Quantitative genetic variance in experimental fly populations evolving with or without environmental heterogeneity

Reduced within-population quantitative genetic variation is associated with climate harshness in maritime pine

How evolutionary forces interact to maintain genetic variation within populations has been a matter of extensive theoretical debates. While mutation and exogenous gene flow increase genetic variation, stabilizing selection and genetic drift are expected to deplete it. To date, levels of genetic variation observed in natural populations are hard to predict without accounting for other processes, such as balancing selection in heterogeneous environments. We aimed to empirically test three hypotheses: (i) admixed populations have higher quantitative genetic variation due to introgression from other gene pools, (ii) quantitative genetic variation is lower in populations from harsher environments (i.e., experiencing stronger selection), and (iii) quantitative genetic variation is higher in populations from heterogeneous environments. Using growth, phenological and functional trait data from three clonal common gardens and 33 populations (522 clones) of maritime pine (Pinus pinaster Aiton), we estimated the association between the population-specific total genetic variances (i.e., among-clone variances) for these traits and ten population-specific indices related to admixture levels (estimated based on 5165 SNPs), environmental temporal and spatial heterogeneity and climate harshness. Populations experiencing colder winters showed consistently lower genetic variation for early height growth (a fitness-related trait in forest trees) in the three common gardens. Within-population quantitative genetic variation was not associated with environmental heterogeneity or population admixture for any trait. Our results provide empirical support for the potential role of natural selection in reducing genetic variation for early height growth within populations, which indirectly gives insight into the adaptive potential of populations to changing environments.

Genotype-environment interaction and the maintenance of genetic variation: an empirical study of Lobelia inflata (Campanulaceae)

High levels of genetic variation are often observed in natural populations, suggesting the action of processes such as frequency-dependent selection, heterozygote advantage and variable selection. However, the maintenance of genetic variation in fitness-related traits remains incompletely explained. The extent of genetic variation in obligately self-fertilizing populations of Lobelia inflata (Campanulaceae L.) strongly implies balancing selection. Lobelia inflata thus offers an exceptional opportunity for an empirical test of genotype-environment interaction (G × E) as a variance-maintaining mechanism under fluctuating selection: L. inflata is monocarpic and reproduces only by seed, facilitating assessment of lifetime fitness; genome-wide homozygosity precludes some mechanisms of balancing selection, and microsatellites are, in effect, genotypic lineage markers. Here, we find support for the temporal G × E hypothesis using a manipulated space-for-time approach across four environments: a field environment, an outdoor experimental plot and two differing growth-chamber environments. High genetic variance was confirmed: 83 field-collected individuals consisted of 45 distinct microsatellite lineages with, on average, 4.5 alleles per locus. Rank-order fitness, measured as lifetime fruit production in 16 replicated multilocus genotypes, changed significantly across environments. Phenotypic differences among microsatellite lineages were detected. Results thus support the G × E hypothesis in principle. However, the evaluation of the effect size of this mechanism and fitness effects of life-history traits will require a long-term study of fluctuating selection on labelled genotypes in the field.

Small population size and low genomic diversity have no effect on fitness in experimental translocations of a wild fish

Little empirical work in nature has quantified how wild populations with varying effective population sizes and genetic diversity perform when exposed to a gradient of ecologically important environmental conditions. To achieve this, juvenile brook trout from 12 isolated populations or closed metapopulations that differ substantially in population size and genetic diversity were transplanted to previously fishless ponds spanning a wide gradient of ecologically important variables. We evaluated the effect of genome-wide variation, effective population size (N_e), pond habitat, and initial body size on two fitness correlates (survival and growth). Genetic variables had no effect on either fitness correlate, which was determined primarily by habitat (pond temperature, depth, and pH) and initial body size. These results suggest that some vertebrate populations with low genomic diversity, low N_e, and long-term isolation can represent important sources of variation and are capable of maintaining fitness in, and ultimately persisting and adapting to, changing environments. Our results also reinforce the paramount importance of improving available habitat and slowing habitat degradation for species conservation.

Additive genetic variance for lifetime fitness and the capacity for adaptation in an annual plant

The immediate capacity for adaptation under current environmental conditions is directly proportional to the additive genetic variance for fitness, V_A (W). Mean absolute fitness, W ¯ , is predicted to change at the rate V A ( W ) W ¯ , according to Fisher's Fundamental Theorem of Natural Selection. Despite ample research evaluating degree of local adaptation, direct assessment of V_A (W) and the capacity for ongoing adaptation is exceedingly rare. We estimated V_A (W) and W ¯ in three pedigreed populations of annual Chamaecrista fasciculata, over three years in the wild. Contrasting with common expectations, we found significant V_A (W) in all populations and years, predicting increased mean fitness in subsequent generations (0.83 to 6.12 seeds per individual). Further, we detected two cases predicting "evolutionary rescue," where selection on standing V_A (W) was expected to increase fitness of declining populations ( W ¯ < 1.0) to levels consistent with population sustainability and growth. Within populations, inter-annual differences in genetic expression of fitness were striking. Significant genotype-by-year interactions reflected modest correlations between breeding values across years, indicating temporally variable selection at the genotypic level that could contribute to maintaining V_A (W). By directly estimating V_A (W) and total lifetime W ¯ , our study presents an experimental approach for studies of adaptive capacity in the wild.

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.

A comparison of stable and fluctuating resources with respect to evolutionary adaptation and life-history traits using individual-based modeling and machine learning

There are three non-mutually-exclusive key strategies evolved by gene pools to cope with fluctuating food resource availability, including evolutionary adaptation, phenotypic plasticity, and migration. We focus primarily on evolutionary adaptation and behavioral plasticity, which is a type of phenotypic plasticity, resulting in life-history changes as ways of dealing with fluctuations in food resource availability. Using EcoSim, a predator-prey individual-based model, we compare individuals with stable food resources with those in environments where there are fluctuating food resources in terms of adaptation through behavioral plasticity and evolution. The purpose of our study is to determine whether evolution and behavioral plasticity truly play a role in adapting to an environment with fluctuating food resources, as well as to determine whether there are specific gene divergences between gene pools in fluctuating food resource environments versus gene pools where food resources are relatively stable. An important result of our study is that individuals in environments that are unstable with respect to food resource availability exhibited significant differences in behaviors versus those in environments with stable food resources. Although behavioral plasticity facilitates a rapid response to unstable food conditions, our study revealed the evolution of perceptual traits such as vision range in reaction to fluctuating food resources, indicating the importance of evolution in adapting to unstable resource environments in the long run. Moreover, using decision trees, we found that there were significant behavioral gene divergences between individuals in environments with fluctuating food resources as opposed to individuals in environments with stable food resources.

Genetic conflict with a parasitic nematode disrupts the legume-rhizobia mutualism

Genetic variation for partner quality in mutualisms is an evolutionary paradox. One possible resolution to this puzzle is that there is a tradeoff between partner quality and other fitness‐related traits. Here, we tested whether susceptibility to parasitism is one such tradeoff in the mutualism between legumes and nitrogen‐fixing bacteria (rhizobia). We performed two greenhouse experiments with the legume Medicago truncatula. In the first, we inoculated each plant with the rhizobia Ensifer meliloti and with one of 40 genotypes of the parasitic root‐knot nematode Meloidogyne hapla. In the second experiment, we inoculated all plants with rhizobia and half of the plants with a genetically variable population of nematodes. Using the number of nematode galls as a proxy for infection severity, we found that plant genotypes differed in susceptibility to nematode infection, and nematode genotypes differed in infectivity. Second, we showed that there was a genetic correlation between the number of mutualistic structures formed by rhizobia (nodules) and the number of parasitic structures formed by nematodes (galls). Finally, we found that nematodes disrupt the rhizobia mutualism: nematode‐infected plants formed fewer nodules and had less nodule biomass than uninfected plants. Our results demonstrate that there is genetic conflict between attracting rhizobia and repelling nematodes in Medicago. If genetic conflict with parasitism is a general feature of mutualism, it could account for the maintenance of genetic variation in partner quality and influence the evolutionary dynamics of positive species interactions.

Experimental evidence that density mediates negative frequency-dependent selection on aggression

Aggression can be beneficial in competitive environments if aggressive individuals are more likely to access resources than non-aggressive individuals. However, variation in aggressive behaviour persists within populations, suggesting that high levels of aggression might not always be favoured. The goal of this study was to experimentally assess the effects of population density and phenotypic frequency on selection on aggression in a competitive environment. We compared survival of two strains of Drosophila melanogaster that differ in aggression across three density treatments and five frequency treatments (single strain groups, equal numbers of each strain and strains mixed at 3:1 and 1:3 ratios) during a period of limited resources. While there was no difference in survival across single-strain treatments, survival was strongly density dependent, with declining survival as density increased. Furthermore, at medium and high densities, there was evidence of negative frequency-dependent selection, where rare strains experienced greater survival than common strains. However, there was no evidence of negative frequency-dependent selection at low density. Our results indicate that the benefits of aggression during periods of limited resources can depend on the interaction between the phenotypic composition of populations and population density, both of which are mechanisms that could maintain variation in aggressive behaviours within natural populations.

Rapid trait evolution drives increased speed and variance in experimental range expansions

Range expansions are central to two ecological issues reshaping patterns of global biodiversity: biological invasions and climate change. Traditional theory considers range expansion as the outcome of the demographic processes of birth, death and dispersal, while ignoring the evolutionary implications of such processes. Recent research suggests evolution could also play a critical role in determining expansion speed but controlled experiments are lacking. Here we use flour beetles (Tribolium castaneum) to show experimentally that mean expansion speed and stochastic variation in speed are both increased by rapid evolution of traits at the expansion edge. We find that higher dispersal ability and lower intrinsic growth rates evolve at the expansion edge compared with spatially nonevolving controls. Furthermore, evolution of these traits is variable, leading to enhanced variance in speed among replicate population expansions. Our results demonstrate that evolutionary processes must be considered alongside demographic ones to better understand and predict range expansions.

Spatial structure provides unique opportunities for evolution during range expansions. Here, the authors show experimentally using the red flour beetle, Tribolium castaneum, that dispersal and growth can evolve through spatial processes, increasing expansion speed and its variance.

Environmental change mediates mate choice for an extended phenotype, but not for mate quality

Sexual cues, including extended phenotypes, are expected to be reliable indicators of male genetic quality and/or provide information on parental quality. However, the reliability of these cues may be dependent on stability of the environment, with heterogeneity affecting how selection acts on such traits. Here, we test how environmental change mediates mate choice for multiple sexual traits, including an extended phenotype--the structure of male-built nests - in stickleback fish. First, we manipulated the dissolved oxygen (DO) content of water to create high or low DO environments in which male fish built nests. Then we recorded the mate choice of females encountering these males (and their nests), under either the same or reversed DO conditions. Males in high DO environments built more compact nests than those in low DO conditions and males adjusted their nest structure in response to changing conditions. Female mate choice for extended phenotype (male nests) was environmentally dependent (females chose more compact nests in high DO conditions), while female choice for male phenotype was not (females chose large, vigorous males regardless of DO level). Examining mate choice in this dynamic context suggests that females evaluate the reliability of multiple sexual cues, taking into account environmental heterogeneity.

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.