Humans as the world's greatest evolutionary force

Genomic analysis of an emerging multiresistant Staphylococcus aureus strain rapidly spreading in cystic fibrosis patients revealed the presence of an antibiotic inducible bacteriophage

Background

Staphylococcus aureus is a major human pathogen responsible for a variety of nosocomial and community-acquired infections. Recent reports show that the prevalence of Methicillin-Resistant S. aureus (MRSA) infections in cystic fibrosis (CF) patients is increasing. In 2006 in Marseille, France, we have detected an atypical MRSA strain with a specific antibiotic susceptibility profile and a unique growth phenotype. Because of the clinical importance of the spread of such strain among CF patients we decided to sequence the genome of one representative isolate (strain CF-Marseille) to compare this to the published genome sequences. We also conducted a retrospective epidemiological analysis on all S. aureus isolated from 2002 to 2007 in CF patients from our institution.

Results

CF-Marseille is multidrug resistant, has a hetero-Glycopeptide-Intermediate resistance S. aureus phenotype, grows on Cepacia agar with intense orange pigmentation and has a thickened cell wall. Phylogenetic analyses using Complete Genome Hybridization and Multi Locus VNTR Assay showed that CF-Marseille was closely related to strain Mu50, representing vancomycin-resistant S. aureus. Analysis of CF-Marseille shows a similar core genome to that of previously sequenced MRSA strains but with a different genomic organization due to the presence of specific mobile genetic elements i.e. a new SCCmec type IV mosaic cassette that has integrated the pUB110 plasmid, and a new phage closely related to phiETA3. Moreover this phage could be seen by electron microscopy when mobilized with several antibiotics commonly used in CF patients including, tobramycin, ciprofloxacin, cotrimoxazole, or imipenem. Phylogenetic analysis of phenotypically similar h-GISA in our study also suggests that CF patients are colonized by polyclonal populations of MRSA that represents an incredible reservoir for lateral gene transfer.

Conclusion

In conclusion, we demonstrated the emergence and spreading of a new isolate of MRSA in CF patients in Marseille, France, that has probably been selected in the airways by antibiotic pressure. Antibiotic-mediated phage induction may result in high-frequency transfer and the unintended consequence of promoting the spread of virulence and/or antibiotic resistance determinants. The emergence of well-adapted MRSA is worrying in such population chronically colonized and receiving many antibiotics and represents a model for emergence of uncontrollable super bugs in a specific niche.

Reviewers

This article was reviewed by Eric Bapteste, Pierre Pontarotti, and Igor Zhulin. For the full reviews, please go to the Reviewers' comments section.

Human predators outpace other agents of trait change in the wild

The observable traits of wild populations are continually shaped and reshaped by the environment and numerous agents of natural selection, including predators. In stark contrast with most predators, humans now typically exploit high proportions of prey populations and target large, reproductive-aged adults. Consequently, organisms subject to consistent and strong 'harvest selection' by fishers, hunters, and plant harvesters may be expected to show particularly rapid and dramatic changes in phenotype. However, a comparison of the rate at which phenotypic changes in exploited taxa occurs relative to other systems has never been undertaken. Here, we show that average phenotypic changes in 40 human-harvested systems are much more rapid than changes reported in studies examining not only natural (n = 20 systems) but also other human-driven (n = 25 systems) perturbations in the wild, outpacing them by >300% and 50%, respectively. Accordingly, harvested organisms show some of the most abrupt trait changes ever observed in wild populations, providing a new appreciation for how fast phenotypes are capable of changing. These changes, which include average declines of almost 20% in size-related traits and shifts in life history traits of nearly 25%, are most rapid in commercially exploited systems and, thus, have profound conservation and economic implications. Specifically, the widespread potential for transitively rapid and large effects on size- or life history-mediated ecological dynamics might imperil populations, industries, and ecosystems.

Environmental change and the option value of genetic diversity

Rapid anthropogenic environmental change is altering selection pressures on natural plant populations. However, it is difficult to predict easily the novel selection pressures to which populations will be exposed. There is heavy reliance on plant genetic diversity for future crop security in agriculture and industry, but the implications of genetic diversity for natural populations receives less attention. Here, we examine the links between the genetic diversity of natural populations and aspects of plant performance and fitness. We argue that accumulating evidence demonstrates the future benefit or 'option value' of genetic diversity within natural populations when subject to anthropogenic environmental changes. Consequently, the loss of that diversity will hinder their ability to adapt to changing environments and is, therefore, of serious concern.

Fishery-induced selection on an Alpine whitefish: quantifying genetic and environmental effects on individual growth rate

Size-selective fishing, environmental changes and reproductive strategies are expected to affect life-history traits such as the individual growth rate. The relative contribution of these factors is not clear, particularly whether size-selective fishing can have a substantial impact on the genetics and hence on the evolution of individual growth rates in wild populations. We analysed a 25-year monitoring survey of an isolated population of the Alpine whitefish Coregonus palaea. We determined the selection differentials on growth rate, the actual change of growth rate over time and indicators of reproductive strategies that may potentially change over time. The selection differential can be reliably estimated in our study population because almost all the fish are harvested within their first years of life, i.e. few fish escape fishing mortality. We found a marked decline in average adult growth rate over the 25 years and a significant selection differential for adult growth, but no evidence for any linear change in reproductive strategies over time. Assuming that the heritability of growth in this whitefish corresponds to what was found in other salmonids, about a third of the observed decline in growth rate would be linked to fishery-induced evolution. Size-selective fishing seems to affect substantially the genetics of individual growth in our study population.

Susceptibility to neonicotinoids and risk of resistance development in the brown planthopper, Nilaparvata lugens (Stål) (Homoptera: Delphacidae)

BACKGROUND

In recent years, outbreaks of the brown planthopper, Nilaparvata lugens (Stål), have occurred more frequently in China. The objective of this study was to determine the susceptibility of N. lugens to neonicotinoids and other insecticides in major rice production areas in China.

RESULTS

Results indicated that substantial variations in the susceptibility to different insecticides existed in N. lugens. Field populations had developed variable resistance levels to neonicotinoids, with a high resistance level to imidacloprid (RR: 135.3-301.3-fold), a medium resistance level to imidaclothiz (RR: 35-41.2-fold), a low resistance level to thiamethoxam (up to 9.9-fold) and no resistance to dinotefuran, nitenpyram and thiacloprid (RR < 3-fold). Further examinations indicated that a field population had developed medium resistance level to fipronil (up to 10.5-fold), and some field populations had evolved a low resistance level to buprofezin. In addition, N. lugens had been able to develop 1424-fold resistance to imidacloprid in the laboratory after the insect was selected with imidacloprid for 26 generations.

CONCLUSION

Long-term use of imidacloprid in a wide range of rice-growing areas might be associated with high levels of resistance in N. lugens. Therefore, insecticide resistance management strategies must be developed to prevent further increase in resistance.

Speciation and the evolution of gamete recognition genes: pattern and process

Proteins on gamete surfaces are major determinants of fertilization success, particularly in free-spawning animals. Molecular analyses of these simple genetic systems show rapid evolution, positive selection, accelerated coalescence and, sometimes, extensive polymorphism. Careful analysis of the behavior of sperm produced by males with different gamete alleles shows that these alleles can deliver significant functional differences. Three forms of allele-specific fertilization advantage have been shown: assortative mating based on gamete type, rare allele advantage and heterozygote superiority. Models suggest that sperm and egg proteins may be coevolutionary partners that can alternate between directional selection for high fertilization ability and cyclic adaptation of eggs and sperm driven by sexual conflict. These processes act within allopatric populations and may accelerate their divergence if gamete adaptations in separate demes reduce cross-fertilization. Reproductive character displacement by reinforcement may play a diversifying role when previously allopatric populations rejoin. In circumstance that might prove to be common, divergence in sympatry can be driven by sexual conflict or by association of mating types with ecological differences. The ecology of fertilization, especially the degree of sperm competition and egg death via polyspermy, are important determinants of the strength and direction of selection on gametes. Free-spawning animals allow careful analysis of gamete recognition -from the behavior of adults and interactions of gametes, to molecular patterns of allele divergence. Future research efforts on the evolutionary consequences of fertilization ecology, and the interaction between extensive variation in egg surface proteins and sperm fertilization ability, are particularly needed.

A reservoir of drug-resistant pathogenic bacteria in asymptomatic hosts

The population genetics of pathogenic bacteria has been intensively studied in order to understand the spread of disease and the evolution of virulence and drug resistance. However, much less attention has been paid to bacterial carriage populations, which inhabit hosts without producing disease. Since new virulent strains that cause disease can be recruited from the carriage population of bacteria, our understanding of infectious disease is seriously incomplete without knowledge on the population structure of pathogenic bacteria living in an asymptomatic host. We report the first extensive survey of the abundance and diversity of a human pathogen in asymptomatic animal hosts. We have found that asymptomatic swine from livestock productions frequently carry populations of Salmonella enterica with a broad range of drug-resistant strains and genetic diversity greatly exceeding that previously described. This study shows how agricultural practice and human intervention may lead and influence the evolution of a hidden reservoir of pathogens, with important implications for human health.

Sea lice escape predation on their host

Parasites seldom have predators but often fall victim to those of their hosts. How parasites respond to host predation can have important consequences for both hosts and parasites, though empirical investigations are rare. The exposure of wild juvenile salmon to sea lice (Lepeophtheirus salmonis) from salmon farms allowed us to study a novel ecological interaction: the response of sea lice to predation on their juvenile pink and chum salmon hosts by two salmonid predators-coho smolts and cut-throat trout. In approximately 70% of trials in which a predator consumed a parasitized prey, lice escaped predation by swimming or moving directly onto the predator. This trophic transmission is strongly male biased, probably because behaviour and morphology constrain female movement and transmission. These findings highlight the potential for sea lice to be transmitted up marine food webs in areas of intensive salmon aquaculture, with implications for louse population dynamics and predatory salmonid health.

The effects of the genetic background on herbicide resistance fitness cost and its associated dominance in Arabidopsis thaliana

The advantage of the resistance conferred by a mutation can sometimes be offset by a high fitness-cost penalty. This balance will affect possible fate of the resistance allele. Few studies have explored the impact of the genetic background on the expression of the resistance fitness cost and none has attempted to measure the variation in fitness-cost dominance. However, both the fitness penalty and its dominance may modify evolutionary trajectory and outcome. Here the impact of Arabidopsis thaliana intraspecific genetic diversity on fitness cost and its associated dominance was investigated by analysing 12 quantitative traits in crosses between a mutant conferring resistance to the herbicide 2,4-D and nine different natural genetic backgrounds. Fitness cost values were found to be more affected by intraspecific genetic diversity than fitness cost dominance, even though this effect depends on the quantitative trait measured. This observation has implications for the choice of the best strategy for preventing herbicide resistance development. In addition, our results pinpoint a potential compensatory improvement of the resistance fitness cost and its associated dominance by the genetic diversity locally present within a species.

Targeting QseC signaling and virulence for antibiotic development

Many bacterial pathogens rely on a conserved membrane histidine sensor kinase, QseC, to respond to host adrenergic signaling molecules and bacterial signals in order to promote the expression of virulence factors. Using a high-throughput screen, we identified a small molecule, LED209, that inhibits the binding of signals to QseC, preventing its autophosphorylation and consequently inhibiting QseC-mediated activation of virulence gene expression. LED209 is not toxic and does not inhibit pathogen growth; however, this compound markedly inhibits the virulence of several pathogens in vitro and in vivo in animals. Inhibition of signaling offers a strategy for the development of broad-spectrum antimicrobial drugs.

The rate of environmental change drives adaptation to an antibiotic sink

Recent accelerated trends of human-induced global changes are providing many examples of adaptation to novel environments. Although the rate of environmental change can vary dramatically, its effect on evolving populations is unknown. A crucial feature explaining the adaptation to harsh environments is the supply of beneficial mutations via immigration from a 'source' population. In this study, we tested the effect of immigration on adaptation to increasing concentrations of antibiotics. Using experimental population of Pseudomonas aeruginosa, a pathogenic bacterium, we show that higher immigration rates and a slow increase in antibiotic concentration result in a more rapid evolution of resistance; however, a high immigration rate combined with rapid increases in concentration resulted in higher maximal levels of resistance. These findings, which support recent theoretical work, have important implications for the control of antibiotic resistance because they show that rapid rates of change can produce variants with the ability to resist future treatments.

Diversification of rice yellow mottle virus and related viruses spans the history of agriculture from the neolithic to the present

The mechanisms of evolution of plant viruses are being unraveled, yet the timescale of their evolution remains an enigma. To address this critical issue, the divergence time of plant viruses at the intra- and inter-specific levels was assessed. The time of the most recent common ancestor (TMRCA) of Rice yellow mottle virus (RYMV; genus Sobemovirus) was calculated by a Bayesian coalescent analysis of the coat protein sequences of 253 isolates collected between 1966 and 2006 from all over Africa. It is inferred that RYMV diversified approximately 200 years ago in Africa, i.e., centuries after rice was domesticated or introduced, and decades before epidemics were reported. The divergence time of sobemoviruses and viruses of related genera was subsequently assessed using the age of RYMV under a relaxed molecular clock for calibration. The divergence time between sobemoviruses and related viruses was estimated to be approximately 9,000 years, that between sobemoviruses and poleroviruses approximately 5,000 years, and that among sobemoviruses approximately 3,000 years. The TMRCA of closely related pairs of sobemoviruses, poleroviruses, and luteoviruses was approximately 500 years, which is a measure of the time associated with plant virus speciation. It is concluded that the diversification of RYMV and related viruses has spanned the history of agriculture, from the Neolithic age to the present.

Glyphosate-resistant weeds of South American cropping systems: an overview

Herbicide resistance is an evolutionary event resulting from intense herbicide selection over genetically diverse weed populations. In South America, orchard, cereal and legume cropping systems show a strong dependence on glyphosate to control weeds. The goal of this report is to review the current knowledge on cases of evolved glyphosate-resistant weeds in South American agriculture. The first reports of glyphosate resistance include populations of highly diverse taxa (Lolium multiflorum Lam., Conyza bonariensis L., C. canadensis L.). In all instances, resistance evolution followed intense glyphosate use in fruit fields of Chile and Brazil. In fruit orchards from Colombia, Parthenium hysterophorus L. has shown the ability to withstand high glyphosate rates. The recent appearance of glyphosate-resistant Sorghum halepense L. and Euphorbia heterophylla L. in glyphosate-resistant soybean fields of Argentina and Brazil, respectively, is of major concern. The evolution of glyphosate resistance has clearly taken place in those agroecosystems where glyphosate exerts a strong and continuous selection pressure on weeds. The massive adoption of no-till practices together with the utilization of glyphosate-resistant soybean crops are factors encouraging increase in glyphosate use. This phenomenon has been more evident in Argentina and Brazil. The exclusive reliance on glyphosate as the main tool for weed management results in agroecosystems biologically more prone to glyphosate resistance evolution.

The evolution of fungal drug resistance: modulating the trajectory from genotype to phenotype

The emergence of drug resistance in pathogenic microorganisms provides an excellent example of microbial evolution that has had profound consequences for human health. The widespread use of antimicrobial agents in medicine and agriculture exerts strong selection for the evolution of drug resistance. Selection acts on the phenotypic consequences of resistance mutations, which are influenced by the genetic variation in particular genomes. Recent studies have revealed a mechanism by which the molecular chaperone heat shock protein 90 (Hsp90) can alter the relationship between genotype and phenotype in an environmentally contingent manner, thereby 'sculpting' the course of evolution. Harnessing Hsp90 holds great promise for treating life-threatening infectious diseases.

Antibiotic-resistant soil bacteria in transgenic plant fields

Understanding the prevalence and polymorphism of antibiotic resistance genes in soil bacteria and their potential to be transferred horizontally is required to evaluate the likelihood and ecological (and possibly clinical) consequences of the transfer of these genes from transgenic plants to soil bacteria. In this study, we combined culture-dependent and -independent approaches to study the prevalence and diversity of bla genes in soil bacteria and the potential impact that a 10-successive-year culture of the transgenic Bt176 corn, which has a blaTEM marker gene, could have had on the soil bacterial community. The bla gene encoding resistance to ampicillin belongs to the beta-lactam antibiotic family, which is widely used in medicine but is readily compromised by bacterial antibiotic resistance. Our results indicate that soil bacteria are naturally resistant to a broad spectrum of beta-lactam antibiotics, including the third cephalosporin generation, which has a slightly stronger discriminating effect on soil isolates than other cephalosporins. These high resistance levels for a wide range of antibiotics are partly due to the polymorphism of bla genes, which occur frequently among soil bacteria. The blaTEM116 gene of the transgenic corn Bt176 investigated here is among those frequently found, thus reducing any risk of introducing a new bacterial resistance trait from the transgenic material. In addition, no significant differences were observed in bacterial antibiotic-resistance levels between transgenic and nontransgenic corn fields, although the bacterial populations were different.

The epidemic of antibiotic-resistant infections: a call to action for the medical community from the Infectious Diseases Society of America

The ongoing explosion of antibiotic-resistant infections continues to plague global and US health care. Meanwhile, an equally alarming decline has occurred in the research and development of new antibiotics to deal with the threat. In response to this microbial "perfect storm," in 2001, the federal Interagency Task Force on Antimicrobial Resistance released the "Action Plan to Combat Antimicrobial Resistance; Part 1: Domestic" to strengthen the response in the United States. The Infectious Diseases Society of America (IDSA) followed in 2004 with its own report, "Bad Bugs, No Drugs: As Antibiotic Discovery Stagnates, A Public Health Crisis Brews," which proposed incentives to reinvigorate pharmaceutical investment in antibiotic research and development. The IDSA's subsequent lobbying efforts led to the introduction of promising legislation in the 109 th US Congress (January 2005-December 2006). Unfortunately, the legislation was not enacted. During the 110 th Congress, the IDSA has continued to work with congressional leaders on promising legislation to address antibiotic-resistant infection. Nevertheless, despite intensive public relations and lobbying efforts, it remains unclear whether sufficiently robust legislation will be enacted. In the meantime, microbes continue to become more resistant, the antibiotic pipeline continues to diminish, and the majority of the public remains unaware of this critical situation. The result of insufficient federal funding; insufficient surveillance, prevention, and control; insufficient research and development activities; misguided regulation of antibiotics in agriculture and, in particular, for food animals; and insufficient overall coordination of US (and international) efforts could mean a literal return to the preantibiotic era for many types of infections. If we are to address the antimicrobial resistance crisis, a concerted, grassroots effort led by the medical community will be required.

Adaptation to the cost of resistance in a haploid clonally reproducing organism: the role of mutation, migration and selection

A model of compensatory evolution with respect to fungicide resistance in a haploid clonally reproducing fungus is developed in which compensatory mutations mitigate fitness costs associated with resistance. The role of mutation, migration and selection in invasion of rare genotypes when the environment changes from unsprayed to sprayed and from sprayed to unsprayed is analysed in detail. In some circumstances (ignoring back mutations) stable internal steady-state values for multiple genotypes can be obtained. In these cases a threshold value (f*) for the fraction of the population exposed to the fungicide can be derived for the transition between different steady-state conditions. Conditions are derived for invasion-when-rare of resistant genotypes at boundary equilibria established sometime after the onset of spraying and conversely of sensitive genotypes sometime after the cessation of spraying are derived. In these cases conditions are presented for (a) the invasion of a resistant genotype with a compensatory mutation (resistant-compensated) into a sensitive-uncompensated population that has re-equilibrated following the onset of spraying and (b) the invasion of a susceptible-uncompensated genotype into a resistant-compensated population that has re-equilibrated following the cessation of spraying, provided certain conditions are met. A resistant-compensated genotype may be fixed (or at near-fixation) in the population following a period of spraying, provided the mean intrinsic growth rate of the resistant-compensated genotype in a sprayed environment (over exposed and non-exposed parts of the population) is greater than that of the susceptible-uncompensated genotype. The fraction of the population exposed (the efficiency of spraying) is critical in this respect. However, it is possible for a sensitive-uncompensated genotype to invade provided there is no fitness gain associated with the resistant-compensated genotype, introduction by migration occurs following equilibration of the population to the new environment, and competitive effects are re-imposed when spraying ceases. We further derive a threshold level for the resident resistant-compensated population to reduce to following the cessation of spraying, such that the introduced susceptible-uncompensated genotype will invade. These results will be of use in determining the long-term persistence of resistance in a pathogen population once a fungicide is no longer effective and removed from use.

Parallel evolution of multidrug-resistance in Salmonella enterica isolated from swine

The increase in frequency of Salmonella enterica resistant to antibiotics in food-producing animals is of great concern to public health. Determining the rate at which different resistance phenotypes are generated and maintained in the environment is thus of great importance. The distribution and evolution of antibiotic resistance and multidrug-resistance in 362 Salmonella stains as part of a cross-sectional study of the Canadian swine industry were investigated. The susceptibility of all isolates to 12 antimicrobial agents was tested and the statistical and phylogenetic distribution of resistance among strains characterized via multilocus sequence typing was studied to test the origin of multidrug-resistance in Salmonella. More than 25% of all isolates were multidrug-resistant, with predominance in serotype Typhimurium, a serotype of vital importance to public health. The strong associations between resistance phenotypes, which differ among serotypes and which is supported by the significant genetic distance between serotypes, was indicative of the independent acquisition of multidrug-resistance in at least two different serotypes, i.e. Typhimurium and Derby. The independent origin of multidrug-resistance in Salmonella indicates that strong selective pressures are present in the environment of the bacteria and that statistical and phylogenetic studies of antibiotic resistance are an essential part in the understanding and the control of the epidemic.

The biology and future prospects of antivirulence therapies

The emergence and increasing prevalence of bacterial strains that are resistant to available antibiotics demand the discovery of new therapeutic approaches. Targeting bacterial virulence is an alternative approach to antimicrobial therapy that offers promising opportunities to inhibit pathogenesis and its consequences without placing immediate life-or-death pressure on the target bacterium. Certain virulence factors have been shown to be potential targets for drug design and therapeutic intervention, whereas new insights are crucial for exploiting others. Targeting virulence represents a new paradigm to empower the clinician to prevent and treat infectious diseases.

Influenza: Biology, Infection, and Control

The growth of the human population has profoundly affected the global ecosystem, influencing the animal population balance, the availability of fresh water, arable land, biotic production, and atmospheric gases. The human ecological impact has significantly accelerated the evolutionary change of numerous organisms. For example, the production of human medicine and food has resulted in the rapid evolution of drug-resistant pathogenic organisms as well as plants and insects resistant to pesticides (Palumbi, 2001). Recently, the nutritional support of the human population has relied on the vast monoculture of domestic mammals and birds, which has facilitated the emergence of pathogenic enzootic organisms that infect both animals and humans. This chapter will focus on the global threat to human health represented by the highly contagious enzootic virus influenza. It will also discuss current efforts and future improvements to protect humans from global influenza epidemics and pandemics.

Evolution of pathogens in a man-made world

Human activities have resulted in substantial, large-scale environmental modifications, especially in the past century. Ecologists and evolutionary biologists are increasingly coming to realize that parasites and pathogens, like free-living organisms, evolve as the consequence of these anthropogenic changes. Although this area now commands the attention of a variety of researchers, a broad predictive framework is lacking, mainly because the links between human activities, the environment and parasite evolution are complex. From empirical and theoretical examples chosen in the literature, we give an overview of the ways in which humans can directly or indirectly influence the evolution of different traits in parasites (e.g. specificity, virulence, polymorphism). We discuss the role of direct and indirect factors as diverse as habitat fragmentation, pollution, biodiversity loss, climate change, introduction of species, use of vaccines and antibiotics, ageing of the population, etc. We also present challenging questions for further research. Understanding the links between anthropogenic changes and parasite evolution needs to become a cornerstone of public health planning, economic development and conservation biology.

Delaying weed adaptation to herbicide by environmental heterogeneity: a simulation approach

BACKGROUND

Environmental heterogeneity in space or time can drive the evolutionary trajectory of an adaptive trait. This concept could be of practical significance in pesticide resistance management that aims to delay the evolution of a resistance allele. Using a population genetics model, the dynamics of herbicide resistance in a weed species was simulated in a heterogeneous environment with alternation of two unrelated herbicides in time, in space or in both time and space. The level of the environmental heterogeneity (habitat grain) was simulated by a variation in the size of the herbicide-treated areas.

RESULTS

The model confirms that several strategies based on habitat heterogeneity efficiently slow down and even prevent resistance evolution. For a recessive resistant trait in outcrossing species, a medium level of environmental heterogeneity (intermediate habitat grain) was found to be the best for delaying herbicide resistance, as previously observed for insecticide resistance management. In selfing species or for a dominant resistant trait in outcrossing species, a low level of environmental heterogeneity (coarse-grained habitat) was more efficient in delaying resistance evolution when heterogeneity in both space and time were considered.

CONCLUSION

This model suggests that the choice of optimal tactics for delaying herbicide resistance by enhanced heterogeneity in space or time firstly depends on the interactions between the breeding system and the dominance of the resistance allele in the presence of herbicide, then on the value of the fitness cost and lastly on the dominance of this fitness cost.

Targeting virulence: a new paradigm for antimicrobial therapy

Clinically significant antibiotic resistance has evolved against virtually every antibiotic deployed. Yet the development of new classes of antibiotics has lagged far behind our growing need for such drugs. Rather than focusing on therapeutics that target in vitro viability, much like conventional antibiotics, an alternative approach is to target functions essential for infection, such as virulence factors required to cause host damage and disease. This approach has several potential advantages including expanding the repertoire of bacterial targets, preserving the host endogenous microbiome, and exerting less selective pressure, which may result in decreased resistance. We review new approaches to targeting virulence, discuss their advantages and disadvantages, and propose that in addition to targeting virulence, new antimicrobial development strategies should be expanded to include targeting bacterial gene functions that are essential for in vivo viability. We highlight both new advances in identifying these functions and prospects for antimicrobial discovery targeting this unexploited area.

Conceptual bases for quantifying the role of the environment on gene evolution: the participation of positive selection and neutral evolution

To demonstrate that a given change in the environment has contributed to the emergence of a given genotypic and phenotypic shift during the course of evolution, one should ask to what extent such shifts would have occurred without environmental change. Of course, such tests are rarely practical but phenotypic novelties can still be correlated to genomic shifts in response to environmental changes if enough information is available. We surveyed and re-evaluated the published data in order to estimate the role of environmental changes on the course of species and genomic evolution. Only a few published examples clearly demonstrate a causal link between a given environmental change and the fixation of a genomic variant resulting in functional modification (gain, loss or alteration of function). Many others suggested a link between a given phenotypic shift and a given environmental change but failed to identify the underlying genomic determinant(s) and/or the associated functional consequence(s). The proportion of genotypic and phenotypic variation that is fixed concomitantly with environmental changes is often considered adaptive and hence, the result of positive selection, even though alternative causes, such as genetic drift, are rarely investigated. Therefore, the second aim herein is to review evidence for the mechanisms leading to fixation.

Survey of susceptibilities to monosultap, triazophos, fipronil, and abamectin in Chilo suppressalis (Lepidoptera: Crambidae)

To provide a foundation for national resistance management of the Asiatic rice borer, Chilo suppressalis (Walker) (Lepidoptera: Crambidae), a study was carried out to determine dose-response and susceptibility changes over a 5-yr period in the insect from representative rice, Oryza sativa L., production regions. In total, 11 populations were collected from 2002 to 2006 in seven rice-growing provinces in China, and they were used to examine their susceptibility levels to monosultap, triazophos, fipronil, and abamectin. Results indicated that most populations had increased tolerance to monosultap. Several field populations, especially those in the southeastern Zhejiang Province, were highly or extremely highly resistant to triazophos (resistance ratio [RR] = 52.57-899.93-fold), and some populations in Anhui, Jiangsu, Shanghai, and the northern rice regions were susceptible or had a low level of resistance to triazophos (RR = 1.00-10.69). Results also showed that most field populations were susceptible to fipronil (RR < 3), but the populations from Ruian and Cangnan, Zhejiang, in 2006 showed moderate levels of resistance to fipronil (RR = 20.99-25.35). All 11 field populations collected in 2002-2006 were susceptible to abamectin (RR < 5). The tolerance levels in the rice stem borer exhibited an increasing trend (or with fluctuation) over a 5-yr period for different insecticides, and they reached a maximal level in 2006 for all four insecticides. Analysis of regional resistance ratios indicated that the history and intensity of insecticide application are the major driving forces for the resistance evolution in C. suppressalis. Strategic development of insecticide resistance management also is proposed.

Size-selective harvesting alters life histories of a temperate sex-changing fish

Selective mortality, whether caused naturally by predation or through the influence of harvest practices, initiates changes within populations when individuals possessing certain heritable traits have increased fitness. Theory predicts that increased mortality rates will select for changes in a number of different life history characteristics. For example, fishing often targets larger individuals and has been shown repeatedly to alter population size structure and growth rates, and the timing of maturation. For sex-changing species, selective fishing practices can affect additional traits such as the mature population sex ratio and the timing of sexual transformation. Using historical comparisons, we examined the effects of exploitation on life history characteristics of California sheephead, Semicossyphus pulcher, a temperate protogynous (female-male sex changer) labrid that inhabits nearshore rocky environments from central California, USA, to southern Baja California, Mexico. Recreational fishing intensified and an unregulated commercial live-fish fishery developed rapidly in southern California between the historical and current studies. Collections of S. pulcher from three locations (Bahia Tortugas, Catalina Island, and San Nicolas Island) in 1998 were compared with data collected 20-30 years previously to ascertain fishery-induced changes in life history traits. At Bahia Tortugas, where fishing by the artisanal community remained light and annual survivorship stayed high, we observed no changes in size structure or shifts in the timing of maturation or the timing of sex change. In contrast, where recreational (Catalina) and commercial (San Nicolas) fishing intensified and annual survivorship correspondingly declined, males and females shifted significantly to smaller body sizes, females matured earlier and changed sex into males at both smaller sizes and younger ages and appeared to have a reduced maximum lifespan. Mature sex ratios (female:male) increased at San Nicolas, despite a twofold reduction in the mean time spent as a mature female. Proper fisheries management requires measures to prevent sex ratio skew, sperm limitation, and reproductive failure because populations of sequential hermaphrodites are more sensitive to size-selective harvest than separate-sex species. This is especially true for S. pulcher, where different segments of the fishery (commercial vs. recreational) selectively target distinct sizes and therefore sexes in different locations.

LmrR is a transcriptional repressor of expression of the multidrug ABC transporter LmrCD in Lactococcus lactis

LmrCD is an ABC-type multidrug transporter in Lactococcus lactis. LmrR encodes a putative transcriptional regulator. In a DeltalmrR strain, lmrCD is up-regulated. LmrR binds the promoter region of lmrCD and interacts with drugs that cause lmrCD up-regulation. This suggests that LmrR is a drug-dependent transcriptional regulator of lmrCD expression.

Eco-evolutionary vs. habitat contributions to invasion in salmon: experimental evaluation in the wild

Although trait evolution over contemporary timescales is well documented, its influence on ecological dynamics in the wild has received much less attention particularly compared to traditional ecological and environmental factors. For example, evolution over ecologically relevant timescales is expected in populations that colonize new habitats, where it should theoretically enhance fitness, associated vital rates of survival and reproduction, and population growth potential. Nonetheless, success of exotic species is much more commonly attributed to ecological aspects of habitat quality and 'escape from enemies' in the invaded range. Here, we consider contemporary evolution of vital rates in introduced Chinook salmon (Oncorhynchus tshawytscha) that quickly colonized New Zealand and diverged over c. 26 generations. By using experimental translocations, we partitioned the roles of evolution and habitat quality in modifying geographical patterns of vital rates. Variation in habitat quality within the new range had the greatest influence on broad geographical patterns of vital rates, but locally adapted salmon still exhibited more than double the vital rate performance, and hence fitness, of nonlocal counterparts. The scope of this fitness evolution far exceeds the scale of divergence in trait values for these populations, or even the expected fitness effects of particular traits. These results suggest that contemporary evolution can be an important part of the eco-evolutionary dynamics of invasions and highlight the need for studies of the emergent fitness and ecological consequences of such evolution, rather than just changes in trait values.

Selective harvesting and habitat loss produce long-term life history changes in a mouflon population

We examined the long-term effects (28 years) of habitat loss and phenotype-based selective harvest on body mass, horn size, and horn shape of mouflon (Ovis gmelini musimon) in southern France. This population has experienced habitat deterioration (loss of 50.8% of open area) since its introduction in 1956 and unrestricted selective hunting of the largest horned males since 1973. Both processes are predicted to lead to a decrease in phenotype quality by decreasing habitat quality and by reducing the reproductive contribution of individuals carrying traits that are targeted by hunters. Body mass and body size of both sexes and horn measurements of males markedly decreased (by 3.4-38.3%) in all age classes from the 1970s. Lamb body mass varied in relation to the spatiotemporal variation of habitat closure within the hunting-free reserve, suggesting that habitat closure explains part of these changes. However, the fact that there was no significant spatial variation in body mass in the early part of the study, when a decline in phenotypic quality already had occurred, provided support for the influence of selective harvesting. We also found that the allometric relationship between horn breadth and horn length changed over the study period. For a given horn length, horn breadth was lower during the second part of the study. This result, as well as changes in horn curve diameter, supports the interpretation that selective harvesting of males based on their horn configuration had evolutionary consequences for horn shape, since this phenotypic trait is less likely to be affected by changes in habitat characteristics. Moreover, males required more time (approximately four years) to develop a desirable trophy, suggesting that trophy hunting favors the reproductive contribution of animals with slow-growing horns. Managers should exploit hunters' desire for trophy males to finance management strategies which ensure a balance between the population and its environment. However, for long-term sustainable exploitation, harvest strategy should also ensure that selectively targeted males are allowed to contribute genetically to the next generations.

Increased sedentariness in European Blackbirds following urbanization: a consequence of local adaptation?

Urbanization changes local environmental conditions and may lead to altered selection regimes for life history traits of organisms thriving in cities. Previous studies have reported changes in breeding phenology and even trends toward increased sedentariness in migratory bird species colonizing urban areas. However, does the change in migratory propensity simply represent a phenotypic adjustment to local urban environment, or is it genetically based and hence the result of local adaptation? To test this, we hand-raised European Blackbirds (Turdus merula) from urban and forest populations, quantified their nocturnal activity and fat deposition covering two complete migratory cycles and examined the consequences of a reduced migratory propensity for the timing of gonadal development (a physiological measure of the seasonal timing of reproduction). Although nocturnal activities differed strikingly between fall and spring seasons, with low activities during the fall and high activities during the spring seasons, our data confirm, even in birds kept from early life under common-garden conditions, a change toward reduced migratoriness in urban blackbirds. The first score of a principal component analysis including amount of nocturnal activity and fat deposition, defined as migratory disposition, was lower in urban than in forest males particularly during their first year, whereas females did not differ. The results suggest that the intrinsic but male-biased difference is genetically determined, although early developmental effects cannot be excluded. Moreover, individuals with low migratory disposition developed their gonads earlier, resulting in longer reproductive seasons. Since urban conditions facilitate earlier breeding, intrinsic shifts to sedentariness thus seem to be adaptive in urban habitats. These results corroborate the idea that urbanization has evolutionary consequences for life history traits such as migratory behavior.

The Evolution of Dispersal in Reserve Networks

The fragmentation of an environment into developed and protected areas may influence selection pressure on dispersal by increasing the chance of moving from a favorable to an unfavorable habitat. We theoretically explore this possibility through two cases: (1) marine systems in which reduced predation and/or increased feeding drive the evolution of planktonic larval duration and (2) more generally, where stochasticity in reproductive yield drives the evolution of the proportion of offspring dispersing. Model results indicate that habitat fragmentation generally shifts selection pressure toward reduced dispersal, particularly when areas outside reserves are uninhabitable. However, shifts to increased dispersal may occur when temporal heterogeneity is the primary selective force and constant-quota harvest occurs outside reserves. In addition, model results suggest the potential for changes in the genetic variability in dispersal after habitat fragmentation. The predicted evolutionary changes in dispersal will depend on factors such as the relative genetic and environmental contributions to dispersal-related traits and the extent of anthropogenic impacts outside reserves. If the predicted evolutionary changes are biologically attainable, they may suggest altering current guidelines for the appropriate size and spacing of marine reserves necessary to achieve conservation and fisheries goals.