scholarly journals The ABCs of Experimental Evolution

2013 ◽  
Vol 2013 ◽  
pp. 1-7
Author(s):  
Zaid Abdo ◽  
Mathew Stein ◽  
Andrzej Wojtowicz ◽  
Kim M. Pepin
Keyword(s):  
Statistical Inference ◽  
Experimental Evolution ◽  
Selection Pressure ◽  
Sequence Data ◽  
Mechanistic Model ◽  
Evolutionary Process ◽  
Microbial Evolution ◽  
Simple Method ◽  
Underlying Mechanisms ◽  
Many Sources

Microbial evolution is complex and is influenced by many sources of variation. Experimental evolution is no exception, although it is more controlled, easily replicated, and typically devoid of interactions between species. Mathematical modeling of the evolutionary process can help in understanding the underlying mechanisms that drive outcome of such experiments. These models can be complex and parameter rich, limiting their feasibility for statistical inference. In this paper, we introduce the use of Approximate Bayesian Computation (ABC) as a tool for statistical inference in the study of experimental evolution. ABC is a fast and simple method for fitting complex models to data. We utilize this method, coupled with a mechanistic model of experimental evolution, to study the evolution process of bacteriophage ϕX174 under benign selection pressure. Our results highlight three mutation-selection scenarios that could explain this process: high mutation/low selection pressure, low mutation/high selection pressure, and low mutation/low selection pressure, with posterior support of 19%, 9.5%, and 71.5% for each of these scenarios, respectively. Sequence data support the first candidate. Though surprising, this scenario was not improbable based on our analysis.

scholarly journals Sequence analysis of heparan sulphate and heparin oligosaccharides

1999 ◽  
Vol 339 (3) ◽  
pp. 767-773 ◽  
Author(s):  
Romain R. VIVÈS ◽  
David A. PYE ◽  
Markku SALMIVIRTA ◽  
John J. HOPWOOD ◽  
Ulf LINDAHL ◽  
...  
Keyword(s):  
Sequence Analysis ◽  
Protein Interactions ◽  
Sequence Data ◽  
Specific Binding ◽  
Heparan Sulphate ◽  
Biologically Active ◽  
Simple Method ◽  
Gag Protein ◽  
Specific Binding Sites ◽  
Strong Anion Exchange

The biological activity of heparan sulphate (HS) and heparin largely depends on internal oligosaccharide sequences that provide specific binding sites for an extensive range of proteins. Identification of such structures is crucial for the complete understanding of glycosaminoglycan (GAG)-protein interactions. We describe here a simple method of sequence analysis relying on the specific tagging of the sugar reducing end by 3H radiolabelling, the combination of chemical scission and specific enzymic digestion to generate intermediate fragments, and the analysis of the generated products by strong-anion-exchange HPLC. We present full sequence data on microgram quantities of four unknown oligosaccharides (three HS-derived hexasaccharides and one heparin-derived octasaccharide) which illustrate the utility and relative simplicity of the technique. The results clearly show that it is also possible to read sequences of inhomogeneous preparations. Application of this technique to biologically active oligosaccharides should accelerate progress in the understanding of HS and heparin structure-function relationships and provide new insights into the primary structure of these polysaccharides.

Energy Transfer in a Linear Turbulence Model

2018 ◽  
Author(s):  
Bendegúz Dezső Bak ◽  
Tamás Kalmár-Nagy
Keyword(s):  
Energy Transfer ◽  
Energy Spectrum ◽  
Isotropic Turbulence ◽  
Mechanistic Model ◽  
Viscous Friction ◽  
Scaling Exponent ◽  
Engineering Systems ◽  
Simple Method ◽  
The Masses ◽  
Binary Tree Structure

Energy transfer is present in many natural and engineering systems which include different scales. It is important to study the energy cascade (which refers to the energy transfer among the different scales) of such systems. A well-known example is turbulent flow in which the kinetic energy of large vortices is transferred to smaller ones. Below a threshold vortex scale the energy is dissipated due to viscous friction. We introduce a mechanistic model of turbulence which consists of masses connected by springs arranged in a binary tree structure. To represent the various scales, the masses are gradually decreased in lower levels. The bottom level of the model contains dampers to provide dissipation. We define the energy spectrum of the model as the fraction of the total energy stored in each level. A simple method is provided to calculate this spectrum in the asymptotic limit, and the spectra of systems having different stiffness distributions are calculated. We find the stiffness distribution for which the energy spectrum has the same scaling exponent (−5/3) as the Kolmogorov spectrum of 3D homogeneous, isotropic turbulence.

scholarly journals Intrinsic Noise and the Design of the Genetic Machinery

1983 ◽  
Vol 36 (1) ◽  
pp. 77 ◽  
Author(s):  
DC Reanney ◽  
DG MacPhee ◽  
J Pressing
Keyword(s):  
Life Style ◽  
Selection Pressure ◽  
Evolutionary Process ◽  
Intrinsic Noise ◽  
Darwinian Theory ◽  
Transmission Of Information ◽  
Genetic Mechanisms ◽  
Translational Mechanisms

Darwinian theory envisages 'selection pressure' as a stress imposed on the genotype by the environment. However, noise in the replicative and translational mechanisms in itself imposes a significant 'pressure' on the adaptive fitness of the organism. We propose that the biosphere has been shaped by both extrinsic (environmental) and intrinsic (noise-generated) factors. Because noise has been a remorseless and ever-present background to the evolutionary process, adaptations to this intrinsic pressure include not only a variety of familiar genetic mechanisms but also many anatomical and life-style characteristics that focus on the transmission of information between generations.

scholarly journals Recurrent hybridization underlies the evolution of novelty in Gentiana (Gentianaceae) in the Qinghai-Tibetan Plateau

AoB Plants ◽  
2020 ◽  
Author(s):  
Peng-Cheng Fu ◽  
Alex D Twyford ◽  
Shan-Shan Sun ◽  
Hong-Yu Wang ◽  
Ming-Ze Xia ◽  
...  
Keyword(s):  
Tibetan Plateau ◽  
Sequence Data ◽  
Evolutionary Process ◽  
Source Area ◽  
Nuclear Data ◽  
Population History ◽  
Plastid Genomes ◽  
Key Factor ◽  
History Of ◽  
Postglacial Expansion

Abstract The Qinghai-Tibetan Plateau (QTP) and adjacent areas are centers of diversity for several alpine groups. Although the QTP acted as a source area for diversification of the alpine genus Gentiana, the evolutionary process underlying diversity in this genus, especially the formation of narrow endemics, is still poorly understood. Hybridization has been proposed as a driver of plant endemism in the QTP but few cases have been documented with genetic data. Here, we describe a new endemic species in Gentiana section Cruciata as G. hoae sp. nov., and explore its evolutionary history with complete plastid genomes and nuclear ribosomal ITS sequence data. Genetic divergence within G. hoae approximately 3 million years ago was followed by postglacial expansion on the QTP, suggesting Pleistocene glaciations as a key factor shaping the population history of G. hoae. Furthermore, a mismatch between plastid and nuclear data suggest that G. hoae participated in historical hybridization, while population sequencing show this species continues to hybridize with the co-occurring congener G. straminea in three locations. Our results indicate that hybridization may be a common process in the evolution of Gentiana and may be widespread among recently diverged taxa of the QTP.

scholarly journals Evolutionary fine-tuning of background-matching camouflage among geographical populations in the sandy beach tiger beetle

2020 ◽  
Vol 287 (1941) ◽  
pp. 20202315
Author(s):  
Nayuta Yamamoto ◽  
Teiji Sota
Keyword(s):  
Sequence Data ◽  
Evolutionary Process ◽  
Fine Tuning ◽  
Colour Pattern ◽  
Tiger Beetle ◽  
Background Matching ◽  
Geographical Populations ◽  
Geographical Distances ◽  
The Japanese Archipelago ◽  
Colour Patterns

Background-matching camouflage is a widespread adaptation in animals; however, few studies have thoroughly examined its evolutionary process and consequences. The tiger beetle Chaetodera laetescripta exhibits pronounced variation in elytral colour pattern among sandy habitats of different colour in the Japanese Archipelago. In this study, we performed digital image analysis with avian vision modelling to demonstrate that elytral luminance, which is attributed to proportions of elytral colour components, is fine-tuned to match local backgrounds. Field predation experiments with model beetles showed that better luminance matching resulted in a lower attack rate and corresponding lower mortality. Using restriction site-associated DNA (RAD) sequence data, we analysed the dispersal and evolution of colour pattern across geographical locations. We found that sand colour matching occurred irrespective of genetic and geographical distances between populations, suggesting that locally adapted colour patterns evolved after the colonization of these habitats. Given that beetle elytral colour patterns presumably have a quantitative genetic basis, our findings demonstrate that fine-tuning of background-matching camouflage to local habitat conditions can be attained through selection by visual predators, as predicted by the earliest proponent of natural selection.

Error Thresholds in Genetic Algorithms

2006 ◽  
Vol 14 (2) ◽  
pp. 157-182 ◽  
Author(s):  
Gabriela Ochoa
Keyword(s):  
Genetic Algorithms ◽  
Selection Pressure ◽  
Evolutionary Process ◽  
Critical Value ◽  
Mutation Rates ◽  
Genomic Information ◽  
Quasispecies Model ◽  
Error Catastrophe ◽  
Important Notion ◽  
Quasispecies Evolution

The error threshold of replication is an important notion in the quasispecies evolution model; it is a critical mutation rate (error rate) beyond which structures obtained by an evolutionary process are destroyed more frequently than selection can reproduce them. With mutation rates above this critical value, an error catastrophe occurs and the genomic information is irretrievably lost. Therefore, studying the factors that alter this magnitude has important implications in the study of evolution. Here we use a genetic algorithm, instead of the quasispecies model, as the underlying model of evolution, and explore whether the phenomenon of error thresholds is found on finite populations of bit strings evolving on complex landscapes. Our empirical results verify the occurrence of error thresholds in genetic algorithms. In this way, this notion is brought from molecular evolution to evolutionary computation. We also study the effect of modifying the most prominent evolutionary parameters on the magnitude of this critical value, and found that error thresholds depend mainly on the selection pressure and genotype length.

scholarly journals Retroposed New Genes Out of the X in Drosophila

2002 ◽  
Vol 12 (12) ◽  
pp. 1854-1859
Author(s):  
Esther Betrán ◽  
Kevin Thornton ◽  
Manyuan Long
Keyword(s):  
Population Genetics ◽  
Molecular Mechanisms ◽  
Sequence Data ◽  
Evolutionary Process ◽  
Significant Excess ◽  
Link Type ◽  
New Genes ◽  
Asymmetric Pattern ◽  
Unpublished Information

New genes that originated by various molecular mechanisms are an essential component in understanding the evolution of genetic systems. We investigated the pattern of origin of the genes created by retroposition in Drosophila. We surveyed the wholeDrosophila melanogaster genome for such new retrogenes and experimentally analyzed their functionality and evolutionary process. These retrogenes, functional as revealed by the analysis of expression, substitution, and population genetics, show a surprisingly asymmetric pattern in their origin. There is a significant excess of retrogenes that originate from the X chromosome and retropose to autosomes; new genes retroposed from autosomes are scarce. Further, we found that most of these X-derived autosomal retrogenes had evolved a testis expression pattern. These observations may be explained by natural selection favoring those new retrogenes that moved to autosomes and avoided the spermatogenesis X inactivation, and suggest the important role of genome position for the origin of new genes.[The sequence data from this study have been submitted to GenBank under accession nos. AY150701–AY150797. The following individuals kindly provided reagents, samples, or unpublished information as indicated in the paper: M.-L. Wu, F. Lemeunier, and P. Gibert.]

scholarly journals Evolution of Turbulent Horseshoe Vortex System in Front of a Vertical Circular Cylinder in Open Channel

Water ◽  
2019 ◽  
Vol 11 (10) ◽  
pp. 2079 ◽  
Author(s):  
Chen ◽  
Yang ◽  
Wu
Keyword(s):  
Open Channel ◽  
Evolutionary Process ◽  
Reynolds Numbers ◽  
Horseshoe Vortex ◽  
Local Scour ◽  
Time Resolved ◽  
Vortex Interactions ◽  
Initial Stage ◽  
Image Velocimetry ◽  
Underlying Mechanisms

A turbulent horseshoe vortex (HV) system around a wall-mounted cylinder in open channel is characterized by random variations in vortex features and an abundance of vortex interactions. The turbulent HV system is responsible for initiating the local scour process in front of the cylinder. The evolution of the turbulent HV system is investigated statistically and quantitatively with time-resolved particle image velocimetry. The cylinder Reynolds numbers of the flow are 8600, 10,200, and 13,600, respectively. A novel vortex tracking method was proposed to obtain the variations in position, size, and strength of the primary HV (PHV) which dominates the system most of the time. Relationships between the various features of the PHV during its evolutionary process were obtained through correlation analyses. Results show that the dimensionless mean lifespan of the PHV is about 5.0. Statistically, the downstream movement of the PHV toward the cylinder is accompanied with its bed-approaching movement and decreasing in size, and the opposite is true. The circulation strength of the PHV decreases and increases dramatically in the region downstream of its time-averaged position when the PHV approaches and departs from the cylinder, respectively. Meanwhile, mechanisms responsible for the generation, movement, variation, and disappearance of the PHV are re-investigated and enriched based on its interactions with vortices in the separation region and structures in the incoming flow. The obtained change trends of the features of the PHV and the underlying mechanisms for its evolution are valuable for predicting and controlling the initial stage of the local scour in front of cylinders.

scholarly journals Quantifying evolutionary constraints on B-cell affinity maturation

2015 ◽  
Vol 370 (1676) ◽  
pp. 20140244 ◽  
Author(s):  
Connor O. McCoy ◽  
Trevor Bedford ◽  
Vladimir N. Minin ◽  
Philip Bradley ◽  
Harlan Robins ◽  
...  
Keyword(s):  
B Cell ◽  
Empirical Bayes ◽  
High Throughput Sequencing ◽  
Sequence Data ◽  
Evolutionary Process ◽  
Cell Receptor ◽  
Affinity Maturation ◽  
Variable Regions ◽  
Empirical Bayes Estimators ◽  
Stochastic Mapping

The antibody repertoire of each individual is continuously updated by the evolutionary process of B-cell receptor (BCR) mutation and selection. It has recently become possible to gain detailed information concerning this process through high-throughput sequencing. Here, we develop modern statistical molecular evolution methods for the analysis of B-cell sequence data, and then apply them to a very deep short-read dataset of BCRs. We find that the substitution process is conserved across individuals but varies significantly across gene segments. We investigate selection on BCRs using a novel method that side-steps the difficulties encountered by previous work in differentiating between selection and motif-driven mutation; this is done through stochastic mapping and empirical Bayes estimators that compare the evolution of in-frame and out-of-frame rearrangements. We use this new method to derive a per-residue map of selection, which provides a more nuanced view of the constraints on framework and variable regions.

scholarly journals Getting a better picture of microbial evolution en route to a network of genomes

2009 ◽  
Vol 364 (1527) ◽  
pp. 2187-2196 ◽  
Author(s):  
Tal Dagan ◽  
William Martin
Keyword(s):  
Natural Variation ◽  
Evolutionary Process ◽  
Microbial Evolution ◽  
Evolutionary Relationships ◽  
Sequence Comparisons ◽  
Microbial Genomes ◽  
Living Things ◽  
Current Thinking ◽  
Multicellular Organisms ◽  
Looking Glass

Most current thinking about evolution is couched in the concept of trees. The notion of a tree with recursively bifurcating branches representing recurrent divergence events is a plausible metaphor to describe the evolution of multicellular organisms like vertebrates or land plants. But if we try to force the tree metaphor onto the whole of the evolutionary process, things go badly awry, because the more closely we inspect microbial genomes through the looking glass of gene and genome sequence comparisons, the smaller the amount of the data that fits the concept of a bifurcating tree becomes. That is mainly because among microbes, endosymbiosis and lateral gene transfer are important, two mechanisms of natural variation that differ from the kind of natural variation that Darwin had in mind. For such reasons, when it comes to discussing the relationships among all living things, that is, including the microbes and all of their genes rather than just one or a select few, many biologists are now beginning to talk about networks rather than trees in the context of evolutionary relationships among microbial chromosomes. But talk is not enough. If we were to actually construct networks instead of trees to describe the evolutionary process, what would they look like? Here we consider endosymbiosis and an example of a network of genomes involving 181 sequenced prokaryotes and how that squares off with some ideas about early cell evolution.

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