Humans as the world's greatest evolutionary force

Crossroads of Antibiotic Resistance and Biosynthesis

The biosynthesis of antibiotics and self-protection mechanisms employed by antibiotic producers are an integral part of the growing antibiotic resistance threat. The origins of clinically relevant antibiotic resistance genes found in human pathogens have been traced to ancient microbial producers of antibiotics in natural environments. Widespread and frequent antibiotic use amplifies environmental pools of antibiotic resistance genes and increases the likelihood for the selection of a resistance event in human pathogens. This perspective will provide an overview of the origins of antibiotic resistance to highlight the crossroads of antibiotic biosynthesis and producer self-protection that result in clinically relevant resistance mechanisms. Some case studies of synergistic antibiotic combinations, adjuvants, and hybrid antibiotics will also be presented to show how native antibiotic producers manage the emergence of antibiotic resistance.

Targeting virulence factors as an antimicrobial approach: Pigment inhibitors

The fascinating and dangerous colored pathogens contain unique chemically pigmented molecules, which give varied and efficient assistance as virulence factors to the crucial reproduction and growth of microbes. Therefore, multiple novel strategies and inhibitors have been developed in recent years that target virulence factor pigments. However, despite the importance and significance of this topic, it has not yet been comprehensively reviewed. Moreover, research groups around the world have made successful progress against antibacterial infections by targeting pigment production, including our serial works on the discovery of CrtN inhibitors against staphyloxanthin production in Staphylococcus aureus. On the basis of the previous achievements and recent progress of our group in this field, this article will be the first comprehensive review of pigment inhibitors against colored pathogens, especially S. aureus infections, and this article includes design strategies, representative case studies, advantages, limitations, and perspectives to guide future research.

Evolutionary and ecological insights from herbicide-resistant weeds: what have we learned about plant adaptation, and what is left to uncover?

The evolution of herbicide resistance in crop weeds presents one of the greatest challenges to agriculture and the production of food. Herbicide resistance has been studied for more than 60 yr, in the large part by researchers seeking to design effective weed control programs. As an outcome of this work, various unique questions in plant adaptation have been addressed. Here, I collate recent research on the herbicide-resistant problem in light of key questions and themes in evolution and ecology. I highlight discoveries made on herbicide-resistant weeds in three broad areas - the genetic basis of adaptation, evolutionary constraints, experimental evolution - and similarly discuss questions left to be answered. I then develop how one would use herbicide-resistance evolution as a model for studying eco-evolutionary dynamics within a community context. My overall goals are to highlight important findings in the weed science literature that are relevant to themes in plant adaptation and to stimulate the use of herbicide-resistant plants as models for addressing key questions within ecology and evolution.

Spatiotemporal dynamics of fungicide resistance in the wheat pathogen Zymoseptoria tritici in France

BACKGROUND

Management of pesticide resistance is a major issue in modern agricultural systems, particularly in the context of the broader challenge of reducing pesticide use. However, such management must be adapted to resistance dynamics, which remains challenging to predict due to its dependence on many biological traits of pests, interactions with the environment and pesticide use. We retrospectively studied the evolution of reported resistances to four modes of action (benzimidazoles, quinone outside inhibitors, sterol demethylation inhibitors and succinate dehydrogenase inhibitors), in French populations of the wheat pathogen Zymoseptoria tritici.

RESULTS

We used statistical models to analyse the Performance trial network data set (2004-2017; ∼ 70 locations in France yearly). They highlighted contrasting behaviours between phenotypes, for example: (i) stable spatial distributions and colonization front structures over time, and (ii) different frequency growth rates at the national scale and between regions.

CONCLUSION

We provide a quantitative description of the spatiotemporal patterns of resistance evolution for fungicides with several modes of action. Moreover, we highlight some unexpected resistance dynamics in France, with major differences between the north and south. This complex pattern of resistance evolution in French populations is consistent with previous descriptions of dynamics at the European scale. These results should make it easier to anticipate evolution locally and to improve the management of resistance. © 2019 Society of Chemical Industry.

Do plants pay a fitness cost to be resistant to glyphosate?

We reviewed the literature to understand the effects of glyphosate resistance on plant fitness at the molecular, biochemical and physiological levels. A number of correlations between enzyme characteristics and glyphosate resistance imply the existence of a plant fitness cost associated with resistance-conferring mutations in the glyphosate target enzyme, 5-enolpyruvylshikimate-3-phosphate synthase (EPSPS). These biochemical changes result in a tradeoff between the glyphosate resistance of the EPSPS enzyme and its catalytic activity. Mutations that endow the highest resistance are more likely to decrease catalytic activity by reducing the affinity of EPSPS for its natural substrate, and/or slowing the velocity of the enzyme reaction, and are thus very likely to endow a substantial plant fitness cost. Prediction of fitness costs associated with EPSPS gene amplification and overexpression can be more problematic. The validity of cost prediction based on the theory of evolution of gene expression and resource allocation has been cast into doubt by contradictory experimental evidence. Further research providing insights into the role of the EPSPS cassette in weed adaptation, and estimations of the energy budget involved in EPSPS amplification and overexpression are required to understand and predict the biochemical and physiological bases of the fitness cost of glyphosate resistance.

Light pollution affects space use and interaction of two small mammal species irrespective of personality

Background

Artificial light at night (ALAN) is one form of human-induced rapid environmental changes (HIREC) and is strongly interfering with natural dark–light cycles. Some personality types within a species might be better suited to cope with environmental change and therefore might be selected upon under ongoing urbanization.

Results

We used LED street lamps in a large outdoor enclosure to experimentally investigate the effects of ALAN on activity patterns, movement and interaction of individuals of two species, the bank vole (Myodes glareolus) and the striped field mouse (Apodemus agrarius). We analyzed effects combined with individual boldness score. Both species reduced their activity budget during daylight hours. While under natural light conditions home ranges were larger during daylight than during nighttime, this difference vanished under ALAN. Conspecifics showed reduced home range overlap, proximity and activity synchrony when subjected to nighttime illumination. Changes in movement patterns in reaction to ALAN were not associated with differences in boldness score of individuals.

Conclusions

Our results suggest that light pollution can lead to changes in movement patterns and individual interactions in small mammals. This could lead to fitness consequences on the population level.

Electronic supplementary material

The online version of this article (10.1186/s12898-019-0241-0) contains supplementary material, which is available to authorized users.

The Case for Studying Non-Market Food Systems

Markets dominate the world’s food systems. Today’s food systems fail to realize the normative foundations of ecological economics: justice, sustainability, efficiency, and value pluralism. Drawing on empirical and theoretical literature from diverse intellectual traditions, I argue that markets, as an institution for governing food systems, hinder the realization of these objectives. Markets allocate food toward money, not hunger. They encourage shifting costs on others, including nonhuman nature. They rarely signal unsustainability, and in many ways cause it. They do not resemble the efficient markets of economic theory. They organize food systems according to exchange value at the expense of all other social, cultural, spiritual, moral, and environmental values. I argue that food systems can approach the objectives of ecological economics roughly to the degree that they subordinate market mechanisms to social institutions that embody those values. But such “embedding” processes, whether through creating state policy or alternative markets, face steep barriers and can only partially remedy food markets’ inherent shortcomings. Thus, ecological economists should also study, promote, and theorize non-market food systems.

A harvest of weeds yields insight into a case of contemporary evolution

When Charles Darwin was exploring the idea of evolution via natural selection, he looked to domesticated species, with the opening chapter of The Origin of Species titled 'Variation Under Domestication' (Darwin ). Domesticated species such as crops are a great example of artificial selection, which Darwin realized was analogous to natural selection. But growing among those carefully selected crop varieties are the unwelcome and unwanted plants we call weeds. Despite the importance of weeds and long-standing interest in their evolution (Baker ), we still know little about how agricultural weeds evolve, and we often fail to take evolution into account when attempting to manage them (Neve et al. ). Agricultural weeds are subjected to the unique conditions of farm fields, such as frequent soil disturbance and the addition of water and nutrients. They are also confronted with aggressive attempts at their removal via herbicides and mechanical means. As such, they are under intense demographic and selective pressure and can potentially rapidly evolve in response. In this issue of Molecular Ecology, Kuester and co-authors make a rare attempt to understand contemporary evolution in an agricultural weed (Kuester et al. ). They do so using the powerful resurrection approach of comparing ancestors and descendants under common conditions (Franks et al. ). They sampled multiple populations of the weedy plant Ipomoea purpurea at two points in time. A comparison of these greenhouse-grown ancestor and descendent populations showed that, over time, populations had lost significant levels of neutral genetic diversity, consistent with genetic bottlenecks. The authors also found a slight increase, on average, of resistance to the herbicide glyphosate, which is the active ingredient in Roundup(®) . This work is one of a growing number of studies demonstrating rapid evolution in natural populations (Thompson ) and also reveals evidence of both selection and drift in populations of an agricultural weed.

Hygiene Defense Behaviors Used by a Fungus-Growing Ant Depend on the Fungal Pathogen Stages

Parasites and their hosts use different strategies to overcome the defenses of the other, often resulting in an evolutionary arms race. Limited animal studies have explored the differential responses of hosts when challenged by differential parasite loads and different developmental stages of a parasite. The fungus-growing ant Trachymyrmex sp. 10 employs three different hygienic strategies to control fungal pathogens: Grooming the antibiotic-producing metapleural glands (MGs) and planting or weeding their mutualistic fungal crop. By inoculating Trachymyrmex colonies with different parasite concentrations (Metarhizium) or stages (germinated conidia or ungermianted conidia of Metarhizium and Escovopsis), we tested whether ants modulate and change hygienic strategies depending on the nature of the parasite challenge. There was no effect of the concentration of parasite on the frequencies of the defensive behaviors, indicating that the ants did not change defensive strategy according to the level of threat. However, when challenged with conidia of Escovopsis sp. and Metarhizium brunneum that were germinated or not-germinated, the ants adjusted their thygienic behavior to fungal planting and MG grooming behaviors using strategies depending on the conidia germination status. Our study suggests that fungus-growing ants can adjust the use of hygienic strategies based on the nature of the parasites.

Systems Biology of Cold Adaptation in the Polyextremophilic Red Alga Galdieria sulphuraria

Rapid fluctuation of environmental conditions can impose severe stress upon living organisms. Surviving such episodes of stress requires a rapid acclimation response, e.g., by transcriptional and post-transcriptional mechanisms. Persistent change of the environmental context, however, requires longer-term adaptation at the genetic level. Fast-growing unicellular aquatic eukaryotes enable analysis of adaptive responses at the genetic level in a laboratory setting. In this study, we applied continuous cold stress (28°C) to the thermoacidophile red alga G. sulphuraria, which is 14°C below its optimal growth temperature of 42°C. Cold stress was applied for more than 100 generations to identify components that are critical for conferring thermal adaptation. After cold exposure for more than 100 generations, the cold-adapted samples grew ∼30% faster than the starting population. Whole-genome sequencing revealed 757 variants located on 429 genes (6.1% of the transcriptome) encoding molecular functions involved in cell cycle regulation, gene regulation, signaling, morphogenesis, microtubule nucleation, and transmembrane transport. CpG islands located in the intergenic region accumulated a significant number of variants, which is likely a sign of epigenetic remodeling. We present 20 candidate genes and three putative cis-regulatory elements with various functions most affected by temperature. Our work shows that natural selection toward temperature tolerance is a complex systems biology problem that involves gradual reprogramming of an intricate gene network and deeply nested regulators.

Characterizing the cultural niches of North American birds

Efforts to mitigate the current biodiversity crisis require a better understanding of how and why humans value other species. We use Internet query data and citizen science data to characterize public interest in 621 bird species across the United States. We estimate the relative popularity of different birds by quantifying how frequently people use Google to search for species, relative to the rates at which they are encountered in the environment. In intraspecific analyses, we also quantify the degree to which Google searches are limited to, or extend beyond, the places in which people encounter each species. The resulting metrics of popularity and geographic specificity of interest allow us to define aspects of relationships between people and birds within a cultural niche space. We then estimate the influence of species traits and socially constructed labels on niche positions to assess the importance of observations and ideas in shaping public interest in birds. Our analyses show clear effects of migratory strategy, color, degree of association with bird feeders, and, especially, body size on niche position. They also indicate that cultural labels, including "endangered," "introduced," and, especially, "team mascot," are strongly associated with the magnitude and geographic specificity of public interest in birds. Our results provide a framework for exploring complex relationships between humans and other species and enable more informed decision-making across diverse bird conservation strategies and goals.

Considering weed management as a social dilemma bridges individual and collective interests

Weeds pose severe threats to agricultural and natural landscapes worldwide. One major reason for the failure to effectively manage weeds at landscape scales is that current Best Management Practice guidelines, and research on how to improve such guidelines, focus too narrowly on property-level management decisions. Insufficiently considered are the aggregate effects of individual actions to determine landscape-scale outcomes, or whether there are collective practices that would improve weed management outcomes. Here, we frame landscape-scale weed management as a social dilemma, where trade-offs occur between individual and collective interests. We apply a transdisciplinary system approach-integrating the perspectives of ecologists, evolutionary biologists and agronomists into a social science theory of social dilemmas-to four landscape-scale weed management challenges: (i) achieving plant biosecurity, (ii) preventing weed seed contamination, (iii) maintaining herbicide susceptibility and (iv) sustainably using biological control. We describe how these four challenges exhibit characteristics of 'public good problems', wherein effective weed management requires the active contributions of multiple actors, while benefits are not restricted to these contributors. Adequate solutions to address these public good challenges often involve a subset of the eight design principles developed by Elinor Ostrom for 'common pool social dilemmas', together with design principles that reflect the public good nature of the problems. This paper is a call to action for scholars and practitioners to broaden our conceptualization and approaches to weed management problems. Such progress begins by evaluating the public good characteristics of specific weed management challenges and applying context-specific design principles to realize successful and sustainable weed management.

The evolutionary origins of pesticide resistance

Durable crop protection is an essential component of current and future food security. However, the effectiveness of pesticides is threatened by the evolution of resistant pathogens, weeds and insect pests. Pesticides are mostly novel synthetic compounds, and yet target species are often able to evolve resistance soon after a new compound is introduced. Therefore, pesticide resistance provides an interesting case of rapid evolution under strong selective pressures, which can be used to address fundamental questions concerning the evolutionary origins of adaptations to novel conditions. We ask: (i) whether this adaptive potential originates mainly from de novo mutations or from standing variation; (ii) which pre-existing traits could form the basis of resistance adaptations; and (iii) whether recurrence of resistance mechanisms among species results from interbreeding and horizontal gene transfer or from independent parallel evolution. We compare and contrast the three major pesticide groups: insecticides, herbicides and fungicides. Whilst resistance to these three agrochemical classes is to some extent united by the common evolutionary forces at play, there are also important differences. Fungicide resistance appears to evolve, in most cases, by de novo point mutations in the target-site encoding genes; herbicide resistance often evolves through selection of polygenic metabolic resistance from standing variation; and insecticide resistance evolves through a combination of standing variation and de novo mutations in the target site or major metabolic resistance genes. This has practical implications for resistance risk assessment and management, and lessons learnt from pesticide resistance should be applied in the deployment of novel, non-chemical pest-control methods.

Predicting Antimicrobial Resistance and Associated Genomic Features from Whole-Genome Sequencing

Thanks to the genomics revolution, thousands of strain-specific whole-genome sequences are now accessible for a wide range of pathogenic bacteria. This availability enables big data informatics approaches to be used to study the spread and acquisition of antimicrobial resistance (AMR). In this issue of the Journal of Clinical Microbiology, Nguyen et al. (M. Nguyen, S. W. Long, P. F. McDermott, R. J. Olsen, R. Olson, R. L. Stevens, G. H. Tyson, S. Zhao, and J. J. Davis, J Clin Microbiol 57:e01260-18, 2019, https://doi.org/10.1128/JCM.01260-18) report the results obtained with their machine learning models based on whole-genome sequencing data to predict the MICs of antibiotics for 5,728 nontyphoidal Salmonella genomes collected over 15 years in the United States. Their major finding demonstrates that MICs can be predicted with an average accuracy of 95% within ±1 2-fold dilution step (confidence interval, 95% to 95%), an average very major error rate of 2.7%, and an average major error rate of 0.1%. Importantly, these models predict MICs with no a priori information about the underlying gene content or resistance phenotypes of the strains, enabling the possibility to identify AMR determinants and rapidly diagnose and prioritize antibiotic use directly from the organism sequence. Employing such tools to diagnose and limit the spread of resistance-conferring mechanisms could help ameliorate the looming antibiotic resistance crisis.

Evolutionary Rescue Through Partly Heritable Phenotypic Variability

Environmental variation is commonplace, but unpredictable. Populations that encounter a deleterious environment can sometimes avoid extinction by rapid evolutionary adaptation. Phenotypic variability, whereby a single genotype can express multiple different phenotypes, might play an important role in rescuing such populations from extinction. This type of evolutionary bet-hedging need not confer a direct benefit to a single individual, but it may increase the chance of long-term survival of a lineage. Here, we develop a population genetic model to explore how partly heritable phenotypic variability influences the probability of evolutionary rescue and the mean duration of population persistence in changing environments. We find that the probability of population persistence depends nonmonotonically on the degree of phenotypic heritability between generations: some heritability can help avert extinction, but too much heritability removes any benefit of phenotypic variability. Partly heritable phenotypic variation is particularly advantageous when it extends the persistence time of a declining population and thereby increases the chance of rescue via beneficial mutations at linked loci. We discuss the implications of these results in the context of therapies designed to eradicate populations of pathogens or aberrant cellular lineages.

Treatment of Infected Wounds in the Age of Antimicrobial Resistance: Contemporary Alternative Therapeutic Options

As antibiotic resistance increases and antimicrobial options diminish, there is a pressing need to identify and develop new and/or alternative (non-antimicrobial-based) wound therapies. The authors describe the implications of antibiotic resistance on their current wound treatment paradigms and review the most promising non-antibiotic-based antimicrobial agents currently in research and development, with a focus on preclinical and human studies of therapeutic bacteriophages, antimicrobial peptides, cold plasma treatment, photodynamic therapy, honey, silver, and bioelectric dressings.

The Quest for Novel Antimicrobial Compounds: Emerging Trends in Research, Development, and Technologies

Pathogenic antibiotic resistant bacteria pose one of the most important health challenges of the 21st century. The overuse and abuse of antibiotics coupled with the natural evolutionary processes of bacteria has led to this crisis. Only incremental advances in antibiotic development have occurred over the last 30 years. Novel classes of molecules, such as engineered antibodies, antibiotic enhancers, siderophore conjugates, engineered phages, photo-switchable antibiotics, and genome editing facilitated by the CRISPR/Cas system, are providing new avenues to facilitate the development of antimicrobial therapies. The informatics revolution is transforming research and development efforts to discover novel antibiotics. The explosion of nanotechnology and micro-engineering is driving the invention of antimicrobial materials, enabling the cultivation of "uncultivable" microbes and creating specific and rapid diagnostic technologies. Finally, a revival in the ecological aspects of microbial disease management, the growth of prebiotics, and integrated management based on the "One Health" model, provide additional avenues to manage this health crisis. These, and future scientific and technological developments, must be coupled and aligned with sound policy and public awareness to address the risks posed by rising antibiotic resistance.

Eco-evolutionary dynamics in a disturbed world: implications for the maintenance of ecological networks

Past management of exploited species and of conservation issues has often ignored the evolutionary dynamics of species. During the 70s and 80s, evolution was mostly considered a slow process that may be safely ignored for most management issues. However, in recent years, examples of fast evolution have accumulated, suggesting that time scales of evolutionary dynamics (variations in genotype frequencies) and of ecological dynamics (variations in species densities) are often largely comparable, so that complex feedbacks commonly exist between the ecological and the evolutionary context ("eco-evolutionary dynamics"). While a first approach is of course to consider the evolution of a given species, in ecological communities, species are interlinked by interaction networks. In the present article, I discuss how species (co)evolution in such a network context may alter our understanding and predictions for species coexistence, given the disturbed world we live in. I review some concepts and examples suggesting that evolution may enhance the robustness of ecological networks and then show that, in many situations, the reverse may also happen, as evolutionary dynamics can harm diversity maintenance in various ways. I particularly focus on how evolution modifies indirect effects in ecological networks, then move to coevolution and discuss how the outcome of coevolution for species coexistence depends on the type of interaction (mutualistic or antagonistic) that is considered. I also review examples of phenotypes that are known to be important for ecological networks and shown to vary rapidly given global changes. Given all these components, evolution produces indirect eco-evolutionary effects within networks that will ultimately influence the optimal management of the current biodiversity crisis.

Marine Metazoan Modern Mass Extinction: Improving Predictions by Integrating Fossil, Modern, and Physiological Data

Evolution, extinction, and dispersion are fundamental processes affecting marine biodiversity. Until recently, studies of extant marine systems focused mainly on evolution and dispersion, with extinction receiving less attention. Past extinction events have, however, helped shape the evolutionary history of marine ecosystems, with ecological and evolutionary legacies still evident in modern seas. Current anthropogenic global changes increase extinction risk and pose a significant threat to marine ecosystems, which are critical for human use and sustenance. The evaluation of these threats and the likely responses of marine ecosystems requires a better understanding of evolutionary processes that affect marine ecosystems under global change. Here, we discuss how knowledge of ( a) changes in biodiversity of ancient marine ecosystems to past extinctions events, ( b) the patterns of sensitivity and biodiversity loss in modern marine taxa, and ( c) the physiological mechanisms underpinning species' sensitivity to global change can be exploited and integrated to advance our critical thinking in this area.

Risk-Only Assessment of Genetically Engineered Crops Is Risky

The risks of not considering benefits in risk assessment are often overlooked. Risks are also often evaluated without consideration of the broader context. We discuss these two concepts in relation to genetically engineered (GE) crops. The health, environmental, and economic risks and benefits of GE crops are exemplified and presented in the context of modern agriculture. Misattribution of unique risks to GE crops are discussed. It is concluded that the scale of modern agriculture is its distinguishing characteristic and that the greater knowledge around GE crops allows for a more thorough characterization of risk. By considering the benefits and risks in the context of modern agriculture, society will be better served and benefits will be less likely to be forgone.

Antibacterial isoamphipathic oligomers highlight the importance of multimeric lipid aggregation for antibacterial potency

Cationic charge and hydrophobicity have long been understood to drive the potency and selectivity of antimicrobial peptides (AMPs). However, these properties alone struggle to guide broad success in vivo, where AMPs must differentiate bacterial and mammalian cells, while avoiding complex barriers. New parameters describing the biophysical processes of membrane disruption could provide new opportunities for antimicrobial optimization. In this work, we utilize oligothioetheramides (oligoTEAs) to explore the membrane-targeting mechanism of oligomers, which have the same cationic charge and hydrophobicity, yet show a unique ~ 10-fold difference in antibacterial potency. Solution-phase characterization reveals little difference in structure and dynamics. However, fluorescence microscopy of oligomer-treated Staphylococcus aureus mimetic membranes shows multimeric lipid aggregation that correlates with biological activity and helps establish a framework for the kinetic mechanism of action. Surface plasmon resonance supports the kinetic framework and supports lipid aggregation as a driver of antimicrobial function.

Joseph Brown et al. use oligothioetheramides (oligo TEAs) to show that multimeric lipid aggregation in Staphylococcus aureus mimetic membranes correlates with the biological activity of oligoTEAs. These results may explain why antimicrobial peptides with identical cationic charge and hydrophobicity show different biological activity.

Physical tidepool characteristics affect age- and size-class distributions and site fidelity in tidepool sculpin (Oligocottus maculosus)

Rapidly changing environments pose unique challenges to the resident organisms. Tidepools in coastal environments vary in biophysical characteristics spatially and temporally, and how they vary determines their short- and long-term suitability as habitats and therefore influence on the distributions of tidepool organisms. Biophysical effects on distribution could differ between age classes, depending on their intrinsic ontogenetic requirements and dominance relations. In this study, we investigate the influence of physical pool characteristics on the site fidelity and population distribution of tidepool sculpin (Oligocottus maculosus Girard, 1856). We assessed short-term recapture of marked individuals and size-class distribution among four pool sets. The proportion of adults varied between pools primarily in association with water temperature and pool volume. Smaller adult and larger juvenile fish occupied warmer, small-volume pools, whereas larger adults occupied larger, cooler pools. Between 24% and 56% of marked fish were recaptured, with a higher probability of recapture in pools with “smooth” basins than in those with more rugose basins. Few fish moved among study pools, but the proportion of adults declined with repeated sampling, suggesting greater pool fidelity of juveniles. These results illustrate that intrinsic habitat features influence age- and size-class distributions in a resident tidepool sculpin species, with corresponding consequences for site fidelity.

Managing the emergence of pathogen resistance via spatially targeted antimicrobial use

From agriculture to public health to civil engineering, managing antimicrobial resistance presents a considerable challenge. The dynamics underlying resistance evolution reflect inherently spatial processes. Resistant pathogen strains increase in frequency when a strain that emerges in one locale can spread and replace pathogen subpopulations formerly sensitive to the antimicrobial agent. Moreover, the strength of selection for antimicrobial resistance is in part governed by the extent of antimicrobial use. Thus, altering how antimicrobials are used across a landscape can potentially shift the spatial context governing the dynamics of antimicrobial resistance and provide a potent management tool. Here, we model how the efficacy of adjusting antimicrobial use over space to manage antimicrobial resistance is mediated by competition among pathogen strains and the topology of pathogen metapopulations. For several pathogen migration scenarios, we derive critical thresholds for the spatial extent of antimicrobial use below which resistance cannot emerge, and relate these thresholds to (a) the ability to eradicate antimicrobial-sensitive pathogens locally and (b) the strength of the trade-off between resistance ability and competitive performance where antimicrobial use is absent. We find that in metapopulations where patches differ in connectedness, constraining antimicrobial use across space to mitigate resistance evolution only works if the migration of the resistant pathogen is modest; yet, this situation is reversed if the resistant strain has a high colonization rate, with variably connected metapopulations exhibiting less sensitivity to reducing antimicrobial use across space. Furthermore, when pathogens are alternately exposed to sites with and without the antimicrobial, bottlenecking resistant strains through sites without an antimicrobial is only likely to be effective under a strong competition-resistance trade-off. We therefore identify life-history constraints that are likely to suggest which pathogens can most effectively be controlled by a spatially targeted antimicrobial regime. We discuss implications of our results for managing and thinking about antimicrobial resistance evolution in spatially heterogeneous contexts.

Antimicrobial and Antibiofilm Activity of Disubstituted Bis-benzimidazolium Salts

The increased prevalence of antibiotic-resistant bacteria is a critical issue for human health. Developing new antibiotic agents is vital for fighting persistent infections and lowering mortality rates. In this study, we designed lutidine-disubstituted bis-benzimidazolium salts (lutidine-bis-benzimidazolium core with octyl, adamantyl, and cholesteryl lipophilic side chains), and tested their antimicrobial activity, their capacity to inhibit planktonic bacterial and fungal growth, and their ability to inhibit the formation of or disrupt mature methicillin-resistant Staphylococcus aureus (MRSA) biofilms. The antibiofilm activity of these salts was analyzed in terms of their lipophilicity, capacity to induce transmembrane ion transport, perturbation of the cellular membrane, and mechanism of action in the phospholipid bilayer. The synthesized compounds were not active against MRSA biofilms, as the formation of transmembrane channels had no effect on the integrity of the extracellular polymeric substance matrix and only octyl and adamantyl derivatives possessed the capacity to inhibit biofilm formation. The synthesized derivatives could be used as lead candidates for the development of anti-MRSA agents.

The role of plant size in the selection of glyphosate resistance in Sorghum halepense

BACKGROUND

The effect of plant size (seedlings versus young plants versus adult plants) on the phenotypic level of glyphosate resistance and selection intensity (SI) in Sorghum halepense with and without a reduced glyphosate translocation resistance mechanism was evaluated.

RESULTS

Resistance parameters [the 50% lethal dose (LD50 ) and the dose required to cause a 50% reduction in plant growth (GR50 )] in adult plants were notably higher than in seedlings regardless of the resistance status. However, under similar plant size increases, populations comprised of glyphosate-resistant (R) individuals showed higher survival and growth when glyphosate treated compared with glyphosate-susceptible (S) plants. An increase in SI was always evident with increasing glyphosate doses. However, the rate of increase in SI was higher under glyphosate selection of young R and S plants, followed by seedlings and adult R and S plants. However, in conditions of R seedlings coexisting with adult S plants under glyphosate treatment (1000-4000 g ha-1 ), selection against glyphosate resistance was observed.

CONCLUSION

Any increase in size from the seedling stage of R plants translates into an amplification of resistance. Depending on the particular size combinations of spatially coexisting R and S plants, selection for glyphosate resistance may be faster, slower or even not evident. © 2018 Society of Chemical Industry.

Confronting herbicide resistance with cooperative management

BACKGROUND

Resistance of pathogens and pests to antibiotics and pesticides worldwide is rapidly reaching critical levels. The common-pool-resource nature of this problem (i.e. whereby the susceptibility to treatment of target organisms is a shared resource) has been largely overlooked. Using herbicide-resistant weeds as a model system, we developed a discrete-time landscape-scale simulation to investigate how aggregating herbicide management strategies at different spatial scales from individual farms to larger cooperative structures affects the evolution of glyphosate resistance in common waterhemp (Amaranthus tuberculatus).

RESULTS

Our findings indicate that high-efficacy herbicide management strategies practiced at the farm scale are insufficient to slow resistance evolution in A. tuberculatus. When best practices were aggregated at large spatial scales, resistance evolution was hindered; conversely, when poor management practices were aggregated, resistance was exacerbated. Tank mixture-based strategies were more effective than rotation-based strategies in most circumstances, while applying glyphosate alone resulted in the poorest outcomes.

CONCLUSIONS

Our findings highlight the importance of landscape-scale cooperative management for confronting common-pool-resource resistance problems in weeds and other analogous systems. © 2018 The Authors. Pest Management Science published by John Wiley & Sons Ltd on behalf of Society of Chemical Industry.

The opportunity for sexual selection and the evolution of non-responsiveness to pesticides, sterility inducers and contraceptives

We illustrate a method for delaying and possibly eliminating the evolution of non-responsiveness to the treatments now used to control pest populations. Using simulations and estimates of the variance in relative fitness, i.e., the opportunity for selection, in a rat-like mammal, we show that the selection responsible for the evolution of non-responsiveness to pesticides and sterility-inducers, is similar in its action to sexual selection, and for this reason can be orders of magnitude stronger than that which exists for untreated populations. In contrast, we show that when contraceptives are used to reduce the fertility of a pest species, with non-responders embedded within such populations, the opportunity for selection favoring non-responsiveness is reduced to that which is expected by chance alone. In pest species with separate sexes, we show that efforts to control pest populations or to mitigate selection favoring non-responsiveness, are likely to be ineffective when members of one sex are sterilized or killed. We also show that while mating preferences can impede the rate at which resistance evolves, they are more likely to accelerate this process, arguing against the use of sterile male approaches for controlling pests. Our results suggest that contraceptives are more effective at controlling pest populations and slowing the evolution of non-responsiveness than treatments that cause sterilization or death in target species. Furthermore, our results indicate that contraceptives that work differentially on each sex will be most effective in mitigating selection favoring non-responders. Our results have significant implications for the development and application of treatments to manage pests, now and into the future.

An ecological perspective on managing weeds during the great selection for herbicide resistance

More than 70 years after modern agriculture declared a 'war on weeds', they continue to thrive and suppress crop yields. Viewing weeds as an enemy that can be defeated if only a powerful enough technology can be deployed is a losing proposition. The latest evidence for the inadequacy of this approach, rampant evolution of multiple herbicide-resistant weed genotypes and dwindling options for chemical control in many production systems, should be seen as an urgent message to all those concerned with the science and practice of weed management: we need another way of thinking about the weed resistance issue. Fortunately, the theoretical and practical foundation of this alternative approach, ecological weed management, has been in development for decades. Here, we use Barry Commoner's laws of ecology as a conceptual frame for a review of some of the fundamental concepts of ecological weed management. © 2018 Society of Chemical Industry.

Effect of tetramethyl thiuram disulfide (thiram) in relation to tibial dyschondroplasia in chickens

Tetramethyl thiuram disulfide (thiram) is one of the important pesticides, which is extensively used in agriculture, but if it is combined with the cell membrane, then it causes membrane damage, bone morphogenic inactivation, and inhibited angiogenesis. Thiram has been considered a common cause of tibial dyschondrolplasia (TD) in various avian species, because it becomes the part of feed due to environmental contamination and its overuse in agriculture as pesticides or fungicide. However, there is no systematic study on the changes of the correlation indexes with toxic effect of the thiram in chickens. Therefore, we evaluated the toxic effects of thiram on growth performance of chickens, viscera organ index, pathological changes in tissue, and gene expression associated with osteoblast differentiation, vascularization, and tibial bone development. For this study, 1-day chickens (n = 300) were randomly distributed into two equal groups, control group (normal basal diet) and thiram group (adding thiram 40 mg/kg in basal diet). The result presented that thiram group chickens were looking unhealthy, lazy, and showing clinical symptoms like lameness. Thiram treatment significantly reduced the performance of chickens, liver index, and tibial length compared with control group. The toxic effect of thiram increased the visceral organ index (spleen and cardiac), tibia index, and TD severity considerably. It also increased serum Ca²⁺ and P³⁺ concentration and decreased tibial density compared to control chickens but the difference was not significant. Histopathology of tibia and liver showed that there were severe lesions due to toxic effect of thiram. Furthermore, HIF-1α and VEGF antibody localizations were increased and WNT4 localization was reduced significantly in immunohistochemical analysis. This systemic study of toxic effects of thiram in chicken concluded that thiram reduced the growth performance of chickens through decreasing liver index, whereas increasing kidney, cardiac, and spleen index, and induced TD by changing the expressions of VEGF, HIF-1α, and WNT4.

Weed evolution: Genetic differentiation among wild, weedy, and crop radish

Approximately 200 weed species are responsible for more than 90% of crop losses and these comprise less than one percent of all named plant species, suggesting that there are only a few evolutionary routes that lead to weediness. Agricultural weeds can evolve along three main paths: they can be escaped crops, wild species, or crop‐wild hybrids. We tested these three hypotheses in weedy radish, a weed of small grains and an emerging model for investigating the evolution of agricultural weeds, using 21 CAPS and SSR markers scored on 338 individuals from 34 populations representing all major species and sub‐species in the radish genus Raphanus. To test for adaptation of the weeds to the agricultural environment, we estimated genetic differentiation in flowering time in a series of common garden experiments with over 2,400 individuals from 43 populations (all but one of the genotyped populations plus 10 additional populations). Our findings suggest that the agricultural weed radish R. r. raphanistrum is most genetically similar to native populations of R. r. raphanistrum and is likely not a feral crop or crop hybrid. We also show that weedy radish flowers more rapidly than any other Raphanus population or cultivar, which is consistent with rapid adaptation to the frequent and severe disturbance that characterizes agricultural fields.

Human influences on the strength of phenotypic selection

Human activities are driving rapid phenotypic change in many species, with harvesting considered to be a particularly potent evolutionary force. We hypothesized that faster evolutionary change in human-disturbed populations could be caused by a strengthening of phenotypic selection, for example, if human disturbances trigger maladaptation and/or increase the opportunity for selection. We tested this hypothesis by synthesizing 1,366 phenotypic selection coefficients from 37 species exposed to various anthropogenic disturbances, including harvest. We used a paired design that only included studies measuring selection on the same traits in both human-disturbed and control (not obviously human-disturbed "natural") populations. Surprisingly, this meta-analysis did not reveal stronger selection in human-disturbed environments; in fact, we even found some evidence that human disturbances might slightly reduce selection strength. The only clear exceptions were two fisheries showing very strong harvest selection. On closer inspection, we discovered that many disturbances weakened selection by increasing absolute fitness and by decreasing the opportunity for selection-thus explaining what initially seemed a counterintuitive result. We discuss how human disturbances can sometimes weaken rather than strengthen selection, and why measuring the total effect of disturbances on selection is exceedingly difficult. Despite these challenges, documenting human influences on selection can reveal disturbances with particularly strong effects (e.g., fishing), and thus better inform the management of populations exposed to these disturbances.

The Extended Genotype: Microbially Mediated Olfactory Communication

Microbes are now known to influence inter- and intraspecific olfactory signaling systems. They do so by producing metabolites that function as odorants. A unique attribute of such odorants is that they arise as a product of microbial-host interactions. These interactions need not be mutualistic, and indeed can be antagonistic. We develop an integrated ecoevolutionary model to explore microbially mediated olfactory communication and a process model that illustrates the various ways that microbial products might contribute to odorants. This novel approach generates testable predictions, including that selection to incorporate microbial products should be a common feature of infochemicals that communicate identity but not those that communicate fitness or quality. Microbes extend an individual's genotype, but also enhance vulnerability to environmental change.

Antibiotic Resistance in Plant-Pathogenic Bacteria

Antibiotics have been used for the management of relatively few bacterial plant diseases and are largely restricted to high-value fruit crops because of the expense involved. Antibiotic resistance in plant-pathogenic bacteria has become a problem in pathosystems where these antibiotics have been used for many years. Where the genetic basis for resistance has been examined, antibiotic resistance in plant pathogens has most often evolved through the acquisition of a resistance determinant via horizontal gene transfer. For example, the strAB streptomycin-resistance genes occur in Erwinia amylovora, Pseudomonas syringae, and Xanthomonas campestris, and these genes have presumably been acquired from nonpathogenic epiphytic bacteria colocated on plant hosts under antibiotic selection. We currently lack knowledge of the effect of the microbiome of commensal organisms on the potential of plant pathogens to evolve antibiotic resistance. Such knowledge is critical to the development of robust resistance management strategies to ensure the safe and effective continued use of antibiotics in the management of critically important diseases.

Timing and frequency of sublethal exposure modifies the induction and retention of increased insecticide tolerance in wood frogs (Lithobates sylvaticus)

Although the paradigm for increased tolerance to pesticides has been by selection on constitutive (naïve) traits, recent research has shown it can also occur through phenotypic plasticity. However, the time period in which induction can occur, the duration of induced tolerance, and the influence of multiple induction events remain unknown. We hypothesized that the induction of increased pesticide tolerance is limited to early sensitive periods, the magnitude of induced tolerance depends on the number of exposures, and the retention of induced tolerance depends on the time elapsed after an exposure and the number of exposures. To test these hypotheses, we exposed wood frog tadpoles to either a no-carbaryl control (water) or 0.5 mg/L carbaryl at 4 time periods, and later tested their tolerance to carbaryl using time-to-death assays. We discovered that tadpoles induced increased tolerance early and midway but not late in our experiment and their constitutive tolerance increased with age. We found no difference in the magnitude of induced tolerance after a single or 2 exposures. Finally, induced pesticide tolerance was reversed within 6 d but was retained only when tadpoles experienced all 4 consecutive exposures. Phenotypic plasticity provides an immediate response for sensitive amphibian larvae to early pesticide exposures and reduces phenotypic mismatches in aquatic environments contaminated by agrochemicals. Environ Toxicol Chem 2018;37:2188-2197. © 2018 SETAC.

Wicked evolution: Can we address the sociobiological dilemma of pesticide resistance?

Resistance to insecticides and herbicides has cost billions of U.S. dollars in the agricultural sector and could result in millions of lives lost to insect-vectored diseases. We mostly continue to use pesticides as if resistance is a temporary issue that will be addressed by commercialization of new pesticides with novel modes of action. However, current evidence suggests that insect and weed evolution may outstrip our ability to replace outmoded chemicals and other control mechanisms. To avoid this outcome, we must address the mix of ecological, genetic, economic, and sociopolitical factors that prevent implementation of sustainable pest management practices. We offer an ambitious proposition.

Adaptive Networks for Restoration Ecology

The urgent need to restore biodiversity and ecosystem functioning challenges ecology as a predictive science. Restoration ecology would benefit from evolutionary principles embedded within a framework that combines adaptive network models and the phylogenetic structure of ecological interactions. Adaptive network models capture feedbacks between trait evolution, species abundances, and interactions to explain resilience and functional diversity within communities. Phylogenetically-structured network data, increasingly available via next-generation sequencing, inform constraints affecting interaction rewiring. Combined, these approaches can predict eco-evolutionary changes triggered by community manipulation practices, such as translocations and eradications of invasive species. We discuss theoretical and methodological opportunities to bridge network models and data from restoration projects and propose how this can be applied to the functional restoration of ecological interactions.

Toxicity of various road-deicing salts to Asian clams (Corbicula fluminea)

Humans are altering environments by destroying habitats, introducing species, and releasing pollution. One emergent pollutant is the salinization of freshwater habitats from road-deicing salts. Government agencies have set thresholds to protect freshwater ecosystems, yet these values are exceeded in many systems. The present study investigated the tolerance of Asian clams (Corbicula fluminea), a common invasive bivalve, to the common road salt (sodium chloride [NaCl]) and 2 alternatives (magnesium chloride [MgCl₂ ] and calcium chloride [CaCl₂ ]). Experiments conducted at 4 and 8 d revealed that Asian clams are very salt tolerant. The median lethal concentration after 4 d of exposure (LC50_4-d ) estimate was 2162 mg Cl^- /L for MgCl₂ , 3554 mg Cl^- /L for CaCl₂ , and more than 22 581 mg Cl^- /L for NaCl, which were all significantly different from each other (p ≤ 0.05). The LC50_8-d values were significantly different (p ≤ 0.05) from each other and from the LC50_4-d values, and were estimated to be 1769 mg Cl^- /L for MgCl₂ , 2235 Cl^- /L for CaCl₂ , and 10 069 mg Cl^- /L for NaCl. Mortality was determined using 2 methods: either no response after exposure or no response after being in freshwater following exposure. For the majority of the LC50s, these methods were not significantly different (p > 0.05). The high salt tolerance of Asian clams is a concern because of their transportation in ballast water between aquatic ecosystems. Furthermore, salt-tolerant organisms may outcompete sensitive organisms in salinized ecosystems, which may alter ecosystem services. Environ Toxicol Chem 2018;37:1839-1845. © 2018 SETAC.

Harvesting changes mating behaviour in European lobster

Removing individuals from a wild population can affect the availability of prospective mates and the outcome of competitive interactions, with subsequent effects on mating patterns and sexual selection. Consequently, the rate of harvest-induced evolution is predicted to be strongly dependent on the strength and dynamics of sexual selection, yet there is limited empirical knowledge on the interplay between selective harvesting and the mating systems of exploited species. In this study, we used genetic parentage assignment to compare mating patterns of the highly valued and overexploited European lobster (Homarus gammarus) in a designated lobster reserve and nearby fished area in southern Norway. In the area open to fishing, the fishery is regulated by a closed season, a minimum legal size and a ban on the harvest of egg-bearing females. Due to the differences in size and sex-specific fishing mortality between the two areas, males and females are of approximately equal average size in the fished area, whereas males tend to be larger in the reserve. Our results show that females would mate with males larger than their own body size, but the relative size difference was significantly larger in the reserve. Sexual selection acted positively on both body size and claw size in males in the reserve, while it was nonsignificant in fished areas. This strongly suggests that size truncation of males by fishing reduces the variability of traits that sexual selection acts upon. If fisheries continue to target large individuals (particularly males) with higher relative reproductive success, the weakening of sexual selection will likely accelerate fisheries-induced evolution towards smaller body size.

Genetic adaptation as a biological buffer against climate change: Potential and limitations

Climate change profoundly impacts ecosystems and their biota, resulting in range shifts, novel interactions, food web alterations, changed intensities of host-parasite interactions, and extinctions. An increasing number of studies have documented evolutionary changes in traits such as phenology and thermal tolerance. In this opinion paper, we argue that, while evolutionary responses have the potential to provide a buffer against extinctions or range shifts, a number of constraints and complexities blur this simple prediction. First, there are limits to evolutionary potential both in terms of genetic variation and demographic effects, and these limits differ strongly among taxa and populations. Second, there can be costs associated with genetic adaptation, such as a reduced evolutionary potential towards other (human-induced) environmental stressors or direct fitness costs due to tradeoffs. Third, the differential capacity of taxa to genetically respond to climate change results in novel interactions because different organism groups respond to a different degree with local compared to regional (dispersal and range shift) responses. These complexities result in additional changes in the selection pressures on populations. We conclude that evolution can provide an initial buffer against climate change for some taxa and populations but does not guarantee their survival. It does not necessarily result in reduced extinction risks across the range of taxa in a region or continent. Yet, considering evolution is crucial, as it is likely to strongly change how biota will respond to climate change and will impact which taxa will be the winners or losers at the local, metacommunity and regional scales.

Transcriptome response of the foundation plant Spartina alterniflora to the Deepwater Horizon oil spill

Despite the severe impacts of the Deepwater Horizon oil spill, the foundation plant species Spartina alterniflora proved resilient to heavy oiling, providing an opportunity to identify mechanisms of response to the anthropogenic stress of crude oil exposure. We assessed plants from oil-affected and unaffected populations using a custom DNA microarray to identify genomewide transcription patterns and gene expression networks that respond to crude oil exposure. In addition, we used T-DNA insertion lines of the model grass Brachypodium distachyon to assess the contribution of four novel candidate genes to crude oil response. Responses in S. alterniflora to hydrocarbon exposure across the transcriptome as well as xenobiotic specific response pathways had little overlap with those previously identified in the model plant Arabidopsis thaliana. Among T-DNA insertion lines of B. distachyon, we found additional support for two candidate genes, one (ATTPS21) involved in volatile production, and the other (SUVH5) involved in epigenetic regulation of gene expression, that may be important in the response to crude oil. The architecture of crude oil response in S. alterniflora is unique from that of the model species A. thaliana, suggesting that xenobiotic response may be highly variable across plant species. In addition, further investigations of regulatory networks may benefit from more information about epigenetic response pathways.

Orangutans venture out of the rainforest and into the Anthropocene

Conservation benefits from understanding how adaptability and threat interact to determine a taxon's vulnerability. Recognizing how interactions with humans have shaped taxa such as the critically endangered orangutan (Pongo spp.) offers insights into this relationship. Orangutans are viewed as icons of wild nature, and most efforts to prevent their extinction have focused on protecting minimally disturbed habitat, with limited success. We synthesize fossil, archeological, genetic, and behavioral evidence to demonstrate that at least 70,000 years of human influence have shaped orangutan distribution, abundance, and ecology and will likely continue to do so in the future. Our findings indicate that orangutans are vulnerable to hunting but appear flexible in response to some other human activities. This highlights the need for a multifaceted, landscape-level approach to orangutan conservation that leverages sound policy and cooperation among government, private sector, and community stakeholders to prevent hunting, mitigate human-orangutan conflict, and preserve and reconnect remaining natural forests. Broad cooperation can be encouraged through incentives and strategies that focus on the common interests and concerns of different stakeholders. Orangutans provide an illustrative example of how acknowledging the long and pervasive influence of humans can improve strategies to preserve biodiversity in the Anthropocene.