allowing deleterious mutations to accumulate at an elevated rate. We find only limited support for more rapid molecular evolution in selfing lineages. Overall, our analyses indicate that the evolution of breeding system in this group is unlikely to be explained solely by available mutational models.

Sex may need more than one

The positive replies to our original paper (West et al., 1999) leave us in the pleasurable position of being able to keep our ®nal comments short. Kondrashov (1999) demonstrates what Seger (1999) called `physics envy'. The idea that the Mutational Deterministic hypothesis can be easily validated or rejected, once the minimum rate of deleterious mutations per genome per generation (U) is known, sounds great, especially if the magical number is U > 1. However, quantitative predictions (and assumptions) are almost always model-speci®c, so that there is unlikely to be a single, uncontroversial value, even if we ignore the large con®dence limits that are placed on estimates of U (see West et al., 1999). For instance, with reasonable levels of epistasis, a value of U > 1.5 is required (Charlesworth, 1990). If stochastic effects (which are unavoidable during the early phases of any clonal invasion) or variation in the extent of epistasis are included, then U > 2.0 is required (Howard, 1994; Otto & Feldman, 1997). In addition, irrespective of the value of U, the Mutational Deterministic hypothesis absolutely requires synergistic epistasis between deleterious mutations (Kondrashov, 1982). The idea that a single value of U will resolve the issue seems to us somewhat optimistic. We agree with Kondrashov (1999) that our particular form of pluralist explanation is required for only a small fraction (»0.2 < U < »2.0) of the entire parameter space (0 < U < ¥). However, that `small fraction' is the relevant parameter space: it is where the majority of estimates of the mutation rate in sexual species fall (West et al., 1999). A pressing goal now is to determine the virulence of parasites in the wild, and whether they in fact evolve to infect locally common host genotypes. If the latter is not true, or if parasites are not suf®ciently virulent to drive host gene frequency dynamics, then both the parasite-driven Red Queen and our particular form of pluralism are falsi®ed. We agree with Lenski (1999) that different factors may be responsible for the evolutionary origin and maintenance of sex. As we said, our discussion concerned the maintenance of sex. We also agree that experiments with Escherichia coli offer an exceptional opportunity to test for `a general tendency for genetic structures to exhibit synergistic epistasis among deleterious mutations' (Elena & Lenski, 1997). We note, however, that such experiments cannot test whether synergistic epistasis occurs in a type of organism where sexual reproduction predominates. Do larger, more complex genomes with higher mutation rates lead to synergistic epistasis (Szathmary, 1993; Falush, 1998; Hurst & Smith, 1998)? Do the higher numbers of parasites in larger species help cause truncation selection against individuals with large numbers of mutations? Estimating relevant parameters can be much harder in more complex and sexual species (West et al., 1998), but such results are crucial. We hope eventually to have a range of estimates of the mutation rate and the extent of epistasis from a number of sexual and asexual species, so that a whole slew of more subtle questions can be addressed. Red®eld's (1999) comments give us the opportunity to make the following points, orthogonal to our discussion of plurality. (1) Theoretical models suggest that the rate of crossing over is far more important than chromosome number in determining the effective amount of recombination (Burt, unpublished observations). (2) Variation in recombination rates across species are consistent with Red Queen and mutational models (Burt & Bell, 1987;

ENVIRONMENTAL STRESS AND THE MAINTENANCE OF SEX IN A FRESHWATER SNAIL.

Synergism among mutations can lead to an advantage to sexual reproduction, provided mutation rates are high enough (the mutational deterministic hypothesis). Here we tested the idea that competition for food can increase the advantage to sexual reproduction, perhaps by increasing the synergism among mutations in asexual individuals. We compared the survivorship of sexual and asexual snails (Potamopyrgus antipodarum) under two treatments: starved and fed. We predicted higher mortality for asexual snails when starved, but found that sexual and asexual individuals survived at the same rate, independent of treatment. These results suggest that the distribution of sex in this snail may not be explained by variation in competition among populations.

Test of synergistic interactions among deleterious mutations in bacteria

Identifying the forces responsible for the origin and maintenance of sexuality remains one of the greatest unsolved problems in biology. The mutational deterministic hypothesis postulates that sex is an adaptation that allows deleterious mutations to be purged from the genome; it requires synergistic interactions, which means that two mutations would be more harmful together than expected from their separate effects. We generated 225 genotypes of Escherichia coli carrying one, two or three successive mutations and measured their fitness relative to an unmutated competitor. The relationship between mutation number and average fitness is nearly log-linear. We also constructed 27 recombinant genotypes having pairs of mutations whose separate and combined effects on fitness were determined. Several pairs exhibit significant interactions for fitness, but they are antagonistic as often as they are synergistic. These results do not support the mutational deterministic hypothesis for the evolution of sex.

Selection Against Deleterious Mutations and the Maintenance of Biparental Sex

The mutational deterministic hypothesis postulates an advantage to sexual over asexual reproduction when mutation rates are on the order of 1.0 per genome per generation, provided that selection takes the form of a synergistic epistasis. While the efficacy of this mechanism has been investigated for infinite populations, its ability to protect sex in finite populations exhibiting stochastic dynamics remains untested. Stochastic processes have the potential to undermine protection for sex in two ways: (1) asexual lineages derived from sexual ancestors may, by chance, be founded by individuals bearing fewer than the equilibrium mean number of mutations, and (2) once established, such lineages will undergo random perturbations in the rates at which they grow and accumulate mutations. In the present study, I show using computer simulation that sexual populations of as many as 10,000 individuals are susceptible to invasion by asexual lineages for mutation rates higher than predicted under the mutational deterministic hypothesis. My simulations differ from previous investigations in that they model the progress of asexual lineages into sexual populations as both stochastic and deterministic processes for various mutation rates, selection regimes, and population sizes. It is suggested that ecological factors, such as parasitism or release from competition, could interact with selection against deleterious mutations to protect sex. To provide the sole explanation for sex, however, may require that selection against deleterious mutations be accompanied by mutation rates on the order of 2.0 per genome per generation.