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287 results for “Response to selection”
Data from: Genome scan reveals selection acting on genes linked to stress response in wild pearl millet
Uncovering genomic regions involved in adaption is a major goal in evolutionary biology. High-throughput sequencing now makes it possible to tackle this challenge in nonmodel species. Yet, despite the increasing number of methods targeted to specifically detect genomic footprints of selection, the complex demography of natural populations often causes high rates of false positive in gene discoveries. The aim of this study was to identify climate adaptations in wild pearl millet populations, Cenchrus americanus ssp. monodii. We focused on two climate gradients, one in Mali and one in Niger. We used a two-step strategy to limit false-positive outliers. First, we considered gradients as biological replicates and performed RNA sequencing of four populations at the extremities. We combined four methods—three based on differentiation among populations and one based on diversity patterns within populations—to identify outlier SNPs from a set of 87 218 high-quality SNPs. Among 11 155 contigs of pearl millet reference transcriptome, 540 exhibited selection signals as evidenced by at least one of the four methods. In a second step, we genotyped 762 samples in 11 additional populations distributed along the gradients using SNPs from the detected contigs and random SNPs as control. We further assessed selection on this large data set using a differentiation-based method and a method based on correlations with environmental variables based. Four contigs displayed consistent signatures between the four extreme and 11 additional populations, two of which were linked to abiotic and biotic stress responses.
Data from: The incidental response to uniform natural selection
When populations are exposed to novel conditions of growth they often become adapted to a similar extent, and at the same time evolve some degree of impairment in their original environment. They may also come to vary widely with respect to characters which are uncorrelated with fitness, as the result of chance genetic associations among the founders, when these are a small sample from a large and variable ancestral population. I report an experiment in which 240 replicate lines of the unicellular chlorophyte Chlamydomonas were derived from primarily photoautotrophic ancestors and cultured as heterotrophs in the dark. All adapted to the dark and were impaired in the light after several hundred generations of culture. They also displayed a wide range of colony morphologies that were uncorrelated with fitness. This incidental response to selection probably arose through random variation in the initial composition of the lines. The differences between closely related species or varieties may likewise arise, in similar circumstances, by sampling error rather than natural selection.
Data from: The response of correlated traits following cessation of fishery-induced selection
The application of evolutionary principles to the management of fisheries has gained considerable attention recently. Harvesting of fish may apply directional or disruptive selection to key life history traits and evidence for fishery-induced evolution is growing. The traits that are directly selected upon are often correlated (genetically or phenotypically) with a suite of interrelated physiological, behavioral, and morphological characters. A question that has received comparatively little attention is whether or not, after cessation of fishery-induced selection, these correlated traits revert back to previous states. Here, we empirically examine this question. In experiments with the Atlantic silverside, Menidia menidia, we applied size-selective culling for 5 generations and then maintained the lines a further 5 generations under random harvesting. We found that some traits do return to pre-harvesting levels (e.g., larval viability), some partially recover (e.g., egg volume, size at hatch), and others show no sign of change (e.g., food consumption rate, vertebral number). Such correlations among characters could, in theory, greatly accelerate or decelerate the recovery of fish populations. These results may explain why some fish stocks fail to recover after fishing pressure is relaxed.
Data from: Response to selection on cold tolerance is constrained by inbreeding
The evolutionary potential of any given population is of fundamental importance for its longer-term prospects. Modern land-use practices often result in small and isolated populations, increasing extinction risk through reduced genetic diversity caused by inbreeding or drift. Concomitant genetic erosion may further interfere with a population's evolutionary potential. In this study we investigate the consequences of inbreeding on evolutionary potential (the ability to increase cold resistance) in the tropical butterfly Bicyclus anynana. We applied artificial selection to chill-coma recovery time, starting from three levels of inbreeding (outbred control, one or two full-sib matings). Ten generations of selection produced highly divergent phenotypes, with the lines selected for increased cold tolerance showing by ca. 28% shorter recovery times after cold exposure relative to unselected controls. Correlated responses to selection in 10 life history and stress resistance traits were essentially absent. Inbred lines showed a weaker response to selection, thus indicating a reduced evolutionary potential. Inbreeding depression was still measurable in some traits after the course of selection. Traits more closely related to fitness showed a clear fitness rebound, suggesting a trait-specific impact of purging. Our findings have important implications for the longer-term survival of small populations in fragmented landscapes.
Data from: Age-dependent female responses to a male ejaculate signal alter demographic opportunities for selection
A central tenet of evolutionary explanations for ageing is that the strength of selection wanes with age. However, data on age-specific expression and benefits of sexually selected traits are lacking—particularly for traits subject to sexual conflict. We addressed this by using as a model the responses of Drosophila melanogaster females of different ages to receipt of sex peptide (SP), a seminal fluid protein transferred with sperm during mating. SP can mediate sexual conflict, benefitting males while causing fitness costs in females. Virgin and mated females of all ages showed significantly reduced receptivity in response to SP. However, only young virgin females also showed increased egg laying; hence, there was a narrow demographic window of maximal responses to SP. Males gained significant 'per mating' fitness benefits only when mating with young females. The pattern completely reversed in matings with older females, where SP transfer was costly. The overall benefits of SP transfer (hence opportunity for selection) therefore reversed with female age. The data reveal a new example of demographic variation in the strength of selection, with convergence and conflicts of interest between males and ageing females occurring over different facets of responses to a sexually antagonistic trait.
Data from: Predicting the response to simultaneous selection: genetic architecture and physiological constraints
A great deal is known about the evolutionary significance of body size and development time. They are determined by the non-linear interaction of three physiological traits: two hormonal events and growth rate. In this study we investigate how the genetic architecture of the underlying three physiological traits affects the simultaneous response to selection on the two life history traits in the hawk moth Manduca sexta. The genetic architecture suggests that when the two life history traits are both selected in the same direction (to increase or decrease) the response to selection is primarily determined by the hormonal mechanism. When the life history traits are selected in opposite directions (one to increase and one to decrease) the response to selection is primarily determined by factors that affect the growth rate. To determine how the physiological traits affect the response to selection of the life history traits, we simulated the predicted response to ten generations of selection. 83% of our predictions were supported by the simulation. The main components of this physiological framework also exist in unicellular organisms, vertebrates and plants and can thus provide a robust framework for understanding how underlying physiology can determine the simultaneous evolution of life history traits.
Data from: Application of a dense genetic map for assessment of genomic responses to selection and inbreeding in Heliothis virescens
Adaptation of pest species to laboratory conditions and selection for resistance to toxins in the laboratory are expected to cause inbreeding and genetic bottlenecks that reduce genetic variation. Heliothis virescens, a major cotton pest, has been colonized in the laboratory many times, and a few laboratory colonies have been selected for Bacillus thuringiensis (Bt) resistance. We developed 350-bp double-digest restriction-site associated DNA-sequencing (ddRAD-seq) molecular markers to examine and compare changes in genetic variation associated with laboratory adaptation, artificial selection and inbreeding in this nonmodel insect species. We found that allelic and nucleotide diversity declined dramatically in laboratory-reared H. virescens as compared with field-collected populations. The declines were primarily a result of the loss of low frequency alleles present in field-collected H. virescens. A further, albeit modest decline in genetic diversity was observed in a Bt-selected population. The greatest decline was seen in H. virescens that were sib-mated for 10 generations, in which more than 80% of loci were fixed for a single allele. To determine which regions of the genome were resistant to fixation in our sib-mated line, we generated a dense intraspecific linkage map containing three PCR-based and 659 ddRAD-seq markers. Markers that retained polymorphism were observed in small clusters spread over multiple linkage groups, but this clustering was not statistically significant. Overall, we have confirmed and extended the general expectations for reduced genetic diversity in laboratory colonies, provided tools for further genomic analyses and produced highly homozygous genomic DNA for future whole genome sequencing of H. virescens.
Data from: Recommendations for using msBayes to incorporate uncertainty in selecting an ABC model prior: a response to Oaks et al.
Prior specification is an essential component of parameter estimation and model comparison in Approximate Bayesian computation (ABC). Oaks et al. present a simulation-based power analysis of msBayes and conclude that msBayes has low power to detect genuinely random divergence times across taxa, and suggest the cause is Lindley's paradox. Although the predictions are similar, we show that their findings are more fundamentally explained by insufficient prior sampling that arises with poorly chosen wide priors that critically undersample nonsimultaneous divergence histories of high likelihood. In a reanalysis of their data on Philippine Island vertebrates, we show how this problem can be circumvented by expanding upon a previously developed procedure that accommodates uncertainty in prior selection using Bayesian model averaging. When these procedures are used, msBayes supports recent divergences without support for synchronous divergence in the Oaks et al. data and we further present a simulation analysis that demonstrates that msBayes can have high power to detect asynchronous divergence under narrower priors for divergence time. Our findings highlight the need for exploration of plausible parameter space and prior sampling efficiency for ABC samplers in high dimensions. We discus potential improvements to msBayes and conclude that when used appropriately with model averaging, msBayes remains an effective and powerful tool.
Data from: Evolution of pre- and post-copulatory traits in male Drosophila melanogaster as a correlated response to selection for resistance to cold stress
Background: In Drosophila melanogaster the fitness of males depends on a broad array of reproductive traits classified as pre- and post-copulatory traits. Exposure to cold stress, can reduce sperm number, male mating ability and courtship behavior. Therefore, it is expected that the adaptation to cold stress will involve changes in pre- and post-copulatory traits. Such evolution of reproductive traits in response to cold stress is not well studied. Methods: We selected replicate populations of D. melanogaster for resistance to cold shock. Over 37–46 generations of selection, we investigated pre- and post-copulatory traits such as mating latency, copulation duration, mating frequency, male fertility, fitness (progeny production) and sperm competitive ability in male flies subjected to cold shock and those not subjected to cold shock. Results: We found that post cold shock, the males from the selected populations had a significantly lower mating latency along with, higher mating frequency, fertility, sperm competitive ability and number of progeny relative to the control populations. Conclusion: While most studies of experimental evolution of cold stress resistance have documented the evolution of survivorship in response to selection, our study clearly shows that adaptation to cold stress involves rapid changes in the pre- and post-copulatory traits. Additionally, improved performances under stressful conditions need not necessarily trade-off with performance under benign conditions.
Data from: Testing for a genetic response to sexual selection in a wild Drosophila population
In accordance with the consensus that sexual selection is responsible for the rapid evolution of display traits on macroevolutionary scales, microevolutionary studies suggest sexual selection is a widespread and often strong form of directional selection in nature. However, empirical evidence for the contemporary evolution of sexually selected traits remains weak. In this study we used a novel application of quantitative genetic breeding designs to test for a genetic response to sexual selection on eight chemical display traits in a field population of the fly, Drosophila serrata. Using our quantitative genetic approach, we were able to detect a genetically-based difference in means between groups of males descended from either successful or random wild males for one of these display traits, the diene (Z,Z)-5,9-C27:2. Our experimental results, in combination with previous lab studies on this system, suggest that both natural selection and sexual selection may be influencing the evolutionary trajectories of these traits in nature, limiting the capacity for a contemporary evolutionary response.
Data from: Evolution of phenotype-environment associations by genetic responses to selection and phenotypic plasticity in a temporally autocorrelated environment
Covariation between population-mean phenotypes and environmental variables, sometimes termed a 'phenotype-environment association' (PEA), can result from phenotypic plasticity, genetic responses to natural selection, or both. PEAs can potentially provide information on the evolutionary dynamics of a particular set of populations, but this requires a full theoretical characterization of PEAs and their evolution. Here, we derive formulas for the expected PEA in a temporally fluctuating environment for a quantitative trait with a linear reaction norm. We compare several biologically relevant scenarios, including constant versus evolving plasticity, and the situation where an environment affects both development and selection but at different time periods. We find that PEAs are determined not only by biological factors (e.g., magnitude of plasticity, genetic variation), but also environmental factors, such as the association between the environments of development and of selection, and in some cases the level of temporal autocorrelation. We also describe how a PEA can be used to estimate the relationship between an optimum phenotype and an environmental variable (i.e., the environmental sensitivity of selection), an important parameter for determining the extinction risk of populations experiencing environmental change. We illustrate this ability using published data on the predator-induced morphological responses of tadpoles to predation risk.
Data from: Synergism and antagonism of proximate mechanisms enable and constrain the response to simultaneous selection on body size and development time: an empirical test using experimental evolution
Natural selection acts on multiple traits simultaneously. How mechanisms underlying such traits enable or constrain their response to simultaneous selection is poorly understood. We show how antagonism and synergism among three traits at the developmental level enable or constrain evolutionary change in response to simultaneous selection on two focal traits at the phenotypic level. After 10 generations of 25% simultaneous directional selection on all four combinations of body size and development time in Manduca sexta (Sphingidae), the changes in the three developmental traits predict 93% of the response of development time and 100% of the response of body size. When the two focal traits were under synergistic selection, the response to simultaneous selection was enabled by juvenile hormone and ecdysteroids and constrained by growth rate. When the two focal traits were under antagonistic selection, the response to selection was due primarily to change in growth rate and constrained by the two hormonal traits. The approach used here reduces the complexity of the developmental and endocrine mechanisms to three proxy traits. This generates explicit predictions for the evolutionary response to selection that are based on biologically informed mechanisms. This approach has broad applicability to a diverse range of taxa, including algae, plants, amphibians, mammals, and insects.
Data from: Roads elicit negative movement and habitat-selection responses by wolverines (Gulo gulo luscus)
Wildlife behavior when crossing roads is likely to mirror natural responses to predation risk including not responding, pausing, avoiding, or increasing speed during crossing. We generated coarse-scale behavioral predictions based on these expectations that could be assessed with GPS radiotelemetry. We evaluated our predictions using an integrated step-selection analysis of wolverine (Gulo gulo luscus) space use in relation to spatially and temporally dynamic vehicle traffic on industrial roads in northern Alberta. We compared support for alternative models of road avoidance, increased speed near roads, and road avoidance and increased speed near roads. We predicted that wolverines would avoid roads and increase their speed near roads and that these behaviors would increase with traffic volume. We found that vehicle traffic was relatively low (0 – 30 vehicles/12 hours) but important for explaining wolverine space use. Top winter and summer models indicated that wolverines avoided and increased speed near roads. Wolverine movement but not avoidance increased with traffic volume. We suggest that movement is a fine-scaled response that is more responsive to vehicle traffic than habitat selection. We show that roads, regardless of traffic volume, reduce the quality of wolverine habitats and act as barriers to movement and that higher-traffic roads might be most deleterious. We suggest that wildlife behavior near roads should be viewed as a continuum and that accurate modeling of behavior when near roads requires quantification of both movement and habitat selection. Mitigating the effects of roads on wolverines would require clustering roads, road closures, or access management.
Data from: Dynamic antagonism between phytochromes and PIF-family bHLHs induces selective reciprocal responses to light and shade in a rapidly responsive transcriptional network in Arabidopsis
Plants respond to shade-modulated light-signals, via the phytochrome (phy) system, by adaptive changes, collectively termed the shade avoidance syndrome (SAS). To examine the roles of the Phy-Interacting bHLH Factors, PIF1, 3, 4 and 5, in relaying this information to the transcriptional network, we compared the genome-wide expression profiles of wild-type and quadruple pif (pifq) mutants in response to shade. The data identify a subset of genes, enriched in transcription-factor-encoding loci, that respond rapidly (within 1 h), in a PIF-dependent manner, to the shade signal, and that contain promoter-located G-box-sequence motifs (CACGTG), known to be preferred PIF binding sites. These genes are thus potential direct targets of phy-PIF signaling that function in the primary transcriptional circuitry controlling downstream response-elaboration. A second subset of PIF-dependent, early-response genes, lacking G-box motifs, are enriched for auxin-responsive loci, suggestive of being indirect targets of phy-PIF signaling involved in the rapid cell-expansion known to be induced by shade. A meta-analysis comparing deetiolation- and shade-responsive transcriptomes identifies a further subset of G-box-containing genes that reciprocally display rapid repression and induction in response to light and shade signals at the inception of deetiolation and shade-avoidance, respectively. Collectively, these data define a core set of transcriptional and hormonal (auxin, cytokinin) processes that appear to be dynamically poised to react rapidly to changes in the light environment via perturbations in the mutually antagonistic actions of the phys and PIFs. Data from comparative analysis of the quadruple pifq and all triple pif-mutant combinations in response to light and shade, confirm that the PIF-quartet members act with overlapping redundancy on seedling morphogenesis and transcriptional regulation, but that the individual PIFs contribute differentially to these responses.
Data from: Dearth of polymorphism associated with a sustained response to selection for flowering time in maize
Background: Long term selection experiments bring unique insights on the genetic architecture of quantitative traits and their evolvability. Indeed, they are utilized to (i) monitor changes in allele frequencies and assess the effects of genomic regions involved traits determinism; (ii) evaluate the role of standing variation versus new mutations during adaptation; (iii) investigate the contribution of non allelic interactions. Here we describe genetic and phenotypic evolution of two independent Divergent Selection Experiments (DSEs) for flowering time conducted during 16 years from two early maize inbred lines. Results: Our experimental design uses selfing as the mating system and small population sizes, so that two independent families evolved within each population, Late and Early. Observed patterns are strikingly similar between the two DSEs. We observed a significant response to selection in both directions during the first 7 generations of selection. Within Early families, the response is linear through 16 generations, consistent with the maintenance of genetic variance. Within Late families and despite maintenance of significant genetic variation across 17 generations, the response to selection reached a plateau after 7 generations. This plateau is likely caused by physiological limits. Residual heterozygosity in the initial inbreds can partly explain the observed responses as evidenced by 42 markers derived from both Methyl-Sensitive Amplification- and Amplified Fragment Length- Polymorphisms. Among the 42, a subset of 13 markers most of which are in high linkage disequilibrium, display a strong association with flowering time variation. Their fast fixation throughout DSEs' pedigrees results in strong genetic differentiation between populations and families. Conclusions: Our results reveal a paradox between the sustainability of the response to selection and the associated dearth of polymorphisms. Among other hypotheses, we discuss the maintenance of heritable variation by few mutations with strong epistatic interactions whose effects are modified by continuous changes of the genetic background through time.
Data from: Environmentally induced changes in correlated responses to selection reveal variable pleiotropy across a complex genetic network
Selection in novel environments can lead to a coordinated evolutionary response across a suite of characters. Environmental conditions can also potentially induce changes in the genetic architecture of complex traits, which in turn could alter the pattern of the multivariate response to selection. We describe a factorial selection experiment using the nematode Caenorhabditis remanei in which two different stress-related phenotypes (heat and oxidative stress resistance) were selected under three different environmental conditions. The pattern of covariation in the evolutionary response between phenotypes or across environments differed depending on the environment in which selection occurred, including asymmetrical responses to selection in some cases. These results indicate that variation in pleiotropy across the stress response network is highly sensitive to the external environment. Our findings highlight the complexity of the interaction between genes and environment that influences the ability of organisms to acclimate to novel environments. They also make clear the need to identify the underlying genetic basis of genetic correlations in order understand how patterns of pleiotropy are distributed across complex genetic networks.
Unidirectional response to bidirectional selection on body size. I. Phenotypic, life history and endocrine response
Anthropogenic perturbations such as harvesting often select against a large body size and are predicted to induce rapid evolution towards smaller body sizes and earlier maturation. However, body-size evolvability and, hence, adaptability to anthropogenic perturbations remain seldom evaluated in wild populations. Here, we use a laboratory experiment over 6 generations to measure the ability of wild-caught medaka fish (Oryzias latipes) to evolve in response to bidirectional size-dependent selection mimicking opposite harvest regimes. Specifically, we imposed selection against a small body size (Large line), against a large body size (Small line) or random selection (Control line), and measured correlated responses across multiple phenotypic, life-history and endocrine traits. As expected, the Large line evolved faster somatic growth and delayed maturation, but also evolved smaller body sizes at hatch, with no change in average levels of pituitary gene expressions of luteinizing, follicle-stimulating or growth (GH) hormones. In contrast, the Small medaka line was unable to evolve smaller body sizes or earlier maturation, but evolved smaller body sizes at hatch and showed marginally-significant signs of increased reproductive investment, including larger egg sizes and elevated pituitary GH production. Natural selection on medaka body size was too weak to significantly hinder the effect of artificial selection, indicating that the asymmetric body-size response to size-dependent selection reflected an asymmetry in body-size evolvability. Our results show that trait evolvability may be contingent upon the direction of selection, and that a detailed knowledge of trait evolutionary potential is needed to forecast population response to anthropogenic change.
Investigation of Genetic Predictors of the Response to Selective Serotonin Re-uptake Inhibitors (SSRI) Treatment
ClinicalTrials.gov study NCT03927950. IPD Sharing: NO. Countries: 1. Publications: 0.
Threshold Response of Lumbar Selective Nerve Root Block in Predicting Good Outcome Following Lumbar Foraminotomy
ClinicalTrials.gov study NCT03801356. IPD Sharing: NO. Countries: 1. Publications: 0.
A Study With Upadacitinib (ABT-494) in Subjects From China and Selected Countries With Moderately to Severely Active Rheumatoid Arthritis Who Have Had an Inadequate Response to Conventional Synthetic
ClinicalTrials.gov study NCT02955212. IPD Sharing: YES. Countries: 3. Publications: 0.
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