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66 results for “fitness landscapes”
Agricultural landscape simplification affects wild plant fitness indirectly through herbivore-mediated changes in floral display
<p>As natural landscapes are modified and converted into simplified agricultural landscapes, the community composition and interactions of organisms persisting in these modified landscapes are altered. While many studies examine the consequences of these changing interactions for crops, few have evaluated the effects on wild plants. Here, we examine how pollinator and herbivore interactions affect fitness for wild resident and phytometer plants at sites along a landscape gradient ranging from natural to highly simplified. We tested the direct and indirect effects of landscape composition on plant traits and fitness mediated by insect interactions. For phytometer plants exposed to herbivores, we found that greater landscape complexity corresponded with elevated herbivore damage, which reduced total flower production but increased individual flower size. Though larger flowers increased pollination, the reduction in flowers ultimately reduced plant fitness. Herbivory was also higher in complex landscapes for resident plants, but overall damage was low and therefore did not have a cascading effect on floral display and fitness. This work highlights that landscape composition directly affects patterns of herbivory with cascading effects on pollination and wild plant fitness. Further, the absence of fitness consequences for resident plants suggests that they may be adapted to their local insect community. </p>
Agricultural landscape simplification affects wild plant fitness indirectly through herbivore-mediated changes in floral display
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Data from: Host-parasite coevolution promotes innovation through deformations in fitness landscapes
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Data from The Multi-Funnel Structure of TSP Fitness Landscapes: A Visual Exploration
<p>Landscape data for "The Multi-Funnel Structure of TSP Fitness Landscapes: A Visual Exploration", G. Ochoa, N. Veerapen, D. Whitley and E. Burke. Artificial Evolution (EA 2015), 26-28 October 2015, Lyon, France.</p>
Data used to produce figures in "Monotonicity of Fitness Landscapes and Mutation Rate Control"
<p>Data used in Figures 2, 3, 4, 6, 7, 8, 9 and 10 of the manuscript "Monotonicity of Fitness Landscapes and Mutation Rate Control"</p>
Fitness landscape of substrate-adaptive mutations in evolved APC transporters
<p>Growth rate calculations:</p> <p>Single colonies of <em>S. cerevisiae</em> Δ10AA pADHXC3GH-<em>GOI</em> were inoculated in YB media supplemented with 4 mm NH<sub>4</sub><sup>+</sup> and 0.1 mg/ml ampicillin, and grown until late logarithmic phase. The cultures were pelleted at 750 × <em>g</em> for 10 min at 30 °C and washed with YB media. The wells in the microplate were filled with the amino acids of interest to a final concentration of 2 mM and with culture cells to a final OD<sub>600</sub> of 0.04, to a final total well volume of 200 µl. Sterile water was added in the space between the wells to avoid evaporation. The prepared microplates included three biological replicates of the strains with the plasmid containing the gene of interest (GOI) and one biological replicate of the strain with the empty vector. The absorbance in each well was measured at 600 nm in 30 min intervals without shaking of the microplate, at 30 °C for 72 h in a SpectraMax ABS Plus plate reader. The data sets (CSV files) are the raw optical density readings from the growth assays, along with plate layout metadata (CSV files). The growth rates were derived based on the Baranyi growth model, using the <em>growthrates</em> package in <em>R</em>.</p> <p>Included transporter genes:</p> <p>Mutated transporters (script growth_rates_mutants_Baranyi2.r)</p> <p><em>AGP1</em>, <em>AGP1</em>-N, <em>AGP1</em>-V,<em> AGP1</em>-NV, <em>AGP1</em>-G, <em>AGP1</em>-T, <em>PUT4</em>, <em>PUT4</em>-S</p> <p>Wild-type transporters (script growth_rates_wild_types_Baranyi2.r)</p> <p><em>AGP1</em>, <em>BAP2</em>, <em>CAN1</em>, <em>HIP1</em>, <em>LYP1</em>, <em>MMP1</em>, <em>PUT4</em></p> <p> </p> <p>Plasmid sequences (Genbank files):</p> <p>pADHXC3GH-AGP1, pADHXC3GH-BAP2, pADHXC3GH-CAN1, pADHXC3GH-HIP1, pADHXC3GH-LYP1, pADHXC3GH-MMP1, pADHXC3GH-PUT4-S L207S, pADHXC3GH-PUT4, pADHXC3GH</p> <p> </p> <p>Measureing relative membrane fluorescence (all transporters in this study have C-terminal GFP tags):</p> <p>Micrographs were analyzed with ImageJ using the script analyse_cell_perimeter.ijm</p>
Data and code for the GECCO 2024 paper: "Understanding fitness landscapes in morpho-evolution via local optima networks"
<p>The LON and algorithm run data is available in data/ </p> <p>To run the LON extraction:</p> <p>From gymrem2d-lons/ModularER_2D, run python3 setup.py</p> <p>Direct encoding: python3 lons.py --file direct.cfg</p> <p>LSystem: python3 lons.py --file lsystem.cfg </p> <p>CPPN: python3 lons.py --file cppn.cfg</p> <p> </p>
Hybridization alters the shape of the genotypic fitness landscape, increasing access to novel fitness peaks during adaptive radiation
<p>Estimating the complex relationship between fitness and genotype or phenotype (i.e. the adaptive landscape) is one of the central goals of evolutionary biology. However, adaptive walks connecting genotypes to organismal fitness, speciation, and novel ecological niches are still poorly understood and processes for surmounting fitness valleys remain controversial. One outstanding system for addressing these connections is a recent adaptive radiation of ecologically and morphologically novel pupfishes (a generalist, molluscivore, and scale-eater) endemic to San Salvador Island, Bahamas. We leveraged whole-genome sequencing of 139 hybrids from two independent field fitness experiments to identify the genomic basis of fitness, estimate genotypic fitness networks, and measure the accessibility of adaptive walks on the fitness landscape. We identified 132 SNPs that were significantly associated with fitness in field enclosures. Six out of the 13 regions most strongly associated with fitness contained differentially expressed genes and fixed SNPs between trophic specialists; one gene (<em>mettl21e</em>) was also misexpressed in lab-reared hybrids, suggesting a potential intrinsic genetic incompatibility. We then constructed genotypic fitness networks from adaptive alleles and show that scale-eating specialists are the most isolated of the three species on these networks. Intriguingly, introgressed and<em> de novo</em> variants reduced fitness landscape ruggedness as compared to standing variation, increasing the accessibility of genotypic fitness paths from generalist to specialists. Our results suggest that adaptive introgression and <em>de novo</em> mutations alter the shape of the fitness landscape, providing key connections in adaptive walks circumventing fitness valleys and triggering the evolution of novelty during adaptive radiation.</p>
Constrained Fitness Landscape Analysis of Vehicle Routing Problems
<p>The repository is a set of Jupyter notebooks and datasets used in the article titled: “Constrained Fitness Landscape Analysis for Capacitated Vehicle routing problems.” The main objective is to give the tools for reproducing the results shown in the paper.</p>
Fitness landscapes reveal context-dependent benefits of oviposition behaviour
<p><span>Resource choice behaviour has enormous fitness consequences and can drive niche expansion. However, individual behavioural choices are often mediated by context, determined by past experience. Do such context-dependent behaviours reflect maladaptive variation, or are they locally adaptive? Using Tribolium castaneum (the red flour beetle), we demonstrate that context-dependent oviposition behaviour reflects distinct, context-specific local fitness peaks. We measured offspring fitness to generate fitness landscapes as a function of all possible oviposition behaviours (i.e., combinations of fecundity and resource preference) in a habitat containing optimal and suboptimal resource patches. We did this by experimentally manipulating female egg allocation across patches, which allowed us to assess behaviours not typically observed in the laboratory. We found that females from different age and competition contexts exhibit distinct behaviours which optimize different fitness components, linked in a tradeoff. With prior exposure to strong competition and increasing age, females produce few but fast-developing offspring that are advantageous under high resource competition. In contrast, young naïve females produce significantly more (but slower-developing) offspring, which is beneficial under weak competition. Systematically mapping complete context-dependent fitness landscapes is thus critical to infer behavioural optimality and offers predictive power in novel contexts. </span></p>
Hybridization alters the shape of the genotypic fitness landscape, increasing access to novel fitness peaks during adaptive radiation
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The evolutionary dynamics and fitness landscape of clonal hematopoiesis
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Data from: Rapid within- and transgenerational changes in thermal tolerance and fitness in variable thermal landscapes
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Data from: Landscape homogenization strengthens the fitness benefits of plant species' centrality in pollination networks
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Data from: Fitness landscapes of human microsatellites
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Fitness landscapes reveal context-dependent benefits of oviposition behaviour
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Epigenetic variation can promote adaptation by smoothing rugged fitness landscapes
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Data from: Crossing fitness valleys: empirical estimation of adaptive landscape associated with polymorphic mimicry
Characterising the fitness landscapes associated with polymorphic adaptive traits enables the investigation of the mechanisms allowing transitions between fitness peaks. Here, we explore how natural selection can promote genetic mechanisms preventing heterozygous phenotypes from falling into non-adaptive valleys. Polymorphic mimicry is an ideal system to investigate such fitness landscapes, because the direction of selection acting on complex mimetic colour patterns can be predicted by the local mimetic community composition. Using more than 5,000 artificial butterflies displaying colour patterns exhibited by the polymorphic Müllerian mimic Heliconius numata, we directly tested the role of wild predators in shaping fitness landscapes. We compared predation rates on mimetic phenotypes (homozygotes at the supergene controlling colour pattern), intermediate phenotypes (heterozygotes), exotic morphs (absent from the local community) and palatable cryptic phenotypes. Exotic morphs were significantly more attacked than local morphs, highlighting predators' discriminatory capacities. Overall, intermediates were attacked twice as much as local homozygotes, suggesting the existence of deep fitness valleys promoting strict dominance and reduced recombination between supergene alleles. By including information on predators' colour perception, we also showed that protection on intermediates strongly depends on their phenotypic similarity to homozygous phenotypes and that ridges exist between similar phenotypes, which may facilitate divergence in colour patterns.
Data from: Contrasting habitat and landscape effects on the fitness of a long-lived grassland plant under forest encroachment: do they provide evidence for extinction debt?
1. Habitat loss, fragmentation and transformation threaten the persistence of many species worldwide. Population and individual fitness are often compromised in small, degraded and isolated habitats, but extinction can be a slow process and extinction debts are common. 2. Long-lived species are prone to persist as remnant populations in low quality habitats for a long time, but the population and individual-level mechanisms of extinction debt remain poorly explored so far. 3. We here investigate the mechanisms involved in the long-term persistence of the common grassland specialist, long-lived, clonal plant Aphyllanthes monspeliensis L. (Asparagaceae). after forest encroachment into semi-natural Mediterranean calcareous grasslands in Catalonia (NE Iberian Peninsula). For this purpose we assess vegetative (aboveground and belowground) and reproductive plant performance indicators and their habitat and landscape (current and historical) drivers. 4. We confirm the existence of an extinction debt for this species, since current plant frequency is related to historical but not current connectivity, and we also find a positive effect of historical connectivity on seed set. In addition, current tree cover negatively affects individual size and aboveground/belowground biomass ratio, and biotic soil acidification leads to a reduction in the flowering probability of individuals and stems. 5. However, we also find that current connectivity negatively affects flowering and that tree cover enhances seed set. The forestation process, thus, also exerts a positive effect on some fitness traits, probably by providing a moister environment. 6. Synthesis. Habitat loss and deterioration result in a decreased vegetative performance of Aphyllanthes monspeliensis, a grassland specialist, but show contrasting effects on its reproductive performance. However, further forest encroachment would increase light competition and soil acidification, threatening its persistence and promoting the payment of the extinction debt if no conservation measures are taken.
Data from: Analysis of statistical correlations between properties of adaptive walks in fitness landscapes
The fitness landscape metaphor has been central in our way of thinking about adaptation. In this scenario, adaptive walks are an idealized dynamics that mimics the uphill movement of an evolving population towards a fitness peak of the landscape. Recent works in experimental evolution have demonstrated that the constraints imposed by epistasis are responsible for reducing the number of accessible mutational pathways towards fitness peaks. Here we exhaustively analyze the statistical properties of adaptive walks for two empirical fitness landscapes and for theoretical NK landscapes. Some general scenario can be drawn from our simulation study. Regardless the dynamics, we observe that the shortest paths are more regularly used. Although the accessibility of a given fitness peak is reasonably correlated to the number of monotonic pathways towards it, the two quantities are not exactly proportional. A negative correlation predictability and mean path divergence is established, and so with the decrease of the number of effective mutational pathways ensues the convergence of the attraction basin of fitness peaks. On the other hand, other features are not conserved among fitness landscapes, such as the relationship between accessibility and predictability.
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