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Neutral evolution

Mauro Santos, Manuel Sapage, Margarida Matos, Susana A M Varela
A spatially explicit, individual-based simulation model is used to study the spread of an allele for mate-choice copying (MCC) through horizontal cultural transmission when female innate preferences do or do not coevolve with a male viability-increasing trait. Evolution of MCC is unlikely when innate female preferences coevolve with the trait, as copier females cannot express a higher preference than non-copier females for high-fitness males. However, if a genetic polymorphism for innate preference persists in the population, MCC can evolve by indirect selection through hitchhiking: the copying allele hitchhikes on the male trait...
March 23, 2017: Evolution; International Journal of Organic Evolution
Tommaso Biagini, Giovanni Chillemi, Gianluigi Mazzoccoli, Alessandro Grottesi, Caterina Fusilli, Daniele Capocefalo, Stefano Castellana, Angelo Luigi Vescovi, Tommaso Mazza
Molecular dynamics (MD) simulation allows one to predict the time evolution of a system of interacting particles. It is widely used in physics, chemistry and biology to address specific questions about the structural properties and dynamical mechanisms of model systems. MD earned a great success in genome research, as it proved to be beneficial in sorting pathogenic from neutral genomic mutations. Considering their computational requirements, simulations are commonly performed on HPC computing devices, which are generally expensive and hard to administer...
February 18, 2017: Briefings in Bioinformatics
Jun Chen, Sylvain Glémin, Martin Lascoux
A central question in evolutionary biology is why some species have more genetic diversity than others and a no less important question is why selection efficacy varies among species. Although these questions have started to be tackled in animals, they have not been addressed to the same extent in plants. Here, we estimated nucleotide diversity at synonymous, πS, and nonsynonymous sites, πN, and a measure of the efficacy of selection, the ratio πN/πS, in 34 animal and 28 plant species using full genome data...
February 25, 2017: Molecular Biology and Evolution
Gisang Park, Yong-Il Kim, Young Heon Kim, Mira Park, Kyu Yeon Jang, Hyunjoon Song, Ki Min Nam
The evolution of the phase and morphology of FeOOH nanorods prepared by a hydrothermal method is studied via X-ray diffraction (XRD) and in situ transmission electron microscopy. The FeOOH nanorod with a tetragonal structure (β-FeOOH) is gradually converted into a rhombohedral Fe2O3 nanorod by a simple thermal treatment. The existence of an intermediate FeOOH structure with high lattice strains during the phase transition is identified by Rietveld analysis using XRD. The electrochemical properties of the nanorods are investigated based on the crystal phases to elucidate their relative catalytic activities...
March 22, 2017: Nanoscale
Esmeralda Vizzi, Oscar A Piñeros, M Daniela Oropeza, Laura Naranjo, José A Suárez, Rixio Fernández, José L Zambrano, Argelia Celis, Ferdinando Liprandi
BACKGROUND: Rotavirus (RV) is the most common cause of severe childhood diarrhea worldwide. Despite Venezuela was among the first developing countries to introduce RV vaccines into their national immunization schedules, RV is still contributing to the burden of diarrhea. Concerns exist about the selective pressure that RV vaccines could exert on the predominant types and/or emergence of new strains. RESULTS: To assess the impact of RV vaccines on the genotype distribution 1 year after the vaccination was implemented, a total of 912 fecal specimens, collected from children with acute gastroenteritis in Caracas from February 2007 to April 2008, were screened, of which 169 (18...
March 21, 2017: Virology Journal
Kenneth B Hoehn, Gerton Lunter, Oliver G Pybus
Phylogenetic methods have shown promise in understanding the development of broadly neutralizing antibody lineages (bNAbs). However, the mutational process that generates these lineages -- somatic hypermutation -- is biased by hotspot motifs, which violates important assumptions in most phylogenetic substitution models. Here, we develop a modified GY94-type substitution model that partially accounts for this context-dependency while preserving independence of sites during calculation. This model shows a substantially better fit to three well-characterized bNAb lineages than the standard GY94 model...
March 17, 2017: Genetics
Sahar Shirani, Ferdi L Hellweger
Molecular observations reveal substantial biogeographic patterns of cyanobacteria within systems of connected lakes. An important question is the relative role of environmental selection and neutral processes in the biogeography of these systems. Here, we quantify the effect of genetic drift and dispersal limitation by simulating individual cyanobacteria cells using an agent-based model (ABM). In the model, cells grow (divide), die, and migrate between lakes. Each cell has a full genome that is subject to neutral mutation (i...
March 16, 2017: Microbial Ecology
D N Wagner, T Z Baris, D I Dayan, X Du, M F Oleksiak, D L Crawford
It has been suggested that adaptive evolution on ecological timescales shapes communities. However, adaptation among environments relies on isolation or large selection coefficients that exceed migration effects. This reliance is tempered if adaptation is polygenic-does not depend on one allele completely replacing another but instead requires small allele frequency changes at many loci. Thus, whether individuals can evolve adaptation to fine-scale habitat variation (for example, microhabitats) is not resolved...
March 15, 2017: Heredity
ThirumalaiSelvi Ulaganathan, Michal T Boniecki, Elizabeth Foran, Vitaliy Buravenkov, Naama Mizrachi, Ehud Banin, William Helbert, Miroslaw Cygler
Ulvan is a complex sulfated polysaccharide biosynthesized by green seaweed and contains predominantly rhamnose, xylose, and uronic acid sugars. Ulvan-degrading enzymes have only recently been identified and added to the CAZy ( ) database as family PL24, but neither their structure nor catalytic mechanism(s) are yet known. Several homologous, new ulvan lyases, have been discovered in Pseudoalteromonas sp. strain PLSV, Alteromonas LOR, and Nonlabens ulvanivorans, defining a new family PL25, with the lyase encoded by the gene PLSV_3936 being one of them...
March 23, 2017: ACS Chemical Biology
Nathan G Marculis, Roger Lui, Mark A Lewis
We investigate the inside dynamics of solutions to integrodifference equations to understand the genetic consequences of a population with nonoverlapping generations undergoing range expansion. To obtain the inside dynamics, we decompose the solution into neutral genetic components. The inside dynamics are given by the spatiotemporal evolution of the neutral genetic components. We consider thin-tailed dispersal kernels and a variety of per capita growth rate functions to classify the traveling wave solutions as either pushed or pulled fronts...
March 13, 2017: Bulletin of Mathematical Biology
Michael B Doud, Scott E Hensley, Jesse D Bloom
Identifying viral mutations that confer escape from antibodies is crucial for understanding the interplay between immunity and viral evolution. We describe a high-throughput approach to quantify the selection that monoclonal antibodies exert on all single amino-acid mutations to a viral protein. This approach, mutational antigenic profiling, involves creating all replication-competent protein variants of a virus, selecting with antibody, and using deep sequencing to identify enriched mutations. We use mutational antigenic profiling to comprehensively identify mutations that enable influenza virus to escape four monoclonal antibodies targeting hemagglutinin, and validate key findings with neutralization assays...
March 2017: PLoS Pathogens
Jeanna A Bugaytsova, Oscar Björnham, Yevgen A Chernov, Pär Gideonsson, Sara Henriksson, Melissa Mendez, Rolf Sjöström, Jafar Mahdavi, Anna Shevtsova, Dag Ilver, Kristof Moonens, Macarena P Quintana-Hayashi, Roman Moskalenko, Christopher Aisenbrey, Göran Bylund, Alexej Schmidt, Anna Åberg, Kristoffer Brännström, Verena Königer, Susanne Vikström, Lena Rakhimova, Anders Hofer, Johan Ögren, Hui Liu, Matthew D Goldman, Jeannette M Whitmire, Jörgen Ådén, Justine Younson, Charles G Kelly, Robert H Gilman, Abhijit Chowdhury, Asish K Mukhopadhyay, G Balakrish Nair, Konstantinos S Papadakos, Beatriz Martinez-Gonzalez, Dionyssios N Sgouras, Lars Engstrand, Magnus Unemo, Dan Danielsson, Sebastian Suerbaum, Stefan Oscarson, Ludmilla A Morozova-Roche, Anders Olofsson, Gerhard Gröbner, Jan Holgersson, Anders Esberg, Nicklas Strömberg, Maréne Landström, Angela M Eldridge, Brett A Chromy, Lori M Hansen, Jay V Solnick, Sara K Lindén, Rainer Haas, Andre Dubois, D Scott Merrell, Staffan Schedin, Han Remaut, Anna Arnqvist, Douglas E Berg, Thomas Borén
The BabA adhesin mediates high-affinity binding of Helicobacter pylori to the ABO blood group antigen-glycosylated gastric mucosa. Here we show that BabA is acid responsive-binding is reduced at low pH and restored by acid neutralization. Acid responsiveness differs among strains; often correlates with different intragastric regions and evolves during chronic infection and disease progression; and depends on pH sensor sequences in BabA and on pH reversible formation of high-affinity binding BabA multimers. We propose that BabA's extraordinary reversible acid responsiveness enables tight mucosal bacterial adherence while also allowing an effective escape from epithelial cells and mucus that are shed into the acidic bactericidal lumen and that bio-selection and changes in BabA binding properties through mutation and recombination with babA-related genes are selected by differences among individuals and by changes in gastric acidity over time...
March 8, 2017: Cell Host & Microbe
Ran Long, Yu Li, Yan Liu, Shuangming Chen, Xusheng Zheng, Chao Gao, Chaohua He, Nanshan Chen, Zeming Qi, Li Song, Jun Jiang, Junfa Zhu, Yujie Xiong
Photocatalytic conversion of CO2 to CH4 - a carbon-neutral fuel represents an appealing approach to remedy the current energy and environmental crisis; however, it suffers from the large production of CO and H2 by side reactions. The design of catalytic sites for CO2 adsorption and activation holds the key to address this grand challenge. In this article, we develop highly selective sites for photocatalytic conversion of CO2 to CH4 by isolating Cu atoms in Pd lattice. According to our synchrotron-radiation characterizations and theoretical simulations, the isolation of Cu atoms in Pd lattice can play dual roles in the enhancement of CO2-to-CH4 conversion: (1) providing the paired Cu-Pd sites for the enhanced CO2 adsorption and the suppressed H2 evolution; and (2) elevating the d-band center of Cu sites for the improved CO2 activation...
March 9, 2017: Journal of the American Chemical Society
Sònia Casillas, Antonio Barbadilla
Molecular population genetics aims to explain genetic variation and molecular evolution from population genetics principles. The field was born 50 years ago with the first measures of genetic variation in allozyme loci, continued with the nucleotide sequencing era, and is currently in the era of population genomics. During this period, molecular population genetics has been revolutionized by progress in data acquisition and theoretical developments. The conceptual elegance of the neutral theory of molecular evolution or the footprint carved by natural selection on the patterns of genetic variation are two examples of the vast number of inspiring findings of population genetics research...
March 2017: Genetics
Zachary K Goldsmith, Aparna K Harshan, James B Gerken, Márton Vörös, Giulia Galli, Shannon S Stahl, Sharon Hammes-Schiffer
NiFe oxyhydroxide materials are highly active electrocatalysts for the oxygen evolution reaction (OER), an important process for carbon-neutral energy storage. Recent spectroscopic and computational studies increasingly support iron as the site of catalytic activity but differ with respect to the relevant iron redox state. A combination of hybrid periodic density functional theory calculations and spectroelectrochemical experiments elucidate the electronic structure and redox thermodynamics of Ni-only and mixed NiFe oxyhydroxide thin-film electrocatalysts...
March 6, 2017: Proceedings of the National Academy of Sciences of the United States of America
Julia Minicka, Santiago F Elena, Natasza Borodynko-Filas, Błażej Rubiś, Beata Hasiów-Jaroszewska
BACKGROUND: Pepino mosaic virus (PepMV) is an emerging plant pathogen that infects tomatoes worldwide. Understanding the factors that influence its evolutionary success is essential for developing new control strategies that may be more robust against the evolution of new viral strains. One of these evolutionary factors is the distribution of mutational fitness effect (DMFE), that is, the fraction of mutations that are lethal, deleterious, neutral, and beneficial on a given viral strain and host species...
March 6, 2017: BMC Evolutionary Biology
David Beauparlant, Peter Rusert, Carsten Magnus, Claus Kadelka, Jacqueline Weber, Therese Uhr, Osvaldo Zagordi, Corinna Oberle, Maria J Duenas-Decamp, Paul R Clapham, Karin J Metzner, Huldrych F Günthard, Alexandra Trkola
A hallmark of HIV-1 infection is the continuously declining number of the virus' predominant target cells, activated CD4+ T cells. With diminishing CD4+ T cell levels, the capacity to utilize alternate cell types and receptors, including cells that express low CD4 receptor levels such as macrophages, thus becomes crucial. To explore evolutionary paths that allow HIV-1 to acquire a wider host cell range by infecting cells with lower CD4 levels, we dissected the evolution of the envelope-CD4 interaction under in vitro culture conditions that mimicked the decline of CD4high target cells, using a prototypic subtype B, R5-tropic strain...
March 2017: PLoS Pathogens
Bin Liu, Yu-Fei Zhao, Hui-Qing Peng, Zhen-Yu Zhang, Chun-Kit Sit, Muk-Fung Yuen, Tie-Rui Zhang, Chun-Sing Lee, Wen-Jun Zhang
Novel 3D Ni1-x Cox Se2 mesoporous nanosheet networks with tunable stoichiometry are successfully synthesized on Ni foam (Ni1-x Cox Se2 MNSN/NF with x ranging from 0 to 0.35). The collective effects of special morphological design and electronic structure engineering enable the integrated electrocatalyst to have very high activity for hydrogen evolution reaction (HER) and excellent stability in a wide pH range. Ni0.89 Co0.11 Se2 MNSN/NF is revealed to exhibit an overpotential (η10 ) of 85 mV at -10 mA cm(-2) in alkaline medium (pH 14) and η10 of 52 mV in acidic solution (pH 0), which are the best among all selenide-based electrocatalysts reported thus far...
March 6, 2017: Advanced Materials
Kazuya Kobayashi
Biodiversity has long been a source of wonder and scientific curiosity. Theoretically, the co-occurrence of competitive species requires niche differentiation, and such differences are well known; however, the neutral theory, which assumes the equivalence of all individuals regardless of the species in a biological community, has successfully recreated observed patterns of biodiversity. In this research, the evolution of sex allocation is demonstrated to be the key to resolving why the neutral theory works well, despite the observed species differences...
March 6, 2017: Scientific Reports
F Débarre
The theoretical investigation of how spatial structure affects the evolution of social behavior has mostly been done under the assumption that parent-offspring strategy transmission is perfect, i.e., for genetically transmitted traits, that mutation is very weak or absent. Here, we investigate the evolution of social behavior in structured populations under arbitrary mutation probabilities. We consider populations of fixed size N, structured such that in the absence of selection, all individuals have the same probability of reproducing or dying (neutral reproductive values are the all same)...
February 28, 2017: Journal of Theoretical Biology
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