Living in a jar: genetic variation and differentiation among laboratory strains of the red flour beetle

The red flour beetle, Tribolium castaneum, is a common pest, which has become an important model study organism, especially in genetic, ecological and evolutionary research. Although almost all studies on this species have been conducted using established laboratory strains, very little is known about the loss of genetic diversity within the strains and genetic divergence between different laboratory stocks. In this study, five long‐term laboratory strains and one wild strain were examined for genetic variation at 12 microsatellite loci, which were designed using publicly available sequences. One of the laboratory strains is resistant to phosphine and one to organophosphorous insecticides. All strains had significant amounts of molecular variation, but genetic diversity in the laboratory strains was lower than in the wild‐derived strain used as control. We observed significant molecular divergence among the strains, however, the relationship between them reflected resistance status rather than geographic origins. We found no evidence for recent bottlenecks, but the wild‐derived population showed signs of demographic expansion. A novel multivariate method, multiple co‐inertia analysis, revealed that the two loci contributing most to the divergence between the resistant strains were located on the eighth chromosome, near genes associated with insecticide resistance.     

Evolutionary biology of starvation resistance: what we have learned from Drosophila

Most animals face periods of food shortage and are thus expected to evolve adaptations enhancing starvation resistance (SR). Most of our knowledge of the genetic and physiological bases of those adaptations, their evolutionary correlates and trade-offs, and patterns of within- and among-population variation, comes from studies on Drosophila. In this review, we attempt to synthesize the various facets of evolutionary biology of SR emerging from those studies. Heritable variation for SR is ubiquitous in Drosophila populations, allowing for large responses to experimental selection. Individual flies can also inducibly increase their SR in response to mild nutritional stress (dietary restriction). Both the evolutionary change and the physiological plasticity involve increased accumulation of lipids, changes in carbohydrate and lipid metabolism and reduction in reproduction. They are also typically associated with greater resistance to desiccation and oxidative stress, and with prolonged development and lifespan. These responses are increasingly seen as facets of a shift of the physiology towards a 'survival mode', which helps the animal to survive hard times. The last decade has seen a great progress in revealing the molecular bases of induced responses to starvation, and the first genes contributing to genetic variation in SR have been identified. In contrast, little progress has been made in understanding the ecological significance of SR in Drosophila; in particular it remains unclear to what extent geographical variation in SR reflect differences in natural selection acting on this trait rather than correlated responses to selection on other traits. Drosophila offers a unique opportunity for an integrated study of the manifold aspects of adaptation to nutritional stress. Given that at least some major molecular mechanisms of response to nutritional stress seem common to animals, the insights from Drosophila are likely to apply more generally than just to dipterans or insects.     

高等植物热激转录因子生物学特性及其在非生物胁迫适应中的作用

热激转录因子(HSFs)参与了植物生长发育的调控以及多种非生物胁迫适应基因的表达调控。HSFs通常形成同源三聚体,激活转录活性从而发挥功能。本文综述了热激转录因子的基本结构、亚细胞定位、转录调控、功能多样性及其在植物适应极端温度、盐害、干旱、强光和氧化胁迫等非生物胁迫过程中的作用。HSFs是提高高等植物抗多重胁迫的优质候选基因,对其深入研究具有重要的应用价值。未来,通过生物基因工程等手段利用HSFs提高各类作物抗性具有广阔的发展前景。     

Good genes, oxidative stress and condition-dependent sexual signals

The immune and the detoxication systems of animals are characterized by allelic polymorphisms, which underlie individual differences in ability to combat assaults from pathogens and toxic compounds. Previous studies have shown that females may improve offspring survival by selecting mates on the basis of sexual ornaments and signals that honestly reveal health. In many cases the expression of these ornaments appears to be particularly sensitive to oxidative stress. Activated immune and detoxication systems often generate oxidative stress by an extensive production of reactive metabolites and free radicals. Given that tolerance or resistance to toxic compounds and pathogens can be inherited, female choice should promote the evolution of male ornaments that reliably reveal the status of the bearers' level of oxidative stress. Hence, oxidative stress may be one important agent linking the expression of sexual ornaments to genetic variation in fitness-related traits, thus promoting the evolution of female mate choice and male sexual ornamentation, a controversial issue in evolutionary biology ever since Darwin.     

Genome-wide association analysis of oxidative stress resistance in Drosophila melanogaster

Background

Aerobic organisms are susceptible to damage by reactive oxygen species. Oxidative stress resistance is a quantitative trait with population variation attributable to the interplay between genetic and environmental factors. Drosophila melanogaster provides an ideal system to study the genetics of variation for resistance to oxidative stress.

Methods and Findings

We used 167 wild-derived inbred lines of the Drosophila Genetic Reference Panel for a genome-wide association study of acute oxidative stress resistance to two oxidizing agents, paraquat and menadione sodium bisulfite. We found significant genetic variation for both stressors. Single nucleotide polymorphisms (SNPs) associated with variation in oxidative stress resistance were often sex-specific and agent-dependent, with a small subset common for both sexes or treatments. Associated SNPs had moderately large effects, with an inverse relationship between effect size and allele frequency. Linear models with up to 12 SNPs explained 67–79% and 56–66% of the phenotypic variance for resistance to paraquat and menadione sodium bisulfite, respectively. Many genes implicated were novel with no known role in oxidative stress resistance. Bioinformatics analyses revealed a cellular network comprising DNA metabolism and neuronal development, consistent with targets of oxidative stress-inducing agents. We confirmed associations of seven candidate genes associated with natural variation in oxidative stress resistance through mutational analysis.

Conclusions

We identified novel candidate genes associated with variation in resistance to oxidative stress that have context-dependent effects. These results form the basis for future translational studies to identify oxidative stress susceptibility/resistance genes that are evolutionary conserved and might play a role in human disease.     

Cryptic genetic variation is enriched for potential adaptations

Cryptic genetic variation accumulates under weakened selection and has been proposed as a source of evolutionary innovations. Weakened selection may, however, also lead to the accumulation of strongly deleterious or lethal alleles, swamping the effect of any potentially adaptive alleles when they are revealed. Here I model variation that is partially shielded from selection, assuming that unconditionally deleterious variation is more strongly deleterious than variation that is potentially adaptive in a future environment. I find that cryptic genetic variation can be substantially enriched for potential adaptations under a broad range of realistic parameter values, including those applicable to alternative splices and readthrough products generated by the yeast prion [PSI+]. This enrichment is dramatically stronger when multiple simultaneous changes are required to generate a potentially adaptive phenotype. Cryptic genetic variation is likely to be an effective source of useful adaptations at a time of environmental change, relative to an equivalent source of variation that has not spent time in a hidden state.     

HOW REPEATABLE IS ADAPTIVE EVOLUTION? THE ROLE OF GEOGRAPHICAL ORIGIN AND FOUNDER EFFECTS IN LABORATORY ADAPTATION

The importance of contingency versus predictability in evolution has been a long-standing issue, particularly the interaction between genetic background, founder effects, and selection. Here we address experimentally the effects of genetic background and founder events on the repeatability of laboratory adaptation in Drosophila subobscura populations for several functional traits. We found disparate starting points for adaptation among laboratory populations derived from independently sampled wild populations for all traits. With respect to the subsequent evolutionary rate during laboratory adaptation, starvation resistance varied considerably among foundations such that the outcome of laboratory evolution is rather unpredictable for this particular trait, even in direction. In contrast, the laboratory evolution of traits closely related to fitness was less contingent on the circumstances of foundation. These findings suggest that the initial laboratory evolution of weakly selected characters may be unpredictable, even when the key adaptations under evolutionary domestication are predictable with respect to their trajectories.     

The Role of Oxidative Stress in the Longevity and Insecticide Resistance Phenotype of the Major Malaria Vectors Anopheles arabiensis and Anopheles funestus

Oxidative stress plays numerous biological roles, both functional and pathological. The role of oxidative stress in various epidemiologically relevant biological traits in Anopheles mosquitoes is not well established. In this study, the effects of oxidative stress on the longevity and insecticide resistance phenotype in the major malaria vector species An. arabiensis and An. funestus were examined. Responses to dietary copper sulphate and hydrogen peroxide were used as proxies for the oxidative stress phenotype by determining the effect of copper on longevity and hydrogen peroxide lethal dose. Glutathione peroxidase and catalase activities were determined colorimetrically. Oxidative burden was quantified as protein carbonyl content. Changes in insecticide resistance phenotype were monitored by WHO bioassay. Insecticide resistant individuals showed an increased capacity for coping with oxidative stress, mediated by increased glutathione peroxidase and catalase activity. This effect was observed in both species, as well as in laboratory strains and F₁ individuals derived from wild-caught An. funestus mothers. Phenotypic capacity for coping with oxidative stress was greatest in strains with elevated Cytochrome P450 activity. Synergism of oxidative stress defence enzymes by dietary supplementation with haematin, 3-Amino-1, 2, 4-triazole and Sodium diethyldithiocarbamate significantly increased pyrethroid-induced mortality in An. arabiensis and An. funestus. It is therefore concluded that defence against oxidative stress underlies the augmentation of the insecticide resistance phenotype associated with multiple blood-feeding. This is because multiple blood-feeding ultimately leads to a reduction of oxidative stress in insecticide resistant females, and also reduces the oxidative burden induced by DDT and pyrethroids, by inducing increased glutathione peroxidase activity. This study highlights the importance of oxidative stress in the longevity and insecticide resistance phenotype in malaria vectors.     

A comparative survey of the frequency and distribution of polymorphism in the genome of Xenopus tropicalis

Naturally occurring DNA sequence variation within a species underlies evolutionary adaptation and can give rise to phenotypic changes that provide novel insight into biological questions. This variation exists in laboratory populations just as in wild populations and, in addition to being a source of useful alleles for genetic studies, can impact efforts to identify induced mutations in sequence-based genetic screens. The Western clawed frog Xenopus tropicalis (X. tropicalis) has been adopted as a model system for studying the genetic control of embryonic development and a variety of other areas of research. Its diploid genome has been extensively sequenced and efforts are underway to isolate mutants by phenotype- and genotype-based approaches. Here, we describe a study of genetic polymorphism in laboratory strains of X. tropicalis. Polymorphism was detected in the coding and non-coding regions of developmental genes distributed widely across the genome. Laboratory strains exhibit unexpectedly high frequencies of genetic polymorphism, with alleles carrying a variety of synonymous and non-synonymous codon substitutions and nucleotide insertions/deletions. Inter-strain comparisons of polymorphism uncover a high proportion of shared alleles between Nigerian and Ivory Coast strains, in spite of their distinct geographical origins. These observations will likely influence the design of future sequence-based mutation screens, particularly those using DNA mismatch-based detection methods which can be disrupted by the presence of naturally occurring sequence variants. The existence of a significant reservoir of alleles also suggests that existing laboratory stocks may be a useful source of novel alleles for mapping and functional studies.     

Sperm competition in mammals

Female promiscuity can lead to the spermatazoa of several males 'competing' to fertilize the ova of a single female. Such promiscuity is relatively common among mammals and has resulted in a suite of adaptations associated with sperm competition. In the last decade, laboratory scientists using experimental techniques have clarified the physiological and behavioural mechanisms that result from sperm competition. Field biologists have collected data on a variety of mammals to test predictions of sperm competition theory. Unfortunately, theories developed and tested in laboratory situations do not always explain variation in behaviour observed in field studies.     

Redox physiology in animal function:The struggle of living in an oxidant environment

A strong focus of ecological research for several decades has been to understand the factors underlying the variation in animal life-histories. In recent times, ecological studies have begun to show that oxidative stress may represent another important modulator of competitive trade-offs among fitness traits or of positively integrated patterns of traits. Therefore, incorporating mechanisms underlying oxidative physiology into evolutionary ecology has the potential to help understand variation in life-histo...     

The consequence of natural selection on genetic variation in the mouse

Laboratory mouse strains are known to have emerged from recent interbreeding between individuals of Mus musculus isolated populations. As a result of this breeding history, the collection of polymorphisms observed between laboratory mouse strains is likely to harbor the effects of natural selection between reproductively isolated populations. Until now no study has systematically investigated the consequences of this breeding history on gene evolution. Here we have used a novel, unbiased evolutionary approach to predict the founder origin of laboratory mouse strains and to assess the balance between ancient and newly emerged mutations in the founder subspecies. Our results confirm a contribution from at least four distinct subspecies. Additionally, our method allowed us to identify regions of relaxed selective constraint among laboratory mouse strains. This unique structure of variation is likely to have significant consequences on the use of mouse to find genes underlying phenotypic variation.     

Genetic improvement of Amblyseius finlandicus (Acari: Phytoseiidae): laboratory selection for resistance to azinphosmethyl and dimethoate

Amblyseius finlandicus (Oudemans) was selected in the laboratory for resistance to azinphosmethyl and dimethoate by subjecting adult females to increasing concentrations of dried residues of dimethoate and azinphosmethyl on detached bean leaves. The first eight selections were done with dimethoate. Slide-dip bioassays indicated selection with dimethoate increased dimethoate resistance 1.8-fold and azinphosmethyl resistance 2.6-fold. These resistances appeared to be quite stable: a 1.2 to 1.3-fold decrease in resistance ratios was observed in a subculture after 10 months without selections. No decrease was observed after 9 months without selections in a pooled colony that consisted of both resistant and susceptible mites. The dimethoate-selected colony was subsequently selected eight times with azinphosmethyl. About 15 % of the mites survived the last selection round with 2,500 ppm, which is 2.5 times the highest recommended field rate in Finnish apple orchards. At the end of the selection program, based on slide-dip bioassays, the total increase in resistance to dimethoate was about two-fold and to azinphosmethyl about 5.4-fold compared to the unselected base colony from which the selected colony was derived. The LC₅₀ value for azinphosmethyl was 14 times higher in the selected colony (451.3 ppm a.i.) compared to the most susceptible colony tested. A similar level of resistance to both pesticides was achieved after six azinphosmethyl selections on a mixed colony that was initiated by pooling mites from five field-collected colonies and the dimethoate-selected lines. Year-to-year variation in azinphosmethyl LC₅₀ values of the unselected base colony was high, with values varying from 83.8 to 348.7 ppm a.i., demonstrating the need to test a reference strain in each bioassay. Results of the azinphosmethyl selections and the subsequent slide-dip bioassays suggest that the resistant strain could tolerate field rates of azinphosmethyl (300–950 ppm a.i.) used in Finnish apple orchards.     

Adaptations of Cave Fishes with some Comparisons to Deep-sea Fishes

I provide my retrospective and prospective views on adaptations of cave fishes. I emphasize the history of my insights into cave adaptation from 45 years of research using surface, cave-spring, and cave species of amblyopsid fishes. My approach has been to use natural experiments and to always consider multiple hypotheses. To clarify evolutionary adaptations, I show the importance of a broad comparative approach which includes studies of morphology, metabolic physiology, foraging behavior, life history, and ecology. And I show that the most important agents of selection, of darkness and attendant low food supply, are best understood in the context of rigor, variability, and predictability. I also present my insights from what I consider the most insightful contributions on deep-sea fishes. The contributions are those of Marshall in studies of morphology in relation to energy economy of pelagic and benthic species, Childress in studies of physiological and biochemical adaptations with depth for pelagic species, and Koslow in studies on population biology and life history of bathybenthic and benthic sea-mount species. Compared to caves, I suggest that the extremes of metabolic and life history adaptations of deep-sea fish are explained by a longer evolutionary history and a much greater habitat range, food supply, and predation risk. Finally, I take a retrospective view of what we have learned about cave fishes. I discuss possible evolutionary mechanisms that can explain the trends with increasing cave adaptation in amblyopsid fishes, especially progenesis and the pleiotropic effects of the stress resistance syndrome. Finally, based on insights from deep-sea fishes, and emerging new techniques, I suggest what cave fish biologists should do in the future.