Black and orange coloration predict success during male–male competition in the guppy

Investigating how intrasexual competition and intersexual mate choice act within a system is crucial to understanding the maintenance and diversity of sexually-dimorphic traits. These two processes can act in concert by selecting for the same trait, or in opposition by selecting for different extremes of the same trait; they can also act on different traits, potentially increasing trait complexity. We asked whether male–male competition and female mate choice act on the same male traits using Trinidadian guppies, which exhibit sexual size dimorphism and male-limited color patterns consisting of different colors arranged along the body and fins. We used behavioral assays to assess the relationship between color and competitive success and then compared our results to the plethora of data on female choice and color in our study population. Males initiated more contests if they were larger than their competitor. Males won contests more often if they had more black coloration than their competitor, and the effect of black was stronger when males had less orange than their competitor. Additionally, males won more often if they had either more structural color (iridescence) and more orange, or less structural color and less orange than their competitor, suggesting multiple combinations of color traits predict success. Females from our study population exhibit a strong preference for more orange coloration. Thus, traits favored in male contests differ from those favored by intersexual selection in this population. These results suggest that inter- and intrasexual selection, when acting concurrently, can promote increased complexity of sexually selected traits.

Cascading indirect genetic effects in a clonal vertebrate

Understanding how individual differences arise and how their effects propagate through groups are fundamental issues in biology. Individual differences can arise from indirect genetic effects (IGE): genetically based variation in the conspecifics with which an individual interacts. Using a clonal species, the Amazon molly (Poecilia formosa), we test the hypothesis that IGE can propagate to influence phenotypes of the individuals that do not experience them firsthand. We tested this by exposing genetically identical Amazon mollies to conspecific social partners of different clonal lineages, and then moving these focal individuals to new social groups in which they were the only member to have experienced the IGE. We found that genetically different social environments resulted in the focal animals experiencing different levels of aggression, and that these IGE carried over into new social groups to influence the behaviour of naive individuals. These data reveal that IGE can cascade beyond the individuals that experience them. Opportunity for cascading IGE is ubiquitous, especially in species with long-distance dispersal or fission-fusion group dynamics. Cascades could amplify (or mitigate) the effects of IGE on trait variation and on evolutionary trajectories. Expansion of the IGE framework to include cascading and other types of carry-over effects will therefore improve understanding of individual variation and social evolution and allow more accurate prediction of population response to changing environments.

A large and diverse autosomal haplotype is associated with sex-linked colour polymorphism in the guppy

Male colour patterns of the Trinidadian guppy (Poecilia reticulata) are typified by extreme variation governed by both natural and sexual selection. Since guppy colour patterns are often inherited faithfully from fathers to sons, it has been hypothesised that many of the colour trait genes must be physically linked to sex determining loci as a ‘supergene’ on the sex chromosome. Here, we phenotype and genotype four guppy ‘Iso-Y lines’, where colour was inherited along the patriline for 40 generations. Using an unbiased phenotyping method, we confirm the breeding design was successful in creating four distinct colour patterns. We find that genetic differentiation among the Iso-Y lines is repeatedly associated with a diverse haplotype on an autosome (LG1), not the sex chromosome (LG12). Moreover, the LG1 haplotype exhibits elevated linkage disequilibrium and evidence of sex-specific diversity in the natural source population. We hypothesise that colour pattern polymorphism is driven by Y-autosome epistasis.

Extreme colour pattern variation in male Trinidadian guppies are influenced by natural selection and sexual selection. Here, the authors phenotype and genotype four guppy lineages finding that colour pattern is associated with a diverse haplotype on an autosome.

Indirect Genetic Effects: A Cross-disciplinary Perspective on Empirical Studies

Indirect genetic effects (IGE) occur when an individual's phenotype is influenced by genetic variation in conspecifics. Opportunities for IGE are ubiquitous, and, when present, IGE have profound implications for behavioral, evolutionary, agricultural, and biomedical genetics. Despite their importance, the empirical study of IGE lags behind the development of theory. In large part, this lag can be attributed to the fact that measuring IGE, and deconvoluting them from the direct genetic effects of an individual's own genotype, is subject to many potential pitfalls. In this Perspective, we describe current challenges that empiricists across all disciplines will encounter in measuring and understanding IGE. Using ideas and examples spanning evolutionary, agricultural, and biomedical genetics, we also describe potential solutions to these challenges, focusing on opportunities provided by recent advances in genomic, monitoring, and phenotyping technologies. We hope that this cross-disciplinary assessment will advance the goal of understanding the pervasive effects of conspecific interactions in biology.

Using Delaunay triangulation to sample whole-specimen color from digital images

Color variation is one of the most obvious examples of variation in nature, but biologically meaningful quantification and interpretation of variation in color and complex patterns are challenging. Many current methods for assessing variation in color patterns classify color patterns using categorical measures and provide aggregate measures that ignore spatial pattern, or both, losing potentially important aspects of color pattern.Here, we present Colormesh, a novel method for analyzing complex color patterns that offers unique capabilities. Our approach is based on unsupervised color quantification combined with geometric morphometrics to identify regions of putative spatial homology across samples, from histology sections to whole organisms. Colormesh quantifies color at individual sampling points across the whole sample.We demonstrate the utility of Colormesh using digital images of Trinidadian guppies (Poecilia reticulata), for which the evolution of color has been frequently studied. Guppies have repeatedly evolved in response to ecological differences between up- and downstream locations in Trinidadian rivers, resulting in extensive parallel evolution of many phenotypes. Previous studies have, for example, compared the area and quantity of discrete color (e.g., area of orange, number of black spots) between these up- and downstream locations neglecting spatial placement of these areas. Using the Colormesh pipeline, we show that patterns of whole-animal color variation do not match expectations suggested by previous work.Colormesh can be deployed to address a much wider range of questions about color pattern variation than previous approaches. Colormesh is thus especially suited for analyses that seek to identify the biologically important aspects of color pattern when there are multiple competing hypotheses or even no a priori hypotheses at all.

Can You Trust Who You See? The Evolution of Socially Cued Anticipatory Plasticity

AbstractThe social environment can affect development and fitness. However, we do not know how selection acts on individuals that cue developmental pathways using features of the social environment. Socially cued anticipatory plasticity (SCAP) is a hypothetical strategy whereby juveniles use social cues to alter development to match their adult phenotype to the social environment that they expect to encounter. While intuitively appealing, the evolution of such plasticity is a puzzle, because the cue changes when individuals use it. Can socially cued plasticity evolve when such a feedback occurs? We use individual-based simulations to model evolution of SCAP in an environment that fluctuates between favoring each of two discrete phenotypes. We found that socially cued plasticity evolved, but only when strong selection acted on survival rather than on fecundity differences between adult phenotypes. In this case, the social cue reliably predicted which phenotype would be favored on maturation. Surprisingly, costs to plasticity increased the range of conditions under which it was adaptive. In the absence of costs, evolution led to a state where SCAP individuals could not effectively respond to environmental changes. Costs to plasticity lowered the proportion of the population that used SCAP, which in turn increased the reliability of the social cue and allowed individuals that used socially cued plasticity to switch between the favored phenotypes more consistently. Our results suggest that the evolution of adaptive plasticity in response to social cues may represent a larger class of problems in which evolution is hard to predict because of feedbacks among critical processes.

Nonparallel transcriptional divergence during parallel adaptation

How underlying mechanisms bias evolution toward predictable outcomes remains an area of active debate. In this study, we leveraged phenotypic plasticity and parallel adaptation across independent lineages of Trinidadian guppies (Poecilia reticulata) to assess the predictability of gene expression evolution during parallel adaptation. Trinidadian guppies have repeatedly and independently adapted to high- and low-predation environments in the wild. We combined this natural experiment with a laboratory breeding design to attribute transcriptional variation to the genetic influences of population of origin and developmental plasticity in response to rearing with or without predators. We observed substantial gene expression plasticity, as well as the evolution of expression plasticity itself, across populations. Genes exhibiting expression plasticity within populations were more likely to also differ in expression between populations, with the direction of population differences more likely to be opposite those of plasticity. While we found more overlap than expected by chance in genes differentially expressed between high- and low-predation populations from distinct evolutionary lineages, the majority of differentially expressed genes were not shared between lineages. Our data suggest alternative transcriptional configurations associated with shared phenotypes, highlighting a role for transcriptional flexibility in the parallel phenotypic evolution of a species known for rapid adaptation.

Sex differences in the plasticity of life history in response to social environment

Predicting how social environment affects life history variation is critical to understanding if, and when, selection favors alternative life history development, especially in systems in which social interactions change over time or space. Although sexual selection theory predicts that males and females should respond differently to variation in the social environment, few studies have examined the responses of both male and female phenotypes to the same gradient of social environment. In this study, we used a livebearing fish to determine how males and females altered their life histories in response to variation in the social environment during development. We found that both males and females delayed maturity and attained larger sizes when their social environment included adults, in contrast to developing in juvenile-only environments. The magnitude of this effect differed substantially between the sexes. The common pattern of response in the sexes suggested that life history trade-offs, rather than sexual selection, is responsible for these changes in life history expression. These effects make the relationship between genotype and phenotype depend strongly on the environment experienced by each individual. These results indicate that social environment is an important driver of life history variation in sailfin mollies and can be at least as important as abiotic effects.

Paternal exposure to a common pharmaceutical (Ritalin) has transgenerational effects on the behaviour of Trinidadian guppies

Evidence is emerging that paternal effects, the nongenetic influence of fathers on their offspring, can be transgenerational, spanning several generations. Methylphenidate hydrochloride (MPH; e.g. Ritalin) is a dopaminergic drug that is highly prescribed to adolescent males for the treatment of Attention-deficit/hyperactivity disorder. It has been suggested that MPH could cause transgenerational effects because MPH can affect the male germline in rodents and because paternal effects have been observed in individuals taking similar drugs (e.g. cocaine). Despite these concerns, the transgenerational effects of paternal MPH exposure are unknown. Therefore, we exposed male and female Trinidadian guppies (Poecilia reticulata) to a low, chronic dose of MPH and observed that MPH affected the anxiety/exploratory behaviour of males, but not females. Because of this male-specific effect, we investigated the transgenerational effects of MPH through the paternal line. We observed behavioural effects of paternal MPH exposure on offspring and great-grandoffspring that were not directly administered the drug, making this the first study to demonstrate that paternal MPH exposure can affect descendants. These effects were not due to differential mortality or fecundity between control and MPH lines. These results highlight the transgenerational potential of MPH.

Mating Preference for Novel Phenotypes Can Be Explained by General Neophilia in Female Guppies

AbstractUnderstanding how genetic variation is maintained in ecologically important traits is a fundamental question in evolutionary biology. Male Trinidadian guppies (Poecilia reticulata) exhibit extreme genetic diversity in color patterns within populations, which is believed to be promoted by a female mating preference for rare or novel patterns. However, the origins of this preference remain unclear. Here, we test the hypothesis that mating preference for novel phenotypes is a by-product of general neophilia that evolved in response to selection in nonmating contexts. We measured among-female variation in preference for eight different, novel stimuli that spanned four ecological contexts: mate choice, exploration, foraging, and social (but nonsexual) interactions. Females exhibited preference for novelty in six out of eight tests. Individual variation in preference for novelty was positively correlated among all eight types of stimuli. Furthermore, factor analysis revealed a single axis of general neophilia that accounts for 61% of individual variation in preference for novel color patterns. The single-factor structure of neophilia suggests that interest in novelty is governed primarily by shared processes that transcend context. Because neophilia likely has a sizable heritable component, our results provide evidence that mating preference for novel phenotypes may be a nonadaptive by-product of natural selection on neophilia.

Habituation underpins preference for mates with novel phenotypes in the guppy

Populations harbour enormous genetic diversity in ecologically important traits. Understanding the processes that maintain this variation is a long-standing challenge in evolutionary biology. Recent evidence indicates that a mating preference for novel sexual signals can be a powerful force maintaining genetic diversity. However, the proximate underpinnings of this preference, and its generality, remain unclear. Here, we test the hypothesis that preference for novel sexual signals is underpinned by habituation, a nearly ubiquitous form of learning whereby individuals become less responsive to repetitive stimuli. We use the Trinidadian guppy ( Poecilia reticulata), in which male colour patterns are diverse yet heritable. We show that repeated exposure to males with a given colour pattern reduces female interest in males with that pattern, and that interest recovers following brief isolation. These results fulfil two core criteria of habituation: responsiveness decline and spontaneous recovery. To distinguish habituation from sensory adaptation and fatigue, we also demonstrate stimulus specificity and dishabituation. These results provide the first evidence that habituation causes a preference for novel sexual signals, addressing the mechanistic underpinnings of this mating preference. Given the pervasiveness of habituation among taxa and sensory contexts, our findings suggest that preference for novelty may play an underappreciated role in mate choice and the maintenance of genetic variation.

Sources of elevated heavy metal concentrations in sediments and benthic marine invertebrates of the western Antarctic Peninsula

Antarctica is one of the least anthropogenically-impacted areas of the world. Metal sources to the marine environment include localised activities of research stations and glacial meltwater containing metals of lithogenic origin. In this study, concentrations of nine metals (Cd, Co, Cr, Cu, Fe, Mn, Ni, Pb, Zn) were examined in three species of benthic invertebrates collected from four locations near Rothera Research Station on the western Antarctic Peninsula: Laternula elliptica (mudclam, filter feeder), Nacella concinna (limpet, grazer) and Odontaster validus (seastar, predator and scavenger). In addition, metals were evaluated in sediments at the same locations. Metal concentrations in different body tissues of invertebrates were equivalent to values recorded in industrialized non-polar sites and were attributed to natural sources including sediment input resulting from glacial erosion of local granodioritic rocks. Anthropogenic activities at Rothera Research Station appeared to have some impact on metal concentrations in the sampled invertebrates, with concentrations of several metals higher in L. elliptica near the runway and aircraft activities, but this was not a trend that was detected in the other species. Sediment analysis from two sites near the station showed lower metal concentrations than the control site 5 km distant and was attributed to differences in bedrock metal content. Differences in metal concentrations between organisms were attributed to feeding mechanisms and habitat, as well as depuration routes. L. elliptica kidneys showed significantly higher concentrations of eight metals, with some an order of magnitude greater than other organs, and the internal structure of O. validus had significantly higher Ni. This study supports previous assessments of N. concinna and L. elliptica as good biomonitors of metal concentrations and suggests O. validus as an additional biomonitor for use in future Antarctic metal monitoring programs.

Consistent female preference for rare and unfamiliar male color patterns in wild guppy populations

How genetic variation is maintained in ecologically important traits is a central question in evolutionary biology. Male Trinidadian guppies, Poecilia reticulata, exhibit high genetic diversity in color patterns within populations, and field and laboratory studies implicate negative frequency-dependent selection in maintaining this variation. However, behavioral and ecological processes that mediate this selection in natural populations are poorly understood. We evaluated female mate preference in 11 natural guppy populations, including paired populations from high- and low-predation habitats, to determine if this behavior is responsible for negative frequency-dependent selection and to evaluate its prevalence in nature. Females directed significantly more attention to males with rare and unfamiliar color patterns than to males with common patterns. Female attention also increased with the area of male orange coloration, but this preference was independent of the preference for rare and unfamiliar patterns. We also found an overall effect of predation regime; females from high-predation populations directed more attention toward males than those from low-predation populations. Again, however, the habitat-linked preference was statistically independent from the preference for rare and unfamiliar patterns. Because previous research indicates that female attention to males predicts male mating success, we conclude that the prevalence of female preference for males with rare and unfamiliar color patterns across many natural populations supports the hypothesis that female preference is an important process underlying the maintenance of high genetic variation in guppy color patterns.

Pervasive Linked Selection and Intermediate-Frequency Alleles Are Implicated in an Evolve-and-Resequencing Experiment of Drosophila simulans

We develop analytical and simulation tools for evolve-and-resequencing experiments and apply them to a new study of rapid evolution in Drosophila simulans Likelihood test statistics applied to pooled population sequencing data suggest parallel evolution of 138 SNPs across the genome. This number is reduced by orders of magnitude from previous studies (thousands or tens of thousands), owing to differences in both experimental design and statistical analysis. Whole genome simulations calibrated from Drosophila genetic data sets indicate that major features of the genome-wide response could be explained by as few as 30 loci under strong directional selection with a corresponding hitchhiking effect. Smaller effect loci are likely also responding, but are below the detection limit of the experiment. Finally, SNPs showing strong parallel evolution in the experiment are intermediate in frequency in the natural population (usually 30-70%) indicative of balancing selection in nature. These loci also exhibit elevated differentiation among natural populations of D. simulans, suggesting environmental heterogeneity as a potential balancing mechanism.

Why does the magnitude of genotype-by-environment interaction vary?

Genotype-by-environment interaction (G × E), that is, genetic variation in phenotypic plasticity, is a central concept in ecology and evolutionary biology. G×E has wide-ranging implications for trait development and for understanding how organisms will respond to environmental change. Although G × E has been extensively documented, its presence and magnitude vary dramatically across populations and traits. Despite this, we still know little about why G × E is so evident in some traits and populations, but minimal or absent in others. To encourage synthetic research in this area, we review diverse hypotheses for the underlying biological causes of variation in G × E. We extract common themes from these hypotheses to develop a more synthetic understanding of variation in G × E and suggest some important next steps.

Advancing behavioural genomics by considering timescale

Animal behavioural traits often covary with gene expression, pointing towards a genomic constraint on organismal responses to environmental cues. This pattern highlights a gap in our understanding of the time course of environmentally responsive gene expression, and moreover, how these dynamics are regulated. Advances in behavioural genomics explore how gene expression dynamics are correlated with behavioural traits that range from stable to highly labile. We consider the idea that certain genomic regulatory mechanisms may predict the timescale of an environmental effect on behaviour. This temporally minded approach could inform both organismal and evolutionary questions ranging from the remediation of early life social trauma to understanding the evolution of trait plasticity.

Pleiotropy, constraint, and modularity in the evolution of life histories: insights from genomic analyses

Multicellular organisms display an enormous range of life history (LH) strategies and present an evolutionary conundrum; despite strong natural selection, LH traits are characterized by high levels of genetic variation. To understand the evolution of life histories and maintenance of this variation, the specific phenotypic effects of segregating alleles and the genetic networks in which they act need to be elucidated. In particular, the extent to which LH evolution is constrained by the pleiotropy of alleles contributing to LH variation is generally unknown. Here, we review recent empirical results that shed light on this question, with an emphasis on studies employing genomic analyses. While genome-scale analyses are increasingly practical and affordable, they face limitations of genetic resolution and statistical power. We describe new research approaches that we believe can produce new insights and evaluate their promise and applicability to different kinds of organisms. Two approaches seem particularly promising: experiments that manipulate selection in multiple dimensions and measure phenotypic and genomic response and analytical approaches that take into account genome-wide associations between markers and phenotypes, rather than applying a traditional marker-by-marker approach.

Stimulation of the Drosophila immune system alters genome-wide nucleosome occupancy

In eukaryotes, nucleosomes participate in all DNA-templated events by regulating access to the underlying DNA sequence. However, nucleosome dynamics during a genome response have not been well characterized [1,2]. We stimulated Drosophila S2 cells with heat-killed Gram-negative bacteria Salmonella typhimurium, and mapped genome-wide nucleosome occupancy at high temporal resolution by MNase-seq using Illumina HiSeq 2500. We show widespread nucleosome occupancy change in S2 cells during the immune response, with the significant nucleosomal loss occurring at 4 h after stimulation. Data have been deposited to the Gene Expression Omnibus (GEO) database repository with the dataset identifier GSE64507.

Vitellogenin family gene expression does not increase Drosophila lifespan or fecundity

One of the most striking patterns in comparative biology is the negative correlation between lifespan and fecundity observed in comparisons among species. This pattern is consistent with the idea that organisms need to allocate a fixed energy budget among competing demands of growth, development, reproduction and somatic maintenance. However, exceptions to this pattern have been observed in many social insects, including ants, bees, and termites.  In honey bees ( Apismellifera), Vitellogenin ( Vg), a yolk protein precursor, has been implicated in mediating the long lifespan and high fecundity of queen bees. To determine if Vg-like proteins can regulate lifespan in insects generally, we examined the effects of expression of ApisVg and Drosophila CG31150 (a Vg-like gene recently identified as cv-d) on Drosophilamelanogaster lifespan and fecundity using the RU486-inducible GeneSwitch system. For all genotypes tested, overexpression of Vg and CG31150 decreased Drosophila lifespan and did not affect total or age-specific fecundity. We also detected an apparent effect of the GeneSwitch system itself, wherein RU486 exposure (or the GAL4 expression it induces) led to a significant increase in longevity and decrease in fecundity in our fly strains. This result is consistent with the pattern reported in a recent meta-analysis of Drosophila aging studies, where transgenic constructs of the UAS/GAL4 expression system that should have no effect (e.g. an uninduced GeneSwitch) significantly extended lifespan in some genetic backgrounds. Our results suggest that Vg-family genes are not major regulators of Drosophila life history traits, and highlight the importance of using appropriate controls in aging studies.

Phenotypic and genomic plasticity of alternative male reproductive tactics in sailfin mollies

A major goal of modern evolutionary biology is to understand the causes and consequences of phenotypic plasticity, the ability of a single genotype to produce multiple phenotypes in response to variable environments. While ecological and quantitative genetic studies have evaluated models of the evolution of adaptive plasticity, some long-standing questions about plasticity require more mechanistic approaches. Here, we address two of those questions: does plasticity facilitate adaptive evolution? And do physiological costs place limits on plasticity? We examine these questions by comparing genetically and plastically regulated behavioural variation in sailfin mollies (Poecilia latipinna), which exhibit striking variation in plasticity for male mating behaviour. In this species, some genotypes respond plastically to a change in the social environment by switching between primarily courting and primarily sneaking behaviour. In contrast, other genotypes have fixed mating strategies (either courting or sneaking) and do not display plasticity. We found that genetic and plastic variation in behaviour were accompanied by partially, but not completely overlapping changes in brain gene expression, in partial support of models that predict that plasticity can facilitate adaptive evolution. We also found that behavioural plasticity was accompanied by broader and more robust changes in brain gene expression, suggesting a substantial physiological cost to plasticity. We also observed that sneaking behaviour, but not courting, was associated with upregulation of genes involved in learning and memory, suggesting that sneaking is more cognitively demanding than courtship.

Genomic basis of aging and life-history evolution in Drosophila melanogaster

Natural diversity in aging and other life-history patterns is a hallmark of organismal variation. Related species, populations, and individuals within populations show genetically based variation in life span and other aspects of age-related performance. Population differences are especially informative because these differences can be large relative to within-population variation and because they occur in organisms with otherwise similar genomes. We used experimental evolution to produce populations divergent for life span and late-age fertility and then used deep genome sequencing to detect sequence variants with nucleotide-level resolution. Several genes and genome regions showed strong signatures of selection, and the same regions were implicated in independent comparisons, suggesting that the same alleles were selected in replicate lines. Genes related to oogenesis, immunity, and protein degradation were implicated as important modifiers of late-life performance. Expression profiling and functional annotation narrowed the list of strong candidate genes to 38, most of which are novel candidates for regulating aging. Life span and early age fecundity were negatively correlated among populations; therefore, the alleles we identified also are candidate regulators of a major life-history trade-off. More generally, we argue that hitchhiking mapping can be a powerful tool for uncovering the molecular bases of quantitative genetic variation.

Mutation and the evolution of ageing: from biometrics to system genetics

A notable success for evolutionary genetics during the past century was to generate a coherent, quantitative explanation for an apparent evolutionary paradox: the tendency for multicellular organisms to show declining fitness with age (senescence, often referred to simply as 'ageing'). This general theory is now widely accepted and explains most of the features of senescence that are observed in natural and laboratory populations, but specific instantiations of that theory have been more controversial. To date, most of the empirical tests of these models have relied on data generated from biometric experiments. Modern population genetics and genomics provide new, and probably more powerful, ways to test ideas that are still controversial more than half a century after the original theory was developed. System-genetic experiments have the potential to address both evolutionary and mechanistic questions about ageing by identifying causal loci and the genetic networks with which they interact. Both the biometrical approaches and the newer approaches are reviewed here, with an emphasis on the challenges and limitations that each method faces.

Sleep, aging, and lifespan in Drosophila

Background

Epidemiological studies in humans suggest that a decrease in daily sleep duration is associated with reduced lifespan, but this issue remains controversial. Other studies in humans also show that both sleep quantity and sleep quality decrease with age. Drosophila melanogaster is a useful model to study aging and sleep, and inheriting mutations affecting the potassium current Shaker results in flies that sleep less and have a shorter lifespan. However, whether the link between short sleep and reduced longevity exists also in wild-type flies is unknown. Similarly, it is unknown whether such a link depends on sleep amount per se, rather than on other factors such as waking activity. Also, sleep quality has been shown to decrease in old flies, but it remains unclear whether aging-related sleep fragmentation is a generalized phenomenon.

Results

We compared 3 short sleeping mutant lines (Hk¹, Hk^Y and Hk²) carrying a mutation in Hyperkinetic, which codes for the beta subunit of the Shaker channel, to wild-type siblings throughout their entire lifespan (all flies kept at 20°C). Hk¹ and Hk^Y mutants were short sleeping relative to wild-type controls from day 3 after eclosure, and Hk² flies became short sleepers about two weeks later. All 3 Hk mutant lines had reduced lifespan relative to wild-type flies. Total sleep time showed a trend to increase in all lines with age, but the effect was most pronounced in Hk¹ and Hk^Y flies. In both mutant and wild-type lines sleep quality did not decay with age, but the strong preference for sleep at night declined starting in "middle age". Using Cox regression analysis we found that in Hk¹ and Hk^Y mutants and their control lines there was a negative relationship between total sleep amount during the first 2 and 4 weeks of age and hazard (individual risk of death), while no association was found in Hk² flies and their wild-type controls. Hk¹ and Hk^Y mutants and their control lines also showed an association between total daily wake activity over the first 2 and 4 weeks of age and hazard. However, when both sleep duration and wake activity were used in the same regression, the effects of activity were much reduced, while most of the sleep effects remained significant. Finally, Hk¹ flies and wild-type siblings were also tested at 25°C, and results were similar to those at 20°C. Namely, Hk¹ mutants were short sleeping, hyperactive, and short lived relative to controls, and sleep quality in both groups did not decrease with age.

Conclusions

Different Hk mutations affect the sleep phenotype, and do so in an age-dependent manner. In 4 of the 6 lines tested sleep associates significantly with lifespan variation even after any effect of activity is removed, but activity does not associate significantly with lifespan after the effects of sleep are removed. Thus, in addition to environmental factors and genetic background, sleep may also affect longevity. Sleep quality does not necessarily decay as flies age, suggesting that aging-related sleep fragmentation may also depend on many factors, including genetic background and rearing conditions.

A genomewide assessment of inbreeding depression: gene number, function, and mode of action

Although the genetic basis of inbreeding depression is still being debated, most fitness effects are thought to be the result of increased homozygosity for recessive or partially recessive deleterious alleles rather than the loss of overdominant genes. It is unknown how many loci are associated with inbreeding depression, the genes or gene pathways involved, or their mode of action. To uncover genes associated with variation in fitness following inbreeding, we generated a set of inbred lines of Drosophila melanogaster for which only the third chromosome varied among lines and measured male competitive reproductive success among these lines to estimate inbreeding depression. Male competitive reproductive success for different lines validated our prediction that equally inbred lines show variation in inbreeding depression. To begin to assess the molecular basis of inbreeding depression for male competitive reproductive success, we detected variation in whole-genome gene expression across these inbred lines with commercially available high-density oligonucleotide microarrays. A total of 567 genes were differentially expressed among these inbred lines, indicating that inbreeding directly or indirectly affects a large number of genes: genes that are disproportionately involved in metabolism, stress and defense responses. Subsequently, we generated a set of outbred lines by crossing the highest inbreeding depression lines to each other and contrasted gene expression between parental inbred lines and F(1) hybrids with transcript abundance as a quantitative phenotype to determine the mode of action of the genes associated with inbreeding depression. Although our results indicated that approximately 75% of all genes involved in inbreeding depression were additive, partially additive, or dominant, about 25% of all genes expressed patterns of overdominance. These results should be viewed with caution given that they may be confounded by issues of statistical inference or associative overdominance.

Age, but not experience, affects courtship gene expression in male Drosophila melanogaster

Mutation screens in model organisms have helped identify the foundation of many fundamental organismal phenotypes. An emerging question in evolutionary and behavioral biology is the extent to which these “developmental” genes contribute to the subtle individual variation that characterizes natural populations. A related question is whether individual differences arise from static differences in gene expression that arose during previous life stages, or whether they are due to dynamic regulation of expression during the life stage under investigation. Here, we address these questions using genes that have been discovered to control the development of normal courtship behavior in male Drosophila melanogaster. We examined whether these genes have static or dynamic expression in the heads of adult male flies of different ages and with different levels of social experience. We found that 16 genes of the 25 genes examined were statically expressed, and 9 genes were dynamically expressed with changes related to adult age. No genes exhibited rapid dynamic expression changes due to social experience or age*experience interaction. We therefore conclude that a majority of fly “courtship” genes are statically expressed, while a minority are regulated in adults with respect to age, but not with respect to relevant social experience. These results are consistent with those from a recent microarray analysis that found none of the canonical courtship genes changed expression in male flies after brief exposure to females.

Evolution and mechanisms of long life and high fertility in queen honey bees

Honey bees (Apis mellifera) are eusocial insects that exhibit striking caste-specific differences in longevity. Queen honey bees live on average 1-2 years whereas workers live on average 15-38 days in the summer and 150-200 days in the winter. Previous studies of senescence in the honey bee have focused on establishing the importance of extrinsic mortality factors (predation, weather) and behavior (nursing and foraging) in worker bee longevity. However, few studies have tried to elucidate the mechanisms that allow queen honey bees to achieve their long lifespan without sacrificing fecundity. Here, we review both types of studies and emphasize the importance of understanding both proximate and ultimate causes of the unusual life history of honey bee queens.

Natural genetic variation in complex mating behaviors of male Drosophila melanogaster

Mating behavior, including courtship and copulation, is a main component of male fitness, especially in species with no parental care. Variation in this behavior can thus be a target for mate choice and sexual selection, and can lead to evolution. The fruit fly, Drosophila melanogaster, has well-documented complex male courtship comprised of a sequence behaviors, and is an ideal model for behavior-genetic analysis. In order to evaluate genetic differences in the temporal pattern of mating behavior, we developed a high-throughput method that allows us to document the progression of male courtship and copulation using an ordinal scale (male mating progression scale, MMP). Using this method, we document natural genetic variation in the temporal pattern of behavior that was not detected using other metrics. This method was robust enough to detect genetic variation in this trait for males placed with both virgin and mated female targets.

Senescence in the worker honey bee Apis Mellifera

Honey bees are social insects that exhibit striking caste-specific differences in longevity. Queen honey bees live on average 1-2 years, whereas workers live 2-6 weeks in the summer and about 20 weeks in the winter. It is not clear whether queen-worker differences in longevity are due to intrinsic physiological differences in the rate of senescence, to differential exposure to extrinsic factors such as predation and adverse environmental conditions, or both. To determine if the relatively short lifespan of worker bees involves senescence, we measured age-specific resistance to three different physiological stressors (starvation, thermal, and oxidative stress) while eliminating age-related differences in foraging activity and minimizing age-related differences in energy expenditure. Despite these manipulations, older worker bees were still significantly less resistant to all three stressors than were younger bees. These results indicate that the regulation of worker bee lifespan involves senescence, in addition to extrinsic factors.

Age specificity of inbreeding load in Drosophila melanogaster and implications for the evolution of late-life mortality plateaus

Current evolutionary theories explain the origin of aging as a byproduct of the decline in the force of natural selection with age. These theories seem inconsistent with the well-documented occurrence of late-life mortality plateaus, since under traditional evolutionary models mortality rates should increase monotonically after sexual maturity. However, the equilibrium frequencies of deleterious alleles affecting late life are lower than predicted under traditional models, and thus evolutionary models can accommodate mortality plateaus if deleterious alleles are allowed to have effects spanning a range of neighboring age classes. Here we test the degree of age specificity of segregating alleles affecting fitness in Drosophila melanogaster. We assessed age specificity by measuring the homozygous fitness effects of segregating alleles across the adult life span and calculated genetic correlations of these effects across age classes. For both males and females, we found that allelic effects are age specific with effects extending over 1-2 weeks across all age classes, consistent with modified mutation-accumulation theory. These results indicate that a modified mutation-accumulation theory can both explain the origin of senescence and predict late-life mortality plateaus.

Vitellogenin, juvenile hormone, insulin signaling, and queen honey bee longevity

In most animals, longevity is achieved at the expense of fertility, but queen honey bees do not show this tradeoff. Queens are both long-lived and fertile, whereas workers, derived from the same genome, are both relatively short-lived and normally sterile. It has been suggested, on the basis of results from workers, that vitellogenin (Vg), best known as a yolk protein synthesized in the abdominal fat body, acts as an antioxidant to promote longevity in queen bees. We explored this hypothesis, as well as related roles of insulin-IGF-1 signaling and juvenile hormone. Vg was expressed in thorax and head fat body cells in an age-dependent manner, with old queens showing much higher expression than workers. In contrast, Vg expression in worker head was much lower. Queens also were more resistant to oxidative stress than workers. These results support the hypothesis that caste-specific differences in Vg expression are involved in queen longevity. Consistent with predictions from Drosophila, old queens had lower head expression of insulin-like peptide and its putative receptors than did old workers. Juvenile hormone affected the expression of Vg and insulin-IGF-1 signaling genes in opposite directions. These results suggest that conserved and species-specific mechanisms interact to regulate queen bee longevity without sacrificing fecundity.

Frequency-dependent survival in natural guppy populations

The maintenance of genetic variation in traits under natural selection is a long-standing paradox in evolutionary biology. Of the processes capable of maintaining variation, negative frequency-dependent selection (where rare types are favoured by selection) is the most powerful, at least in theory; however, few experimental studies have confirmed that this process operates in nature. One of the most extreme, unexplained genetic polymorphisms is seen in the colour patterns of male guppies (Poecilia reticulata). Here we manipulated the frequencies of males with different colour patterns in three natural populations to estimate survival rates, and found that rare phenotypes had a highly significant survival advantage compared to common phenotypes. Evidence from humans and other species implicates frequency-dependent survival in the maintenance of molecular, morphological and health-related polymorphisms. As a controlled manipulation in nature, this study provides unequivocal support for frequency-dependent survival--an evolutionary process capable of maintaining extreme polymorphism.

Quantitative trait locus analysis of male mating success and sperm competition in Drosophila melanogaster

Much of sexual selection theory depends on assumptions about the genetic basis of variation in male mating success and sperm competitive ability. Despite intense interest in this topic, few genes have been identified that contribute to variation in these traits. Here we report the results of quantitative trait locus (QTL) analyses of mating success of male Drosophila melanogaster when exposed to virgin females, remating success of males with previously mated females, and both defense and offense components of sperm competition. We found two to four significant QTLs for remating success, but no QTLs for mating success, even though mating success was more genetically variable than remating success in the recombinant inbred lines used in this study. By combining these results with data from previous gene-expression experiments, we were able to identify three X-linked candidate genes for variation in remating ability. For two of these genes, QTL and expression data were completely concordant with respect to directionality of effects: high mating success was associated with high levels of gene expression and with beneficial QTL effects on the trait. We found equivocal evidence for genetic variation in sperm offense and defense in the recombinant inbred lines, and we did not find any significant QTLs for either sperm competition trait.

Segregating variation in the transcriptome: cis regulation and additivity of effects

Properties of genes underlying variation in complex traits are largely unknown, especially for variation that segregates within populations. Here, we evaluate allelic effects, cis and trans regulation, and dominance patterns of transcripts that are genetically variable in a natural population of Drosophila melanogaster. Our results indicate that genetic variation due to the third chromosome causes mainly additive and nearly additive effects on gene expression, that cis and trans effects on gene expression are numerically about equal, and that cis effects account for more genetic variation than do trans effects. We also evaluated patterns of variation in different functional categories and determined that genes involved in metabolic processes are overrepresented among variable transcripts, but those involved in development, transcription regulation, and signal transduction are underrepresented. However, transcripts for proteins known to be involved in protein-protein interactions are proportionally represented among variable transcripts.

Gene expression patterns associated with queen honey bee longevity

The oxidative stress theory of aging proposes that accumulation of oxidative damage is the main proximate cause of aging and that lifespan is determined by the rate at which this damage occurs. Two predictions from this theory are that long-lived organisms produce fewer ROS or have increased antioxidant production. Based in these predictions, molecular mechanisms to promote longevity could include either changes in the regulation of mitochondrial genes that affect ROS production or elevated expression of antioxidant genes. We explored these possibilities in the honey bee, a good model for the study of aging because it has a caste system in which the same genome produces both a long-lived queen and a short-lived worker. We measured mRNA levels for genes encoding eight of the most prominent antioxidant enzymes and five mitochondrial proteins involved in respiration. The expression of antioxidant genes generally decreased with age in queens, but not in workers. Expression of most mitochondrial genes, in particular CytC, was higher in young queens, but these genes showed a faster age-related decline relative to workers. One exception to this trend was COX-I in thorax. This resulted in higher COX-I/CytC ratios in old queens compared to old workers, which suggests caste-specific differences in mitochondrial function that might be related to the caste-specific differences in longevity. Queen honey bee longevity appears to have evolved via mechanisms other than increased antioxidant gene expression.