Genomic evidence that resource-based trade-offs limit host-range expansion in a seed beetle

Repeatability of evolution and genomic predictions of temperature adaptation in seed beetles

Climate warming is threatening biodiversity by increasing temperatures beyond the optima of many ectotherms. Owing to the inherent non-linear relationship between temperature and the rate of cellular processes, such shifts towards hot temperature are predicted to impose stronger selection compared with corresponding shifts towards cold temperature. This suggests that when adaptation to warming occurs, it should be relatively rapid and predictable. Here we tested this hypothesis from the level of single-nucleotide polymorphisms to life-history traits in the beetle Callosobruchus maculatus. We conducted an evolve-and-resequence experiment on three genetic backgrounds of the beetle reared at hot or cold temperature. Indeed, we find that phenotypic evolution was faster and more repeatable at hot temperature. However, at the genomic level, adaptation to heat was less repeatable when compared across genetic backgrounds. As a result, genomic predictions of phenotypic adaptation in populations exposed to hot temperature were accurate within, but not between, backgrounds. These results seem best explained by genetic redundancy and an increased importance of epistasis during adaptation to heat, and imply that the same mechanisms that exert strong selection and increase repeatability of phenotypic evolution at hot temperature reduce repeatability at the genomic level. Thus, predictions of adaptation in key phenotypes from genomic data may become increasingly difficult as climates warm.

Nonlinear transcriptomic responses to compounded environmental changes across temperature and resources in a pest beetle, Callosobruchus maculatus (Coleoptera: Chrysomelidae)

Many species are experiencing drastic and multidimensional changes to their environment due to anthropogenic events. These multidimensional changes may act nonadditively on physiological and life history responses, and thus may not be predicted by responses to single dimensional environmental changes. Therefore, work is needed to understand species' responses to multiple aspects of change. We used whole-transcriptomic RNA-Sequencing and life history assays to uncover responses to singly-applied shifts in resource or temperature environmental dimensions, in comparison to combined, multidimensional change, in the crop pest seed beetle, Callosobruchus maculatus. We found that multidimensional change caused larger fecundity, developmental period and offspring viability life history changes than predicted by additive effects of 1-dimensional changes. In addition, there was little overlap between genes differentially expressed under multidimensional treatment versus under altered resource or temperature conditions alone. Moreover, 115 genes exhibited significant resource × temperature interaction effects on expression, including those involved in energy metabolism, detoxification, and enhanced formation of cuticle structural components. We conclude that single dimensional changes alone cannot determine life history and transcriptomic responses to multidimensional environmental change. These results highlight the importance of studying multidimensional environmental change for understanding the molecular and phenotypic responses that may allow organisms including insects to rapidly adapt simultaneously to multiple aspects of environmental change.

Correlated responses to selection across diverse environments during experimental evolution of Tetrahymena thermophila

Correlated responses to selection have long been observed and studied; however, it remains unclear when they will arise, and in what direction. To contribute to a growing understanding of correlated responses to selection, we used experimental evolution of the ciliate Tetrahymena thermophila to study direct and correlated responses in a variety of different environmental conditions. One experiment focused on adaptation to two different temperatures and the correlated responses across temperatures. Another experiment used inhibitory concentrations of a variety of compounds to test direct and correlated responses to selection. We found that all populations adapted to the environments in which they evolved. We also found many cases of correlated evolution across environments; few conditions resulted in trade-offs and many resulted in a positive correlated response. Surprisingly, in many instances, the correlated response was of a larger magnitude than the direct response. We find that ancestral fitness predicts the extent of adaptation, consistent with diminishing returns epistasis. Unexpectedly, we also find that this pattern of diminishing returns holds across environments regardless of the environment in which evolution occurs. We also found that the correlated response is asymmetric across environments, that is, the fitness of a population evolved in one environment and assayed in a second was inversely related to the fitness of a population evolved in the second environment and assayed in the first. These results support the notion that positive correlated responses to selection across environments are frequent, and worth further study.

Evolution repeats itself in replicate long-term studies in the wild

The extent to which evolution is repeatable remains debated. Here, we study changes over time in the frequency of cryptic color-pattern morphs in 10 replicate long-term field studies of a stick insect, each spanning at least a decade (across 30 years of total data). We find predictable "up-and-down" fluctuations in stripe frequency in all populations, representing repeatable evolutionary dynamics based on standing genetic variation. A field experiment demonstrates that these fluctuations involve negative frequency-dependent natural selection (NFDS). These fluctuations rely on demographic and selective variability that pushes populations away from equilibrium, such that they can reliably move back toward it via NFDS. Last, we show that the origin of new cryptic forms is associated with multiple structural genomic variants such that which mutations arise affects evolution at larger temporal scales. Thus, evolution from existing variation is predictable and repeatable, but mutation adds complexity even for traits evolving deterministically under natural selection.

Understanding the joint evolution of dispersal and host specialisation using phytophagous arthropods as a model group

Theory generally predicts that host specialisation and dispersal should evolve jointly. Indeed, many models predict that specialists should be poor dispersers to avoid landing on unsuitable hosts while generalists will have high dispersal abilities. Phytophagous arthropods are an excellent group to test this prediction, given extensive variation in their host range and dispersal abilities. Here, we explore the degree to which the empirical literature on this group is in accordance with theoretical predictions. We first briefly outline the theoretical reasons to expect such a correlation. We then report empirical studies that measured both dispersal and the degree of specialisation in phytophagous arthropods. We find a correlation between dispersal and levels of specialisation in some studies, but with wide variation in this result. We then review theoretical attributes of species and environment that may blur this correlation, namely environmental grain, temporal heterogeneity, habitat selection, genetic architecture, and coevolution between plants and herbivores. We argue that theoretical models fail to account for important aspects, such as phenotypic plasticity and the impact of selective forces stemming from other biotic interactions, on both dispersal and specialisation. Next, we review empirical caveats in the study of this interplay. We find that studies use different measures of both dispersal and specialisation, hampering comparisons. Moreover, several studies do not provide independent measures of these two traits. Finally, variation in these traits may occur at scales that are not being considered. We conclude that this correlation is likely not to be expected from large-scale comparative analyses as it is highly context dependent and should not be considered in isolation from the factors that modulate it, such as environmental scale and heterogeneity, intrinsic traits or biotic interactions. A stronger crosstalk between theoretical and empirical studies is needed to understand better the prevalence and basis of the correlation between dispersal and specialisation.

Performance of a parasitic plant and its effects on hosts depends on the interactions between parasite seed family and host species

Root hemiparasitic plants act as keystone species influencing plant community composition through their differential suppression of host species. Their own performance also strongly depends on interactions with host species. However, little is known about the roles of parasite genetic variation vs. plasticity in these interactions. We grew plants from eight maternal families of the root hemiparasite Rhinanthus alectorolophus with six potential host species (two grasses, two legumes and two forbs) and without a host and measured fitness-related and morphological traits of the parasite, host biomass and overall productivity. Parasite biomass and other traits showed strong plastic variation in response to different host species, but were also affected by parasite maternal family. Parasite seed families responded differently to the hosts, indicating genetic variation that could serve as the basis for adaptation to different host plants. However, there were no negative correlations in the performance of families across different hosts, indicating that R. alectorolophus has plastic generalist genotypes and is not constrained in its use of different host species by trade-offs in performance. Parasite effects on host biomass (which may indicate virulence) and total productivity (host + parasite biomass) depended on the specific combination of parasite family and host species. Mean biomass of hosts with a parasite family and mean biomass of that family tended to be negatively correlated, suggesting selection for maximum resource extraction from the hosts. Specialization of generalist root hemiparasites may be restricted by a lack of trade-offs in performance across hosts, together with strong spatial and temporal variation in host species availability. The genetic variation in the effects on different hosts highlights the importance of genetic diversity of hemiparasites for their effects on plant community structure and productivity and for the success of using them to restore grassland diversity.

A possible genomic footprint of polygenic adaptation on population divergence in seed beetles?

Efforts to unravel the genomic basis of incipient speciation are hampered by a mismatch between our toolkit and our understanding of the ecology and genetics of adaptation. While the former is focused on detecting selective sweeps involving few independently acting or linked speciation genes, the latter states that divergence typically occurs in polygenic traits under stabilizing selection. Here, we ask whether a role of stabilizing selection on polygenic traits in population divergence may be unveiled by using a phenotypically informed integrative approach, based on genome‐wide variation segregating in divergent populations. We compare three divergent populations of seed beetles (Callosobruchus maculatus) where previous work has demonstrated a prominent role for stabilizing selection on, and population divergence in, key life history traits that reflect rate‐dependent metabolic processes. We derive and assess predictions regarding the expected pattern of covariation between genetic variation segregating within populations and genetic differentiation between populations. Population differentiation was considerable (mean F_ST = 0.23–0.26) and was primarily built by genes showing high selective constraints and an imbalance in inferred selection in different populations (positive Tajima's D_NS in one and negative in one), and this set of genes was enriched with genes with a metabolic function. Repeatability of relative population differentiation was low at the level of individual genes but higher at the level of broad functional classes, again spotlighting metabolic genes. Absolute differentiation (d_XY) showed a very different general pattern at this scale of divergence, more consistent with an important role for genetic drift. Although our exploration is consistent with stabilizing selection on polygenic metabolic phenotypes as an important engine of genome‐wide relative population divergence and incipient speciation in our study system, we note that it is exceedingly difficult to firmly exclude other scenarios.

A polygenic architecture with habitat-dependent effects underlies ecological differentiation in Silene

Ecological differentiation can drive speciation but it is unclear how the genetic architecture of habitat-dependent fitness contributes to lineage divergence. We investigated the genetic architecture of cumulative flowering, a fitness component, in second-generation hybrids between Silene dioica and Silene latifolia transplanted into the natural habitat of each species. We used reduced-representation sequencing and Bayesian sparse linear mixed models (BSLMMs) to analyze the genetic control of cumulative flowering in each habitat. Our results point to a polygenic architecture of cumulative flowering. Allelic effects were mostly beneficial or deleterious in one habitat and neutral in the other. Positive-effect alleles often were derived from the native species, whereas negative-effect alleles, at other loci, tended to originate from the non-native species. We conclude that ecological differentiation is governed and maintained by many loci with small, habitat-dependent effects consistent with conditional neutrality. This pattern may result from differences in selection targets in the two habitats and from environmentally dependent deleterious load. Our results further suggest that selection for native alleles and against non-native alleles acts as a barrier to gene flow between species.

Jack-of-all-trades paradigm meets long-term data: Generalist herbivores are more widespread and locally less abundant

Insect herbivores are relatively specialized. Why this is so is not clear. We examine assumptions about associations between local abundance and dietary specialization using an 18-year data set of caterpillar-plant interactions in Ecuador. Our data consist of caterpillar-plant associations and include standardized plot-based samples and general collections of caterpillars, allowing for diet breadth and abundance estimates across spatial scales for 1917 morphospecies. We find that more specialized caterpillars are locally more abundant than generalists, consistent with a key component of the 'jack of all trades, master of none' hypothesis. As the diet breadth of species increased, generalists were not as abundant in any one location, but they had broader occupancy across the landscape, which is a pattern that could reflect high plant beta diversity and is consistent with an alternative neutral hypothesis. Our finding that more specialized species can be both rare and common highlights the ecological complexity of specialization.

Disparate genetic variants associated with distinct components of cowpea resistance to the seed beetle Callosobruchus maculatus

Polygenic genome-wide association mapping identified two regions of the cowpea genome associated with different components of resistance to its major post-harvest pest, the seed beetle Callosobruchus maculatus. Cowpea (Vigna unguiculata) is an important grain and fodder crop in arid and semi-arid regions of Africa, Asia, and South America, where the cowpea seed beetle, Callosobruchus maculatus, is a serious post-harvest pest. Development of cultivars resistant to C. maculatus population growth in storage could increase grain yield and quality and reduce reliance on insecticides. Here, we use a MAGIC (multi-parent, advanced-generation intercross) population of cowpea consisting of 305 recombinant inbred lines (RILs) to identify genetic variants associated with resistance to seed beetles. Because inferences regarding the genetic basis of resistance may depend on the source of the pest or the assay protocol, we used two divergent geographic populations of C. maculatus and two complementary assays to measure several aspects of resistance. Using polygenic genome-wide association mapping models, we found that the cowpea RILs harbor substantial additive-genetic variation for most resistance measures. Variation in several components of resistance, including larval development time and survival, was largely explained by one or several linked loci on chromosome 5. A second region on chromosome 8 explained increased seed resistance via the induction of early-exiting larvae. Neither of these regions contained genes previously associated with resistance to insects that infest grain legumes. We found some evidence of gene-gene interactions affecting resistance, but epistasis did not contribute substantially to resistance variation in this mapping population. The combination of mostly high heritabilities and a relatively consistent and simple genetic architecture increases the feasibility of breeding for enhanced resistance to C. maculatus.

Genomic time-series data show that gene flow maintains high genetic diversity despite substantial genetic drift in a butterfly species

Effective population size affects the efficacy of selection, rate of evolution by drift, and neutral diversity levels. When species are subdivided into multiple populations connected by gene flow, evolutionary processes can depend on global or local effective population sizes. Theory predicts that high levels of diversity might be maintained by gene flow, even very low levels of gene flow, consistent with species long-term effective population size, but tests of this idea are mostly lacking. Here, we show that Lycaeides buttery populations maintain low contemporary (variance) effective population sizes (e.g., ~200 individuals) and thus evolve rapidly by genetic drift. In contrast, populations harbored high levels of genetic diversity consistent with an effective population size several orders of magnitude larger. We hypothesized that the differences in the magnitude and variability of contemporary versus long-term effective population sizes were caused by gene flow of sufficient magnitude to maintain diversity but only subtly affect evolution on generational time scales. Consistent with this hypothesis, we detected low but non-trivial gene flow among populations. Furthermore, using short-term population-genomic time-series data, we documented patterns consistent with predictions from this hypothesis, including a weak but detectable excess of evolutionary change in the direction of the mean (migrant gene pool) allele frequencies across populations, and consistency in the direction of allele frequency change over time. The documented decoupling of diversity levels and short-term change by drift in Lycaeides has implications for our understanding of contemporary evolution and the maintenance of genetic variation in the wild.

The evolution of coevolution in the study of species interactions

The study of reciprocal adaptation in interacting species has been an active and inspiring area of evolutionary research for nearly 60 years. Perhaps owing to its great natural history and potential consequences spanning population divergence to species diversification, coevolution continues to capture the imagination of biologists. Here we trace developments following Ehrlich and Raven's classic paper, with a particular focus on the modern influence of two studies by Dr. May Berenbaum in the 1980s. This series of classic work presented a compelling example exhibiting the macroevolutionary patterns predicted by Ehrlich and Raven and also formalized a microevolutionary approach to measuring selection, functional traits, and understanding reciprocal adaptation between plants and their herbivores. Following this breakthrough was a wave of research focusing on diversifying macroevolutionary patterns, mechanistic chemical ecology, and natural selection on populations within and across community types. Accordingly, we breakdown coevolutionary theory into specific hypotheses at different scales: reciprocal adaptation between populations within a community, differential coevolution among communities, lineage divergence, and phylogenetic patterns. We highlight progress as well as persistent gaps, especially the link between reciprocal adaptation and diversification.

Adaptation and correlated fitness responses over two time scales in Drosophila suzukii populations evolving in different environments

The process of local adaptation involves differential changes in fitness over time across different environments. Although experimental evolution studies have extensively tested for patterns of local adaptation at a single time point, there is relatively little research that examines fitness more than once during the time course of adaptation. We allowed replicate populations of the fruit pest Drosophila suzukii to evolve in one of eight different fruit media. After five generations, populations with the highest initial levels of maladaptation had mostly gone extinct, whereas experimental populations evolving on cherry, strawberry and cranberry media had survived. We measured the fitness of each surviving population in each of the three fruit media after five and after 26 generations of evolution. After five generations, adaptation to each medium was associated with increased fitness in the two other media. This was also true after 26 generations, except when populations that evolved on cranberry medium developed on cherry medium. These results suggest that, in the theoretical framework of a fitness landscape, the fitness optima of cherry and cranberry media are the furthest apart. Our results show that studying how fitness changes across several environments and across multiple generations provides insights into the dynamics of local adaptation that would not be evident if fitness were analysed at a single point in time. By allowing a qualitative mapping of an experimental fitness landscape, our approach will improve our understanding of the ecological factors that drive the evolution of local adaptation in D. suzukii.

The role of maternal effects on offspring performance in familiar and novel environments

Maternal effects are an important evolutionary force that may either facilitate adaptation to a new environment or buffer against unfavourable conditions. The degree of variation in traits expressed by siblings from different mothers is often sensitive to environmental conditions. This could generate a Maternal-by-Environment interaction (M × E) that inflates estimates of Genotype-by-Environment effects (G × E). We aimed to test for environment-specific maternal effects (M × E) using a paternal full-sib/half-sib breeding design in the seed beetle Callosobruchus maculatus, where we split and reared offspring from the same mother on two different bean host types-original and novel. Our quantitative genetic analysis indicated that maternal effects were very small on both host types for all the measured life-history traits. There was also little evidence that maternal oviposition preference for a particular host type predicted her offspring's performance on that host. Further, additive genetic variance for most traits was relatively high on both hosts. While there was higher heritability for offspring reared in the novel host, there was no evidence for G × Es, and most cross-host genetic correlations were positive. This suggests that offspring from the same family ranked similarly for performance on both host types. Our results point to a genetic basis of host adaptation in the seed beetle, rather than maternal effects. Even so, we encourage researchers to test for potential M × Es because, due to a lack of testing, it remains unclear how often they arise.

A population-genomic approach for estimating selection on polygenic traits in heterogeneous environments

Strong selection can cause rapid evolutionary change, but temporal fluctuations in the form, direction and intensity of selection can limit net evolutionary change over longer time periods. Fluctuating selection could affect molecular diversity levels and the evolution of plasticity and ecological specialization. Nonetheless, this phenomenon remains understudied, in part because of analytical limitations and the general difficulty of detecting selection that does not occur in a consistent manner. Herein, I fill this analytical gap by presenting an approximate Bayesian computation (ABC) method to detect and quantify fluctuating selection on polygenic traits from population genomic time-series data. I propose a model for environment-dependent phenotypic selection. The evolutionary genetic consequences of selection are then modelled based on a genotype-phenotype map. Using simulations, I show that the proposed method generates accurate and precise estimates of selection when the generative model for the data is similar to the model assumed by the method. The performance of the method when applied to an evolve-and-resequence study of host adaptation in the cowpea seed beetle (Callosobruchus maculatus) was more idiosyncratic and depended on specific analytical choices. Despite some limitations, these results suggest the proposed method provides a powerful approach to connect the causes of (variable) selection to traits and genome-wide patterns of evolution. Documentation and open-source computer software (fsabc) implementing this method are available from github (https://github.com/zgompert/fsabc.git).

Intercontinental genomic parallelism in multiple three-spined stickleback adaptive radiations

Parallelism, the evolution of similar traits in populations diversifying in similar conditions, provides strong evidence of adaptation by natural selection. Many studies of parallelism focus on comparisons of different ecotypes or contrasting environments, defined a priori, which could upwardly bias the apparent prevalence of parallelism. Here, we estimated genomic parallelism associated with components of environmental and phenotypic variation at an intercontinental scale across four freshwater adaptive radiations (Alaska, British Columbia, Iceland and Scotland) of the three-spined stickleback (Gasterosteus aculeatus). We combined large-scale biological sampling and phenotyping with restriction site associated DNA sequencing (RAD-Seq) data from 73 freshwater lake populations and four marine ones (1,380 fish) to associate genome-wide allele frequencies with continuous distributions of environmental and phenotypic variation. Our three main findings demonstrate that (1) quantitative variation in phenotypes and environments can predict genomic parallelism; (2) genomic parallelism at the early stages of adaptive radiations, even at large geographic scales, is founded on standing variation; and (3) similar environments are a better predictor of genome-wide parallelism than similar phenotypes. Overall, this study validates the importance and predictive power of major phenotypic and environmental factors likely to influence the emergence of common patterns of genomic divergence, providing a clearer picture than analyses of dichotomous phenotypes and environments.

Measuring the effect of environmental stress on inbreeding depression alone obscures the relative importance of inbreeding-stress interactions on overall fitness in Callosobruchus maculatus

Environmental stress can have a profound effect on inbreeding depression. Quantifying this effect is of particular importance in threatened populations, which are often simultaneously subject to both inbreeding and environmental stress. But while the prevalence of inbreeding-stress interactions is well known, the importance and broader applicability of such interactions in conservation are not clearly understood. We used seed beetles, Callosobruchus maculatus, as a model system to quantify how environmental stressors (here host quality and temperature stress) interact with inbreeding as measured by changes in the magnitude of inbreeding depression, δ, as well as the relative importance of inbreeding-stress interactions to overall fitness. We found that while both environmental stressors caused substantial inbreeding-stress interactions as measured by change in δ, the relative importance of these interactions to overall survival was modest. This suggests that assessing inbreeding-stress interactions within the framework of δ alone may give an inaccurate representation of the relevance of interactions to population persistence. Furthermore, we found that the effect of environmental stress on fitness, but not inbreeding depression, varied strongly among populations. These results suggest that the outcomes of inbreeding-stress interactions are not easily generalized, an important consideration in conservation settings.

What We Don't Know About Diet-Breadth Evolution in Herbivorous Insects

Half a million species of herbivorous insects have been described. Most of them are diet specialists, using only a few plant species as hosts. Biologists suspect that their specificity is key to their diversity. But why do herbivorous insects tend to be diet specialists? In this review, we catalog a broad range of explanations. We review the evidence for each and suggest lines of research to obtain the evidence we lack. We then draw attention to a second major question, namely how changes in diet breadth affect the rest of a species’ biology. In particular, we know little about how changes in diet breadth feed back on genetic architecture, the population genetic environment, and other aspects of a species’ ecology. Knowing more about how generalists and specialists differ should go a long way toward sorting out potential explanations of specificity, and yield a deeper understanding of herbivorous insect diversity.

Predicting patch occupancy reveals the complexity of host range expansion

Specialized plant-insect interactions are a defining feature of life on earth, yet we are only beginning to understand the factors that set limits on host ranges in herbivorous insects. To better understand the recent adoption of alfalfa as a host plant by the Melissa blue butterfly, we quantified arthropod assemblages and plant metabolites across a wide geographic region while controlling for climate and dispersal inferred from population genomic variation. The presence of the butterfly is successfully predicted by direct and indirect effects of plant traits and interactions with other species. Results are consistent with the predictions of a theoretical model of parasite host range in which specialization is an epiphenomenon of the many barriers to be overcome rather than a consequence of trade-offs in developmental physiology.

Colonization of Marginal Host Plants by Seed Beetles (Coleoptera: Chrysomelidae): Effects of Geographic Source and Genetic Admixture

The ability to adapt to a novel host plant may vary among insect populations with different genetic histories, and colonization of a marginal host may be facilitated by genetic admixture of disparate populations. We assembled populations of the seed beetle, Callosobruchus maculatus (F.), from four continents, and compared their ability to infest two hosts, lentil and pea. We also formed two cross-continent hybrids (Africa × N.A. and Africa × S.A.). In pre-selection assays, survival was only ~3% in lentil and ~40% in pea. For three replicate populations per line, colonization success on lentil was measured as cumulative exit holes after 75-175 d. On pea, we estimated the change in larval survival after five generations of selection. Females in all lines laid few eggs on lentil, and survival of F1 larvae was uniformly <5%. Subsequently, however, the lines diverged considerably in population growth. Performance on lentil was highest in the Africa × N.A. hybrid, which produced far more adults (mean > 11,000) than either parental line. At the other extreme, Asian populations on lentil appeared to have gone extinct. The Africa × N.A. line also exhibited the highest survival on pea, and again performed better than either parent line. However, no line displayed a rapid increase in survival on pea, as is sometimes observed on lentil. Our results demonstrate that geographic populations can vary substantially in their responses to the same novel resource. In addition, genetic admixtures (potentially caused by long-distance transport of infested seeds) may facilitate colonization of an initially poor host.

Combining Experimental Evolution and Genomics to Understand How Seed Beetles Adapt to a Marginal Host Plant

Genes that affect adaptive traits have been identified, but our knowledge of the genetic basis of adaptation in a more general sense (across multiple traits) remains limited. We combined population-genomic analyses of evolve-and-resequence experiments, genome-wide association mapping of performance traits, and analyses of gene expression to fill this knowledge gap and shed light on the genomics of adaptation to a marginal host (lentil) by the seed beetle Callosobruchus maculatus. Using population-genomic approaches, we detected modest parallelism in allele frequency change across replicate lines during adaptation to lentil. Mapping populations derived from each lentil-adapted line revealed a polygenic basis for two host-specific performance traits (weight and development time), which had low to modest heritabilities. We found less evidence of parallelism in genotype-phenotype associations across these lines than in allele frequency changes during the experiments. Differential gene expression caused by differences in recent evolutionary history exceeded that caused by immediate rearing host. Together, the three genomic datasets suggest that genes affecting traits other than weight and development time are likely to be the main causes of parallel evolution and that detoxification genes (especially cytochrome P450s and beta-glucosidase) could be especially important for colonization of lentil by C. maculatus.

How to better predict long-term benefits and risks in weed biocontrol: an evolutionary perspective

Classical biological control (also called importation biological control) of weeds has a remarkable track record for efficiency and safety, but further improvement is still needed, particularly to account for potential evolutionary changes after release. Here, we discuss the increasing yet limited evidence of post-introduction evolution and describe approaches to predict evolutionary change. Recent advances include using experimental evolution studies over several generations that combine -omics tools with behavioral bioassays. This novel approach in weed biocontrol is well suited to explore the potential for rapid evolutionary change in real-time and thus can be used to estimate more accurately potential benefits and risks of agents before their importation. We outline this approach with a chrysomelid beetle used to control invasive common ragweed.

The host range of Aphis gossypii is dependent on aphid genetic background and feeding experience

Background

A polyphagous insect herbivore has a wide range of host plants. However, it has been found that many polyphagous herbivores commonly exhibit a strong preference for a subset of species in their broad host range, and various host biotypes exist in herbivore populations. Nutrition and secondary metabolites in plants affect herbivore preference and performance, but it is still not clear which factors determine the host range and host preference of polyphagous herbivores.

Method

Cotton-melon aphids, Aphis gossypii Glover, collected from cotton and cucumber crops, were used in this study. The genetic backgrounds of these aphids were detected using microsatellite PCR and six genotypes were evaluated. Performance of these six aphid genotypes on excised leaves and plants of cotton and cucumber seedlings were examined through a reciprocal transplant experiment. In order to detect whether the feeding experience on artificial diet would alter aphid host range, the six genotypes of aphids fed on artificial diet for seven days were transferred onto cotton and cucumber leaves, and then their population growth on these two host plants was surveyed.

Results

Aphids from cotton and cucumber plants could not colonize the excised leaves and intact plants of cucumber and cotton seedlings, respectively. All six genotypes of aphids collected from cotton and cucumber plants could survive and produce offspring on artificial diet, which lacked plant secondary metabolites. The feeding experience on the artificial diet did not alter the ability of all six genotypes to use their native host plants. However, after feeding on this artificial diet for seven days, two aphid genotypes from cotton and one from cucumber acquired the ability to use both of the excised leaves from cucumber and cotton plants. The two aphid genotypes from cotton conditioned by the feeding experience on artificial diet and then reared on excised cucumber leaves for >12 generations still maintained the ability to use intact cotton plants but did not establish a population on cucumber plants. However, one cucumber genotype conditioned by artificial diet and then reared on excised cotton leaves could use both the intact cotton and cucumber plants, showing that the expansion of host range was mediated by feeding experience.

Conclusion

Feeding experience on artificial diet induced the expansion of host range of the cucurbit-specialized A. gossypii, and this expansion was genotype-specific. We speculated that feeding on a constant set of host plants in the life cycle of aphids may contribute to the formation of host specialization.

Components of Cowpea Resistance to the Seed Beetle Callosobruchus maculatus (Coleoptera: Chrysomelidae: Bruchinae)

Cowpea, Vigna unguiculata (L.) Walp., serves as a major source of dietary protein in many tropical and subtropical regions around the world. To identify loci associated with agronomically desirable traits, eight elite cowpea cultivars were systematically inter-crossed for eight generations to yield 305 recombinant inbred lines. Here, we investigated whether these founder parents also possess resistance to the seed beetle Callosobruchus maculatus (F.), a highly destructive post-harvest pest. We estimated larval survival in seeds, egg-to-adult development time, adult mass at emergence, and seed acceptance for oviposition. Survival varied significantly among cowpea cultivars, but the pattern was complicated by an unexpected source of mortality; on three cultivars, mature larvae in a substantial fraction of seeds (20-36%) exited seeds prematurely, and consequently failed to molt into viable adults. Even if such seeds were eliminated from the analysis, survival in the remaining seeds varied from 49 to 92% across the eight parents. Development time and body mass also differed among hosts, with particularly slow larval development on three closely related cultivars. Egg-laying females readily accepted all cultivars except one with a moderately rugose seed coat. Overall, suitability ranks of the eight cultivars depended on beetle trait; a cultivar that received the most eggs (IT82E-18) also conferred low survival. However, one cultivar (IT93K-503-1) was a relatively poor host for all traits. Given the magnitude of variation among parental cultivars, future assays of genotyped recombinant progeny can identify genomic regions and candidate genes associated with resistance to seed beetles.

Variable Responses to Novel Hosts by Populations of the Seed Beetle Callosobruchus maculatus (Coleoptera: Chrysomelidae: Bruchinae)

Cosmopolitan pests can consist of geographic populations that differ in their current host ranges or in their ability to colonize a novel host. We compared the responses of cowpea-adapted, seed-beetle populations (Callosobruchus maculatus [F.] (Coleoptera: Chrysomelidae: Bruchinae)) from Africa, North America, and South America to four novel legumes: chickpea, lentil, mung bean, and pea. We also qualitatively compared these results to those obtained earlier for an Asian population. For each host, we measured larval survival to adult emergence and used both no-choice and choice tests to estimate host acceptance. The pattern of larval survival was similar among populations: high or moderately high survival on cowpea, mung bean, and chickpea, intermediate survival on pea, and very low survival on lentil. One exception was unusually high survival of African larvae on pea, and there was modest variation among populations for survival on lentil. The African population was also an outlier with respect to host acceptance; under no-choice conditions, African females showed a much greater propensity to accept the two least preferred hosts, chickpea and lentil. However, greater acceptance of these hosts by African females was not evident in choice tests. Inferences about population differences in host acceptance can thus strongly depend on experimental protocol. Future selection experiments can be used to determine whether the observed population differences in initial performance will affect the probability of producing self-sustaining populations on a marginal crop host.

Antagonistic pleiotropy for carbon use is rare in new mutations

Pleiotropic effects of mutations underlie diverse biological phenomena such as ageing and specialization. In particular, antagonistic pleiotropy ("AP": when a mutation has opposite fitness effects in different environments) generates tradeoffs, which may constrain adaptation. Models of adaptation typically assume that AP is common - especially among large-effect mutations - and that pleiotropic effect sizes are positively correlated. Empirical tests of these assumptions have focused on de novo beneficial mutations arising under strong selection. However, most mutations are actually deleterious or neutral, and may contribute to standing genetic variation that can subsequently drive adaptation. We quantified the incidence, nature, and effect size of pleiotropy for carbon utilization across 80 single mutations in Escherichia coli that arose under mutation accumulation (i.e., weak selection). Although ∼46% of the mutations were pleiotropic, only 11% showed AP; among beneficial mutations, only ∼4% showed AP. In some environments, AP was more common in large-effect mutations; and AP effect sizes across environments were often negatively correlated. Thus, AP for carbon use is generally rare (especially among beneficial mutations); is not consistently enriched in large-effect mutations; and often involves weakly deleterious antagonistic effects. Our unbiased quantification of mutational effects therefore suggests that antagonistic pleiotropy may be unlikely to cause maladaptive tradeoffs.

Genetic drift precluded adaptation of an insect seed predator to a novel host plant in a long-term selection experiment

Host specialization is considered a primary driver of the enormous diversity of herbivorous insects. Trade-offs in host use are hypothesized to promote this specialization, but they have mostly been studied in generalist herbivores. We conducted a multi-generation selection experiment to examine the adaptation of the specialist seed-feeding bug, Lygaeus equestris, to three novel host plants (Helianthus annuus, Verbascum thapsus and Centaurea phrygia) and to test whether trade-offs promote specialization. During the selection experiment, body size of L. equestris increased more on the novel host plant H. annuus compared to the primary host plant, Vincetoxicum hirundinaria, but this effect was not observed in other fitness related traits. In addition to selection, genetic drift caused variation among the experimental herbivore populations in their ability to exploit the host plants. Microsatellite data indicated that the level of within-population genetic variation decreased and population differentiation increased more in the selection line feeding on H. annuus compared to V. hirundinaria. We found a negative correlation between genetic differentiation and heterozygosity at the end of the experiment, suggesting that differentiation was significantly affected by genetic drift. We did not find fitness trade-offs between L. equestris feeding on the four hosts. Thus, trade-offs do not seem to promote specialization in L. equestris. Our results suggest that this insect herbivore is not likely to adapt to a novel host species in a time-scale of 20 generations despite sufficient genetic variation and that genetic drift disrupted the response to selection.

Natural selection and the predictability of evolution in Timema stick insects

Predicting evolution remains difficult. We studied the evolution of cryptic body coloration and pattern in a stick insect using 25 years of field data, experiments, and genomics. We found that evolution is more difficult to predict when it involves a balance between multiple selective factors and uncertainty in environmental conditions than when it involves feedback loops that cause consistent back-and-forth fluctuations. Specifically, changes in color-morph frequencies are modestly predictable through time (r² = 0.14) and driven by complex selective regimes and yearly fluctuations in climate. In contrast, temporal changes in pattern-morph frequencies are highly predictable due to negative frequency-dependent selection (r² = 0.86). For both traits, however, natural selection drives evolution around a dynamic equilibrium, providing some predictability to the process.

Evolution of larval competitiveness and associated life-history traits in response to host shifts in a seed beetle

Resource competition is frequently strong among parasites that feed within small discrete resource patches, such as seeds or fruits. The properties of a host can influence the behavioural, morphological and life-history traits of associated parasites, including traits that mediate competition within the host. For seed parasites, host size may be an especially important determinant of competitive ability. Using the seed beetle, Callosobruchus maculatus, we performed replicated, reciprocal host shifts to examine the role of seed size in determining larval competitiveness and associated traits. Populations ancestrally associated with either a small host (mung bean) or a large one (cowpea) were switched to each other's host for 36 generations. Compared to control lines (those remaining on the ancestral host), lines switched from the small host to the large host evolved greater tolerance of co-occurring larvae within seeds (indicated by an increase in the frequency of small seeds yielding two adults), smaller egg size and higher fecundity. Each change occurred in the direction predicted by the traits of populations already adapted to cowpea. However, we did not observe the expected decline in adult mass following the shift to the larger host. Moreover, lines switched from the large host (cowpea) to the small host (mung bean) did not evolve the predicted increase in larval competitiveness or egg size, but did exhibit the predicted increase in body mass. Our results thus provide mixed support for the hypothesis that host size determines the evolution of competition-related traits of seed beetles. Evolutionary responses to the two host shifts were consistent among replicate lines, but the evolution of larval competition was asymmetric, with larval competitiveness evolving as predicted in one direction of host shift, but not the reverse. Nevertheless, our results indicate that switching hosts is sufficient to produce repeatable and rapid changes in the competition strategy and fitness-related traits of insect populations.

Trait Correlations in the Genomics Era

Thinking about the evolutionary causes and consequences of trait correlations has been dominated by quantitative genetics theory that is focused on hypothetical loci. Since this theory was initially developed, technology has enabled the identification of specific genetic variants that contribute to trait correlations. Here, we review studies of the genetic basis of trait correlations to ask: What has this new information taught us? We find that causal variants can be pleiotropic and/or linked in different ways, indicating that pleiotropy and linkage are not alternative genetic mechanisms. Further, many trait correlations have a polygenic basis, suggesting that both pleiotropy and linkage likely contribute. We discuss implications of these findings for the evolutionary causes and consequences of trait correlations.