High nucleotide polymorphism and rapid decay of linkage disequilibrium in wild populations of Caenorhabditis remanei

The common ancestor of the self-fertilizing nematodes Caenorhabditis elegans and C. briggsae must have reproduced by obligate outcrossing, like most species in this genus. However, we have only a limited understanding about how genetic variation is patterned in such male-female (gonochoristic) Caenorhabditis species. Here, we report results from surveying nucleotide variation of six nuclear loci in a broad geographic sample of wild isolates of the gonochoristic C. remanei. We find high levels of diversity in this species, with silent-site diversity averaging 4.7%, implying an effective population size close to 1 million. Additionally, the pattern of polymorphisms reveals little evidence for population structure or deviation from neutral expectations, suggesting that the sampled C. remanei populations approximate panmixis and demographic equilibrium. Combined with the observation that linkage disequilibrium between pairs of polymorphic sites decays rapidly with distance, this suggests that C. remanei will provide an excellent system for identifying the genetic targets of natural selection from deviant patterns of polymorphism and linkage disequilibrium. The patterns revealed in this obligately outcrossing species may provide a useful model of the evolutionary circumstances in C. elegans' gonochoristic progenitor. This will be especially important if self-fertilization evolved recently in C. elegans history, because most of the evolutionary time separating C. elegans from its known relatives would have occurred in a state of obligate outcrossing.     

Selection at linked sites in the partial selfer Caenorhabditis elegans

Natural selection can produce a correlation between local recombination rates and levels of neutral DNA polymorphism as a consequence of genetic hitchhiking and background selection. Theory suggests that selection at linked sites should affect patterns of neutral variation in partially selfing populations more dramatically than in outcrossing populations. However, empirical investigations of selection at linked sites have focused primarily on outcrossing species. To assess the potential role of selection as a determinant of neutral polymorphism in the context of partial self-fertilization, we conducted a multivariate analysis of single-nucleotide polymorphism (SNP) density throughout the genome of the nematode Caenorhabditis elegans. We based the analysis on a published SNP data set and partitioned the genome into windows to calculate SNP densities, recombination rates, and gene densities across all six chromosomes. Our analyses identify a strong, positive correlation between recombination rate and neutral polymorphism (as estimated by noncoding SNP density) across the genome of C. elegans. Furthermore, we find that levels of neutral polymorphism are lower in gene-dense regions than in gene-poor regions in some analyses. Analyses incorporating local estimates of divergence between C. elegans and C. briggsae indicate that a mutational explanation alone is unlikely to explain the observed patterns. Consequently, we interpret these findings as evidence that natural selection shapes genome-wide patterns of neutral polymorphism in C. elegans. Our study provides the first demonstration of such an effect in a partially selfing animal. Explicit models of genetic hitchhiking and background selection can each adequately describe the relationship between recombination rate and SNP density, but only when they incorporate selfing rate. Clarification of the relative roles of genetic hitchhiking and background selection in C. elegans awaits the development of specific theoretical predictions that account for partial self-fertilization and biased sex ratios.     

High local genetic diversity and low outcrossing rate in Caenorhabditis elegans natural populations

BACKGROUND: Caenorhabditis elegans is a major model system in biology, yet very little is known about its biology outside the laboratory. In particular, its unusual mode of reproduction with self-fertile hermaphrodites and facultative males raises the question of its frequency of outcrossing in natural populations. RESULTS: We describe the first analysis of C. elegans individuals sampled directly from natural populations. C. elegans is found predominantly in the dauer stage and with a very low frequency of males versus hermaphrodites. Whereas C. elegans was previously shown to display a low worldwide genetic diversity, we find by comparison a surprisingly high local genetic diversity of C. elegans populations; this local diversity is contributed in great part by immigration of new alleles rather than by mutation. Our results on heterozygote frequency, male frequency, and linkage disequilibrium furthermore show that selfing is the predominant mode of reproduction in C. elegans natural populations but that infrequent outcrossing events occur, at a rate of approximately 1%. CONCLUSIONS: Our results give a first insight in the biology of C. elegans in the natural populations. They demonstrate that local populations of C. elegans are genetically diverse and that a low frequency of outcrossing allows for the recombination of these locally diverse genotypes.     

Temporal dynamics and linkage disequilibrium in natural Caenorhabditis elegans populations

Caenorhabditis elegans is a major laboratory model system yet a newcomer to the field of population genetics, and relatively little is known of its biology in the wild. Recent studies of natural populations at a single time point revealed strong spatial population structure and suggested that these populations may be very dynamic. We have therefore studied several natural C. elegans populations over time and genotyped them at polymorphic microsatellite loci. While some populations appear to be genetically stable over the course of observation, others seem to go extinct, with full replacement of multilocus genotypes upon regrowth. The frequency of heterozygotes indicates that outcrossing occurs at a mean frequency of 1.7% and is variable between populations. However, in genetically stable populations, linkage disequilibrium between different chromosomes can be maintained over several years at a level much higher than expected from the heterozygote frequency. C. elegans seems to follow metapopulation dynamics, and the maintenance of linkage disequilibrium despite a low yet significant level of outcrossing suggests that selection may act against the progeny of outcrossings.     

Population genetics of Caenorhabditis elegans: the paradox of low polymorphism in a widespread species

Caenorhabditis elegans has become one of the most widely used model research organisms, yet we have little information on evolutionary processes and recent evolutionary history of this widespread species. We examined patterns of variation at 20 microsatellite loci in a sample of 23 natural isolates of C. elegans from various parts of the world. One-half of the loci were monomorphic among all strains, and overall genetic variation at microsatellite loci was low, relative to most other species. Some population structure was detected, but there was no association between the genetic and geographic distances among different natural isolates. Thus, despite the nearly worldwide occurrence of C. elegans, little evidence was found for local adaptation in strains derived from different parts of the world. The low levels of genetic variation within and among populations suggest that recent colonization and population expansion might have occurred. However, the patterns of variation are not consistent with population expansion. A possible explanation for the observed patterns is the action of background selection to reduce polymorphism, coupled with ongoing gene flow among populations worldwide.     

Predominance of outcrossing in Lymnaea stagnalis despite low apparent fitness costs of self-fertilization

We have quantified the natural mating system in eight populations of the simultaneously hermaphroditic aquatic snail Lymnaea stagnalis, and studied the ecological and genetic forces that may be directing mating system evolution in this species. We investigated whether the natural mating system can be explained by the availability of mates, by the differential survival of self- and cross-fertilized snails in nature, and by the effects of mating system on parental fecundity and early survival. The natural mating system of L. stagnalis was found to be predominantly cross-fertilizing. Density of snails in the populations had no relationship with the mating system, suggesting that outcrossing rates are not limited by mate availability at the population densities observed. Contrary to expectations for outcrossing species, we detected no evidence for inbreeding depression in survival in nature with inferential population genetic methods. Further, experimental manipulations of mating system in the laboratory revealed that self-fertilization had no effect on parental fecundity, and only minor effects on offspring survival. Predominance of cross-fertilization despite low apparent fitness costs of self-fertilization is at odds with the paradigm that high self-fertilization depression is necessary for maintenance of cross-fertilization in self-compatible hermaphrodites.     

Reproductive assurance through self-fertilization does not vary with population size in the alien invasive plant Datura stramonium

Autonomous self-fertilization is suggested to be associated with invasiveness in plants because it offers reproductive assurance when there is a shortage of suitable mates or pollinators. Given that shortages of mates and pollinators are a common cause of Allee effects in small plant populations, we predict that the benefits of self-fertilization in terms of reproductive assurance should be greatest in small populations. We tested this idea for the invasive herb Datura stramonium , a self-fertilizing species which is also cross-pollinated to some extent by insects (mainly hawkmoths and honeybees). During two consecutive years, we studied 20 and 55 populations, respectively, of different sizes. Untreated flowers of D. stramonium showed high levels of fruit and seed set in all populations studied. Although, fruit and seed set were generally reduced by about 90% in flowers in which self-fertilization was prevented through emasculation, this effect did not vary according to population size. By using a natural color (anthocyanin) dimorphism in 12 populations, we showed that the average outcrossing rate was low (1.3%) and that there was no relationship between outcrossing rate and population size. Pollen removal from flowers also did not vary according to population size, suggesting that the pollinator visitation rate is not lower in small populations. However, decreasing deviations of observed from expected fruit set with population size imply that small populations may have an increased chance of extinction due to demographic stochasticity. Overall, our results suggest that reproductive assurance through self-fertilization in invasive plants may be important for all stages of population establishment, and not just in the founder population.     

Do males facilitate the spread of novel phenotypes within populations of the androdioecious nematode Caenorhabditis elegans?

In the androdioecious nematode Caenorhabditis elegans, self-fertilization is the predominant mode of reproduction. Nevertheless, males do occur, and it is still unclear if these represent a selective advantage or merely an evolutionary relict. In this study, we first tested the hypothesis that the production of males might benefit invaders to resident populations. We added single, GFP-marked worms to established laboratory populations and followed GFP frequencies over time. Mated hermaphrodites and also males were more successful in invading resident populations if compared to single, unmated hermaphrodites. The observed higher frequencies should increase the likelihood that any of the associated invading alleles persist. Second, we tested the hypothesis that males and, thus, higher outcrossing rates, are specifically favored under changing environmental conditions. After an outbred population was subjected to changing stress or to control laboratory conditions, we measured the male maintenance of the resulting populations. Interestingly all populations, experimental and control alike, showed high male maintenance, suggesting that persistence of males is also favored under standard laboratory conditions.     

SEXUAL PARTNERS FOR THE STRESSED: FACULTATIVE OUTCROSSING IN THE SELF-FERTILIZING NEMATODE CAENORHABDITIS ELEGANS

Sexual reproduction shuffles genetic variation, potentially enhancing the evolutionary response to environmental change. Many asexual organisms respond to stress by generating facultative sexual reproduction, presumably as a means of escaping the trap of low genetic diversity. Self-fertilizing organisms are subject to similar genetic limitations: the consistent loss of genetic diversity within lineages restricts the production of variation through recombination. Selfing organisms may therefore benefit from a similar shift in mating strategy during periods of stress. We determined the effects of environmental stress via starvation and passage through the stress-resistant dauer stage on mating system dynamics of Caenorhabditis elegans , which reproduces predominantly through self-fertilization but is capable of outcrossing in the presence of males. Starvation elevated male frequencies in a strain-specific manner through differential male survival during dauer exposure and increased outcrossing rates after dauer exposure. In the most responsive strain, the mating system changed from predominantly selfing to almost exclusively outcrossing. Like facultative sex in asexual organisms, facultative outcrossing in C. elegans may periodically facilitate adaptation under stress. Such a shift in reproductive strategy should have a major impact on evolutionary change within these populations and may be a previously unrecognized feature of other highly selfing organisms.     

Subdivision and haplotype structure in natural populations of Arabidopsis lyrata

High levels of inbreeding are expected to cause a strong reduction in levels of genetic variability, effective recombination rates and in adaptation compared with related outcrossing populations. We examined patterns of DNA polymorphism at five nuclear loci and one chloroplast locus within and between four populations of the outcrossing plant Arabidopsis lyrata, a close relative of the highly self-fertilizing model species A. thaliana. The observed patterns are compared with species-wide polymorphism at orthologous loci, as well as within- and between-population patterns at other studied loci in A. thaliana. In addition to evidence for much higher average within-population diversity, species-wide levels of silent polymorphism are generally higher in A. lyrata than in A. thaliana, unlike the results from a previous study of the ADH locus. However, polymorphism is also low in the North American A. lyrata subspecies lyrata compared with the European subspecies petraea, suggesting either a population bottleneck in North American populations or recent admixture involving diverged European populations. Differentiation between the two subspecies is strong, although there are few fixed differences, suggesting that their isolation is recent. Estimates of intralocus recombination rates and analysis of haplotype structure in European A. lyrata populations indicate lower recombination than predicted based on the variability together with physical recombination rates estimated from A. thaliana. This may be due to strong population subdivision, or to recent departures from demographic equilibrium such as a bottleneck or population admixture. Alternatively, there may be consistently lower recombination rates in the outcrossing species. In contrast, estimates of recombination rates from species-wide samples of A. thaliana are close to the values expected assuming a high rate of self-fertilization. Complex population histories in both A. thaliana and A. lyrata complicate theoretical predictions and empirical tests of the effects of inbreeding on polymorphism and molecular evolution.     

Patterns of molecular evolution in Caenorhabditis preclude ancient origins of selfing

The evolution of self-fertilization can mediate pronounced changes in genomes as a by-product of a drastic reduction in effective population size and the concomitant accumulation of slightly deleterious mutations by genetic drift. In the nematode genus Caenorhabditis, a highly selfing lifestyle has evolved twice independently, thus permitting an opportunity to test for the effects of mode of reproduction on patterns of molecular evolution on a genomic scale. Here we contrast rates of nucleotide substitution and codon usage bias among thousands of orthologous groups of genes in six species of Caenorhabditis, including the classic model organism Caenorhabditis elegans. Despite evidence that weak selection on synonymous codon usage is pervasive in the history of all species in this genus, we find little difference among species in the patterns of codon usage bias and in replacement-site substitution. Applying a model of relaxed selection on codon usage to the C. elegans and C. briggsae lineages suggests that self-fertilization is unlikely to have evolved more than approximately 4 million years ago, which is less than a quarter of the time since they shared a common ancestor with outcrossing species. We conclude that the profound changes in mating behavior, physiology, and developmental mechanisms that accompanied the transition from an obligately outcrossing to a primarily selfing mode of reproduction evolved in the not-too-distant past.     

The proximate determinants of sex ratio in C. elegans populations

The soil nematode Caenorhabditis elegans is an example of a species in which self-fertilizing hermaphrodites predominate, but functional males continue to persist--allowing outcrossing to persevere at low levels. Hermaphrodites can produce male progeny as a consequence of sex chromosome non-disjunction or via outcrossing with males. Consequently, the genetics of sex determination coupled with the efficiency by which males find, inseminate and obtain fertilizations with hermaphrodites will influence the frequency at which males and outcrossing occurs in such populations. Behavioural and physiological traits with a heritable basis, as well as ecological characters, may influence male reproductive success and therefore sex ratio. Because sex ratio is tied to male reproductive success, sex ratio greatly affects outcrossing rates, patterns of genetic variation, and the ability of natural selection to act within populations. In this paper we explore the determinants of male frequency in C. elegans with a mathematical model and experimental data. We address the role of the genetic machinery of sex determination via sex chromosome non-disjunction on sex ratio and the influence of physiological components of C. elegans' life history that contribute to variation in sex ratio by way of male reproductive success. Finally, we discuss the short-term and long-term factors that are likely to affect sex ratio and breeding system evolution in species like C. elegans.     

Inbreeding and outbreeding depression in Caenorhabditis nematodes

The nematode Caenorhabditis elegans reproduces primarily by self-fertilization of hermaphrodites, yet males are present at low frequencies in natural populations (androdioecy). The ancestral state of C. elegans was probably gonochorism (separate males and females), as in its relative C. remanei. Males may be maintained in C. elegans because outcrossed individuals escape inbreeding depression. The level of inbreeding depression is, however, expected to be low in such a highly selfing species, compared with an outcrosser like C. remanei. To investigate these issues, we measured life-history traits in the progeny of inbred versus outcrossed C. elegans and C. remanei individuals derived from recently isolated natural populations. In addition, we maintained inbred lines of C. remanei through 13 generations of full-sibling mating. Highly inbred C. remanei showed dramatic reductions in brood size and relative fitness compared to outcrossed individuals, with evidence of both direct genetic and maternal-effect inbreeding depression. This decline in fitness accumulated over time, causing extinction of nearly 90% of inbred lines, with no evidence of purging of deleterious mutations from the remaining lines. In contrast, pure strains of C. elegans performed better than crosses between strains, indicating outbreeding depression. The results are discussed in relation to the evolution of androdioecy and the effect of mating system on the level of inbreeding depression.     

INBREEDING EFFECTS IN CLARKIA TEMBLORIENSIS (ONAGRACEAE) POPULATIONS WITH DIFFERENT NATURAL OUTCROSSING RATES

Inbreeding depression is commonly observed in natural populations. The deleterious effects of forced inbreeding are often thought to be less pronounced in populations with self-pollinating mating systems than in primarily outcrossing populations. We tested this hypothesis by comparing the performance of plants produced by artificial self- and cross-pollination from three populations whose outcrossing rate estimates were 0.03, 0.26, and 0.58. Outcrossing rates and inbreeding coefficients were estimated using isozyme polymorphisms as genetic markers. Analysis of F statistics suggests that biparental inbreeding as well as self-fertilization contribute to the level of homozygosity in the seed crop. Biparental inbreeding will reduce the heterozygosity of progeny produced by outcrossing, relative to random outcrossing expectations, and hence will reduce the effects of outcrossing versus self-fertilization. Heterotic selection may increase the average heterozygosity during the life history. Selfed and outcrossed seeds from all three populations were equally likely to germinate and survive to reproduce. However, inbreeding depression was observed in fecundity traits of plants surviving to reproduction in all three populations. Even in the population whose natural self-fertilization rate was 97%, plants grown from seed produced by self-pollination produced fewer fruits and less total seed weight than plants grown from outcrossed seed. There was no detectable inbreeding depression in estimated lifetime fitness. Inbreeding effects for all reproductive yield characters were most severe in the accession from the most outcrossing population and least severe in the accession from the most self-fertilizing population.     

Genetic variation for outcrossing among Caenorhabditis elegans isolates

The evolution of breeding systems results from the existence of genetic variation and selective forces favoring different outcrossing rates. In this study we determine the extent of genetic variation for characters directly related to outcrossing, such as male frequency, male mating ability, and male reproductive success, in several wild isolates of the nematode Caenorhabditis elegans. This species is characterized by an androdioecious breeding system in which males occur with hermaphrodites that can either self-fertilize or outcross with males. We find genetic variation for all characters measured, but also find that environmental variation is a large fraction of the total phenotypic variance. We further determine the existence of substantial genetic variation for population competitive performance in several laboratory environments. However, these measures are uncorrelated with outcrossing characters. The data presented here contribute to an understanding of male maintenance in natural populations through their role in outcrossing.     

Evolution of outcrossing in experimental populations of Caenorhabditis elegans

Caenorhabditis elegans can reproduce exclusively by self-fertilization. Yet, males can be maintained in laboratory populations, a phenomenon that continues to puzzle biologists. In this study we evaluated the role of males in facilitating adaptation to novel environments. For this, we contrasted the evolution of a fitness component exclusive to outcrossing in experimental populations of different mating systems. We introgressed a modifier of outcrossing into a hybrid population derived from several wild isolates to transform the wild-type androdioecious mating system into a dioecious mating system. By genotyping 375 single-nucleotide polymorphisms we show that the two populations had similar standing genetic diversity available for adaptation, despite the occurrence of selection during their derivation. We then performed replicated experimental evolution under the two mating systems from starting conditions of either high or low levels of diversity, under defined environmental conditions of discrete non-overlapping generations, constant density at high population sizes (N = 10⁴), no obvious spatial structure and abundant food resources. During 100 generations measurements of sex ratios and male competitive performance showed: 1) adaptation to the novel environment; 2) directional selection on male frequency under androdioecy; 3) optimal outcrossing rates of 0.5 under androdioecy; 4) the existence of initial inbreeding depression; and finally 5) that the strength of directional selection on male competitive performance does not depend on male frequencies. Taken together, these results suggest that androdioecious males are maintained at intermediate frequencies because outcrossing is adaptive.     

Patterns of nucleotide polymorphism distinguish temperate and tropical wild isolates of Caenorhabditis briggsae

Caenorhabditis briggsae provides a natural comparison species for the model nematode C. elegans, given their similar morphology, life history, and hermaphroditic mode of reproduction. Despite C. briggsae boasting a published genome sequence and establishing Caenorhabditis as a model genus for genetics and development, little is known about genetic variation across the geographic range of this species. In this study, we greatly expand the collection of natural isolates and characterize patterns of nucleotide variation for six loci in 63 strains from three continents. The pattern of polymorphisms reveals differentiation between C. briggsae strains found in temperate localities in the northern hemisphere from those sampled near the Tropic of Cancer, with diversity within the tropical region comparable to what is found for C. elegans in Europe. As in C. elegans, linkage disequilibrium is pervasive, although recombination is evident among some variant sites, indicating that outcrossing has occurred at a low rate in the history of the sample. In contrast to C. elegans, temperate regions harbor extremely little variation, perhaps reflecting colonization and recent expansion of C. briggsae into northern latitudes. We discuss these findings in relation to their implications for selection, demographic history, and the persistence of self-fertilization.     

Allee effect and self-fertilization in hermaphrodites: reproductive assurance in demographically stable populations

The fact that selfing increases seed set (reproductive assurance) has often been put forward as an important selective force for the evolution of selfing. However, the role of reproductive assurance in hermaphroditic populations is far from being clear because of a lack of theoretical work. Here, I propose a theoretical model that analyzes self-fertilization in the presence of reproductive assurance. Because reproductive assurance directly influences the per capita growth rate, I developed an explicit demographic model for partial selfers in the presence of reproductive assurance, specifically when outcrossing is limited by the possibility of pollen transfer (Allee effect). Mating system parameters are derived as a function of the underlying demographical parameters. The functional link between population demography and mating system parameters (reproductive assurance, selfing rate) can be characterized. The demographic model permits the analysis of the evolution of self-fertilization in stable populations when reproductive assurance occurs. The model reveals some counterintuitive results such as the fact that increasing the fraction of selfed ovules can, in certain circumstances, increase the fraction of outcrossed ovules. Moreover, I demonstrate that reproductive assurance per se cannot account for the evolution of stable mixed selfing rates. Also, the model reveals that the extinction of outcrossing populations depends on small changes in population density (ecological perturbations), while the transition from outcrossing to selfing can, in certain cases, lead the population to extinction (evolutionary suicide). More generally, this paper highlights the fact that self-fertilization affects both the dynamics of individuals and the dynamics of selfing genes in hermaphroditic populations.     

Allee effect and self-fertilization in hermaphrodites: reproductive assurance in a structured metapopulation

Reproductive assurance through selfing during colonization events or when population densities are low has often been put forward as a mechanism selecting for the evolution of self-fertilization. Such arguments emphasize on the role of both local demography and metapopulation processes. We developed a model for the evolution of self-fertilization in a structured metapopulation in which local densities are not steady because of population growth. Reproduction by selfing is density-independent (reproductive assurance) but selfed seeds endure inbreeding depression, whereas reproduction by outcrossing is density-dependent (Allee effect). First, we derived an analytical criterion for metapopulation viability as a function of the selfing rate and metapopulation parameters. We show that outcrossers can develop a viable metapopulation when they produce a high amount of dispersal seeds that counterbalances their incapacity to found new populations from low densities. Second, the model shows there is a positive feedback between demography and outcrossing rates, leading to either complete outcrossing or selfing. Specifically, we illustrate that inbreeding depression can paradoxically favor the evolution of selfing because of its negative effect on density. Also, complete outcrossing can be selected despite pollen limitation, although it does not provide a full seed set. This model underlines the influence of the mating system both on demography and gene dynamics in a metapopulation context.