Salt concentration in substrate modulates the composition of bacterial and yeast microbiomes of Drosophila melanogaster

Aim: Microbiomes influence the physiology and behavior of multicellular organisms and contribute to their adaptation to changing environmental conditions. However, yeast and bacterial microbiota have usually been studied separately; therefore, the interaction between bacterial and yeast communities in the gut of Drosophila melanogaster (D. melanogaster) is often overlooked. In this study, we investigate the correlation between bacterial and yeast communities in the gut of D. melanogaster. Methods: We studied the shifts in the joint microbiome of Drosophila melanogaster, encompassing both yeasts and bacteria, during adaptation to substrate with varying salt concentrations (0%, 2%, 4%, and 7%) using plating for both yeasts and bacteria and NGS-sequencing of variable 16S rRNA gene regions for bacteria. Results: The microbiome of flies and their substrates was gradually altered at moderate NaCl concentrations (2% and 4% compared with the 0% control) and completely transformed at high salt concentrations (7%). The relative abundance of Acetobacter, potentially beneficial to D. melanogaster, decreased as NaCl concentration increased, whereas the relative abundance of the more halotolerant lactobacilli first increased, peaking at 4% NaCl, and then declined dramatically at 7%. At this salinity level, potentially pathogenic bacteria of the genera Leuconostoc and Providencia were dominant. The yeast microbiome of D. melanogaster also undergoes significant changes with an increase in salt concentration in the substrate. The total yeast abundance undergoes nonlinear changes: it is lowest at 0% salt concentration and highest at 2%-4%. At a 7% concentration, the yeast abundance in flies and their substrate is lower than at 2%-4% but significantly higher than at 0%. Conclusions: The abundance and diversity of bacteria that are potentially beneficial to the flies decreased, while the proportion of potential pathogens, Leuconostoc and Providencia, increased with an increase in salt concentration in the substrate. In samples with a relatively high abundance and/or diversity of yeasts, the corresponding indicators for bacteria were often lowered, and vice versa. This may be due to the greater halotolerance of yeasts compared to bacteria and may also indicate antagonism between these groups of microorganisms.

Self-strengthen luminescent hydrogel

For typical synthetic materials, continue mechanical loading usually cause damage and even failure, because they are closed systems, without substance exchange with surroundings and structural reconstruction after damage. Double-network (DN) hydrogels have recently been demonstrated to generate radicals under mechanical loading. In this work, DN hydrogel provided with sustained monomer and lanthanide complex supply undergo self-growth, and thus simultaneous self-strengthen in both mechanical performance and luminescence intensity are realized through bond rupture-initiated mechanoradical polymerization. This strategy proves the feasibility of imparting desired functions to the DN hydrogel by mechanical stamping, and provides a new strategy for the design of luminescent soft materials with high fatigue resistance.

Meta-analytic evidence that animals rarely avoid inbreeding

Animals are usually expected to avoid mating with relatives (kin avoidance) as incestuous mating can lead to the expression of inbreeding depression. Yet, theoretical models predict that unbiased mating with regards to kinship should be common, and that under some conditions, the inclusive fitness benefits associated with inbreeding can even lead to a preference for mating with kin. This mismatch between empirical and theoretical expectations generates uncertainty as to the prevalence of inbreeding avoidance in animals. Here, we synthesized 677 effect sizes from 139 experimental studies of mate choice for kin versus non-kin in diploid animals, representing 40 years of research, using a meta-analytical approach. Our meta-analysis revealed little support for the widely held view that animals avoid mating with kin, despite clear evidence of publication bias. Instead, unbiased mating with regards to kinship appears widespread across animals and experimental conditions. The significance of a variety of moderators was explored using meta-regressions, revealing that the degree of relatedness and prior experience with kin explained some variation in the effect sizes. Yet, we found no difference in kin avoidance between males and females, choice and no-choice experiments, mated and virgin animals or between humans and animals. Our findings highlight the need to rethink the widely held view that inbreeding avoidance is a given in experimental studies.

Variable inbreeding depression may explain associations between the mating system and herbicide resistance in the common morning glory

Inbreeding depression is a central parameter underlying mating system variation in nature and one that can be altered by environmental stress. Although a variety of systems show that inbreeding depression tends to increase under stressful conditions, we have very little understanding across most organisms how the level of inbreeding depression may change as a result of adaptation to stressors. In this work we examined the potential that inbreeding depression varied among lineages of Ipomoea purpurea artificially evolved to exhibit divergent levels of herbicide resistance. We examined inbreeding depression in a variety of fitness-related traits in both the growth chamber and in the field, and paired this work with an examination of gene expression changes. We found that, while inbreeding depression was present across many of the traits, lineages artificially selected for increased herbicide resistance often showed no evidence of inbreeding depression in the presence of herbicide, and in fact, showed evidence of outbreeding depression in some traits compared to nonselected control lines and lineages selected for increased herbicide susceptibility. Further, at the transcriptome level, the resistant selection lines had differing patterns of gene expression according to breeding type (inbred vs. outcrossed) compared to the control and susceptible selection lines. Our data together indicate that inbreeding depression may be lessened in populations that are adapting to regimes of strong selection.

Yeasts affect tolerance of Drosophila melanogaster to food substrate with high NaCl concentration

The ability of model animal species, such as Drosophila melanogaster, to adapt quickly to various adverse conditions has been shown in many experimental evolution studies. It is usually assumed by default that such adaptation is due to changes in the gene pool of the studied population of macroorganisms. At the same time, it is known that microbiome can influence biological processes in macroorganisms. In order to assess the possible impact of microbiome on adaptation, we performed an evolutionary experiment in which some D. melanogaster lines were reared on a food substrate with high NaCl concentration while the others were reared on the standard (favourable) substrate. We evaluated the reproductive efficiency of experimental lines on the high salt substrate three years after the experiment started. Our tests confirmed that the lines reared on the salty substrate became more tolerant to high NaCl concentration. Moreover, we found that pre-inoculation of the high salt medium with homogenized salt-tolerant flies tended to improve reproductive efficiency of naïve flies on this medium (compared to pre-inoculation with homogenized control flies). The analysis of yeast microbiome in fly homogenates revealed significant differences in number and species richness of yeasts between salt-tolerant and control lines. We also found that some individual yeast lines extracted from the salt-tolerant flies improved reproductive efficiency of naïve flies on salty substrate (compared to baker's yeast and no yeast controls), whereas the effect of the yeast lines extracted from the control flies tended to be smaller. The yeast Starmerella bacillaris extracted from the salt-tolerant flies showed the strongest positive effect. This yeast is abundant in all salt-tolerant lines, and very rare or absent in all control lines. The results are consistent with the hypothesis that some components of the yeast microbiome of D. melanogaster contribute to to flies' tolerance to food substrate with high NaCl concentration.

Kin recognition and co-operative foraging in Drosophila melanogaster larvae

A long-standing goal for biologists and social scientists is to understand the factors that lead to the evolution and maintenance of co-operative behaviour between conspecifics. To that end, the fruit fly, Drosophila melanogaster, is becoming an increasingly popular model species to study sociality; however, most of the research to date has focused on adult behaviours. In this study, we set out to examine group-feeding behaviour by larvae and to determine whether the degree of relatedness between individuals mediates the expression co-operation. In a series of assays, we manipulated the average degree of relatedness in groups of third-instar larvae that were faced with resource scarcity, and measured the size, frequency and composition of feeding clusters, as well as the fitness benefits associated with co-operation. Our results suggest that larval D. melanogaster are capable of kin recognition (something that has not been previously described in this species), as clusters were more numerous, larger and involved more larvae, when more closely related kin were present in the social environment. These findings are discussed in the context of the correlated fitness-associated benefits of co-operation, the potential mechanisms by which individuals may recognize kin, and how that kinship may play an important role in facilitating the manifestation of this co-operative behaviour.

Evolution of ageing as a tangle of trade-offs: energy versus function

Despite tremendous progress in recent years, our understanding of the evolution of ageing is still incomplete. A dominant paradigm maintains that ageing evolves due to the competing energy demands of reproduction and somatic maintenance leading to slow accumulation of unrepaired cellular damage with age. However, the centrality of energy trade-offs in ageing has been increasingly challenged as studies in different organisms have uncoupled the trade-off between reproduction and longevity. An emerging theory is that ageing instead is caused by biological processes that are optimized for early-life function but become harmful when they continue to run-on unabated in late life. This idea builds on the realization that early-life regulation of gene expression can break down in late life because natural selection is too weak to optimize it. Empirical evidence increasingly supports the hypothesis that suboptimal gene expression in adulthood can result in physiological malfunction leading to organismal senescence. We argue that the current state of the art in the study of ageing contradicts the widely held view that energy trade-offs between growth, reproduction, and longevity are the universal underpinning of senescence. Future research should focus on understanding the relative contribution of energy and function trade-offs to the evolution and expression of ageing.

Ecological specialization in populations adapted to constant versus heterogeneous environments

Populations vary in their degree of ecological specialization. An intuitive, but often untested, hypothesis is that populations evolving under greater environmental heterogeneity will evolve to be less specialized. How important is environmental heterogeneity in explaining among-population variation in specialization? We assessed juvenile viability of 20 Drosophila melanogaster populations evolving under one of four regimes: (1) a salt-enriched environment, (2) a cadmium-enriched environment, (3) a temporally varying environment, and (4) a spatially varying environment. Juvenile viability was tested in both the original selective environments and a set of novel environments. In both the original and novel environments, populations from the constant cadmium regime had the lowest average viability and the highest variance in viability across environments but populations from the other three regimes were similar. Our results suggest that variation in specialization among these populations is most simply explained as a pleiotropic by-product of adaptation to specific environments rather than resulting from a history of exposure to environmental heterogeneity.

Spatial environmental complexity mediates sexual conflict and sexual selection in Drosophila melanogaster

Sexual selection is an important agent of evolutionary change, but the strength and direction of selection often vary over space and time. One potential source of heterogeneity may lie in the opportunity for male-male and/or male-female interactions imposed by the spatial environment. It has been suggested that increased spatial complexity permits sexual selection to act in a complementary fashion with natural selection (hastening the loss of deleterious alleles and/or promoting the spread of beneficial alleles) via two (not mutually exclusive) pathways. In the first scenario, sexual selection potentially acts more strongly on males in complex environments, allowing males of greater genetic "quality" a greater chance of outcompeting rivals, with benefits manifested indirectly in offspring. In the second scenario, increased spatial complexity reduces opportunities for males to antagonistically harm females, allowing females (especially those of greater potential fecundities) to achieve greater reproductive success (direct fitness benefits). Here, using Drosophila melanogaster, we explore the importance of these mechanisms by measuring direct and indirect fitness of females housed in simple vial environments or in vials in which spatial complexity has been increased. We find strong evidence in favor of the female conflict-mediated pathway as individuals in complex environments remated less frequently and produced more offspring than those housed in a simpler spatial environment, but no difference in the fitness of sons or daughters. We discuss these results in the context of other recent studies and what they mean for our understanding of how sexual selection operates.

Responses of a legume to inbreeding and the intensity of novel and familiar stresses

It is often assumed that the negative effects of inbreeding on fitness (inbreeding depression, ID) are particularly strong under stressful conditions. However, ID may be relatively mild under types of stress that plant populations have experienced for a long time, because environment-specific deleterious alleles may already have been purged. We examined the performance of open- and self-pollinated progeny of the short-lived calcareous grassland plant Anthyllis vulneraria under three intensities of each of five types of stress. Drought, nutrient deficiency, and defoliation were chosen as stresses typical for the habitat of origin, while shade and waterlogging were expected to be novel, unfamiliar stresses for A. vulneraria. The stresses reduced plant biomass by up to 91%, and the responses of the plants were mostly in line with the functional equilibrium hypothesis. There was significant ID in biomass (δ = 0.17), leaf chlorophyll content, and the number of root nodules of the legume, but the magnitude of ID was independent of the stress treatments. In particular, there was no significant interaction between inbreeding and the intensity of any stress type, and ID was not higher under novel than under familiar stresses. In addition, phenotypic plasticity in biomass allocation, leaf functional traits and in root nodulation of the legume to the various stress treatments was not influenced by inbreeding. Our findings do not support the common hypothesis of stronger ID under stressful environments, not even if the stresses are novel to the plants.

Interactions of inbreeding and stress by poor host quality in a root hemiparasite

BACKGROUND AND AIMS

Populations of many hemiparasitic plants are fragmented and threatened by inbreeding depression (ID). In addition, they may also be strongly affected by a lack of suitable host species. However, nothing is known about possible interactive effects of inbreeding and host quality for parasitic plants. Poor host quality represents a special type of biotic stress and the magnitude of ID is often expected to be higher in more stressful environments.

METHODS

We studied the effects of inbreeding and the quality of host species for the declining root hemiparasite Rhinanthus alectorolophus Selfed and open-pollinated parasites from two natural populations were grown (1) with 13 potential host species and (2) with 15 four-species mixtures.

KEY RESULTS

ID differed among host species and mixtures. In the first experiment, ID was highest in parasites grown with good hosts and declined with stress intensity. In the second experiment, ID was not influenced by stress intensity, but was highest in mixtures of hosts from only one functional group and lowest in mixtures containing three functional groups. Both parasite performance with individual host species and the damage to these host species differed between parasites from the two study populations.

CONCLUSIONS

Our results contradict the common assumption that ID is generally higher in more stressful environments. In addition, they support the importance of diverse host communities for hemiparasitic plants. The differences in host quality between the two parasite populations indicate genetic variation in the adaptation to individual hosts and in host-specific virulence. However, inbreeding did not affect specific host-parasite interactions.

Experimental Evolution of Gene Expression and Plasticity in Alternative Selective Regimes

Little is known of how gene expression and its plasticity evolves as populations adapt to different environmental regimes. Expression is expected to evolve adaptively in all populations but only those populations experiencing environmental heterogeneity are expected to show adaptive evolution of plasticity. We measured the transcriptome in a cadmium-enriched diet and a salt-enriched diet for experimental populations of Drosophila melanogaster that evolved for ~130 generations in one of four selective regimes: two constant regimes maintained in either cadmium or salt diets and two heterogeneous regimes that varied either temporally or spatially between the two diets. For populations evolving in constant regimes, we find a strong signature of counter-gradient evolution; the evolved expression differences between populations adapted to alternative diets is opposite to the plastic response of the ancestral population that is naïve to both diets. Based on expression patterns in the ancestral populations, we identify a set of genes for which we predict selection in heterogeneous regimes to result in increases in plasticity and we find the expected pattern. In contrast, a set of genes where we predicted reduced plasticity did not follow expectation. Nonetheless, both gene sets showed a pattern consistent with adaptive expression evolution in heterogeneous regimes, highlighting the difference between observing “optimal” plasticity and improvements in environment-specific expression. Looking across all genes, there is evidence in all regimes of differences in biased allele expression across environments (“allelic plasticity”) and this is more common among genes with plasticity in total expression.

Different developmental environments change how genes are expressed and what phenotypes are produced. Here we examine how the responsiveness of gene expression to different environments (“expression plasticity”) evolves in populations adapted to constant environments or heterogeneous ones (temporal or spatial heterogeneity) using experimental populations of D. melanogaster. We find the plastic response of the ancestral population that is naïve to both environments is generally opposed by the evolved differences between populations adapted to alternative environments. Populations that live in heterogeneous environments show evidence of adaptive expression evolution in genes predicted to evolve changes in plasticity.

Does Genetic Variation Maintained by Environmental Heterogeneity Facilitate Adaptation to Novel Selection?

Environmental heterogeneity helps maintain genetic variation in fitness. Therefore, one might predict that populations living in heterogeneous environments have higher adaptive potential than populations living in homogeneous environments. Such a prediction could be useful in guiding conservation priorities without requiring detailed genetic studies. However, this prediction will be true only if the additional genetic variation maintained by environmental heterogeneity can be used to respond to novel selection. Here we examine the effect of environmental heterogeneity on future adaptability using replicated experimental Drosophila melanogaster populations that had previously evolved for ∼100 generations under one of four selective regimes: constant salt-enriched larvae medium, constant cadmium-enriched larvae medium, and two heterogeneous regimes that vary either temporally or spatially between the two media. Replicates of these experimental populations were subjected to a novel heat stress while being maintained in their original larval diet selection regimes. Adaptation to increased temperature was measured with respect to female productivity and male siring success after ∼20 generations. For female productivity, there was evidence of adaptation overall and heterogeneous populations had a larger adaptive response than homogeneous populations. There was less evidence of adaptation overall for male siring success and no support for faster adaptation in heterogeneous populations.

Indirect selection of thermal tolerance during experimental evolution of Drosophila melanogaster

Natural selection alters the distribution of a trait in a population and indirectly alters the distribution of genetically correlated traits. Long-standing models of thermal adaptation assume that trade-offs exist between fitness at different temperatures; however, experimental evolution often fails to reveal such trade-offs. Here, we show that adaptation to benign temperatures in experimental populations of Drosophila melanogaster resulted in correlated responses at the boundaries of the thermal niche. Specifically, adaptation to fluctuating temperatures (16-25°C) decreased tolerance of extreme heat. Surprisingly, flies adapted to a constant temperature of 25°C had greater cold tolerance than did flies adapted to other thermal conditions, including a constant temperature of 16°C. As our populations were never exposed to extreme temperatures during selection, divergence of thermal tolerance likely reflects indirect selection of standing genetic variation via linkage or pleiotropy. We found no relationship between heat and cold tolerances in these populations. Our results show that the thermal niche evolves by direct and indirect selection, in ways that are more complicated than assumed by theoretical models.

Environmental versus anthropogenic effects on population adaptive divergence in the freshwater snail Lymnaea stagnalis

Repeated pesticide contaminations of lentic freshwater systems located within agricultural landscapes may affect population evolution in non-target organisms, especially in species with a fully aquatic life cycle and low dispersal ability. The issue of evolutionary impact of pollutants is therefore conceptually important for ecotoxicologists. The impact of historical exposure to pesticides on genetic divergence was investigated in the freshwater gastropod Lymnaea stagnalis, using a set of 14 populations from contrasted environments in terms of pesticide and other anthropogenic pressures. The hypothesis of population adaptive divergence was tested on 11 life-history traits, using Q(ST)-F(ST) comparisons. Despite strong neutral differentiation (mean F(ST) = 0.291), five adult traits or parameters were found to be under divergent selection. Conversely, two early expressed traits showed a pattern consistent with uniform selection or trait canalization, and four adult traits appeared to evolve neutrally. Divergent selection patterns were mostly consistent with a habitat effect, opposing pond to ditch and channel populations. Comparatively, pesticide and other human pressures had little correspondence with evolutionary patterns, despite hatching rate impairment associated with global anthropogenic pressure. Globally, analyses revealed high genetic variation both at neutral markers and fitness-related traits in a species used as model in ecotoxicology, providing empirical support for the need to account for genetic and evolutionary components of population response in ecological risk assessment.

Genome-wide patterns of genetic variation within and among alternative selective regimes

Environmental heterogeneity has been hypothesized to influence levels of genetic variation but the effect of heterogeneity depends on (i) the form of heterogeneity, (ii) whether ecologically relevant or neutral loci are being considered, and (iii) the genetic basis of ecological adaptation. We surveyed genome-wide SNP diversity in replicate experimental Drosophila melanogaster populations with equal census sizes that evolved for 42 generations under one of four selection regimes: (i) salt-enriched environment (Salt), (ii) cadmium-enriched environment (Cad), (iii) temporally (Temp) or (iv) spatially (Spatial) variable environments. There was significant differentiation between all pairs of treatments but the greatest differentiation occurred between the two homogenous treatments (Cad and Salt). For sites likely under differential ecological selection (and those closely linked to them), the pattern of within-population diversity π followed the expectation from classic antagonistic selection theory: Spatial>Temp>Salt≈Cad. However, neutral diversity unlinked to selected sites followed a different pattern: Spatial>Salt≈Cad>Temp. As implicated by the latter result, measures of F_ST among replicate populations within treatments are consistent with differences in effective population sizes among selective regimes despite equal census sizes. Though there are clear changes in the rank order of treatments when contrasting selected and neutral sites with respect to π, the rank ordering of treatments with respect to F_ST appears reasonably consistent between site categories. These results demonstrate that alternative selective regimes affect within- and among-population diversity differently for different site types.

Evolutionary biologists seek to understand the factors affecting genetic variation. While it is intuitive that environmental heterogeneity should increase levels of variation, theoretical models showed that spatial and temporal heterogeneity differ in how likely they are to maintain polymorphisms affecting fitness. We evolved experimental populations of fruit flies in constant environments or in temporally or spatially varying environments, then examined levels of sequence variation across the genome. For sites associated with ecological selection, polymorphism patterns matched the theoretical expectations with variation greatest in populations evolving in spatially heterogeneous environments, less variation in populations evolving in temporally heterogeneous environments, and least variation in populations evolving in constant environments. However, a different pattern was observed at sites not associated with differential ecological selection (i.e., most of the genome). For these sites, levels of variation were highest at spatially heterogeneous populations but lowest for temporally heterogeneous populations. Populations evolving under temporal heterogeneity also showed the greatest differentiation from one another, suggesting that this selection regime caused more genetic drift than other selection regimes. These results illustrate that environmental heterogeneity affects levels of variation not only at sites subject to differential ecological selection but also genome-wide, though spatial and temporal heterogeneity affect diversity differently.

Decreased accumulation of cadmium in Drosophila selected for resistance suggests a mechanism independent of metallothionein

Heavy metals, including cadmium, are common contaminants in environments subject to human activity. Responses to exposure in the fruit fly, Drosophila melanogaster, are dosage-dependent and resistance is selectable. While metallothionein-mediated sequestration has been extensively studied as a mechanism of cadmium resistance, a link between selection for resistance and an increased accumulation of cadmium has yet to be demonstrated. To address this need, we have selected wild-type flies for cadmium resistance for 20 generations and tested metal content using mass spectrometry. Resistant flies were observed to contain lower levels of cadmium, arguing for a mechanism of cadmium resistance that is not mediated by increased sequestration. This, coupled with genetic evidence suggesting the involvement of factors located on the X chromosome, suggests a gene other than metallothionein may be involved in resistance in this line.

Selfing, adaptation and background selection in finite populations

Classic deterministic genetic models of the evolution of selfing predict species should be either completely outcrossing or completely selfing. However, even species considered high selfers outcross to a small degree (e.g. Arabidopsis thaliana and Caenorhabditis elegans). This discrepancy between theory and data may exist because the classic models ignore the effects of drift interacting with selection, that is, Hill-Robertson effects. High selfing rates make the effective rate of recombination near zero, which is expected to cause the build-up of negative disequilibria in finite populations. Despite the transmission advantage associated with complete selfing, low levels of outcrossing may be favoured because of the benefits of increasing the effective rate of recombination to dissipate negative disequilibria. Using multilocus simulations, we confirm that selfing reduces effective population size through background selection and causes negative disequilibria between selected sites. Consequently, the rate of adaptation is substantially reduced in strong selfers. When selfing rate is allowed to evolve, populations evolve to be either strong outcrossers or strong selfers, depending on the parameter values. Amongst selfers, low, but nonzero, levels of outcrossing can be maintained by selection even when all mutations are deleterious; more outcrossing is maintained with higher rates of deleterious mutation. The addition of beneficial mutations can (i) lead to a quantitative increase in the degree of outcrossing amongst stronger selfers but (ii) may cause outcrossing species to evolve into stronger selfers.

Temporal variation favors the evolution of generalists in experimental populations of Drosophila melanogaster

In variable environments, selection should favor generalists that maintain fitness across a range of conditions. However, costs of adaptation may generate fitness trade-offs and lead to some compromise between specialization and generalization that maximizes fitness. Here, we evaluate the evolution of specialization and generalization in 20 populations of Drosophila melanogaster experimentally evolved in constant and variable thermal environments for 3 years. We developed genotypes from each population at two temperatures after which we measured fecundity across eight temperatures. We predicted that constant environments would select for thermal specialists and that variable environments would select for thermal generalists. Contrary to our predictions, specialists and generalists did not evolve in constant and spatially variable environments, respectively. However, temporal variation produced a type of generalist that has rarely been considered by theoretical models of developmental plasticity. Specifically, genotypes from the temporally variable selective environment were more fecund across all temperatures than were genotypes from other environments. These patterns suggest certain allelic effects and should inspire new directions for modeling adaptation to fluctuating environments.