Evolution in agriculture: the application of evolutionary approaches to the management of biotic interactions in agro-ecosystems

Addressing the Challenges of Pathogen Evolution on the World's Arable Crops

Advances in genomic and molecular technologies coupled with an increasing understanding of the fine structure of many resistance and infectivity genes, have opened up a new era of hope in controlling the many plant pathogens that continue to be a major source of loss in arable crops. Some new approaches are under consideration including the use of nonhost resistance and the targeting of critical developmental constraints. However, the major thrust of these genomic and molecular approaches is to enhance the identification of resistance genes, to increase their ease of manipulation through marker and gene editing technologies and to lock a range of resistance genes together in simply manipulable resistance gene cassettes. All these approaches essentially continue a strategy that assumes the ability to construct genetic-based resistance barriers that are insurmountable to target pathogens. Here we show how the recent advances in knowledge and marker technologies can be used to generate more durable disease resistance strategies that are based on broad evolutionary principles aimed at presenting pathogens with a shifting, landscape of fluctuating directional selection.

Restriction site associated DNA (RAD) for de novo sequencing and marker discovery in sugarcane borer, Diatraea saccharalis Fab. (Lepidoptera: Crambidae)

We present the development of a genomic library using RADseq (restriction site associated DNA sequencing) protocol for marker discovery that can be applied on evolutionary studies of the sugarcane borer Diatraea saccharalis, an important South American insect pest. A RADtag protocol combined with Illumina paired-end sequencing allowed de novo discovery of 12 811 SNPs and a high-quality assembly of 122.8M paired-end reads from six individuals, representing 40 Gb of sequencing data. Approximately 1.7 Mb of the sugarcane borer genome distributed over 5289 minicontigs were obtained upon assembly of second reads from first reads RADtag loci where at least one SNP was discovered and genotyped. Minicontig lengths ranged from 200 to 611 bp and were used for functional annotation and microsatellite discovery. These markers will be used in future studies to understand gene flow and adaptation to host plants and control tactics.

How humans drive speciation as well as extinction

A central topic for conservation science is evaluating how human activities influence global species diversity. Humanity exacerbates extinction rates. But by what mechanisms does humanity drive the emergence of new species? We review human-mediated speciation, compare speciation and known extinctions, and discuss the challenges of using net species diversity as a conservation objective. Humans drive rapid evolution through relocation, domestication, hunting and novel ecosystem creation-and emerging technologies could eventually provide additional mechanisms. The number of species relocated, domesticated and hunted during the Holocene is of comparable magnitude to the number of observed extinctions. While instances of human-mediated speciation are known, the overall effect these mechanisms have upon speciation rates has not yet been quantified. We also explore the importance of anthropogenic influence upon divergence in microorganisms. Even if human activities resulted in no net loss of species diversity by balancing speciation and extinction rates, this would probably be deemed unacceptable. We discuss why, based upon 'no net loss' conservation literature-considering phylogenetic diversity and other metrics, risk aversion, taboo trade-offs and spatial heterogeneity. We conclude that evaluating speciation alongside extinction could result in more nuanced understanding of biosphere trends, clarifying what it is we actually value about biodiversity.

Insight into the durability of plant resistance to aphids from a demo-genetic study of Aphis gossypii in melon crops

Resistance breakdown has been observed following the deployment of plant cultivars resistant to pests. Assessing the durability of a resistance requires long-term experiments at least at a regional scale. We collected such data for melon resistance conferred by the Vat gene cluster to melon aphids. We examined landscape-level populations of Aphis gossypii collected in 2004-2015, from melon-producing regions with and without the deployment of Vat resistance and with different climates. We conducted demo-genetic analyses of the aphid populations on Vat and non-Vat plants during the cropping seasons. The Vat resistance decreased the density of aphid populations in all areas and changed the genetic structure and composition of these populations. Two bottlenecks were identified in the dynamics of adapted clones, due to the low levels of production of dispersal morphs and winter extinction. Our results suggest that (i) Vat resistance will not be durable in the Lesser Antilles, where no bottleneck affected the dynamics of adapted clones, (ii) Vat resistance will be durable in south-west France, where both bottlenecks affected the dynamics of adapted clones and (iii) Vat resistance will be less durable in south-east France, where only one of the two bottlenecks was observed.

Evolution and Phylogenetic Diversity of Yam Species (Dioscorea spp.): Implication for Conservation and Agricultural Practices

Yams (Dioscorea spp.) consist of approximately 600 species. Presently, these species are threatened by genetic erosion due to many factors such as pest attacks and farming practices. In parallel, complex taxonomic boundaries in this genus makes it more challenging to properly address the genetic diversity of yam and manage its germplasm. As a first step toward evaluating and preserving the genetic diversity yam species, we use a phylogenetic diversity (PD) approach that has the advantage to investigate phylogenetic relationships and test hypotheses of species monophyly while alleviating to the problem of ploidy variation within and among species. The Bayesian phylogenetic analysis of 62 accessions from 7 species from three regions of Cameroon showed that most Dioscorea sections were monophyletic, but species within sections were generally non-monophyletic. The wild species D. praehensilis and cultivated D. cayenensis were the species with the highest PD. At the opposite, D. esculenta has a low PD and future studies should focus on this species to properly address its conservation status. We also show that wild species show a stronger genetic structure than cultivated species, which potentially reflects the management of the yam germplasm by farmers. These findings show that phylogenetic diversity is a promising approach for an initial investigation of genetic diversity in a crop consisting of closely related species.

The Urochloa Foliar Blight and Collar Rot Pathogen Rhizoctonia solani AG-1 IA Emerged in South America Via a Host Shift from Rice

The fungus Rhizoctonia solani anastomosis group (AG)-1 IA emerged in the early 1990s as an important pathogen causing foliar blight and collar rot on pastures of the genus Urochloa (signalgrass) in South America. We tested the hypothesis that this pathogen emerged following a host shift or jump as a result of geographical overlapping of host species. The genetic structure of host and regional populations of R. solani AG-1 IA infecting signalgrass, rice, and soybean in Colombia and Brazil was analyzed using nine microsatellite loci in 350 isolates to measure population differentiation and infer the pathogen reproductive system. Phylogeographical analyses based on the microsatellite loci and on three DNA sequence loci were used to infer historical migration patterns and test hypotheses about the origin of the current pathogen populations. Cross pathogenicity assays were conducted to measure the degree of host specialization in populations sampled from different hosts. The combined analyses indicate that the pathogen populations currently infecting Urochloa in Colombia and Brazil most likely originated from a population that originally infected rice. R. solani AG-1 IA populations infecting Urochloa exhibit a mixed reproductive system including both sexual reproduction and long-distance dispersal of adapted clones, most likely on infected seed. The pathogen population on Urochloa has a genetic structure consistent with a high evolutionary potential and showed evidence for host specialization.

Fitness trade-offs in pest management and intercropping with colour: an evolutionary framework and potential application

An important modern goal of plant science research is to develop tools for agriculturalists effective at curbing yield losses to insect herbivores, but resistance evolution continuously threatens the efficacy of pest management strategies. The high-dose/refuge strategy has been employed with some success to curb pest adaptation, and has been shown to be most effective when fitness costs (fitness trade-offs) of resistance are high. Here, I use eco-evolutionary reasoning to demonstrate the general importance of fitness trade-offs for pest control, showing that strong fitness trade-offs mitigate the threat of pest adaptation, even if adaptation were to occur. I argue that novel pest management strategies evoking strong fitness trade-offs are the most likely to persist in the face of unbridled pest adaptation, and offer the manipulation of crop colours as a worked example of one potentially effective strategy against insect herbivores.

Stochastic eco-evolutionary model of a prey-predator community

We are interested in the impact of natural selection in a prey-predator community. We introduce an individual-based model of the community that takes into account both prey and predator phenotypes. Our aim is to understand the phenotypic coevolution of prey and predators. The community evolves as a multi-type birth and death process with mutations. We first consider the infinite particle approximation of the process without mutation. In this limit, the process can be approximated by a system of differential equations. We prove the existence of a unique globally asymptotically stable equilibrium under specific conditions on the interaction among prey individuals. When mutations are rare, the community evolves on the mutational scale according to a Markovian jump process. This process describes the successive equilibria of the prey-predator community and extends the polymorphic evolutionary sequence to a coevolutionary framework. We then assume that mutations have a small impact on phenotypes and consider the evolution of monomorphic prey and predator populations. The limit of small mutation steps leads to a system of two differential equations which is a version of the canonical equation of adaptive dynamics for the prey-predator coevolution. We illustrate these different limits with an example of prey-predator community that takes into account different prey defense mechanisms. We observe through simulations how these various prey strategies impact the community.

Playing on a pathogen's weakness: using evolution to guide sustainable plant disease control strategies

Wild plants and their associated pathogens are involved in ongoing interactions over millennia that have been modified by coevolutionary processes to limit the spatial extent and temporal duration of disease epidemics. These interactions are disrupted by modern agricultural practices and social activities, such as intensified monoculture using superior varieties and international trading of agricultural commodities. These activities, when supplemented with high resource inputs and the broad application of agrochemicals, create conditions uniquely conducive to widespread plant disease epidemics and rapid pathogen evolution. To be effective and durable, sustainable disease management requires a significant shift in emphasis to overtly include ecoevolutionary principles in the design of adaptive management programs aimed at minimizing the evolutionary potential of plant pathogens by reducing their genetic variation, stabilizing their evolutionary dynamics, and preventing dissemination of pathogen variants carrying new infectivity or resistance to agrochemicals.

Crop pathogen emergence and evolution in agro-ecological landscapes

Remnant areas hosting natural vegetation in agricultural landscapes can impact the disease epidemiology and evolutionary dynamics of crop pathogens. However, the potential consequences for crop diseases of the composition, the spatial configuration and the persistence time of the agro-ecological interface - the area where crops and remnant vegetation are in contact - have been poorly studied. Here, we develop a demographic-genetic simulation model to study how the spatial and temporal distribution of remnant wild vegetation patches embedded in an agricultural landscape can drive the emergence of a crop pathogen and its subsequent specialization on the crop host. We found that landscape structures that promoted larger pathogen populations on the wild host facilitated the emergence of a crop pathogen, but such landscape structures also reduced the potential for the pathogen population to adapt to the crop. In addition, the evolutionary trajectory of the pathogen population was determined by interactions between the factors describing the landscape structure and those describing the pathogen life histories. Our study contributes to a better understanding of how the shift of land-use patterns in agricultural landscapes might influence crop diseases to provide predictive tools to evaluate management practices.

Enhanced science-stakeholder communication to improve ecosystem model performances for climate change impact assessments

In recent years, climate impact assessments of relevance to the agricultural and forestry sectors have received considerable attention. Current ecosystem models commonly capture the effect of a warmer climate on biomass production, but they rarely sufficiently capture potential losses caused by pests, pathogens and extreme weather events. In addition, alternative management regimes may not be integrated in the models. A way to improve the quality of climate impact assessments is to increase the science-stakeholder collaboration, and in a two-way dialog link empirical experience and impact modelling with policy and strategies for sustainable management. In this paper we give a brief overview of different ecosystem modelling methods, discuss how to include ecological and management aspects, and highlight the importance of science-stakeholder communication. By this, we hope to stimulate a discussion among the science-stakeholder communities on how to quantify the potential for climate change adaptation by improving the realism in the models.

Crop domestication and its impact on naturally selected trophic interactions

Crop domestication is the process of artificially selecting plants to increase their suitability to human requirements: taste, yield, storage, and cultivation practices. There is increasing evidence that crop domestication can profoundly alter interactions among plants, herbivores, and their natural enemies. Overall, little is known about how these interactions are affected by domestication in the geographical ranges where these crops originate, where they are sympatric with the ancestral plant and share the associated arthropod community. In general, domestication consistently has reduced chemical resistance against herbivorous insects, improving herbivore and natural enemy performance on crop plants. More studies are needed to understand how changes in morphology and resistance-related traits arising from domestication may interact with environmental variation to affect species interactions across multiple scales in agroecosystems and natural ecosystems.

The evolution of fungicide resistance

Fungicides are widely used in developed agricultural systems to control disease and safeguard crop yield and quality. Over time, however, resistance to many of the most effective fungicides has emerged and spread in pathogen populations, compromising disease control. This review describes the development of resistance using case histories based on four important diseases of temperate cereal crops: eyespot (Oculimacula yallundae and Oculimacula acuformis), Septoria tritici blotch (Zymoseptoria tritici), powdery mildew (Blumeria graminis), and Fusarium ear blight (a complex of Fusarium and Microdochium spp). The sequential emergence of variant genotypes of these pathogens with reduced sensitivity to the most active single-site fungicides, methyl benzimidazole carbamates, demethylation inhibitors, quinone outside inhibitors, and succinate dehydrogenase inhibitors illustrates an ongoing evolutionary process in response to the introduction and use of different chemical classes. Analysis of the molecular mechanisms and genetic basis of resistance has provided more rapid and precise methods for detecting and monitoring the incidence of resistance in field populations, but when or where resistance will occur remains difficult to predict. The extent to which the predictability of resistance evolution can be improved by laboratory mutagenesis studies and fitness measurements, comparison between pathogens, and reconstruction of evolutionary pathways is discussed. Risk models based on fungal life cycles, fungicide properties, and exposure to the fungicide are now being refined to take account of additional traits associated with the rate of pathogen evolution. Experimental data on the selection of specific mutations or resistant genotypes in pathogen populations in response to fungicide treatments can be used in models evaluating the most effective strategies for reducing or preventing resistance. Resistance management based on robust scientific evidence is vital to prolong the effective life of fungicides and safeguard their future use in crop protection.

The influence of genetic drift and selection on quantitative traits in a plant pathogenic fungus

Genetic drift and selection are ubiquitous evolutionary forces acting to shape genetic variation in populations. While their relative importance has been well studied in plants and animals, less is known about their relative importance in fungal pathogens. Because agro-ecosystems are more homogeneous environments than natural ecosystems, stabilizing selection may play a stronger role than genetic drift or diversifying selection in shaping genetic variation among populations of fungal pathogens in agro-ecosystems. We tested this hypothesis by conducting a Q_ST/F_ST analysis using agricultural populations of the barley pathogen Rhynchosporium commune. Population divergence for eight quantitative traits (Q_ST) was compared with divergence at eight neutral microsatellite loci (F_ST) for 126 pathogen strains originating from nine globally distributed field populations to infer the effects of genetic drift and types of selection acting on each trait. Our analyses indicated that five of the eight traits had Q_ST values significantly lower than F_ST, consistent with stabilizing selection, whereas one trait, growth under heat stress (22°C), showed evidence of diversifying selection and local adaptation (Q_ST>F_ST). Estimates of heritability were high for all traits (means ranging between 0.55–0.84), and average heritability across traits was negatively correlated with microsatellite gene diversity. Some trait pairs were genetically correlated and there was significant evidence for a trade-off between spore size and spore number, and between melanization and growth under benign temperature. Our findings indicate that many ecologically and agriculturally important traits are under stabilizing selection in R. commune and that high within-population genetic variation is maintained for these traits.

Applying evolutionary biology to address global challenges

Two categories of evolutionary challenges result from escalating human impacts on the planet. The first arises from cancers, pathogens, and pests that evolve too quickly and the second, from the inability of many valued species to adapt quickly enough. Applied evolutionary biology provides a suite of strategies to address these global challenges that threaten human health, food security, and biodiversity. This Review highlights both progress and gaps in genetic, developmental, and environmental manipulations across the life sciences that either target the rate and direction of evolution or reduce the mismatch between organisms and human-altered environments. Increased development and application of these underused tools will be vital in meeting current and future targets for sustainable development.

Expanding the eco-evolutionary context of herbicide resistance research

The potential for human-driven evolution in economically and environmentally important organisms in medicine, agriculture and conservation management is now widely recognised. The evolution of herbicide resistance in weeds is a classic example of rapid adaptation in the face of human-mediated selection. Management strategies that aim to slow or prevent the evolution of herbicide resistance must be informed by an understanding of the ecological and evolutionary factors that drive selection in weed populations. Here, we argue for a greater focus on the ultimate causes of selection for resistance in herbicide resistance studies. The emerging fields of eco-evolutionary dynamics and applied evolutionary biology offer a means to achieve this goal and to consider herbicide resistance in a broader and sometimes novel context. Four relevant research questions are presented, which examine (i) the impact of herbicide dose on selection for resistance, (ii) plant fitness in herbicide resistance studies, (iii) the efficacy of herbicide rotations and mixtures and (iv) the impacts of gene flow on resistance evolution and spread. In all cases, fundamental ecology and evolution have the potential to offer new insights into herbicide resistance evolution and management.

Achieving sustainable plant disease management through evolutionary principles

Plants and their pathogens are engaged in continuous evolutionary battles and sustainable disease management requires novel systems to create environments conducive for short-term and long-term disease control. In this opinion article, we argue that knowledge of the fundamental factors that drive host-pathogen coevolution in wild systems can provide new insights into disease development in agriculture. Such evolutionary principles can be used to guide the formulation of sustainable disease management strategies which can minimize disease epidemics while simultaneously reducing pressure on pathogens to evolve increased infectivity and aggressiveness. To ensure agricultural sustainability, disease management programs that reflect the dynamism of pathogen population structure are essential and evolutionary biologists should play an increasing role in their design.

Plant succession as an integrator of contrasting ecological time scales

Ecologists have studied plant succession for over a hundred years, yet our understanding of the nature of this process is incomplete, particularly in relation to its response to new human perturbations and the need to manipulate it during ecological restoration. We demonstrate how plant succession can be understood better when it is placed in the broadest possible temporal context. We further show how plant succession can be central to the development of a framework that integrates a spectrum of ecological processes, which occur over time scales ranging from seconds to millions of years. This novel framework helps us understand the impacts of human perturbations on successional trajectories, ecosystem recovery, and global environmental change.

Guiding deployment of resistance in cereals using evolutionary principles

Genetically controlled resistance provides plant breeders with an efficient means of controlling plant disease, but this approach has been constrained by practical difficulties associated with combining many resistance genes together and strong evolutionary responses from pathogen populations leading to subsequent resistance breakdown. However, continuing advances in molecular marker technologies are revolutionizing the ability to rapidly and reliably manipulate resistances of all types - major gene, adult plant and quantitative resistance loci singly or multiply into individual host lines. Here, we argue that these advances provide major opportunities to deliberately design deployment strategies in cereals that can take advantage of the evolutionary pressures faced by target pathogens. Different combinations of genes deployed either within single host individuals or between different individuals within or among crops, can be used to reduce the size of pathogen populations and generate patterns of disruptive selection. This will simultaneously limit immediate epidemic development and reduce the probability of subsequent evolutionary change in the pathogen for broader infectivity or increased aggressiveness. The same general principles are relevant to the control of noncereal diseases, but the most efficacious controls will vary reflecting the range of genetic options available and their fit with specific ecology and life-history combinations.

Identifying geographic hot spots of reassortment in a multipartite plant virus

Reassortment between different species or strains plays a key role in the evolution of multipartite plant viruses and can have important epidemiological implications. Identifying geographic locations where reassortant lineages are most likely to emerge could be a valuable strategy for informing disease management and surveillance efforts. We developed a predictive framework to identify potential geographic hot spots of reassortment based upon spatially explicit analyses of genome constellation diversity. To demonstrate the utility of this approach, we examined spatial variation in the potential for reassortment among Cardamom bushy dwarf virus (CBDV; Nanoviridae, Babuvirus) isolates in Northeast India. Using sequence data corresponding to six discrete genome components for 163 CBDV isolates, a quantitative measure of genome constellation diversity was obtained for locations across the sampling region. Two key areas were identified where viruses with highly distinct genome constellations cocirculate, and these locations were designated as possible geographic hot spots of reassortment, where novel reassortant lineages could emerge. Our study demonstrates that the potential for reassortment can be spatially dependent in multipartite plant viruses and highlights the use of evolutionary analyses to identify locations which could be actively managed to facilitate the prevention of outbreaks involving novel reassortant strains.

Pathogen population dynamics in agricultural landscapes: the Ddal modelling framework

Modelling processes that occur at the landscape scale is gaining more and more attention from theoretical ecologists to agricultural managers. Most of the approaches found in the literature lack applicability for managers or, on the opposite, lack a sound theoretical basis. Based on the metapopulation concept, we propose here a modelling approach for landscape epidemiology that takes advantage of theoretical results developed in the metapopulation context while considering realistic landscapes structures. A landscape simulator makes it possible to represent both the field pattern and the spatial distribution of crops. The pathogen population dynamics are then described through a matrix population model both stage- and space-structured. In addition to a classical invasion analysis we present a stochastic simulation experiment and provide a complete framework for performing a sensitivity analysis integrating the landscape as an input factor. We illustrate our approach using an example to evaluate whether the agricultural landscape composition and structure may prevent and mitigate the development of an epidemic. Although designed for a fungal foliar disease, our modelling approach is easily adaptable to other organisms.

Ecological effects of environmental change

This Special Issue of Ecology Letters presents contributions from an international meeting organised by Centre National de la Recherche Scientifique (CNRS) and Ecology Letters on the broad theme of ecological effects of global environmental change. The objectives of these articles are to synthesise, hypothesise and illustrate the ecological effects of environmental change drivers and their interactions, including habitat loss and fragmentation, pollution, invasive species and climate change. A range of disciplines is represented, including stoichiometry, cell biology, genetics, evolution and biodiversity conservation. The authors emphasise the need to account for several key ecological factors and different spatial and temporal scales in global change research. They also stress the importance of ecosystem complexity through approaches such as functional group and network analyses, and of mechanisms and predictive models with respect to environmental responses to global change across an ecological continuum: population, communities and ecosystems. Lastly, these articles provide important insights and recommendations for environmental conservation and management, as well as highlighting future research priorities.

When virulence originates from non-agricultural hosts: new insights into plant breeding

Monogenic plant resistance breakdown is a model for testing evolution in action in pathogens. As a rule, plant pathologists argue that virulence - the allele that allows pathogens to overcome resistance - is due to a new mutation at the avirulence locus within the native/endemic population that infects susceptible crops. In this article, we develop an alternative and neglected scenario where a given virulence pre-exists in a non-agricultural host and might be accidentally released or introduced on the matching resistant cultivar in the field. The main difference between the two scenarios is the divergence time expected between the avirulent and the virulent populations. As a consequence, population genetic approaches such as genome scans and Approximate Bayesian Computation methods allow explicit testing of the two scenarios by timing the divergence. This review then explores the fundamental implications of this alternative scenario for plant breeding, including the invasion of virulence or the evolution of more aggressive hybrids, and proposes concrete solutions to achieve a sustainable resistance.

Is agriculture driving the diversification of the Bemisia tabaci species complex (Hemiptera: Sternorrhyncha: Aleyrodidae)?: Dating, diversification and biogeographic evidence revealed

BACKGROUND

Humans and insect herbivores are competing for the same food crops and have been for thousands of years. Despite considerable advances in crop pest management, losses due to insects remain considerable. The global homogenisation of agriculture has supported the range expansion of numerous insect pests and has been driven in part by human-assisted dispersal supported through rapid global trade and low-cost air passenger transport. One of these pests, is the whitefly, Bemisia tabaci, a cryptic species complex that contains some of the world's most damaging pests of agriculture. The complex shows considerable genetic diversity and strong phylogeographic relationships. One consequence of the considerable impact that members of the B. tabaci complex have on agriculture, is the view that human activity, particularly in relation to agricultural practices, such as use of insecticides, has driven the diversification found within the species complex. This has been particularly so in the case of two members of the complex, Middle East-Asia Minor 1 (MEAM1) and Mediterranean (MED), which have become globally distributed invasive species. An alternative hypothesis is that diversification is due to paleogeographic and paleoclimatological changes.

RESULTS

The idea that human activity is driving speciation within the B. tabaci complex has never been tested, but the increased interest in fossil whiteflies and the growth in molecular data have enabled us to apply a relaxed molecular clock and so estimate divergence dates for the major lineages within the B. tabaci species complex. The divergence estimates do not support the view that human activity has been a major driver of diversification.

CONCLUSIONS

Our analysis suggests that the major lineages within the complex arose approximately 60-30 mya and the highly invasive MED and MEAM1 split from the rest of the species complex around 12 mya well before the evolution of Homo sapiens and agriculture. Furthermore, the divergence dates coincide with a period of global diversification that occurred broadly across the plant and animal kingdoms and was most likely associated with major climatic and tectonic events.

Herbicide-resistant weeds: from research and knowledge to future needs

Synthetic herbicides have been used globally to control weeds in major field crops. This has imposed a strong selection for any trait that enables plant populations to survive and reproduce in the presence of the herbicide. Herbicide resistance in weeds must be minimized because it is a major limiting factor to food security in global agriculture. This represents a huge challenge that will require great research efforts to develop control strategies as alternatives to the dominant and almost exclusive practice of weed control by herbicides. Weed scientists, plant ecologists and evolutionary biologists should join forces and work towards an improved and more integrated understanding of resistance across all scales. This approach will likely facilitate the design of innovative solutions to the global herbicide resistance challenge.

Adaptive evolution of a generalist parasitoid: implications for the effectiveness of biological control agents

The use of alternative hosts imposes divergent selection pressures on parasitoid populations. In response to selective pressures, these populations may follow different evolutionary trajectories. Divergent natural selection could promote local host adaptation in populations, translating into direct benefits for biological control, thereby increasing their effectiveness on the target host. Alternatively, adaptive phenotypic plasticity could be favored over local adaptation in temporal and spatially heterogeneous environments. We investigated the existence of local host adaptation in Aphidius ervi, an important biological control agent, by examining different traits related to infectivity (preference) and virulence (a proxy of parasitoid fitness) on different aphid-host species. The results showed significant differences in parasitoid infectivity on their natal host compared with the non-natal hosts. However, parasitoids showed a similar high fitness on both natal and non-natal hosts, thus supporting a lack of host adaptation in these introduced parasitoid populations. Our results highlight the role of phenotypic plasticity in fitness-related traits of parasitoids, enabling them to maximize fitness on alternative hosts. This could be used to increase the effectiveness of biological control. In addition, A. ervi females showed significant differences in infectivity and virulence across the tested host range, thus suggesting a possible host phylogeny effect for those traits.

Molecular genetics and genomics generate new insights into invertebrate pest invasions

Invertebrate pest invasions and outbreaks are associated with high social, economic, and ecological costs, and their significance will intensify with an increasing pressure on agricultural productivity as a result of human population growth and climate change. New molecular genetic and genomic techniques are available and accessible, but have been grossly underutilized in studies of invertebrate pest invasions, despite that they are useful tools for applied pest management and for understanding fundamental features of pest invasions including pest population demographics and adaptation of pests to novel and/or changing environments. Here, we review current applications of molecular genetics and genomics in the study of invertebrate pest invasions and outbreaks, and we highlight shortcomings from the current body of research. We then discuss recent conceptual and methodological advances in the areas of molecular genetics/genomics and data analysis, and we highlight how these advances will further our understanding of the demographic, ecological, and evolutionary features of invertebrate pest invasions. We are now well equipped to use molecular data to understand invertebrate dispersal and adaptation, and this knowledge has valuable applications in agriculture at a time when these are critically required.

Worldwide population genetic structure of the oriental fruit moth (Grapholita molesta), a globally invasive pest

Background

Invasive pest species have large impacts on agricultural crop yields, and understanding their population dynamics is important for ensuring food security. The oriental fruit moth Grapholita molesta is a cosmopolitan pest of stone and pome fruit species including peach and apple, and historical records indicate that it has invaded North and South America, Europe, Australia and Africa from its putative native range in Asia over the past century.

Results

We used 13 microsatellite loci, including nine newly developed markers, to characterize global population structure of G. molesta. Approximately 15 individuals from each of 26 globally distributed populations were genotyped. A weak but significant global pattern of isolation-by-distance was found, and G. molesta populations were geographically structured on a continental scale. Evidence does not support that G. molesta was introduced to North America from Japan as previously proposed. However, G. molesta was probably introduced from North America to The Azores, South Africa, and Brazil, and from East Asia to Australia. Shared ancestry was inferred between populations from Western Europe and from Brazil, although it remains unresolved whether an introduction occurred from Europe to Brazil, or vice versa. Both genetic diversity and levels of inbreeding were surprisingly high across the range of G. molesta and were not higher or lower overall in introduced areas compared to native areas. There is little evidence for multiple introductions to each continent (except in the case of South America), or for admixture between populations from different origins.

Conclusions

Cross-continental introductions of G. molesta appear to be infrequent, which is surprising given its rapid worldwide expansion over the past century. We suggest that area-wide spread via transport of fruits and other plant materials is a major mechanism of ongoing invasion, and management efforts should therefore target local and regional farming communities and distribution networks.

Simulating evolutionary responses of an introgressed insect resistance trait for ecological effect assessment of transgene flow: a model for supporting informed decision-making in environmental risk assessment

Predicting outcomes of transgene flow from arable crops requires a system perspective that considers ecological and evolutionary processes within a landscape context. In Europe, the arable weed Raphanus raphanistrum is a potential hybridization partner of oilseed rape, and the two species are ecologically linked through the common herbivores Meligethes spp. Observations in Switzerland show that high densities of Meligethes beetles maintained by oilseed rape crops can lead to considerable damage on R. raphanistrum. We asked how increased insect resistance in R. raphanistrum - as might be acquired through introgression from transgenic oilseed rape - would affect seed production under natural herbivore pressure. In simulation experiments, plants protected against Meligethes beetles produced about twice as many seeds as unprotected plants. All stages in the development of reproductive structures from buds to pods were negatively affected by the herbivore, with the transition from buds to flowers being the most vulnerable. We conclude that resistance to Meligethes beetles could confer a considerable selective advantage upon R. raphanistrum in regions where oilseed rape is widely grown.

Experimental measures of pathogen competition and relative fitness

Competition among pathogen strains for limited host resources can have a profound effect on pathogen evolution. A better understanding of the principles and consequences of competition can be useful in designing more sustainable disease management strategies. The competitive ability and relative fitness of a pathogen strain are determined by its intrinsic biological properties, the resistance and heterogeneity of the corresponding host population, the population density and genetic relatedness of the competing strains, and the physical environment. Competitive ability can be inferred indirectly from fitness components, such as basic reproduction rate or transmission rate. However, pathogen strains that exhibit higher fitness components when they infect a host alone may not exhibit a competitive advantage when they co-infect the same host. The most comprehensive measures of competitive ability and relative fitness come from calculating selection coefficients in a mixed infection in a field setting. Mark-release-recapture experiments can be used to estimate fitness costs associated with unnecessary virulence and fungicide resistance.

Biologically Based Methods for Pest Management in Agriculture under Changing Climates: Challenges and Future Directions

The current changes in global climatic regimes present a significant societal challenge, affecting in all likelihood insect physiology, biochemistry, biogeography and population dynamics. With the increasing resistance of many insect pest species to chemical insecticides and an increasing organic food market, pest control strategies are slowly shifting towards more sustainable, ecologically sound and economically viable options. Biologically based pest management strategies present such opportunities through predation or parasitism of pests and plant direct or indirect defense mechanisms that can all be important components of sustainable integrated pest management programs. Inevitably, the efficacy of biological control systems is highly dependent on natural enemy-prey interactions, which will likely be modified by changing climates. Therefore, knowledge of how insect pests and their natural enemies respond to climate variation is of fundamental importance in understanding biological insect pest management under global climate change. Here, we discuss biological control, its challenges under climate change scenarios and how increased global temperatures will require adaptive management strategies to cope with changing status of insects and their natural enemies.

Stress for invasion success? Temperature stress of preceding generations modifies the response to insecticide stress in an invasive pest insect

Adaptation to stressful environments is one important factor influencing species invasion success. Tolerance to one stress may be complicated by exposure to other stressors experienced by the preceding generations. We studied whether parental temperature stress affects tolerance to insecticide in the invasive Colorado potato beetle Leptinotarsa decemlineata. Field-collected pyrethroid-resistant beetles were reared under either stressful (17°C) or favourable (23°C) insecticide-free environments for three generations. Then, larvae were exposed to pyrethroid insecticides in common garden conditions (23°C). Beetles were in general tolerant to stress. The parental temperature stress alone affected beetles positively (increased adult weight) but it impaired their tolerance to insecticide exposure. In contrast, offspring from the favourable temperature regime showed compensatory weight gain in response to insecticide exposure. Our study emphasizes the potential of cross-generational effects modifying species stress tolerance. When resistant pest populations invade benign environments, a re-application of insecticides may enhance their performance via hormetic effects. In turn, opposite effects may arise if parental generations have been exposed to temperature stress. Thus, the outcome of management practices of invasive pest species is difficult to predict unless we also incorporate knowledge of the evolutionary and recent (preceding generations) stress history of the given populations into pest management.

Shared influence of pathogen and host genetics on a trade-off between latent period and spore production capacity in the wheat pathogen, Puccinia triticina

Crop pathogens are notorious for their rapid adaptation to their host. We still know little about the evolution of their life cycles and whether there might be trade-offs between fitness components, limiting the evolutionary potential of these pathogens. In this study, we explored a trade-off between spore production capacity and latent period in Puccinia triticina, a fungal pathogen causing leaf rust on wheat. Using a simple multivariate (manova) technique, we showed that the covariance between the two traits is under shared control of host and pathogen, with contributions from host genotype (57%), pathogen genotype (18.4%) and genotype × genotype interactions (12.5%). We also found variation in sign and strength of genetic correlations for the pathogen, when measured on different host varieties. Our results suggest that these important pathogen life-history traits do not freely respond to directional selection and that precise evolutionary trajectories are contingent on the genetic identity of the interacting host and pathogen.

No evidence for change in oviposition behaviour of Helicoverpa armigera (Hübner) (Lepidoptera: Noctuidae) after widespread adoption of transgenic insecticidal cotton

Cotton growing landscapes in Australia have been dominated by dual-toxin transgenic Bt varieties since 2004. The cotton crop has thus effectively become a sink for the main target pest, Helicoverpa armigera. Theory predicts that there should be strong selection on female moths to avoid laying on such plants. We assessed oviposition, collected from two cotton-growing regions, by female moths when given a choice of tobacco, cotton and cabbage. Earlier work in the 1980s and 1990s on populations from the same geographic locations indicated these hosts were on average ranked as high, mid and low preference plants, respectively, and that host rankings had a heritable component. In the present study, we found no change in the relative ranking of hosts by females, with most eggs being laid on tobacco, then cotton and least on cabbage. As in earlier work, some females laid most eggs on cotton and aspects of oviposition behaviour had a heritable component. Certainly, cotton is not avoided as a host, and the implications of these finding for managing resistance to Bt cotton are discussed.

Evolved polygenic herbicide resistance in Lolium rigidum by low-dose herbicide selection within standing genetic variation

The interaction between environment and genetic traits under selection is the basis of evolution. In this study, we have investigated the genetic basis of herbicide resistance in a highly characterized initially herbicide-susceptible Lolium rigidum population recurrently selected with low (below recommended label) doses of the herbicide diclofop-methyl. We report the variability in herbicide resistance levels observed in F₁ families and the segregation of resistance observed in F₂ and back-cross (BC) families. The selected herbicide resistance phenotypic trait(s) appear to be under complex polygenic control. The estimation of the effective minimum number of genes (N_E), depending on the herbicide dose used, reveals at least three resistance genes had been enriched. A joint scaling test indicates that an additive-dominance model best explains gene interactions in parental, F₁, F₂ and BC families. The Mendelian study of six F₂ and two BC segregating families confirmed involvement of more than one resistance gene. Cross-pollinated L. rigidum under selection at low herbicide dose can rapidly evolve polygenic broad-spectrum herbicide resistance by quantitative accumulation of additive genes of small effect. This can be minimized by using herbicides at the recommended dose which causes high mortality acting outside the normal range of phenotypic variation for herbicide susceptibility.

Evolving while invading: rapid adaptive evolution in juvenile development time for a biological control organism colonizing a high-elevation environment

We report evidence of adaptive evolution in juvenile development time on a decadal timescale for the cinnabar moth Tyria jacobaeae (Lepidoptera: Arctiidae) colonizing new habitats and hosts from the Willamette Valley to the Coast Range and Cascades Mountains in Oregon. Four lines of evidence reveal shorter egg to pupa juvenile development times evolved in the mountains, where cooler temperatures shorten the growing season: (i) field observations showed that the mountain populations have shorter phenological development; (ii) a common garden experiment revealed genetic determination of phenotypic differences in juvenile development time between Willamette Valley and mountain populations correlated with the growing season; (iii) a laboratory experiment rearing offspring from parental crosses within and between Willamette Valley and Cascades populations demonstrated polygenic inheritance, high heritability, and genetic determination of phenotypic differences in development times; and (iv) statistical tests that exclude random processes (founder effect, genetic drift) in favor of natural selection as explanations for observed differences in phenology. These results support the hypothesis that rapid adaptation to the cooler mountain climate occurred in populations established from populations in the warmer valley climate. Our findings should motivate regulators to require evaluation of evolutionary potential of candidate biological control organisms prior to release.