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"Natural selection"

Kit D Longden
Color is famous for not existing in the external world: our brains create the perception of color from the spatial and temporal patterns of the wavelength and intensity of light. For an intangible quality, we have detailed knowledge of its origins and consequences. Much is known about the organization and evolution of the first phases of color processing, the filtering of light in the eye and processing in the retina, and about the final phases, the roles of color in behavior and natural selection. To understand how color processing in the central brain has evolved, we need well-defined pathways or circuitry where we can gauge how color contributes to the computations involved in specific behaviors...
October 24, 2016: Current Biology: CB
Pedro Jordano
Species-specific traits constrain the ways organisms interact in nature. Some pairwise interactions among coexisting species simply do not occur; they are impossible to observe despite the fact that partners coexist in the same place. The author discusses these 'forbidden links' of species interaction networks. Photo: a sphingid moth, Manduca sexta visiting a flower of Tocoyena formosa (Rubiaceae) in the Brazilian Cerrado; tongue and corolla tube lengths approximately 100 mm. Courtesy of Felipe Amorim. Sazatornil, F...
November 2016: Journal of Animal Ecology
Annat Haber, Ian Dworkin
The structure of environmentally induced phenotypic covariation can influence the effective strength and magnitude of natural selection. Yet our understanding of the factors that contribute to and influence the evolutionary lability of such covariation is poor. Most studies have either examined environmental variation without accounting for covariation, or examined phenotypic and genetic covariation without distinguishing the environmental component. In this study we examined the effect of mutational perturbations on different properties of environmental covariation, as well as mean shape...
October 25, 2016: Evolution; International Journal of Organic Evolution
Julie B Hébert, Sonja J Scheffer, David J Hawthorne
Evolutionary radiations have been well documented in plants and insects, and natural selection may often underly these radiations. If radiations are adaptive, the diversity of species could be due to ecological speciation in these lineages. Agromyzid flies exhibit patterns of repeated host-associated radiations. We investigated whether host-associated population divergence and evidence of divergent selection exist in the leaf miner Phytomyza glabricola on its sympatric host plants, the holly species, Ilex coriacea and I...
September 2016: Ecology and Evolution
Arif Uddin, Monisha Nath Choudhury, Supriyo Chakraborty
The mitochondrially encoded NADH:ubiquinone oxidoreductase core subunit 1 (MT-ND1) gene is a subunit of the respiratory chain complex I and involved in the first step of the electron transport chain of oxidative phosphorylation (OXPHOS). To understand the pattern of compositional properties, codon usage and expression level of mitochondrial ND1 genes in pisces, aves, and mammals, we used bioinformatic approaches as no work was reported earlier. In this study, a perl script was used for calculating nucleotide contents and different codon usage bias parameters...
October 24, 2016: Mitochondrial DNA. Part A. DNA Mapping, Sequencing, and Analysis
Peter R Wiecha, Arnaud Arbouet, Christian Girard, Aurélie Lecestre, Guilhem Larrieu, Vincent Paillard
The rational design of photonic nanostructures consists of anticipating their optical response from systematic variations of simple models. This strategy, however, has limited success when multiple objectives are simultaneously targeted, because it requires demanding computational schemes. To this end, evolutionary algorithms can drive the morphology of a nano-object towards an optimum through several cycles of selection, mutation and cross-over, mimicking the process of natural selection. Here, we present a numerical technique that can allow the design of photonic nanostructures with optical properties optimized along several arbitrary objectives...
October 24, 2016: Nature Nanotechnology
S Des Roches, R Sollmann, K Calhoun, A Rothstein, E B Rosenblum
Measuring links among genotype, phenotype, and survival in the wild has long been a focus of studies of adaptation. We conducted a four-year capture-recapture study to measure survival by genotype and phenotype in the Southwestern Fence Lizard (Sceloporus cowlesi) at the White Sands ecotone (transition area between white sands and dark soil habitats). We report several unanticipated findings. First, in contrast with previous work showing that cryptic blanched colouration in S. cowlesi from the heart of the dunes is associated with mutations in the melanocortin-1 receptor gene (Mc1r), ecotonal S...
October 24, 2016: Molecular Ecology
Gorana G Stamenković, Valentina S Ćirković, Marina M Šiljić, Jelena V Blagojević, Aleksandra M Knežević, Ivana D Joksić, Maja P Stanojević
The aim of this study was to estimate substitution rate and imprints of natural selection on parvovirus B19 genotype 1. Studied datasets included 137 near complete coding B19 genomes (positions 665 to 4851) for phylogenetic and substitution rate analysis and 146 and 214 partial genomes for selection analyses in open reading frames ORF1 and ORF2, respectively, collected 1973-2012 and including 9 newly sequenced isolates from Serbia. Phylogenetic clustering assigned majority of studied isolates to G1A. Nucleotide substitution rate for total coding DNA was 1...
October 24, 2016: Scientific Reports
Seila Omer, Timothy J Harlow, Johann Peter Gogarten
Finding a signature of purifying selection in a gene is usually interpreted as evidence for the gene providing a function that is targeted by natural selection. This opinion offers a very different hypothesis: purifying selection may be due to removing harmful mutations from the population, that is, the gene and its encoded protein become harmful after a mutation occurred, possibly because the mutated protein interferes with the translation machinery, or because of toxicity of the misfolded protein. Finding a signature of purifying selection should not automatically be considered proof of the gene's selectable function...
October 20, 2016: Trends in Microbiology
Evangelina Silva-Santiago, Juan Pablo Pardo, Rolando Hernández-Muñoz, Armando Aranda-Anzaldo
During the interphase the nuclear DNA of metazoan cells is organized in supercoiled loops anchored to constituents of a nuclear substructure or compartment known as the nuclear matrix. The stable interactions between DNA and the nuclear matrix (NM) correspond to a set of topological relationships that define a nuclear higher-order structure (NHOS). Current evidence suggests that the NHOS is cell-type-specific. Biophysical evidence and theoretical models suggest that thermodynamic and structural constraints drive the actualization of DNA-NM interactions...
October 19, 2016: Gene
Daniel Nichol, Mark Robertson-Tessi, Peter Jeavons, Alexander R A Anderson
Non-genetic variation in phenotypes, or bet-hedging, has been observed as a driver of drug resistance in both bacterial infections and cancers. Here, we study how bet-hedging emerges in the genotype-phenotype mapping through a simple interaction model: a molecular switch. We use simple Chemical Reaction Networks to implement stochastic switches that map gene products to phenotypes and investigate the impact of structurally distinct mappings on the evolution of phenotypic heterogeneity. Bet-hedging naturally emerges within this model and is robust to evolutionary loss through mutations to both the expression of individual genes and to the network itself...
October 21, 2016: Genetics
Yohann Nédélec, Joaquín Sanz, Golshid Baharian, Zachary A Szpiech, Alain Pacis, Anne Dumaine, Jean-Christophe Grenier, Andrew Freiman, Aaron J Sams, Steven Hebert, Ariane Pagé Sabourin, Francesca Luca, Ran Blekhman, Ryan D Hernandez, Roger Pique-Regi, Jenny Tung, Vania Yotova, Luis B Barreiro
Individuals from different populations vary considerably in their susceptibility to immune-related diseases. To understand how genetic variation and natural selection contribute to these differences, we tested for the effects of African versus European ancestry on the transcriptional response of primary macrophages to live bacterial pathogens. A total of 9.3% of macrophage-expressed genes show ancestry-associated differences in the gene regulatory response to infection, and African ancestry specifically predicts a stronger inflammatory response and reduced intracellular bacterial growth...
October 20, 2016: Cell
Hélène Quach, Maxime Rotival, Julien Pothlichet, Yong-Hwee Eddie Loh, Michael Dannemann, Nora Zidane, Guillaume Laval, Etienne Patin, Christine Harmant, Marie Lopez, Matthieu Deschamps, Nadia Naffakh, Darragh Duffy, Anja Coen, Geert Leroux-Roels, Frederic Clément, Anne Boland, Jean-François Deleuze, Janet Kelso, Matthew L Albert, Lluis Quintana-Murci
Humans differ in the outcome that follows exposure to life-threatening pathogens, yet the extent of population differences in immune responses and their genetic and evolutionary determinants remain undefined. Here, we characterized, using RNA sequencing, the transcriptional response of primary monocytes from Africans and Europeans to bacterial and viral stimuli-ligands activating Toll-like receptor pathways (TLR1/2, TLR4, and TLR7/8) and influenza virus-and mapped expression quantitative trait loci (eQTLs)...
October 20, 2016: Cell
Kerry A Geiler-Samerotte, Yuan O Zhu, Benjamin E Goulet, David W Hall, Mark L Siegal
The protein-folding chaperone Hsp90 has been proposed to buffer the phenotypic effects of mutations. The potential for Hsp90 and other putative buffers to increase robustness to mutation has had major impact on disease models, quantitative genetics, and evolutionary theory. But Hsp90 sometimes contradicts expectations for a buffer by potentiating rapid phenotypic changes that would otherwise not occur. Here, we quantify Hsp90's ability to buffer or potentiate (i.e., diminish or enhance) the effects of genetic variation on single-cell morphological features in budding yeast...
October 2016: PLoS Biology
Szabolcs Makai, László Tamás, Angéla Juhász
Wheat has been cultivated for 10000 years and ever since the origin of hexaploid wheat it has been exempt from natural selection. Instead, it was under the constant selective pressure of human agriculture from harvest to sowing during every year, producing a vast array of varieties. Wheat has been adopted globally, accumulating variation for genes involved in yield traits, environmental adaptation and resistance. However, one small but important part of the wheat genome has hardly changed: the regulatory regions of both the x- and y-type high molecular weight glutenin subunit (HMW-GS) genes, which are alone responsible for approximately 12% of the grain protein content...
2016: Frontiers in Plant Science
Anton Suvorov, Nicholas O Jensen, Camilla R Sharkey, M Stanley Fujimoto, Paul Bodily, Haley M Cahill Wightman, T Heath Ogden, Mark J Clement, Seth M Bybee
Gene duplication plays a central role in adaptation to novel environments by providing new genetic material for functional divergence and evolution of biological complexity. Several evolutionary models have been proposed for gene duplication to explain how new gene copies are preserved by natural selection but these models have rarely been tested using empirical data. Opsin proteins, when combined with a chromophore, form a photopigment that is responsible for the absorption of light, the first step in the phototransduction cascade...
October 18, 2016: Molecular Ecology
Shauna M Baillie, Andrew M Muir, Michael J Hansen, Charles C Krueger, Paul Bentzen
BACKGROUND: Adaptive radiation involving a colonizing phenotype that rapidly evolves into at least one other ecological variant, or ecotype, has been observed in a variety of freshwater fishes in post-glacial environments. However, few studies consider how phenotypic traits vary with regard to neutral genetic partitioning along ecological gradients. Here, we present the first detailed investigation of lake trout Salvelinus namaycush that considers variation as a cline rather than discriminatory among ecotypes...
October 19, 2016: BMC Evolutionary Biology
Ricky-John Spencer, James U Van Dyke, Michael B Thompson
Ecological traps are threats to organisms, and exist in a range of biological systems. A subset of ecological trap theory is the "ethological trap," whereby behaviors canalized by past natural selection become traps when environments change rapidly. Invasive predators are major threats to imperiled species and their ability to exploit canalized behaviors of naive prey is particularly important for the establishment of the predator and the decline of the native prey. Our study uses ecological theory to demonstrate that invasive predator controls require shifts in management priorities...
October 2016: Ecological Applications: a Publication of the Ecological Society of America
Mahendra Kumar Prajapat, Isha Shroff, R G Brajesh, Supreet Saini
Cooperation benefits individual cells in a microbial population by helping accomplish tasks which are difficult or non-beneficial for individuals in the population to carry out by themselves. Hence, numerous examples exist of bacteria cooperating and working towards a common objective. The sharing of a common public good via quorum sensing is one of the ways of cooperation among individuals of many microbial populations. However, cheaters exploit cooperators in a population by not contributing to the production of the common goods but enjoy benefits from goods secreted by cooperating individuals...
October 18, 2016: Molecular BioSystems
Mareike Cora Janiak
All living organisms need to consume nutrients to grow, survive, and reproduce, making the successful acquisition of food resources a powerful selective pressure. However, acquiring food is only part of the challenge. While all animals spend much of their daily activity budget hunting, searching for, or otherwise procuring food, a large part of what is involved in overall nutrition occurs once the meal has been swallowed. Most nutritional components are too complex for immediate use and must be broken down into simpler compounds, which can then be absorbed by the body...
September 2016: Evolutionary Anthropology
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