Jekyll or Hyde? The genome (and more) of Nesidiocoris tenuis, a zoophytophagous predatory bug that is both a biological control agent and a pest.

Nesidiocoris tenuis (Reuter) is an efficient predatory biological control agent used throughout the Mediterranean Basin in tomato crops but regarded as a pest in northern European countries. From the family Miridae, it is an economically important insect yet very little is known in terms of genetic information and no genomic or transcriptomic studies have been published. Here, we use a linked-read sequencing strategy on a single female N. tenuis. From this, we assembled the 355 Mbp genome and delivered an ab initio, homology-based and evidence-based annotation. Along the way, the bacterial "contamination" was removed from the assembly. In addition, bacterial lateral gene transfer (LGT) candidates were detected in the N. tenuis genome. The complete gene set is composed of 24 688 genes; the associated proteins were compared to other hemipterans (Cimex lectularis, Halyomorpha halys and Acyrthosiphon pisum). We visualized the genome using various cytogenetic techniques, such as karyotyping, CGH and GISH, indicating a karyotype of 2n = 32. Additional analyses include the localization of 18S rDNA and unique satellite probes as well as pooled sequencing to assess nucleotide diversity and neutrality of the commercial population. This is one of the first mirid genomes to be released and the first of a mirid biological control agent.

Facilitators of adaptation and antifungal resistance mechanisms in clinically relevant fungi.

Opportunistic fungal pathogens can cause a diverse range of diseases in humans. The increasing rate of fungal infections caused by strains that are resistant to commonly used antifungals results in difficulty to treat diseases, with accompanying high mortality rates. Existing and newly emerging molecular resistance mechanisms rapidly spread in fungal populations and need to be monitored. Fungi exhibit a diversity of mechanisms to maintain physiological resilience and create genetic variation; processes which eventually lead to the selection and spread of resistant fungal pathogens. To prevent and anticipate this dispersion, the role of evolutionary factors that drive fungal adaptation should be investigated. In this review, we provide an overview of resistance mechanisms against commonly used antifungal compounds in the clinic and for which fungal resistance has been reported. Furthermore, we aim to summarize and elucidate potent generators of genetic variability across the fungal kingdom that aid adaptation to stressful environments. This knowledge can lead to recognizing potential niches that facilitate fast resistance development and can provide leads for new management strategies to battle the emerging resistant populations in the clinic and the environment.

[Polymicrobial infections: ecosystems with special properties]. / Polymicrobiële infecties: ecosystemen met bijzondere eigenschappen.

Bacteria often live together in complex communities. Insight into these microbial ecosystems is essential to make it possible to intervene when these ecosystems lead to disease. Bacteria do not only respond to their host, but they also affect each other, which may have far-reaching consequences for the course of the disease. In this article we describe that clinical isolates in a polymicrobial infection can be seen as ecosystems. These ecosystems often have properties that separate isolates do not have; they may, for example, be more virulent or more resistant to antibiotics. We therefore emphasise that the whole is greater than the sum of its parts, even for infections.

The plastic fly: the effect of sustained fluctuations in adult food supply on life-history traits.

Many adult traits in Drosophila melanogaster show phenotypic plasticity, and the effects of diet on traits such as lifespan and reproduction are well explored. Although plasticity in response to food is still present in older flies, it is unknown how sustained environmental variation affects life-history traits. Here, we explore how such life-long fluctuations of food supply affect weight and survival in groups of flies and affect weight, survival and reproduction in individual flies. In both experiments, we kept adults on constant high or low food and compared these to flies that experienced fluctuations of food either once or twice a week. For these 'yoyo' groups, the initial food level and the duration of the dietary variation differed during adulthood, creating four 'yoyo' fly groups. In groups of flies, survival and weight were affected by adult food. However, for individuals, survival and reproduction, but not weight, were affected by adult food, indicating that single and group housing of female flies affects life-history trajectories. Remarkably, both the manner and extent to which life-history traits varied in relation to food depended on whether flies initially experienced high or low food after eclosion. We therefore conclude that the expression of life-history traits in adult life is affected not only by adult plasticity, but also by early adult life experiences. This is an important but often overlooked factor in studies of life-history evolution and may explain variation in life-history experiments.

Footprints of selection in wild populations of Bicyclus anynana along a latitudinal cline.

One of the major questions in ecology and evolutionary biology is how variation in the genome enables species to adapt to divergent environments. Here, we study footprints of thermal selection in candidate genes in six wild populations of the afrotropical butterfly Bicyclus anynana sampled along a c. 3000 km latitudinal cline. We sequenced coding regions of 31 selected genes with known functions in metabolism, pigment production, development and heat shock responses. These include genes for which we expect a priori a role in thermal adaptation and, thus, varying selection pressures along a latitudinal cline, and genes we do not expect to vary clinally and can be used as controls. We identified amino acid substitution polymorphisms in 13 genes and tested these for clinal variation by correlation analysis of allele frequencies with latitude. In addition, we used two F(ST) -based outlier methods to identify loci with higher population differentiation than expected under neutral evolution, while accounting for potentially confounding effects of population structure and demographic history. Two metabolic enzymes of the glycolytic pathway, UGP and Treh, showed clinal variation. The same loci showed elevated population differentiation and were identified as significant outliers. We found no evidence of clines in the pigmentation genes, heat shock proteins and developmental genes. However, we identified outlier loci in more localized parts of the range in the pigmentation genes yellow and black. We discuss that the observed clinal variation and elevated population divergence in UGP and Treh may reflect adaptation to a geographic thermal gradient.

Quality-quantity trade-off of human offspring under adverse environmental conditions.

A central paradigm in life-history theory is the trade-off between offspring number and quality. Several studies have investigated this trade-off in humans, but data are inconclusive, perhaps because prosperous socio-cultural factors mask the trade-off. Therefore, we studied 2461 offspring groups in an area under adverse conditions in northern Ghana with high fertility and mortality rates. In a linear mixed model controlling for differences in age and tribe of the mother and socioeconomic status, each additional child in the offspring group resulted in a 2.3% (95% CI 1.9-2.6%, P < 0.001) lower proportional survival of the offspring. Furthermore, we made use of the polygamous population structure and compared offspring of co-wives in 388 households, thus controlling for variation in resources between compounds. Here, offspring survival decreased 2.8% (95% CI 2.3-4.0%, P < 0.001) for each increase in offspring number. We interpret these data as an apparent quality-quantity trade-off in human offspring.

Genomic studies in ageing research: the need to integrate genetic and gene expression approaches.

Genome-wide and hypothesis-based approaches to the study of ageing and longevity have been dominated by genetic investigations. To identify essential mechanisms of a complex trait such as ageing in higher species, a holistic understanding of interacting pathways is required. More information on such interactions is expected to be obtained from global gene expression analysis if combined with genetic studies. Genetic sequence variation often provides a functional gene marker for the trait, whereas a gene expression profile may provide a quantitative biomarker representing complex cellular pathway interactions contributing to the trait. Thus far, gene expression studies have associated multiple pathways to ageing including mitochondrial electron transport and the oxidative stress response. However, most of the studies are underpowered to detect small age-changes. A systematic survey of gene expression changes as a function of age in human individuals and animal models is lacking. Well designed gene expression studies, especially at the level of biological processes, will provide hypotheses on gene-environmental interactions determining biological ageing rate. Cross-sectional studies monitoring the profile as a chronological marker of ageing must be integrated with prospective studies indicating which profiles represent biomarkers preceding and predicting physiological decline and mortality. New study designs such as the Leiden Longevity Study, including two generations of subjects from longevity families, aim to achieve these combined approaches.

Evolutionary dynamics of multilocus microsatellite arrangements in the genome of the butterfly Bicyclus anynana, with implications for other Lepidoptera.

The sequences flanking microsatellites isolated from the butterfly Bicyclus anynana display high levels of similarity among different loci. We examined sequence data for evidence of the two mechanisms most likely to generate these similarities, namely recombination mediated events, such as unequal crossing over or gene conversion and through transposition of mobile elements (MEs). Many sequences contained tandemly arranged microsatellites, lending support to recombination as the multiplication mechanism. There is, however, also support for ME-mediated multiplication of microsatellites and their flanking sequences. Homology with a known Lepidopteran ME was found in B. anynana microsatellite regions, and polymorphic microsatellite markers with partial similarities in their flanking sequences were passed on to the next generation independently, indicating that they are not linked. Therefore, the rise of these similarities appears to be mediated through both processes, either as an interaction between the two, or by each being responsible for part of the observations. A large proportion of microsatellites embedded in repetitive DNA is representative for most studied butterflies and moths, and a BLAST survey of the B. anynana sequences revealed four short microsatellite-associated sequences that were present in many species of Lepidoptera. The similarities usually start to deviate beyond these sequences, which suggests that they define the extremes of a repeated unit. Further study of these conserved sequences may help to understand the mechanism underlying the multiplication events, and answer the question of why these redundancies are predominantly found in this insect group.

Extraordinary long life spans in fruit-feeding butterflies can provide window on evolution of life span and aging.

Information on the life span of organisms in the field is essential for elucidating the evolution of life span and aging. We present mark-recapture data (>30,000 marked individuals, >4000 recaptured at least once) on 47 species of fruit-feeding butterflies in a tropical forest in Uganda. The data reveal adult life spans in the field for several species that are significantly longer than previously recorded in Lepidoptera (butterflies and moths). Longevity records for species of which more than 100 individuals were recaptured ranged from 67 (Bicyclus auricruda) to 293 days (Euphaedra medon). In contrast to the majority of Lepidoptera which are short-lived, these all show exceptionally long life spans, and may thus help to better identify factors that affect aging, particularly when combined with information on temporal patterns in reproduction, strategies to avoid predation, and nutritional ecology. These key traits are readily measurable in butterflies and thus studies on fruit-feeding butterflies have much potential for gaining insight into the evolution of life span and aging, especially given the tradition of field-research on butterflies.

Realized correlated responses to artificial selection on pre-adult life-history traits in a butterfly.

We use artificial selection experiments targeted on egg size, development time or pupal mass within a single butterfly population followed by a common-garden experiment to explore the interactions among these life-history traits. Relationships were predicted to be negative between egg size and development time, but to be positive between development time and body size and between egg size and body size. Correlated responses to selection were in part inconsistent with these predictions. Although there was evidence for a positive genetic correlation between egg and body size, there was no support for genetic correlations between larval development time and either egg size or pupal mass. Phenotypic correlations among the three target traits of selection gave comparable results for the relationships between egg mass and development time (no association) as well as between egg mass and pupal mass (positive association), but not for the relation between development time and pupal mass (negative phenotypic correlation). In summary, correlated responses to selection as well as phenotypic correlations were rather unpredictable. The impact of variation in acquisition and allocation of energy as well as of the benign conditions used deserve further investigation.

Methuselah life history in a variety of conditions, implications for the use of mutants in longevity research.

The laboratory has yielded many long-lived mutants of several model-organisms in the past few years. Many of the resulting claims for extended longevity have been nuanced or shown to be restricted to specific conditions, including environments and genetic backgrounds. Here, we test whether the long-lived mutant fruit fly methuselah (mth(1)) displays its apparent superiority in longevity and stress resistance in different environments, at different ages and in correlated traits. The results demonstrate that stress resistance at different times in life is not consistently higher in the mutant relative to its progenitor strain (w(1118)). Furthermore, the mth(1) genotype only leads to an increase in longevity in an environment where reproduction is not stimulated. Also, virgin and mated life span were compared and showed that mating negatively affects life span, especially in the mth(1) individuals. This reduced the life span enhancing effect of the mutation to zero. This apparent environment and mating dependent trade-off between longevity and reproduction supports the disposable soma theory of ageing. We conclude that these data can only provide limited information on natural variation. The data show the need to uncover the full complexity of variation in such traits in natural environments.

C. elegans DAF-12, Nuclear Hormone Receptors and human longevity and disease at old age.

In Caenorhabditis elegans, DAF-12 appears to be a decisive checkpoint for many life history traits including longevity. The daf-12 gene encodes a Nuclear Hormone Receptor (NHR) and is member of a superfamily that is abundantly represented throughout the animal kingdom, including humans. It is, however, unclear which of the human receptor representatives are most similar to DAF-12, and what their role is in determining human longevity and disease at old age. Using a sequence similarity search, we identified human NHRs similar to C. elegans DAF-12 and found that, based on sequence similarity, Liver X Receptor A and B are most similar to C. elegans DAF-12, followed by the Pregnane X Receptor, Vitamin D Receptor, Constitutive Andosteron Receptor and the Farnesoid X Receptor. Their biological functions include, amongst others, detoxification and immunomodulation. Both are processes that are involved in protecting the body from harmful environmental influences. Furthermore, the DAF-12 signalling systems seem to be functionally conserved and all six human NHRs have cholesterol derived compounds as their ligands. We conclude that the DAF-12 signalling system seems to be evolutionary conserved and that NHRs in man are critical for body homeostasis and survival. Genomic variations in these NHRs or their target genes are prime candidates for the regulation of human lifespan and disease at old age.

Sexual functionality of Leptopilina clavipes (Hymenoptera: Figitidae) after reversing Wolbachia-induced parthenogenesis.

Females infected with parthenogenesis-inducing Wolbachia bacteria can be cured from their infection by antibiotic treatment, resulting in male production. In most cases, however, these males are either sexually not fully functional, or infected females have lost the ability to reproduce sexually. We studied the decay of sexual function in males and females of the parasitoid Leptopilina clavipes. In western Europe, infected and uninfected populations occur allopatrically, allowing for an investigation of both male and female sexual function. This was made by comparing females and males induced from different parthenogenetic populations with those from naturally occurring uninfected populations. Our results indicate that although males show a decay of sexual function, they are still able to fertilize uninfected females. Infected females, however, do not fertilize their eggs after mating with males from uninfected populations. The absence of genomic incompatibilities suggests that these effects are due to the difference in mode of reproduction.

The evolutionary genetics of egg size plasticity in a butterfly.

Abstract The evolution of phenotypic plasticity requires that it is adaptive, genetically determined, and exhibits sufficient genetic variation. For the tropical butterfly Bicyclus anynana there is evidence that temperature-mediated plasticity in egg size is an adaptation to predictable seasonal change. Here we set out to investigate heritability in egg size and genetic variation in the plastic response to temperature in this species, using a half-sib breeding design. Egg size of individual females was first measured at a high temperature 4 days after eclosion. Females were then transferred to a low temperature and egg size was measured after acclimation periods of 6 and 12 days respectively. Overall, additive genetic variance explained only 3-11% of the total phenotypic variance, whereas maternal effects were more pronounced. Genotype-environment interactions and cross-environmental correlations of less than unity suggest that there is potential for short-term evolutionary change. Our findings strengthen the support for the adaptive nature of temperature-mediated plasticity in egg size.

The effects of larval density on adult life-history traits in three species of Drosophila.

There is evidence that longevity and starvation resistance are determined by a common genetic mechanism. Starvation resistance in Drosophila strongly correlates with both fat content and longevity, and is affected by density during rearing. In this study, we examine how three species, Drosophila melanogaster, Drosophila ananassae and Drosophila willistoni, respond to three larval density treatments. Starvation resistance after adult eclosion, and after 2 days of feeding, and longevity were examined in each sex. D. willistoni reacted differently to larval density than the other two species. This species showed an effect of density on longevity whilst D. ananassae and D. melanogaster showed no such effects. The results also indicate that starvation resistance is not solely determined by fat content. Resistance to starvation at two time points after eclosion differed among species. This may reflect differences in resource acquisition and allocation, and we discuss our findings in relation to how selection may operate in the different species.

Genetic and environmental sources of egg size variation in the butterfly Bicyclus anynana.

By dividing families of the tropical butterfly, Bicyclus anynana, among different larval (including early pupal) and adult (including late pupal) temperatures, we investigate the genetic and environmental effects on egg size. Both sources of variation affected egg size to similar extents. As previously found in other arthropods, egg size tended to increase at lower temperatures. Our data suggest that the plastic response in egg size can be induced during the pupal stage. Females reared as larvae at the same high temperature tended to lay larger eggs when transferred to a lower temperature, either as prepupae or pupae, compared to those remaining at the high temperature. Additionally, females reared as larvae at different temperatures, but maintained at the same temperature from the early pupal stage onwards, laid larger eggs after larval growth at a low temperature. Heritability estimates for egg size were about 0.4 (parent-offspring regression) and 0.2 (variance component estimates using the full-sib families). Although there seemed to be some variation in the plastic response to temperature among families, genotype-environment interactions were nonsignificant.

Chemical defence in a sawfly: genetic components of variation in relevant life-history traits.

Larvae of several tenthredinid sawfly species readily release droplets of haemolymph through their integument when attacked by predators. This defence mechanism via 'bleeding' is characterised by a low integument resistance and a high haemolymph deterrence. Both traits are variable, and negatively correlated among species. We sought to determine if such differences in the propensity to bleed also occur intraspecifically by studying the heritability of traits potentially associated with the bleeding phenomenon in the turnip sawfly Athalia rosae ruficornis Jakovlev (Hymenoptera: Tenthredinidae, Allantinae). For three European populations, heritabilities were estimated in the laboratory in a parent-offspring and a full-sib design for haemolymph deterrence (measured as concentration of sequestered glucosinolate), integument resistance, body mass of eonymph and adult, and developmental time. Within A. rosae, no significant negative phenotypic correlation was found between the two traits directly related to the defence mechanism: integument resistance and haemolymph deterrence. However, the significant heritabilities found for these traits in the full-sib analysis (0.39 and 0.35, respectively, for males in the Swiss population) show that the variation has a genetic component. While full-sib analysis revealed highly significant heritabilities for most traits in all the three populations, parent-offspring regression revealed little or no evidence of heritable variation. Effects of common environment for siblings and variation in the host-plant quality between insect generations are likely to be the main factors explaining these differences. A consequence of such host-plant variation in the wild might be that genetic variation of such chemical defensive traits is largely invisible to natural selection.

Cellular basis of wing size variation in Drosophila melanogaster: a comparison of latitudinal clines on two continents.

We investigated the cellular basis of two extensive, continuous, latitudinal, genetic, body size clines of Drosophila melanogaster by measuring wing area and cell size in the wing blade of adult flies reared under standard, laboratory conditions. We report that the contribution of cell size to an Australian cline is much smaller than that to a South American cline. The data suggest that neither cell size nor cell number were the targets of selection, but rather wing area itself, or a trait closely related to it. We hypothesize that the differences between the continents were caused by differences in the initial pattern of genetic variation for the cell traits and/or by the direction of selection on the source populations of the clines. Despite large differences between continents in the cellular basis of the latitudinal variation, multiple regression analysis, using the individual variation within populations, showed that the relationship between cell size and cell number was changed with latitude in the same way in the two clines. The relative contribution of cell number to wing area variation increased with latitude, probably because of compensatory interactions with cell size as a consequence of the latitudinal increase in cell number. Our findings are discussed in relation to the cellular basis of evolutionary change in laboratory thermal selection lines and natural populations along latitudinal clines.

The evolutionary genetics of ageing and longevity.

Evolutionary theories of ageing are based on the observation that the efficacy of natural selection decreases with age. This is because, even without ageing, individuals will die of environmental causes, such as predation, disease and accidents. Ageing is thought to have evolved as the result of optimising fitness early in life. A second process, namely the progressive accumulation of mutations with effects late in life, will reinforce this result. Longevity of a species is therefore determined by the amount of environmental mortality caused by the ecology of a species. The experimental data concerning the relative roles of both processes are reviewed here. Recent discoveries of the levelling of mortality curves, and of age specific mutations in mutation accumulation lines of Drosophila melanogaster, require adjustments to the original models of the evolution of ageing and species longevity. These adjustments do not invalidate the underlying rationale of evolutionary theories of ageing. With current developments in QTL mapping and genetic association studies, the unravelling of the ageing process has the potential to progress rapidly.

On the developmental theory of ageing. II. The effect of developmental temperature on longevity in relation to adult body size in D. melanogaster.

Flies from a wild type strain of Drosophila melanogaster, previously kept at 25 degrees C, were reared at either 20, 25 or 29 degrees C. As expected, developmental time and adult body size decreased with increasing temperature. Adult longevity of flies reared at 25 degrees C was slightly greater than that of flies raised at 20 or 29 degrees C when measured at all three temperatures. This may reflect the laboratory history of the strain. On the whole, it appeared that longevity was independent of adult body size. These results support our previous conclusion (Zwaan et al., 1991) that developmental time and body size are not causally related to longevity in 'environmental' studies. It is stressed, that genetic analysis is needed to investigate the reputed correlation between development and ageing.