Contrasting patterns of synonymous and nonsynonymous sequence evolution in asexual and sexual freshwater snail lineages

In asexual lineages, both synonymous and nonsynonymous sequence polymorphism may be reduced due to severe founder effects when asexual lineages originate. However, mildly deleterious (nonsynonymous) mutations may accumulate after asexual lineages are formed, because the efficiency of purifying selection is reduced even in the nonrecombining mitochondrial genome. Here we examine patterns of synonymous and nonsynonymous mitochondrial sequence polymorphism in asexual and sexual lineages of the freshwater snail Campeloma. Using clade-specific estimates, we found that synonymous sequence polymorphism was significantly reduced by 75% in asexuals relative to sexuals, whereas nonsynonymous sequence polymorphism did not differ significantly between sexuals and asexuals. Two asexual clades had high negative values for Tajima's D statistic. Coalescent simulations confirmed that various bottleneck scenarios can account for this result. We also used branch-specific estimates of the ratio of amino acid to silent substitutions, K(a)/K(s). Our study revealed that K(a)/K(s) ratios are six times higher in terminal branches of independent asexual lineages compared to sexuals. Coalescent-based reconstruction of gene networks for all sexual and asexual clades indicated that nonsynonymous mutations occurred at a higher frequency in recently derived asexual haplotypes. These findings suggest that patterns of synonymous and nonsynonymous nucleotide polymorphism in asexual snail lineages may be shaped by both severe founder effect and relaxed purifying selection.     

EVOLUTIONARY FEEDBACKS BETWEEN REPRODUCTIVE MODE AND MUTATION RATE EXACERBATE THE PARADOX OF SEX

Evolutionary theory suggests that low mutation rates should favor the persistence of asexuals. Additionally, given the observation that most nonneutral mutations are deleterious, asexuality may strengthen selection for reduced mutation rates. This reciprocal relationship raises the possibility of a positive feedback loop between sex and mutation rate. We explored the consequences of this evolutionary feedback with an individual‐based model in which a sexual population is continually challenged by the introduction of asexual clones. We found that asexuals were more likely to spread in a population when mutation rates were able to evolve relative to a model in which mutation rates were held constant. In fact, under evolving mutation rates, asexuals were able to spread to fixation even when sexuals faced no cost of sex whatsoever. The added success of asexuals was the result of their ability to evolve lower mutation rates and thereby slow the process of mutation accumulation that otherwise limited their spread. Given the existence of ample mutation rate variation in natural populations, our findings show that the evolutionary feedback between sex and mutation rate may intensify the “paradox of sex,” supporting the argument that deleterious mutation accumulation alone is likely insufficient to overcome the reproductive advantage of asexual competitors in the short term.     

Range expansions of sexual versus asexual organisms: Effects of reproductive assurance and migration load

It is generally considered that sexual organisms show faster evolutionary adaptation than asexual organisms because sexuals can accumulate adaptive mutations through recombination. Yet, empirical evidence often shows that the geographic range size of sexual species is narrower than that of closely related asexual species, which may seem as if asexuals can adapt to more varied environments. Two potential explanations for this apparent contradiction considered by the existing theory are reproduction assurance and migration load. Here, we consider both reproductive assurance and migration load within a single model to comparatively examine their effects on range expansions of sexuals and asexuals across an environmental gradient. The model shows that higher dispersal propensity decreases sexuals' disadvantage in reproductive assurance while increasing their disadvantage in migration load. Moreover, lower mutation rate constrains adaptation more strongly in asexuals than in sexuals. Thus, high dispersal propensity and high mutation rates promote that asexuals have wider range sizes than sexuals. Intriguingly, our model reveals that sexuals can have wider geographic range sizes than asexuals under low dispersal propensity and low mutation rates, a pattern consistent with a few exceptional empirical cases. Combining reproductive assurance and migration load provides a useful perspective to better understand the relationships between species' mating systems and their geographic ranges.     

Existence of two sexual races in the planarian species switching between asexual and sexual reproduction

In certain planarian species that are able to switch between asexual and sexual reproduction, determining whether a sexual has the ability to switch to the asexual state is problematic, which renders the definition of sexuals controversial. We experimentally show the existence of two sexual races, acquired and innate, in the planarian Dugesia ryukyuensis. Acquired sexuals used in this study were experimentally switched from asexuals. Inbreeding of acquired sexuals produced both innate sexuals and asexuals, but inbreeding of innate sexuals produced innate sexuals only and no asexuals. Acquired sexuals, but not innate sexuals, were forced to become asexuals by ablation and regeneration (asexual induction). This suggests that acquired sexuals somehow retain asexual potential, while innate sexuals do not. We also found that acquired sexuals have the potential to develop hyperplastic and supernumerary ovaries, while innate sexuals do not. In this regard, acquired sexuals were more prolific than innate sexuals. The differences between acquired and innate sexuals will provide a structure for examining the mechanism underlying asexual and sexual reproduction in planarians.     

The evolution of geographic parthenogenesis in Timema walking-sticks

Phylogenetic studies of asexual lineages and their sexual progenitors are useful for inferring the causes of geographical parthenogenesis and testing hypotheses regarding the evolution of sex. With five known parthenogens and well-studied ecology, Timema walking-sticks are a useful system for studying these questions. Timema are mainly endemic to California and they exhibit the common pattern of geographical parthenogenesis, with asexuals exhibiting more-northerly distributions. Neighbour-joining and maximum-parsimony analyses of 416 bp of mitochondrial cytochrome oxidase I (COI) from 168 individuals were used to infer general phylogenetic relationships, resulting in three major phylogeographical subdivisions: a Northern clade; a Santa Barbara clade; and a Southern clade. A nested cladistic analysis, comparing intra- and interspecific haplotypic variation on a geographical scale, revealed that the overall pattern of geographical parthenogenesis in Timema could be attributed to historical range expansion. These results suggest that geographical parthenogenesis is the result of more-extensive northerly dispersal of asexuals than sexuals.     

Molecular evidence for ancient asexuality in timema stick insects

Asexuality is rare in animals in spite of its apparent advantage relative to sexual reproduction, indicating that it must be associated with profound costs [1-9]. One expectation is that reproductive advantages gained by new asexual lineages will be quickly eroded over time [3, 5-7]. Ancient asexual taxa that have evolved and adapted without sex would be "scandalous" exceptions to this rule, but it is often difficult to exclude the possibility that putative asexuals deploy some form of "cryptic" sex, or have abandoned sex more recently than estimated from divergence times to sexual relatives [10]. Here we provide evidence, from high intraspecific divergence of mitochondrial sequence and nuclear allele divergence patterns, that several independently derived Timema stick-insect lineages have persisted without recombination for more than a million generations. Nuclear alleles in the asexual lineages displayed significantly higher intraindividual divergences than in related sexual species. In addition, within two asexuals, nuclear allele phylogenies suggested the presence of two clades, with sequences from the same individual appearing in both clades. These data strongly support ancient asexuality in Timema and validate the genus as an exceptional opportunity to attack the question of how asexual reproduction can be maintained over long periods of evolutionary time.     

LOWER MITE INFESTATIONS IN AN ASEXUAL GECKO COMPARED WITH ITS SEXUAL ANCESTORS

What advantage do sexually reproducing organisms gain from their mode of reproduction that compensates for their twofold loss in reproductive rate relative to their asexual counterparts? One version of the Red Queen hypothesis suggests that selective pressure from parasites is strongest on the most common genotype in a population, and thus genetically identical clonal lineages are more vulnerable to parasitism over time than genetically diverse sexual lineages. Our surveys of the ectoparasites of an asexual gecko and its two sexual ancestral species show that the sexuals have a higher prevalence, abundance, and mean intensity of mites than asexuals sharing the same habitat. Our experimental data indicate that in one sexual/asexual pair this pattern is at least partly attributable to higher attachment rates of mites to sexuals. Such a difference may occur as a result of exceptionally high susceptibility of the sexuals to mites because of their low genetic diversity (relative to other more-outbred sexual species) and their potentially high stress levels, or as a result of exceptionally low susceptibility of the asexuals to mites because of their high levels of heterozygosity.     

Recent and ancient asexuality in Timema walkingsticks

Determining the evolutionary age of asexual lineages should help in inferring the temporal scale under which asexuality and sex evolve and assessing selective factors involved in the evolution of asexuality. We used 416 bp of the mitochondrial COI gene to infer phylogenetic relationships of virtually all known Timema walkingstick species, including extensive intraspecific sampling for all five of the asexuals and their close sexual relatives. The asexuals T. douglasi and T. shepardii were very closely related to each other and evolutionarily young (less than 0.5 million years old). For the asexuals T. monikensis and T. tahoe, evidence for antiquity was weak since only one population of each was sampled, intraspecific divergences were low, and genetic distances to related sexuals were high: maximum-likelihood molecular-clock age estimates ranged from 0.26 to 2.39 million years in T. monikensis and from 0.29-1.06 million years in T. tahoe. By contrast, T. genevieve was inferred to be an ancient asexual, with an age of 0.81 to 1.42 million years. The main correlate of the age of asexual lineages was their geographic position, with younger asexuals being found further north.     

Twigs on the tree of life? Neutral and selective models for integrating macroevolutionary patterns with microevolutionary processes in the analysis of asexuality

Neutral models characterize evolutionary or ecological patterns expected in the absence of specific causal processes, such as natural selection or ecological interactions. In this study, we describe and evaluate three neutral models that can, in principle, help to explain the apparent 'twigginess' of asexual lineages on phylogenetic trees without involving the negative consequences predicted for the absence of recombination and genetic exchange between individuals. Previously, such phylogenetic twiggyness of asexual lineages has been uncritically interpreted as evidence that asexuality is associated with elevated extinction rates and thus represents an evolutionary dead end. Our first model uses simple phylogenetic simulations to illustrate that, with sexual reproduction as the ancestral state, low transition rates to stable asexuality, or low rates of ascertained 'speciation' in asexuals, can generate twiggy distributions of asexuality, in the absence of high extinction rates for asexual lineages. The second model, developed by Janko et   al . (2008 ), shows that a dynamic equilibrium between origins and neutral losses of asexuals can, under some conditions, generate a relatively low mean age of asexual lineages. The third model posits that the risk of extinction for asexual lineages may be higher than that of sexuals simply because asexuals inhabit higher latitudes or altitudes, and not due to effects of their reproductive systems. Such neutral models are useful in that they allow quantitative evaluation of whether empirical data, such as phylogenetic and phylogeographic patterns of sex and asexuality, indeed support the idea that asexually reproducing lineages persist over shorter evolutionary periods than sexual lineages, due to such processes as mutation accumulation, slower rates of adaptive evolution, or relatively lower levels of genetic variability.     

Radical amino acid mutations persist longer in the absence of sex

Harmful mutations are ubiquitous and inevitable, and the rate at which these mutations are removed from populations is a critical determinant of evolutionary fate. Closely related sexual and asexual taxa provide a particularly powerful setting to study deleterious mutation elimination because sexual reproduction should facilitate mutational clearance by reducing selective interference between sites and by allowing the production of offspring with different mutational complements than their parents. Here, we compared the rate of removal of conservative (i.e., similar biochemical properties) and radical (i.e., distinct biochemical properties) nonsynonymous mutations from mitochondrial genomes of sexual versus asexual Potamopyrgus antipodarum, a New Zealand freshwater snail characterized by coexisting and ecologically similar sexual and asexual lineages. Our analyses revealed that radical nonsynonymous mutations are cleared at higher rates than conservative changes and that sexual lineages eliminate radical changes more rapidly than asexual counterparts. These results are consistent with reduced efficacy of purifying selection in asexual lineages allowing harmful mutations to remain polymorphic longer than in sexual lineages. Together, these data illuminate some of the population‐level processes contributing to mitochondrial mutation accumulation and suggest that mutation accumulation could influence the outcome of competition between sexual and asexual lineages.     

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.     

Discordance between nuclear and mitochondrial genomes in sexual and asexual lineages of the freshwater snail Potamopyrgus antipodarum

The presence and extent of mitonuclear discordance in coexisting sexual and asexual lineages provides insight into 1) how and when asexual lineages emerged, and 2) the spatial and temporal scales at which the ecological and evolutionary processes influencing the evolution of sexual and asexual reproduction occur. Here, we used nuclear single‐nucleotide polymorphism (SNP) markers and a mitochondrial gene to characterize phylogeographic structure and the extent of mitonuclear discordance in Potamopyrgus antipodarum. This New Zealand freshwater snail is often used to study the evolution and maintenance of sex because obligately sexual and obligately asexual individuals often coexist. While our data indicate that sexual and asexual P. antipodarum sampled from the same lake population are often genetically similar, suggesting recent origin of these asexuals from sympatric sexual P. antipodarum, we also found significantly more population structure in sexuals vs. asexuals. This latter result suggests that some asexual lineages originated in other lakes and/or in the relatively distant past. When comparing mitochondrial and nuclear population genetic structure, we discovered that one mitochondrial haplotype (‘1A’) was rare in sexuals, but common and widespread in asexuals. Haplotype 1A frequency and nuclear genetic diversity were not associated, suggesting that the commonness of this haplotype cannot be attributed entirely to genetic drift and pointing instead to a role for selection.     

Population structure, parasitism, and survivorship of sexual and autodiploid parthenogenetic Campeloma limum

Two theories for the maintenance of sexual reproduction, the Red Queen hypothesis and mutation accumulation, suggest that the dispersal rates of sexuals and asexuals may determine the elimination or persistence of asexuals. Under higher dispersal rates of asexuals, asexuals may temporarily escape virulent parasites and reduce the effects of deleterious mutations. In the present study, I examine the population structure, parasite loads, and juvenile survivorship of Campeloma limum sexuals and autodiploid parthenogens from the southeastern U.S. Atlantic coastal plain. Using mtDNA sequence variation, it is shown that parthenogenetic haplotypes with limited sequence divergence are geographically widespread throughout this region and there is no significant population differentiation over a broad geographical scale. Sexual C. limum populations show significant mtDNA differentiation among and within river drainages and there is significant isolation by distance. These patterns are consistent with a recent origin and range expansion of parthenogens. Prevalence of infection by digenetic trematodes is significantly higher in autodiploid parthenogens, and the variance of prevalence is also higher in autodiploid parthenogens. I argue that the latter pattern indicates that unparasitized parthenogens have temporarily escaped these virulent parasites, but recolonization of these populations by trematodes results in high infection levels (> 40%), possibly due to reduced variation in resistance genes. I also examined whether the survivorship of juvenile sexuals and parthenogens varied under different stress levels. Sexual juveniles had twofold higher survivorship in all environments. Compared to polyploid parthenogens, autodiploid parthenogens may be less buffered against the effects of deleterious recessive alleles. I propose that the combined effects of higher parasitism and reduced juvenile survivorship of these autodiploid parthenogens accounts for the spatial distribution of sexual and parthenogenetic C. limum in the Atlantic coastal plain. Parthenogens may persist by higher dispersal rates into marginal habitats where there is a temporary escape from digenetic trematodes and competition with sexuals.     

Genetic load in sexual and asexual diploids: segregation, dominance and genetic drift

In diploid organisms, sexual reproduction rearranges allelic combinations between loci (recombination) as well as within loci (segregation). Several studies have analyzed the effect of segregation on the genetic load due to recurrent deleterious mutations, but considered infinite populations, thus neglecting the effects of genetic drift. Here, we use single-locus models to explore the combined effects of segregation, selection, and drift. We find that, for partly recessive deleterious alleles, segregation affects both the deterministic component of the change in allele frequencies and the stochastic component due to drift. As a result, we find that the mutation load may be far greater in asexuals than in sexuals in finite and/or subdivided populations. In finite populations, this effect arises primarily because, in the absence of segregation, heterozygotes may reach high frequencies due to drift, while homozygotes are still efficiently selected against; this is not possible with segregation, as matings between heterozygotes constantly produce new homozygotes. If deleterious alleles are partly, but not fully recessive, this causes an excess load in asexuals at intermediate population sizes. In subdivided populations without extinction, drift mostly occurs locally, which reduces the efficiency of selection in both sexuals and asexuals, but does not lead to global fixation. Yet, local drift is stronger in asexuals than in sexuals, leading to a higher mutation load in asexuals. In metapopulations with turnover, global drift becomes again important, leading to similar results as in finite, unstructured populations. Overall, the mutation load that arises through the absence of segregation in asexuals may greatly exceed previous predictions that ignored genetic drift.     

Aging asexual lineages and the evolutionary maintenance of sex

Finite populations of asexual and highly selfing species suffer from a reduced efficacy of selection. Such populations are thought to decline in fitness over time due to accumulating slightly deleterious mutations or failing to adapt to changing conditions. These within‐population processes that lead nonrecombining species to extinction may help maintain sex and outcrossing through species level selection. Although inefficient selection is proposed to elevate extinction rates over time, previous models of species selection for sex assumed constant diversification rates. For sex to persist, classic models require that asexual species diversify at rates lower than sexual species; the validity of this requirement is questionable, both conceptually and empirically. We extend past models by allowing asexual lineages to decline in diversification rates as they age, that is nonrecombining lineages “senesce” in diversification rates. At equilibrium, senescing diversification rates maintain sex even when asexual lineages, at young ages, diversify faster than their sexual progenitors. In such cases, the age distribution of asexual lineages contains a peak at intermediate values rather than showing the exponential decline predicted by the classic model. Coexistence requires only that the average rate of diversification in asexuals be lower than that of sexuals.     

The cost of males in Daphnia pulex

Sex is paradoxical, because asexuals should replace their sexual ancestors by avoiding the demographic cost of producing males (hereafter referred to as the cost‐of‐males). Despite the large body of theoretical and empirical work dealing with the paradox of sex, the cost‐of‐males assumption has been rarely tested. In the present study, we tested the cost‐of‐males assumption in the cladoceran Daphnia pulex. Populations of this species consist of both cyclically parthenogenetic (i.e. sexuals) and obligately parthenogenetic (i.e. asexuals) lineages. In addition, some of the asexual lineages produce only female offspring, whereas others produce functional males, which can mate with sexual females. We compared the reproductive investment of sexuals, male‐producing asexuals, and non‐male‐producing asexuals when raised separately under various environmental conditions. We also determined the outcome of competition between pair‐wise combinations of these reproductive modes. The cost of males was evident when sexual and asexual females were raised separately: sexuals produced fewer female offspring. However, there was no cost of males when reproductive modes were raised in pairs, as sexuals won the competition with asexuals. Our results directly relate to the field conditions experienced by D. pulex. Sexuals might suffer the cost of males at the beginning of the season, when resource competition is low; but when conditions deteriorate as the population approaches carrying capacity, sexuals seem to be better competitors in spite of male production.     

Parasites and sexual reproduction in psychid moths

Persistence of sexual reproduction among coexisting asexual competitors has been a major paradox in evolutionary biology. The number of empirical studies is still very limited, as few systems with coexisting sexual and strictly asexual lineages have been found. We studied the ecological mechanisms behind the simultaneous coexistence of a sexually and an asexually reproducing closely related species of psychid moth in Central Finland between 1999 and 2001. The two species compete for the same resources and are often infected by the same hymenopteran parasitoids. They are extremely morphologically and behaviorally similar and can be separated only by their reproductive strategy (sexual vs. asexual) or by genetic markers. We compared the life-history traits of these species in two locations where they coexist to test predictions of the cost-of-sex hypothesis. We did not find any difference in female size, number of larvae, or offspring survival between the sexuals and asexuals, indicating that sexuals are subject to cost of sex. We also used genetic markers to check and exclude the possibility of Wolbachia bacteria infection inducing parthenogenesis. None of the samples was infected by Wolbachia and, thus, it is unlikely that these bacteria could affect our results. We sampled 38 locations to study the prevalence of parasitoids and the moths' reproductive strategy. We found a strong positive correlation between prevalence of sexual reproduction and prevalence of parasitoids. In locations where parasitoids are rare asexuals exist in high densities, whereas in locations with a high parasitoid load the sexual species was dominant. Spatial distribution alone does not explain the results. We suggest that the parasite hypothesis for sex may offer an explanation for the persistence of sexual moths in this system.     

Equal fecundity in asexual and sexual mollies (<Emphasis Type="Italic">Poecilia</Emphasis>)

The evolution and maintenance of sexual reproduction is still one of the major unresolved problems in evolutionary biology. Sexual reproduction is fraught with a number of costs as compared to asexual reproduction. For example, sexuals have to produce males, which–given a 1:1 sex ratio—results in a two-fold advantage for asexuals that do not produce males. Consequently, asexuals will outperform and replace sexuals over time assuming everything else is equal. Nonetheless, a few cases of closely related asexuals and sexuals have been documented to coexist stably in natural systems. We investigated the presence of a two-fold cost in a unique system of three closely related fish species: the asexual Amazon Molly (Poecilia formosa), and two sexual species, Sailfin Molly (P. latipinna) and Atlantic Molly (P. mexicana). Amazon Molly reproduce gynogenetically (by sperm dependent parthenogenesis) and always coexist with one of the sexual species, which serves as sperm donor. In the laboratory, we compared reproductive output between P. formosa and P. mexicana as well as P. formosa and P. latipinna. We found no differences in the fecundity in either comparison of a sexual and the asexual species. Under the assumption of a 1:1 sex ratio, the asexual Amazon Molly should consequently have a full two-fold advantage and be able to outcompete sexuals over time. Hence, the coexistence of the species pairs in nature presents a paradox still to be solved.