Factors enforcing the species boundary between the human pathogens Cryptococcus neoformans and Cryptococcus deneoformans

Hybridization has resulted in the origin and variation in extant species, and hybrids continue to arise despite pre- and post-zygotic barriers that limit their formation and evolutionary success. One important system that maintains species boundaries in prokaryotes and eukaryotes is the mismatch repair pathway, which blocks recombination between divergent DNA sequences. Previous studies illuminated the role of the mismatch repair component Msh2 in blocking genetic recombination between divergent DNA during meiosis. Loss of Msh2 results in increased interspecific genetic recombination in bacterial and yeast models, and increased viability of progeny derived from yeast hybrid crosses. Hybrid isolates of two pathogenic fungal Cryptococcus species, Cryptococcus neoformans and Cryptococcus deneoformans, are isolated regularly from both clinical and environmental sources. In the present study, we sought to determine if loss of Msh2 would relax the species boundary between C. neoformans and C. deneoformans. We found that crosses between these two species in which both parents lack Msh2 produced hybrid progeny with increased viability and high levels of aneuploidy. Whole-genome sequencing revealed few instances of recombination among hybrid progeny and did not identify increased levels of recombination in progeny derived from parents lacking Msh2. Several hybrid progeny produced structures associated with sexual reproduction when incubated alone on nutrient-rich medium in light, a novel phenotype in Cryptococcus. These findings represent a unique, unexpected case where rendering the mismatch repair system defective did not result in increased meiotic recombination across a species boundary. This suggests that alternative pathways or other mismatch repair components limit meiotic recombination between homeologous DNA and enforce species boundaries in the basidiomycete Cryptococcus species.     

Drastic fitness loss in human immunodeficiency virus type 1 upon serial bottleneck events

Muller's ratchet predicts fitness losses in small populations of asexual organisms because of the irreversible accumulation of deleterious mutations and genetic drift. This effect should be enhanced if population bottlenecks intervene and fixation of mutations is not compensated by recombination. To study whether Muller's ratchet could operate in a retrovirus, 10 biological clones were derived from a human immunodeficiency virus type 1 (HIV-1) field isolate by MT-4 plaque assay. Each clone was subjected to 15 plaque-to-plaque passages. Surprisingly, genetic deterioration of viral clones was very drastic, and only 4 of the 10 initial clones were able to produce viable progeny after the serial plaque transfers. Two of the initial clones stopped forming plaques at passage 7, two others stopped at passage 13, and only four of the remaining six clones yielded infectious virus. Of these four, three displayed important fitness losses. Thus, despite virions carrying two copies of genomic RNA and the system displaying frequent recombination, HIV-1 manifested a drastic fitness loss as a result of an accentuation of Muller's ratchet effect.     

THE CONTRIBUTION OF NEW MUTATIONS TO GENOTYPE-ENVIRONMENT INTERACTION FOR FITNESS IN DROSOPHILA MELANOGASTER

Many studies have documented the existence of genotype-environment interaction (GEI) for traits closely related to fitness in natural populations. A type of GEI that is commonly observed is changes in the fitness ranking of genetic groups (families, clones, or inbred lines) in different environments. We refer to such changes in ranking as crossing of reaction norms for fitness. A common interpretation of crossing of reaction norms for fitness is that selection favors different alleles in the different environments (i.e., that “trade-offs” exist). If this is the case, selection could maintain genetic variation, and even lead to reproductive isolation between subpopulations using different environments. Even if the same alleles are favored in every environment, however, deleterious mutations that vary in the magnitude of their effect depending on environment could cause reaction norms for fitness to cross. If deleterious mutations with environment-dependent effects are responsible for maintaining much of the variation leading to crossing of reaction norms for fitness in natural populations, it should be possible to observe crossing of reaction norms for fitness among otherwise genetically identical lines bearing newly arisen spontaneous mutations. We examined the contribution of new mutations to GEI for fitness in Drosophila melanogaster. Eighteen lines were derived from a common, highly inbred base stock, and maintained at a population size of 10 pairs for over 200 generations, to allow them to accumulate spontaneous mutations. Because of the small population size of the lines, selection against mildly deleterious mutations should have been relatively ineffective. The lines were tested for productivity (number of surviving adult progeny from a standard number of parents) in five different environmental treatments, comprising different food media, temperatures, and levels of competition. The lines showed highly significant GEI for productivity, owing largely to considerable changes in ranking in the different environments. We conclude that mutations that are deleterious on average, but whose quantitative effects depend on environment, could be responsible for maintaining much of the variation leading to crossing of reaction norms for fitness that has been observed in samples of D. melanogaster from the wild.     

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.     

EFFECTS OF DIFFERENT LEVELS OF INBREEDING ON FITNESS COMPONENTS IN MIMULUS GUTTATUS

Recent theoretical work has shown that there can be selection favoring the maintenance of sexual reproduction and the evolution of increased recombination when deleterious mutations at different loci interact synergistically, such that the logarithm of fitness declines at a greater than linear rate with the number of harmful mutations per genome. The purpose of this experimental study was to determine whether synergism exists for genes affecting fitness components in two partially selfing populations of the monkey flower Mimulus guttatus. For each wild population, a large randomly mated base population was constructed and many independent lines, inbred to differing degrees, were extracted from this base population. Lines with expected inbreeding coefficients of 0, 0.25, 0.5, and 0.75 were raised simultaneously in the greenhouse and were scored for germination, flowering, flower production, and pollen viability. All fitness traits except germination success declined with increased inbreeding, but in spite of the substantial inbreeding depression found in this study, relatively little evidence of synergistic epistasis was found. The only trait that showed evidence of synergism was pollen viability. These results indicate that synergism is not strong for the fitness components measured in this study. The evidence for synergism from other published studies is also reviewed.     

On the evolutionary advantage of fitness-associated recombination

The adaptive value of recombination remains something of a puzzle. One of the basic problems is that recombination not only creates new and advantageous genetic combinations, but also breaks down existing good ones. A negative correlation between the fitness of an individual and its recombination rate would result in prolonged integrity of fitter genetic combinations while enabling less fit ones to produce new combinations. Such a correlation could be mediated by various factors, including stress responses, age, or direct DNA damage. For haploid population models, we show that an allele for such fitness-associated recombination (FAR) can spread both in asexual populations and in populations reproducing sexually at any uniform recombination rate. FAR also carries an advantage for the population as a whole, resulting in a higher average fitness at mutation-selection balance. These results are demonstrated in populations adapting to new environments as well as in well-adapted populations coping with deleterious mutations. Current experimental results providing evidence for the existence of FAR in nature are discussed.     

Rapid evolutionary escape by large populations from local fitness peaks is likely in nature

Fitness interactions between loci in the genome, or epistasis, can result in mutations that are individually deleterious but jointly beneficial. Such epistasis gives rise to multiple peaks on the genotypic fitness landscape. The problem of evolutionary escape from such local peaks has been a central problem of evolutionary genetics for at least 75 years. Much attention has focused on models of small populations, in which the sequential fixation of valley genotypes carrying individually deleterious mutations operates most quickly owing to genetic drift. However, valley genotypes can also be subject to mutation while transiently segregating, giving rise to copies of the high fitness escape genotype carrying the jointly beneficial mutations. In the absence of genetic recombination, these mutations may then fix simultaneously. The time for this process declines sharply with increasing population size, and it eventually comes to dominate evolutionary behavior. Here we develop an analytic expression for N(crit), the critical population size that defines the boundary between these regimes, which shows that both are likely to operate in nature. Frequent recombination may disrupt high-fitness escape genotypes produced in populations larger than N(crit) before they reach fixation, defining a third regime whose rate again slows with increasing population size. We develop a novel expression for this critical recombination rate, which shows that in large populations the simultaneous fixation of mutations that are beneficial only jointly is unlikely to be disrupted by genetic recombination if their map distance is on the order of the size of single genes. Thus, counterintuitively, mass selection alone offers a biologically realistic resolution to the problem of evolutionary escape from local fitness peaks in natural populations.     

Intralocus sexual conflict,adaptive sex allocation,and the heritability of fitness

Intralocus sexual conflict arises when selection favours alternative fitness optima in males and females. Unresolved conflict can create negative between‐sex genetic correlations for fitness, such that high‐fitness parents produce high‐fitness progeny of their same sex, but low‐fitness progeny of the opposite sex. This cost of sexual conflict could be mitigated if high‐fitness parents bias sex allocation to produce more offspring of their same sex. Previous studies of the brown anole lizard (Anolis sagrei) show that viability selection on body size is sexually antagonistic, favouring large males and smaller females. However, sexual conflict over body size may be partially mitigated by adaptive sex allocation: large males sire more sons than daughters, whereas small males sire more daughters than sons. We explored the evolutionary implications of these phenomena by assessing the additive genetic (co)variance of fitness within and between sexes in a wild population. We measured two components of fitness: viability of adults over the breeding season, and the number of their progeny that survived to sexual maturity, which includes components of parental reproductive success and offspring viability (RS^V). Viability of parents was not correlated with adult viability of their sons or daughters. RS^V was positively correlated between sires and their offspring, but not between dams and their offspring. Neither component of fitness was significantly heritable, and neither exhibited negative between‐sex genetic correlations that would indicate unresolved sexual conflict. Rather, our results are more consistent with predictions regarding adaptive sex allocation in that, as the number of sons produced by a sire increased, the adult viability of his male progeny increased.     

The mixed mating system of Impatiens capensis and infection by a foliar rust pathogen: patterns of resistance and fitness consequences

Outcrossing by hosts may offer protection from natural enemies adapted to parental genotypes by creating diverse progeny that differ from their parents through genetic recombination. However, past experimental work addressing the relationship between mating system and disease in offspring has given conflicting results, suggesting that outcrossing might also cause the dissolution of resistant genotypes. To determine if selfed progeny are more susceptible to disease caused by the heteroecious rust, Puccinia recondita, or if selfing preserves existing resistant genotypes, we used a factorial design to compare levels of infection of selfed and outcrossed progeny of Impatiens capensis, a woodland annual with a mixed mating system. We compared the level of host infection when exposed to three pathogen sources in the field: the sympatric rust population, and two allopatric rust populations. Outcrossed progeny exposed to sympatric rust had higher infection scores than selfed progeny exposed to the same rust, suggesting that outcrossing breaks up resistant genotypes. In addition, there was a trend for the rust to be more infective on sympatric rather than allopatric hosts. We also examined whether rust infection differentially alters the fitness of selfed and outcrossed progeny. Outcrossed plants that escaped infection had higher fitness, as measured by fruit production, than selfed plants, but there was no difference in fitness between infected selfed and infected outcrossed plants. Thus, outcrossing was advantageous in the absence of disease, but there was no fitness difference between selfed and outcrossed progeny in the presence of disease. In sum, our results indicate that interactions with pathogens can eliminate or reverse the advantage of outcrossing.     

Genome structure and the benefit of sex

We examine the behavior of sexual and asexual populations in modular multipeaked fitness landscapes and show that sexuals can systematically reach different, higher fitness adaptive peaks than asexuals. Whereas asexuals must move against selection to escape local optima, sexuals reach higher fitness peaks reliably because they create specific genetic variants that "skip over" fitness valleys, moving from peak to peak in the fitness landscape. This occurs because recombination can supply combinations of mutations in functional composites or "modules," that may include individually deleterious mutations. Thus when a beneficial module is substituted for another less-fit module by sexual recombination it provides a genetic variant that would require either several specific simultaneous mutations in an asexual population or a sequence of individual mutations some of which would be selected against. This effect requires modular genomes, such that subsets of strongly epistatic mutations are tightly physically linked. We argue that such a structure is provided simply by virtue of the fact that genomes contain many genes each containing many strongly epistatic nucleotides. We briefly discuss the connections with "building blocks" in the evolutionary computation literature. We conclude that there are conditions in which sexuals can systematically evolve high-fitness genotypes that are essentially unevolvable for asexuals.     

Patterns of the purging of deleterious genes with synergistic interactions in different breeding schemes

 The purging of deleterious genes for increasing progeny fitness and/or avoiding extinction in breeding programs, particularly with endangered species, has become of increased interest in recent years. Some studies have shown that purging can be effective only for deleterious genes of multiplicative, large effects, such as lethal or sublethal genes. In the present study, we examine the effectiveness of purging viability genes of synergistic, small effect with continuous selfing, full-sib mating, or half-sib mating, by computer simulation. A diploid breeding population with a constant progeny size of 10, 50 or 200 is simulated, one of the three breeding schemes referred to above is practiced over ten generations, and the patterns of purging, progeny survival and population extinction are examined. The rate and amount of purging generally increase with high dominance, strong synergism, high genetic load and low inbreeding. Progeny survival can increase only for a progeny size larger than 50 using schemes of mild inbreeding when there is a high level of dominance and strong synergism. The probability of extinction could greatly increase up to 100% for a progeny size of 10, but mostly is less than 10% for a progeny size larger than 50 in terms of the genetic load examined. The implications of these simulated results for purging deleterious genes of small effect in small breeding populations are discussed. Received: 5 July 1998 / Accepted: 5 August 1998     

Evolutionary rescue by compensatory mutations is constrained by genomic and environmental backgrounds

Since deleterious mutations may be rescued by secondary mutations during evolution, compensatory evolution could identify genetic solutions leading to therapeutic targets. Here, we tested this hypothesis and examined whether these solutions would be universal or would need to be adapted to one's genetic and environmental makeups. We performed experimental evolutionary rescue in a yeast disease model for the Wiskott–Aldrich syndrome in two genetic backgrounds and carbon sources. We found that multiple aspects of the evolutionary rescue outcome depend on the genotype, the environment, or a combination thereof. Specifically, the compensatory mutation rate and type, the molecular rescue mechanism, the genetic target, and the associated fitness cost varied across contexts. The course of compensatory evolution is therefore highly contingent on the initial conditions in which the deleterious mutation occurs. In addition, these results reveal biologically favored therapeutic targets for the Wiskott–Aldrich syndrome, including the target of an unrelated clinically approved drug. Our results experimentally illustrate the importance of epistasis and environmental evolutionary constraints that shape the adaptive landscape and evolutionary rate of molecular networks.     

Accumulation of deleterious mutations in small abiotic populations of RNA

The accumulation of slightly deleterious mutations in populations leads to the buildup of a genetic load and can cause the extinction of populations of small size. Mutation-accumulation experiments have been used to study this process in a wide variety of organisms, yet the exact mutational underpinnings of genetic loads and their fitness consequences remain poorly characterized. Here, we use an abiotic system of RNA populations evolving continuously in vitro to examine the molecular events that can instigate a genetic load. By tracking the fitness decline of ligase ribozyme populations with bottleneck sizes between 100 and 3000 molecules, we detected the appearance and subsequent fixation of both slightly deleterious mutations and advantageous mutations. Smaller populations went extinct in significantly fewer generations than did larger ones, supporting the notion of a mutational meltdown. These data suggest that mutation accumulation was an important evolutionary force in the prebiotic RNA world and that mechanisms such as recombination to ameliorate genetic loads may have been in place early in the history of life.     

An Experimental Test for Synergistic Epistasis and Its Application in Chlamydomonas

Theoretically, one of the most general benefits of sex is given by its function in facilitating selection against deleterious mutations. This advantage of sex may be deterministic if deleterious mutations affect the fitness of an individual in a synergistic way, i.e., if mutations increase each others' negative fitness effect. We present a new test for synergistic epistasis that considers the skewness of the log fitness distribution of offspring from a cross. We applied this test to data of the unicellular alga Chlamydomonas moewussii. For this purpose, two crosses were made: one between two strains that are presumed to have accumulated slightly deleterious mutations, the other between two strains without a history of mutation accumulation. Fitness was measured by estimating the two parameters of logistic growth in batch culture, the maximum growth rate (r) and the carrying capacity (K). The finding of a negatively skewed distribution for K in the accumulation cross suggests synergism between mutations affecting the carrying capacity, while the absence of skewness for r in both crosses is consistent with independent effects of mutations affecting this parameter. The results suggest a possible alternative explanation for the general observation that sex is related to constant environments, where selection on K predominates, while asexual reproduction is found in more variable environments, where selection on r is more important.     

Relative effects of segregation and recombination on the evolution of sex in finite diploid populations

The mechanism of reproducing more viable offspring in response to selection is a major factor influencing the advantages of sex. In diploids, sexual reproduction combines genotype by recombination and segregation. Theoretical studies of sexual reproduction have investigated the advantage of recombination in haploids. However, the potential advantage of segregation in diploids is less studied. This study aimed to quantify the relative contribution of recombination and segregation to the evolution of sex in finite diploids by using multilocus simulations. The mean fitness of a sexually or asexually reproduced population was calculated to describe the long-term effects of sex. The evolutionary fate of a sex or recombination modifier was also monitored to investigate the short-term effects of sex. Two different scenarios of mutations were considered: (1) only deleterious mutations were present and (2) a combination of deleterious and beneficial mutations. Results showed that the combined effects of segregation and recombination strongly contributed to the evolution of sex in diploids. If deleterious mutations were only present, segregation efficiently slowed down the speed of Muller''s ratchet. As the recombination level was increased, the accumulation of deleterious mutations was totally inhibited and recombination substantially contributed to the evolution of sex. The presence of beneficial mutations evidently increased the fixation rate of a recombination modifier. We also observed that the twofold cost of sex was easily to overcome in diploids if a sex modifier caused a moderate frequency of sex.     

Mating behavior as an indicator of quality of Drosophila subobscura males?

According to current theoretical predictions, any deleterious mutations that reduce nonsexual fitness may have a negative influence on mating success. This means that sexual selection may remove deleterious mutations from the populations. Males of good genetic quality should be more successful in mating, compared to the males of lower genetic quality. As mating success is a condition dependent trait, large fractions of the genome may be a target of sexual selection and many behavioral traits are likely to be condition dependent. We manipulated the genetic quality of Drosophila subobscura males by inducing mutations with ionizing radiation and observed the effects of the obtained heterozygous mutations on male mating behavior: courtship occurrence, courtship latency, mating occurrence, latency to mating and duration of mating. We found possible effects of mutations. Females mated more frequently with male progeny of nonirradiated males and that these males courted females faster compared to the male progeny of irradiated males. Our findings indicate a possible important role of sexual selection in purging deleterious mutations.     

Estimation of deleterious genomic mutation parameters in natural populations by accounting for variable mutation effects across loci

The genomes of all organisms are subject to continuous bombardment of deleterious genomic mutations (DGM). Our ability to accurately estimate various parameters of DGM has profound significance in population and evolutionary genetics. The Deng-Lynch method can estimate the parameters of DGM in natural selfing and outcrossing populations. This method assumes constant fitness effects of DGM and hence is biased under variable fitness effects of DGM. Here, we develop a statistical method to estimate DGM parameters by considering variable mutation effects across loci. Under variable mutation effects, the mean fitness and genetic variance for fitness of parental and progeny generations across selfing/outcrossing in outcrossing/selfing populations and the covariance between mean fitness of parents and that of their progeny are functions of DGM parameters: the genomic mutation rate U, average homozygous effect s, average dominance coefficient h, and covariance of selection and dominance coefficients cov(h, s). The DGM parameters can be estimated by the algorithms we developed herein, which may yield improved estimation of DGM parameters over the Deng-Lynch method as demonstrated by our simulation studies. Importantly, this method is the first one to characterize cov(h, s) for DGM.     

Deleterious mutations and the genetic variance of male fitness components in Mimulus guttatus

Deleterious mutations are relevant to a broad range of questions in genetics and evolutionary biology. I present an application of the "biometric method" for estimating mutational parameters for male fitness characters of the yellow monkeyflower, Mimulus guttatus. The biometric method rests on two critical assumptions. The first is that experimental inbreeding changes genotype frequencies without changing allele frequencies; i.e., there is no genetic purging during the experiment. I satisfy this condition by employing a breeding design in which the parents are randomly extracted, fully homozygous inbred lines. The second is that all genetic variation is attributable to deleterious mutations maintained in mutation-selection balance. I explicitly test this hypothesis using likelihood ratios. Of the three deleterious mutation models tested, the first two are rejected for all characters. The failure of these models is due to an excess of additive genetic variation relative to the expectation under mutation-selection balance. The third model is not rejected for either of two log-transformed male fitness traits. However, this model imposes only "weak conditions" and is not sufficiently detailed to provide estimates for mutational parameters. The implication is that, if biometric methods are going to yield useful parameter estimates, they will need to consider mutational models more complicated than those typically employed in experimental studies.     

The “balance” argument and the evolution of sex

The “balance” argument suggests that if sex were maladaptive at the individual level, it would be quickly lost from species with asexual/sexual alternation. Williams has suggested an “Aphid-Rotifer” model for such species. It has the following characteristics (a) parthenogenesis is favoured when the environment is stable (b) when the environment changes qualitatively, sex generates offspring with an increased fitness variance compared to parthenogenetic progeny (c) if selection is intense and sib competition occurs then sex is favoured. It is argued here that condition (b) is not essential to the model. An increased fitness variance may be generated by the recombination of unfavourable mutations when one or more of the following occur; (1) founder effects (2) inbreeding (3) haplo-diploidy (4) intra-male competition. Parthenogenesis sustains an advantage when selection is relaxed and the possession of mutations is not reflected in differences in fitness. Sex is favoured when selection is intense and fitness reflects the possession of unfavourable mutations.     

The effects of pathogen infection and mutation on life-history characters in Arabidopsis thaliana

The nature of the interaction among deleterious mutations is important to models in many areas of evolutionary biology. In addition, interactions between genetic and environmental factors may affect the predictions of such models. Individuals of unknown genotypes of Arabidopsis thaliana, ecotype Marburg, were exposed to five levels of chemical (EMS) mutagenesis and three levels of Pseudomonas syringae infection. Survival, growth and flowering characteristics of each individual were measured. The logarithm of fitness is expected to be a linear function of mutation number if mutations act independently. Furthermore, the expected number of mutations should be approximately a linear function of time of exposure to mutagen. Therefore, nonlinear effects of mutagen exposure on the logarithm of fitness characters would suggest epistasis between mutations. Similarly, if pathogen infection and mutation act independently of each other, their effects should be additive on a log scale. Statistical interactions between these factors would suggest they do not act independently; particularly, if highly mutated individuals suffer more when infected than do less mutated individuals, this suggests that pathogens and mutations act synergistically. Pseudomonas-infected individuals were shown to have an increased probability of flowering under conditions of short day length, but to ultimately produce fewer flowers than uninfected individuals. This suggests a plastic response to stress and, despite that response, an ultimately deleterious effect of infection on fitness. Leaf rosette growth was negatively and linearly related to the expected number of mutations, and the effects of mutation on different life-cycle stages appeared to be uncorrelated. No significant interactions between pathogen and mutation main effects were found. These results suggest that mutations act multiplicatively with each other and with pathogen infection in determining individual fitness.