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fitness landscape

Vadim I Agol, Anatoly P Gmyl
Reproduction of RNA viruses is typically error-prone due to the infidelity of their replicative machinery and the usual lack of proofreading mechanisms. The error rates may be close to those that kill the virus. Consequently, populations of RNA viruses are represented by heterogeneous sets of genomes with various levels of fitness. This is especially consequential when viruses encounter various bottlenecks and new infections are initiated by a single or few deviating genomes. Nevertheless, RNA viruses are able to maintain their identity by conservation of major functional elements...
June 2018: Microbiology and Molecular Biology Reviews: MMBR
Belén Cotes, Mónica González, Emilio Benítez, Eva De Mas, Gemma Clemente-Orta, Mercedes Campos, Estefanía Rodríguez
The promotion of native vegetation as a habitat for natural enemies, which could increase their abundance and fitness, is especially useful in highly simplified settings such as Mediterranean greenhouse landscapes. Spiders as generalist predators may also be involved in intra-guild predation. However, the niche complementarity provided by spiders as a group means that increased spider diversity may facilitate complementary control actions. In this study, the interactions between spiders, the two major horticultural pests, Bemisia tabaci and Frankliniella occidentalis , and their naturally occurring predators and parasitoids were evaluated in a mix of 21 newly planted shrubs selected for habitat management in a highly disturbed horticultural system...
March 14, 2018: Insects
Yoann Anciaux, Luis-Miguel Chevin, Ophélie Ronce, Guillaume Martin
Evolutionary rescue describes a situation where adaptive evolution prevents the extinction of a population facing a stressing environment. Models of evolutionary rescue could in principle be used to predict the level of stress beyond which extinction becomes likely for species of conservation concern, or conversely the treatment levels most likely to limit the emergence of resistant pests or pathogens. Stress levels are known to affect both the rate of population decline (demographic effect) and the speed of adaptation (evolutionary effect), but the latter aspect has received less attention...
March 13, 2018: Genetics
Katherine M Malan, I Moser
The notion and characterisation of fitness landscapes has helped understand the performance of heuristic algorithms on complex optimisation problems. Many practical problems, however, are constrained, and when significant areas of the search space are infeasible, researchers have intuitively resorted to a variety of constraint-handling techniques intended to help the algorithm manoeuvre through infeasible areas and towards feasible regions of better fitness. It is clear that providing constraint-related feedback to the algorithm to influence its choice of solutions overlays the violation landscape with the fitness landscape in unpredictable ways whose effects on the algorithm cannot be directly measured...
March 12, 2018: Evolutionary Computation
Cheryl Holzmeyer
While academic open access, open data and open science initiatives have proliferated in recent years, facilitating new research resources for health promotion, open initiatives are not one-size-fits-all. Health research particularly illustrates how open initiatives may serve various interests and ends. Open initiatives not only foster new pathways of research access; they also discipline research in new ways, especially when associated with new regimes of research use and peer review, while participating in innovation ecosystems that often perpetuate existing systemic biases toward commercial biomedicine...
March 7, 2018: Health Promotion International
Pengfei Tian, John M Louis, James L Baber, Annie Aniana, Robert Best
Efficient and accurate models to predict the fitness of a sequence would be extremely valuable in protein design. We have explored the use of statistical potentials for the coevolutionary fitness landscape, extracted from known protein sequences, in conjuction with Monte Carlo simulations, as a tool for design. As proof of principle, we created a series of predicted high-fitness sequences for three different protein folds, representative of different structural classes: the GA (all-α) and GB (α/β) binding domains of streptococcal protein G, and an SH3 (all-β) domain...
March 7, 2018: Angewandte Chemie
W Ebeling, R Feistel
In 1971, Manfred Eigen extended the principles of Darwinian evolution to chemical processes, from catalytic networks to the emergence of information processing at the molecular level, leading to the emergence of life. In this paper, we investigate some very general characteristics of this scenario, such as the valuation process of phenotypic traits in a high-dimensional fitness landscape, the effect of spatial compartmentation on the valuation, and the self-organized transition from structural to symbolic genetic information of replicating chain molecules...
March 1, 2018: European Biophysics Journal: EBJ
Michael Sievers, Kirsten M Parris, Stephen E Swearer, Robin Hale
Around cities, natural wetlands are rapidly being destroyed and replaced with wetlands constructed to treat stormwater. Although the intended purpose of these wetlands is to manage urban stormwater, they are inhabited by wildlife that might be exposed to contaminants. These effects will be exacerbated if animals are unable to differentiate between stormwater treatment wetlands of varying quality and some function as 'ecological traps' (i.e. habitats that animals prefer despite fitness being lower than in other habitats)...
March 1, 2018: Ecological Applications: a Publication of the Ecological Society of America
Kristina Crona
We show that genetic recombination can be a powerful mechanism for escaping suboptimal peaks. Recent studies of empirical fitness landscapes reveal complex gene interactions and multiple peaks. However, classical work on recombination largely ignores the effect of complex gene interactions. Briefly, we restrict to fitness landscapes where the global peak is difficult to access. If the optimal genotype can be generated by shuffling genes present in the population, then recombination will produce the genotype...
2018: PloS One
Aysan Ghasemzadeh, Marta Małgorzata Ter Haar, Masoud Shams-Bakhsh, Walter Pirovano, Vitantonio Pantaleo
Next-generation sequencing has opened the door to the reconstruction of viral populations and examination of the composition of mutant spectra in infected cells, tissues, and host organisms. In this chapter we present details on the use of the Shannon entropy method to estimate the site-specific nucleotide relative variability of turnip crinkle virus, a positive (+) stranded RNA plant virus, in a large dataset of short RNAs of Cicer arietinum L., a natural reservoir of the virus. We propose this method as a viral metagenomics tool to provide a more detailed description of the viral quasispecies in infected plant tissue...
2018: Methods in Molecular Biology
Robert A Francis, Jimmy D Taylor, Eric Dibble, Bronson Strickland, Vanessa M Petro, Christine Easterwood, Guiming Wang
Animal habitat selection, among other ecological phenomena, is spatially scale dependent. Habitat selection by American beavers Castor canadensis (hereafter, beaver) has been studied at singular spatial scales, but to date no research addresses multi-scale selection. Our objectives were to determine if beaver habitat selection was specialized to semiaquatic habitats and if variables explaining habitat selection are consistent between landscape and fine spatial scales. We built maximum entropy (MaxEnt) models to relate landscape-scale presence-only data to landscape variables, and used generalized linear mixed models to evaluate fine spatial scale habitat selection using global positioning system (GPS) relocation data...
December 2017: Current Zoology
Farren Curtis, Xiayue Li, Timothy Rose, Alvaro Vazquez-Mayagoitia, Saswata Bhattacharya, Luca M Ghiringhelli, Noa Marom
We present the implementation of GAtor, a massively parallel, first principles genetic algorithm (GA) for molecular crystal structure prediction. GAtor is written in Python and currently interfaces with the FHI-aims code to perform local optimizations and energy evaluations using dispersion-inclusive density functional theory (DFT). GAtor offers a variety of fitness evaluation, selection, crossover, and mutation schemes. Breeding operators designed specifically for molecular crystals provide a balance between exploration and exploitation...
February 26, 2018: Journal of Chemical Theory and Computation
Jonathan P Lynch
I propose that reduced root development would be advantageous for drought resistance in high-input agroecosystems. Selection regimes for crop ancestors and landraces include multiple stresses, intense competition, and variable resource distribution, which favored prolific root production, developmental plasticity in response to resource availability, and maintenance of unspecialized root tissues. High-input agroecosystems have removed many of these constraints to root function. Therefore, root phenotypes that focus on water capture at the expense of ancestral adaptations would be better suited to high-input agroecosystems...
February 17, 2018: Journal of Experimental Botany
Kai Chen, Kevin S Burgess, Xiang-Yun Yang, Ya-Huang Luo, Lian-Ming Gao, De-Zhu Li
The diversity of traits associated with plant regeneration is often shaped by functional trade-offs where plants typically do not excel at every function because resources allocated to one function cannot be allocated to another. By analyzing correlations among seed traits, empirical studies have shown that there is a trade-off between seedling development and the occupation of new habitats, although only a small range of taxa have been tested; whether such trade-off exists in a biodiverse and complex landscape remains unclear...
February 2018: Ecology and Evolution
John N Allan, Richard R Furman
The emergence of targeted therapy for patients with chronic lymphocytic leukemia (CLL) has permanently altered the therapeutic landscape. In both upfront and relapsed settings, safe and effective oral kinase inhibitors are available which rival the responses and durability seen with standard chemo immunotherapy regimens. In 2016, ibrutinib was granted Federal Drug Administration approval for first-line therapy in patients with CLL. While its role as initial therapy for older, unfit or deleted 17p CLL patients is less controversial, its role as first-line treatment for younger fit patients is less clear, begging the question, what is the optimal treatment for these patients, novel agents or standard CIT strategies? In this review, we aim to provide guidance for what we believe is the optimal management of young fit patients with CLL...
March 2018: Best Practice & Research. Clinical Haematology
Elizabeth C Hair, Alexa R Romberg, Raymond Niaura, David B Abrams, Morgane A Bennett, Haijun Xiao, Jessica M Rath, Lindsay Pitzer, Donna Vallone
Introduction: Among youth, the frequency and prevalence of using more than one tobacco (small cigar, cigarette, and hookah) or nicotine-containing product (e-cigarettes-ENDS) are changing. These shifts pose challenges for regulation, intervention, and prevention campaigns because of scant longitudinal data on the stability of use patterns in this changing product landscape. Methods: A nationally representative longitudinal survey of 15- to 21-year olds (n = 15,275) was used to describe transitions between never use, noncurrent use, and past 30-day use of combustible tobacco, e-cigarettes (ENDS), and dual use of both kinds of products...
February 13, 2018: Nicotine & Tobacco Research: Official Journal of the Society for Research on Nicotine and Tobacco
David B Saakian
We consider many-site mutation-recombination models of evolution with selection. We are looking for situations where the recombination increases the mean fitness of the population, and there is an optimal recombination rate. We found two fitness landscapes supporting such nonmonotonic behavior of the mean fitness versus the recombination rate. The first case is related to the evolution near the error threshold on a neutral-network-like fitness landscape, for moderate genome lengths and large population. The more realistic case is the second one, in which we consider the evolutionary dynamics of a finite population on a rugged fitness landscape (the smooth fitness landscape plus some random contributions to the fitness)...
January 2018: Physical Review. E
Paul Grassein, Patrice Delarue, Harold Abraham Scheraga, Gia G Maisuradze, Patrick Senet
Protein folding/unfolding can be analysed experimentally at a local scale by monitoring the physical properties of local probes as a function of the temperature, as for example the distance between fluorophores or the values of chemical shifts of backbone atoms. Here, the analytical Lifson-Roig model for the helix-coil transition is modified to analyse local thermal unfolding of the fast-folder W protein of bacteriophage lambda (gpW) simulated by all-atom molecular dynamics (MD) simulations in explicit solvent at fifteen different temperatures...
February 15, 2018: Journal of Physical Chemistry. B
Michael Manhart, Bharat V Adkar, Eugene I Shakhnovich
Mutations in a microbial population can increase the frequency of a genotype not only by increasing its exponential growth rate, but also by decreasing its lag time or adjusting the yield (resource efficiency). The contribution of multiple life-history traits to selection is a critical question for evolutionary biology as we seek to predict the evolutionary fates of mutations. Here we use a model of microbial growth to show that there are two distinct components of selection corresponding to the growth and lag phases, while the yield modulates their relative importance...
February 14, 2018: Proceedings. Biological Sciences
Jeroen Everaars, Josef Settele, Carsten F Dormann
Solitary bees are important but declining wild pollinators. During daily foraging in agricultural landscapes, they encounter a mosaic of patches with nest and foraging habitat and unsuitable matrix. It is insufficiently clear how spatial allocation of nesting and foraging resources and foraging traits of bees affect their daily foraging performance. We investigated potential brood cell construction (as proxy of fitness), number of visited flowers, foraging habitat visitation and foraging distance (pollination proxies) with the model SOLBEE (simulating pollen transport by solitary bees, tested and validated in an earlier study), for landscapes varying in landscape fragmentation and spatial allocation of nesting and foraging resources...
2018: PloS One
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