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https://www.readbyqxmd.com/read/29141909/local-fitness-landscapes-predict-yeast-evolutionary-dynamics-in-directionally-changing-environments
#1
Florien A Gorter, Mark G M Aarts, Bas J Zwaan, J Arjan G M de Visser
The fitness landscape is a concept that is widely used for understanding and predicting evolutionary adaptation. The topography of the fitness landscape depends critically on the environment, with potentially far-reaching consequences for evolution under changing conditions. However, few studies have assessed directly how empirical fitness landscapes change across conditions, or validated the predicted consequences of such change. We previously evolved replicate yeast populations in the presence of either gradually increasing or constant high concentrations of the heavy metals cadmium (Cd), nickel (Ni), and zinc (Zn), and analysed their phenotypic and genomic changes...
November 15, 2017: Genetics
https://www.readbyqxmd.com/read/29141660/xcell-digitally-portraying-the-tissue-cellular-heterogeneity-landscape
#2
Dvir Aran, Zicheng Hu, Atul J Butte
Tissues are complex milieus consisting of numerous cell types. Several recent methods have attempted to enumerate cell subsets from transcriptomes. However, the available methods have used limited sources for training and give only a partial portrayal of the full cellular landscape. Here we present xCell, a novel gene signature-based method, and use it to infer 64 immune and stromal cell types. We harmonized 1822 pure human cell type transcriptomes from various sources and employed a curve fitting approach for linear comparison of cell types and introduced a novel spillover compensation technique for separating them...
November 15, 2017: Genome Biology
https://www.readbyqxmd.com/read/29138394/critical-mutation-rate-has-an-exponential-dependence-on-population-size-for-eukaryotic-length-genomes-with-crossover
#3
Elizabeth Aston, Alastair Channon, Roman V Belavkin, Danna R Gifford, Rok Krašovec, Christopher G Knight
The critical mutation rate (CMR) determines the shift between survival-of-the-fittest and survival of individuals with greater mutational robustness ("flattest"). We identify an inverse relationship between CMR and sequence length in an in silico system with a two-peak fitness landscape; CMR decreases to no more than five orders of magnitude above estimates of eukaryotic per base mutation rate. We confirm the CMR reduces exponentially at low population sizes, irrespective of peak radius and distance, and increases with the number of genetic crossovers...
November 14, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29138304/refactoring-the-genetic-code-for-increased-evolvability
#4
Gur Pines, James D Winkler, Assaf Pines, Ryan T Gill
The standard genetic code is robust to mutations during transcription and translation. Point mutations are likely to be synonymous or to preserve the chemical properties of the original amino acid. Saturation mutagenesis experiments suggest that in some cases the best-performing mutant requires replacement of more than a single nucleotide within a codon. These replacements are essentially inaccessible to common error-based laboratory engineering techniques that alter a single nucleotide per mutation event, due to the extreme rarity of adjacent mutations...
November 14, 2017: MBio
https://www.readbyqxmd.com/read/29137670/modelling-and-mapping-tick-dynamics-using-volunteered-observations
#5
Irene Garcia-Martí, Raúl Zurita-Milla, Arnold J H van Vliet, Willem Takken
BACKGROUND: Tick populations and tick-borne infections have steadily increased since the mid-1990s posing an ever-increasing risk to public health. Yet, modelling tick dynamics remains challenging because of the lack of data and knowledge on this complex phenomenon. Here we present an approach to model and map tick dynamics using volunteered data. This approach is illustrated with 9 years of data collected by a group of trained volunteers who sampled active questing ticks (AQT) on a monthly basis and for 15 locations in the Netherlands...
November 14, 2017: International Journal of Health Geographics
https://www.readbyqxmd.com/read/29133448/origin-of-life-in-a-digital-microcosm
#6
Nitash C G, Thomas LaBar, Arend Hintze, Christoph Adami
While all organisms on Earth share a common descent, there is no consensus on whether the origin of the ancestral self-replicator was a one-off event or whether it only represented the final survivor of multiple origins. Here, we use the digital evolution system Avida to study the origin of self-replicating computer programs. By using a computational system, we avoid many of the uncertainties inherent in any biochemical system of self-replicators (while running the risk of ignoring a fundamental aspect of biochemistry)...
December 28, 2017: Philosophical Transactions. Series A, Mathematical, Physical, and Engineering Sciences
https://www.readbyqxmd.com/read/29133391/adaptive-benefits-from-small-mutation-supplies-in-an-antibiotic-resistance-enzyme
#7
Merijn L M Salverda, Jeroen Koomen, Bertha Koopmanschap, Mark P Zwart, J Arjan G M de Visser
Populations with large mutation supplies adapt via the "greedy" substitution of the fittest genotype available, leading to fast and repeatable short-term responses. At longer time scales, smaller mutation supplies may in theory lead to larger improvements when distant high-fitness genotypes more readily evolve from lower-fitness intermediates. Here we test for long-term adaptive benefits from small mutation supplies using in vitro evolution of an antibiotic-degrading enzyme in the presence of a novel antibiotic...
November 13, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/29127445/negative-epistasis-in-experimental-rna-fitness-landscapes
#8
REVIEW
Devin P Bendixsen, Bjørn Østman, Eric J Hayden
Mutations and their effects on fitness are a fundamental component of evolution. The effects of some mutations change in the presence of other mutations, and this is referred to as epistasis. Epistasis can occur between mutations in different genes or within the same gene. A systematic study of epistasis requires the analysis of numerous mutations and their combinations, which has recently become feasible with advancements in DNA synthesis and sequencing. Here we review the mutational effects and epistatic interactions within RNA molecules revealed by several recent high-throughput mutational studies involving two ribozymes studied in vitro, as well as a tRNA and a snoRNA studied in yeast...
November 10, 2017: Journal of Molecular Evolution
https://www.readbyqxmd.com/read/29114046/pulsed-evolution-shaped-modern-vertebrate-body-sizes
#9
Michael J Landis, Joshua G Schraiber
The relative importance of different modes of evolution in shaping phenotypic diversity remains a hotly debated question. Fossil data suggest that stasis may be a common mode of evolution, while modern data suggest some lineages experience very fast rates of evolution. One way to reconcile these observations is to imagine that evolution proceeds in pulses, rather than in increments, on geological timescales. To test this hypothesis, we developed a maximum-likelihood framework for fitting Lévy processes to comparative morphological data...
November 7, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/29113978/additive-phenotypes-underlie-epistasis-of-fitness-effects
#10
Andrew M Sackman, Darin R Rokyta
Gene interactions, or epistasis, play a large role in determining evolutionary outcomes. The ruggedness of fitness landscapes, and thus the predictability of evolution and the accessibility of high-fitness genotypes, is determined largely by the pervasiveness of epistasis and the degree of correlation between similar genotypes. We created all possible pairings of three sets of five beneficial first-step mutations fixed during adaptive walks under three different regimes: selection on growth rate alone, on growth rate and thermal stability, and on growth rate and pH stability...
November 7, 2017: Genetics
https://www.readbyqxmd.com/read/29104505/effect-of-population-size-and-mutation-rate-on-the-evolution-of-rna-sequences-on-an-adaptive-landscape-determined-by-rna-folding
#11
Ali R Vahdati, Kathleen Sprouffske, Andreas Wagner
The dynamics of populations evolving on an adaptive landscape depends on multiple factors, including the structure of the landscape, the rate of mutations, and effective population size. Existing theoretical work often makes ad hoc and simplifying assumptions about landscape structure, whereas experimental work can vary important parameters only to a limited extent. We here overcome some of these limitations by simulating the adaptive evolution of RNA molecules, whose fitness is determined by the thermodynamics of RNA secondary structure folding...
2017: International Journal of Biological Sciences
https://www.readbyqxmd.com/read/29093220/parasite-infection-induces-size-dependent-host-dispersal-consequences-for-parasite-persistence
#12
Akira Terui, Keita Ooue, Hirokazu Urabe, Futoshi Nakamura
Host dispersal is now recognized as a key predictor of the landscape-level persistence and expansion of parasites. However, current theories treat post-infection dispersal propensities as a fixed trait, and the plastic nature of host's responses to parasite infection has long been underappreciated. Here, we present a mark-recapture experiment in a single host-parasite system (larval parasites of the freshwater mussel Margaritifera laevis and its salmonid fish host Oncorhynchus masou masou) and provide, to our knowledge, the first empirical evidence that parasite infection induces size-dependent host dispersal in the field...
November 15, 2017: Proceedings. Biological Sciences
https://www.readbyqxmd.com/read/29092002/pstab-prediction-of-stable-mutants-unfolding-curves-stability-maps-and-protein-electrostatic-frustration
#13
Soundhararajan Gopi, Devanshu Devanshu, Praveen Krishna, Athi N Naganathan
Summary: We present a web-server for rapid prediction of changes in protein stabilities over a range of temperatures and experimental conditions upon single- or multiple-point substitutions of charged residues. Potential mutants are identified by a charge-shuffling procedure while the stability changes (i.e. an unfolding curve) are predicted employing an ensemble-based statistical-mechanical model. We expect this server to be a simple yet detailed tool for engineering stabilities, identifying electrostatically frustrated residues, generating local stability maps and in constructing fitness landscapes...
October 28, 2017: Bioinformatics
https://www.readbyqxmd.com/read/29080363/genomics-meets-applied-ecology-characterizing-habitat-quality-for-sloths-in-a-tropical-agro-ecosystem
#14
Emily D Fountain, Jung Koo Kang, Douglas J Tempel, Per J Palsbøll, Jonathan N Pauli, M Zachariah Peery
Understanding how habitat quality in heterogeneous landscapes governs the distribution and fitness of individuals is a fundamental aspect of ecology. While mean individual fitness is generally considered a key to assessing habitat quality, a comprehensive understanding of habitat quality in heterogeneous landscapes requires estimates of dispersal rates among habitat types. The increasing accessibility of genomic approaches, combined with field-based demographic methods, provides novel opportunities for incorporating dispersal estimation into assessments of habitat quality...
October 28, 2017: Molecular Ecology
https://www.readbyqxmd.com/read/29072444/a-free-energy-barrier-caused-by-the-refolding-of-an-oligomeric-intermediate-controls-the-lag-time-of-amyloid-formation-by-hiapp
#15
Arnaldo L Serrano, Justin P Lomont, Ling-Hsien Tu, Daniel P Raleigh, Martin T Zanni
Transiently populated oligomers formed en route to amyloid fibrils may constitute the most toxic aggregates associated with many amyloid-associated diseases. Most nucleation theories used to describe amyloid aggregation predict low oligomer concentrations and do not take into account free energy costs that may be associated with structural rearrangements between the oligomer and fiber states. We have used isotope labeling and two-dimensional infrared spectroscopy to spectrally resolve an oligomeric intermediate during the aggregation of the human islet amyloid protein (hIAPP or amylin), the protein associated with type II diabetes...
November 7, 2017: Journal of the American Chemical Society
https://www.readbyqxmd.com/read/29069345/adaptive-evolution-under-extreme-genetic-drift-in-oxidatively-stressed-caenorhabditis-elegans
#16
Stephen F Christy, Riana I Wernick, Michael J Lue, Griselda Velasco, Dana K Howe, Dee R Denver, Suzanne Estes
A mutation-accumulation (MA) experiment with Caenorhabditis elegans nematodes was conducted in which replicate, independently evolving lines were initiated from a low-fitness mitochondrial electron transport chain mutant, gas-1 . The original intent of the study was to assess the effect of ETC dysfunction involving elevated reactive oxygen species (ROS) production on patterns of spontaneous germline mutation. In contrast to results of standard MA experiments, gas-1 MA lines evolved slightly higher mean fitness alongside reduced among-line genetic variance compared to their ancestor...
October 23, 2017: Genome Biology and Evolution
https://www.readbyqxmd.com/read/29062891/the-landscape-of-transcription-errors-in-eukaryotic-cells
#17
Jean-Francois Gout, Weiyi Li, Clark Fritsch, Annie Li, Suraiya Haroon, Larry Singh, Ding Hua, Hossein Fazelinia, Zach Smith, Steven Seeholzer, Kelley Thomas, Michael Lynch, Marc Vermulst
Accurate transcription is required for the faithful expression of genetic information. To understand the molecular mechanisms that control the fidelity of transcription, we used novel sequencing technology to provide the first comprehensive analysis of the fidelity of transcription in eukaryotic cells. Our results demonstrate that transcription errors can occur in any gene, at any location, and affect every aspect of protein structure and function. In addition, we show that multiple proteins safeguard the fidelity of transcription and provide evidence suggesting that errors that evade these layers of RNA quality control profoundly affect the physiology of living cells...
October 2017: Science Advances
https://www.readbyqxmd.com/read/29062002/the-space-of-genotypes-is-a-network-of-networks-implications-for-evolutionary-and-extinction-dynamics
#18
Pablo Yubero, Susanna Manrubia, Jacobo Aguirre
The forcing that environmental variation exerts on populations causes continuous changes with only two possible evolutionary outcomes: adaptation or extinction. Here we address this topic by studying the transient dynamics of populations on complex fitness landscapes. There are three important features of realistic landscapes of relevance in the evolutionary process: fitness landscapes are rough but correlated, their fitness values depend on the current environment, and many (often most) genotypes do not yield viable phenotypes...
October 23, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29061895/the-topology-of-evolutionary-novelty-and-innovation-in-macroevolution
#19
REVIEW
Douglas H Erwin
Sewall Wright's fitness landscape introduced the concept of evolutionary spaces in 1932. George Gaylord Simpson modified this to an adaptive, phenotypic landscape in 1944 and since then evolutionary spaces have played an important role in evolutionary theory through fitness and adaptive landscapes, phenotypic and functional trait spaces, morphospaces and related concepts. Although the topology of such spaces is highly variable, from locally Euclidean to pre-topological, evolutionary change has often been interpreted as a search through a pre-existing space of possibilities, with novelty arising by accessing previously inaccessible or difficult to reach regions of a space...
December 5, 2017: Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences
https://www.readbyqxmd.com/read/29054926/biomolecular-coevolution-and-its-applications-going-from-structure-prediction-toward-signaling-epistasis-and-function
#20
REVIEW
Mehari B Zerihun, Alexander Schug
Evolution leads to considerable changes in the sequence of biomolecules, while their overall structure and function remain quite conserved. The wealth of genomic sequences, the 'Biological Big Data', modern sequencing techniques provide allows us to investigate biomolecular evolution with unprecedented detail. Sophisticated statistical models can infer residue pair mutations resulting from spatial proximity. The introduction of predicted spatial adjacencies as constraints in biomolecular structure prediction workflows has transformed the field of protein and RNA structure prediction toward accuracies approaching the experimental resolution limit...
October 20, 2017: Biochemical Society Transactions
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