The accumulation of deleterious mutations within the frozen niche variation hypothesis

Phenotypic plasticity rather than genotype drives reproductive choices in Hydra populations

Facultative clonality is associated with complex life cycles where sexual and asexual forms can be exposed to contrasting selection pressures. Facultatively clonal animals often have distinct developmental capabilities that depend on reproductive mode (e.g., negligible senescence and exceptional regeneration ability in asexual individuals, which are lacking in sexual individuals). Understanding how these differences in life history strategies evolved is hampered by limited knowledge of the population structure underlying sexual and asexual forms in nature. Here we studied genetic differentiation of coexisting sexual and asexual Hydra oligactis polyps, a freshwater cnidarian where reproductive mode-dependent life history patterns are observed. We collected asexual and sexual polyps from 13 Central European water bodies and used restriction-site associated DNA sequencing to infer population structure. We detected high relatedness among populations and signs that hydras might spread with resting eggs through zoochory. We found no genetic structure with respect to mode of reproduction (asexual vs. sexual). On the other hand, clear evidence was found for phenotypic plasticity in mode of reproduction, as polyps inferred to be clones differed in reproductive mode. Moreover, we detected two cases of apparent sex change (males and females found within the same clonal lineages) in this species with supposedly stable sexes. Our study describes population genetic structure in Hydra for the first time, highlights the role of phenotypic plasticity in generating patterns of life history variation, and contributes to understanding the evolution of reproductive mode-dependent life history variation in coexisting asexual and sexual forms.

No evidence for accumulation of deleterious mutations and fitness degradation in clonal fish hybrids: Abandoning sex without regrets

Despite its inherent costs, sexual reproduction is ubiquitous in nature, and the mechanisms to protect it from a competitive displacement by asexuality remain unclear. Popular mutation-based explanations, like the Muller's ratchet and the Kondrashov's hatchet, assume that purifying selection may not halt the accumulation of deleterious mutations in the nonrecombining genomes, ultimately leading to their degeneration. However, empirical evidence is scarce and it remains particularly unclear whether mutational degradation proceeds fast enough to ensure the decay of clonal organisms and to prevent them from outcompeting their sexual counterparts. To test this hypothesis, we jointly analysed the exome sequences and the fitness-related phenotypic traits of the sexually reproducing fish species and their clonal hybrids, whose evolutionary ages ranged from F1 generations to 300 ky. As expected, mutations tended to accumulate in the clonal genomes in a time-dependent manner. However, contrary to the predictions, we found no trend towards increased nonsynonymity of mutations acquired by clones, nor higher radicality of their amino acid substitutions. Moreover, there was no evidence for fitness degeneration in the old clones compared with that in the younger ones. In summary, although an efficacy of purifying selection may still be reduced in the asexual genomes, our data indicate that its efficiency is not drastically decreased. Even the oldest investigated clone was found to be too young to suffer fitness consequences from a mutation accumulation. This suggests that mechanisms other than mutation accumulation may be needed to explain the competitive advantage of sex in the short term.

Evolution of asexual Daphnia pulex in Japan: variations and covariations of the digestive, morphological and life history traits

Background

Several genetic lineages of obligate parthenogenetic Daphnia pulex, a common zooplankton species, have invaded Japan from North America. Among these, a lineage named JPN1 is thought to have started colonization as a single genotype several hundred to thousand years ago and subsequently produced many genotypes in Japan. To examine the phenotypic variations due to ecological drivers diverging the genotypes in new habitats, we measured heritability and variation in 17 traits, including life history, morphology and digestive traits, and the genetic distance among the D. pulex JPN1 genotypes in Japan.

Results

We found that most of the traits measured varied significantly among the genotypes and that heritability was highest in the morphological traits, followed by the digestive and life history traits. In addition, 93% of the variation in these traits was explained by the first three components in the principal component analysis, implying that variation of these heritable traits is not random but rather converged into a few directions. These relations among traits revealed the potential importance of predation pressures and food conditions as factors for diverging and selecting different genotypes. However, the magnitude of the difference in any single trait group did not correlate with the genetic distance.

Conclusions

Our findings show that the divergent traits evolved within D. pulex JPN1 lineage without genetic recombination, since their ancestral clone invaded Japan. Large variations and covariations of the phenotypic traits, irrespective of the genetic distance among the genotypes, support the view that the invasive success of D. pulex JPN1 was promoted by a genetic architecture that allowed for large phenotypic variations with a limited number of functionally important mutations without recombination.

Electronic supplementary material

The online version of this article (10.1186/s12862-019-1453-9) contains supplementary material, which is available to authorized users.

Higher ploidy is associated with reduced range breadth in the Potentilleae tribe

PREMISE OF THE STUDY

Polyploids are predicted to have greater niche breadth and larger ranges than diploids because of higher ecological tolerances, self-compatibility, and increased genetic variation. However, empirical support for this prediction is mixed, and most studies compare diploids and polyploids, rather than accounting for quantitative variation in ploidy. We test the prediction that species of higher ploidy have greater range breadth and abiotic breadth than those of lower ploidy.

METHODS

We estimate range breadth (latitudinal range, altitudinal range, and range size) and abiotic breadth (range in temperature, precipitation, and ultraviolet-B irradiance) for 109 species in the Potentilleae tribe of Rosaceae. We assess the contribution of ploidy to variation in range breadth, while accounting for shared evolutionary history and time of species divergence using phylogenetic comparative methods.

KEY RESULTS

Ploidy varied widely among species from 2× to 12×. Phylogenetic relatedness explained little of the variation in ploidy, range breadth, and abiotic breadth. Transitions to higher ploidy were associated with reduced latitudinal and altitudinal ranges, smaller overall range size, and reduced abiotic breadth for temperature and UV-B.

CONCLUSIONS

In contrast to predictions, this study shows that transitions to higher ploidy are associated with reduced range size and abiotic breadth. It also highlights the importance of considering continuous variation in ploidy when evaluating ecological correlates with ploidy. We discuss how genome duplication may contribute to the observed negative relationship between ploidy and range breadth.

Evolution of risk preference is determined by reproduction dynamics, life history, and population size

Alternative behavioral strategies typically differ in their associated risks, meaning that a different variance in fitness-related outcomes characterizes each behavior. Understanding how selection acts on risk preference is crucial to interpreting and predicting behavior. Despite much research, most theoretical frameworks have been laid out as optimization problems from the individual's perspective, and the influence of population dynamics has been underappreciated. We use agent-based simulations that implement competition between two simple behavioral strategies to illuminate effects of population dynamics on risk-taking. We explore the effects of inter-generational reproduction dynamics, population size, the number of decisions throughout an individual's life, and simple alternate distributions of risk. We find that these factors, very often ignored in empirical and theoretical studies of behavior, can have significant and non-intuitive impacts on the selection of alternative behavioral strategies. Our results demonstrate that simple rules regarding predicted risk preference do not hold across the complete range of each of the factors we studied; we propose intuitive interpretations for the dynamics within each regime. We suggest that studies of behavioral strategies should explicitly take into account the species' life history and the ecological context in which selection acted on the risk-related behavior of the organism of interest.

Seasonal niche partitioning and coexistence of amphimictic and parthenogenetic lineages of Heterocypris barbara (Crustacea: Ostracoda)

Sympatry of amphimictic and parthenogenetic lineages in species with mixed reproductive systems is rarely observed in nature. On Lampedusa Island (Pelagie Islands, Italy), amphimictic and parthenogenetic lineages of Heterocypris barbara (Gauthier and Brehm, 1928) co-occur in a temporary pond. Their sympatric persistence calls for an ecological differentiation. We investigated the role of seasonal variation of temperature and photoperiod conditions by two different approaches: microcosms set up by inundation of dry sediments from the temporary pond and life-table experiments. Microcosms recreate conditions similar to the field and in their sediments random samples of resting eggs of both amphimictic and parthenogenetic females are stored. Life-table experiments supplied individual-based estimates of survivorship, adult life span, fecundity, and sex ratio in the progeny. We carried out the experiments at 24 °C and a photoperiod of 12 h light (L) : 12 h dark (D) (simulating fall conditions) and at 16 °C and a photoperiod of 10 h L : 14 h D (simulating winter conditions). Males and amphimictic females were the most numerous forms at 24 °C and 12 h L : 12 h D; parthenogenetic females were dominant at 16 °C and 10 h L : 14 h D. Life-table experiments showed that amphimictic forms do not complete development at 16 °C and 10 h L : 14 h D. Our results suggest that sympatry of amphimictic and parthenogenetic females in the field depends on seasonal niche partitioning and the storage effect of resting eggs that allows survival through adverse-season conditions.

Multigenerational demographic responses of sexual and asexual Artemia to chronic genotoxicity by a reference mutagen

Genotoxins are capable of multigenerational impacts on natural populations via DNA damage and mutations. Sexual reproduction is assumed to reduce the long term consequences of genotoxicity for individual fitness and should therefore reduce population level effects. However, rather few empirical studies have quantified the magnitude of this effect. We tried to analyse the multigenerational demographic responses of sexual Artemia franciscana and asexual Artemia parthenogenetica due to chronic genotoxicity by a reference mutagen, ethyl methane sulfonate (EMS). A prospective (elasticity analysis) and retrospective (differences and contributions) perturbation analysis was carried out to understand the interactions of life history traits with population growth rate λ by comparing elasticities, differences and contributions of vital rates to λ. None of the previous studies have compared the effects of chronic genotoxicity using prospective and retrospective perturbation analyses in a sexual and asexual species over generations. The behaviour of a population with lower growth rate in the presence of genotoxicants in the field was studied by simulating reduced fertilities in the LTRE design. The results of prospective and retrospective perturbation analyses of effects on λ showed that population growth rate was proportionally more sensitive to juvenile survival whereas the effect of EMS on juvenile fertility contributed more to the variations in population growth rate in both the species and this effect was due to the high growth rate of Artemia. Simulations of lower population growth rate in the model showed that adult fertility and survival are also of importance. Sexual reproduction substantially mitigated the long term consequences of genetic damage, although these would be greater if population growth rate were lower. So multigenerational population level consequences of genotoxicity were much greater in an asexual species. So asexual species, and those with a parthenogenetic phase in their life cycle, may be particularly vulnerable to the effects of environmental mutagens. Ecological risk assessments should include information from multigenerational studies, as responses to genotoxicity may vary depending on the life history strategies and reproductive modes of the species under consideration. Single generation studies may under or over-estimate risks.

Differential responses of sexual and asexual Artemia to genotoxicity by a reference mutagen: Is the comet assay a reliable predictor of population level responses?

The impact of chronic genotoxicity to natural populations is always questioned due to their reproductive surplus. We used a comet assay to quantify primary DNA damage after exposure to a reference mutagen ethyl methane sulfonate in two species of crustacean with different reproductive strategies (sexual Artemia franciscana and asexual Artemia parthenogenetica). We then assessed whether this predicted individual performance and population growth rate over three generations. Artemia were exposed to different chronic concentrations (0.78mM, 1.01mM, 1.24mM and 1.48mM) of ethyl methane sulfonate from instar 1 onwards for 3 h, 24 h, 7 days, 14 days and 21 days and percentage tail DNA values were used for comparisons between species. The percentage tail DNA values showed consistently elevated values up to 7 days and showed a reduction from 14 days onwards in A. franciscana. Whilst in A. parthenogenetica such a reduction was evident on 21 days assessment. The values of percentage tail DNA after 21 days were compared with population level fitness parameters, growth, survival, fecundity and population growth rate to know whether primary DNA damage as measured by comet assay is a reliable biomarker. Substantial increase in tail DNA values was associated with substantial reductions in all the fitness parameters in the parental generation of A. franciscana and parental, F1 and F2 generations of A. parthenogenetica. So comet results were more predictive in asexual species over generations. These results pointed to the importance of predicting biomarker responses from multigenerational consequences considering life history traits and reproductive strategies in ecological risk assessments.

Ecological equivalence: a realistic assumption for niche theory as a testable alternative to neutral theory

BACKGROUND

Hubbell's 2001 neutral theory unifies biodiversity and biogeography by modelling steady-state distributions of species richness and abundances across spatio-temporal scales. Accurate predictions have issued from its core premise that all species have identical vital rates. Yet no ecologist believes that species are identical in reality. Here I explain this paradox in terms of the ecological equivalence that species must achieve at their coexistence equilibrium, defined by zero net fitness for all regardless of intrinsic differences between them. I show that the distinction of realised from intrinsic vital rates is crucial to evaluating community resilience.

PRINCIPAL FINDINGS

An analysis of competitive interactions reveals how zero-sum patterns of abundance emerge for species with contrasting life-history traits as for identical species. I develop a stochastic model to simulate community assembly from a random drift of invasions sustaining the dynamics of recruitment following deaths and extinctions. Species are allocated identical intrinsic vital rates for neutral dynamics, or random intrinsic vital rates and competitive abilities for niche dynamics either on a continuous scale or between dominant-fugitive extremes. Resulting communities have steady-state distributions of the same type for more or less extremely differentiated species as for identical species. All produce negatively skewed log-normal distributions of species abundance, zero-sum relationships of total abundance to area, and Arrhenius relationships of species to area. Intrinsically identical species nevertheless support fewer total individuals, because their densities impact as strongly on each other as on themselves. Truly neutral communities have measurably lower abundance/area and higher species/abundance ratios.

CONCLUSIONS

Neutral scenarios can be parameterized as null hypotheses for testing competitive release, which is a sure signal of niche dynamics. Ignoring the true strength of interactions between and within species risks a substantial misrepresentation of community resilience to habitat loss.

Can differences in autonomous selfing ability explain differences in range size among sister-taxa pairs of Collinsia (Plantaginaceae)? An extension of Baker's Law

Species with greater selfing ability are predicted to be better adapted for colonizing new habitats (Baker's Law). Here, we tested an expansion of this hypothesis: that species proficient at autonomous selfing have larger range sizes than their less proficient sister taxa. We also tested competing hypotheses regarding seed production and niche breadth on range size. Floral traits affecting the proficiency of autonomous selfing were measured and seed production was calculated for six sister-taxa pairs in the clade Collinsia. We tested for the hypothesized effects of these variables on elevational distribution and range size. We found that species most proficient at selfing had significantly larger range sizes than their sister-taxa that were less proficient at selfing. Species proficient at autonomous selfing occupied a higher mean elevation than their sister taxa, but they did not differ in their total elevational range. Species with greater seed production did not have larger range sizes. Our results extend Baker's Law, suggesting that species proficient at autonomous selfing are better adapted to establish new populations and thus can more readily expand their range. Autonomous selfing ability may play a vital role in explaining variance in range size among other species.

A combinational theory for maintenance of sex

Sexual reproduction implies high costs, but it is difficult to give evidence for evolutionary advantages that would explain the predominance of meiotic sex in eukaryotes. A combinational theory discussing evolution, maintenance and loss of sex may resolve the problem. The main function of sex is the restoration of DNA and consequently a higher quality of offspring. Recombination at meiosis evolved, perhaps, as a repair mechanism of DNA strand damages. This mechanism is most efficient for DNA restoration in multicellular eukaryotes, because the initial cell starts with a re-optimized genome, which is passed to all the daughter cells. Meiosis acts also as creator of variation in haploid stages, in which selection can purge most efficiently deleterious mutations. A prolonged diploid phase buffers the effects of deleterious recessive alleles as well as epigenetic defects and is thus optimal for prolonged growth periods. For complex multicellular organisms, the main advantage of sexuality is thus the alternation of diploid and haploid stages, combining advantages of both. A loss of sex is constrained by several, partly group-specific, developmental features. Hybridization may trigger shifts from sexual to asexual reproduction, but crossing barriers of the parental sexual species limit this process. For the concerted break-up of meiosis-outcrossing cycles plus silencing of secondary features, various group-specific changes in the regulatory system may be required. An establishment of asexuals requires special functional modifications and environmental opportunities. Costs for maintenance of meiotic sex are consequently lower than a shift to asexual reproduction.

Climate and agricultural context shape reproductive mode variation in an aphid crop pest

In aphids, reproductive mode is generally assumed to be selected for by winter climate. Sexual lineages produce frost-resistant eggs, conferring an advantage in regions with cold winters, while asexual lineages predominate in regions with mild winters. However, habitat and resource heterogeneities are known to exert a strong influence on sex maintenance and might modulate the effect of climate on aphid reproductive strategies. We carried out a hierarchical sampling in northern France to investigate whether reproductive mode variation of the aphid Rhopalosiphum padi is driven by winter climate conditions, by habitat and resource heterogeneities represented by a range of host plants or by both factors. We confirmed the coexistence in R. padi populations of two genetic clusters associated with distinct reproductive strategies. Asexual lineages predominated, whatever the surveyed year and location. However, we detected a between-year variation in the local contribution of both clusters, presumably associated with preceding winter severity. No evidence for host-driven niche differentiation was found in the field on six Poaceae among sexual and asexual lineages. Two dominant multilocus genotypes ( approximately 70% of the sample), having persisted over a 10-year period, were equally abundant on different plant species and locations, indicating their large ecological tolerance. Our results fit theoretical predictions of the influence of winter climate on the balance between sexual and asexual lineages. They also highlight the importance of current agricultural practices which seem to favour a small number of asexual generalist genotypes and their migration across large areas of monotonous environments.

Temporal differentiation and spatial coexistence of sexual and facultative asexual lineages of an aphid species at mating sites

Cases of coexisting sexual and asexual relatives are puzzling, as evolutionary theory predicts that competition for the same ecological niches should lead to the exclusion of one or the other population. In the cyclically parthenogenetic aphid, Rhopalosiphum padi, sexual and facultative asexual lineages are admixed in space at the time of sexual reproduction. We investigated how the interaction of reproductive mode and environment can lead to temporal niche differentiation. We demonstrated theoretically that differential sensitivity of sexual and facultatively asexual aphids to an environmental parameter (mating host suitability) shapes the two strategies: whereas the sexual lineages switch earlier to the production of sexual forms, the facultative asexual lineages delay and spread out their investment in sexual reproduction. This predicted pattern of niche specialization is in agreement with the temporal structure revealed in natura by demographic and genetic data. We propose that partial loss of sex by one pool of aphids and subsequent reduction in gene flow between lineages may favour temporal specialization through disruptive selection.

The complex causality of geographical parthenogenesis

Asexual organisms usually have larger and more northern distributions than their sexual relatives. This phenomenon, called geographical parthenogenesis, has been controversially attributed to predispositions in certain taxa; advantages of polyploidy and/or hybrid origin; better colonizing abilities because of uniparental reproduction; introgression of apomixis into sexuals; niche differentiation of clones; or biotic interactions. This review on apomictic plants demonstrates that each of these factors alone has not been able to explain the observed distributions. Establishment of the complex regulatory system of apomixis requires taxonomic and geographical predispositions; hybridization and/or polyploidization do create diversity, but they do not necessarily result in large distributions; colonizing abilities depend on clonal diversity and are outweighed by sexuals by self-compatibility and higher potentials for speciation; niche differentiation, ploidy levels and selfing keep sympatric sexuals and apomicts separated; and the impact of biotic interactions on distributions is uncertain. In conclusion, the distributional success of apomicts has a complex causality and depends on certain circumstances and combinations of factors. The rare establishment of apomixis may help to explain the predominance of sexuality on the large scale.

Outcomes of reciprocal invasions between genetically diverse and genetically uniform populations of Daphnia obtusa (Kurz)

Ecological theory predicts that genetic variation produced by sexual reproduction results in niche diversification and provides a competitive advantage both to facilitate invasion into genetically uniform asexual populations and to withstand invasion by asexual competitors. We tested the hypothesis that a large group of diverse clones of Daphnia obtusa has greater competitive advantage when invading into genetically uniform populations of this species than a smaller group with inherently less genetic diversity. We compared competitive outcomes to those of genetically uniform groups of small and large size invading into genetically diverse populations. Genetically diverse invaders of initially large group size increased their representation by more than those of initially small size; in contrast, genetically uniform invaders of initially large group size diminished on average by more than those of initially small size. These results demonstrate an advantage to the genetic variation produced by sexual reproduction, both in invasion and resisting invasion, which we attribute to competitive release experienced by individuals in genetically diverse populations.

Population models of sperm-dependent parthenogenesis

Organisms that reproduce by sperm-dependent parthenogenesis are asexual clones that require sperm of a sexual host to initiate egg production, without the genome of the sperm contributing genetic information to the zygote. Although sperm-dependent parthenogenesis has some of the disadvantages of sex (requiring a mate) without the counterbalancing advantages (mixing of parental genotypes), it appears amongst a wide variety of species. We develop initial models for the density-dependent dynamics of animal populations with sperm-dependent parthenogenesis (pseudogamy or gynogenesis), based on the known biology of the common Enchytraeid worm Lumbricillus lineatus. Its sperm-dependent parthenogenetic populations are reproductive parasites of the hermaphrodite sexual form. Our logistic models reveal two alternative requirements for coexistence at density-dependent equilibria: (i) If the two forms differ in competitive ability, the form with the lower intrinsic birth rate must be compensated by a more than proportionately lower competitive impact from the other, relative to intraspecific competition, (ii) If the two forms differ in their intrinsic capacity to exploit resources, the sperm-dependent parthenogen must be superior in this respect and must have a lower intrinsic birth rate. In general for crowded environments we expect a sperm-dependent parthenogen to compete strongly for limiting resources with the sexual sibling species. Its competitive impact is likely to be weakened by its genetic uniformity, however, and this may suffice to cancel any advantage of higher intrinsic growth rate obtained from reproductive investment only in egg production. We discuss likely thresholds of coexistence for other sperm-dependent parthenogens. The fish Poeciliopsis monacha-lucida likewise obtains an intrinsic growth advantage from reduced investment in male gametes, and so its persistence is likely to depend on it being a poor competitor. The planarian Schmidtea polychroa obtains no such intrinsic benefit because it produces fertile sperm, and its persistence may depend on superior resource exploitation.