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Data from: The relation between the neutrality index for mitochondrial genes and the distribution of mutational effects on fitness
We explore factors affecting patterns of polymorphism and divergence (as captured by the neutrality index) at mammalian mitochondrial loci. To do this, we develop a population genetic model that incorporates a fraction of neutral amino acid sites, mutational bias, and a probability distribution of selection coefficients against new nonsynonymous mutations. We confirm, by reanalyzing publicly available data sets, that the mitochondrial cyt-b gene shows a broad range of neutrality indices across mammalian taxa, and explore the biological factors that can explain this observation. We find that observed patterns of differences in the neutrality index, polymorphism and divergence are not caused by differences in mutational bias. They can, however, be explained by a combination of a small fraction of neutral amino acid sites, weak selection acting on most amino acid mutations, and differences in effective population size among taxa.
Data from: Covariance among premating, postcopulatory and viability fitness components in Drosophila melanogaster and their influence on paternity measurement
In polyandrous mating systems, male fitness depends on success in premating, postcopulatory, and offspring viability episodes of selection. We tracked male success across all of these episodes simultaneously, using transgenic Drosophila melanogaster with ubiquitously expressed green fluorescent protein (i.e., GFP) in a series of competitive and non-competitive matings. This approach permitted us to track paternity-specific viability over all life stages and to distinguish true competitive fertilization success from differential early offspring viability. Relationships between episodes of selection were generally not present when paternity was measured in eggs, however positive correlations between sperm competitive success and offspring viability became significant when paternity was measured in adult offspring. Additionally, we found a significant male × female interaction on hatching success and a lack of repeatability of offspring viability across a focal male's matings, which may underly the limited number of correlations found between episodes of selection.
Data from: Linking system-wide impacts of RNA polymerase mutations to the fitness cost of rifampin resistance in Pseudomonas aeruginosa
Fitness costs play a key role in the evolutionary dynamics of antibiotic resistance in bacteria by generating selection against resistance in the absence of antibiotics. Although the genetic basis of antibiotic resistance is well understood, the precise molecular mechanisms linking the genetic basis of resistance to its fitness cost remain poorly characterized. Here, we examine how the system-wide impacts of mutations in the RNA polymerase (RNAP) gene rpoB shape the fitness cost of rifampin resistance in Pseudomonas aeruginosa. Rifampin resistance mutations reduce transcriptional efficiency, and this explains 76% of the variation in fitness among rpoB mutants. The pleiotropic consequence of rpoB mutations is that mutants show altered relative transcript levels of essential genes. We find no evidence that global transcriptional responses have an impact on the fitness cost of rifampin resistance as revealed by transcriptome sequencing (RNA-Seq). Global changes in the transcriptional profiles of rpoB mutants compared to the transcriptional profile of the rifampin-sensitive ancestral strain are subtle, demonstrating that the transcriptional regulatory network of P. aeruginosa is robust to the decreased transcriptional efficiency associated with rpoB mutations. On a smaller scale, we find that rifampin resistance mutations increase the expression of RNAP due to decreased termination at an attenuator upstream from rpoB, and we argue that this helps to minimize the cost of rifampin resistance by buffering against reduced RNAP activity. In summary, our study shows that it is possible to dissect the molecular mechanisms underpinning variation in the cost of rifampin resistance and highlights the importance of genome-wide buffering of relative transcript levels in providing robustness against resistance mutations. IMPORTANCE Antibiotic resistance mutations carry fitness costs. Relative to the characteristics of their antibiotic-sensitive ancestors, resistant mutants show reduced growth rates and competitive abilities. Fitness cost plays an important role in the evolution of antibiotic resistance in the absence of antibiotics; however, the molecular mechanisms underlying these fitness costs is not well understood. We applied a systems-level approach to dissect the molecular underpinnings of the fitness costs associated with rifampin resistance in P. aeruginosa and showed that most of the variation in fitness cost can be explained by the direct effect of resistance mutations on the enzymatic activity of the mutated gene. Pleiotropic changes in transcriptional profiles are subtle at a genome-wide scale, suggesting that the gene regulatory network of P. aeruginosa is robust in the face of the direct effects of resistance mutations.
Data from: On the (un)predictability of a large intragenic fitness landscape
The study of fitness landscapes, which aims at mapping genotypes to fitness, is receiving ever-increasing attention. Novel experimental approaches combined with next-generation sequencing (NGS) methods enable accurate and extensive studies of the fitness effects of mutations, allowing us to test theoretical predictions and improve our understanding of the shape of the true underlying fitness landscape and its implications for the predictability and repeatability of evolution. Here, we present a uniquely large multiallelic fitness landscape comprising 640 engineered mutants that represent all possible combinations of 13 amino acid-changing mutations at 6 sites in the heat-shock protein Hsp90 in Saccharomyces cerevisiae under elevated salinity. Despite a prevalent pattern of negative epistasis in the landscape, we find that the global fitness peak is reached via four positively epistatic mutations. Combining traditional and extending recently proposed theoretical and statistical approaches, we quantify features of the global multiallelic fitness landscape. Using subsets of the data, we demonstrate that extrapolation beyond a known part of the landscape is difficult owing to both local ruggedness and amino acid-specific epistatic hotspots and that inference is additionally confounded by the nonrandom choice of mutations for experimental fitness landscapes.
Data from: Dual tree complex wavelet transform based signal denoising method exploiting neighbourhood dependencies and goodness of fit test
A novel signal denoising method is proposed whereby goodness of fit (GOF) test in combination with a majority classifications based neighbourhood filtering is employed on complex wavelet coefficients obtained by applying dual tree complex wavelet transform (DTCWT) on a noisy signal. The DT-CWT has proven to be a better tool for signal denoising as compared to the conventional discrete wavelet transform (DWT) owing to its approximate translation invariance. The proposed framework exploits statistical neighbourhood dependencies by performing the GOF test locally on the DT-CWT coefficients for their preliminary classification/detection as signal or noise. Next, a deterministic neighbourhood filtering approach based on majority noise classifications is employed to detect false classification of signal coefficients as noise (via the GOF test) which are subsequently restored. The proposed method shows competitive performance against the state of the art in signal denoising.
Data from: Lifetime fitness in wild baboons: tradeoffs and individual heterogeneity in quality
Understanding the evolution of life histories requires information on how life histories vary among individuals, and how such variation predicts individual fitness. Using complete life histories for females in a well-studied population of wild baboons, we tested two non-exclusive hypotheses about the relationships among survival, reproduction, and fitness: the quality hypothesis, which predicts positive correlations between life history traits, mediated by variation in resource acquisition, and the tradeoff hypothesis, which predicts negative correlations between life history traits, mediated by tradeoffs in resource allocation. In support of the quality hypothesis, we found that females with higher rates of offspring survival were themselves better at surviving. Further, after statistically controlling for variation in female quality, we found evidence for two types of tradeoffs: females who produced surviving offspring at a slower rate had longer lifespans than those who produced surviving offspring at a faster rate, and females who produced surviving offspring at a slower rate had a higher overall proportion of offspring survive infancy than females who produced surviving offspring at a faster rate. Importantly, these tradeoffs were evident even when accounting for: (i) the influence of offspring survival on maternal birth rate, (ii) the dependence of offspring survival on maternal survival, and (iii) potential age-related changes in birth rate and/or offspring survival. Our results shed light on why tradeoffs are evident in some populations, while variation in individual quality masks tradeoffs in others.
Data from: The fitness effects of a pale mutant in the aposematic seed bug Lygaeus simulans indicate pleiotropy between warning coloration and life history
Conspicuous warning colours that signal chemical or other defences are common in the natural world. For instance, such aposematic warning patterns of red-and-black or yellow-and-black are common among insect taxa, particularly in the order Hemiptera, often forming the basis of Batesian and/or Müllerian mimicry rings. In addition, it has been repeatedly noted that colour polymorphisms or mutants that influence pigmentation can show pleiotropy with other behavioural, physiological or life-history traits. Here we describe a pale mutant of the seed bug Lygaeus simulans that appeared in our lab population in 2012, which differs in colour to the wild-type bugs. Through multigenerational experimental crosses between wild-type and pale mutant L. simulans, we first show that the pale phenotype segregates as a single Mendelian locus, with the pale allele being recessive to the wild-type. Next, we show (1) that there is a large heterozygous advantage in terms of fecundity, (2) that pale females suffer reduced longevity, and (3) that pale males have increased body length compared to wild-type homozygotes. Our data therefore suggest that the colour locus is pleiotropic with a number of life-history traits, opening the door for a more complete genetic analysis of aposematic colouration in this species. In addition, this phenotype will be useful as a visible genetic marker, providing a tool for investigating sperm competition and other post-copulatory drivers of sexual selection in this species.
Data from: Host use dynamics in a heterogeneous fitness landscape generates oscillations in host range and diversification
Colonization of novel hosts is thought to play an important role in parasite diversification, yet little consensus has been achieved about the macroevolutionary consequences of changes in host use. Here we offer a mechanistic basis for the origins of parasite diversity by simulating lineages evolved in silico. We describe an individual-based model in which (i) parasites undergo sexual reproduction limited by genetic proximity, (ii) hosts are uniformly distributed along a one-dimensional resource gradient, and (iii) host use is determined by the interaction between the phenotype of the parasite and a heterogeneous fitness landscape. We found two main effects of host use on the evolution of a parasite lineage. First, the colonization of a novel host allowed parasites to explore new areas of the resource space, increasing phenotypic and genotypic variation. Second, hosts produced heterogeneity in the parasite fitness landscape, which led to reproductive isolation and therefore, speciation. As a validation of the model, we analyzed empirical data from Nymphalidae butterflies and their host plants. We then assessed the number of hosts used by parasite lineages and the diversity of resources they encompass. In both simulated and empirical systems, host diversity emerged as the main predictor of parasite species richness.
Data from: Fitness decline in spontaneous mutation accumulation lines of Caenorhabditis elegans with varying effective population sizes
The rate and fitness effects of new mutations have been investigated by mutation accumulation (MA) experiments in which organisms are maintained at a constant minimal population size to facilitate the accumulation of mutations with minimal efficacy of selection. We evolved 35 MA lines of Caenorhabditis elegans in parallel for 409 generations at three population sizes (N = 1, 10, and 100), representing the first spontaneous long-term MA experiment at varying population sizes with corresponding differences in the efficacy of selection. Productivity and survivorship in the N = 1 lines declined by 44% and 12%, respectively. The average effects of deleterious mutations in N = 1 lines are estimated to be 16.4% for productivity and 11.8% for survivorship. Larger populations (N = 10 and 100) did not suffer a significant decline in fitness traits despite a lengthy and sustained regime of consecutive bottlenecks exceeding 400 generations. Together, these results suggest that fitness decline in very small populations is dominated by mutations with large deleterious effects. It is possible that the MA lines at larger population sizes contain a load of cryptic deleterious mutations of small to moderate effects that would be revealed in more challenging environments.
Data from: Fitness consequences of altered feeding behavior in immune-challenged mosquitoes
Background: Malaria-infected mosquitoes have been reported to be more likely to take a blood meal when parasites are infectious than when non-infectious. This change in feeding behavior increases the likelihood of malaria transmission, and has been considered an example of parasite manipulation of host behavior. However, immune challenge with heat-killed Escherichia coli induces the same behavior, suggesting that altered feeding behavior may be driven by adaptive responses of hosts to cope with an immune response, rather than by parasite-specific factors. Here we tested the alternative hypothesis that down-regulated feeding behavior prior to infectiousness is a mosquito adaptation that increases fitness during infection. Methods: We measured the impact of immune challenge and blood feeding on the fitness of individual mosquitoes. After an initial blood meal, Anopheles stephensi Liston mosquitoes were experimentally challenged with heat-killed E. coli at a dose known to mimic the same temporal changes in mosquito feeding behavior as active malaria infection. We then tracked daily egg production and survivorship of females maintained on blood-feeding regimes that either mimicked down-regulated feeding behaviors observed during early malaria infection, or were fed on a four-day feeding cycle typically associated with uninfected mosquitoes. Results: Restricting access to blood meals enhanced mosquito survival but lowered lifetime reproduction. Immune- challenge did not impact either fitness component. Combining fecundity and survival to estimate the population- scale intrinsic rate of increase (r), we found that, contrary to the mosquito adaptation hypothesis, mosquito fitness decreased if blood feeding was delayed following an immune challenge. Conclusions: Our data provide no support for the idea that malaria-induced suppression of blood feeding is an adaptation by mosquitoes to reduce the impact of immune challenge. Alternatively, the behavioral alterations may be neither host nor parasite adaptations, but rather a consequence of constraints imposed on feeding by activation of the mosquito immune response, i.e. non-adaptive illness-induced anorexia. Future work incorporating field conditions and different immune challenges could further clarify the effect of altered feeding on mosquito and parasite fitness.
Data from: Microbiome interactions shape host fitness
Gut bacteria can affect key aspects of host fitness, such as development, fecundity, and lifespan, while the host, in turn, shapes the gut microbiome. However, it is unclear to what extent individual species versus community interactions within the microbiome are linked to host fitness. Here, we combinatorially dissect the natural microbiome of Drosophila melanogaster and reveal that interactions between bacteria shape host fitness through life history tradeoffs. Empirically, we made germ-free flies colonized with each possible combination of the five core species of fly gut bacteria. We measured the resulting bacterial community abundances and fly fitness traits, including development, reproduction, and lifespan. The fly gut promoted bacterial diversity, which, in turn, accelerated development, reproduction, and aging: Flies that reproduced more died sooner. From these measurements, we calculated the impact of bacterial interactions on fly fitness by adapting the mathematics of genetic epistasis to the microbiome. Development and fecundity converged with higher diversity, suggesting minimal dependence on interactions. However, host lifespan and microbiome abundances were highly dependent on interactions between bacterial species. Higher-order interactions (involving three, four, and five species) occurred in 13–44% of possible cases depending on the trait, with the same interactions affecting multiple traits, a reflection of the life history tradeoff. Overall, we found these interactions were frequently context-dependent and often had the same magnitude as individual species themselves, indicating that the interactions can be as important as the individual species in gut microbiomes.
Data from: Effects of aphid parasitism on host plant fitness in an aphid-host relationship.
Aphids are serious agricultural insect pests which exploit the phloem sap of host plants and thus transmit pathogens to their hosts. However, the degree to which aphid parsitism affects the fitness of the host plants is not well understood. The aphid, Macrosiphoniella yomogicola, parasitizes the mugwort Artemisia montana in Japan. During summer most mugworts carry aphids, but most aphid colonies die out after the budding of A. montana inflorescences in late summer. A few aphid colonies survive to late autumn, at which point sexuparae appear to later lay overwintering eggs after copulation. The death of the aphid colonies seems to cause by biochemical changes in the phloem sap in the host plant coincident with the budding of inflorescences. The surviving aphid colonies may suppress the budding of inflorescences to allow persistence of their genetic line into the following year. Our investigations demonstrate that aphid parasitism did not affect host plant growth, but that it did significantly decrease the number of inflorescences and the average weight of floral buds. Our results indicate that aphid parasitism has a strong negative effect on the fitness of host plants. The manner in which the aphids suppress floral budding in their hosts is worth examining from the perspective of the evolution of aphid-plant interactions.
Data from: Direct and indirect effects of early-life environment on lifetime fitness of bighorn ewes
Cohort effects, when a common environment affects long-term performance, can have a major impact on population dynamics. Very few studies of wild animals have obtained the necessary data to study the mechanisms leading to cohort effects. We exploited 42 years of individual-based data on bighorn sheep to test for causal links between birth density, body mass, age at first reproduction, longevity, and lifetime reproductive success using path analysis. Specifically, we investigated whether the effect of early-life environment on lifetime fitness was the result of indirect effects through body mass or direct effects of early-life environment on fitness. Additionally, we evaluated whether the effects of early-life environment where dependant on the environment experienced during adulthood. Contrary to expectation, the effect on lifetime reproductive success mediated through body mass was weak compared to the effects found via a delay in age at first reproduction, reduced longevity, and the direct effect of birth density. Birth density also had an important indirect effect on lifetime reproductive success through reduced longevity, but only when adult density was high. Our results show that the potential long-term consequences of a harsh early-life environment on fitness are likely to be underestimated if investigations are limited to body mass instead of fitness at several life stages, or if the interactions between past and present environment is ignored.
Data from: Male competition fitness landscapes predict both forward and reverse speciation
Speciation is facilitated when selection generates a rugged fitness landscape such that populations occupy different peaks separated by valleys. Competition for food resources is a strong ecological force that can generate such divergent selection. However, it is unclear whether intrasexual competition over resources that provide mating opportunities can generate rugged fitness landscapes that foster speciation. Here we use highly variable male F2 hybrids of benthic and limnetic threespine sticklebacks, Gasterosteus aculeatus Linnaeus, 1758, to quantify the male competition fitness landscape. We find that disruptive sexual selection generates two fitness peaks corresponding closely to the male phenotypes of the two parental species, favouring divergence. Most surprisingly, an additional region of high fitness favours novel hybrid phenotypes that correspond to those observed in a recent case of reverse speciation after anthropogenic disturbance. Our results reveal that sexual selection through male competition plays an integral role in both forward and reverse speciation.
Data from: Environmental heterogeneity generates opposite gene-by-environment interactions for two fitness-related traits within a population
Theory predicts that environmental heterogeneity offers a potential solution to the maintenance of genetic variation within populations, but empirical evidence remains sparse. The livebearing fish Xiphophorus variatus exhibits polymorphism at a single locus, with different alleles resulting in up to five distinct melanistic "tailspot" patterns within populations. We investigated the effects of heterogeneity in two ubiquitous environmental variables (temperature and food availability) on two fitness-related traits (upper thermal limits and body condition) in two different tailspot types (wildtype and upper cut crescent). We found gene-by-environment (GxE) interactions between tailspot type and food level affecting upper thermal limits (UTL), as well as between tailspot type and thermal environment affecting body condition. Exploring mechanistic bases underlying these GxE patterns, we found no differences between tailspot types in hsp70 gene expression despite significant overall increases in expression under both thermal and food stress. Similarly, there was no difference in routine metabolic rates between the tailspot types. The reversal of relative performance of the two tailspot types under different environmental conditions revealed a mechanism by which environmental heterogeneity can balance polymorphism within populations through selection on different fitness-related traits.
Data from: Exploring variation in fitness surfaces over time or space
As the number of studies estimating selection on multiple traits has increased in recent years, fitness surfaces have become a fundamental tool for understanding multivariate selection and evolution. However, rigorous statistical comparisons of multivariate selection surfaces over time or space have been limited to parametric analyses of selection coefficients estimated using a quadratic regression model. Although parametric comparisons are useful when selection is approximately linear or quadratic in nature, they are limited when confronting the complex nature of rugged fitness surfaces. Here, I present a novel solution to comparing non-parametric fitness surfaces over time or space. Using a Tucker3 tensor decomposition, which is essentially a higher-order principal components analysis, I show how major features of fitness surfaces can be compared statistically. Combined with a bootstrap algorithm, I develop three statistical tests that identify 1) Differences in the shape of non-parametric fitness surfaces, 2) Differences in the contribution of each surface to variation in fitness across time or space, and 3) Specific areas of the surfaces (trait combinations) that vary significantly over time or space. I illustrate the tensor decomposition and statistical analyses using idealized fitness surfaces.
Data from: Nutritional geometry and fitness consequences in Drosophila suzukii, the Spotted-Wing Drosophila
Since its arrival to North America less than a decade ago, the invasive Spotted-Wing Drosophila (Drosophila suzukii) has inflicted substantial economic losses on soft fruit agriculture due to its ability to oviposit into ripening fruits. More effective management approaches for this species are needed, but little is known about the factors that influence behavioral choices made by D. suzukii when selecting hosts, or the consequences that their offspring experience when developing in different environments. Using a nutritional geometry methodology, we found that the ratio of proteins-to-carbohydrates (P:C) present in media greatly influenced adult D. suzukii behavior and subsequent offspring development. Whereas adult flies showed a strong bias in their oviposition and association behaviors toward carbohydrate-rich foods, larval survival and eclosion rate were strongly dependent on protein availability. Here, we explore the preference–performance hypothesis (PPH), in which females are predicted to oviposit on medias that provide the greatest offspring benefits, in regard to its relevance in D. suzukii behavior and consequences for management. Our results provide valuable insight into the ecology and evolution of this species that may hopefully lead to more effective management strategies.
Data from: Rates of fitness decline and rebound suggest pervasive epistasis
Unraveling the factors that determine the rate of adaptation is a major question in evolutionary biology. One key parameter is the effect of a new mutation on fitness, which invariably depends on the environment and genetic background. The fate of a mutation also depends on population size, which determines the amount of drift it will experience. Here, we manipulate both population size and genotype composition and follow adaptation of 23 distinct Escherichia coli genotypes. These have previously accumulated mutations under intense genetic drift and encompass a substantial fitness variation. A simple rule is uncovered: the net fitness change is negatively correlated with the fitness of the genotype in which new mutations appear—a signature of epistasis. We find that Fisher's geometrical model can account for the observed patterns of fitness change and infer the parameters of this model that best fit the data, using Approximate Bayesian Computation. We estimate a genomic mutation rate of 0.01 per generation for fitness altering mutations, albeit with a large confidence interval, a mean fitness effect of mutations of −0.01, and an effective number of traits nine in mutS− E. coli. This framework can be extended to confront a broader range of models with data and test different classes of fitness landscape models.
Data from: Fitness consequences of artificial selection on relative male genital size
Male genitalia often show remarkable differences among related species in size, shape and complexity. Across poeciliid fishes, the elongated fin (gonopodium) that males use to inseminate females ranges from 18 to 53% of body length. Relative genital size therefore varies greatly among species. In contrast, there is often tight within-species allometric scaling, which suggests strong selection against genital–body size combinations that deviate from a species' natural line of allometry. We tested this constraint by artificially selecting on the allometric intercept, creating lines of males with relatively longer or shorter gonopodia than occur naturally for a given body size in mosquitofish, Gambusia holbrooki. We show that relative genital length is heritable and diverged 7.6–8.9% between our up-selected and down-selected lines, with correlated changes in body shape. However, deviation from the natural line of allometry does not affect male success in assays of attractiveness, swimming performance and, crucially, reproductive success (paternity).
Compact Markov-modulated models for multiclass trace fitting
<p>This is the dataset used in the paper "Compact Markov-modulated models for multiclass trace fitting" by G. Casale, A. Sansottera, P. Cremonesi to appear in European Journal of Operational Research. Please check the README.TXT file for details on the dataset. </p>
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