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fitness landscape

Ina Monika Margret Heidinger, Silke Hein, Heike Feldhaar, Hans-Joachim Poethke
In the highly fragmented landscape of central Europe, dispersal is of particular importance as it determines the long-term survival of animal populations. Dispersal not only secures the re-colonization of patches where populations went extinct, it may also rescue small populations and thus prevent local extinction events. As dispersal involves different individual fitness costs, the decision to disperse should not be random but context-dependent and often will be biased towards a certain group of individuals (e...
October 24, 2016: Insect Science
Amanda M West, Paul H Evangelista, Catherine S Jarnevich, Nicholas E Young, Thomas J Stohlgren, Colin Talbert, Marian Talbert, Jeffrey Morisette, Ryan Anderson
Early detection of invasive plant species is vital for the management of natural resources and protection of ecosystem processes. The use of satellite remote sensing for mapping the distribution of invasive plants is becoming more common, however conventional imaging software and classification methods have been shown to be unreliable. In this study, we test and evaluate the use of five species distribution model techniques fit with satellite remote sensing data to map invasive tamarisk (Tamarix spp.) along the Arkansas River in Southeastern Colorado...
October 11, 2016: Journal of Visualized Experiments: JoVE
Carrie A Deans, Spencer T Behmer, Justin Fiene, Gregory A Sword
Plant soluble protein and digestible carbohydrate content significantly affect insect herbivore fitness, but studies reporting plant protein and carbohydrate content are rare. Instead, the elements nitrogen and carbon often are used as surrogates for plant protein and digestible carbohydrate content, respectively. However, this is problematic for two reasons. First, carbon is found in all organic molecules, which precludes strong correlations with ecologically important dietary macronutrients (e.g., digestible carbohydrates, the primary energy source for most insect herbivores)...
October 13, 2016: Journal of Chemical Ecology
Lars Qviller, Hildegunn Viljugrein, Leif Egil Loe, Erling L Meisingset, Atle Mysterud
BACKGROUND: Many wingless ectoparasites have a limited capacity for active movement and are therefore primarily dependent on hitchhiking on their hosts for transportation. The distribution of the tick Ixodes ricinus is expected to depend mainly on transportation by hosts and tick subsequent survival in areas where they drop off. In Europe, the most important hosts of adult female I. ricinus are cervids. The extensive space use of large hosts provides a much larger dispersal potential for I...
October 13, 2016: Parasites & Vectors
C Emi Fergus, Andrew O Finley, Patricia A Soranno, Tyler Wagner
The nutrient-water color paradigm is a framework to characterize lake trophic status by relating lake primary productivity to both nutrients and water color, the colored component of dissolved organic carbon. Total phosphorus (TP), a limiting nutrient, and water color, a strong light attenuator, influence lake chlorophyll a concentrations (CHL). But, these relationships have been shown in previous studies to be highly variable, which may be related to differences in lake and catchment geomorphology, the forms of nutrients and carbon entering the system, and lake community composition...
2016: PloS One
Benjamin J Schoville, Kyle S Brown, Jacob A Harris, Jayne Wilkins
The Middle Stone Age (MSA) is associated with early evidence for symbolic material culture and complex technological innovations. However, one of the most visible aspects of MSA technologies are unretouched triangular stone points that appear in the archaeological record as early as 500,000 years ago in Africa and persist throughout the MSA. How these tools were being used and discarded across a changing Pleistocene landscape can provide insight into how MSA populations prioritized technological and foraging decisions...
2016: PloS One
Vladimiras Oleinikovas, Giorgio Saladino, Benjamin P Cossins, Francesco L Gervasio
Cryptic pockets, i.e. sites on protein targets that only become apparent when drugs bind, provide a promising alternative to classical binding sites for drug development. Here we investigate the nature and dynamical properties of cryptic sites in four pharmacologically relevant targets, while comparing the efficacy of various simulation-based approaches in discovering them. We find that the studied cryptic sites do not correspond to local minima in the computed conformational free energy landscape of the unliganded proteins...
October 11, 2016: Journal of the American Chemical Society
David B Saakian, Tatiana Yakushkina, Chin-Kun Hu
We propose a modification of the Crow-Kimura and Eigen models of biological molecular evolution to include a mutator gene that causes both an increase in the mutation rate and a change in the fitness landscape. This mutator effect relates to a wide range of biomedical problems. There are three possible phases: mutator phase, mixed phase and non-selective phase. We calculate the phase structure, the mean fitness and the fraction of the mutator allele in the population, which can be applied to describe cancer development and RNA viruses...
October 10, 2016: Scientific Reports
Sean C Hackett, Michael B Bonsall
The evolution of resistance to pesticides by insect pests is a significant challenge for sustainable agriculture. For transgenic crops expressing Bacillus thuringiensis (Bt), crystalline (Cry) toxins resistance evolution may be delayed by the high-dose/refuge strategy in which a non-toxic refuge is planted to promote the survival of susceptible insects. The high-dose/refuge strategy may interact with fitness costs associated with resistance alleles to further delay resistance. However, while a diverse range of fitness costs are reported in the field, they are typically represented as a fixed reduction in survival or viability which is insensitive to ecological conditions such as competition...
October 2016: Journal of Applied Ecology
Saskya van Nouhuys, Minna Kohonen, Anne Duplouy
The success of maternally transmitted endosymbiotic bacteria, such as Wolbachia, is directly linked to their host reproduction but in direct conflict with other parasites that kill the host before it reaches reproductive maturity. Therefore, symbionts that have evolved strategies to increase their host's ability to evade lethal parasites may have high penetrance, while detrimental symbionts would be selected against, leading to lower penetrance or extinction from the host population. In a natural population of the parasitoid wasp Hyposoter horticola in the Åland Islands (Finland), the Wolbachia strain wHho persists at an intermediate prevalence (∼50%)...
October 1, 2016: Journal of Experimental Biology
Fabio Daolio, Arnaud Liefooghe, Sébastien Verel, Hernán Aguirre, Kiyoshi Tanaka
In this paper, we attempt to understand and to contrast the impact of problem features on the performance of randomized search heuristics for black-box multi-objective combinatorial optimization problems. At first, we measure the performance of two conventional dominance-based approaches with unbounded archive on a benchmark of enumerable binary optimization problems with tunable ruggedness, objective space dimension, and objective correlation (ρMNK-landscapes). Precisely, we investigate the expected runtime required by a global evolutionary optimization algorithm with an ergodic variation operator (GSEMO) and by a neighborhood-based local search heuristic (PLS), to identify a [Formula: see text]-approximation of the Pareto set...
September 30, 2016: Evolutionary Computation
Elsa Y León Marroquin, José A Herrera González, Miguel A Camacho López, José E Villarreal Barajas, Olivia A García-Garduño
Radiochromic film has become an important tool to verify dose distributions for intensity-modulated radiotherapy (IMRT) and quality assurance (QA) procedures. A new radiochromic film model, EBT3, has recently become available, whose composition and thickness of the sensitive layer are the same as those of previous EBT2 films. However, a matte polyester layer was added to EBT3 to prevent the formation of Newton's rings. Furthermore, the symmetrical design of EBT3 allows the user to eliminate side-orientation dependence...
2016: Journal of Applied Clinical Medical Physics
Alita R Burmeister, Richard E Lenski, Justin R Meyer
The origin of new and complex structures and functions is fundamental for shaping the diversity of life. Such key innovations are rare because they require multiple interacting changes. We sought to understand how the adaptive landscape led to an innovation whereby bacteriophage λ evolved the new ability to exploit a receptor, OmpF, on Escherichia coli cells. Previous work showed that this ability evolved repeatedly, despite requiring four mutations in one virus gene. Here, we examine how this innovation evolved by studying six intermediate genotypes of λ isolated during independent transitions to exploit OmpF and comparing them to their ancestor...
September 28, 2016: Proceedings. Biological Sciences
Daniel T Harris, Ningyan Wang, Timothy P Riley, Scott D Anderson, Nishant K Singh, Erik Procko, Brian M Baker, David M Kranz
Proteins are often engineered to have higher affinity for their ligands in order to achieve therapeutic benefit. For example, many studies have used phage- or yeast-display libraries of mutants within complementarity determining regions (CDRs) to affinity mature antibodies and T cell receptors (TCRs). However, these approaches do not allow rapid assessment or evolution across the entire interface. By combining directed evolution with deep sequencing it is now possible to generate sequence fitness landscapes that survey the impact of every amino acid substitution across the entire protein-protein interface...
September 28, 2016: Journal of Biological Chemistry
Jesus F San-Miguel, Hermann Einsele, Philippe Moreau
: Panobinostat is an oral pan-histone deacetylase inhibitor developed by Novartis. Panobinostat acts via epigenetic modification and inhibition of the aggresome pathway. In August 2015, the European Commission authorized panobinostat for use in combination with bortezomib and dexamethasone for the treatment of relapsed or relapsed and refractory multiple myeloma (MM) in patients who have received ≥2 prior regimens including bortezomib and an immunomodulatory drug. In January 2016, the National Institute for Health and Care Excellence recommended panobinostat for use in the same combination and patient population...
September 27, 2016: Advances in Therapy
Chele Martínez-Martí, María V Jiménez-Franco, J Andrew Royle, José A Palazón, José F Calvo
Occurrence models that account for imperfect detection of species are increasingly used for estimating geographical range, for determining species-landscape relations and to prioritize conservation actions worldwide. In 2010, we conducted a large-scale survey in Río Muni, the mainland territory of Equatorial Guinea, which aimed to estimate the probabilities of occurrence and detection of threatened mammals based on environmental covariates, and to identify priority areas for conservation. Interviews with hunters were designed to record presence/absence data of seven species (golden cat, leopard, forest elephant, forest buffalo, western gorilla, chimpanzee and mandrill) in 225 sites throughout the region...
September 26, 2016: Scientific Reports
Marco Basile, Francesco Valerio, Rosario Balestrieri, Mario Posillico, Rodolfo Bucci, Tiziana Altea, Bruno De Cinti, Giorgio Matteucci
Environmental heterogeneity affects not only the distribution of a species but also its local abundance. High heterogeneity due to habitat alteration and fragmentation can influence the realized niche of a species, lowering habitat suitability as well as reducing local abundance. We investigate whether a relationship exists between habitat suitability and abundance and whether both are affected by fragmentation. Our aim was to assess the predictive power of such a relationship to derive advice for environmental management...
2016: PeerJ
Diego Pesce, Niles Lehman, J Arjan G M de Visser
The origin and evolution of sex, and the associated role of recombination, present a major problem in biology. Sex typically involves recombination of closely related DNA or RNA sequences, which is fundamentally a random process that creates but also breaks up beneficial allele combinations. Directed evolution experiments, which combine in vitro mutation and recombination protocols with in vitro or in vivo selection, have proved to be an effective approach for improving functionality of nucleic acids and enzymes...
October 19, 2016: Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences
Kavita Jain, Sona John
We study a continuous time model for the frequency distribution of an infinitely large asexual population in which both beneficial and deleterious mutations occur and fitness is additive. When beneficial mutations are ignored, the exact solution for the frequency distribution is known to be a Poisson distribution. Here we include beneficial mutations and obtain exact expressions for the frequency distribution at all times using an eigenfunction expansion method. We find that the stationary distribution is non-Poissonian and related to the Bessel function of the first kind...
September 9, 2016: Theoretical Population Biology
Chelsie K Sievers, Luli S Zou, Perry J Pickhardt, Kristina A Matkowskyj, Dawn M Albrecht, Linda Clipson, Jeffery W Bacher, B Dustin Pooler, Fouad J Moawad, Brooks D Cash, Mark Reichelderfer, Tien N Vo, Michael A Newton, Bret R Larget, Richard B Halberg
OBJECTIVE AND DESIGN: The goal of the study was to determine whether the mutational profile of early colorectal polyps correlated with growth behaviour. The growth of small polyps (6-9 mm) that were first identified during routine screening of patients was monitored over time by interval imaging with CT colonography. Mutations in these lesions with known growth rates were identified by targeted next-generation sequencing. The timing of mutational events was estimated using computer modelling and statistical inference considering several parameters including allele frequency and fitness...
September 8, 2016: Gut
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