Experimental Evidence for the Negative Effects of Self-Fertilization on the Adaptive Potential of Populations

Population genetic structure in a self-compatible hermaphroditic snail is driven by drift independently of its contemporary mating system

Genetic drift, gene flow, and natural selection commonly influence population genetic diversity. In populations of self-compatible hermaphrodites, the mating system (e.g., self-fertilization) further reduces individual heterozygosity. Furthermore, selfing, as a form of inbreeding, significantly impacts genetic drift by reducing effective population size (N e). This can potentially accelerate genetic drift, particularly in small populations where self-fertilization is likely during founder events. To investigate the roles of genetic drift and contemporary mating system in populations of the freshwater snail Lymnaea stagnalis, we examined their effective population sizes (N e) and Tajima's D values, which reflect genetic drift over extended time periods, as well as estimates of within-population selfing rates and pairwise relatedness reflecting contemporary mating system. We used 4054 SNP markers obtained using restriction site associated DNA (RAD) sequencing from individuals in five snail populations originating from geographically closely located ponds. We found strong population genetic structure and differences in genetic diversity among populations. Covariation between genetic diversity and N e estimates and Tajima's D values suggested drift being an important determinant of genetic diversity and structure in these populations. However, this effect was independent of the contemporary mating system, as indicated by the similarity of selfing rates and relatedness estimates among populations. Thus, founder events (possibly including historical inbreeding) and/or drift due to small sizes of L. stagnalis populations are likely to explain their genetic structure and limit within-population genetic diversity.

Weak response to selection on stigma-anther distance in a primarily selfing population of yellow monkeyflower

Stebbins hypothesized that selfing lineages are evolutionary dead ends because they lack adaptive potential. While selfing populations often possess limited nucleotide variability compared with closely related outcrossers, reductions in the genetic variability of quantitative characters remain unclear, especially for key traits determining selfing rates. Yellow monkeyflower (Mimulus guttatus) populations generally outcross and maintain extensive quantitative genetic variation in floral traits. Here, we study the Joy Road population (Bodega Bay, CA, USA) of M. guttatus, where individuals exhibit stigma-anther distances (SAD) typical of primarily selfing monkeyflowers. We show that this population is closely related to nearby conspecifics on the Pacific Coast with a modest 33% reduction in genome-wide variation compared with a more highly outcrossing population. A five-generation artificial selection experiment challenged the hypothesis that the Joy Road population harbours comparatively low evolutionary potential in stigma-anther distance, a critical determinant of selfing rate in Mimulus. Artificial selection generated a weak phenotypic response, with low realized heritabilities (0.020-0.028) falling 84% below those measured for floral characters in more highly outcrossing M. guttatus. These results demonstrate substantial declines in evolutionary potential with a transition toward selfing. Whether these findings explain infrequent reversals to outcrossing or general limits on adaptation in selfers requires further investigation.

Ongoing convergent evolution of a selfing syndrome threatens plant-pollinator interactions

Plant-pollinator interactions evolved early in the angiosperm radiation. Ongoing environmental changes are however leading to pollinator declines that may cause pollen limitation to plants and change the evolutionary pressures shaping plant mating systems. We used resurrection ecology methodology to contrast ancestors and contemporary descendants in four natural populations of the field pansy (Viola arvensis) in the Paris region (France), a depauperate pollinator environment. We combine population genetics analysis, phenotypic measurements and behavioural tests on a common garden experiment. Population genetics analysis reveals 27% increase in realized selfing rates in the field during this period. We documented trait evolution towards smaller and less conspicuous corollas, reduced nectar production and reduced attractiveness to bumblebees, with these trait shifts convergent across the four studied populations. We demonstrate the rapid evolution of a selfing syndrome in the four studied plant populations, associated with a weakening of the interactions with pollinators over the last three decades. This study demonstrates that plant mating systems can evolve rapidly in natural populations in the face of ongoing environmental changes. The rapid evolution towards a selfing syndrome may in turn further accelerate pollinator declines, in an eco-evolutionary feedback loop with broader implications to natural ecosystems.

Parallel evolution of morphological and genomic selfing syndromes accompany the breakdown of heterostyly

Evolutionary transitions from outcrossing to selfing in flowering plants have convergent morphological and genomic signatures and can involve parallel evolution within related lineages. Adaptive evolution of morphological traits is often assumed to evolve faster than nonadaptive features of the genomic selfing syndrome. We investigated phenotypic and genomic changes associated with transitions from distyly to homostyly in the Primula oreodoxa complex. We determined whether the transition to selfing occurred more than once and investigated stages in the evolution of morphological and genomic selfing syndromes using 22 floral traits and both nuclear and plastid genomic data from 25 populations. Two independent transitions were detected representing an earlier and a more recently derived selfing lineage. The older lineage exhibited classic features of the morphological and genomic selfing syndrome. Although features of both selfing syndromes were less developed in the younger selfing lineage, they exhibited parallel development with the older selfing lineage. This finding contrasts with the prediction that some genomic changes should lag behind adaptive changes to morphological traits. Our findings highlight the value of comparative studies on the timing and extent of transitions from outcrossing to selfing between related lineages for investigating the tempo of morphological and molecular evolution.

Propensity for selfing varies within a population of hermaphroditic snails: coexistence of selfers, outcrossers and mixed-mating individuals

To understand mating-system evolution in self-compatible hermaphrodites, variation in selfing rates is highly relevant. Empirical studies are rarely designed to capture variation between individuals, instead often comparing species and populations. Yet, evolution primarily occurs within populations, rendering among-individual variation essential. Observed individual selfing rates depend on the environment (e.g. differences in mate availability) and individuals' propensity for selfing. We quantified individual variation in selfing propensity in the snail Radix balthica by conducting laboratory mating trials that manipulated mate availability (low versus moderate) and estimating selfing rates from progeny arrays. We also measured female lifetime fitness. We found substantial among-individual variation in selfing propensity, including pure selfers (32%), pure outcrossers (31%) and mixed-mating individuals that selfed and outcrossed (37%). Experimental levels of mate availability did not significantly affect selfing rates. Selfers had reduced female liftetime fitness. Our results show that the propensity for selfing can differ considerably among individuals, with similar proportions of selfers, outcrossers and mixed maters. As mate availability did not affect selfing, our 'moderate' experimental level of mate availability might still have been too low to prompt selfers to outcross. This and the observed fitness differences also cautiously suggest that investigating the heritability of selfing propensities might be worthwhile in this population.

Purging due to self-fertilization does not prevent accumulation of expansion load

As species expand their geographic ranges, colonizing populations face novel ecological conditions, such as new environments and limited mates, and suffer from evolutionary consequences of demographic change through bottlenecks and mutation load accumulation. Self-fertilization is often observed at species range edges and, in addition to countering the lack of mates, is hypothesized as an evolutionary advantage against load accumulation through increased homozygosity and purging. We study how selfing impacts the accumulation of genetic load during range expansion via purging and/or speed of colonization. Using simulations, we disentangle inbreeding effects due to demography versus due to selfing and find that selfers expand faster, but still accumulate load, regardless of mating system. The severity of variants contributing to this load, however, differs across mating system: higher selfing rates purge large-effect recessive variants leaving a burden of smaller-effect alleles. We compare these predictions to the mixed-mating plant Arabis alpina, using whole-genome sequences from refugial outcrossing populations versus expanded selfing populations. Empirical results indicate accumulation of expansion load along with evidence of purging in selfing populations, concordant with our simulations, suggesting that while purging is a benefit of selfing evolving during range expansions, it is not sufficient to prevent load accumulation due to range expansion.

The potential for floral evolution in response to competing selection pressures following the loss of hawkmoth pollination in Ruellia humilis

PREMISE

In the absence of hawkmoth pollinators, chasmogamous (CH) flowers of Ruellia humilis self-pollinate by two secondary mechanisms. Other floral visitors might exert selection on CH floral traits to restore outcrossing, but at the same time preferential predation of CH seeds generates selection to increase the allocation of resources to cleistogamous (CL) flowers.

METHODS

To assess the potential for an evolutionary response to these competing selection pressures, we estimated additive genetic variances ( σ A 2 ${\sigma }_{{\rm{A}}}^{2}$ ) and covariances for 14 reproductive traits and three fitness components in a Missouri population lacking hawkmoth pollinators.

RESULTS

We found significant σ A 2 ${\sigma }_{{\rm{A}}}^{2}$ for all 11 floral traits and two measures of resource allocation to CL flowers, indicating the potential for a short-term response to selection on most reproductive traits. Selection generated by seed predators is predicted to increase the percentage of CL flowers by 0.24% per generation, and mean stigma-anther separation is predicted to decrease as a correlated response, increasing the fraction of plants that engage in prior selfing. However, the initial response to this selection is opposed by strong directional dominance.

CONCLUSIONS

The predicted evolutionary decrease in the number of CH flowers available for potential outcrossing, combined with the apparent preclusion of potential diurnal pollinators by the pollen-harvesting activities of sweat bees, suggest that 100% cleistogamy is the likely outcome of evolution in the absence of hawkmoths. However, rare mutations with large effects, such as delaying budbreak until after sunrise, could provide pathways for the restoration of outcrossing that are not reachable by gradual quantitative-genetic evolution.

Extreme mitochondrial DNA divergence underlies genetic conflict over sex determination

Cytoplasmic male sterility (CMS) is a form of genetic conflict over sex determination that results from differences in modes of inheritance between genomic compartments.^1-3 Indeed, maternally transmitted (usually mitochondrial) genes sometimes enhance their transmission by suppressing the male function in a hermaphroditic organism to the detriment of biparentally inherited nuclear genes. Therefore, these hermaphrodites become functionally female and may coexist with regular hermaphrodites in so-called gynodioecious populations.³ CMS has been known in plants since Darwin's times⁴ but is previously unknown in the animal kingdom.^5-8 We relate the first observation of CMS in animals. It occurs in a freshwater snail population, where some individuals appear unable to sire offspring in controlled crosses and show anatomical, physiological, and behavioral characters consistent with a suppression of the male function. Male sterility is associated with a mitochondrial lineage that underwent a spectacular acceleration of DNA substitution rates, affecting the entire mitochondrial genome-this acceleration concerns both synonymous and non-synonymous substitutions and therefore results from increased mitogenome mutation rates. Consequently, mitochondrial haplotype divergence within the population is exceptionally high, matching that observed between snail taxa that diverged 475 million years ago. This result is reminiscent of similar accelerations in mitogenome evolution observed in plant clades where gynodioecy is frequent,^9,10 both being consistent with arms-race evolution of genome regions implicated in CMS.^11,12 Our study shows that genomic conflicts can trigger independent evolution of similar sex-determination systems in plants and animals and dramatically accelerate molecular evolution.

Understanding the drivers of dispersal evolution in range expansions and their ecological consequences

Research has conclusively demonstrated the potential for dispersal evolution in range expansions and shifts, however the degree of dispersal evolution observed has varied substantially among organisms. Further, it is unknown how the factors influencing dispersal evolution might impact other ecological processes at play. We use an individual-based model to investigate the effects of the underlying genetics of dispersal and mode of reproduction in range expansions and shifts. Consistent with predictions from stationary populations, dispersal evolution increases with sexual reproduction and loci number. Contrary to our predictions, however, increased dispersal does not always improve a population’s ability to track changing conditions. The mate finding Allee effect inherent to sexual reproduction increases extinction risk during range shifts, counteracting the beneficial effect of increased dispersal evolution. Our results demonstrate the importance of considering both ecological and evolutionary processes for understanding range expansions and shifts.

Multiple Sources of Introduction of North American Arabidopsis thaliana from across Eurasia

Large-scale movement of organisms across their habitable range, or migration, is an important evolutionary process that can shape genetic diversity and influence the adaptive spread of alleles. Although human migrations have been studied in great detail with modern and ancient genomes, recent anthropogenic influence on reducing the biogeographical constraints on the migration of nonnative species has presented opportunities in several study systems to ask the questions about how repeated introductions shape genetic diversity in the introduced range. We present an extensive overview of population structure of North American Arabidopsis thaliana by studying a set of 500 whole-genome sequenced and over 2,800 RAD-seq genotyped individuals in the context of global diversity represented by Afro-Eurasian genomes. We use methods based on haplotype and rare-allele sharing as well as phylogenetic modeling to identify likely sources of introductions of extant N. American A. thaliana from the native range in Africa and Eurasia. We find evidence of admixture among the introduced lineages having increased haplotype diversity and reduced mutational load. We also detect signals of selection in immune-system-related genes that may impart qualitative disease resistance to pathogens of bacterial and oomycete origin. We conclude that multiple introductions to a nonnative range can rapidly enhance the adaptive potential of a colonizing species by increasing haplotypic diversity through admixture. Our results lay the foundation for further investigations into the functional significance of admixture.

Selfing rate variation within species is unrelated to life-history traits or geographic range position

PREMISE

In plants, populations and species vary widely along the continuum from outcrossing to selfing. Life-history traits and ecological circumstances influence among-species variation in selfing rates, but their general role in explaining intraspecific variation is unknown. Using a database of plant species, we test whether life-history traits, geographic range position, or abundance predict selfing rate variation among populations.

METHODS

We identified species where selfing rates were estimated in at least three populations at known locations. Two key life-history traits (generation time and growth form) were used to predict within-species selfing rate variation. Populations sampled within a species' native range were assessed for proximity to the nearest edge and abundance. Finally, we conducted linear and segmented regressions to determine functional relationships between selfing rate and geographic range position within species.

RESULTS

Selfing rates for woody species varied less than for herbs, which is explained by the lower average selfing rate of woody species. Relationships between selfing and peripherality or abundance significantly varied among species in their direction and magnitude. However, there was no general pattern of increased selfing toward range edges. A power analysis shows that tests of this hypothesis require studying many (i.e., 40+) populations.

CONCLUSIONS

Intraspecific variation in plant mating systems is often substantial yet remains difficult to explain. Beyond sampling more populations, future tests of biogeographic hypotheses will benefit from phylogeographic information concerning specific range edges, the study of traits influencing mating system (e.g., herkogamy), and measures of abundance at local scales (e.g., population density).

Genetics of quantitative traits with dominance under stabilizing and directional selection in partially selfing species

Recurrent self-fertilization is thought to lead to reduced adaptive potential by decreasing the genetic diversity of populations, thus leading selfing lineages down an evolutionary "blind alley." Although well supported theoretically, empirical support for reduced adaptability in selfing species is limited. One limitation of classical theoretical models is that they assume pure additivity of the fitness-related traits that are under stabilizing selection, despite ample evidence that quantitative traits are subject to dominance. Here, we relax this assumption and explore the effect of dominance on a fitness-related trait under stabilizing selection for populations that differ in selfing rates. By decomposing the genetic variance into additional components specific to inbred populations, we show that dominance components can explain a substantial part of the genetic variance of inbred populations. We also show that ignoring these components leads to an upward bias in the predicted response to selection. Finally, we show that when considering the effect of dominance, the short-term evolutionary potential of populations remains comparable across the entire gradient in outcrossing rates, and genetic associations can even make selfing populations more evolvable on the longer term, reconciling theoretical, and empirical results.

Genomic characterization of selfing in the cyclic parthenogen Daphnia magna

Inbreeding refers to the fusion of related individuals' gametes, with self-fertilization (selfing) being an extreme form of inbreeding-involving gametes produced by the same individual. Selfing is expected to reduce heterozygosity by an average of 50% in one generation; however, little is known about the empirical variation on a genome level surrounding this figure and the factors that affect variation. We selfed genotypes of the cyclic parthenogen Daphnia magna and analysed whole genomes of mothers and selfed offspring, observing the predicted 50% heterozygosity reduction on average. We also saw substantial variation around this value and significant differences among mother-offspring pairs. Crossover analysis confirmed the known trend of recombination occurring more often towards the telomeres. This effect was shown, through simulations, to increase the variance of heterozygosity reduction compared to when a uniform distribution of crossovers was used. Similarly, we simulated inbred line production after several generations of selfing and we observed higher variance in achieved homozygosity when we consider a higher recombination rate towards the telomeres. Our empirical and simulation study highlights that the expected mean values of heterozygosity reduction show remarkable variation, which can help understand, for example, differences among inbred individuals.

Addressing Darwin's dilemma: Can pseudo-overdominance explain persistent inbreeding depression and load?

Darwin spent years investigating the effects of self-fertilization, concluding that "nature abhors perpetual self-fertilization." Given that selection purges inbred populations of strongly deleterious mutations and drift fixes mild mutations, why does inbreeding depression (ID) persist in highly inbred taxa and why do no purely selfing taxa exist? Background selection, associations and interference among loci, and drift within small inbred populations all limit selection while often increasing fixation. These mechanisms help to explain why more inbred populations in most species consistently show more fixed load. This drift load is manifest in the considerable heterosis regularly observed in between-population crosses. Such heterosis results in subsequent high ID, suggesting a mechanism by which small populations could retain variation and inbreeding load. Multiple deleterious recessive mutations linked in repulsion generate pseudo-overdominance. Many tightly linked load loci could generate a balanced segregating load high enough to sustain ID over many generations. Such pseudo-overdominance blocks (or "PODs") are more likely to occur in regions of low recombination. They should also result in clear genetic signatures including genomic hotspots of heterozygosity; distinct haplotypes supporting alleles at intermediate frequency; and high linkage disequilibrium in and around POD regions. Simulation and empirical studies tend to support these predictions. Additional simulations and comparative genomic analyses should explore POD dynamics in greater detail to resolve whether PODs exist in sufficient strength and number to account for why ID and load persist within inbred lineages.

Population Genomics of the "Arcanum" Species Group in Wild Tomatoes: Evidence for Separate Origins of Two Self-Compatible Lineages

Given their diverse mating systems and recent divergence, wild tomatoes (Solanum section Lycopersicon) have become an attractive model system to study ecological divergence, the build-up of reproductive barriers, and the causes and consequences of the breakdown of self-incompatibility. Here we report on a lesser-studied group of species known as the "Arcanum" group, comprising the nominal species Solanum arcanum, Solanum chmielewskii, and Solanum neorickii. The latter two taxa are self-compatible but are thought to self-fertilize at different rates, given their distinct manifestations of the morphological "selfing syndrome." Based on experimental crossings and transcriptome sequencing of a total of 39 different genotypes from as many accessions representing each species' geographic range, we provide compelling evidence for deep genealogical divisions within S. arcanum; only the self-incompatible lineage known as "var. marañón" has close genealogical ties to the two self-compatible species. Moreover, there is evidence under multiple inference schemes for different geographic subsets of S. arcanum var. marañón being closest to S. chmielewskii and S. neorickii, respectively. To broadly characterize the population-genomic consequences of these recent mating-system transitions and their associated speciation events, we fit demographic models indicating strong reductions in effective population size, congruent with reduced nucleotide and S-locus diversity in the two independently derived self-compatible species.

Postglacial ecotype formation under outcrossing and self-fertilization in Arabidopsis lyrata

The formation of ecotypes has been invoked as an important driver of postglacial biodiversity, because many species colonized heterogeneous habitats and experienced divergent selection. Ecotype formation has been predominantly studied in outcrossing taxa, while far less attention has been paid to the implications of mating system shifts. Here, we addressed whether substrate-related ecotypes exist in selfing and outcrossing populations of Arabidopsis lyrata subsp. lyrata and whether the genomic footprint differs between mating systems. The North American subspecies colonized both rocky and sandy habitats during postglacial range expansion and shifted the mating system from predominantly outcrossing to predominantly selfing in a number of regions. We performed an association study on pooled whole-genome sequence data of 20 selfing or outcrossing populations, which suggested genes involved in adaptation to substrate. Motivated by enriched gene ontology terms, we compared root growth between plants from the two substrates in a common environment and found that plants originating from sand grew roots faster and produced more side roots, independent of mating system. Furthermore, single nucleotide polymorphisms associated with substrate-related ecotypes were more clustered among selfing populations. Our study provides evidence for substrate-related ecotypes in A. lyrata and divergence in the genomic footprint between mating systems. The latter is the likely result of selfing populations having experienced divergent selection on larger genomic regions due to higher genome-wide linkage disequilibrium.

Genetic variability of morpho-physiological response to phosphorus deficiency in Tunisian populations of Brachypodium hybridum

Brachypodium hybridum (Poaceae) is widely distributed in the dry environments in Mediterranean basin, due to its high tolerance to drought. Investigating the natural variation of B. hybridum in response to environmental stresses is crucial for unraveling the genetic network of its stress tolerance. 79 B. hybridum lines from eight Tunisian populations were screened for their performance to low P availability using morpho-physiological parameters. ANOVA showed that treatment and population*treatment factors were the most contributors in the explained variance for the majority of parameters. A considerable population differentiation was detected in control and under P level (Qst = 0.77 vs Qst = 0.62). This suggests that B. hybridum exhibit an adaptive differential response to P deficiency related environmental conditions. Results revealed that Raouad and Sejnen lines were the most tolerant to P deficiency followed by Haouaria and Enfidha lines. The remaining populations were classified as sensitive. This pattern suggests that coastal populations were more tolerant to P deficiency than the inland ones. A slightly higher heritability was evidenced under low P level for most of traits, indicating that the direct selection under P deficiency is more reliable than an indirect one under optimal P supply.

Evolution: Selfing Takes Species Down Stebbins's Blind Alley

Shifts from outcrossing to selfing have occurred thousands of times across the tree of life. By reducing the size of the gene pool, selfing should limit adaptive potential. A refreshing empirical experiment with snails supports this long-standing hypothesis.

How does selfing affect the genetic variance of quantitative traits? An updated meta-analysis on empirical results in angiosperm species

Most theoretical works predict that selfing should reduce the level of additive genetic variance available for quantitative traits within natural populations. Despite a growing number of quantitative genetic studies undertaken during the last two decades, this prediction is still not well supported empirically. To resolve this issue and confirm or reject theoretical predictions, we reviewed quantitative trait heritability estimates from natural plant populations with different rates of self-fertilization and carried out a meta-analysis. In accordance with models of polygenic traits under stabilizing selection, we found that the fraction of additive genetic variance is negatively correlated with the selfing rate. Although the mating system explains a moderate fraction of the variance, the mean reduction of narrow-sense heritability values between strictly allogamous and predominantly selfing populations is strong, around 60%. Because some nonadditive components of genetic variance become selectable under inbreeding, we determine whether self-fertilization affects the relative contribution of these components to genetic variance by comparing narrow-sense heritability estimates from outcrossing populations with broad-sense heritability estimated in autogamous populations. Results suggest that these nonadditive components of variance may restore some genetic variance in predominantly selfing populations; it remains, however, uncertain how these nonadditive components will contribute to adaptation.

Evolution of sex ratio through gene loss

Several species of Caenorhabditis nematodes, including Caenorhabditis elegans, have recently evolved self-fertile hermaphrodites from female/male ancestors. These hermaphrodites can either self-fertilize or mate with males, and the extent of outcrossing determines subsequent male frequency. Using experimental evolution, the authors show that a gene family with a historical role in sperm competition plays a large role in regulating male frequency after self-fertility evolves. By reducing, but not completely eliminating outcrossing, loss of the mss genes contributes to adaptive tuning of the sex ratio in a newly self-fertile species.

The maintenance of males at intermediate frequencies is an important evolutionary problem. Several species of Caenorhabditis nematodes have evolved a mating system in which selfing hermaphrodites and males coexist. While selfing produces XX hermaphrodites, cross-fertilization produces 50% XO male progeny. Thus, male mating success dictates the sex ratio. Here, we focus on the contribution of the male secreted short (mss) gene family to male mating success, sex ratio, and population growth. The mss family is essential for sperm competitiveness in gonochoristic species, but has been lost in parallel in androdioecious species. Using a transgene to restore mss function to the androdioecious Caenorhabditis briggsae, we examined how mating system and population subdivision influence the fitness of the mss+ genotype. Consistent with theoretical expectations, when mss+ and mss-null (i.e., wild type) genotypes compete, mss+ is positively selected in both mixed-mating and strictly outcrossing situations, though more strongly in the latter. Thus, while sexual mode alone affects the fitness of mss+, it is insufficient to explain its parallel loss. However, in genetically homogenous androdioecious populations, mss+ both increases male frequency and depresses population growth. We propose that the lack of inbreeding depression and the strong subdivision that characterize natural Caenorhabditis populations impose selection on sex ratio that makes loss of mss adaptive after self-fertility evolves.

Sexual selection and inbreeding: Two efficient ways to limit the accumulation of deleterious mutations

Theory and empirical data showed that two processes can boost selection against deleterious mutations, thus facilitating the purging of the mutation load: inbreeding, by exposing recessive deleterious alleles to selection in homozygous form, and sexual selection, by enhancing the relative reproductive success of males with small mutation loads. These processes tend to be mutually exclusive because sexual selection is reduced under mating systems that promote inbreeding, such as self‐fertilization in hermaphrodites. We estimated the relative efficiency of inbreeding and sexual selection at purging the genetic load, using 50 generations of experimental evolution, in a hermaphroditic snail (Physa acuta). To this end, we generated lines that were exposed to various intensities of inbreeding, sexual selection (on the male function), and nonsexual selection (on the female function). We measured how these regimes affected the mutation load, quantified through the survival of outcrossed and selfed juveniles. We found that juvenile survival strongly decreased in outbred lines with reduced male selection, but not when female selection was relaxed, showing that male‐specific sexual selection does purge deleterious mutations. However, in lines exposed to inbreeding, where sexual selection was also relaxed, survival did not decrease, and even increased for self‐fertilized juveniles, showing that purging through inbreeding can compensate for the absence of sexual selection. Our results point to the further question of whether a mixed strategy combining the advantages of both mechanisms of genetic purging could be evolutionary stable.

Whole-genome sequencing reveals the extent of heterozygosity in a preferentially self-fertilizing hermaphroditic vertebrate

The mangrove rivulus, Kryptolebias marmoratus, is one of only two self-fertilizing hermaphroditic fish species and inhabits mangrove forests. While selfing can be advantageous, it reduces heterozygosity and decreases genetic diversity. Studies using microsatellites found that there are variable levels of selfing among populations of K. marmoratus, but overall, there is a low rate of outcrossing and, therefore, low heterozygosity. In this study, we used whole-genome data to assess the levels of heterozygosity in different lineages of the mangrove rivulus and infer the phylogenetic relationships among those lineages. We sequenced whole genomes from 15 lineages that were completely homozygous at microsatellite loci and used single nucleotide polymorphisms (SNPs) to determine heterozygosity levels. More variation was uncovered than in studies using microsatellite data because of the resolution of full genome sequencing data. Moreover, missense polymorphisms were found most often in genes associated with immune function and reproduction. Inferred phylogenetic relationships suggest that lineages largely group by their geographic distribution. The use of whole-genome data provided further insight into genetic diversity in this unique species. Although this study was limited by the number of lineages that were available, these data suggest that there is previously undescribed variation within lineages of K. marmoratus that could have functional consequences and (or) inform us about the limits to selfing (e.g., genetic load, accumulation of deleterious mutations) and selection that might favor the maintenance of heterozygosity. These results highlight the need to sequence additional individuals within and among lineages.

Advances in Fasciola hepatica research using 'omics' technologies

The liver fluke Fasciola hepatica is an economically important pathogen of livestock worldwide, as well as being an important neglected zoonosis. Parasite control is reliant on the use of drugs, particularly triclabendazole, which is effective against multiple parasite stages. However, the spread of parasites resistant to triclabendazole has intensified the pursuit for novel control strategies. Emerging 'omics' technologies are helping advance our understanding of liver fluke biology, specifically the molecules that act at the host-parasite interface and are central to infection, virulence and long-term survival within the definitive host. This review discusses the technological sequencing advances that have facilitated the unbiased analysis of liver fluke biology, resulting in an extensive range of 'omics' datasets. In addition, we highlight the 'omics' studies of host responses to F. hepatica infection that, when combined with the parasite datasets, provide the opportunity for integrated analyses of host-parasite interactions. These extensive datasets will form the foundation for future in-depth analysis of F. hepatica biology and development, and the search for new drug or vaccine interventions.

Recombination Alters the Dynamics of Adaptation on Standing Variation in Laboratory Yeast Populations

The rates and selective effects of beneficial mutations, together with population genetic factors such as population size and recombination rate, determine the outcomes of adaptation and the signatures this process leaves in patterns of genetic diversity. Previous experimental studies of microbial evolution have focused primarily on initially clonal populations, finding that adaptation is characterized by new strongly selected beneficial mutations that sweep rapidly to fixation. Here, we study evolution in diverse outcrossed yeast populations, tracking the rate and genetic basis of adaptation over time. We combine time-serial measurements of fitness and allele frequency changes in 18 populations of budding yeast evolved at different outcrossing rates to infer the drivers of adaptation on standing genetic variation. In contrast to initially clonal populations, we find that adaptation is driven by a large number of weakly selected, linked variants. Populations undergoing different rates of outcrossing make use of this selected variation differently: whereas asexual populations evolve via rapid, inefficient, and highly variable fixation of clones, sexual populations adapt continuously by gradually breaking down linkage disequilibrium between selected variants. Our results demonstrate how recombination can sustain adaptation over long timescales by inducing a transition from selection on genotypes to selection on individual alleles, and show how pervasive linked selection can affect evolutionary dynamics.

Bioinvasion Triggers Rapid Evolution of Life Histories in Freshwater Snails

Biological invasions offer interesting situations for observing how novel interactions between closely related, formerly allopatric species may trigger phenotypic evolution in situ. Assuming that successful invaders are usually filtered to be competitively dominant, invasive and native species may follow different trajectories. Natives may evolve traits that minimize the negative impact of competition, while trait shifts in invasives should mostly reflect expansion dynamics, through selection for colonization ability and transiently enhanced mutation load at the colonization front. These ideas were tested through a large-scale common-garden experiment measuring life-history traits in two closely related snail species, one invasive and one native, co-occurring in a network of freshwater ponds in Guadeloupe. We looked for evidence of recent evolution by comparing uninvaded or recently invaded sites with long-invaded ones. The native species adopted a life history favoring rapid population growth (i.e., increased fecundity, earlier reproduction, and increased juvenile survival) that may increase its prospects of coexistence with the more competitive invader. We discuss why these effects are more likely to result from genetic change than from maternal effects. The invader exhibited slightly decreased overall performances in recently colonized sites, consistent with a moderate expansion load resulting from local founder effects. Our study highlights a rare example of rapid life-history evolution following invasion.

The Evolutionary Interplay between Adaptation and Self-Fertilization

Genome-wide surveys of nucleotide polymorphisms, obtained from next-generation sequencing, have uncovered numerous examples of adaptation in self-fertilizing organisms, especially regarding changes to climate, geography, and reproductive systems. Yet existing models for inferring attributes of adaptive mutations often assume idealized outcrossing populations, which risks mischaracterizing properties of these variants. Recent theoretical work is emphasizing how various aspects of self-fertilization affects adaptation, yet empirical data on these properties are lacking. We review theoretical and empirical studies demonstrating how self-fertilization alters the process of adaptation, illustrated using examples from current sequencing projects. We propose ideas for how future research can more accurately quantify aspects of adaptation in self-fertilizers, including incorporating the effects of standing variation, demographic history, and polygenic adaptation.

Analysis of large-scale next-generation sequencing datasets are finding more examples of adaptive evolution at the genomic level.

Advances in theoretical work has demonstrated how self-fertilisation affects different aspects of adaptation in these organisms, compared to outcrossers.

Current software and statistical methods do not take different mating systems into account, which risks mischaracterising the presence or strength of adaptive mutations from genome scans.

Development of new mathematical and statistical methods that explicitly consider self-fertilization and associated demographic effects will enable researchers to more accurately quantify adaptation in these organisms.