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287 results for “Response to selection”
Sexual selection buffers the negative consequences of population fragmentation on adaptive plastic responses to increasing temperatures
<p class="MsoNormal"><span>Whether sexual selection facilitates or hampers the ability to plastically respond to novel environments might depend on population structure, via its effects on </span><span>sexual interactions and associated fitness payoffs</span><span>. Using experimentally evolved lines </span><span>of the seed beetle <em>Callosobruchus maculatus,</em> we tested whether individuals evolving under different sexual selection (monogamy vs polygamy) and population spatial structure (metapopulation vs undivided populations) treatments differed in their response across developmental thermal conditions (control, hot or stressful) in a range of fitness and fitness-associated traits. We found that individuals from subdivided populations had lower lifetime reproductive success (LRS) at hot temperatures, but only in lines evolving under relaxed sexual selection, revealing a complex interaction between sexual selection, population structure, and thermal environmental stress on fitness. We also found an effect of population structure on several traits, including fertility and adult emergence success, under exposure to high thermal conditions. Finally, we found a strong negative effect of hot and stressful temperatures in fitness and associated traits. Our results show that population structure can exacerbate the impact of a warming climate, potentially leading to declines in population viability, but that sexual selection can buffer the negative influence of population subdivision on adaptation to warm temperatures</span><span>.</span></p>
A Functional Response in Resource Selection Links Multi-Scale Responses of a Large Carnivore to Human Mortality Risk
<p>This repository contains code and data to reproduce results from the manuscript 'A Functional Response in Resource Selection Links Multi-Scale Responses of a Large Carnivore to Human Mortality Risk'. </p>
Inter- and intraspecific selection in alien plants: how population growth, functional traits and climate responses change with residence time
<p><strong>Aim: </strong>When alien species are introduced to new ranges, climate or trait mismatches may initially constrain their population growth. However, inter- and intraspecific selection in the new environment should cause population growth rates to increase with residence time. Using a species-for-time approach, we test whether with increasing residence time (a) negative effects of climatic mismatches between the species' new and native range on population growth weaken, and (b) functional traits converge towards values that maximize population growth in the new range.</p> <p><strong>Location:</strong> Germany.</p> <p><strong>Time period: </strong>12,000 years BP to present.</p> <p><strong>Major taxa studied: </strong>46 plant species of the Asteraceae family.</p> <p><strong>Methods:</strong> We set up a common-garden mesocosm-experiment using annual plant species with a wide range of residence times (7-12,000 years) and followed their population dynamics over two years. We calculated climatic distance between the common garden and the species' native range. We also measured key functional traits of each species to analyse trait-demography relationships and test trait convergence with increasing residence time.</p> <p><strong>Results: </strong>We found no support for the hypothesis that negative effects of climatic mismatches on population growth weaken with residence time. However, seed mass had a clear negative effect on population growth. As expected under such strong directional selection between or within species, increasing residence time led seed mass to converge to low values that increase population growth. Accordingly, population growth tended to increase with residence time.</p> <p><strong>Main conclusions: </strong>We identify trait but not climatic mismatches as important constraints on population growth of invaders. Understanding how inter- and intraspecific selection shapes functional traits of alien species should improve the predictability of future invasions and help understanding limits to the population growth and spread of invaders already present. In a broader context, this study contributes to the conceptual integration of invasion biology with community, functional, and population ecology.</p>
Adaptive immune response selects for increased body size - dataset
<p>The dataset for the manuscript " Adaptive immune response selects for increased body size ". The dataset is packed in ZIP archive 'Dataset_Ejsmond_etal_2022.zip' with variables and description of variables saved in Matlab workspaces.</p>
Data and code from: Opposite, but insufficient, phenological responses to climate in two circumpolar seabirds: relative roles of phenotypic plasticity and selection
<p><span>The magnitude of climate change has been greatest in the Arctic, accelerating climate-induced shifts in phenology, but wildlife responses vary. Variation may be due to the relative importance of phenotypic plasticity or phenotypic selection.</span></p> <p><span>Here, we examine and contrast the environmental drivers of plasticity in breeding phenology of two circumpolar seabirds at their receding summer range limit using unique datasets of marked individuals </span><span>covering </span><span>25 and 30</span><span> years</span><span>. Based on prior knowledge of the local ecosystems, we predicted that climate would generate opposing patterns of plasticity in the two populations.</span></p> <p><span>Laying phenology of kittiwakes in the Gulf of Alaska was associated with a large-scale climate oscillation (Pacific Decadal Oscillation) while the Arctic-breeding murres adjusted </span><span>laying to sea-ice conditions. Kittiwakes laid earlier after experiencing colder climate about two years prior and laying dates did not advance over the study, but murres laid earlier when warmer climate led to earlier spring sea-ice break-up, and murre laying dates advanced by one week since 1990. Selection favoured earlier laying in both species.</span></p> <p><span>Both populations adjusted breeding phenology to environmental variation, but we anticipate opposing effects on phenology with continued climate change. Ice-constrained species can likely adapt to some extent because plasticity can provide the necessary shift to this physical barrier, although individuals were only able to adjust by ~one week while ice conditions advanced by over a month</span><span>. </span><span>In more temperate regions</span><span>,</span><span> where phenology is driven by bottom-up effects, plasticity and selection counteract one another leading to limited adaptability. We provide insights into the likely adjustments by Arctic marine animals to an increasingly warmer and ice-less summer.</span></p>
Off-target integron activity leads to rapid plasmid compensatory evolution in response to antibiotic selection pressure
Integrons are mobile genetic elements that have played an important role in the dissemination of antibiotic resistance. As shown previously (Souque et al, 2021), the integron can generate under stress combinatorial variation in resistance cassette expression by cassette re-shuffling, accelerating the evolution of resistance. However, the flexibility of the integron integrase site recognition motif hints at potential off-target effects of the integrase on the rest of the genome that may have important evolutionary consequences. Here we test this hypothesis by selecting for increased piperacillin resistance populations of <em>P.aeruginosa</em> with a mobile integron containing a hard-to-mobilise beta-lactamase cassette to minimize the potential for adaptive cassette re-shuffling. We found that integron activity can both decrease overall survival rate but also improve the fitness of the surviving populations. Off-target inversions mediated by the integron accelerated plasmid adaptation by disrupting costly conjugative genes otherwise mutated in control populations lacking a functional integrase. Plasmids containing integron-mediated inversions were associated with lower plasmid costs and higher stability than plasmids carrying mutations, albeit at a cost of reduced conjugative ability. These findings highlight the potential for integrons to create structural variation that can drive bacterial evolution, and they provide an interesting example showing how antibiotic pressure can drive the loss of conjugative genes.
European badger (Meles meles) responses to low-intensity, selective culling: using mark recapture and relatedness data to assess social perturbation
<p>Culling the main wildlife host of bovine tuberculosis in Great Britain (GB) and Ireland, the European badger (Meles meles) to reduce infections in cattle, has been employed in both territories. In GB, this has been controversial, with results suggesting that culling induces disturbance to badger social structure, facilitating wider disease dissemination. Previous analyses hypothesized that even very low-level, selective culling may cause similar deleterious effects by increasing ranging of individuals and greater mixing between social-groups. To assess this hypothesis, a novel, prospective, landscape-scale 'before-and-after' Test and vaccinate or remove (TVR) study was implemented. Test-positive badgers were culled and test-negative badgers were BCG vaccinated and released. Mark-recapture metrics of badger ranging and genetic metrics of social group relatedness did not change significantly over the study period. However, selective culling was associated with a localised reduction in social-group relatedness in culled groups. Synthesis and application: Ecological context is important; extrapolation across territories and other disease epidemiological-systems (epi-systems) is likely to be challenging. However, we demonstrate that small-scale, selective removal of test-positive badgers was not associated with metrics of increased ranging but was associated with localised changes in social-group relatedness. This adds to the evidence base on badger control options for policy makers.</p>
Data from: Widespread bird species show idiosyncratic responses in residual body mass to selective logging and edge effects in the Colombian Western Andes
<p>This dataset consists of banding data (N = 1589 captures, 129 bird species), including morphological and breeding biology measures, collected from understory birds in subtropical cloudforest at roughly 2000 m.a.s.l. in the municipality of El Cairo in Colombia's Western Andes (Serrania de los Paraguas range). Roughly 8,350 net hours were divided into two three-month field seasons (June-August 2017 and January-March 2018), both corresponding to local dry seasons. Birds were banded along 500-meter transects in forest interior across a gradient of forest fragment patch sizes (N = 8 fragments, area range = 10-173 ha) and a private ~750 ha reserve (Reserva Natural Cerro El Ingles) in the same landscape. Each non-hummingbird capture was fitted with an aluminum leg band with a unique combination, and we collected data on mass, tarsus length, wing chord, pectoral muscle score, cloacal protuberance and brood patch score, and age and sex (where possible due to plumage differences). We captured 101 species (including 6 boreal migrants) in 844 captures (53%) during the January-March sampling period and 102 species in 745 captures during the June-August sampling period; each site was sampled during both sampling periods. The most captured bird families were Trochilidae (24 spp., 36% of total captures), Thraupidae (17 spp.), Tyrannidae (16 spp.), Furnariidae (14 spp.), and Turdidae (6 spp.).</p> <p>A subset of these data (uploaded as a separate file) were used to calculate body condition indices for 20 species of commonly captured birds (N = 984 captures) that occured across much of the patch size gradient (at least 8 out of 14 transects), and were related to fragment area and measures of edge and selective logging effects (see Jones et al. 2022). In this file, we include all predictor variables necessary to run the generalized linear mixed models in Jones et al. (2022), including proportion forest cover within 1 km (a proxy for patch size), edge density, average distance to forest edge from the netting transect, average canopy cover and height along the transect, multivariate measures of understory plant density, large-diameter tree density, and vertical vegetation structure, elevation of each transect, and average yearly rainfall for each transect.</p>
A dual selection system for directed evolution to identify allosteric transcription factor PobR variants responsive to different aromatic compounds
<p>This dataset includes all the raw data of our characterization experiments during the work titled “A dual selection system for directed evolution to identify allosteric transcription factor PobR variants responsive to different aromatic compounds”.</p>
Questionnaire Response About Weight Of Criteria For Selecting Online Course Using Weighted Product Method
<p>This dataset is a response to a questionnaire that we already delivered to some Institut Teknologi Sepuluh Nopember Surabaya students. In this questionnaire, they chose which criteria are important for selecting an online course, and by that data, we can get the weights of each criteria and we use that data to do our Weighted Product selection.</p>
Sexual selection moderates heat stress response in males and females
<p><span>1. </span><span>A widespread effect of climate change is the displacement of organisms from their thermal optima. The associated thermal stress imposed by climate change has been argued to have a particularly strong impact on male reproduction but evidence for this postulated sex-specific stress response is equivocal. </span></p> <p><span>2. </span><span>One important factor that may explain intra- and interspecific variation in stress responses is sexual selection, which is predicted to magnify negative effects of stress. Nevertheless, empirical studies exploring the </span><span>interplay of sexual selection and heat stress </span><span>are still scarce. </span></p> <p><span>3. </span><span>We tested experimentally for an interaction between sexual selection and thermal stress in the red flour beetle Tribolium castaneum by contrasting heat responses in male and female reproductive success between setups of enforced monogamy versus polygamy. </span></p> <p><span>4. </span><span>We found that polygamy magnifies detrimental effects of heat stress in males but relaxes the observed negative effects in females. Our results suggest that sexual selection can reverse sex differences in thermal sensitivity, and may therefore alter sex-specific selection on alleles associated with heat tolerance. </span></p> <p><span>5. </span><span>Assuming that sexual selection and natural selection are aligned to favour the same genetic variants under environmental stress, our findings support the idea that sexual selection on males may promote the adaptation to current global warming.</span></p>
Weak response to selection on stigma-anther distance in a primarily selfing population of yellow monkeyflower
<p>Stebbins hypothesized that selfing lineages are evolutionary dead ends because they lack adaptive potential. While selfing populations often harbor limited nucleotide variability compared to closely related outcrossers, reductions in the genetic variability of quantitative characters remain unclear, especially for key traits determining selfing rates. Yellow monkeyflower (<em>Mimulus guttatus</em>) populations generally outcross and maintain extensive quantitative genetic variation in floral traits. Here, we study the Joy Road population (Bodega Bay, California, USA) of <em>M. guttatus</em>, where individuals exhibit stigma-anther distances typical of primarily selfing monkeyflowers. We show that this population is closely related to nearby conspecifics on the Pacific coast with a modest 33% reduction in genome-wide variation compared to a more highly outcrossing population. A five-generation artificial selection experiment challenged the hypothesis that the Joy Road population harbors comparatively low evolutionary potential in the stigma-anther distance, a critical determinant of selfing rate in <em>Mimulus</em>. Artificial selection generated a weak phenotypic response, with low realized heritabilities (0.020-0.028) falling 84% below those measured for floral characters in more highly outcrossing <em>M. guttatus</em>. These results demonstrate substantial declines in evolutionary potential with a transition toward selfing. Whether these findings explain infrequent reversals to outcrossing or general limits on adaptation in selfers requires further investigation.</p>
Data from: Sexually discordant selection is associated with trait specific morphological changes and a complex genomic response
<p>Sexes often have differing fitness optima, potentially generating intra-locus sexual conflict, as each sex bears a genetic 'load' of alleles beneficial to the other sex. One strategy to evaluate conflict in the genome is to artificially select populations discordantly, against established sexual dimorphism, reintroducing attenuated conflict. We investigate a long-term artificial selection experiment reversing sexual size dimorphism in <em>Drosophila melanogaster</em> during ~350 generations of sexually discordant selection. We explore morphological and genomic changes to identify loci under selection between the sexes in discordantly and concordantly size selected treatments. Despite substantial changes to overall size, concordant selection maintained ancestral sexual dimorphism. However, discordant selection altered size dimorphism in a trait-specific manner. We observe multiple, possible soft selective sweeps in the genome, with size related genes showing signs of selection. Patterns of genomic differentiation between the sexes within lineages identified potential sites maintained by sexual conflict. One discordant selected lineage shows a pattern of elevated genomic differentiation between males and females, on chromosome 3L, consistent with the maintenance of sexual conflict. Our results suggest visible signs of conflict and differentially segregating alleles between the sexes due to discordant selection.</p>
Functional responses in habitat selection as a management tool to evaluate agri-environment schemes for farmland birds
<p>The folder "functional_responses.zip" contains data analyzed for "Functional responses in habitat selection as a management tool to evaluate agri-environment schemes for farmland birds"</p> <p>The raw LPIS/IACS data are owned by the Saxon State Ministry for Energy, Climate Protection, Environment and Agriculture; they hold sensitive information and hence cannot be made publicly available. They can be requested from the agency for research purposes.</p> <p>Processed data are retrievable from .RDATA in "rdata_mixed_model" and "rdata_functional_responses" folders.</p> <p>"rscript" folder contains R functions of JAGS codes (jags_code.R), data processing (process.R), utility functions (utils.R), and figures (figure_all.R or figure_all_by_sp.R).</p> <p>Dg: Common whitethroat (Curruca communis)</p> <p>Fl: Eurasian skylark (Alauda arvensis)</p> <p>G: Yellowhammer (Emberiza citrinella)</p> <p>Ga: Corn bunting (Emberiza calandra)</p> <p> </p> <p>If you have questions regarding data, please contact ryo.ogawa@uni-bonn.de.</p>
Microgeographic divergence of functional responses among salamanders under antagonistic selection from apex predators
A predator's functional response determines predator–prey interactions by describing the relationship between the number of prey available and the number eaten. Its shape and parameters fundamentally govern the dynamic equilibrium of predator–prey interactions and their joint abundances. Yet, estimates of these key parameters generally assume stasis in space and time and ignore the potential for local adaptation to alter feeding responses and the stability of trophic dynamics. Here, we evaluate if functional responses diverge among populations of spotted salamander ( Ambystoma maculatum ) larvae that face antagonistic selection on feeding strategies based on their own risk of predation. Common garden experiments revealed that spotted salamander from ponds with varying predation risks differed in their functional responses, suggesting an evolutionary response. Applying mechanistic equations, we discovered that the combined changes in attack rates, handling times and shape of the functional response enhanced feeding rate in environments with high densities of gape-limited predators. We suggest how these parameter changes could alter community equilibria and other emergent properties of food webs. Community ecologists might often need to consider how local evolution at fine scales alters key relationships in ways that alter local diversity patterns, food web dynamics, resource gradients and community responses to disturbance.
Immune selection determines tumor antigenicity and influences response to checkpoint inhibitors
<p>R markdown files and source data to reproduce figures from the manuscript "Immune selection determines tumor antigenicity and influences response to checkpoint inhibitors"</p>
Immune selection determines tumor antigenicity and influences response to checkpoint inhibitors - Dataset
<p>Dataset used from the publication "Tumor and Microenvironment Evolution during Immunotherapy with Nivolumab" published in </p> <p>Cell. 2017 Nov 2;171(4):934-949.e16.</p> <p> doi: 10.1016/j.cell.2017.09.028. Epub 2017 Oct 12.</p>
Soil moisture incidentally selects for microbes that facilitate locally adaptive plant response
<p>We examined the role of the plant vs the environment in selecting for beneficial microbes to plants in their home moisture environment, in either wet vs dry conditions. To this end, we first conditioned soil microbial communities, selecting for either dry- or wet-adapted soil microbial communities, either with or without plants. After 3 plant generations, we conducted a full reciprocal transplant of each soil community onto wet- and dry-treated plants, using the soil from the prior 3 generations as an inoculum. From plants inoculated with these ‘evolved’ soils, we measured plant biomass and height. We also measured soil nitrogen of the inoculum, and measured inoculum respiration across a water content gradient. <br> </p>
Data from: Increased male-induced harm in response to female-limited selection: interactive effects between intra- and interlocus sexual conflict?
<p><span>Interlocus sexual conflict (IRSC) occurs because of shared interactions that have opposite effects on male and female fitness. Typically, it is assumed that loci involved in IRSC have sex-limited expression and are thus not directly affected by selective pressures acting on the other sex. However, if loci involved in IRSC have pleiotropic effects in the other sex, intersexual selection can shape the evolutionary dynamics of conflict escalation and resolution, as well as the evolution of reproductive traits linked to IRSC loci, and vice versa. Here we used an artificial selection approach in</span><span> Japanese quail (<em>Coturnix</em> <em>japonica</em>) to test if female-limited selection on reproductive investment affects the amount of harm caused by males during mating. We found that males originating from lines selected for high female reproductive investment caused more oxidative damage in the female reproductive tract than males originating from lines selected for low female reproductive investment. This male-induced damage was specific to the oviduct and not found in other female tissues, suggesting that it was ejaculate-mediated. Our results suggest that intersexual selection shapes the evolution of IRSC and that male-induced harm may contribute to the maintenance of variation in female reproductive investment.</span></p>
Contaminated sediment in the Detroit River selects for evolved CYP1A and p53 responses in wild brown bullhead (Ameiurus nebulosus) populations
<div> <div> <p><span>In a previous study, adaptive responses to a single polycyclic aromatic hydrocarbon (PAH), benzo[a]pyrene (BaP), were identified in brown bullhead (</span><span><em>Ameiurus nebulosu</em>s</span><span>) captured from contaminated sites across the Great Lakes. The tumor suppressor p53 and phase I toxin metabolizing CYP1A genes showed a protective and refractory response, respectively, up to the F1 generation (Williams and Hubberstey, 2014). As an extension to the first study, bullhead were exposed to sediment collected from sites along the Detroit River to see if these adaptive responses are attainable when fish from a contaminated site are exposed to a mixture of contaminants, instead of a single compound. p53 and CYP1A proteins were measured in both studies with the addition of phase II glutathione-s-transferase (GST) activity in the second. Three treatment groups were measured: acute (treated immediately), cleared (depurated for three months and subsequent treatment), and farm raised F1 offspring. All three treatment groups were exposed to clean and contaminated sediment for 24 and 96 hours. </span><span>Acute fish from contaminated sites exposed to contaminated sediment revealed an initial elevated p53 response that was not reached in cleared fish exposed to contaminated sediment. Instead, cleared and F1 bullhead from clean and contaminated sites had overlapping p53 expression patterns in response to contaminated sediment by 96 hours. Acute fish from contaminated sites exposed to contaminated sediment revealed refractory CYP1A expression, which disappeared in cleared fish and whose F1 refractory response overlapped with clean site F1 offspring. Decreasing GST activity was evident in both clean and contaminated fish over time, with clean site fish responding to contaminated sediment more deliberately. By 96 hours, the response patterns of F1 offspring from clean and contaminated sites to clean and contaminated sediment exposures were similar. </span><span> </span></p> </div> <div> <p><span>Because p53, CYP1A and GST activity responses to contaminated sediment dosing overlapped in clean and contaminated farm-raised F1 offspring, these results suggest that contaminated fish have acclimated to the contaminants present in their environments by reaching a tolerance threshold and no evidence of adaptation was detected in these biomarkers. </span></p> </div> </div>
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