A coevolution analysis for identifying protein-protein interactions by Fourier transform.

Directory of Open Access Journals (Sweden)

Changchuan Yin

Full Text Available Protein-protein interactions (PPIs play key roles in life processes, such as signal transduction, transcription regulations, and immune response, etc. Identification of PPIs enables better understanding of the functional networks within a cell. Common experimental methods for identifying PPIs are time consuming and expensive. However, recent developments in computational approaches for inferring PPIs from protein sequences based on coevolution theory avoid these problems. In the coevolution theory model, interacted proteins may show coevolutionary mutations and have similar phylogenetic trees. The existing coevolution methods depend on multiple sequence alignments (MSA; however, the MSA-based coevolution methods often produce high false positive interactions. In this paper, we present a computational method using an alignment-free approach to accurately detect PPIs and reduce false positives. In the method, protein sequences are numerically represented by biochemical properties of amino acids, which reflect the structural and functional differences of proteins. Fourier transform is applied to the numerical representation of protein sequences to capture the dissimilarities of protein sequences in biophysical context. The method is assessed for predicting PPIs in Ebola virus. The results indicate strong coevolution between the protein pairs (NP-VP24, NP-VP30, NP-VP40, VP24-VP30, VP24-VP40, and VP30-VP40. The method is also validated for PPIs in influenza and E.coli genomes. Since our method can reduce false positive and increase the specificity of PPI prediction, it offers an effective tool to understand mechanisms of disease pathogens and find potential targets for drug design. The Python programs in this study are available to public at URL (https://github.com/cyinbox/PPI.

Coevolution of nutrigenomics and society: ethical considerations

NARCIS (Netherlands)

Korthals, M.

2011-01-01

To optimize the coevolution of nutrigenomics and society (ie, the reciprocal stimulation of both developments), I analyzed chances for a fruitful match between normative concepts and strategies of both developments. Nutrigenomics embodies =3 normative concepts. First, food is exclusively interpreted

Catchment coevolution: A useful framework for improving predictions of hydrological change?

Science.gov (United States)

Troch, Peter A.

2017-04-01

The notion that landscape features have co-evolved over time is well known in the Earth sciences. Hydrologists have recently called for a more rigorous connection between emerging spatial patterns of landscape features and the hydrological response of catchments, and have termed this concept catchment coevolution. In this presentation we present a general framework of catchment coevolution that could improve predictions of hydrologic change. We first present empirical evidence of the interaction and feedback of landscape evolution and changes in hydrological response. From this review it is clear that the independent drivers of catchment coevolution are climate, geology, and tectonics. We identify common currency that allows comparing the levels of activity of these independent drivers, such that, at least conceptually, we can quantify the rate of evolution or aging. Knowing the hydrologic age of a catchment by itself is not very meaningful without linking age to hydrologic response. Two avenues of investigation have been used to understand the relationship between (differences in) age and hydrological response: (i) one that is based on relating present landscape features to runoff processes that are hypothesized to be responsible for the current fingerprints in the landscape; and (ii) one that takes advantage of an experimental design known as space-for-time substitution. Both methods have yielded significant insights in the hydrologic response of landscapes with different histories. If we want to make accurate predictions of hydrologic change, we will also need to be able to predict how the catchment will further coevolve in association with changes in the activity levels of the drivers (e.g., climate). There is ample evidence in the literature that suggests that whole-system prediction of catchment coevolution is, at least in principle, plausible. With this imperative we outline a research agenda that implements the concepts of catchment coevolution for building

HIV-1 protease-substrate coevolution in nelfinavir resistance.

Science.gov (United States)

Kolli, Madhavi; Ozen, Ayşegül; Kurt-Yilmaz, Nese; Schiffer, Celia A

2014-07-01

Resistance to various human immunodeficiency virus type 1 (HIV-1) protease inhibitors (PIs) challenges the effectiveness of therapies in treating HIV-1-infected individuals and AIDS patients. The virus accumulates mutations within the protease (PR) that render the PIs less potent. Occasionally, Gag sequences also coevolve with mutations at PR cleavage sites contributing to drug resistance. In this study, we investigated the structural basis of coevolution of the p1-p6 cleavage site with the nelfinavir (NFV) resistance D30N/N88D protease mutations by determining crystal structures of wild-type and NFV-resistant HIV-1 protease in complex with p1-p6 substrate peptide variants with L449F and/or S451N. Alterations of residue 30's interaction with the substrate are compensated by the coevolving L449F and S451N cleavage site mutations. This interdependency in the PR-p1-p6 interactions enhances intermolecular contacts and reinforces the overall fit of the substrate within the substrate envelope, likely enabling coevolution to sustain substrate recognition and cleavage in the presence of PR resistance mutations. Resistance to human immunodeficiency virus type 1 (HIV-1) protease inhibitors challenges the effectiveness of therapies in treating HIV-1-infected individuals and AIDS patients. Mutations in HIV-1 protease selected under the pressure of protease inhibitors render the inhibitors less potent. Occasionally, Gag sequences also mutate and coevolve with protease, contributing to maintenance of viral fitness and to drug resistance. In this study, we investigated the structural basis of coevolution at the Gag p1-p6 cleavage site with the nelfinavir (NFV) resistance D30N/N88D protease mutations. Our structural analysis reveals the interdependency of protease-substrate interactions and how coevolution may restore substrate recognition and cleavage in the presence of protease drug resistance mutations. Copyright © 2014, American Society for Microbiology. All Rights Reserved.

Physical mode of bacteria and virus coevolution

Science.gov (United States)

Han, Pu; Niestemski, Liang; Deem, Michael

2013-03-01

Single-cell hosts such as bacteria or archaea possess an adaptive, heritable immune system that protects them from viral invasion. This system, known as the CRISPR-Cas system, allows the host to recognize and incorporate short foreign DNA or RNA sequences from viruses or plasmids. The sequences form what are called ``spacers'' in the CRISPR. Spacers in the CRISPR loci provide a record of the host and predator coevolution history. We develop a physical model to study the dynamics of this coevolution due to immune pressure. Hosts and viruses reproduce, die, and evolve due to viral infection pressure, host immune pressure, and mutation. We will discuss the differing effects of point mutation and recombination on CRISPR evolution. We will also discuss the effect of different spacer deletion mechanisms. We will describe population structure of hosts and viruses, how spacer diversity depends on position within CRISPR, and match of the CRISPR spacers to the virus population.

The potential of a population genomics approach to analyse geographic mosaics of plant–insect coevolution

NARCIS (Netherlands)

Vermeer, K.M.C.A.; Dicke, M.; Jong, de P.W.

2011-01-01

A central issue in the evolutionary ecology of species interactions is coevolution, which involves the reciprocal selection between individuals of interacting species. Understanding the importance of coevolution in shaping species interactions requires the consideration of spatial variation in their

Co-evolution as Tool for Diversifying Flavor and Aroma Profiles of Wines

Directory of Open Access Journals (Sweden)

Peter Morrison-Whittle

2018-05-01

Full Text Available The products of microbial metabolism form an integral part of human industry and have been shaped by evolutionary processes, accidentally and deliberately, for thousands of years. In the production of wine, a great many flavor and aroma compounds are produced by yeast species and are the targets of research for commercial breeding programs. Here we demonstrate how co-evolution with multiple species can generate novel interactions through serial co-culture in grape juice. We find that after ~65 generations, co-evolved strains and strains evolved independently show significantly different growth aspects and exhibit significantly different metabolite profiles. We show significant impact of co-evolution of Candida glabrata and Pichia kudriavzevii on the production of metabolites that affect the flavor and aroma of experimental wines. While co-evolved strains do exhibit novel interactions that affect the reproductive success of interacting species, we found no evidence of cross-feeding behavior. Our findings yield promising avenues for developing commercial yeast strains by using co-evolution to diversify the metabolic output of target species without relying on genetic modification or breeding technologies. Such approaches open up exciting new possibilities for harnessing microbial co-evolution in areas of agriculture and food related research generally.

Coevolution of variability models and related software artifacts

DEFF Research Database (Denmark)

Passos, Leonardo; Teixeira, Leopoldo; Dinztner, Nicolas

2015-01-01

models coevolve with other artifact types, we study a large and complex real-world variant-rich software system: the Linux kernel. Specifically, we extract variability-coevolution patterns capturing changes in the variability model of the Linux kernel with subsequent changes in Makefiles and C source...

Coevolution of game and network structure with adjustable linking

Science.gov (United States)

Qin, Shao-Meng; Zhang, Guo-Yong; Chen, Yong

2009-12-01

Most papers about the evolutionary game on graph assume the statistic network structure. However, in the real world, social interaction could change the relationship among people. And the change of social structure will also affect people’s strategies. We build a coevolution model of prisoner’s dilemma game and network structure to study the dynamic interaction in the real world. Differing from other coevolution models, players rewire their network connections according to the density of cooperation and other players’ payoffs. We use a parameter α to control the effect of payoff in the process of rewiring. Based on the asynchronous update rule and Monte Carlo simulation, we find that, when players prefer to rewire their links to those who are richer, the temptation can increase the cooperation density.

Data from: Rapid multiple-level coevolution in experimental populations of yeast killer and non-killer strains

NARCIS (Netherlands)

Pieczynska, M.D.; Wloch-Salamon, D.; Korona, R.; Visser, de J.A.G.M.

2016-01-01

Coevolution between different biological entities is considered an important evolutionary mechanism at all levels of biological organization. Here we provide evidence for coevolution of a yeast killer strain (K) carrying cytoplasmic dsRNA viruses coding for anti-competitor toxins and an isogenic

Heuristic urban transportation network design method, a multilayer coevolution approach

Science.gov (United States)

Ding, Rui; Ujang, Norsidah; Hamid, Hussain bin; Manan, Mohd Shahrudin Abd; Li, Rong; Wu, Jianjun

2017-08-01

The design of urban transportation networks plays a key role in the urban planning process, and the coevolution of urban networks has recently garnered significant attention in literature. However, most of these recent articles are based on networks that are essentially planar. In this research, we propose a heuristic multilayer urban network coevolution model with lower layer network and upper layer network that are associated with growth and stimulate one another. We first use the relative neighbourhood graph and the Gabriel graph to simulate the structure of rail and road networks, respectively. With simulation we find that when a specific number of nodes are added, the total travel cost ratio between an expanded network and the initial lower layer network has the lowest value. The cooperation strength Λ and the changeable parameter average operation speed ratio Θ show that transit users' route choices change dramatically through the coevolution process and that their decisions, in turn, affect the multilayer network structure. We also note that the simulated relation between the Gini coefficient of the betweenness centrality, Θ and Λ have an optimal point for network design. This research could inspire the analysis of urban network topology features and the assessment of urban growth trends.

CMCpy: Genetic Code-Message Coevolution Models in Python

Science.gov (United States)

Becich, Peter J.; Stark, Brian P.; Bhat, Harish S.; Ardell, David H.

2013-01-01

Code-message coevolution (CMC) models represent coevolution of a genetic code and a population of protein-coding genes (“messages”). Formally, CMC models are sets of quasispecies coupled together for fitness through a shared genetic code. Although CMC models display plausible explanations for the origin of multiple genetic code traits by natural selection, useful modern implementations of CMC models are not currently available. To meet this need we present CMCpy, an object-oriented Python API and command-line executable front-end that can reproduce all published results of CMC models. CMCpy implements multiple solvers for leading eigenpairs of quasispecies models. We also present novel analytical results that extend and generalize applications of perturbation theory to quasispecies models and pioneer the application of a homotopy method for quasispecies with non-unique maximally fit genotypes. Our results therefore facilitate the computational and analytical study of a variety of evolutionary systems. CMCpy is free open-source software available from http://pypi.python.org/pypi/CMCpy/. PMID:23532367

Studying the co-evolution of protein families with the Mirrortree web server.

Science.gov (United States)

Ochoa, David; Pazos, Florencio

2010-05-15

The Mirrortree server allows to graphically and interactively study the co-evolution of two protein families, and investigate their possible interactions and functional relationships in a taxonomic context. The server includes the possibility of starting from single sequences and hence it can be used by non-expert users. The web server is freely available at http://csbg.cnb.csic.es/mtserver. It was tested in the main web browsers. Adobe Flash Player is required at the client side to perform the interactive assessment of co-evolution. pazos@cnb.csic.es Supplementary data are available at Bioinformatics online.

Coevolution of amino acid residues in the key photosynthetic enzyme Rubisco

Directory of Open Access Journals (Sweden)

Kapralov Maxim V

2011-09-01

Full Text Available Abstract Background One of the key forces shaping proteins is coevolution of amino acid residues. Knowing which residues coevolve in a particular protein may facilitate our understanding of protein evolution, structure and function, and help to identify substitutions that may lead to desired changes in enzyme kinetics. Rubisco, the most abundant enzyme in biosphere, plays an essential role in the process of carbon fixation through photosynthesis, thus facilitating life on Earth. This makes Rubisco an important model system for studying the dynamics of protein fitness optimization on the evolutionary landscape. In this study we investigated the selective and coevolutionary forces acting on large subunit of land plants Rubisco using Markov models of codon substitution and clustering approaches applied to amino acid substitution histories. Results We found that both selection and coevolution shape Rubisco, and that positively selected and coevolving residues have their specifically favored amino acid composition and pairing preference. The mapping of these residues on the known Rubisco tertiary structures showed that the coevolving residues tend to be in closer proximity with each other compared to the background, while positively selected residues tend to be further away from each other. This study also reveals that the residues under positive selection or coevolutionary force are located within functionally important regions and that some residues are targets of both positive selection and coevolution at the same time. Conclusion Our results demonstrate that coevolution of residues is common in Rubisco of land plants and that there is an overlap between coevolving and positively selected residues. Knowledge of which Rubisco residues are coevolving and positively selected could be used for further work on structural modeling and identification of substitutions that may be changed in order to improve efficiency of this important enzyme in crops.

Coevolution of coloration and colour vision?

Science.gov (United States)

Lind, Olle; Henze, Miriam J; Kelber, Almut; Osorio, Daniel

2017-07-05

The evolutionary relationship between signals and animal senses has broad significance, with potential consequences for speciation, and for the efficacy and honesty of biological communication. Here we outline current understanding of the diversity of colour vision in two contrasting groups: the phylogenetically conservative birds, and the more variable butterflies. Evidence for coevolution of colour signals and vision exists in both groups, but is limited to observations of phenotypic differences between visual systems, which might be correlated with coloration. Here, to illustrate how one might interpret the evolutionary significance of such differences, we used colour vision modelling based on an avian eye to evaluate the effects of variation in three key characters: photoreceptor spectral sensitivity, oil droplet pigmentation and the proportions of different photoreceptor types. The models predict that physiologically realistic changes in any one character will have little effect, but complementary shifts in all three can substantially affect discriminability of three types of natural spectra. These observations about the adaptive landscape of colour vision may help to explain the general conservatism of photoreceptor spectral sensitivities in birds. This approach can be extended to other types of eye and spectra to inform future work on coevolution of coloration and colour vision.This article is part of the themed issue 'Animal coloration: production, perception, function and application'. © 2017 The Author(s).

Co-evolution of social networks and continuous actor attributes

NARCIS (Netherlands)

Niezink, Nynke M.D.; Snijders, Tom A.B.

2017-01-01

Social networks and the attributes of the actors in these networks are not static; they may develop interdependently over time. The stochastic actor-oriented model allows for statistical inference on the mechanisms driving this co-evolution process. In earlier versions of this model, dynamic actor

Plastid–Nuclear Interaction and Accelerated Coevolution in Plastid Ribosomal Genes in Geraniaceae

Science.gov (United States)

Weng, Mao-Lun; Ruhlman, Tracey A.; Jansen, Robert K.

2016-01-01

Plastids and mitochondria have many protein complexes that include subunits encoded by organelle and nuclear genomes. In animal cells, compensatory evolution between mitochondrial and nuclear-encoded subunits was identified and the high mitochondrial mutation rates were hypothesized to drive compensatory evolution in nuclear genomes. In plant cells, compensatory evolution between plastid and nucleus has rarely been investigated in a phylogenetic framework. To investigate plastid–nuclear coevolution, we focused on plastid ribosomal protein genes that are encoded by plastid and nuclear genomes from 27 Geraniales species. Substitution rates were compared for five sets of genes representing plastid- and nuclear-encoded ribosomal subunit proteins targeted to the cytosol or the plastid as well as nonribosomal protein controls. We found that nonsynonymous substitution rates (dN) and the ratios of nonsynonymous to synonymous substitution rates (ω) were accelerated in both plastid- (CpRP) and nuclear-encoded subunits (NuCpRP) of the plastid ribosome relative to control sequences. Our analyses revealed strong signals of cytonuclear coevolution between plastid- and nuclear-encoded subunits, in which nonsynonymous substitutions in CpRP and NuCpRP tend to occur along the same branches in the Geraniaceae phylogeny. This coevolution pattern cannot be explained by physical interaction between amino acid residues. The forces driving accelerated coevolution varied with cellular compartment of the sequence. Increased ω in CpRP was mainly due to intensified positive selection whereas increased ω in NuCpRP was caused by relaxed purifying selection. In addition, the many indels identified in plastid rRNA genes in Geraniaceae may have contributed to changes in plastid subunits. PMID:27190001

Host-parasite coevolution can promote the evolution of seed banking as a bet-hedging strategy.

Science.gov (United States)

Verin, Mélissa; Tellier, Aurélien

2018-04-20

Seed (egg) banking is a common bet-hedging strategy maximizing the fitness of organisms facing environmental unpredictability by the delayed emergence of offspring. Yet, this condition often requires fast and drastic stochastic shifts between good and bad years. We hypothesize that the host seed banking strategy can evolve in response to coevolution with parasites because the coevolutionary cycles promote a gradually changing environment over longer times than seed persistence. We study the evolution of host germination fraction as a quantitative trait using both pairwise competition and multiple mutant competition methods, while the germination locus can be genetically linked or unlinked with the host locus under coevolution. In a gene-for-gene model of coevolution, hosts evolve a seed bank strategy under unstable coevolutionary cycles promoted by moderate to high costs of resistance or strong disease severity. Moreover, when assuming genetic linkage between coevolving and germination loci, the resistant genotype always evolves seed banking in contrast to susceptible hosts. Under a matching-allele interaction, both hosts' genotypes exhibit the same seed banking strategy irrespective of the genetic linkage between loci. We suggest host-parasite coevolution as an additional hypothesis for the evolution of seed banking as a temporal bet-hedging strategy. © 2018 The Author(s). Evolution © 2018 The Society for the Study of Evolution.

Wing patterning genes and coevolution of Müllerian mimicry in Heliconius butterflies: Support from phylogeography, cophylogeny, and divergence times.

Science.gov (United States)

Hoyal Cuthill, Jennifer F; Charleston, Michael

2015-12-01

Examples of long-term coevolution are rare among free-living organisms. Müllerian mimicry in Heliconius butterflies had been suggested as a key example of coevolution by early genetic studies. However, research over the last two decades has been dominated by the idea that the best-studied comimics, H. erato and H. melpomene, did not coevolve at all. Recently sequenced genes associated with wing color pattern phenotype offer a new opportunity to resolve this controversy. Here, we test the hypothesis of coevolution between H. erato and H. melpomene using Bayesian multilocus analysis of five color pattern genes and five neutral genetic markers. We first explore the extent of phylogenetic agreement versus conflict between the different genes. Coevolution is then tested against three aspects of the mimicry diversifications: phylogenetic branching patterns, divergence times, and, for the first time, phylogeographic histories. We show that all three lines of evidence are compatible with strict coevolution of the diverse mimicry wing patterns, contrary to some recent suggestions. Instead, these findings tally with a coevolutionary diversification driven primarily by the ecological force of Müllerian mimicry. © 2015 The Author(s). Evolution © 2015 The Society for the Study of Evolution.

Plastid-Nuclear Interaction and Accelerated Coevolution in Plastid Ribosomal Genes in Geraniaceae.

Science.gov (United States)

Weng, Mao-Lun; Ruhlman, Tracey A; Jansen, Robert K

2016-06-27

Plastids and mitochondria have many protein complexes that include subunits encoded by organelle and nuclear genomes. In animal cells, compensatory evolution between mitochondrial and nuclear-encoded subunits was identified and the high mitochondrial mutation rates were hypothesized to drive compensatory evolution in nuclear genomes. In plant cells, compensatory evolution between plastid and nucleus has rarely been investigated in a phylogenetic framework. To investigate plastid-nuclear coevolution, we focused on plastid ribosomal protein genes that are encoded by plastid and nuclear genomes from 27 Geraniales species. Substitution rates were compared for five sets of genes representing plastid- and nuclear-encoded ribosomal subunit proteins targeted to the cytosol or the plastid as well as nonribosomal protein controls. We found that nonsynonymous substitution rates (dN) and the ratios of nonsynonymous to synonymous substitution rates (ω) were accelerated in both plastid- (CpRP) and nuclear-encoded subunits (NuCpRP) of the plastid ribosome relative to control sequences. Our analyses revealed strong signals of cytonuclear coevolution between plastid- and nuclear-encoded subunits, in which nonsynonymous substitutions in CpRP and NuCpRP tend to occur along the same branches in the Geraniaceae phylogeny. This coevolution pattern cannot be explained by physical interaction between amino acid residues. The forces driving accelerated coevolution varied with cellular compartment of the sequence. Increased ω in CpRP was mainly due to intensified positive selection whereas increased ω in NuCpRP was caused by relaxed purifying selection. In addition, the many indels identified in plastid rRNA genes in Geraniaceae may have contributed to changes in plastid subunits. © The Author 2016. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

Multispecies Coevolution Particle Swarm Optimization Based on Previous Search History

Directory of Open Access Journals (Sweden)

Danping Wang

2017-01-01

Full Text Available A hybrid coevolution particle swarm optimization algorithm with dynamic multispecies strategy based on K-means clustering and nonrevisit strategy based on Binary Space Partitioning fitness tree (called MCPSO-PSH is proposed. Previous search history memorized into the Binary Space Partitioning fitness tree can effectively restrain the individuals’ revisit phenomenon. The whole population is partitioned into several subspecies and cooperative coevolution is realized by an information communication mechanism between subspecies, which can enhance the global search ability of particles and avoid premature convergence to local optimum. To demonstrate the power of the method, comparisons between the proposed algorithm and state-of-the-art algorithms are grouped into two categories: 10 basic benchmark functions (10-dimensional and 30-dimensional, 10 CEC2005 benchmark functions (30-dimensional, and a real-world problem (multilevel image segmentation problems. Experimental results show that MCPSO-PSH displays a competitive performance compared to the other swarm-based or evolutionary algorithms in terms of solution accuracy and statistical tests.

The co-evolution of gossip and friendship in workplace social networks

NARCIS (Netherlands)

Ellwardt, Lea; Steglich, Christian; Wittek, Rafael

2012-01-01

This study investigates the co-evolution of friendship and gossip in organizations. Two contradicting perspectives are tested. The social capital perspective predicts that friendship causes gossip between employees, defined as informal evaluative talking about absent colleagues. The evolutionary

Dilemma solving by the coevolution of networks and strategy in a 2 x 2 game.

Science.gov (United States)

Tanimoto, Jun

2007-08-01

A 2 x 2 game model implemented by a coevolution mechanism of both networks and strategy, inspired by the work of Zimmermann and Eguiluz [Phys. Rev. E72, 056118 (2005)] is established. Network adaptation is the manner in which an existing link between two agents is destroyed and how a new one is established to replace it. The strategy is defined as whether an agent offers cooperation (C) or defection (D) . Both the networks and strategy are synchronously renovated in a simulation time step. A series of numerical experiments, considering various 2 x 2 game structures, reveals that the proposed coevolution mechanism can solve dilemmas in several game classes. The effect of solving a dilemma means mutual-cooperation reciprocity (R reciprocity), which is brought about by emerging several cooperative hub agents who have plenty of links. This effect can be primarily observed in game classes of the prisoner's dilemma and stag hunt. The coevolution mechanism, however, seems counterproductive for game classes of leader and hero, where the alternating reciprocity (ST reciprocity) is meaningful.

Self-organization towards optimally interdependent networks by means of coevolution

International Nuclear Information System (INIS)

Wang, Zhen; Szolnoki, Attila; Perc, Matjaž

2014-01-01

Coevolution between strategy and network structure is established as a means to arrive at the optimal conditions needed to resolve social dilemmas. Yet recent research has highlighted that the interdependence between networks may be just as important as the structure of an individual network. We therefore introduce the coevolution of strategy and network interdependence to see whether this can give rise to elevated levels of cooperation in the prisoner's dilemma game. We show that the interdependence between networks self-organizes so as to yield optimal conditions for the evolution of cooperation. Even under extremely adverse conditions, cooperators can prevail where on isolated networks they would perish. This is due to the spontaneous emergence of a two-class society, with only the upper class being allowed to control and take advantage of the interdependence. Spatial patterns reveal that cooperators, once arriving at the upper class, are much more competent than defectors in sustaining compact clusters of followers. Indeed, the asymmetric exploitation of interdependence confers to them a strong evolutionary advantage that may resolve even the toughest of social dilemmas. (paper)

Dynamical trade-offs arise from antagonistic coevolution and decrease intraspecific diversity.

Science.gov (United States)

Huang, Weini; Traulsen, Arne; Werner, Benjamin; Hiltunen, Teppo; Becks, Lutz

2017-12-12

Trade-offs play an important role in evolution. Without trade-offs, evolution would maximize fitness of all traits leading to a "master of all traits". The shape of trade-offs has been shown to determine evolutionary trajectories and is often assumed to be static and independent of the actual evolutionary process. Here we propose that coevolution leads to a dynamical trade-off. We test this hypothesis in a microbial predator-prey system and show that the bacterial growth-defense trade-off changes from concave to convex, i.e., defense is effective and cheap initially, but gets costly when predators coevolve. We further explore the impact of such dynamical trade-offs by a novel mathematical model incorporating de novo mutations for both species. Predator and prey populations diversify rapidly leading to higher prey diversity when the trade-off is concave (cheap). Coevolution results in more convex (costly) trade-offs and lower prey diversity compared to the scenario where only the prey evolves.

Assembly constraints drive co-evolution among ribosomal constituents.

Science.gov (United States)

Mallik, Saurav; Akashi, Hiroshi; Kundu, Sudip

2015-06-23

Ribosome biogenesis, a central and essential cellular process, occurs through sequential association and mutual co-folding of protein-RNA constituents in a well-defined assembly pathway. Here, we construct a network of co-evolving nucleotide/amino acid residues within the ribosome and demonstrate that assembly constraints are strong predictors of co-evolutionary patterns. Predictors of co-evolution include a wide spectrum of structural reconstitution events, such as cooperativity phenomenon, protein-induced rRNA reconstitutions, molecular packing of different rRNA domains, protein-rRNA recognition, etc. A correlation between folding rate of small globular proteins and their topological features is known. We have introduced an analogous topological characteristic for co-evolutionary network of ribosome, which allows us to differentiate between rRNA regions subjected to rapid reconstitutions from those hindered by kinetic traps. Furthermore, co-evolutionary patterns provide a biological basis for deleterious mutation sites and further allow prediction of potential antibiotic targeting sites. Understanding assembly pathways of multicomponent macromolecules remains a key challenge in biophysics. Our study provides a 'proof of concept' that directly relates co-evolution to biophysical interactions during multicomponent assembly and suggests predictive power to identify candidates for critical functional interactions as well as for assembly-blocking antibiotic target sites. © The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.

The Coevolution of Life and Environment on Mars: An Ecosystem Perspective on the Robotic Exploration of Biosignatures

Science.gov (United States)

2018-01-01

Abstract Earth's biological and environmental evolution are intertwined and inseparable. This coevolution has become a fundamental concept in astrobiology and is key to the search for life beyond our planet. In the case of Mars, whether a coevolution took place is unknown, but analyzing the factors at play shows the uniqueness of each planetary experiment regardless of similarities. Early Earth and early Mars shared traits. However, biological processes on Mars, if any, would have had to proceed within the distinctive context of an irreversible atmospheric collapse, greater climate variability, and specific planetary characteristics. In that, Mars is an important test bed for comparing the effects of a unique set of spatiotemporal changes on an Earth-like, yet different, planet. Many questions remain unanswered about Mars' early environment. Nevertheless, existing data sets provide a foundation for an intellectual framework where notional coevolution models can be explored. In this framework, the focus is shifted from planetary-scale habitability to the prospect of habitats, microbial ecotones, pathways to biological dispersal, biomass repositories, and their meaning for exploration. Critically, as we search for biosignatures, this focus demonstrates the importance of starting to think of early Mars as a biosphere and vigorously integrating an ecosystem approach to landing site selection and exploration. Key Words: Astrobiology—Biosignatures—Coevolution of Earth and life—Mars. Astrobiology 18, 1–27. PMID:29252008

The Coevolution of Life and Environment on Mars: An Ecosystem Perspective on the Robotic Exploration of Biosignatures.

Science.gov (United States)

Cabrol, Nathalie A

2018-01-01

Earth's biological and environmental evolution are intertwined and inseparable. This coevolution has become a fundamental concept in astrobiology and is key to the search for life beyond our planet. In the case of Mars, whether a coevolution took place is unknown, but analyzing the factors at play shows the uniqueness of each planetary experiment regardless of similarities. Early Earth and early Mars shared traits. However, biological processes on Mars, if any, would have had to proceed within the distinctive context of an irreversible atmospheric collapse, greater climate variability, and specific planetary characteristics. In that, Mars is an important test bed for comparing the effects of a unique set of spatiotemporal changes on an Earth-like, yet different, planet. Many questions remain unanswered about Mars' early environment. Nevertheless, existing data sets provide a foundation for an intellectual framework where notional coevolution models can be explored. In this framework, the focus is shifted from planetary-scale habitability to the prospect of habitats, microbial ecotones, pathways to biological dispersal, biomass repositories, and their meaning for exploration. Critically, as we search for biosignatures, this focus demonstrates the importance of starting to think of early Mars as a biosphere and vigorously integrating an ecosystem approach to landing site selection and exploration. Key Words: Astrobiology-Biosignatures-Coevolution of Earth and life-Mars. Astrobiology 18, 1-27.

Coevolution study of mitochondria respiratory chain proteins: toward the understanding of protein--protein interaction.

Science.gov (United States)

Yang, Ming; Ge, Yan; Wu, Jiayan; Xiao, Jingfa; Yu, Jun

2011-05-20

Coevolution can be seen as the interdependency between evolutionary histories. In the context of protein evolution, functional correlation proteins are ever-present coordinated evolutionary characters without disruption of organismal integrity. As to complex system, there are two forms of protein--protein interactions in vivo, which refer to inter-complex interaction and intra-complex interaction. In this paper, we studied the difference of coevolution characters between inter-complex interaction and intra-complex interaction using "Mirror tree" method on the respiratory chain (RC) proteins. We divided the correlation coefficients of every pairwise RC proteins into two groups corresponding to the binary protein--protein interaction in intra-complex and the binary protein--protein interaction in inter-complex, respectively. A dramatical discrepancy is detected between the coevolution characters of the two sets of protein interactions (Wilcoxon test, p-value = 4.4 × 10(-6)). Our finding reveals some critical information on coevolutionary study and assists the mechanical investigation of protein--protein interaction. Furthermore, the results also provide some unique clue for supramolecular organization of protein complexes in the mitochondrial inner membrane. More detailed binding sites map and genome information of nuclear encoded RC proteins will be extraordinary valuable for the further mitochondria dynamics study. Copyright © 2011. Published by Elsevier Ltd.

Coevolution of Cryptosporidium tyzzeri and the house mouse (Mus musculus)

Czech Academy of Sciences Publication Activity Database

Kváč, Martin; McEvoy, J.; Loudová, M.; Stenger, B.; Sak, Bohumil; Květoňová, Dana; Ditrich, Oleg; Rašková, Veronika; Moriarty, E.; Rost, M.; Macholán, Miloš; Piálek, Jaroslav

2013-01-01

Roč. 43, č. 10 (2013), s. 805-817 ISSN 0020-7519 R&D Projects: GA ČR GA206/08/0640; GA MŠk(CZ) LH11061 Institutional support: RVO:60077344 ; RVO:67985904 ; RVO:68081766 Keywords : Cryptosporidium tyzzeri * house mouse * hybrid zone * coevolution Subject RIV: EG - Zoology; GJ - Animal Vermins ; Diseases, Veterinary Medicine (BC-A) Impact factor: 3.404, year: 2013

The coevolution of long-term pair bonds and cooperation.

Science.gov (United States)

Song, Z; Feldman, M W

2013-05-01

The evolution of social traits may not only depend on but also change the social structure of the population. In particular, the evolution of pairwise cooperation, such as biparental care, depends on the pair-matching distribution of the population, and the latter often emerges as a collective outcome of individual pair-bonding traits, which are also under selection. Here, we develop an analytical model and individual-based simulations to study the coevolution of long-term pair bonds and cooperation in parental care, where partners play a Snowdrift game in each breeding season. We illustrate that long-term pair bonds may coevolve with cooperation when bonding cost is below a threshold. As long-term pair bonds lead to assortative interactions through pair-matching dynamics, they may promote the prevalence of cooperation. In addition to the pay-off matrix of a single game, the evolutionarily stable equilibrium also depends on bonding cost and accidental divorce rate, and it is determined by a form of balancing selection because the benefit from pair-bond maintenance diminishes as the frequency of cooperators increases. Our findings highlight the importance of ecological factors affecting social bonding cost and stability in understanding the coevolution of social behaviour and social structures, which may lead to the diversity of biological social systems. © 2013 The Authors. Journal of Evolutionary Biology © 2013 European Society For Evolutionary Biology.

Rogue sperm indicate sexually antagonistic coevolution in nematodes.

Directory of Open Access Journals (Sweden)

Ronald E Ellis

2014-07-01

Full Text Available Intense reproductive competition often continues long after animals finish mating. In many species, sperm from one male compete with those from others to find and fertilize oocytes. Since this competition occurs inside the female reproductive tract, she often influences the outcome through physical or chemical factors, leading to cryptic female choice. Finally, traits that help males compete with each other are sometimes harmful to females, and female countermeasures may thwart the interests of males, which can lead to an arms race between the sexes known as sexually antagonistic coevolution. New studies from Caenorhabditis nematodes suggest that males compete with each other by producing sperm that migrate aggressively and that these sperm may be more likely to win access to oocytes. However, one byproduct of this competition appears to be an increased probability that these sperm will go astray, invading the ovary, prematurely activating oocytes, and sometimes crossing basement membranes and leaving the gonad altogether. These harmful effects are sometimes observed in crosses between animals of the same species but are most easily detected in interspecies crosses, leading to dramatically lowered fitness, presumably because the competitiveness of the sperm and the associated female countermeasures are not precisely matched. This mismatch is most obvious in crosses involving individuals from androdioecious species (which have both hermaphrodites and males, as predicted by the lower levels of sperm competition these species experience. These results suggest a striking example of sexually antagonistic coevolution and dramatically expand the value of nematodes as a laboratory system for studying postcopulatory interactions.

Co-Evolutions of Ecosystems, Societies, and Economy in Dryland Asia

Science.gov (United States)

Chen, Jiquan; Ouyang, Zutao; John, Ranjeet; Dong, Gang; Fan, Peilei

2015-04-01

This presentation aims at the interactive changes of the natural system (NS) and the human system (HS) as well as the feedbacks in time and space for dryland Asia where multiple administrative units from several countries experience similar climates, ecosystems, cultures, and traditions but different governments, land uses, economic development, and demographic changes (e.g., ethnical composition). We compiled and examined the changes in major measures for ecosystems (e.g., PAR, LAI, GPP, ET), economy (GDP, export/import, EGS), and human demography (e.g., population, health, education) between 1981 through 2011 (30+ variables) for six Central Asian countries (Afghanistan, Turkmenistan, Tajikistan, Uzbekistan, Kazakhstan, Kyrgyzstan) and two East Asian countries (Mongolia and China). Particular attention was made to understand the co-evolutions of the ratios between the elements of HS and NS, such as: GDP: GPP, PET: FWW, R: PDSI, EGS: GPP, etc., so that feedbacks and interactions can be empirically studied. Spatial and temporal changes of each measure, as well as their ratios, were quantified to highlight the relative contributions of human activities (e.g., policy) and biophysical changes (e.g., climate). We found some tight connections between the HS and NS variables, but the co-evolutions have to be understood in the context of governments, policy, and other major institutional shifts.

Coevolution of antibiotic production and counter-resistance in soil bacteria.

Science.gov (United States)

Laskaris, Paris; Tolba, Sahar; Calvo-Bado, Leo; Wellington, Elizabeth M; Wellington, Liz

2010-03-01

We present evidence for the coexistence and coevolution of antibiotic resistance and biosynthesis genes in soil bacteria. The distribution of the streptomycin (strA) and viomycin (vph) resistance genes was examined in Streptomyces isolates. strA and vph were found either within a biosynthetic gene cluster or independently. Streptomyces griseus strains possessing the streptomycin cluster formed part of a clonal complex. All S. griseus strains possessing solely strA belonged to two clades; both were closely related to the streptomycin producers. Other more distantly related S. griseus strains did not contain strA. S. griseus strains with only vph also formed two clades, but they were more distantly related to the producers and to one another. The expression of the strA gene was constitutive in a resistance-only strain whereas streptomycin producers showed peak strA expression in late log phase that correlates with the switch on of streptomycin biosynthesis. While there is evidence that antibiotics have diverse roles in nature, our data clearly support the coevolution of resistance in the presence of antibiotic biosynthetic capability within closely related soil dwelling bacteria. This reinforces the view that, for some antibiotics at least, the primary role is one of antibiosis during competition in soil for resources.

Coevolution analysis of Hepatitis C virus genome to identify the structural and functional dependency network of viral proteins

Science.gov (United States)

Champeimont, Raphaël; Laine, Elodie; Hu, Shuang-Wei; Penin, Francois; Carbone, Alessandra

2016-05-01

A novel computational approach of coevolution analysis allowed us to reconstruct the protein-protein interaction network of the Hepatitis C Virus (HCV) at the residue resolution. For the first time, coevolution analysis of an entire viral genome was realized, based on a limited set of protein sequences with high sequence identity within genotypes. The identified coevolving residues constitute highly relevant predictions of protein-protein interactions for further experimental identification of HCV protein complexes. The method can be used to analyse other viral genomes and to predict the associated protein interaction networks.

Transition management as a model for managing processes of co-evolution towards sustainable development

NARCIS (Netherlands)

R. Kemp (René); D.A. Loorbach (Derk); J. Rotmans (Jan)

2007-01-01

textabstractSustainable development requires changes in socio-technical systems and wider societal change - in beliefs, values and governance that co-evolve with technology changes. In this article we present a practical model for managing processes of co-evolution: transition management. Transition

Co-evolution of Industry Strategies and Government Policies: The Case of the Brazilian Automotive Industry

Directory of Open Access Journals (Sweden)

Roberto Gonzalez Duarte

2017-07-01

Full Text Available This study examines the evolution of the automotive industry in Brazil and its key drivers. We argue that the rules of the game – industry policies – are an outcome of exchanges between the host government and industry. These arise from changes in economic and political environments and interdependence between industry and the country’s economy. To this end, we draw upon literature on institutions and co-evolution to understand the industry footprint over a 50-year period, as well as its relationship with changes in government policies. This study generates new insights on institutional and co-evolution political perspectives by showing that the rules of the game are not only the making of the government, but are also the result of interdependencies between industry and government.

On Design Mining: Coevolution and Surrogate Models.

Science.gov (United States)

Preen, Richard J; Bull, Larry

2017-01-01

Design mining is the use of computational intelligence techniques to iteratively search and model the attribute space of physical objects evaluated directly through rapid prototyping to meet given objectives. It enables the exploitation of novel materials and processes without formal models or complex simulation. In this article, we focus upon the coevolutionary nature of the design process when it is decomposed into concurrent sub-design-threads due to the overall complexity of the task. Using an abstract, tunable model of coevolution, we consider strategies to sample subthread designs for whole-system testing and how best to construct and use surrogate models within the coevolutionary scenario. Drawing on our findings, we then describe the effective design of an array of six heterogeneous vertical-axis wind turbines.

The Coevolution of Life and Environment on Mars: An Ecosystem Perspective on the Robotic Exploration of Biosignatures

Science.gov (United States)

Cabrol, Nathalie A.

2018-01-01

Earth's biological and environmental evolution are intertwined and inseparable. This coevolution has become a fundamental concept in astrobiology and is key to the search for life beyond our planet. In the case of Mars, whether a coevolution took place is unknown, but analyzing the factors at play shows the uniqueness of each planetary experiment regardless of similarities. Early Earth and early Mars shared traits. However, biological processes on Mars, if any, would have had to proceed within the distinctive context of an irreversible atmospheric collapse, greater climate variability, and specific planetary characteristics. In that, Mars is an important test bed for comparing the effects of a unique set of spatiotemporal changes on an Earth-like, yet different, planet. Many questions remain unanswered about Mars' early environment. Nevertheless, existing data sets provide a foundation for an intellectual framework where notional coevolution models can be explored. In this framework, the focus is shifted from planetary-scale habitability to the prospect of habitats, microbial ecotones, pathways to biological dispersal, biomass repositories, and their meaning for exploration. Critically, as we search for biosignatures, this focus demonstrates the importance of starting to think of early Mars as a biosphere and vigorously integrating an ecosystem approach to landing site selection and exploration.

Coevolution of landesque capital intensive agriculture and sociopolitical hierarchy.

Science.gov (United States)

Sheehan, Oliver; Watts, Joseph; Gray, Russell D; Atkinson, Quentin D

2018-04-03

One of the defining trends of the Holocene has been the emergence of complex societies. Two essential features of complex societies are intensive resource use and sociopolitical hierarchy. Although it is widely agreed that these two phenomena are associated cross-culturally and have both contributed to the rise of complex societies, the causality underlying their relationship has been the subject of longstanding debate. Materialist theories of cultural evolution tend to view resource intensification as driving the development of hierarchy, but the reverse order of causation has also been advocated, along with a range of intermediate views. Phylogenetic methods have the potential to test between these different causal models. Here we report the results of a phylogenetic study that modeled the coevolution of one type of resource intensification-the development of landesque capital intensive agriculture-with political complexity and social stratification in a sample of 155 Austronesian-speaking societies. We found support for the coevolution of landesque capital with both political complexity and social stratification, but the contingent and nondeterministic nature of both of these relationships was clear. There was no indication that intensification was the "prime mover" in either relationship. Instead, the relationship between intensification and social stratification was broadly reciprocal, whereas political complexity was more of a driver than a result of intensification. These results challenge the materialist view and emphasize the importance of both material and social factors in the evolution of complex societies, as well as the complex and multifactorial nature of cultural evolution. Copyright © 2018 the Author(s). Published by PNAS.

On meme--gene coevolution.

Science.gov (United States)

Bull, L; Holland, O; Blackmore, S

2000-01-01

In this article we examine the effects of the emergence of a new replicator, memes, on the evolution of a pre-existing replicator, genes. Using a version of the NKCS model we examine the effects of increasing the rate of meme evolution in relation to the rate of gene evolution, for various degrees of interdependence between the two replicators. That is, the effects of memes' (suggested) more rapid rate of evolution in comparison to that of genes is investigated using a tunable model of coevolution. It is found that, for almost any degree of interdependence between the two replicators, as the rate of meme evolution increases, a phase transition-like dynamic occurs under which memes have a significantly detrimental effect on the evolution of genes, quickly resulting in the cessation of effective gene evolution. Conversely, the memes experience a sharp increase in benefit from increasing their rate of evolution. We then examine the effects of enabling genes to reduce the percentage of gene-detrimental evolutionary steps taken by memes. Here a critical region emerges as the comparative rate of meme evolution increases, such that if genes cannot effectively select memes a high percentage of the time, they suffer from meme evolution as if they had almost no selective capability.

Cross-Resistance: A Consequence of Bi-partite Host-Parasite Coevolution

Science.gov (United States)

Joop, Gerrit

2018-01-01

Host-parasite coevolution can influence interactions of the host and parasite with the wider ecological community. One way that this may manifest is in cross-resistance towards other parasites, which has been observed to occur in some host-parasite evolution experiments. In this paper, we test for cross-resistance towards Bacillus thuringiensis and Pseudomonas entomophila in the red flour beetle Tribolium castaneum, which was previously allowed to coevolve with the generalist entomopathogenic fungus Beauveria bassiana. We combine survival and gene expression assays upon infection to test for cross-resistance and underlying mechanisms. We show that larvae of T. castaneum that evolved with B. bassiana under coevolutionary conditions were positively cross-resistant to the bacterium B. thuringiensis, but not P. entomophila. Positive cross-resistance was mirrored at the gene expression level with markers that were representative of the oral route of infection being upregulated upon B. bassiana exposure. We find that positive cross-resistance towards B. thuringiensis evolved in T. castaneum as a consequence of its coevolutionary interactions with B. bassiana. This cross-resistance appears to be a consequence of resistance to oral toxicity. The fact that coevolution with B. bassiana results in resistance to B. thuringiensis, but not P. entomophila implies that B. thuringiensis and B. bassiana may share mechanisms of infection or toxicity not shared by P. entomophila. This supports previous suggestions that B. bassiana may possess Cry-like toxins, similar to those found in B. thuringiensis, which allow it to infect orally. PMID:29495405

Cross-Resistance: A Consequence of Bi-partite Host-Parasite Coevolution

Directory of Open Access Journals (Sweden)

Tilottama Biswas

2018-02-01

Full Text Available Host-parasite coevolution can influence interactions of the host and parasite with the wider ecological community. One way that this may manifest is in cross-resistance towards other parasites, which has been observed to occur in some host-parasite evolution experiments. In this paper, we test for cross-resistance towards Bacillus thuringiensis and Pseudomonas entomophila in the red flour beetle Tribolium castaneum, which was previously allowed to coevolve with the generalist entomopathogenic fungus Beauveria bassiana. We combine survival and gene expression assays upon infection to test for cross-resistance and underlying mechanisms. We show that larvae of T. castaneum that evolved with B. bassiana under coevolutionary conditions were positively cross-resistant to the bacterium B. thuringiensis, but not P. entomophila. Positive cross-resistance was mirrored at the gene expression level with markers that were representative of the oral route of infection being upregulated upon B. bassiana exposure. We find that positive cross-resistance towards B. thuringiensis evolved in T. castaneum as a consequence of its coevolutionary interactions with B. bassiana. This cross-resistance appears to be a consequence of resistance to oral toxicity. The fact that coevolution with B. bassiana results in resistance to B. thuringiensis, but not P. entomophila implies that B. thuringiensis and B. bassiana may share mechanisms of infection or toxicity not shared by P. entomophila. This supports previous suggestions that B. bassiana may possess Cry-like toxins, similar to those found in B. thuringiensis, which allow it to infect orally.

Practical aspects of protein co-evolution.

Science.gov (United States)

Ochoa, David; Pazos, Florencio

2014-01-01

Co-evolution is a fundamental aspect of Evolutionary Theory. At the molecular level, co-evolutionary linkages between protein families have been used as indicators of protein interactions and functional relationships from long ago. Due to the complexity of the problem and the amount of genomic data required for these approaches to achieve good performances, it took a relatively long time from the appearance of the first ideas and concepts to the quotidian application of these approaches and their incorporation to the standard toolboxes of bioinformaticians and molecular biologists. Today, these methodologies are mature (both in terms of performance and usability/implementation), and the genomic information that feeds them large enough to allow their general application. This review tries to summarize the current landscape of co-evolution-based methodologies, with a strong emphasis on describing interesting cases where their application to important biological systems, alone or in combination with other computational and experimental approaches, allowed getting new insight into these.

Coexistence via coevolution driven by reduced allelochemical effects and increased tolerance to competition between invasive and native plants.

Science.gov (United States)

Huang, Fangfang; Lankau, Richard; Peng, Shaolin

2018-04-01

Coevolution can promote long-term coexistence of two competing species if selection acts to reduce the fitness inequality between competitors and/or strengthen negative frequency dependence within each population. However, clear coevolution between plant competitors has been rarely documented. Plant invasions offer opportunities to capture the process of coevolution. Here we investigated how the developing relationship between an invasive forb, Alliaria petiolata, and a native competitor, Pilea pumila, may affect their long-term coexistence, by testing the competitive effects of populations of varying lengths of co-occurrence on each other across a chronosequence of invasion history. Alliaria petiolata and P. pumila tended to develop greater tolerance to competition over invasion history. Their coexistence was promoted more by increases in stabilizing relative to equalizing processes. These changes likely stem in part from reductions in allelopathic traits in the invader and evolution of tolerance in the native. These results suggested that some native species can evolve tolerance against the competitive effects of strong invaders, which likely promoted their persistence in invaded communities. However, the potential for coevolutionary rescue of competing populations is likely to vary across native species, and evolutionary processes should not be expected to compensate for the ecological consequences of exotic invasions. © 2017 The Authors. New Phytologist © 2017 New Phytologist Trust.

The role of ecology, neutral processes and antagonistic coevolution in an apparent sexual arms race.

Science.gov (United States)

Perry, Jennifer C; Garroway, Colin J; Rowe, Locke

2017-09-01

Some of the strongest examples of a sexual 'arms race' come from observations of correlated evolution in sexually antagonistic traits among populations. However, it remains unclear whether these cases truly represent sexually antagonistic coevolution; alternatively, ecological or neutral processes might also drive correlated evolution. To investigate these alternatives, we evaluated the contributions of intersex genetic correlations, ecological context, neutral genetic divergence and sexual coevolution in the correlated evolution of antagonistic traits among populations of Gerris incognitus water striders. We could not detect intersex genetic correlations for these sexually antagonistic traits. Ecological variation was related to population variation in the key female antagonistic trait (spine length, a defence against males), as well as body size. Nevertheless, population covariation between sexually antagonistic traits remained substantial and significant even after accounting for all of these processes. Our results therefore provide strong evidence for a contemporary sexual arms race. © 2017 John Wiley & Sons Ltd/CNRS.

The Coevolution of "Tyrannosaurus" & Its Prey: Could "Tyrannosaurus" Chase down & Kill a "Triceratops" for Lunch?

Science.gov (United States)

May, S. Randolph

2014-01-01

Students will analyze the coevolution of the predator-prey relationships between "Tyrannosaurus rex" and its prey species using analyses of animal speeds from fossilized trackways, prey-animal armaments, adaptive behaviors, bite marks on prey-animal fossils, predator-prey ratios, and scavenger competition. The students will be asked to…

Culture–gene coevolution of individualism–collectivism and the serotonin transporter gene

Science.gov (United States)

Chiao, Joan Y.; Blizinsky, Katherine D.

2010-01-01

Culture–gene coevolutionary theory posits that cultural values have evolved, are adaptive and influence the social and physical environments under which genetic selection operates. Here, we examined the association between cultural values of individualism–collectivism and allelic frequency of the serotonin transporter functional polymorphism (5-HTTLPR) as well as the role this culture–gene association may play in explaining global variability in prevalence of pathogens and affective disorders. We found evidence that collectivistic cultures were significantly more likely to comprise individuals carrying the short (S) allele of the 5-HTTLPR across 29 nations. Results further show that historical pathogen prevalence predicts cultural variability in individualism–collectivism owing to genetic selection of the S allele. Additionally, cultural values and frequency of S allele carriers negatively predict global prevalence of anxiety and mood disorder. Finally, mediation analyses further indicate that increased frequency of S allele carriers predicted decreased anxiety and mood disorder prevalence owing to increased collectivistic cultural values. Taken together, our findings suggest culture–gene coevolution between allelic frequency of 5-HTTLPR and cultural values of individualism–collectivism and support the notion that cultural values buffer genetically susceptible populations from increased prevalence of affective disorders. Implications of the current findings for understanding culture–gene coevolution of human brain and behaviour as well as how this coevolutionary process may contribute to global variation in pathogen prevalence and epidemiology of affective disorders, such as anxiety and depression, are discussed. PMID:19864286

Culture-gene coevolution of individualism-collectivism and the serotonin transporter gene.

Science.gov (United States)

Chiao, Joan Y; Blizinsky, Katherine D

2010-02-22

Culture-gene coevolutionary theory posits that cultural values have evolved, are adaptive and influence the social and physical environments under which genetic selection operates. Here, we examined the association between cultural values of individualism-collectivism and allelic frequency of the serotonin transporter functional polymorphism (5-HTTLPR) as well as the role this culture-gene association may play in explaining global variability in prevalence of pathogens and affective disorders. We found evidence that collectivistic cultures were significantly more likely to comprise individuals carrying the short (S) allele of the 5-HTTLPR across 29 nations. Results further show that historical pathogen prevalence predicts cultural variability in individualism-collectivism owing to genetic selection of the S allele. Additionally, cultural values and frequency of S allele carriers negatively predict global prevalence of anxiety and mood disorder. Finally, mediation analyses further indicate that increased frequency of S allele carriers predicted decreased anxiety and mood disorder prevalence owing to increased collectivistic cultural values. Taken together, our findings suggest culture-gene coevolution between allelic frequency of 5-HTTLPR and cultural values of individualism-collectivism and support the notion that cultural values buffer genetically susceptible populations from increased prevalence of affective disorders. Implications of the current findings for understanding culture-gene coevolution of human brain and behaviour as well as how this coevolutionary process may contribute to global variation in pathogen prevalence and epidemiology of affective disorders, such as anxiety and depression, are discussed.

Plant lock and ant key: pairwise coevolution of an exclusion filter in an ant-plant mutualism.

Science.gov (United States)

Brouat, C; Garcia, N; Andary, C; McKey, D

2001-10-22

Although observations suggest pairwise coevolution in specific ant-plant symbioses, coevolutionary processes have rarely been demonstrated. We report on, what is to the authors' knowledge, the strongest evidence yet for reciprocal adaptation of morphological characters in a species-specific ant-plant mutualism. The plant character is the prostoma, which is a small unlignified organ at the apex of the domatia in which symbiotic ants excavate an entrance hole. Each myrmecophyte in the genus Leonardoxa has evolved a prostoma with a different shape. By performing precise measurements on the prostomata of three related myrmecophytes, on their specific associated ants and on the entrance holes excavated by symbiotic ants at the prostomata, we showed that correspondence of the plant and ant traits forms a morphological and behavioural filter. We have strong evidence for coevolution between the dimensions and shape of the symbiotic ants and the prostoma in one of the three ant-Leonardoxa associations.

Host specificity and coevolution of Flavobacteriaceae endosymbionts within the siphonous green seaweed Bryopsis.

Science.gov (United States)

Hollants, Joke; Leliaert, Frederik; Verbruggen, Heroen; De Clerck, Olivier; Willems, Anne

2013-06-01

The siphonous green seaweed Bryopsis harbors complex intracellular bacterial communities. Previous studies demonstrated that certain species form close, obligate associations with Flavobacteriaceae. A predominant imprint of host evolutionary history on the presence of these bacteria suggests a highly specialized association. In this study we elaborate on previous results by expanding the taxon sampling and testing for host-symbiont coevolution Therefore, we optimized a PCR protocol to directly and specifically amplify Flavobacteriaceae endosymbiont 16S rRNA gene sequences, which allowed us to screen a large number of algal samples without the need for cultivation or surface sterilization. We analyzed 146 Bryopsis samples, and 92 additional samples belonging to the Bryopsidales and other orders within the class Ulvophyceae. Results indicate that the Flavobacteriaceae endosymbionts are restricted to Bryopsis, and only occur within specific, warm-temperate and tropical clades of the genus. Statistical analyses (AMOVA) demonstrate a significant non-random host-symbiont association. Comparison of bacterial 16S rRNA and Bryopsis rbcL phylogenies, however, reveal complex host-symbiont evolutionary associations, whereby closely related hosts predominantly harbor genetically similar endosymbionts. Bacterial genotypes are rarely confined to a single Bryopsis species and most Bryopsis species harbored several Flavobacteriaceae, obscuring a clear pattern of coevolution. Copyright © 2013 Elsevier Inc. All rights reserved.

The coevolution of recognition and social behavior.

Science.gov (United States)

Smead, Rory; Forber, Patrick

2016-05-26

Recognition of behavioral types can facilitate the evolution of cooperation by enabling altruistic behavior to be directed at other cooperators and withheld from defectors. While much is known about the tendency for recognition to promote cooperation, relatively little is known about whether such a capacity can coevolve with the social behavior it supports. Here we use evolutionary game theory and multi-population dynamics to model the coevolution of social behavior and recognition. We show that conditional harming behavior enables the evolution and stability of social recognition, whereas conditional helping leads to a deterioration of recognition ability. Expanding the model to include a complex game where both helping and harming interactions are possible, we find that conditional harming behavior can stabilize recognition, and thereby lead to the evolution of conditional helping. Our model identifies a novel hypothesis for the evolution of cooperation: conditional harm may have coevolved with recognition first, thereby helping to establish the mechanisms necessary for the evolution of cooperation.

Coevolution of Artificial Agents Using Evolutionary Computation in Bargaining Game

Directory of Open Access Journals (Sweden)

Sangwook Lee

2015-01-01

Full Text Available Analysis of bargaining game using evolutionary computation is essential issue in the field of game theory. This paper investigates the interaction and coevolutionary process among heterogeneous artificial agents using evolutionary computation (EC in the bargaining game. In particular, the game performance with regard to payoff through the interaction and coevolution of agents is studied. We present three kinds of EC based agents (EC-agent participating in the bargaining game: genetic algorithm (GA, particle swarm optimization (PSO, and differential evolution (DE. The agents’ performance with regard to changing condition is compared. From the simulation results it is found that the PSO-agent is superior to the other agents.

Socio-hydrologic Perspectives of the Co-evolution of Humans and Water in the Tarim River Basin, Western China

Science.gov (United States)

Liu, Ye; Tian, Fuqiang; Hu, Heping; Liu, Dengfeng; Sivapalan, Murugesu

2013-04-01

Socio-hydrology studies the co-evolution of coupled human-water systems, which is of great importance for long-term sustainable water resource management in basins suffering from serious eco-environmental degradation. Process socio-hydrology can benefit from the exploring the patterns of historical co-evolution of coupled human-water systems as a way to discovering the organizing principles that may underpin their co-evolution. As a self-organized entity, the human-water system in a river basin would evolve into certain steady states over a sufficiently long time but then could also experience sudden shifts due to internal or external disturbances that exceed system thresholds. In this study, we discuss three steady states (also called stages in the social sciences, including natural, human exploitation and recovery stages) and transitions between these during the past 1500 years in the Tarim River Basin of Western China, which a rich history of civilization including its place in the famous Silk Road that connected China to Europe. Specifically, during the natural stage with a sound environment that existed before the 19th century, shifts in the ecohydrological regime were mainly caused by environmental changes such river channel migration and climate change. During the human exploitation stages in the 5th and again in the 19th-20th centuries, however, humans gradually became the main drivers for system evolution, during which the basin experienced rapid population growth, fast socio-economic development and intense human activities. By the 1970s, after 200 years of colonization, the Tarim River Basin evolved into a new regime with vulnerable ecosystem and water system, and suffered from serious water shortages and desertification. Human society then began to take a critical look into the effects of their activities and reappraise the impact of human development on the ecohydrological system, which eventually led the basin into a treatment and recovery stage

Convergent coevolution in the domestication of coral mushrooms by fungus-growing ants

DEFF Research Database (Denmark)

Munkacsi, A.B.; Pan, J.J.; Villesen, P.

2004-01-01

family Pterulaceae using phylogenetic reconstructions based on broad taxon sampling, including the first mushroom collected from the garden of an ant species in the A. pilosum group. The domestication of the pterulaceous cultivar is independent from the domestication of the gilled mushrooms cultivated...... of parallel coevolution, where the symbionts of each functional group are members of monophyletic groups. However, there is one outstanding exception in the fungus-growing ant system, the unidentified cultivar grown only by ants in the Apterostigma pilosum group. We classify this cultivar in the coral-mushroom...

Cooperation enhanced by the coevolution of teaching activity in evolutionary prisoner's dilemma games with voluntary participation.

Science.gov (United States)

Shen, Chen; Chu, Chen; Geng, Yini; Jin, Jiahua; Chen, Fei; Shi, Lei

2018-01-01

Voluntary participation, as an additional strategy involved in repeated games, has been proved to be an efficient way to promote the evolution of cooperation theoretically and empirically. Besides, current studies show that the coevolution of teaching activity can promote cooperation. Thus, inspired by aforementioned above, we investigate the effect of coevolution of teaching activity on the evolution of cooperation for prisoner's dilemma game with voluntary participation: when the focal player successfully enforces its strategy on the opponent, his teaching ability will get an increase. Through numerical simulation, we have shown that voluntary participation could effectively promote the fraction of cooperation, which is also affected by the value of increment. Furthermore, we investigate the influence of the increment value on the density of different strategies and find that there exists an optimal increment value that plays an utmost role on the evolutionary dynamics. With regard to this observation, we unveil that an optimal value of increment can lead to strongest heterogeneity in agents' teaching ability, further promoting the evolution of cooperation.

Cooperation enhanced by the coevolution of teaching activity in evolutionary prisoner's dilemma games with voluntary participation.

Directory of Open Access Journals (Sweden)

Chen Shen

Full Text Available Voluntary participation, as an additional strategy involved in repeated games, has been proved to be an efficient way to promote the evolution of cooperation theoretically and empirically. Besides, current studies show that the coevolution of teaching activity can promote cooperation. Thus, inspired by aforementioned above, we investigate the effect of coevolution of teaching activity on the evolution of cooperation for prisoner's dilemma game with voluntary participation: when the focal player successfully enforces its strategy on the opponent, his teaching ability will get an increase. Through numerical simulation, we have shown that voluntary participation could effectively promote the fraction of cooperation, which is also affected by the value of increment. Furthermore, we investigate the influence of the increment value on the density of different strategies and find that there exists an optimal increment value that plays an utmost role on the evolutionary dynamics. With regard to this observation, we unveil that an optimal value of increment can lead to strongest heterogeneity in agents' teaching ability, further promoting the evolution of cooperation.

Cosmological coevolution of Yang-Mills fields and perfect fluids

International Nuclear Information System (INIS)

Barrow, John D.; Jin, Yoshida; Maeda, Kei-ichi

2005-01-01

We study the coevolution of Yang-Mills fields and perfect fluids in Bianchi type I universes. We investigate numerically the evolution of the universe and the Yang-Mills fields during the radiation and dust eras of a universe that is almost isotropic. The Yang-Mills field undergoes small amplitude chaotic oscillations, as do the three expansion scale factors which are also displayed by the expansion scale factors of the universe. The results of the numerical simulations are interpreted analytically and compared with past studies of the cosmological evolution of magnetic fields in radiation and dust universes. We find that, whereas magnetic universes are strongly constrained by the microwave background anisotropy, Yang-Mills universes are principally constrained by primordial nucleosynthesis but the bound is comparatively weak with Ω YM rad

Coevolution in host-parasite systems: behavioural strategies of slave-making ants and their hosts.

OpenAIRE

Foitzik, S.; DeHeer, C. J.; Hunjan, D. N.; Herbers, J. M.

2001-01-01

Recently, avian brood parasites and their hosts have emerged as model systems for the study of host-parasite coevolution. However, empirical studies of the highly analogous social parasites, which use the workers of another eusocial species to raise their own young, have never explicitly examined the dynamics of these systems from a coevolutionary perspective. Here, we demonstrate interpopulational variation in behavioural interactions between a socially parasitic slave-maker ant and its host...

Host specificity and coevolution of Flavobacteriaceae endosymbionts within the siphonous green seaweed Bryopsis

OpenAIRE

Hollants, J.; Leliaert, F.; Verbruggen, H.; De Clerck, O.; Willems, A.

2013-01-01

The siphonous green seaweed Bryopsis harbors complex intracellular bacterial communities. Previous studies demonstrated that certain species form close, obligate associations with Flavobacteriaceae. A predominant imprint of host evolutionary history on the presence of these bacteria suggests a highly specialized association. In this study we elaborate on previous results by expanding the taxon sampling and testing for host–symbiont coevolution Therefore, we optimized a PCR protocol to directl...

Phylogenetic placement of an unusual coral mushroom challenges the classic hypothesis of strict coevolution in the apterostigma pilosum group ant-fungus mutualism.

Science.gov (United States)

Dentinger, Bryn T M; Lodge, D Jean; Munkacsi, Andrew B; Desjardin, Dennis E; McLaughlin, David J

2009-08-01

The approximately 50 million-year-old fungus-farming ant mutualism is a classic example of coevolution, involving ants that subsist on asexual, fungal biomass, in turn propagating the fungus clonally through nest-to-nest transmission. Most mutualistic ants cultivate two closely related groups of gilled mushrooms, whereas one small group of ants in the genus Apterostigma cultivates a distantly related lineage comprised of the G2 and G4 groups. The G2 and G4 fungi were previously shown to form a monophyletic group sister to the thread-like coral mushroom family Pterulaceae. Here, we identify an enigmatic coral mushroom that produces both fertile and sterile fruiting structures as the closest free-living relative of the G4 fungi, challenging the monophyly of the Apterostigma-cultivated fungi for the first time. Both nonparametric bootstrap and Bayesian posterior probability support the node leading to the G4 cultivars and a free-living Pterula mushroom. These data suggest three scenarios that contradict the hypothesis of strict coevolution: (1) multiple domestications, (2) escape from domestication, (3) selection of single cultivar lineages from an ancestral mixed-fungus garden. These results illustrate how incomplete phylogenies for coevolved symbionts impede our understanding of the patterns and processes of coevolution.

Comparative Phylogenetic Studies on Schistosoma japonicum and Its Snail Intermediate Host Oncomelania hupensis: Origins, Dispersal and Coevolution.

Directory of Open Access Journals (Sweden)

Stephen W Attwood

Full Text Available Schistosoma japonicum causes major public health problems in China and the Philippines; this parasite, which is transmitted by freshwater snails of the species Oncomelania hupensis, causes the disease intestinal schistosomiasis in humans and cattle. Researchers working on Schistosoma in Africa have described the relationship between the parasites and their snail intermediate hosts as coevolved or even as an evolutionary arms race. In the present study this hypothesis of coevolution is evaluated for S. japonicum and O. hupensis. The origins and radiation of the snails and the parasite across China, and the taxonomic validity of the sub-species of O. hupensis, are also assessed.The findings provide no evidence for coevolution between S. japonicum and O. hupensis, and the phylogeographical analysis suggests a heterochronous radiation of the parasites and snails in response to different palaeogeographical and climatic triggers. The results are consistent with a hypothesis of East to West colonisation of China by Oncomelania with a re-invasion of Japan by O. hupensis from China. The Taiwan population of S. japonicum appears to be recently established in comparison with mainland Chinese populations.The snail and parasite populations of the western mountain region of China (Yunnan and Sichuan appear to have been isolated from Southeast Asian populations since the Pleistocene; this has implications for road and rail links being constructed in the region, which will breach biogeographical barriers between China and Southeast Asia. The results also have implications for the spread of S. japonicum. In the absence of coevolution, the parasite may more readily colonise new snail populations to which it is not locally adapted, or even new intermediate host species; this can facilitate its dispersal into new areas. Additional work is required to assess further the risk of spread of S. japonicum.

Co-evolution of Massive Black Holes and Their Host Galaxies

Science.gov (United States)

Chen, Y. M.

2010-07-01

A scenario of co-evolution of supermassive black holes (SMBHs) and galaxies has been clearly conducted by the important evidence from observational results of quasar host galaxies and the relation between spheroid and SMBH mass. There are a plenty of unresolved problems and questions, some being basic, to be addressed in this scenario. The main goal of the present thesis is focusing on the mysterious scenario including growth of primordial black holes, cosmological evolution of spins and duty cycle of SMBHs, and interaction between the SMBH activity and star formation in galaxies from low to high redshifts. We review the main progress of this field over the past decade since the discovery of Magorrian relation and present comments on some questions in light of our view of points. The key questions to be addressed in this thesis work are: (1) how does the fast growth of primordial black holes influence their evolution? (2) what is the equation to describe the co-evolution of SMBHs and galaxies? (3) what is the mechanism to control the co-evolution? (4) how to transport the fueling gas from kpc scale to the center? It has been suggested that fast growth of primordial black holes via super-Eddington accretion is a promising way to form SMBHs in high redshift universe. Neutrino cooling has been employed and expedites the growth. We consider the Compton heating of the surroundings of the primordial black holes. We find that the realistic accretion rate is only a few percent of the Eddington rate, and the accretion is episodic. It implies that the fast growth via super-Eddington is not feasible. These conclusions have been confirmed by the detailed numerical simulations of Milosavljevic et al. (2008). The difficulties of the fast growth via accretion of baryon particles make the formation of SMBHs elusive in high redshift universe. We developed a new formulation to calculate the duty cycle of SMBHs based on the Soltan argument. We show it can be expressed by the mass

Coevolution of patch-type dependent emigration and patch-type dependent immigration.

Science.gov (United States)

Weigang, Helene C

2017-08-07

The three phases of dispersal - emigration, transfer and immigration - are affecting each other and the former and latter decisions may depend on patch types. Despite the inevitable fact of the complexity of the dispersal process, patch-type dependencies of dispersal decisions modelled as emigration and immigration are usually missing in theoretical dispersal models. Here, I investigate the coevolution of patch-type dependent emigration and patch-type dependent immigration in an extended Hamilton-May model. The dispersing population inhabits a landscape structured into many patches of two types and disperses during a continuous-time season. The trait under consideration is a four dimensional vector consisting of two values for emigration probability from the patches and two values for immigration probability into the patches of each type. Using the adaptive dynamics approach I show that four qualitatively different dispersal strategies may evolve in different parameter regions, including a counterintuitive strategy, where patches of one type are fully dispersed from (emigration probability is one) but individuals nevertheless always immigrate into them during the dispersal season (immigration probability is one). I present examples of evolutionary branching in a wide parameter range, when the patches with high local death rate during the dispersal season guarantee a high expected disperser output. I find that two dispersal strategies can coexist after evolutionary branching: a strategy with full immigration only into the patches with high expected disperser output coexists with a strategy that immigrates into any patch. Stochastic simulations agree with the numerical predictions. Since evolutionary branching is also found when immigration evolves alone, the present study is adding coevolutionary constraints on the emigration traits and hence finds that the coevolution of a higher dimensional trait sometimes hinders evolutionary diversification. Copyright © 2017

Evolutionary responses to a constructed niche: ancient Mesoamericans as a model of gene-culture coevolution.

Directory of Open Access Journals (Sweden)

Tábita Hünemeier

Full Text Available Culture and genetics rely on two distinct but not isolated transmission systems. Cultural processes may change the human selective environment and thereby affect which individuals survive and reproduce. Here, we evaluated whether the modes of subsistence in Native American populations and the frequencies of the ABCA1*Arg230Cys polymorphism were correlated. Further, we examined whether the evolutionary consequences of the agriculturally constructed niche in Mesoamerica could be considered as a gene-culture coevolution model. For this purpose, we genotyped 229 individuals affiliated with 19 Native American populations and added data for 41 other Native American groups (n = 1905 to the analysis. In combination with the SNP cluster of a neutral region, this dataset was then used to unravel the scenario involved in 230Cys evolutionary history. The estimated age of 230Cys is compatible with its origin occurring in the American continent. The correlation of its frequencies with the archeological data on Zea pollen in Mesoamerica/Central America, the neutral coalescent simulations, and the F(ST-based natural selection analysis suggest that maize domestication was the driving force in the increase in the frequencies of 230Cys in this region. These results may represent the first example of a gene-culture coevolution involving an autochthonous American allele.

Comparing the co-evolution of production and test code in open source and industrial developer test processes through repository mining

NARCIS (Netherlands)

Van Rompaey, B.; Zaidman, A.E.; Van Deursen, A.; Demeyer, S.

2008-01-01

This paper represents an extension to our previous work: Mining software repositories to study coevolution of production & test code. Proceedings of the International Conference on Software Testing, Verification, and Validation (ICST), IEEE Computer Society, 2008; doi:10.1109/ICST.2008.47

The Beringian Coevolution Project: Holistic collections of mammals and associated parasites reveal novel perspectives on changing environments in the north

Science.gov (United States)

The Beringian Coevolution Project (BCP), a field program underway in the Arctic since 1999, has focused on building key scientific infrastructure for integrated specimen-based studies on mammals and their associated parasites. BCP has contributed new insights across temporal and spatial scales into...

The aminoacyl-tRNA synthetases had only a marginal role in the origin of the organization of the genetic code: Evidence in favor of the coevolution theory.

Science.gov (United States)

Di Giulio, Massimo

2017-11-07

The coevolution theory of the origin of the genetic code suggests that the organization of the genetic code coevolved with the biosynthetic relationships between amino acids. The mechanism that allowed this coevolution was based on tRNA-like molecules on which-this theory-would postulate the biosynthetic transformations between amino acids to have occurred. This mechanism makes a prediction on how the role conducted by the aminoacyl-tRNA synthetases (ARSs), in the origin of the genetic code, should have been. Indeed, if the biosynthetic transformations between amino acids occurred on tRNA-like molecules, then there was no need to link amino acids to these molecules because amino acids were already charged on tRNA-like molecules, as the coevolution theory suggests. In spite of the fact that ARSs make the genetic code responsible for the first interaction between a component of nucleic acids and that of proteins, for the coevolution theory the role of ARSs should have been entirely marginal in the genetic code origin. Therefore, I have conducted a further analysis of the distribution of the two classes of ARSs and of their subclasses-in the genetic code table-in order to perform a falsification test of the coevolution theory. Indeed, in the case in which the distribution of ARSs within the genetic code would have been highly significant, then the coevolution theory would be falsified since the mechanism on which it is based would not predict a fundamental role of ARSs in the origin of the genetic code. I found that the statistical significance of the distribution of the two classes of ARSs in the table of the genetic code is low or marginal, whereas that of the subclasses of ARSs statistically significant. However, this is in perfect agreement with the postulates of the coevolution theory. Indeed, the only case of statistical significance-regarding the classes of ARSs-is appreciable for the CAG code, whereas for its complement-the UNN/NUN code-only a marginal

Co-evolution of transcriptional silencing proteins and the DNA elements specifying their assembly.

Directory of Open Access Journals (Sweden)

Oliver A Zill

Full Text Available Co-evolution of transcriptional regulatory proteins and their sites of action has been often hypothesized but rarely demonstrated. Here we provide experimental evidence of such co-evolution in yeast silent chromatin, a finding that emerged from studies of hybrids formed between two closely related Saccharomyces species. A unidirectional silencing incompatibility between S. cerevisiae and S. bayanus led to a key discovery: asymmetrical complementation of divergent orthologs of the silent chromatin component Sir4. In S. cerevisiae/S. bayanus interspecies hybrids, ChIP-Seq analysis revealed a restriction against S. cerevisiae Sir4 associating with most S. bayanus silenced regions; in contrast, S. bayanus Sir4 associated with S. cerevisiae silenced loci to an even greater degree than did S. cerevisiae's own Sir4. Functional changes in silencer sequences paralleled changes in Sir4 sequence and a reduction in Sir1 family members in S. cerevisiae. Critically, species-specific silencing of the S. bayanus HMR locus could be reconstituted in S. cerevisiae by co-transfer of the S. bayanus Sir4 and Kos3 (the ancestral relative of Sir1 proteins. As Sir1/Kos3 and Sir4 bind conserved silencer-binding proteins, but not specific DNA sequences, these rapidly evolving proteins served to interpret differences in the two species' silencers presumably involving emergent features created by the regulatory proteins that bind sequences within silencers. The results presented here, and in particular the high resolution ChIP-Seq localization of the Sir4 protein, provided unanticipated insights into the mechanism of silent chromatin assembly in yeast.

Niche construction, sources of selection and trait coevolution.

Science.gov (United States)

Laland, Kevin; Odling-Smee, John; Endler, John

2017-10-06

Organisms modify and choose components of their local environments. This 'niche construction' can alter ecological processes, modify natural selection and contribute to inheritance through ecological legacies. Here, we propose that niche construction initiates and modifies the selection directly affecting the constructor, and on other species, in an orderly, directed and sustained manner. By dependably generating specific environmental states, niche construction co-directs adaptive evolution by imposing a consistent statistical bias on selection. We illustrate how niche construction can generate this evolutionary bias by comparing it with artificial selection. We suggest that it occupies the middle ground between artificial and natural selection. We show how the perspective leads to testable predictions related to: (i) reduced variance in measures of responses to natural selection in the wild; (ii) multiple trait coevolution, including the evolution of sequences of traits and patterns of parallel evolution; and (iii) a positive association between niche construction and biodiversity. More generally, we submit that evolutionary biology would benefit from greater attention to the diverse properties of all sources of selection.

Identification of coevolving residues and coevolution potentials emphasizing structure, bond formation and catalytic coordination in protein evolution.

Directory of Open Access Journals (Sweden)

Daniel Y Little

Full Text Available The structure and function of a protein is dependent on coordinated interactions between its residues. The selective pressures associated with a mutation at one site should therefore depend on the amino acid identity of interacting sites. Mutual information has previously been applied to multiple sequence alignments as a means of detecting coevolutionary interactions. Here, we introduce a refinement of the mutual information method that: 1 removes a significant, non-coevolutionary bias and 2 accounts for heteroscedasticity. Using a large, non-overlapping database of protein alignments, we demonstrate that predicted coevolving residue-pairs tend to lie in close physical proximity. We introduce coevolution potentials as a novel measure of the propensity for the 20 amino acids to pair amongst predicted coevolutionary interactions. Ionic, hydrogen, and disulfide bond-forming pairs exhibited the highest potentials. Finally, we demonstrate that pairs of catalytic residues have a significantly increased likelihood to be identified as coevolving. These correlations to distinct protein features verify the accuracy of our algorithm and are consistent with a model of coevolution in which selective pressures towards preserving residue interactions act to shape the mutational landscape of a protein by restricting the set of admissible neutral mutations.

Studying the co-evolution of production and test code in open source and industrial developer test processes through repository mining

NARCIS (Netherlands)

Zaidman, A.; Van Rompaey, B.; Van Deursen, A.; Demeyer, S.

2010-01-01

Many software production processes advocate rigorous development testing alongside functional code writing, which implies that both test code and production code should co-evolve. To gain insight in the nature of this co-evolution, this paper proposes three views (realized by a tool called TeMo)

Social evolution. Oxytocin-gaze positive loop and the coevolution of human-dog bonds.

Science.gov (United States)

Nagasawa, Miho; Mitsui, Shouhei; En, Shiori; Ohtani, Nobuyo; Ohta, Mitsuaki; Sakuma, Yasuo; Onaka, Tatsushi; Mogi, Kazutaka; Kikusui, Takefumi

2015-04-17

Human-like modes of communication, including mutual gaze, in dogs may have been acquired during domestication with humans. We show that gazing behavior from dogs, but not wolves, increased urinary oxytocin concentrations in owners, which consequently facilitated owners' affiliation and increased oxytocin concentration in dogs. Further, nasally administered oxytocin increased gazing behavior in dogs, which in turn increased urinary oxytocin concentrations in owners. These findings support the existence of an interspecies oxytocin-mediated positive loop facilitated and modulated by gazing, which may have supported the coevolution of human-dog bonding by engaging common modes of communicating social attachment. Copyright © 2015, American Association for the Advancement of Science.

A role for habitat area in the geographic mosaic of coevolution between red crossbills and lodgepole pine.

Science.gov (United States)

Siepielski, A M; Benkman, C W

2005-07-01

Understanding how resource abundance limits adaptive evolution and influences species interactions is an important step towards developing insight into the role of microevolutionary processes in establishing macroevolutionary patterns. We examined how variation in resource abundance (forest area of lodgepole pine Pinus contorta ssp. latifolia) influenced patterns of co-adaptation and coevolution between red crossbill (Loxia curvirostra complex) and lodgepole pine populations. First, we found that crossbill abundance increased logarithmically as forest area increased in mountain ranges lacking a preemptive competitor (pine squirrels Tamiasciurus hudsonicus). Second, seed defences against predation by crossbills increased with increases in crossbill density, suggesting that seed defences have likely evolved in proportion to the intensity of selection that crossbills exert. Third, the average bill size of crossbill populations increased with increasing seed defences, which implies that crossbill offenses increased with increases in seed defences. The large bill size on the largest range is the result of coevolution with lodgepole pine with this crossbill population perhaps speciating. Local adaptation of crossbill populations on smaller ranges, however, is more likely the result of resident crossbills representing a subset of the potential colonists (phenotypic sorting) than of local evolution. In the smallest range, migration and possibly more frequent extinction likely impede local adaptation and may result in maladaptation.

Emergent dynamics of fairness in the spatial coevolution of proposer and responder species in the ultimatum game.

Directory of Open Access Journals (Sweden)

Reiji Suzuki

Full Text Available While spatially local interactions are ubiquitous between coevolving species sharing recourses (e.g., plant-insect interactions, their effects on such coevolution processes of strategies involving the share of a resource are still not clearly understood. We construct a two-dimensional spatial model of the coevolution of the proposer and responder species in the ultimatum game (UG, in which a pair of proposer and responder individuals at each site plays the UG. We investigate the effects of the locality of interactions and the intensity of selection on the emergence of fairness between these species. We show that the lower intensity of selection favors fair strategies in general, and there are no significant differences in the evolution of fairness between the cases with local and global interactions when the intensity of selection is low. However, as the intensity of selection becomes higher, the spatially local interactions contribute to the evolution of fairer strategies more than the global interactions, even though fair strategies become more difficult to evolve. This positive effect of spatial interactions is expected to be due to the mutual benefit of fairness for both proposer and responder species in future generations, which brings about a dynamic evolution process of fairness.

Paternal care and litter size coevolution in mammals.

Science.gov (United States)

Stockley, Paula; Hobson, Liane

2016-04-27

Biparental care of offspring occurs in diverse mammalian genera and is particularly common among species with socially monogamous mating systems. Despite numerous well-documented examples, however, the evolutionary causes and consequences of paternal care in mammals are not well understood. Here, we investigate the evolution of paternal care in relation to offspring production. Using comparative analyses to test for evidence of evolutionary associations between male care and life-history traits, we explore if biparental care is likely to have evolved because of the importance of male care to offspring survival, or if evolutionary increases in offspring production are likely to result from the evolution of biparental care. Overall, we find no evidence that paternal care has evolved in response to benefits of supporting females to rear particularly costly large offspring or litters. Rather, our findings suggest that increases in offspring production are more likely to follow the evolution of paternal care, specifically where males contribute depreciable investment such as provisioning young. Through coevolution with litter size, we conclude that paternal care in mammals is likely to play an important role in stabilizing monogamous mating systems and could ultimately promote the evolution of complex social behaviours. © 2016 The Authors.

Limited ability driven phase transitions in the coevolution process in Axelrod's model

Science.gov (United States)

Wang, Bing; Han, Yuexing; Chen, Luonan; Aihara, Kazuyuki

2009-04-01

We study the coevolution process in Axelrod's model by taking into account of agents' abilities to access information, which is described by a parameter α to control the geographical range of communication. We observe two kinds of phase transitions in both cultural domains and network fragments, which depend on the parameter α. By simulation, we find that not all rewiring processes pervade the dissemination of culture, that is, a very limited ability to access information constrains the cultural dissemination, while an exceptional ability to access information aids the dissemination of culture. Furthermore, by analyzing the network characteristics at the frozen states, we find that there exists a stage at which the network develops to be a small-world network with community structures.

Invasion fitness for gene-culture co-evolution in family-structured populations and an application to cumulative culture under vertical transmission.

Science.gov (United States)

Mullon, Charles; Lehmann, Laurent

2017-08-01

Human evolution depends on the co-evolution between genetically determined behaviors and socially transmitted information. Although vertical transmission of cultural information from parent to offspring is common in hominins, its effects on cumulative cultural evolution are not fully understood. Here, we investigate gene-culture co-evolution in a family-structured population by studying the invasion fitness of a mutant allele that influences a deterministic level of cultural information (e.g., amount of knowledge or skill) to which diploid carriers of the mutant are exposed in subsequent generations. We show that the selection gradient on such a mutant, and the concomitant level of cultural information it generates, can be evaluated analytically under the assumption that the cultural dynamic has a single attractor point, thereby making gene-culture co-evolution in family-structured populations with multigenerational effects mathematically tractable. We apply our result to study how genetically determined phenotypes of individual and social learning co-evolve with the level of adaptive information they generate under vertical transmission. We find that vertical transmission increases adaptive information due to kin selection effects, but when information is transmitted as efficiently between family members as between unrelated individuals, this increase is moderate in diploids. By contrast, we show that the way resource allocation into learning trades off with allocation into reproduction (the "learning-reproduction trade-off") significantly influences levels of adaptive information. We also show that vertical transmission prevents evolutionary branching and may therefore play a qualitative role in gene-culture co-evolutionary dynamics. More generally, our analysis of selection suggests that vertical transmission can significantly increase levels of adaptive information under the biologically plausible condition that information transmission between relatives is

Coevolution between Hispaniolan crossbills and pine: does more time allow for greater phenotypic escalation at lower latitude?

Science.gov (United States)

Parchman, Thomas L; Benkman, Craig W; Mezquida, Eduardo T

2007-09-01

Crossbills (Aves: Loxia) and several conifers have coevolved in predator-prey arms races over the last 10,000 years. However, the extent to which coevolutionary arms races have contributed to the adaptive radiation of crossbills or to any other adaptive radiation is largely unknown. Here we extend our previous studies of geographically structured coevolution by considering a crossbill-conifer interaction that has persisted for a much longer time period and involves a conifer with more variable annual seed production. We examined geographic variation in the cone and seed traits of two sister species of pines, Pinus occidentalis and P. cubensis, on the islands of Hispaniola and Cuba, respectively. We also compared the Hispaniolan crossbill (Loxia megaplaga) to its sister taxa the North American white-winged crossbill (Loxia leucoptera leucoptera). The Hispaniolan crossbill is endemic to Hispaniola whereas Cuba lacks crossbills. In addition and in contrast to previous studies, the variation in selection experienced by these pines due to crossbills is not confounded by the occurrence of selection by tree squirrels (Tamiasciurus and Sciurus). As predicted if P. occidentalis has evolved defenses in response to selection exerted by crossbills, cones of P. occidentalis have scales that are 53% thicker than those of P. cubensis. Cones of P. occidentalis, but not P. cubensis, also have well-developed spines, a known defense against vertebrate seed predators. Consistent with patterns of divergence seen in crossbills coevolving locally with other conifers, the Hispaniolan crossbill has evolved a bill that is 25% deeper than the white-winged crossbill. Together with phylogenetic analyses, our results suggest that predator-prey coevolution between Hispaniolan crossbills and P. occidentalis over approximately 600,000 years has caused substantial morphological evolution in both the crossbill and pine. This also indicates that cone crop fluctuations do not prevent crossbills and

A non-classical phase diagram for virus-bacterial co-evolution mediated by CRISPR

Science.gov (United States)

Han, Pu; Deem, Michael

CRISPR is a newly discovered prokaryotic immune system. Bacteria and archaea with this system incorporate genetic material from invading viruses into their genomes, providing protection against future infection by similar viruses. Due to the cost of CRISPR, bacteria can lose the acquired immunity. We will show an intriguing phase diagram of the virus extinction probability, which when the rate of losing the acquired immunity is small, is more complex than that of the classic predator-prey model. As the CRISPR incorporates genetic material, viruses are under pressure to evolve to escape the recognition by CRISPR, and this co-evolution leads to a non-trivial phase structure that cannot be explained by the classical predator-prey model.

The Co-evolution of Neuroimaging and Psychiatric Neurosurgery.

Science.gov (United States)

Dyster, Timothy G; Mikell, Charles B; Sheth, Sameer A

2016-01-01

The role of neuroimaging in psychiatric neurosurgery has evolved significantly throughout the field's history. Psychiatric neurosurgery initially developed without the benefit of information provided by modern imaging modalities, and thus lesion targets were selected based on contemporary theories of frontal lobe dysfunction in psychiatric disease. However, by the end of the 20th century, the availability of structural and functional magnetic resonance imaging (fMRI) allowed for the development of mechanistic theories attempting to explain the anatamofunctional basis of these disorders, as well as the efficacy of stereotactic neuromodulatory treatments. Neuroimaging now plays a central and ever-expanding role in the neurosurgical management of psychiatric disorders, by influencing the determination of surgical candidates, allowing individualized surgical targeting and planning, and identifying network-level changes in the brain following surgery. In this review, we aim to describe the coevolution of psychiatric neurosurgery and neuroimaging, including ways in which neuroimaging has proved useful in elucidating the therapeutic mechanisms of neuromodulatory procedures. We focus on ablative over stimulation-based procedures given their historical precedence and the greater opportunity they afford for post-operative re-imaging, but also discuss important contributions from the deep brain stimulation (DBS) literature. We conclude with a discussion of how neuroimaging will transition the field of psychiatric neurosurgery into the era of precision medicine.

The Co-evolution of Business Incubators and National Incubator Networks in Emerging Markets

Directory of Open Access Journals (Sweden)

David F. Robinson

2010-11-01

Full Text Available The study proposes a three stage model of the development of business incubation practices in emerging markets. The model addresses the diffusion of incubation practices to new markets, the institutionalization of those practices and the co-evolution of incubators and national networks of incubation. The model is based on interviews conducted in Bolivia, Peru, Chile, Argentina, and Brazil. New incubators in emerging markets often face strong cultural norms and institutional impediments to helping entrepreneurs start new businesses. As incubation becomes better established in a country, incubators provide more advanced technical, legal and market-based advice. Networks of incubators form to share specialized services across many incubators, to allocate government funding to incubators, and to lobby for public and private support of innovation.

Coevolution of Cooperation and Layer Selection Strategy in Multiplex Networks

Directory of Open Access Journals (Sweden)

Katsuki Hayashi

2016-11-01

Full Text Available Recently, the emergent dynamics in multiplex networks, composed of layers of multiple networks, has been discussed extensively in network sciences. However, little is still known about whether and how the evolution of strategy for selecting a layer to participate in can contribute to the emergence of cooperative behaviors in multiplex networks of social interactions. To investigate these issues, we constructed a coevolutionary model of cooperation and layer selection strategies in which each an individual selects one layer from multiple layers of social networks and plays the Prisoner’s Dilemma with neighbors in the selected layer. We found that the proportion of cooperative strategies increased with increasing the number of layers regardless of the degree of dilemma, and this increase occurred due to a cyclic coevolution process of game strategies and layer selection strategies. We also showed that the heterogeneity of links among layers is a key factor for multiplex networks to facilitate the evolution of cooperation, and such positive effects on cooperation were observed regardless of the difference in the stochastic properties of network topologies.

Co-evolution model of Colletotrichum lindemuthianum (melanconiaceae, melanconiales races that occur in some Brazilian regions

Directory of Open Access Journals (Sweden)

Ana Lilia Alzate-Marin

1999-03-01

Full Text Available Colletotrichum lindemuthianum, the causal agent of anthracnose in the common bean (Phaseolus vulgaris L., displays a high level of virulence diversity, which explains the large number of existing pathotypes. Several lines of evidence indicate that such diversity is, at least in part, due to plant and pathogen co-evolution. A co-evolution model based on the binary classification of 25 races identified in Brazil by inoculation of differential cultivars and random amplified polymorphic DNA (RAPD data is proposed. In this model, races 8 and 64 that infected bean cultivar Cornell 49-242 (Are gene and Mexico 222 (Mexico I gene are considered to be sources of two important evolutionary routes. Inferences about undescribed races from Brazil could be made.Colletotrichum lindemuthianum (Sacc. & Magn. Scrib., agente causal da antracnose do feijoeiro comum (Phaseolus vulgaris L., possui alto nível de diversidade de virulência, o que explica o elevado número de patótipos existentes. A partir de trabalhos anteriores sobre a classificação binária de 25 raças identificadas no Brasil e sua relação com agrupamentos RAPD, foi possível construir um modelo de evolução de tais raças. As raças 8 e 64, que foram compatíveis com os cultivares Cornell 49-242 (gene Are e México 222 (gene México I, se apresentam como possíveis origens de duas importantes rotas de evolução. Inferências de raças ainda não detectadas no Brasil puderam ser feitas.

Origin of the cell nucleus, mitosis and sex: roles of intracellular coevolution.

Science.gov (United States)

Cavalier-Smith, Thomas

2010-02-04

The transition from prokaryotes to eukaryotes was the most radical change in cell organisation since life began, with the largest ever burst of gene duplication and novelty. According to the coevolutionary theory of eukaryote origins, the fundamental innovations were the concerted origins of the endomembrane system and cytoskeleton, subsequently recruited to form the cell nucleus and coevolving mitotic apparatus, with numerous genetic eukaryotic novelties inevitable consequences of this compartmentation and novel DNA segregation mechanism. Physical and mutational mechanisms of origin of the nucleus are seldom considered beyond the long-standing assumption that it involved wrapping pre-existing endomembranes around chromatin. Discussions on the origin of sex typically overlook its association with protozoan entry into dormant walled cysts and the likely simultaneous coevolutionary, not sequential, origin of mitosis and meiosis. I elucidate nuclear and mitotic coevolution, explaining the origins of dicer and small centromeric RNAs for positionally controlling centromeric heterochromatin, and how 27 major features of the cell nucleus evolved in four logical stages, making both mechanisms and selective advantages explicit: two initial stages (origin of 30 nm chromatin fibres, enabling DNA compaction; and firmer attachment of endomembranes to heterochromatin) protected DNA and nascent RNA from shearing by novel molecular motors mediating vesicle transport, division, and cytoplasmic motility. Then octagonal nuclear pore complexes (NPCs) arguably evolved from COPII coated vesicle proteins trapped in clumps by Ran GTPase-mediated cisternal fusion that generated the fenestrated nuclear envelope, preventing lethal complete cisternal fusion, and allowing passive protein and RNA exchange. Finally, plugging NPC lumens by an FG-nucleoporin meshwork and adopting karyopherins for nucleocytoplasmic exchange conferred compartmentation advantages. These successive changes took place

The role of insulin C-peptide in the coevolution analyses of the insulin signaling pathway: a hint for its functions.

Directory of Open Access Journals (Sweden)

Shuai Wang

Full Text Available As the linker between the A chain and B chain of proinsulin, C-peptide displays high variability in length and amino acid composition, and has been considered as an inert byproduct of insulin synthesis and processing for many years. Recent studies have suggested that C-peptide can act as a bioactive hormone, exerting various biological effects on the pathophysiology and treatment of diabetes. In this study, we analyzed the coevolution of insulin molecules among vertebrates, aiming at exploring the evolutionary characteristics of insulin molecule, especially the C-peptide. We also calculated the correlations of evolutionary rates between the insulin and the insulin receptor (IR sequences as well as the domain-domain pairs of the ligand and receptor by the mirrortree method. The results revealed distinctive features of C-peptide in insulin intramolecular coevolution and correlated residue substitutions, which partly supported the idea that C-peptide can act as a bioactive hormone, with significant sequence features, as well as a linker assisting the formation of mature insulin during synthesis. Interestingly, the evolution of C-peptide exerted the highest correlation with that of the insulin receptor and its ligand binding domain (LBD, implying a potential relationship with the insulin signaling pathway.

Limited ability driven phase transitions in the coevolution process in Axelrod's model

Energy Technology Data Exchange (ETDEWEB)

Wang Bing [ERATO Aihara Complexity Modelling Project, JST, Institute of Industrial Science, University of Tokyo, 4-6-1 Komaba, Meguro-ku, Tokyo 153-8505 (Japan); Institute of Industrial Science, University of Tokyo, Tokyo (Japan)], E-mail: bingbignmath@gmail.com; Han Yuexing [Graduate School of Information System, University of Electro-Communications, 1-5-1 Chofugaoka, Chofu-Shi, Tokyo (Japan); Chen Luonan [Department of Electrical Engineering and Electronics, Osaka Sangyo University, Daito, Osaka 574-8530 (Japan); Aihara, Kazuyuki [ERATO Aihara Complexity Modelling Project, JST, Institute of Industrial Science, University of Tokyo, 4-6-1 Komaba, Meguro-ku, Tokyo 153-8505 (Japan); Institute of Industrial Science, University of Tokyo, Tokyo (Japan)

2009-04-13

We study the coevolution process in Axelrod's model by taking into account of agents' abilities to access information, which is described by a parameter {alpha} to control the geographical range of communication. We observe two kinds of phase transitions in both cultural domains and network fragments, which depend on the parameter {alpha}. By simulation, we find that not all rewiring processes pervade the dissemination of culture, that is, a very limited ability to access information constrains the cultural dissemination, while an exceptional ability to access information aids the dissemination of culture. Furthermore, by analyzing the network characteristics at the frozen states, we find that there exists a stage at which the network develops to be a small-world network with community structures.

The role of soil moisture on the coevolution of soil and vegetation in mountain grasslands

Science.gov (United States)

Bertoldi, Giacomo; Claudia, Notarnicola; Brenner, Johannes; Castelli, Mariapina; Greifeneder, Felix; Niedrist, Georg; Seeber, Julia; Tappeiner, Ulrike

2016-04-01

One of the key variables controlling the organization of vegetation and the coevolution of soils and landforms is soil moisture content (SMC). For this reason, understanding the controls on the spatial and temporal patterns of SMC is essential to predict how perturbations in vegetation and climate will affect mountain ecosystem functioning. In this contribution, we focus on the dynamic of surface SMC of water-limited alpine grasslands in the Long Term Ecological Research area Mazia Valley in the European Alps. We analyze the impacts of different land managements (meadows versus pastures) and its relationships with climate and topography. The area has been equipped since 2009 with a network of more than 20 stations, measuring SMC and climatic variables and with two eddy-covariance stations, measuring surface fluxes over meadows and pastures. Monthly biomass production data have been collected and detailed soil and spatial soil moisture surveys are available. Moreover, high spatial resolution SMC maps have been derived from satellites Synthetic Aperture Radar Radar (SAR) images (Sentinel 1 and RADARSAT2 images). Both ground surveys and remote sensing observations show persistent landscape-level patterns. Meadows, in general located in flatter areas, tend to be wetter. This leads to higher vegetation productivity and to the development of soils with higher water holding capacity, thus to a positive feedback on SMC. In contrast, pastures, located on steeper slopes with lower vegetation density and higher soil erosion, tend to be drier, leading to a negative feedback on SMC and soil development. This co-evolution of land cover and SMC leads therefore to persistent spatial patterns. In order to understand quantitatively such linked interactions, a sensitivity analysis has been performed with the GEOtop hydrological model. Results show how both abiotic (mainly slope and elevation) and anthropogenic (irrigation and soil management) factors exert a significant control on

Coevolution of parental investment and sexually selected traits drives sex-role divergence.

Science.gov (United States)

Fromhage, Lutz; Jennions, Michael D

2016-08-18

Sex-role evolution theory attempts to explain the origin and direction of male-female differences. A fundamental question is why anisogamy, the difference in gamete size that defines the sexes, has repeatedly led to large differences in subsequent parental care. Here we construct models to confirm predictions that individuals benefit less from caring when they face stronger sexual selection and/or lower certainty of parentage. However, we overturn the widely cited claim that a negative feedback between the operational sex ratio and the opportunity cost of care selects for egalitarian sex roles. We further argue that our model does not predict any effect of the adult sex ratio (ASR) that is independent of the source of ASR variation. Finally, to increase realism and unify earlier models, we allow for coevolution between parental investment and investment in sexually selected traits. Our model confirms that small initial differences in parental investment tend to increase due to positive evolutionary feedback, formally supporting long-standing, but unsubstantiated, verbal arguments.

Energy Levels and Co-evolution of Product Innovation in Supply Chain Clusters

Science.gov (United States)

Ji, Guojun

In the last decade supply chain clusters phenomenon has emerged as a new approach in product innovation studies. This article makes three contributions to the approach by addressing some open issues. The first contribution is to explicitly incorporate the energy levels in the analysis. Hence, the unit of analysis is widened from sectoral systems of innovation to socio-technical systems. Hence, the unit of analysis is widened from sectoral systems of innovation to socio-technical systems. The second contribution is to suggest an analytical distinction between different evolution method, actors involved in them, and the institutions which guide actor's perceptions and activities. Thirdly, the article opens up the black box of institutions, making them an integral part of supply chain. The article provides a coherent conceptual multi-level perspective, using insights from sociology, institutional theory and innovation studies. The perspective is particularly useful to analyze long-term dynamics supply chain clusters phenomenon, shifts from one energy level to another and the co-evolution of product innovation.

Coevolution of network structure and cooperation in the public goods game

International Nuclear Information System (INIS)

Wang Lei; Xia Chengyi; Wang Juan

2013-01-01

Recently, the emergence of cooperation has become a central topic in the evolutionary game field, and coevolution of game dynamics and network topology structure can give us a fresh viewpoint of how the network evolves and cooperation arises. In this paper, we show in detail a picture of the co-evolutionary behaviors between the microscopic structure of the network and cooperation promotion in the public goods game (PGG). Based on a mechanism named after evolutionary preferential attachment (EPA), in which the growth of the network depends on the outcome of PGG dynamics, we explore the structural properties of networks and cooperative behaviors taking place on the networks created by EPA rules. Extensive simulation results indicate that the structure of the resulting networks displays a transition from homogeneous to heterogeneous properties as the selection strength ϵ increases, and the cooperative behaviors have a non-trivial state in which cooperators and defectors can simultaneously occupy the hub nodes in the network. Current results are of interest for us to further understand the cooperation persistence and structure evolution in many natural, social and economical systems. (paper)

Co-evolution of technology and society: The multi-level perspective and a case study, the transition in water supply and personal hygiene in the Netherlands (1850-1930)

NARCIS (Netherlands)

Geels, F.W.

2005-01-01

This article deals with the systems level in Freeman and Perez's innovation typology (incremental, radical, system, techno-economic paradigm). Transitions at this level are understood as changes from one socio-technical system to another, involving co-evolution of technology and society. To

Modeling human-water-systems: towards a comprehensive and spatially distributed assessment of co-evolutions for river basins in Central Europe

OpenAIRE

P. Krahe; E. Nilson; M. Knoche; A.-D. Ebner von Eschenbach

2016-01-01

In the context of river basin and flood risk management there is a growing need to improve the understanding of and the feedbacks between the driving forces “climate and socio-economy” and water systems. We make use of a variety of data resources to illustrate interrelationships between different constituents of the human-water-systems. Taking water storage for energy production as an example we present a first analysis on the co-evolution of socio-economic and hydrological ...

A model of designing as the intersection between uncertainty perception, information processing, and coevolution

DEFF Research Database (Denmark)

Lasso, Sarah Venturim; Cash, Philip; Daalhuizen, Jaap

2016-01-01

, the designer's perceived uncertainty is the motivation to start a process of collecting, exchanging, and integrating knowledge. This has been formalised in Information-Processing Theory and more generally described by authors such as Aurisicchio et al. (2013) who describe design as an information...... takes the first steps towards linking these disparate perspectives in a model of designing that synthesises coevolution and information processing. How designers act has been shown to play an important role in the process of New Product Development (NPD) (See e.g. Badke-Schaub and Frankenberger, 2012...... transformation process. Here the aim of the activity is to reduce the perceived uncertainty through identifying and integrating external information and knowledge within the design team. For2example, when perceiving uncertainty the designer might seek new information online, process this information, and share...

The Role of Microbial Electron Transfer in the Coevolution of the Biosphere and Geosphere.

Science.gov (United States)

Jelen, Benjamin I; Giovannelli, Donato; Falkowski, Paul G

2016-09-08

All life on Earth is dependent on biologically mediated electron transfer (i.e., redox) reactions that are far from thermodynamic equilibrium. Biological redox reactions originally evolved in prokaryotes and ultimately, over the first ∼2.5 billion years of Earth's history, formed a global electronic circuit. To maintain the circuit on a global scale requires that oxidants and reductants be transported; the two major planetary wires that connect global metabolism are geophysical fluids-the atmosphere and the oceans. Because all organisms exchange gases with the environment, the evolution of redox reactions has been a major force in modifying the chemistry at Earth's surface. Here we briefly review the discovery and consequences of redox reactions in microbes with a specific focus on the coevolution of life and geochemical phenomena.

Origin of the cell nucleus, mitosis and sex: roles of intracellular coevolution

Directory of Open Access Journals (Sweden)

Cavalier-Smith Thomas

2010-02-01

Full Text Available Abstract Background The transition from prokaryotes to eukaryotes was the most radical change in cell organisation since life began, with the largest ever burst of gene duplication and novelty. According to the coevolutionary theory of eukaryote origins, the fundamental innovations were the concerted origins of the endomembrane system and cytoskeleton, subsequently recruited to form the cell nucleus and coevolving mitotic apparatus, with numerous genetic eukaryotic novelties inevitable consequences of this compartmentation and novel DNA segregation mechanism. Physical and mutational mechanisms of origin of the nucleus are seldom considered beyond the long-standing assumption that it involved wrapping pre-existing endomembranes around chromatin. Discussions on the origin of sex typically overlook its association with protozoan entry into dormant walled cysts and the likely simultaneous coevolutionary, not sequential, origin of mitosis and meiosis. Results I elucidate nuclear and mitotic coevolution, explaining the origins of dicer and small centromeric RNAs for positionally controlling centromeric heterochromatin, and how 27 major features of the cell nucleus evolved in four logical stages, making both mechanisms and selective advantages explicit: two initial stages (origin of 30 nm chromatin fibres, enabling DNA compaction; and firmer attachment of endomembranes to heterochromatin protected DNA and nascent RNA from shearing by novel molecular motors mediating vesicle transport, division, and cytoplasmic motility. Then octagonal nuclear pore complexes (NPCs arguably evolved from COPII coated vesicle proteins trapped in clumps by Ran GTPase-mediated cisternal fusion that generated the fenestrated nuclear envelope, preventing lethal complete cisternal fusion, and allowing passive protein and RNA exchange. Finally, plugging NPC lumens by an FG-nucleoporin meshwork and adopting karyopherins for nucleocytoplasmic exchange conferred compartmentation

Cooperative Coevolution with Formula-Based Variable Grouping for Large-Scale Global Optimization.

Science.gov (United States)

Wang, Yuping; Liu, Haiyan; Wei, Fei; Zong, Tingting; Li, Xiaodong

2017-08-09

For a large-scale global optimization (LSGO) problem, divide-and-conquer is usually considered an effective strategy to decompose the problem into smaller subproblems, each of which can then be solved individually. Among these decomposition methods, variable grouping is shown to be promising in recent years. Existing variable grouping methods usually assume the problem to be black-box (i.e., assuming that an analytical model of the objective function is unknown), and they attempt to learn appropriate variable grouping that would allow for a better decomposition of the problem. In such cases, these variable grouping methods do not make a direct use of the formula of the objective function. However, it can be argued that many real-world problems are white-box problems, that is, the formulas of objective functions are often known a priori. These formulas of the objective functions provide rich information which can then be used to design an effective variable group method. In this article, a formula-based grouping strategy (FBG) for white-box problems is first proposed. It groups variables directly via the formula of an objective function which usually consists of a finite number of operations (i.e., four arithmetic operations "[Formula: see text]", "[Formula: see text]", "[Formula: see text]", "[Formula: see text]" and composite operations of basic elementary functions). In FBG, the operations are classified into two classes: one resulting in nonseparable variables, and the other resulting in separable variables. In FBG, variables can be automatically grouped into a suitable number of non-interacting subcomponents, with variables in each subcomponent being interdependent. FBG can easily be applied to any white-box problem and can be integrated into a cooperative coevolution framework. Based on FBG, a novel cooperative coevolution algorithm with formula-based variable grouping (so-called CCF) is proposed in this article for decomposing a large-scale white-box problem

Aspiration-based coevolution of link weight promotes cooperation in the spatial prisoner's dilemma game

Science.gov (United States)

Shen, Chen; Chu, Chen; Shi, Lei; Perc, Matjaž; Wang, Zhen

2018-05-01

In this article, we propose an aspiration-based coevolution of link weight, and explore how this set-up affects the evolution of cooperation in the spatial prisoner's dilemma game. In particular, an individual will increase the weight of its link to its neighbours only if the payoff received via this interaction exceeds a pre-defined aspiration. Conversely, if the received payoff is below this aspiration, the link weight with the corresponding neighbour will decrease. Our results show that an appropriate aspiration level leads to a high-cooperation plateau, whereas too high or too low aspiration will impede the evolution of cooperation. We explain these findings with a comprehensive analysis of transition points and with a systematic analysis of typical configuration patterns. The presented results provide further theoretical insights with regards to the impact of different aspiration levels on cooperation in human societies.

Critical mass of public goods and its coevolution with cooperation

Science.gov (United States)

Shi, Dong-Mei; Wang, Bing-Hong

2017-07-01

In this study, the enhancing parameter represented the value of the public goods to the public in public goods game, and was rescaled to a Fermi-Dirac distribution function of critical mass. Public goods were divided into two categories, consumable and reusable public goods, and their coevolution with cooperative behavior was studied. We observed that for both types of public goods, cooperation was promoted as the enhancing parameter increased when the value of critical mass was not very large. An optimal value of critical mass which led to the best cooperation was identified. We also found that cooperations emerged earlier for reusable public goods, and defections became extinct earlier for the consumable public goods. Moreover, we observed that a moderate depreciation rate for public goods resulted in an optimal cooperation, and this range became wider as the enhancing parameter increased. The noise influence on cooperation was studied, and it was shown that cooperation density varied non-monotonically as noise amplitude increased for reusable public goods, whereas decreased monotonically for consumable public goods. Furthermore, existence of the optimal critical mass was also identified in other three regular networks. Finally, simulation results were utilized to analyze the provision of public goods in detail.

The hitchhiker's guide to altruism: gene-culture coevolution, and the internalization of norms.

Science.gov (United States)

Gintis, Herbert

2003-02-21

An internal norm is a pattern of behavior enforced in part by internal sanctions, such as shame, guilt and loss of self-esteem, as opposed to purely external sanctions, such as material rewards and punishment. The ability to internalize norms is widespread among humans, although in some so-called "sociopaths", this capacity is diminished or lacking. Suppose there is one genetic locus that controls the capacity to internalize norms. This model shows that if an internal norm is fitness enhancing, then for plausible patterns of socialization, the allele for internalization of norms is evolutionarily stable. This framework can be used to model Herbert Simon's (1990) explanation of altruism, showing that altruistic norms can "hitchhike" on the general tendency of internal norms to be personally fitness-enhancing. A multi-level selection, gene-culture coevolution argument then explains why individually fitness-reducing internal norms are likely to be prosocial as opposed to socially harmful.

Coevolution between positive reciprocity, punishment, and partner switching in repeated interactions.

Science.gov (United States)

Wubs, Matthias; Bshary, Redouan; Lehmann, Laurent

2016-06-15

Cooperation based on mutual investments can occur between unrelated individuals when they are engaged in repeated interactions. Individuals then need to use a conditional strategy to deter their interaction partners from defecting. Responding to defection such that the future payoff of a defector is reduced relative to cooperating with it is called a partner control mechanism. Three main partner control mechanisms are (i) to switch from cooperation to defection when being defected ('positive reciprocity'), (ii) to actively reduce the payoff of a defecting partner ('punishment'), or (iii) to stop interacting and switch partner ('partner switching'). However, such mechanisms to stabilize cooperation are often studied in isolation from each other. In order to better understand the conditions under which each partner control mechanism tends to be favoured by selection, we here analyse by way of individual-based simulations the coevolution between positive reciprocity, punishment, and partner switching. We show that random interactions in an unstructured population and a high number of rounds increase the likelihood that selection favours partner switching. In contrast, interactions localized in small groups (without genetic structure) increase the likelihood that selection favours punishment and/or positive reciprocity. This study thus highlights the importance of comparing different control mechanisms for cooperation under different conditions. © 2016 The Author(s).

Co-evolution of intelligent socio-technical systems modelling and applications in large scale emergency and transport domains

CERN Document Server

2013-01-01

As the interconnectivity between humans through technical devices is becoming ubiquitous, the next step is already in the making: ambient intelligence, i.e. smart (technical) environments, which will eventually play the same active role in communication as the human players, leading to a co-evolution in all domains where real-time communication is essential. This topical volume, based on the findings of the Socionical European research project, gives equal attention to two highly relevant domains of applications: transport, specifically traffic, dynamics from the viewpoint of a socio-technical interaction and evacuation scenarios for large-scale emergency situations. Care was taken to investigate as much as possible the limits of scalability and to combine the modeling using complex systems science approaches with relevant data analysis.

Genetic and linguistic coevolution in Northern Island Melanesia.

Science.gov (United States)

Hunley, Keith; Dunn, Michael; Lindström, Eva; Reesink, Ger; Terrill, Angela; Healy, Meghan E; Koki, George; Friedlaender, Françoise R; Friedlaender, Jonathan S

2008-10-01

Recent studies have detailed a remarkable degree of genetic and linguistic diversity in Northern Island Melanesia. Here we utilize that diversity to examine two models of genetic and linguistic coevolution. The first model predicts that genetic and linguistic correspondences formed following population splits and isolation at the time of early range expansions into the region. The second is analogous to the genetic model of isolation by distance, and it predicts that genetic and linguistic correspondences formed through continuing genetic and linguistic exchange between neighboring populations. We tested the predictions of the two models by comparing observed and simulated patterns of genetic variation, genetic and linguistic trees, and matrices of genetic, linguistic, and geographic distances. The data consist of 751 autosomal microsatellites and 108 structural linguistic features collected from 33 Northern Island Melanesian populations. The results of the tests indicate that linguistic and genetic exchange have erased any evidence of a splitting and isolation process that might have occurred early in the settlement history of the region. The correlation patterns are also inconsistent with the predictions of the isolation by distance coevolutionary process in the larger Northern Island Melanesian region, but there is strong evidence for the process in the rugged interior of the largest island in the region (New Britain). There we found some of the strongest recorded correlations between genetic, linguistic, and geographic distances. We also found that, throughout the region, linguistic features have generally been less likely to diffuse across population boundaries than genes. The results from our study, based on exceptionally fine-grained data, show that local genetic and linguistic exchange are likely to obscure evidence of the early history of a region, and that language barriers do not particularly hinder genetic exchange. In contrast, global patterns may

Genetic and linguistic coevolution in Northern Island Melanesia.

Directory of Open Access Journals (Sweden)

Keith Hunley

2008-10-01

Full Text Available Recent studies have detailed a remarkable degree of genetic and linguistic diversity in Northern Island Melanesia. Here we utilize that diversity to examine two models of genetic and linguistic coevolution. The first model predicts that genetic and linguistic correspondences formed following population splits and isolation at the time of early range expansions into the region. The second is analogous to the genetic model of isolation by distance, and it predicts that genetic and linguistic correspondences formed through continuing genetic and linguistic exchange between neighboring populations. We tested the predictions of the two models by comparing observed and simulated patterns of genetic variation, genetic and linguistic trees, and matrices of genetic, linguistic, and geographic distances. The data consist of 751 autosomal microsatellites and 108 structural linguistic features collected from 33 Northern Island Melanesian populations. The results of the tests indicate that linguistic and genetic exchange have erased any evidence of a splitting and isolation process that might have occurred early in the settlement history of the region. The correlation patterns are also inconsistent with the predictions of the isolation by distance coevolutionary process in the larger Northern Island Melanesian region, but there is strong evidence for the process in the rugged interior of the largest island in the region (New Britain. There we found some of the strongest recorded correlations between genetic, linguistic, and geographic distances. We also found that, throughout the region, linguistic features have generally been less likely to diffuse across population boundaries than genes. The results from our study, based on exceptionally fine-grained data, show that local genetic and linguistic exchange are likely to obscure evidence of the early history of a region, and that language barriers do not particularly hinder genetic exchange. In contrast

Effects of adaptive degrees of trust on coevolution of quantum strategies on scale-free networks

Science.gov (United States)

Li, Qiang; Chen, Minyou; Perc, Matjaž; Iqbal, Azhar; Abbott, Derek

2013-10-01

We study the impact of adaptive degrees of trust on the evolution of cooperation in the quantum prisoner's dilemma game. In addition to the strategies, links between players are also subject to evolution. Starting with a scale-free interaction network, players adjust trust towards their neighbors based on received payoffs. The latter governs the strategy adoption process, while trust governs the rewiring of links. As soon as the degree of trust towards a neighbor drops to zero, the link is rewired to another randomly chosen player within the network. We find that for small temptations to defect cooperators always dominate, while for intermediate and strong temptations a single quantum strategy is able to outperform all other strategies. In general, reciprocal trust remains within close relationships and favors the dominance of a single strategy. Due to coevolution, the power-law degree distributions transform to Poisson distributions.

Coevolution within a transcriptional network by compensatory trans and cis mutations

KAUST Repository

Kuo, D.

2010-10-26

Transcriptional networks have been shown to evolve very rapidly, prompting questions as to how such changes arise and are tolerated. Recent comparisons of transcriptional networks across species have implicated variations in the cis-acting DNA sequences near genes as the main cause of divergence. What is less clear is how these changes interact with trans-acting changes occurring elsewhere in the genetic circuit. Here, we report the discovery of a system of compensatory trans and cis mutations in the yeast AP-1 transcriptional network that allows for conserved transcriptional regulation despite continued genetic change. We pinpoint a single species, the fungal pathogen Candida glabrata, in which a trans mutation has occurred very recently in a single AP-1 family member, distinguishing it from its Saccharomyces ortholog. Comparison of chromatin immunoprecipitation profiles between Candida and Saccharomyces shows that, despite their different DNA-binding domains, the AP-1 orthologs regulate a conserved block of genes. This conservation is enabled by concomitant changes in the cis-regulatory motifs upstream of each gene. Thus, both trans and cis mutations have perturbed the yeast AP-1 regulatory system in such a way as to compensate for one another. This demonstrates an example of “coevolution” between a DNA-binding transcription factor and its cis-regulatory site, reminiscent of the coevolution of protein binding partners.

Coevolution of bed surface patchiness and channel morphology: 2. Numerical experiments

Science.gov (United States)

Nelson, Peter A.; McDonald, Richard R.; Nelson, Jonathan M.; Dietrich, William E.

2015-01-01

In gravel bed rivers, bed topography and the bed surface grain size distribution evolve simultaneously, but it is not clear how feedbacks between topography and grain sorting affect channel morphology. In this, the second of a pair of papers examining interactions between bed topography and bed surface sorting in gravel bed rivers, we use a two-dimensional morphodynamic model to perform numerical experiments designed to explore the coevolution of both free and forced bars and bed surface patches. Model runs were carried out on a computational grid simulating a 200 m long, 2.75 m wide, straight, rectangular channel, with an initially flat bed at a slope of 0.0137. Over five numerical experiments, we varied (a) whether an obstruction was present, (b) whether the sediment was a gravel mixture or a single size, and (c) whether the bed surface grain size feeds back on the hydraulic roughness field. Experiments with channel obstructions developed a train of alternate bars that became stationary and were connected to the obstruction. Freely migrating alternate bars formed in the experiments without channel obstructions. Simulations incorporating roughness feedbacks between the bed surface and flow field produced flatter, broader, and longer bars than simulations using constant roughness or uniform sediment. Our findings suggest that patches are not simply a by-product of bed topography, but they interact with the evolving bed and influence morphologic evolution.

Diversity patterns amongst herbivorous dinosaurs and plants during the Cretaceous: implications for hypotheses of dinosaur/angiosperm co-evolution.

Science.gov (United States)

Butler, R J; Barrett, P M; Kenrick, P; Penn, M G

2009-03-01

Palaeobiologists frequently attempt to identify examples of co-evolutionary interactions over extended geological timescales. These hypotheses are often intuitively appealing, as co-evolution is so prevalent in extant ecosystems, and are easy to formulate; however, they are much more difficult to test than their modern analogues. Among the more intriguing deep time co-evolutionary scenarios are those that relate changes in Cretaceous dinosaur faunas to the primary radiation of flowering plants. Demonstration of temporal congruence between the diversifications of co-evolving groups is necessary to establish whether co-evolution could have occurred in such cases, but is insufficient to prove whether it actually did take place. Diversity patterns do, however, provide a means for falsifying such hypotheses. We have compiled a new database of Cretaceous dinosaur and plant distributions from information in the primary literature. This is used as the basis for plotting taxonomic diversity and occurrence curves for herbivorous dinosaurs (Sauropodomorpha, Stegosauria, Ankylosauria, Ornithopoda, Ceratopsia, Pachycephalosauria and herbivorous theropods) and major groups of plants (angiosperms, Bennettitales, cycads, cycadophytes, conifers, Filicales and Ginkgoales) that co-occur in dinosaur-bearing formations. Pairwise statistical comparisons were made between various floral and faunal groups to test for any significant similarities in the shapes of their diversity curves through time. We show that, with one possible exception, diversity patterns for major groups of herbivorous dinosaurs are not positively correlated with angiosperm diversity. In other words, at the level of major clades, there is no support for any diffuse co-evolutionary relationship between herbivorous dinosaurs and flowering plants. The diversification of Late Cretaceous pachycephalosaurs (excluding the problematic taxon Stenopelix) shows a positive correlation, but this might be spuriously related to

Co-evolution of insect proteases and plant protease inhibitors.

Science.gov (United States)

Jongsma, Maarten A; Beekwilder, Jules

2011-08-01

Plants are at the basis of the food chain, but there is no such thing as a "free lunch" for herbivores. To promote reproductive success, plants evolved multi-layered defensive tactics to avoid or discourage herbivory. To the detriment of plants, herbivores, in turn, evolved intricate strategies to find, eat, and successfully digest essential plant parts to raise their own offspring. In this battle the digestive tract is the arena determining final victory or defeat as measured by growth or starvation of the herbivore. Earlier, specific molecular opponents were identified as proteases and inhibitors: digestive proteases of herbivores evolved structural motifs to occlude plant protease inhibitors, or alternatively, the insects evolved proteases capable of specifically degrading the host plant inhibitors. In response plant inhibitors evolved hyper-variable and novel protein folds to remain active against potential herbivores. At the level of protease regulation in herbivorous insects, it was shown that inhibition-insensitive digestive proteases are up-regulated when sensitive proteases are inhibited. The way this regulation operates in mammals is known as negative feedback by gut-luminal factors, so-called 'monitor peptides' that are sensitive to the concentration of active enzymes. We propose that regulation of gut enzymes by endogenous luminal factors has been an open invitation to plants to "hijack" this regulation by evolving receptor antagonists, although yet these plant factors have not been identified. In future research the question of the co-evolution of insect proteases and plant inhibitors should, therefore, be better approached from a systems level keeping in mind that evolution is fundamentally opportunistic and that the plant's fitness is primarily improved by lowering the availability of essential amino acids to an herbivore by any available mechanism.

Co-evolution and thresholds in arid floodplain wetland ecosystems.

Science.gov (United States)

Sandi, Steven; Rodriguez, Jose; Riccardi, Gerardo; Wen, Li; Saintilan, Neil

2017-04-01

Vegetation in arid floodplain wetlands consist of water dependent and flood tolerant species that rely on periodical floods in order to maintain healthy conditions. The floodplain often consist of a complex system of marshes, swamps and lagoons interconnected by a network of streams and poorly defined rills. Over time, feedbacks develop between vegetation and flow paths producing areas of flow obstruction and flow concentration, which combined with depositional and erosional process lead to a continuous change on the position and characteristics of inundation areas. This coevolution of flow paths and vegetation can reach a threshold that triggers major channel transformations and abandonment of wetland areas, in a process that is irreversible. The Macquarie Marshes is a floodplain wetland complex in the semi-arid region of north western NSW, Australia. The site is characterised by a low-gradient topography that leads to channel breakdown processes where the river network becomes practically non-existent and the flow extends over large areas of wetland that later re-join and reform channels exiting the system. Due to a combination of climatic and anthropogenic pressures, the wetland ecosystem in the Macquarie Marshes has deteriorated over the past few decades. This has been linked to decreasing inundation frequencies and extent, with whole areas of flood dependent species such as Water Couch and Common Reed undergoing complete succession to terrestrial species and dryland. In this presentation we provide an overview of an ecogeomorphological model that we have developed in order to simulate the complex dynamics of the marshes. The model combines hydrodynamic, vegetation and channel evolution modules. We focus on the vegetation component of the model and the transitional rules to predict wetland invasion by terrestrial vegetation.

Modeling human-water-systems: towards a comprehensive and spatially distributed assessment of co-evolutions for river basins in Central Europe

Directory of Open Access Journals (Sweden)

P. Krahe

2016-05-01

Full Text Available In the context of river basin and flood risk management there is a growing need to improve the understanding of and the feedbacks between the driving forces “climate and socio-economy” and water systems. We make use of a variety of data resources to illustrate interrelationships between different constituents of the human-water-systems. Taking water storage for energy production as an example we present a first analysis on the co-evolution of socio-economic and hydrological indicators. The findings will serve as for the development of conceptual, but fully coupled socio-hydrological models for selected sectors and regions. These models will be used to generate integrated scenarios of the climate and socio-economic change.

Antagonistic Coevolution Drives Whack-a-Mole Sensitivity in Gene Regulatory Networks.

Directory of Open Access Journals (Sweden)

Jeewoen Shin

2015-10-01

Full Text Available Robustness, defined as tolerance to perturbations such as mutations and environmental fluctuations, is pervasive in biological systems. However, robustness often coexists with its counterpart, evolvability--the ability of perturbations to generate new phenotypes. Previous models of gene regulatory network evolution have shown that robustness evolves under stabilizing selection, but it is unclear how robustness and evolvability will emerge in common coevolutionary scenarios. We consider a two-species model of coevolution involving one host and one parasite population. By using two interacting species, key model parameters that determine the fitness landscapes become emergent properties of the model, avoiding the need to impose these parameters externally. In our study, parasites are modeled on species such as cuckoos where mimicry of the host phenotype confers high fitness to the parasite but lower fitness to the host. Here, frequent phenotype changes are favored as each population continually adapts to the other population. Sensitivity evolves at the network level such that point mutations can induce large phenotype changes. Crucially, the sensitive points of the network are broadly distributed throughout the network and continually relocate. Each time sensitive points in the network are mutated, new ones appear to take their place. We have therefore named this phenomenon "whack-a-mole" sensitivity, after a popular fun park game. We predict that this type of sensitivity will evolve under conditions of strong directional selection, an observation that helps interpret existing experimental evidence, for example, during the emergence of bacterial antibiotic resistance.

Coevolution of Interorganizational Psychological Contract and Interorganizational Relationship: A Case Study of Manufacturing Company in China

Directory of Open Access Journals (Sweden)

Wei He

2017-01-01

Full Text Available As the belief of the beholder in an exchange about the obligations that another party should have, interorganizational psychological contract (IPC from a micro perspective provides a new angle to study interorganizational relationship (IOR. This paper studies the interrelation and coevolution of IORs and IPCs by building a system dynamics (SD model. Firstly based on the structural analysis of the interrelations of IPC and IOR, this paper builds the qualitative causal loop diagram of the interrelations. Based on investigation of 55 manufacturing enterprises in China we further draw the stock and flow diagram. Then we apply the data of Jiangxi Motors Co., Ltd., to simulate the model. The results reveal the development and evolution of IORs and IPCs and their interrelations. Furthermore, the sensitivity analysis is conducted and the influences of trust on IORs and IPCs are discussed. Finally managerial implications and some recommendations are provided for the decision-making of developing IORs.

The Co-evolution of Language and the Brain: A Review of Two Contrastive Views (Pinker & Deacon)

DEFF Research Database (Denmark)

Christensen, Ken Ramshøj

2001-01-01

in a larger symbolic computational chain controlled by regions in the frontal parts of the brain. To Deacon, a symbolic learning algorithm drives language acquisition. The increase in size of the human brain in relation to the body may be due to a “cognitive arms race”. Both Pinker and Deacon agree......This article is a review of two contrastive views on the co-evolution of language and the brain – The Language Instinct by Steven Pinker (1994) and The Symbolic Species by Terrence Deacon (1997). As language is a trait unique to mankind it can not be equated with nonlinguistic communication – human...... or nonhuman. This points to a special human brain architecture. Pinker’s claim is that certain areas on the left side of the brain constitute a language organ and that language acquisition is instinctual. To Deacon, however, those areas are non-language-specific computational centers. Moreover, they are parts...

Differential susceptibility to plasticity: a 'missing link' between gene-culture co-evolution and neuropsychiatric spectrum disorders?

Directory of Open Access Journals (Sweden)

Wurzman Rachel

2012-04-01

Full Text Available Abstract Brüne's proposal that erstwhile 'vulnerability' genes need to be reconsidered as 'plasticity' genes, given the potential for certain environments to yield increased positive function in the same domain as potential dysfunction, has implications for psychiatric nosology as well as a more dynamic understanding of the relationship between genes and culture. In addition to validating neuropsychiatric spectrum disorder nosologies by calling for similar methodological shifts in gene-environment-interaction studies, Brüne's position elevates the importance of environmental contexts - inclusive of socio-cultural variables - as mechanisms that contribute to clinical presentation. We assert that when models of susceptibility to plasticity and neuropsychiatric spectrum disorders are concomitantly considered, a new line of inquiry emerges into the co-evolution and co-determination of socio-cultural contexts and endophenotypes. This presents potentially unique opportunities, benefits, challenges, and responsibilities for research and practice in psychiatry. Please see related manuscript: http://www.biomedcentral.com/1741-7015/10/38

The Ecological Dynamics of Natural Selection: Traits and the Coevolution of Community Structure.

Science.gov (United States)

McPeek, Mark A

2017-05-01

Natural selection has both genetic and ecological dynamics. The fitnesses of individuals change with their ecological context, and so the form and strength of selective agents change with abiotic factors and the phenotypes and abundances of interacting species. I use standard models of consumer-resource interactions to explore the ecological dynamics of natural selection and how various trait types influence these dynamics and the resulting structure of a community of coevolving species. Evolutionary optima favored by natural selection depend critically on the abundances of interacting species, and the traits of species can undergo dynamic cycling in limited areas of parameter space. The ecological dynamics of natural selection can also drive shifts from one adaptive peak to another, and these ecologically driven adaptive peak shifts are fundamental to the dynamics of niche differentiation. Moreover, this ecological differentiation is fostered in more productive and more benign environments where species interactions are stronger and where the selection gradients generated by species interactions are stronger. Finally, community structure resulting from coevolution depends fundamentally on the types of traits that underlie species interactions. The ecological dynamics of the process cannot be simplified, neglected, or ignored if we are to build a predictive theory of natural selection.

Coevolution between invasive and native plants driven by chemical competition and soil biota.

Science.gov (United States)

Lankau, Richard A

2012-07-10

Although reciprocal evolutionary responses between interacting species are a driving force behind the diversity of life, pairwise coevolution between plant competitors has received less attention than other species interactions and has been considered relatively less important in explaining ecological patterns. However, the success of species transported across biogeographic boundaries suggests a stronger role for evolutionary relationships in shaping plant interactions. Alliaria petiolata is a Eurasian species that has invaded North American forest understories, where it competes with native understory species in part by producing compounds that directly and indirectly slow the growth of competing species. Here I show that populations of A. petiolata from areas with a greater density of interspecific competitors invest more in a toxic allelochemical under common conditions. Furthermore, populations of a native competitor from areas with highly toxic invaders are more tolerant to competition from the invader, suggesting coevolutionary dynamics between the species. Field reciprocal transplants confirmed that native populations more tolerant to the invader had higher fitness when the invader was common, but these traits came at a cost when the invader was rare. Exotic species are often detrimentally dominant in their new range due to their evolutionary novelty; however, the development of new coevolutionary relationships may act to integrate exotic species into native communities.

Biomimicry of symbiotic multi-species coevolution for discrete and continuous optimization in RFID networks.

Science.gov (United States)

Lin, Na; Chen, Hanning; Jing, Shikai; Liu, Fang; Liang, Xiaodan

2017-03-01

In recent years, symbiosis as a rich source of potential engineering applications and computational model has attracted more and more attentions in the adaptive complex systems and evolution computing domains. Inspired by different symbiotic coevolution forms in nature, this paper proposed a series of multi-swarm particle swarm optimizers called PS 2 Os, which extend the single population particle swarm optimization (PSO) algorithm to interacting multi-swarms model by constructing hierarchical interaction topologies and enhanced dynamical update equations. According to different symbiotic interrelationships, four versions of PS 2 O are initiated to mimic mutualism, commensalism, predation, and competition mechanism, respectively. In the experiments, with five benchmark problems, the proposed algorithms are proved to have considerable potential for solving complex optimization problems. The coevolutionary dynamics of symbiotic species in each PS 2 O version are also studied respectively to demonstrate the heterogeneity of different symbiotic interrelationships that effect on the algorithm's performance. Then PS 2 O is used for solving the radio frequency identification (RFID) network planning (RNP) problem with a mixture of discrete and continuous variables. Simulation results show that the proposed algorithm outperforms the reference algorithms for planning RFID networks, in terms of optimization accuracy and computation robustness.

Visualization on the Web of 20 Years of Crop Rotation and Wildlife Co-Evolutions

Science.gov (United States)

Plumejeaud-Perreau, Christine; Poitevin, Cyril; Bretagnolle, Vincent

2018-05-01

The accumulation of evidences of the effects of intensive agricultural practices against wildlife fauna and flora, and biodiversity in general, has been largely published in scientific papers (Tildman, 1999). However, data serving as sup-port to their conclusions are often kept hidden behind research institutions. This paper presents a data visualization sys-tem opened on the Web allowing citizens to get a comprehensive access to data issued from such kind of research institution, collected for more than 20 years. The Web Information System has been thought in order to ease the comparison of data issues from various databases describing the same object, the agricultural landscape, at different scales and through different observation devices. An interactive visualization is proposed in order to check co-evolution of fauna and flora together with agricultural practices. It mixes aerial orthoimagery produced since 1950 with vectorial data showing the evolutions of agricultural parcels with those of a few sentinel species such as the Montagu's harrier. This is made through a composition of maps, charts and time lines, and specific tools for comparison. A particular concern is given to the observation effort bias in order to show meaningful statistical aggregates.

Adaptive co-evolution of strategies and network leading to optimal cooperation level in spatial prisoner's dilemma game

International Nuclear Information System (INIS)

Han-Shuang, Chen; Zhong-Huai, Hou; Hou-Wen, Xin; Ji-Qian, Zhang

2010-01-01

We study evolutionary prisoner's dilemma game on adaptive networks where a population of players co-evolves with their interaction networks. During the co-evolution process, interacted players with opposite strategies either rewire the link between them with probability p or update their strategies with probability 1 – p depending on their payoffs. Numerical simulation shows that the final network is either split into some disconnected communities whose players share the same strategy within each community or forms a single connected network in which all nodes are in the same strategy. Interestingly, the density of cooperators in the final state can be maximised in an intermediate range of p via the competition between time scale of the network dynamics and that of the node dynamics. Finally, the mean-field analysis helps to understand the results of numerical simulation. Our results may provide some insight into understanding the emergence of cooperation in the real situation where the individuals' behaviour and their relationship adaptively co-evolve. (general)

Co-evolution of elliptical galaxies and their central black holes

International Nuclear Information System (INIS)

Ciotti, I.

2009-01-01

After the discovery that supermassive black holes (SMBHs) are ubiquitous at the center of stellar spheroids and that their mass M BH , in the range 10 6 M-10 9 M, is tightly related to global properties of the host stellar system, the idea of the co-evolution of elliptical galaxies and of their SMBHs has become a central topic of modern astrophysics. Here, I summarize some consequences that can be derived from the galaxy Scaling Laws (SLs) and present a coherent scenario for the formation and evolution of elliptical galaxies and their central SMBHs, focusing in particular on the establishment and maintenance of their SLs. In particular, after a first observationally based part, the discussion focuses on the physical interpretation of the Fundamental Plane. Then, two important processes in principle able to destroy the galaxy and SMBH SLs, namely galaxy merging and cooling flows, are analyzed. Arguments supporting the necessity to clearly distinguish between the origin and maintenance of the different SLs, and the unavoidable occurrence of SMBH feedback on the galaxy ISM in the late stages of galaxy evolution (when elliptical galaxies are sometimes considered as dead, red objects), are then presented. At the end of the paper I will discuss some implications of the recent discovery of super-dense ellipticals in the distant Universe. In particular, I will argue that, if confirmed, these new observations would lead to the conclusion that at early epochs a relation between the stellar mass of the galaxy and the mass of the central SMBH should hold, consistent with the present day Magorrian relation, while the proportionality coefficient between M BH and the scale of velocity dispersion of the hosting spheroids should be significantly smaller than that at the present epoch

Coevolution of the Toll-Like Receptor 4 Complex with Calgranulins and Lipopolysaccharide

Directory of Open Access Journals (Sweden)

Andrea N. Loes

2018-02-01

Full Text Available Toll-like receptor 4 (TLR4 induces inflammation in response to both pathogen- and host-derived molecules. Lipopolysaccharide (LPS recognition by TLR4 has been shown to occur across the amniotes, but endogenous signaling through TLR4 has not been validated outside of placental mammals. To determine whether endogenous danger signaling is also shared across amniotes, we studied the evolution of TLR4-activation by the calgranulin proteins (S100A8, S100A9, and S100A12, a clade of host molecules that potently activate TLR4 in placental mammals. We performed phylogenetic and syntenic analysis and found MRP-126—a gene in birds and reptiles—is likely orthologous to the mammalian calgranulins. We then used an ex vivo TLR4 activation assay to establish that calgranulin pro-inflammatory activity is not specific to placental mammals, but is also exhibited by representative marsupial and sauropsid species. This activity is strongly dependent on the cofactors CD14 and MD-2 for all species studied, suggesting a conserved mode of activation across the amniotes. Ortholog complementation experiments between the calgranulins, TLR4, CD14, and MD-2 revealed extensive lineage specific-coevolution and multi-way interactions between components that are necessary for the activation of NF-κB signaling by calgranulins and LPS. Our work demonstrates that calgranulin activation of TLR4 evolved at least ~320 million years ago and has been conserved in the amniote innate immune system.

A Time-Domain Structural Damage Detection Method Based on Improved Multiparticle Swarm Coevolution Optimization Algorithm

Directory of Open Access Journals (Sweden)

Shao-Fei Jiang

2014-01-01

Full Text Available Optimization techniques have been applied to structural health monitoring and damage detection of civil infrastructures for two decades. The standard particle swarm optimization (PSO is easy to fall into the local optimum and such deficiency also exists in the multiparticle swarm coevolution optimization (MPSCO. This paper presents an improved MPSCO algorithm (IMPSCO firstly and then integrates it with Newmark’s algorithm to localize and quantify the structural damage by using the damage threshold proposed. To validate the proposed method, a numerical simulation and an experimental study of a seven-story steel frame were employed finally, and a comparison was made between the proposed method and the genetic algorithm (GA. The results show threefold: (1 the proposed method not only is capable of localization and quantification of damage, but also has good noise-tolerance; (2 the damage location can be accurately detected using the damage threshold proposed in this paper; and (3 compared with the GA, the IMPSCO algorithm is more efficient and accurate for damage detection problems in general. This implies that the proposed method is applicable and effective in the community of damage detection and structural health monitoring.

Coevolution between a family of parasite virulence effectors and a class of LINE-1 retrotransposons.

Directory of Open Access Journals (Sweden)

Soledad Sacristán

2009-10-01

Full Text Available Parasites are able to evolve rapidly and overcome host defense mechanisms, but the molecular basis of this adaptation is poorly understood. Powdery mildew fungi (Erysiphales, Ascomycota are obligate biotrophic parasites infecting nearly 10,000 plant genera. They obtain their nutrients from host plants through specialized feeding structures known as haustoria. We previously identified the AVR(k1 powdery mildew-specific gene family encoding effectors that contribute to the successful establishment of haustoria. Here, we report the extensive proliferation of the AVR(k1 gene family throughout the genome of B. graminis, with sequences diverging in formae speciales adapted to infect different hosts. Also, importantly, we have discovered that the effectors have coevolved with a particular family of LINE-1 retrotransposons, named TE1a. The coevolution of these two entities indicates a mutual benefit to the association, which could ultimately contribute to parasite adaptation and success. We propose that the association would benefit 1 the powdery mildew fungus, by providing a mechanism for amplifying and diversifying effectors and 2 the associated retrotransposons, by providing a basis for their maintenance through selection in the fungal genome.

Biomimicry of symbiotic multi-species coevolution for discrete and continuous optimization in RFID networks

Directory of Open Access Journals (Sweden)

Na Lin

2017-03-01

Full Text Available In recent years, symbiosis as a rich source of potential engineering applications and computational model has attracted more and more attentions in the adaptive complex systems and evolution computing domains. Inspired by different symbiotic coevolution forms in nature, this paper proposed a series of multi-swarm particle swarm optimizers called PS2Os, which extend the single population particle swarm optimization (PSO algorithm to interacting multi-swarms model by constructing hierarchical interaction topologies and enhanced dynamical update equations. According to different symbiotic interrelationships, four versions of PS2O are initiated to mimic mutualism, commensalism, predation, and competition mechanism, respectively. In the experiments, with five benchmark problems, the proposed algorithms are proved to have considerable potential for solving complex optimization problems. The coevolutionary dynamics of symbiotic species in each PS2O version are also studied respectively to demonstrate the heterogeneity of different symbiotic interrelationships that effect on the algorithm’s performance. Then PS2O is used for solving the radio frequency identification (RFID network planning (RNP problem with a mixture of discrete and continuous variables. Simulation results show that the proposed algorithm outperforms the reference algorithms for planning RFID networks, in terms of optimization accuracy and computation robustness.

Insights into recent and ancient trends in the co-evolution of Earth and life as revealed by microbial genomics

Science.gov (United States)

Anderson, R. E.; Huber, J. A.; Parsons, C.; Stüeken, E.

2017-12-01

Since the origin of life over 4 billion years ago, life has fundamentally altered the habitability of Earth. Similarly, the environment molds the evolutionary trajectory of life itself through natural selection. Microbial genomes retain a "memory" of the co-evolution of life and Earth and can be analyzed to better understand trends and events in both the recent and distant past. To examine evolutionary trends in the more recent past, we have used metagenomics analyses to investigate which environmental factors play the strongest role in driving the evolution of microbes in deep-sea hydrothermal vents, which are thought to have been important habitats in the earliest stages of life's evolution. We have shown that microbial populations in a deep, basalt-hosted system appear to be under stronger purifying selection than populations inhabiting a cooler serpentinizing system less than 20 km away, suggesting that environmental context and geochemistry have an important impact on evolutionary rates and trends. We also found evidence that viruses play an important role in driving evolution in these habitats. Changing environmental conditions may also effect long-term evolutionary trends in Earth's distant past, as revealed by comparative genomics. By reconciling phylogenetic trees for microbial species with trees of metabolic genes, we can determine approximately when crucial metabolic genes began to spread across the tree of life through horizontal gene transfer. Using these methods, we conducted an analysis of the relative timing of the spread of genes related to the nitrogen cycle. Our results indicate that the rate of horizontal gene transfer for important genes related to denitrification increased after the Great Oxidation Event, concurrent with geochemical evidence for increasing availability of nitrate, suggesting that the oxygenation of the atmosphere and surface ocean may have been an important determining factor for the spread of denitrification genes across the

Reciprocal interactions between fluvial processes and riparian plants at multiple scales: ecogeomorphic feedbacks drive coevolution of floodplain morphology and vegetation communities

Science.gov (United States)

Stella, J. C.; Kui, L.; Diehl, R. M.; Bywater-Reyes, S.; Wilcox, A. C.; Shafroth, P. B.; Lightbody, A.

2017-12-01

Fluvial forces interact with woody riparian plants in complex ways to influence the coevolution of river morphology and floodplain plant communities. Here, we report on an integrated suite of multi-disciplinary studies that contrast the responses of plants with different morphologies, tamarisk (Tamarix spp.) and cottonwood (Populus fremontii) in terms of (1) differences in vulnerability to scour and burial during floods; (2) interactions and feedbacks between plants and river morphodynamics; and (3) long-term coevolution of river floodplains and riparian communities following flow regulation from dams. The focus of these studies is sand-bed rivers in arid-land regions where invasion by tamarisk has strongly influenced riverine plant communities and geomorphic processes. We complemented a suite of field-scale flume experiments using live seedlings to quantify the initial stages of plant-river interactions with an analysis of long-term vegetation and geomorphic changes along the dammed Bill Williams River (AZ, USA) using time-series air photographs. Vegetation-fluvial interactions varied with plant characteristics, river hydraulics and sediment conditions, across the wide range of scales we investigated. In the flume studies, tamarisk's denser crowns and stiffer stems induced greater sedimentation compared to cottonwood. This resulted in tamarisk's greater mortality from burial as small seedlings under sediment equilibrium conditions but higher relative survival in larger floods under sediment deficit scenarios, in which more cottonwoods were lost to root scour. Sediment deficit conditions, as occurs downstream of dams, induced both greater scour and greater plant loss. With larger size and at higher densities, plants' vulnerability diminished due to greater root anchoring and canopy effects on hydraulics. At the corridor scale, we observed a pattern of plant encroachment during five decades of flow regulation, in which channel narrowing and simplification was more

The RNA-world and co-evolution hypothesis and the origin of life: Implications, research strategies and perspectives

Science.gov (United States)

Lahav, Noam

1993-01-01

The applicability of the RNA-world and co-evolution hypothesis to the study of the very first stages of the origin of life is discussed. The discussion focuses on the basic differences between the two hypotheses and their implications, with regard to the reconstruction methodology, ribosome emergence, balance between ribozymes and protein enzymes, and their major difficultites. Additional complexities of the two hypotheses, such as membranes and the energy source of the first reactions, are not treated in the present work. A central element in the proposed experimental strategies is the study of the catalytic activites of very small peptides and RNA-like oligomers, according to existing, as well as to yet-to-be-invented scenarios of the two hypothesis under consideration. It is suggested that the novel directed molecular evolution technology, and molecular computational modeling, can be applied to this research. This strategy is assumed to be essential for the suggested goal of future studies of the origin of life, namely, the establishment of a `Primordial Darwinian entity'.

The RNA-world and co-evolution hypotheses and the origin of life: Implications, research strategies and perspectives

Science.gov (United States)

Lahav, Noam

1993-12-01

The applicability of the RNA-world and co-evolution hypotheses to the study of the very first stages of the origin of life is discussed. The discussion focuses on the basic differences between the two hypotheses and their implications, with regard to the reconstruction methodology, ribosome emergence, balance between ribozymes and protein enzymes, and their major difficulties. Additional complexities of the two hypotheses, such as membranes and the energy source of the first reactions, are not treated in the present work. A central element in the proposed experimental strategies is the study of the catalytic activities of very small peptides and RNA-like oligomers, according to existing, as well as to yet-to-be-invented scenarios of the two hypotheses under consideration. It is suggested that the noveldirected molecular evolution technology, andmolecular computational modeling, can be applied to this research. This strategy is assumed to be essential for the suggested goal of future studies of the origin of life, namely, the establishment of a ‘Primordial Darwinian entity’.

Coevolution of honest signaling and cooperative norms by cultural group selection.

Science.gov (United States)

Scheuring, István

2010-08-01

Evolution of cooperative norms is studied in a population where individual and group level selection are both in operation. Individuals play indirect reciprocity game within their group and follow second order norms. Individuals are norm-followers, and imitate their successful group mates. Aside from direct observation individuals can be informed about the previous actions and reputations by information transferred by others. A potential donor estimates the reputation of a potential receiver either by her own observation or by the opinion of the majority of others (indirect observation). Following a previous study (Scheuring, 2009) we assume that norms determine only the probabilities of actions, and mutants can differ in these probabilities. Similarly, we assume that individuals follow a stochastic information transfer strategy. The central question is whether cooperative norm and honest social information transfer can emerge in a population where initially only non-cooperative norms were present, and the transferred information was not sufficiently honest. It is shown that evolution can lead to a cooperative state where information transferred in a reliable manner, where generous cooperative strategies are dominant. This cooperative state emerges along a sharp transition of norms. We studied the characteristics of actions and strategies in this transition by classifying the stochastic norms, and found that a series of more and more judging strategies invade each other before the stabilization of the so-called generous judging strategy. Numerical experiments on the coevolution of social parameters (e.g. probability of direct observation and the number of indirect observers) reveal that it is advantageous to lean on indirect observation even if information transfer is much noisier than for direct observation, which is because to follow the majorities' opinion suppresses information noise meaningfully.

Co-Evolution and Bio-Social Construction: The Kichwa Agroforestry Systems (Chakras in the Ecuadorian Amazonia

Directory of Open Access Journals (Sweden)

Daniel Coq-Huelva

2017-10-01

Full Text Available Polycultured agrarian systems in Ecuadorian Amazonia (also called chakras or swollen gardens are characterised by a market-oriented crop for the generation of monetary income, for example, cocoa, other agricultural products (e.g., banana and cassava, and livestock for family farm consumption. Moreover, a chakra is an outstanding example of agroforestry production, in which ecological, social and economic elements co-evolve from a set of close and strong connections. In this context, the conservation and transformation of their biological subsystems can be understood as the result of complex interactions between anthropogenic and non-anthropogenic factors. In turn, such interactions are essential to provide food and monetary income to the indigenous community. Relevant agency capabilities exist that could cause an agroforestry system to take a different path of co-evolution, that is, towards greater or lesser sustainability associated with different levels of complexity. In conclusion, chakras have key ecological features that can mitigate the impact of human population growth in Amazonia. Additionally, chakras have their own processes of social self-regulation which enhance the possibilities of adaptation of Kichwa communities to changing environmental conditions, being essential elements in local food sovereignty, equitable gender relations and the respect of ancestral wisdom.

Coevolution between human's anticancer activities and functional foods from crop origin center in the world.

Science.gov (United States)

Zeng, Ya-Wen; Du, Juan; Pu, Xiao-Ying; Yang, Jia-Zhen; Yang, Tao; Yang, Shu-Ming; Yang, Xiao-Meng

2015-01-01

Cancer is the leading cause of death around the world. Anticancer activities from many functional food sources have been reported in years, but correlation between cancer prevalence and types of food with anticancer activities from crop origin center in the world as well as food source with human migration are unclear. Hunger from food shortage is the cause of early human evolution from Africa to Asia and later into Eurasia. The richest functional foods are found in crop origin centers, housing about 70% in the world populations. Crop origin centers have lower cancer incidence and mortality in the world, especially Central Asia, Middle East, Southwest China, India and Ethiopia. Asia and Africa with the richest anticancer crops is not only the most important evolution base of humans and origin center of anticancer functional crop, but also is the lowest mortality and incidence of cancers in the world. Cancer prevention of early human migrations was associated with functional foods from crop origin centers, especially Asia with four centers and one subcenter of crop origin, accounting for 58% of the world population. These results reveal that coevolution between human's anticancer activities associated with functional foods for crop origin centers, especially in Asia and Africa.

Replicated population divergence caused by localized coevolution? A test of three hypotheses in the red crossbill-lodgepole pine system.

Science.gov (United States)

Edelaar, P; Benkman, C W

2006-09-01

Several lines of evidence support the hypothesis that local populations of red crossbills (Loxia curvirostra complex) enter into a predator-prey arms race with lodgepole pine (Pinus contorta latifolia) in the absence of competing pine squirrels (Tamiasciurus hudsonicus). Nevertheless, the alternative hypotheses that neutral evolution or factors other than squirrels have caused crossbill population differentiation have not been thoroughly tested. We compared crossbill and pine cone morphology between island populations where squirrels are absent or present, and mainland sites where squirrels are present, in order to distinguish among these hypotheses. All comparisons supported an effect of squirrel absence, not island status, on crossbill and cone morphology. Hence our results provide further evidence that strong localized coevolutionary interactions in a geographic mosaic have driven adaptive population differentiation. In addition, vocal differentiation of crossbills was related to the absence of squirrels, but not to island status. As morphological and vocal differentiation is correlated with reproductive isolation in crossbills, the geographic mosaic of coevolution also seems to promote ecological speciation.

The lack of foundation in the mechanism on which are based the physico-chemical theories for the origin of the genetic code is counterposed to the credible and natural mechanism suggested by the coevolution theory.

Science.gov (United States)

Di Giulio, Massimo

2016-06-21

I analyze the mechanism on which are based the majority of theories that put to the center of the origin of the genetic code the physico-chemical properties of amino acids. As this mechanism is based on excessive mutational steps, I conclude that it could not have been operative or if operative it would not have allowed a full realization of predictions of these theories, because this mechanism contained, evidently, a high indeterminacy. I make that disapproving the four-column theory of the origin of the genetic code (Higgs, 2009) and reply to the criticism that was directed towards the coevolution theory of the origin of the genetic code. In this context, I suggest a new hypothesis that clarifies the mechanism by which the domains of codons of the precursor amino acids would have evolved, as predicted by the coevolution theory. This mechanism would have used particular elongation factors that would have constrained the evolution of all amino acids belonging to a given biosynthetic family to the progenitor pre-tRNA, that for first recognized, the first codons that evolved in a certain codon domain of a determined precursor amino acid. This happened because the elongation factors recognized two characteristics of the progenitor pre-tRNAs of precursor amino acids, which prevented the elongation factors from recognizing the pre-tRNAs belonging to biosynthetic families of different precursor amino acids. Finally, I analyze by means of Fisher's exact test, the distribution, within the genetic code, of the biosynthetic classes of amino acids and the ones of polarity values of amino acids. This analysis would seem to support the biosynthetic classes of amino acids over the ones of polarity values, as the main factor that led to the structuring of the genetic code, with the physico-chemical properties of amino acids playing only a subsidiary role in this evolution. As a whole, the full analysis brings to the conclusion that the coevolution theory of the origin of the

Coevolution between Nuclear-Encoded DNA Replication, Recombination, and Repair Genes and Plastid Genome Complexity.

Science.gov (United States)

Zhang, Jin; Ruhlman, Tracey A; Sabir, Jamal S M; Blazier, John Chris; Weng, Mao-Lun; Park, Seongjun; Jansen, Robert K

2016-02-17

Disruption of DNA replication, recombination, and repair (DNA-RRR) systems has been hypothesized to cause highly elevated nucleotide substitution rates and genome rearrangements in the plastids of angiosperms, but this theory remains untested. To investigate nuclear-plastid genome (plastome) coevolution in Geraniaceae, four different measures of plastome complexity (rearrangements, repeats, nucleotide insertions/deletions, and substitution rates) were evaluated along with substitution rates of 12 nuclear-encoded, plastid-targeted DNA-RRR genes from 27 Geraniales species. Significant correlations were detected for nonsynonymous (dN) but not synonymous (dS) substitution rates for three DNA-RRR genes (uvrB/C, why1, and gyrA) supporting a role for these genes in accelerated plastid genome evolution in Geraniaceae. Furthermore, correlation between dN of uvrB/C and plastome complexity suggests the presence of nucleotide excision repair system in plastids. Significant correlations were also detected between plastome complexity and 13 of the 90 nuclear-encoded organelle-targeted genes investigated. Comparisons revealed significant acceleration of dN in plastid-targeted genes of Geraniales relative to Brassicales suggesting this correlation may be an artifact of elevated rates in this gene set in Geraniaceae. Correlation between dN of plastid-targeted DNA-RRR genes and plastome complexity supports the hypothesis that the aberrant patterns in angiosperm plastome evolution could be caused by dysfunction in DNA-RRR systems. © The Author 2016. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

Sexually antagonistic coevolution for sexual harassment can act as a barrier to further invasions by parthenogenesis.

Science.gov (United States)

Kawatsu, Kazutaka

2013-02-01

The assumption of a twofold cost of sex not only complicates the maintenance of sex but also sets conditions for sexual conflict: in organisms with the twofold cost, males often sexually harass females. Sexual harassment is detrimental to female fitness and thus might help maintain sexual populations if male harassment inflicts a harsher cost on parthenogens than on sexual females (asymmetric harassment cost). However, the generality of this concept is now considered doubtful because selective harassment of parthenogens results in loss of mating opportunities for males. Using three mathematical models, I show here that sexual harassment still can impose the asymmetric cost on parthenogens. First, I apply the Lotka-Volterra model to show the degree of asymmetric harassment cost that permits sex to be maintained stably in the population. Second, using adaptive dynamics, I examine whether sexually antagonistic coevolution for sexual harassment, which occurs only in sexual populations, can promote the asymmetric harassment cost. Finally, an individual-based model, which assumes a spatial structure unlike that in the other two, demonstrates that the asymmetric evolution of harassment cost prevents further invasions of parthenogens from different patches into sexual lineages; these mechanisms may account for allopatric distributions of sexual and parthenogenetic lineages as well as the maintenance of sex.

The coevolution of supermassive black holes and massive galaxies at high redshift

Energy Technology Data Exchange (ETDEWEB)

Lapi, A.; Raimundo, S.; Aversa, R.; Cai, Z.-Y.; Celotti, A.; De Zotti, G.; Danese, L. [SISSA, Via Bonomea 265, I-34136 Trieste (Italy); Negrello, M. [INAF-Osservatorio Astronomico di Padova, Vicolo dell' Osservatorio 5, I-35122 Padova (Italy)

2014-02-20

We exploit the recent, wide samples of far-infrared (FIR) selected galaxies followed up in X-rays and of X-ray/optically selected active galactic nuclei (AGNs) followed up in the FIR band, along with the classic data on AGNs and stellar luminosity functions at high redshift z ≳ 1.5, to probe different stages in the coevolution of supermassive black holes (BHs) and host galaxies. The results of our analysis indicate the following scenario: (1) the star formation in the host galaxy proceeds within a heavily dust-enshrouded medium at an almost constant rate over a timescale ≲ 0.5-1 Gyr and then abruptly declines due to quasar feedback, over the same timescale; (2) part of the interstellar medium loses angular momentum, reaches the circum-nuclear regions at a rate proportional to the star formation, and is temporarily stored in a massive reservoir/proto-torus wherefrom it can be promptly accreted; (3) the BH grows by accretion in a self-regulated regime with radiative power that can slightly exceed the Eddington limit L/L {sub Edd} ≲ 4, particularly at the highest redshifts; (4) for massive BHs, the ensuing energy feedback at its maximum exceeds the stellar one and removes the interstellar gas, thus stopping the star formation and the fueling of the reservoir; (5) afterward, if the latter has retained enough gas, a phase of supply-limited accretion follows, exponentially declining with a timescale of about two e-folding times. We also discuss how the detailed properties and the specific evolution of the reservoir can be investigated via coordinated, high-resolution observations of star-forming, strongly lensed galaxies in the (sub-)mm band with ALMA and in the X-ray band with Chandra and the next-generation X-ray instruments.

Coevolution between flight morphology, vertical stratification and sexual dimorphism: what can we learn from tropical butterflies?

Science.gov (United States)

Graça, M B; Pequeno, P A C L; Franklin, E; Morais, J W

2017-10-01

Occurrence patterns are partly shaped by the affinity of species with habitat conditions. For winged organisms, flight-related attributes are vital for ecological performance. However, due to the different reproductive roles of each sex, we expect divergence in flight energy budget, and consequently different selection responses between sexes. We used tropical frugivorous butterflies as models to investigate coevolution between flight morphology, sex dimorphism and vertical stratification. We studied 94 species of Amazonian fruit-feeding butterflies sampled in seven sites across 3341 ha. We used wing-thorax ratio as a proxy for flight capacity and hierarchical Bayesian modelling to estimate stratum preference. We detected a strong phylogenetic signal in wing-thorax ratio in both sexes. Stouter fast-flying species preferred the canopy, whereas more slender slow-flying species preferred the understorey. However, this relationship was stronger in females than in males, suggesting that female phenotype associates more intimately with habitat conditions. Within species, males were stouter than females and sexual dimorphism was sharper in understorey species. Because trait-habitat relationships were independent from phylogeny, the matching between flight morphology and stratum preference is more likely to reflect adaptive radiation than shared ancestry. This study sheds light on the impact of flight and sexual dimorphism on the evolution and ecological adaptation of flying organisms. © 2017 European Society For Evolutionary Biology. Journal of Evolutionary Biology © 2017 European Society For Evolutionary Biology.

Coevolution of floodplain and riparian forest dynamics on large, meandering rivers

Science.gov (United States)

Stella, J. C.; Riddle, J. D.; Battles, J. J.

2012-12-01

On large meandering rivers, riparian forests coevolve with the floodplains that support them. Floodplain characteristics such as local disturbance regime, deposition rates and sediment texture drive plant community dynamics, which in turn feed back to the abiotic processes. We investigated floodplain and riparian forest coevolution along the along the Sacramento River (California, USA), a large, mediterranean-climate river that has been extensively regulated for 70 years, but whose 160-km middle reach (Red Bluff to Colusa) retains some channel mobility and natural forest stands. Guided by maps of floodplain change over time and current vegetation cover, we conducted an extensive forest inventory and chronosequence analysis to quantify how abiotic conditions and forest structural characteristics such as tree density, basal area and biomass vary with floodplain age. We inventoried 285 fixed-area plots distributed across 19 large point bars within vegetation patches ranging in age from 4 to 107 years. Two successional trajectories were evident: (1) shifting species dominance over time within forested areas, from willow to cottonwood to walnut, boxelder and valley oak; and (2) patches of shrub willow (primarily Salix exigua) that maintained dominance throughout time. Sediment accretion was reduced in the persistent willow plots compared to the successional forest stands, suggesting an association between higher flood energy and arrested succession. Forested stands 40-60 years old were the most extensive across the chronosequence in terms of floodplain area, and supported the highest biomass, species diversity, and functional wildlife habitat. These stands were dominated by Fremont cottonwood (Populus fremontii) and reached their maxima in terms of tree size and biomass at age 50 years. The persistent willow stands reached their structural maxima earlier (32 years) and supported lower biomass. Basal area and abundance of large trees decreased in stands >90 years old

Co-evolution of SNF spliceosomal proteins with their RNA targets in trans-splicing nematodes.

Science.gov (United States)

Strange, Rex Meade; Russelburg, L Peyton; Delaney, Kimberly J

2016-08-01

Although the mechanism of pre-mRNA splicing has been well characterized, the evolution of spliceosomal proteins is poorly understood. The U1A/U2B″/SNF family (hereafter referred to as the SNF family) of RNA binding spliceosomal proteins participates in both the U1 and U2 small interacting nuclear ribonucleoproteins (snRNPs). The highly constrained nature of this system has inhibited an analysis of co-evolutionary trends between the proteins and their RNA binding targets. Here we report accelerated sequence evolution in the SNF protein family in Phylum Nematoda, which has allowed an analysis of protein:RNA co-evolution. In a comparison of SNF genes from ecdysozoan species, we found a correlation between trans-splicing species (nematodes) and increased phylogenetic branch lengths of the SNF protein family, with respect to their sister clade Arthropoda. In particular, we found that nematodes (~70-80 % of pre-mRNAs are trans-spliced) have experienced higher rates of SNF sequence evolution than arthropods (predominantly cis-spliced) at both the nucleotide and amino acid levels. Interestingly, this increased evolutionary rate correlates with the reliance on trans-splicing by nematodes, which would alter the role of the SNF family of spliceosomal proteins. We mapped amino acid substitutions to functionally important regions of the SNF protein, specifically to sites that are predicted to disrupt protein:RNA and protein:protein interactions. Finally, we investigated SNF's RNA targets: the U1 and U2 snRNAs. Both are more divergent in nematodes than arthropods, suggesting the RNAs have co-evolved with SNF in order to maintain the necessarily high affinity interaction that has been characterized in other species.

Metabolic Coevolution in the Bacterial Symbiosis of Whiteflies and Related Plant Sap-Feeding Insects.

Science.gov (United States)

Luan, Jun-Bo; Chen, Wenbo; Hasegawa, Daniel K; Simmons, Alvin M; Wintermantel, William M; Ling, Kai-Shu; Fei, Zhangjun; Liu, Shu-Sheng; Douglas, Angela E

2015-09-15

Genomic decay is a common feature of intracellular bacteria that have entered into symbiosis with plant sap-feeding insects. This study of the whitefly Bemisia tabaci and two bacteria (Portiera aleyrodidarum and Hamiltonella defensa) cohoused in each host cell investigated whether the decay of Portiera metabolism genes is complemented by host and Hamiltonella genes, and compared the metabolic traits of the whitefly symbiosis with other sap-feeding insects (aphids, psyllids, and mealybugs). Parallel genomic and transcriptomic analysis revealed that the host genome contributes multiple metabolic reactions that complement or duplicate Portiera function, and that Hamiltonella may contribute multiple cofactors and one essential amino acid, lysine. Homologs of the Bemisia metabolism genes of insect origin have also been implicated in essential amino acid synthesis in other sap-feeding insect hosts, indicative of parallel coevolution of shared metabolic pathways across multiple symbioses. Further metabolism genes coded in the Bemisia genome are of bacterial origin, but phylogenetically distinct from Portiera, Hamiltonella and horizontally transferred genes identified in other sap-feeding insects. Overall, 75% of the metabolism genes of bacterial origin are functionally unique to one symbiosis, indicating that the evolutionary history of metabolic integration in these symbioses is strongly contingent on the pattern of horizontally acquired genes. Our analysis, further, shows that bacteria with genomic decay enable host acquisition of complex metabolic pathways by multiple independent horizontal gene transfers from exogenous bacteria. Specifically, each horizontally acquired gene can function with other genes in the pathway coded by the symbiont, while facilitating the decay of the symbiont gene coding the same reaction. © The Author(s) 2015. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

Quasi-biweekly oscillations of the South Asian monsoon and its co-evolution in the upper and lower troposphere

Science.gov (United States)

Ortega, Sebastián; Webster, Peter J.; Toma, Violeta; Chang, Hai-Ru

2017-11-01

The Upper Tropospheric Quasi-Biweekly Oscillation (UQBW) of the South Asian monsoon is studied using the potential vorticity field on the 370 K isentrope. The UQBW is shown to be a common occurrence in the upper troposphere during the monsoon, and its typical evolution is described. We suggest that the UQBW is a phenomenon of both the middle and tropical latitudes, owing its existence to the presence of the planetary-scale upper-tropospheric monsoon anticyclone. The UQBW is first identified as Rossby waves originating in the northern flank of the monsoon anticyclone. These Rossby waves break when reaching the Pacific Ocean, and their associated cyclonic PV anomalies move southward to the east of Asia and then westward across the Indian Ocean and Africa advected by the monsoon anticyclone. A strong correlation, or co-evolution, between the UQBW and quasi-biweekly oscillations in the lower troposphere (QBW) is also found. In particular, analysis of vertically-integrated horizontal moisture transport, 850 hPa geopotential, and outgoing long-wave radiation show that the UQBW is usually observed at the same time as, and co-evolves with, the lower tropospheric QBW over South Asia. We discuss the nature of the UQBW, and its possible physical link with the QBW.

A conceptual socio-hydrological model of the co-evolution of humans and water: case study of the Tarim River basin, western China

Science.gov (United States)

Liu, D.; Tian, F.; Lin, M.; Sivapalan, M.

2015-02-01

The complex interactions and feedbacks between humans and water are critically important issues but remain poorly understood in the newly proposed discipline of socio-hydrology (Sivapalan et al., 2012). An exploratory model with the appropriate level of simplification can be valuable for improving our understanding of the co-evolution and self-organization of socio-hydrological systems driven by interactions and feedbacks operating at different scales. In this study, a simplified conceptual socio-hydrological model based on logistic growth curves is developed for the Tarim River basin in western China and is used to illustrate the explanatory power of such a co-evolutionary model. The study area is the main stream of the Tarim River, which is divided into two modeling units. The socio-hydrological system is composed of four sub-systems, i.e., the hydrological, ecological, economic, and social sub-systems. In each modeling unit, the hydrological equation focusing on water balance is coupled to the other three evolutionary equations to represent the dynamics of the social sub-system (denoted by population), the economic sub-system (denoted by irrigated crop area ratio), and the ecological sub-system (denoted by natural vegetation cover), each of which is expressed in terms of a logistic growth curve. Four feedback loops are identified to represent the complex interactions among different sub-systems and different spatial units, of which two are inner loops occurring within each separate unit and the other two are outer loops linking the two modeling units. The feedback mechanisms are incorporated into the constitutive relations for model parameters, i.e., the colonization and mortality rates in the logistic growth curves that are jointly determined by the state variables of all sub-systems. The co-evolution of the Tarim socio-hydrological system is then analyzed with this conceptual model to gain insights into the overall system dynamics and its sensitivity to the

The plurality of values in sustainable agriculture models: diverse lock-in and coevolution patterns

Directory of Open Access Journals (Sweden)

Gael Plumecocq

2018-03-01

Full Text Available In Western economies, several agriculture models coexist. For instance, intensive agriculture organization, which has increased yields while causing major pollution and resource depletion, competes with alternative models, which tackle these sustainability issues and lead to lower yields. An agronomical typology of current agriculture models in Western societies is proposed that describes multiple sustainability issues through an agroecological perspective. However, in order to choose between these agroecological pathways, we must understand their social structure and the principles underlying them. Thus, our purpose is to characterize the institutional aspects of the alternative models using socioeconomic convention theory. We conducted a series of workshops with specialists in the natural sciences (agronomy, landscape ecology, and entomology and social sciences (economics and sociology to describe sustainable agriculture models. This characterization revealed the values underlying six different sustainable agriculture models, their forms of organization, and the institutions governing them. We discuss the implications of the coexistence of these six models in light of sustainable transition issues. From this coexistence perspective, transition (i refers to an intertwined process of legitimation and disqualification, and (ii means seeing pathways as the multiplicity and degree of interconnection between models. Therefore, we (i identified the elements in each model that legitimize its mode of organization, and (ii disqualified the elements that are incompatible with the principles underlying the model's practices. Moreover, we emphasize that multiple transition pathways are possible based on complex, complementary combinations of different models. This revealed the intricate processes of competition and complementarity involving these models. Finally, our study on the coexistence, interdependence, and coevolution of multiple agriculture models

Contrasting Patterns in Mammal–Bacteria Coevolution: Bartonella and Leptospira in Bats and Rodents

Science.gov (United States)

Lei, Bonnie R.; Olival, Kevin J.

2014-01-01

Background Emerging bacterial zoonoses in bats and rodents remain relatively understudied. We conduct the first comparative host–pathogen coevolutionary analyses of bacterial pathogens in these hosts, using Bartonella spp. and Leptospira spp. as a model. Methodology/Principal Findings We used published genetic data for 51 Bartonella genotypes from 24 bat species, 129 Bartonella from 38 rodents, and 26 Leptospira from 20 bats. We generated maximum likelihood and Bayesian phylogenies for hosts and bacteria, and tested for coevoutionary congruence using programs ParaFit, PACO, and Jane. Bartonella spp. and their bat hosts had a significant coevolutionary fit (ParaFitGlobal = 1.9703, P≤0.001; m2 global value = 7.3320, P≤0.0001). Bartonella spp. and rodent hosts also indicated strong overall patterns of cospeciation (ParaFitGlobal = 102.4409, P≤0.001; m2 global value = 86.532, P≤0.0001). In contrast, we were unable to reject independence of speciation events in Leptospira and bats (ParaFitGlobal = 0.0042, P = 0.84; m2 global value = 4.6310, P = 0.5629). Separate analyses of New World and Old World data subsets yielded results congruent with analysis from entire datasets. We also conducted event-based cophylogeny analyses to reconstruct likely evolutionary histories for each group of pathogens and hosts. Leptospira and bats had the greatest number of host switches per parasite (0.731), while Bartonella and rodents had the fewest (0.264). Conclusions/Significance In both bat and rodent hosts, Bartonella exhibits significant coevolution with minimal host switching, while Leptospira in bats lacks evolutionary congruence with its host and has high number of host switches. Reasons underlying these variable coevolutionary patterns in host range are likely due to differences in disease-specific transmission and host ecology. Understanding the coevolutionary patterns and frequency of host-switching events between bacterial pathogens and

Modelling the co-evolution of indirect genetic effects and inherited variability.

Science.gov (United States)

Marjanovic, Jovana; Mulder, Han A; Rönnegård, Lars; Bijma, Piter

2018-03-28

When individuals interact, their phenotypes may be affected not only by their own genes but also by genes in their social partners. This phenomenon is known as Indirect Genetic Effects (IGEs). In aquaculture species and some plants, however, competition not only affects trait levels of individuals, but also inflates variability of trait values among individuals. In the field of quantitative genetics, the variability of trait values has been studied as a quantitative trait in itself, and is often referred to as inherited variability. Such studies, however, consider only the genetic effect of the focal individual on trait variability and do not make a connection to competition. Although the observed phenotypic relationship between competition and variability suggests an underlying genetic relationship, the current quantitative genetic models of IGE and inherited variability do not allow for such a relationship. The lack of quantitative genetic models that connect IGEs to inherited variability limits our understanding of the potential of variability to respond to selection, both in nature and agriculture. Models of trait levels, for example, show that IGEs may considerably change heritable variation in trait values. Currently, we lack the tools to investigate whether this result extends to variability of trait values. Here we present a model that integrates IGEs and inherited variability. In this model, the target phenotype, say growth rate, is a function of the genetic and environmental effects of the focal individual and of the difference in trait value between the social partner and the focal individual, multiplied by a regression coefficient. The regression coefficient is a genetic trait, which is a measure of cooperation; a negative value indicates competition, a positive value cooperation, and an increasing value due to selection indicates the evolution of cooperation. In contrast to the existing quantitative genetic models, our model allows for co-evolution of

Mesozoic fossils (>145 Mya suggest the antiquity of the subgenera of Daphnia and their coevolution with chaoborid predators

Directory of Open Access Journals (Sweden)

Taylor Derek J

2011-05-01

Full Text Available Abstract Background The timescale of the origins of Daphnia O. F. Mueller (Crustacea: Cladocera remains controversial. The origin of the two main subgenera has been associated with the breakup of the supercontinent Pangaea. This vicariance hypothesis is supported by reciprocal monophyly, present day associations with the former Gondwanaland and Laurasia regions, and mitochondrial DNA divergence estimates. However, previous multilocus nuclear DNA sequence divergence estimates at Daphnia. Results We describe new fossils of ephippia from the Khotont site in Mongolia associated with the Jurassic-Cretaceous boundary (about 145 MYA that are morphologically similar to several modern genera of the family Daphniidae, including the two major subgenera of Daphnia, i.e., Daphnia s. str. and Ctenodaphnia. The daphniid fossils co-occurred with fossils of the predaceous phantom midge (Chaoboridae. Conclusions Our findings indicate that the main subgenera of Daphnia are likely much older than previously known from fossils (at least 100 MY older or from nuclear DNA estimates of divergence. The results showing co-occurrence of the main subgenera far from the presumed Laurasia/Gondwanaland dispersal barrier shortly after formation suggests that vicariance from the breakup of Pangaea is an unlikely explanation for the origin of the main subgenera. The fossil impressions also reveal that the coevolution of a dipteran predator (Chaoboridae with the subgenus Daphnia is much older than previously known -- since the Mesozoic.

Distinct co-evolution patterns of genes associated to DNA polymerase III DnaE and PolC

Directory of Open Access Journals (Sweden)

Engelen Stefan

2012-02-01

Full Text Available Abstract Background Bacterial genomes displaying a strong bias between the leading and the lagging strand of DNA replication encode two DNA polymerases III, DnaE and PolC, rather than a single one. Replication is a highly unsymmetrical process, and the presence of two polymerases is therefore not unexpected. Using comparative genomics, we explored whether other processes have evolved in parallel with each polymerase. Results Extending previous in silico heuristics for the analysis of gene co-evolution, we analyzed the function of genes clustering with dnaE and polC. Clusters were highly informative. DnaE co-evolves with the ribosome, the transcription machinery, the core of intermediary metabolism enzymes. It is also connected to the energy-saving enzyme necessary for RNA degradation, polynucleotide phosphorylase. Most of the proteins of this co-evolving set belong to the persistent set in bacterial proteomes, that is fairly ubiquitously distributed. In contrast, PolC co-evolves with RNA degradation enzymes that are present only in the A+T-rich Firmicutes clade, suggesting at least two origins for the degradosome. Conclusion DNA replication involves two machineries, DnaE and PolC. DnaE co-evolves with the core functions of bacterial life. In contrast PolC co-evolves with a set of RNA degradation enzymes that does not derive from the degradosome identified in gamma-Proteobacteria. This suggests that at least two independent RNA degradation pathways existed in the progenote community at the end of the RNA genome world.

Microbes, Mineral Evolution, and the Rise of Microcontinents-Origin and Coevolution of Life with Early Earth.

Science.gov (United States)

Grosch, Eugene G; Hazen, Robert M

2015-10-01

Earth is the most mineralogically diverse planet in our solar system, the direct consequence of a coevolving geosphere and biosphere. We consider the possibility that a microbial biosphere originated and thrived in the early Hadean-Archean Earth subseafloor environment, with fundamental consequences for the complex evolution and habitability of our planet. In this hypothesis paper, we explore possible venues for the origin of life and the direct consequences of microbially mediated, low-temperature hydrothermal alteration of the early oceanic lithosphere. We hypothesize that subsurface fluid-rock-microbe interactions resulted in more efficient hydration of the early oceanic crust, which in turn promoted bulk melting to produce the first evolved fragments of felsic crust. These evolved magmas most likely included sialic or tonalitic sheets, felsic volcaniclastics, and minor rhyolitic intrusions emplaced in an Iceland-type extensional setting as the earliest microcontinents. With the further development of proto-tectonic processes, these buoyant felsic crustal fragments formed the nucleus of intra-oceanic tonalite-trondhjemite-granitoid (TTG) island arcs. Thus microbes, by facilitating extensive hydrothermal alteration of the earliest oceanic crust through bioalteration, promoted mineral diversification and may have been early architects of surface environments and microcontinents on young Earth. We explore how the possible onset of subseafloor fluid-rock-microbe interactions on early Earth accelerated metavolcanic clay mineral formation, crustal melting, and subsequent metamorphic mineral evolution. We also consider environmental factors supporting this earliest step in geosphere-biosphere coevolution and the implications for habitability and mineral evolution on other rocky planets, such as Mars.

Evolution of resistance to a multiple-herbivore community: genetic correlations, diffuse coevolution, and constraints on the plant's response to selection.

Science.gov (United States)

Wise, Michael J; Rausher, Mark D

2013-06-01

Although plants are generally attacked by a community of several species of herbivores, relatively little is known about the strength of natural selection for resistance in multiple-herbivore communities-particularly how the strength of selection differs among herbivores that feed on different plant organs or how strongly genetic correlations in resistance affect the evolutionary responses of the plant. Here, we report on a field study measuring natural selection for resistance in a diverse community of herbivores of Solanum carolinense. Using linear phenotypic-selection analyses, we found that directional selection acted to increase resistance to seven species. Selection was strongest to increase resistance to fruit feeders, followed by flower feeders, then leaf feeders. Selection favored a decrease in resistance to a stem borer. Bootstrapping analyses showed that the plant population contained significant genetic variation for each of 14 measured resistance traits and significant covariances in one-third of the pairwise combinations of resistance traits. These genetic covariances reduced the plant's overall predicted evolutionary response for resistance against the herbivore community by about 60%. Diffuse (co)evolution was widespread in this community, and the diffuse interactions had an overwhelmingly constraining (rather than facilitative) effect on the plant's evolution of resistance. © 2013 The Author(s). Evolution © 2013 The Society for the Study of Evolution.

Mesozoic fossils (>145 Mya) suggest the antiquity of the subgenera of Daphnia and their coevolution with chaoborid predators.

Science.gov (United States)

Kotov, Alexey A; Taylor, Derek J

2011-05-19

The timescale of the origins of Daphnia O. F. Mueller (Crustacea: Cladocera) remains controversial. The origin of the two main subgenera has been associated with the breakup of the supercontinent Pangaea. This vicariance hypothesis is supported by reciprocal monophyly, present day associations with the former Gondwanaland and Laurasia regions, and mitochondrial DNA divergence estimates. However, previous multilocus nuclear DNA sequence divergence estimates at Pangaea. We examined new and existing cladoceran fossils from a Mesozoic Mongolian site, in hopes of gaining insights into the timescale of the evolution of Daphnia. We describe new fossils of ephippia from the Khotont site in Mongolia associated with the Jurassic-Cretaceous boundary (about 145 MYA) that are morphologically similar to several modern genera of the family Daphniidae, including the two major subgenera of Daphnia, i.e., Daphnia s. str. and Ctenodaphnia. The daphniid fossils co-occurred with fossils of the predaceous phantom midge (Chaoboridae). Our findings indicate that the main subgenera of Daphnia are likely much older than previously known from fossils (at least 100 MY older) or from nuclear DNA estimates of divergence. The results showing co-occurrence of the main subgenera far from the presumed Laurasia/Gondwanaland dispersal barrier shortly after formation suggests that vicariance from the breakup of Pangaea is an unlikely explanation for the origin of the main subgenera. The fossil impressions also reveal that the coevolution of a dipteran predator (Chaoboridae) with the subgenus Daphnia is much older than previously known -- since the Mesozoic.

Conflict RNA modification, host-parasite co-evolution, and the origins of DNA and DNA-binding proteins1.

Science.gov (United States)

McLaughlin, Paul J; Keegan, Liam P

2014-08-01

Nearly 150 different enzymatically modified forms of the four canonical residues in RNA have been identified. For instance, enzymes of the ADAR (adenosine deaminase acting on RNA) family convert adenosine residues into inosine in cellular dsRNAs. Recent findings show that DNA endonuclease V enzymes have undergone an evolutionary transition from cleaving 3' to deoxyinosine in DNA and ssDNA to cleaving 3' to inosine in dsRNA and ssRNA in humans. Recent work on dsRNA-binding domains of ADARs and other proteins also shows that a degree of sequence specificity is achieved by direct readout in the minor groove. However, the level of sequence specificity observed is much less than that of DNA major groove-binding helix-turn-helix proteins. We suggest that the evolution of DNA-binding proteins following the RNA to DNA genome transition represents the major advantage that DNA genomes have over RNA genomes. We propose that a hypothetical RNA modification, a RRAR (ribose reductase acting on genomic dsRNA) produced the first stretches of DNA in RNA genomes. We discuss why this is the most satisfactory explanation for the origin of DNA. The evolution of this RNA modification and later steps to DNA genomes are likely to have been driven by cellular genome co-evolution with viruses and intragenomic parasites. RNA modifications continue to be involved in host-virus conflicts; in vertebrates, edited cellular dsRNAs with inosine-uracil base pairs appear to be recognized as self RNA and to suppress activation of innate immune sensors that detect viral dsRNA.

Coevolution and hierarchical interactions of Tomato mosaic virus and the resistance gene Tm-1.

Directory of Open Access Journals (Sweden)

Kazuhiro Ishibashi

Full Text Available During antagonistic coevolution between viruses and their hosts, viruses have a major advantage by evolving more rapidly. Nevertheless, viruses and their hosts coexist and have coevolved, although the processes remain largely unknown. We previously identified Tm-1 that confers resistance to Tomato mosaic virus (ToMV, and revealed that it encodes a protein that binds ToMV replication proteins and inhibits RNA replication. Tm-1 was introgressed from a wild tomato species Solanum habrochaites into the cultivated tomato species Solanum lycopersicum. In this study, we analyzed Tm-1 alleles in S. habrochaites. Although most part of this gene was under purifying selection, a cluster of nonsynonymous substitutions in a small region important for inhibitory activity was identified, suggesting that the region is under positive selection. We then examined the resistance of S. habrochaites plants to ToMV. Approximately 60% of 149 individuals from 24 accessions were resistant to ToMV, while the others accumulated detectable levels of coat protein after inoculation. Unexpectedly, many S. habrochaites plants were observed in which even multiplication of the Tm-1-resistance-breaking ToMV mutant LT1 was inhibited. An amino acid change in the positively selected region of the Tm-1 protein was responsible for the inhibition of LT1 multiplication. This amino acid change allowed Tm-1 to bind LT1 replication proteins without losing the ability to bind replication proteins of wild-type ToMV. The antiviral spectra and biochemical properties suggest that Tm-1 has evolved by changing the strengths of its inhibitory activity rather than diversifying the recognition spectra. In the LT1-resistant S. habrochaites plants inoculated with LT1, mutant viruses emerged whose multiplication was not inhibited by the Tm-1 allele that confers resistance to LT1. However, the resistance-breaking mutants were less competitive than the parental strains in the absence of Tm-1. Based on

Gene loss, adaptive evolution and the co-evolution of plumage coloration genes with opsins in birds.

Science.gov (United States)

Borges, Rui; Khan, Imran; Johnson, Warren E; Gilbert, M Thomas P; Zhang, Guojie; Jarvis, Erich D; O'Brien, Stephen J; Antunes, Agostinho

2015-10-06

The wide range of complex photic systems observed in birds exemplifies one of their key evolutionary adaptions, a well-developed visual system. However, genomic approaches have yet to be used to disentangle the evolutionary mechanisms that govern evolution of avian visual systems. We performed comparative genomic analyses across 48 avian genomes that span extant bird phylogenetic diversity to assess evolutionary changes in the 17 representatives of the opsin gene family and five plumage coloration genes. Our analyses suggest modern birds have maintained a repertoire of up to 15 opsins. Synteny analyses indicate that PARA and PARIE pineal opsins were lost, probably in conjunction with the degeneration of the parietal organ. Eleven of the 15 avian opsins evolved in a non-neutral pattern, confirming the adaptive importance of vision in birds. Visual conopsins sw1, sw2 and lw evolved under negative selection, while the dim-light RH1 photopigment diversified. The evolutionary patterns of sw1 and of violet/ultraviolet sensitivity in birds suggest that avian ancestors had violet-sensitive vision. Additionally, we demonstrate an adaptive association between the RH2 opsin and the MC1R plumage color gene, suggesting that plumage coloration has been photic mediated. At the intra-avian level we observed some unique adaptive patterns. For example, barn owl showed early signs of pseudogenization in RH2, perhaps in response to nocturnal behavior, and penguins had amino acid deletions in RH2 sites responsible for the red shift and retinal binding. These patterns in the barn owl and penguins were convergent with adaptive strategies in nocturnal and aquatic mammals, respectively. We conclude that birds have evolved diverse opsin adaptations through gene loss, adaptive selection and coevolution with plumage coloration, and that differentiated selective patterns at the species level suggest novel photic pressures to influence evolutionary patterns of more-recent lineages.

The co-evolution of microstructure features in self-ion irradiated HT9 at very high damage levels

Energy Technology Data Exchange (ETDEWEB)

Getto, E., E-mail: getto@usna.edu [Department of Mechanical Engineering, United States Naval Academy, Annapolis, MD, 21402 (United States); Department of Nuclear Engineering and Radiological Sciences, University of Michigan, Ann Arbor, MI, 48109 (United States); Vancoevering, G.; Was, G.S. [Department of Nuclear Engineering and Radiological Sciences, University of Michigan, Ann Arbor, MI, 48109 (United States)

2017-02-15

Understanding the void swelling and phase evolution of reactor structural materials at very high damage levels is essential to maintaining safety and longevity of components in Gen IV fast reactors. A combination of ion irradiation and modeling was utilized to understand the microstructure evolution of ferritic-martensitic alloy HT9 at high dpa. Self-ion irradiation experiments were performed on alloy HT9 to determine the co-evolution of voids, dislocations and precipitates up to 650 dpa at 460 °C. Modeling of microstructure evolution was conducted using the modified Radiation Induced Microstructure Evolution (RIME) model, which utilizes a mean field rate theory approach with grouped cluster dynamics. Irradiations were performed with 5 MeV raster-scanned Fe{sup 2+} ions on samples pre-implanted with 10 atom parts per million He. The swelling, dislocation and precipitate evolution at very high dpa was determined using Analytical Electron Microscopy in Scanning Transmission Electron Microscopy (STEM) mode. Experimental results were then interpreted using the RIME model. A microstructure consisting only of dislocations and voids is insufficient to account for the swelling evolution observed experimentally at high damage levels in a complicated microstructure such as irradiated alloy HT9. G phase was found to have a minimal effect on either void or dislocation evolution. M{sub 2}X played two roles; a variable biased sink for defects, and as a vehicle for removal of carbon from solution, thus promoting void growth. When accounting for all microstructure interactions, swelling at high damage levels is a dynamic process that continues to respond to other changes in the microstructure as long as they occur.

Potential arms race in the coevolution of primates and angiosperms: brazzein sweet proteins and gorilla taste receptors.

Science.gov (United States)

Guevara, Elaine E; Veilleux, Carrie C; Saltonstall, Kristin; Caccone, Adalgisa; Mundy, Nicholas I; Bradley, Brenda J

2016-09-01

We explored whether variation in the sweet taste receptor protein T1R3 in primates could contribute to differences in sweet taste repertoire among species, potentially reflecting coevolution with local plants. Specifically, we examined which primates are likely to be sweet "tasters" of brazzein, a protein found in the fruit of the African plant Pentadiplandra brazzeana that tastes intensely sweet to humans, but provides little energy. Sweet proteins like brazzein are thought to mimic the taste of sugars to entice seed dispersers. We examined the evolution of T1R3 and assessed whether primates are likely "deceived" by such biochemical mimicry. Using published and new sequence data for TAS1R3, we characterized 57 primates and other mammals at the two amino acid sites necessary to taste brazzein to determine which species are tasters. We further used dN/dS-based methods to look for statistical evidence of accelerated evolution in this protein across primate lineages. The taster genotype is shared across most catarrhines, suggesting that most African primates can be "tricked" into eating and dispersing P. brazzeana's seeds for little caloric gain. Western gorillas (Gorilla gorilla), however, exhibit derived mutations at the two brazzein-critical positions, and although fruit is a substantial portion of the western gorilla diet, they have not been observed to eat P. brazzeana. Our analyses of protein evolution found no signature of positive selection on TAS1R3 along the gorilla lineage. We propose that the gorilla-specific mutations at the TAS1R3 locus encoding T1R3 could be a counter-adaptation to the false sweet signal of brazzein. © 2016 Wiley Periodicals, Inc.

Should Law Keep Pace with Society? Relative Update Rates Determine the Co-Evolution of Institutional Punishment and Citizen Contributions to Public Goods

Directory of Open Access Journals (Sweden)

Daria Roithmayr

2015-06-01

Full Text Available Until recently, theorists considering the evolution of human cooperation have paid little attention to institutional punishment, a defining feature of large-scale human societies. Compared to individually-administered punishment, institutional punishment offers a unique potential advantage: the ability to control how quickly legal rules of punishment evolve relative to social behavior that legal punishment regulates. However, at what rate should legal rules evolve relative to society to maximize compliance? We investigate this question by modeling the co-evolution of law and cooperation in a public goods game with centralized punishment. We vary the rate at which States update their legal punishment strategy relative to Citizens’ updating of their contribution strategy and observe the effect on Citizen cooperation. We find that when States have unlimited resources, slower State updating lead to more Citizen cooperation: by updating more slowly, States force Citizens to adapt to the legal punishment rules. When States depend on Citizens to finance their punishment activities, however, we find evidence of a ‘Goldilocks’ effect: optimal compliance is achieved when legal rules evolve at a critical evolutionary rate that is slow enough to force citizens to adapt, but fast enough to enable states to quickly respond to outbreaks of citizen lawlessness.

Discovering local patterns of co - evolution: computational aspects and biological examples

Directory of Open Access Journals (Sweden)

Tuller Tamir

2010-01-01

Full Text Available Abstract Background Co-evolution is the process in which two (or more sets of orthologs exhibit a similar or correlative pattern of evolution. Co-evolution is a powerful way to learn about the functional interdependencies between sets of genes and cellular functions and to predict physical interactions. More generally, it can be used for answering fundamental questions about the evolution of biological systems. Orthologs that exhibit a strong signal of co-evolution in a certain part of the evolutionary tree may show a mild signal of co-evolution in other branches of the tree. The major reasons for this phenomenon are noise in the biological input, genes that gain or lose functions, and the fact that some measures of co-evolution relate to rare events such as positive selection. Previous publications in the field dealt with the problem of finding sets of genes that co-evolved along an entire underlying phylogenetic tree, without considering the fact that often co-evolution is local. Results In this work, we describe a new set of biological problems that are related to finding patterns of local co-evolution. We discuss their computational complexity and design algorithms for solving them. These algorithms outperform other bi-clustering methods as they are designed specifically for solving the set of problems mentioned above. We use our approach to trace the co-evolution of fungal, eukaryotic, and mammalian genes at high resolution across the different parts of the corresponding phylogenetic trees. Specifically, we discover regions in the fungi tree that are enriched with positive evolution. We show that metabolic genes exhibit a remarkable level of co-evolution and different patterns of co-evolution in various biological datasets. In addition, we find that protein complexes that are related to gene expression exhibit non-homogenous levels of co-evolution across different parts of the fungi evolutionary line. In the case of mammalian evolution

The E-MOSAICS project: simulating the formation and co-evolution of galaxies and their star cluster populations

Science.gov (United States)

Pfeffer, Joel; Kruijssen, J. M. Diederik; Crain, Robert A.; Bastian, Nate

2018-04-01

We introduce the MOdelling Star cluster population Assembly In Cosmological Simulations within EAGLE (E-MOSAICS) project. E-MOSAICS incorporates models describing the formation, evolution, and disruption of star clusters into the EAGLE galaxy formation simulations, enabling the examination of the co-evolution of star clusters and their host galaxies in a fully cosmological context. A fraction of the star formation rate of dense gas is assumed to yield a cluster population; this fraction and the population's initial properties are governed by the physical properties of the natal gas. The subsequent evolution and disruption of the entire cluster population are followed accounting for two-body relaxation, stellar evolution, and gravitational shocks induced by the local tidal field. This introductory paper presents a detailed description of the model and initial results from a suite of 10 simulations of ˜L⋆ galaxies with disc-like morphologies at z = 0. The simulations broadly reproduce key observed characteristics of young star clusters and globular clusters (GCs), without invoking separate formation mechanisms for each population. The simulated GCs are the surviving population of massive clusters formed at early epochs (z ≳ 1-2), when the characteristic pressures and surface densities of star-forming gas were significantly higher than observed in local galaxies. We examine the influence of the star formation and assembly histories of galaxies on their cluster populations, finding that (at similar present-day mass) earlier-forming galaxies foster a more massive and disruption-resilient cluster population, while galaxies with late mergers are capable of forming massive clusters even at late cosmic epochs. We find that the phenomenological treatment of interstellar gas in EAGLE precludes the accurate modelling of cluster disruption in low-density environments, but infer that simulations incorporating an explicitly modelled cold interstellar gas phase will overcome

21CMMC with a 3D light-cone: the impact of the co-evolution approximation on the astrophysics of reionisation and cosmic dawn.

Science.gov (United States)

Greig, Bradley; Mesinger, Andrei

2018-03-01

We extend 21CMMC, a Monte Carlo Markov Chain sampler of 3D reionisation simulations, to perform parameter estimation directly on 3D light-cones of the cosmic 21cm signal. This brings theoretical analysis closer to the tomographic 21-cm observations achievable with next generation interferometers like HERA and the SKA. Parameter recovery can therefore account for modes which evolve with redshift/frequency. Additionally, simulated data can be more easily corrupted to resemble real data. Using the light-cone version of 21CMMC, we quantify the biases in the recovered astrophysical parameters if we use the 21cm power spectrum from the co-evolution approximation to fit a 3D light-cone mock observation. While ignoring the light-cone effect under most assumptions will not significantly bias the recovered astrophysical parameters, it can lead to an underestimation of the associated uncertainty. However significant biases (˜few - 10 σ) can occur if the 21cm signal evolves rapidly (i.e. the epochs of reionisation and heating overlap significantly) and: (i) foreground removal is very efficient, allowing large physical scales (k {≲} 0.1 Mpc-1) to be used in the analysis or (ii) theoretical modelling is accurate to within ˜10 per cent in the power spectrum amplitude.

Epigenomic Co-localization and Co-evolution Reveal a Key Role for 5hmC as a Communication Hub in the Chromatin Network of ESCs

Directory of Open Access Journals (Sweden)

David Juan

2016-02-01

Full Text Available Summary: Epigenetic communication through histone and cytosine modifications is essential for gene regulation and cell identity. Here, we propose a framework that is based on a chromatin communication model to get insight on the function of epigenetic modifications in ESCs. The epigenetic communication network was inferred from genome-wide location data plus extensive manual annotation. Notably, we found that 5-hydroxymethylcytosine (5hmC is the most-influential hub of this network, connecting DNA demethylation to nucleosome remodeling complexes and to key transcription factors of pluripotency. Moreover, an evolutionary analysis revealed a central role of 5hmC in the co-evolution of chromatin-related proteins. Further analysis of regions where 5hmC co-localizes with specific interactors shows that each interaction points to chromatin remodeling, stemness, differentiation, or metabolism. Our results highlight the importance of cytosine modifications in the epigenetic communication of ESCs. : 5-hydroxymethylcytosine (5hmC plays a key role in the epigenomic communication network of embryonic stem cells. Juan et al. build a communication network based in co-localization of epigenomic data and literature. The analysis of the network and its components reveals that proteins reading and editing 5hmC co-evolve and serve as links between diverse molecular processes.

Host adaptation of Chlamydia pecorum towards low virulence evident in co-evolution of the ompA, incA, and ORF663 Loci.

Science.gov (United States)

Mohamad, Khalil Yousef; Kaltenboeck, Bernhard; Rahman, Kh Shamsur; Magnino, Simone; Sachse, Konrad; Rodolakis, Annie

2014-01-01

Chlamydia (C.) pecorum, an obligate intracellular bacterium, may cause severe diseases in ruminants, swine and koalas, although asymptomatic infections are the norm. Recently, we identified genetic polymorphisms in the ompA, incA and ORF663 genes that potentially differentiate between high-virulence C. pecorum isolates from diseased animals and low-virulence isolates from asymptomatic animals. Here, we expand these findings by including additional ruminant, swine, and koala strains. Coding tandem repeats (CTRs) at the incA locus encoded a variable number of repeats of APA or AGA amino acid motifs. Addition of any non-APA/AGA repeat motif, such as APEVPA, APAVPA, APE, or APAPE, associated with low virulence (PincA CTRs (P = 0.0028). In ORF663, high numbers of 15-mer CTRs correlated with low virulence (P = 0.0001). Correction for ompA phylogram position in ORF663 and incA abolished the correlation between genetic changes and virulence, demonstrating co-evolution of ompA, incA, and ORF663 towards low virulence. Pairwise divergence of ompA, incA, and ORF663 among isolates from healthy animals was significantly higher than among strains isolated from diseased animals (P≤10-5), confirming the longer evolutionary path traversed by low-virulence strains. All three markers combined identified 43 unique strains and 4 pairs of identical strains among all 57 isolates tested, demonstrating the suitability of these markers for epidemiological investigations.

Germ warfare in a microbial mat community: CRISPRs provide insights into the co-evolution of host and viral genomes.

Directory of Open Access Journals (Sweden)

John F Heidelberg

Full Text Available CRISPR arrays and associated cas genes are widespread in bacteria and archaea and confer acquired resistance to viruses. To examine viral immunity in the context of naturally evolving microbial populations we analyzed genomic data from two thermophilic Synechococcus isolates (Syn OS-A and Syn OS-B' as well as a prokaryotic metagenome and viral metagenome derived from microbial mats in hotsprings at Yellowstone National Park. Two distinct CRISPR types, distinguished by the repeat sequence, are found in both the Syn OS-A and Syn OS-B' genomes. The genome of Syn OS-A contains a third CRISPR type with a distinct repeat sequence, which is not found in Syn OS-B', but appears to be shared with other microorganisms that inhabit the mat. The CRISPR repeats identified in the microbial metagenome are highly conserved, while the spacer sequences (hereafter referred to as "viritopes" to emphasize their critical role in viral immunity were mostly unique and had no high identity matches when searched against GenBank. Searching the viritopes against the viral metagenome, however, yielded several matches with high similarity some of which were within a gene identified as a likely viral lysozyme/lysin protein. Analysis of viral metagenome sequences corresponding to this lysozyme/lysin protein revealed several mutations all of which translate into silent or conservative mutations which are unlikely to affect protein function, but may help the virus evade the host CRISPR resistance mechanism. These results demonstrate the varied challenges presented by a natural virus population, and support the notion that the CRISPR/viritope system must be able to adapt quickly to provide host immunity. The ability of metagenomics to track population-level variation in viritope sequences allows for a culture-independent method for evaluating the fast co-evolution of host and viral genomes and its consequence on the structuring of complex microbial communities.

Climate-vegetation-soil interactions and long-term hydrologic partitioning: signatures of catchment co-evolution

Directory of Open Access Journals (Sweden)

P. A. Troch

2013-06-01

subsurface storage release time scales produce significantly more E/P. Vegetation in these catchments have longer access to this additional groundwater source and thus are less prone to water stress. Further analysis reveals that climates that give rise to more (less E/P are associated with catchments that have vegetation with less (more efficient water use parameters. In particular, the climates with tendency to produce more E/P have catchments that have lower % root fraction and less light use efficiency. Our results suggest that their exists strong interactions between climate, vegetation and soil properties that lead to specific hydrologic partitioning at the catchment scale. This co-evolution of catchment vegetation and soils with climate needs to be further explored to improve our capabilities to predict hydrologic partitioning in ungauged basins.

Co-Evolution.

Science.gov (United States)

McGhee, Robert

2002-01-01

Discusses the role of techniques of DNA analysis in assessing the genetic relationships between various species. Focuses on wolf-dog evolution using DNA evidence and historical data about human/wolf-dog relationships. (DDR)

The Co-evolution of Bullying Perpetration, Homophobic Teasing, and a School Friendship Network.

Science.gov (United States)

Merrin, Gabriel J; Haye, Kayla de la; Espelage, Dorothy L; Ewing, Brett; Tucker, Joan S; Hoover, Matthew; Green, Harold D

2018-03-01

Bullying and homophobic teasing behaviors affect the lives of many school aged children, often co-occur, and tend to peak in middle school. While bullying and homophobic teasing behaviors are known to be peer group phenomena, studies typically examine the associations at the individual or school levels. An examination of these behaviors at the peer group level can aid in our understanding of the formation and maintenance of peer groups that engage in these forms of aggressive behavior (selection), and the extent to which friends and the peer group impact individual rates of these aggressive behaviors (influence). In this longitudinal study, we assess the co-evolution of friendship networks, bullying perpetration, and homophobic teasing among middle school students (n = 190) using a Stochastic Actor-Based Model (SABM) for longitudinal networks. Data were collected from 6-8th-grade students (Baseline age 12-15; 53% Female; 47% Male) across three waves of data. The sample was diverse with 58% African American, 31% White, and 11% Hispanic. Since bullying and homophobic teasing behaviors are related yet distinct forms of peer aggression, to capture the unique and combined effects of these behaviors we ran models separately and then together in a competing model. Results indicated that on average individuals with higher rates of bullying perpetration and homophobic teasing were associated with becoming increasingly popular as a friend. However, the effects were not linear, and individuals with the highest rates of bullying perpetration and homophobic teasing were less likely to receive friendship nominations. There was no evidence that bullying perpetration or homophobic teasing were associated with the number of friendship nominations made. Further, there was a preference for individuals to form or maintain friendships with peers who engaged in similar rates of homophobic name-calling; however, this effect was not found for bullying perpetration. Additionally

The co-evolution of microstructure features in self-ion irradiated HT9 at very high damage levels

Science.gov (United States)

Getto, Elizabeth Margaret

The objective of this study was to understand the co-evolution of microstructure features in self-ion irradiated HT9 at very high damage levels. HT9 (heat 84425) was pre-implanted with 10 atom parts per million helium and then irradiated with 5 MeV Fe++ in the temperature range of 440-480°C to 188 dpa. A damage dependence study from 75 to 650 dpa was performed at the peak swelling temperature of 460°C. The swelling, dislocation and precipitate evolution was determined using Analytic Electron Microscopes in both Conventional Transmission electron microscopy (CTEM) and Scanning Transmission Electron Microscopy (STEM) modes. Void swelling reached a nominally linear rate of 0.03%/dpa from 188 to 650 dpa at 460°C. G phase precipitates were observed by 75 dpa and grew linearly up to 650 dpa. M 2X was observed by 250 dpa and peaked in volume fraction at 450 dpa. Dislocation loop evolution was observed up to 650 dpa including a step change in diameter between 375 and 450 dpa; which correlated with nucleation and growth of M2X. The experimental results were interpreted using a rate theory model, the Radiation Induced Microstructure Evolution (RIME), in the damage range from 188 to 650 dpa. A simple system of voids and dislocations was modeled in which the dislocations measured from experiment were used as input, or the dislocations were allowed to evolve dynamically, resulting in swelling that was overestimated by 63% relative to that observed experimentally. G phase had limited effect on the void or dislocation behavior. The behavior of M2X within the microstructure was characterized as a direct effect as a coherent sink, and as an indirect effect in consuming carbon from the matrix, which had the largest impact on both void and dislocation behavior. A slowly monotonically increasing swelling rate was observed both experimentally and computationally, with swelling rates of ˜0.025%/dpa and ˜0.036%/dpa before and after 450 dpa. The agreement in void behavior between

Connecting functional and statistical definitions of genotype by genotype interactions in coevolutionary studies

Directory of Open Access Journals (Sweden)

Katy Denise Heath

2014-04-01

Full Text Available Predicting how species interactions evolve requires that we understand the mechanistic basis of coevolution, and thus the functional genotype-by-genotype interactions (G × G that drive reciprocal natural selection. Theory on host-parasite coevolution provides testable hypotheses for empiricists, but depends upon models of functional G × G that remain loosely tethered to the molecular details of any particular system. In practice, reciprocal cross-infection studies are often used to partition the variation in infection or fitness in a population that is attributable to G × G (statistical G × G. Here we use simulations to demonstrate that within-population statistical G × G likely tells us little about the existence of coevolution, its strength, or the genetic basis of functional G × G. Combined with studies of multiple populations or points in time, mapping and molecular techniques can bridge the gap between natural variation and mechanistic models of coevolution, while model-based statistics can formally confront coevolutionary models with cross-infection data. Together these approaches provide a robust framework for inferring the infection genetics underlying statistical G × G, helping unravel the genetic basis of coevolution.

Coordinated rates of evolution between interacting plastid and nuclear genes in Geraniaceae.

Science.gov (United States)

Zhang, Jin; Ruhlman, Tracey A; Sabir, Jamal; Blazier, J Chris; Jansen, Robert K

2015-03-01

Although gene coevolution has been widely observed within individuals and between different organisms, rarely has this phenomenon been investigated within a phylogenetic framework. The Geraniaceae is an attractive system in which to study plastid-nuclear genome coevolution due to the highly elevated evolutionary rates in plastid genomes. In plants, the plastid-encoded RNA polymerase (PEP) is a protein complex composed of subunits encoded by both plastid (rpoA, rpoB, rpoC1, and rpoC2) and nuclear genes (sig1-6). We used transcriptome and genomic data for 27 species of Geraniales in a systematic evaluation of coevolution between genes encoding subunits of the PEP holoenzyme. We detected strong correlations of dN (nonsynonymous substitutions) but not dS (synonymous substitutions) within rpoB/sig1 and rpoC2/sig2, but not for other plastid/nuclear gene pairs, and identified the correlation of dN/dS ratio between rpoB/C1/C2 and sig1/5/6, rpoC1/C2 and sig2, and rpoB/C2 and sig3 genes. Correlated rates between interacting plastid and nuclear sequences across the Geraniales could result from plastid-nuclear genome coevolution. Analyses of coevolved amino acid positions suggest that structurally mediated coevolution is not the major driver of plastid-nuclear coevolution. The detection of strong correlation of evolutionary rates between SIG and RNAP genes suggests a plausible explanation for plastome-genome incompatibility in Geraniaceae. © 2015 American Society of Plant Biologists. All rights reserved.

Global Operations Coevolution

DEFF Research Database (Denmark)

Slepniov, Dmitrij; Wæhrens, Brian Vejrum; Gubi, Ebbe

2013-01-01

Companies are actively seeking competitive advantage through their choice of location and ownership of operations. The purpose of this chapter is to uncover hidden effects of this development and propose how companies can respond to them. The chapter draws on a case study of a Danish industrial e...... of analysis and involving temporal adaptations. In terms of managerial implications, the study provides managers with lessons for designing a robust system of globally dispersed operations.......Companies are actively seeking competitive advantage through their choice of location and ownership of operations. The purpose of this chapter is to uncover hidden effects of this development and propose how companies can respond to them. The chapter draws on a case study of a Danish industrial...... equipment firm and describes how its operations configuration has been changing over time. The chapter identifies the key determinants of this change and uncovers some of its hidden effects. The chapter closes with propositions for how to respond to these effects through the development of a distinct...

Structure-based Markov random field model for representing evolutionary constraints on functional sites.

Science.gov (United States)

Jeong, Chan-Seok; Kim, Dongsup

2016-02-24

Elucidating the cooperative mechanism of interconnected residues is an important component toward understanding the biological function of a protein. Coevolution analysis has been developed to model the coevolutionary information reflecting structural and functional constraints. Recently, several methods have been developed based on a probabilistic graphical model called the Markov random field (MRF), which have led to significant improvements for coevolution analysis; however, thus far, the performance of these models has mainly been assessed by focusing on the aspect of protein structure. In this study, we built an MRF model whose graphical topology is determined by the residue proximity in the protein structure, and derived a novel positional coevolution estimate utilizing the node weight of the MRF model. This structure-based MRF method was evaluated for three data sets, each of which annotates catalytic site, allosteric site, and comprehensively determined functional site information. We demonstrate that the structure-based MRF architecture can encode the evolutionary information associated with biological function. Furthermore, we show that the node weight can more accurately represent positional coevolution information compared to the edge weight. Lastly, we demonstrate that the structure-based MRF model can be reliably built with only a few aligned sequences in linear time. The results show that adoption of a structure-based architecture could be an acceptable approximation for coevolution modeling with efficient computation complexity.

Controlled experiments of hillslope co-evolution at the Biosphere 2 Landscape Evolution Observatory: toward prediction of coupled hydrological, biogeochemical, and ecological change

Science.gov (United States)

Volkmann, T. H. M.; Sengupta, A.; Pangle, L.; Abramson, N.; Barron-Gafford, G.; Breshears, D. D.; Bugaj, A.; Chorover, J.; Dontsova, K.; Durcik, M.; Ferre, T. P. A.; Harman, C. J.; Hunt, E.; Huxman, T. E.; Kim, M.; Maier, R. M.; Matos, K.; Alves Meira Neto, A.; Meredith, L. K.; Monson, R. K.; Niu, G. Y.; Pelletier, J. D.; Rasmussen, C.; Ruiz, J.; Saleska, S. R.; Schaap, M. G.; Sibayan, M.; Tuller, M.; Van Haren, J. L. M.; Wang, Y.; Zeng, X.; Troch, P. A.

2017-12-01

Understanding the process interactions and feedbacks among water, microbes, plants, and porous geological media is crucial for improving predictions of the response of Earth's critical zone to future climatic conditions. However, the integrated co-evolution of landscapes under change is notoriously difficult to investigate. Laboratory studies are typically limited in spatial and temporal scale, while field studies lack observational density and control. To bridge the gap between controlled lab and uncontrolled field studies, the University of Arizona - Biosphere 2 built a macrocosm experiment of unprecedented scale: the Landscape Evolution Observatory (LEO). LEO consists of three replicated, 330-m2 hillslope landscapes inside a 5000-m2 environmentally controlled facility. The engineered landscapes contain 1-m depth of basaltic tephra ground to homogenous loamy sand that will undergo physical, chemical, and mineralogical changes over many years. Each landscape contains a dense sensor network capable of resolving water, carbon, and energy cycling processes at sub-meter to whole-landscape scale. Embedded sampling devices allow for quantification of biogeochemical processes, and facilitate the use of chemical tracers applied with the artificial rainfall. LEO is now fully operational and intensive forcing experiments have been launched. While operating the massive infrastructure poses significant challenges, LEO has demonstrated the capacity of tracking multi-scale matter and energy fluxes at a level of detail impossible in field experiments. Initial sensor, sampler, and restricted soil coring data are already providing insights into the tight linkages between water flow, weathering, and (micro-) biological community development during incipient landscape evolution. Over the years to come, these interacting processes are anticipated to drive the model systems to increasingly complex states, potentially perturbed by changes in climatic forcing. By intensively monitoring

Seed dispersal in limber and southwestern white pine: Comparing core and peripheral populations

Science.gov (United States)

Diana F. Tomback; Sheridan Samano; Elizabeth L. Pruett; Anna W. Schoettle

2011-01-01

According to the geographic mosaic theory of coevolution (Thompson 2005), the potential for coevolutionary relationships between interacting species varies with the presence of other species within a community. This implies that the strength of coevolution between two species may vary geographically. In this study, we ask whether there is a shift in vertebrate seed...

Cross-linked structure of network evolution

International Nuclear Information System (INIS)

Bassett, Danielle S.; Wymbs, Nicholas F.; Grafton, Scott T.; Porter, Mason A.; Mucha, Peter J.

2014-01-01

We study the temporal co-variation of network co-evolution via the cross-link structure of networks, for which we take advantage of the formalism of hypergraphs to map cross-link structures back to network nodes. We investigate two sets of temporal network data in detail. In a network of coupled nonlinear oscillators, hyperedges that consist of network edges with temporally co-varying weights uncover the driving co-evolution patterns of edge weight dynamics both within and between oscillator communities. In the human brain, networks that represent temporal changes in brain activity during learning exhibit early co-evolution that then settles down with practice. Subsequent decreases in hyperedge size are consistent with emergence of an autonomous subgraph whose dynamics no longer depends on other parts of the network. Our results on real and synthetic networks give a poignant demonstration of the ability of cross-link structure to uncover unexpected co-evolution attributes in both real and synthetic dynamical systems. This, in turn, illustrates the utility of analyzing cross-links for investigating the structure of temporal networks

Cross-linked structure of network evolution

Energy Technology Data Exchange (ETDEWEB)

Bassett, Danielle S., E-mail: dsb@seas.upenn.edu [Department of Bioengineering, University of Pennsylvania, Philadelphia, Pennsylvania 19104 (United States); Department of Physics, University of California, Santa Barbara, California 93106 (United States); Sage Center for the Study of the Mind, University of California, Santa Barbara, California 93106 (United States); Wymbs, Nicholas F.; Grafton, Scott T. [Department of Psychology and UCSB Brain Imaging Center, University of California, Santa Barbara, California 93106 (United States); Porter, Mason A. [Oxford Centre for Industrial and Applied Mathematics, Mathematical Institute, University of Oxford, Oxford OX2 6GG (United Kingdom); CABDyN Complexity Centre, University of Oxford, Oxford, OX1 1HP (United Kingdom); Mucha, Peter J. [Carolina Center for Interdisciplinary Applied Mathematics, Department of Mathematics, University of North Carolina, Chapel Hill, North Carolina 27599 (United States); Department of Applied Physical Sciences, University of North Carolina, Chapel Hill, North Carolina 27599 (United States)

2014-03-15

We study the temporal co-variation of network co-evolution via the cross-link structure of networks, for which we take advantage of the formalism of hypergraphs to map cross-link structures back to network nodes. We investigate two sets of temporal network data in detail. In a network of coupled nonlinear oscillators, hyperedges that consist of network edges with temporally co-varying weights uncover the driving co-evolution patterns of edge weight dynamics both within and between oscillator communities. In the human brain, networks that represent temporal changes in brain activity during learning exhibit early co-evolution that then settles down with practice. Subsequent decreases in hyperedge size are consistent with emergence of an autonomous subgraph whose dynamics no longer depends on other parts of the network. Our results on real and synthetic networks give a poignant demonstration of the ability of cross-link structure to uncover unexpected co-evolution attributes in both real and synthetic dynamical systems. This, in turn, illustrates the utility of analyzing cross-links for investigating the structure of temporal networks.

Design, synthesis and evaluation of a potent substrate analog inhibitor identified by scanning Ala/Phe mutagenesis, mimicking substrate co-evolution, against multidrug-resistant HIV-1 protease

Energy Technology Data Exchange (ETDEWEB)

Yedidi, Ravikiran S. [Department of Biochemistry and Molecular Biology, School of Medicine, Wayne State University, Detroit, MI 48201 (United States); Muhuhi, Joseck M. [Department of Chemistry, Wayne State University, Detroit, MI 48202 (United States); Liu, Zhigang [Department of Biochemistry and Molecular Biology, School of Medicine, Wayne State University, Detroit, MI 48201 (United States); Bencze, Krisztina Z. [Department of Chemistry, Fort Hays State University, Hays, KS 67601 (United States); Koupparis, Kyriacos [Department of Biochemistry and Molecular Biology, School of Medicine, Wayne State University, Detroit, MI 48201 (United States); Department of Chemistry, Wayne State University, Detroit, MI 48202 (United States); O’Connor, Carrie E.; Kovari, Iulia A. [Department of Biochemistry and Molecular Biology, School of Medicine, Wayne State University, Detroit, MI 48201 (United States); Spaller, Mark R. [Department of Chemistry, Wayne State University, Detroit, MI 48202 (United States); Kovari, Ladislau C., E-mail: kovari@med.wayne.edu [Department of Biochemistry and Molecular Biology, School of Medicine, Wayne State University, Detroit, MI 48201 (United States)

2013-09-06

Highlights: •Inhibitors against MDR HIV-1 protease were designed, synthesized and evaluated. •Lead peptide (6a) showed potent inhibition (IC{sub 50}: 4.4 nM) of MDR HIV-1 protease. •(6a) Showed favorable binding isotherms against NL4-3 and MDR proteases. •(6a) Induced perturbations in the {sup 15}N-HSQC spectrum of MDR HIV-1 protease. •Molecular modeling suggested that (6a) may induce total flap closure inMDR protease. -- Abstract: Multidrug-resistant (MDR) clinical isolate-769, human immunodeficiency virus type-1 (HIV-1) protease (PDB ID: (1TW7)), was shown to exhibit wide-open flaps and an expanded active site cavity, causing loss of contacts with protease inhibitors. In the current study, the expanded active site cavity of MDR769 HIV-1 protease was screened with a series of peptide-inhibitors that were designed to mimic the natural substrate cleavage site, capsid/p2. Scanning Ala/Phe chemical mutagenesis approach was incorporated into the design of the peptide series to mimic the substrate co-evolution. Among the peptides synthesized and evaluated, a lead peptide (6a) with potent activity (IC{sub 50}: 4.4 nM) was identified against the MDR769 HIV-1 protease. Isothermal titration calorimetry data showed favorable binding profile for 6aagainst both wild type and MDR769 HIV-1 protease variants. Nuclear magnetic resonance spectrum of {sup 15}N-labeled MDR769 HIV-1 protease in complex with 6a showed some major perturbations in chemical shift, supporting the peptide induced conformational changes in protease. Modeling analysis revealed multiple contacts between 6a and MDR769 HIV-1 protease. The lead peptide-inhibitor, 6a, with high potency and good binding profile can be used as the basis for developing potent small molecule inhibitors against MDR variants of HIV.

Design, synthesis and evaluation of a potent substrate analog inhibitor identified by scanning Ala/Phe mutagenesis, mimicking substrate co-evolution, against multidrug-resistant HIV-1 protease

International Nuclear Information System (INIS)

Yedidi, Ravikiran S.; Muhuhi, Joseck M.; Liu, Zhigang; Bencze, Krisztina Z.; Koupparis, Kyriacos; O’Connor, Carrie E.; Kovari, Iulia A.; Spaller, Mark R.; Kovari, Ladislau C.

2013-01-01

Highlights: •Inhibitors against MDR HIV-1 protease were designed, synthesized and evaluated. •Lead peptide (6a) showed potent inhibition (IC 50 : 4.4 nM) of MDR HIV-1 protease. •(6a) Showed favorable binding isotherms against NL4-3 and MDR proteases. •(6a) Induced perturbations in the 15 N-HSQC spectrum of MDR HIV-1 protease. •Molecular modeling suggested that (6a) may induce total flap closure inMDR protease. -- Abstract: Multidrug-resistant (MDR) clinical isolate-769, human immunodeficiency virus type-1 (HIV-1) protease (PDB ID: (1TW7)), was shown to exhibit wide-open flaps and an expanded active site cavity, causing loss of contacts with protease inhibitors. In the current study, the expanded active site cavity of MDR769 HIV-1 protease was screened with a series of peptide-inhibitors that were designed to mimic the natural substrate cleavage site, capsid/p2. Scanning Ala/Phe chemical mutagenesis approach was incorporated into the design of the peptide series to mimic the substrate co-evolution. Among the peptides synthesized and evaluated, a lead peptide (6a) with potent activity (IC 50 : 4.4 nM) was identified against the MDR769 HIV-1 protease. Isothermal titration calorimetry data showed favorable binding profile for 6aagainst both wild type and MDR769 HIV-1 protease variants. Nuclear magnetic resonance spectrum of 15 N-labeled MDR769 HIV-1 protease in complex with 6a showed some major perturbations in chemical shift, supporting the peptide induced conformational changes in protease. Modeling analysis revealed multiple contacts between 6a and MDR769 HIV-1 protease. The lead peptide-inhibitor, 6a, with high potency and good binding profile can be used as the basis for developing potent small molecule inhibitors against MDR variants of HIV

Co-evolutionary and multi-level dynamics in transitions: The transformation of aviation systems and the shift from propeller to turbojet (1930-1970)

OpenAIRE

Geels, F. W.

2006-01-01

This article deals with system innovation in Freeman and Perez's innovation typology (incremental, radical, system, techno-economic paradigm). This article conceptualises these changes as transitions from one socio-technical system to another. These transitions are co-evolution processes that are not only about technological discontinuities, but also about markets, user practices, regulation, culture, infrastructure and science. In a critical discussion of co-evolution literatures, the articl...

Coevolving parasites and population size shape the evolution of mating behaviour

Directory of Open Access Journals (Sweden)

Kerstes Niels AG

2013-02-01

Full Text Available Abstract Background Coevolution with parasites and population size are both expected to influence the evolution of mating rates. To gain insights into the interaction between these dual selective factors, we used populations from a coevolution experiment with the red flour beetle, Tribolium castaneum, and its microsporidian parasite, Nosema whitei. We maintained each experimental population at two different population sizes. We assayed the mating behaviour of both males and females from coevolved and paired non-coevolved control populations after 24 generations of coevolution with parasites. Results Males from large, coevolved populations (i.e. ancestors were exposed to parasites showed a reduced eagerness to mate compared to males from large, non-coevolved populations. But in small populations, coevolution did not lead to decreased male mating rates. Coevolved females from both large and small populations appeared to be more willing to accept mating than non-coevolved females. Conclusions This study provides unique, experimental insights into the combined roles of coevolving parasites and population size on the evolution of mating rate. Furthermore, we find that males and females respond differently to the same environmental conditions. Our results show that parasites can be key determinants of the sexual behaviour of their hosts.

Phenotype selection reveals coevolution of muscle glycogen and protein and PTEN as a gate keeper for the accretion of muscle mass in adult female mice.

Directory of Open Access Journals (Sweden)

Mandy Sawitzky

Full Text Available We have investigated molecular mechanisms for muscle mass accretion in a non-inbred mouse model (DU6P mice characterized by extreme muscle mass. This extreme muscle mass was developed during 138 generations of phenotype selection for high protein content. Due to the repeated trait selection a complex setting of different mechanisms was expected to be enriched during the selection experiment. In muscle from 29-week female DU6P mice we have identified robust increases of protein kinase B activation (AKT, Ser-473, up to 2-fold if compared to 11- and 54-week DU6P mice or controls. While a number of accepted effectors of AKT activation, including IGF-I, IGF-II, insulin/IGF-receptor, myostatin or integrin-linked kinase (ILK, were not correlated with this increase, phosphatase and tensin homologue deleted on chromosome 10 (PTEN was down-regulated in 29-week female DU6P mice. In addition, higher levels of PTEN phosphorylation were found identifying a second mechanism of PTEN inhibition. Inhibition of PTEN and activation of AKT correlated with specific activation of p70S6 kinase and ribosomal protein S6, reduced phosphorylation of eukaryotic initiation factor 2α (eIF2α and higher rates of protein synthesis in 29-week female DU6P mice. On the other hand, AKT activation also translated into specific inactivation of glycogen synthase kinase 3ß (GSK3ß and an increase of muscular glycogen. In muscles from 29-week female DU6P mice a significant increase of protein/DNA was identified, which was not due to a reduction of protein breakdown or to specific increases of translation initiation. Instead our data support the conclusion that a higher rate of protein translation is contributing to the higher muscle mass in mid-aged female DU6P mice. Our results further reveal coevolution of high protein and high glycogen content during the selection experiment and identify PTEN as gate keeper for muscle mass in mid-aged female DU6P mice.

The interplay between social networks and culture: theoretically and among whales and dolphins

OpenAIRE

Cantor, Mauricio; Whitehead, Hal

2013-01-01

Culture is increasingly being understood as a driver of mammalian phenotypes. Defined as group-specific behaviour transmitted by social learning, culture is shaped by social structure. However, culture can itself affect social structure if individuals preferentially interact with others whose behaviour is similar, or cultural symbols are used to mark groups. Using network formalism, this interplay can be depicted by the coevolution of nodes and edges together with the coevolution of network t...

Co-evolution of human leukocyte antigen (HLA class I ligands with killer-cell immunoglobulin-like receptors (KIR in a genetically diverse population of sub-Saharan Africans.

Directory of Open Access Journals (Sweden)

Paul J Norman

2013-10-01

Full Text Available Interactions between HLA class I molecules and killer-cell immunoglobulin-like receptors (KIR control natural killer cell (NK functions in immunity and reproduction. Encoded by genes on different chromosomes, these polymorphic ligands and receptors correlate highly with disease resistance and susceptibility. Although studied at low-resolution in many populations, high-resolution analysis of combinatorial diversity of HLA class I and KIR is limited to Asian and Amerindian populations with low genetic diversity. At the other end of the spectrum is the West African population investigated here: we studied 235 individuals, including 104 mother-child pairs, from the Ga-Adangbe of Ghana. This population has a rich diversity of 175 KIR variants forming 208 KIR haplotypes, and 81 HLA-A, -B and -C variants forming 190 HLA class I haplotypes. Each individual we studied has a unique compound genotype of HLA class I and KIR, forming 1-14 functional ligand-receptor interactions. Maintaining this exceptionally high polymorphism is balancing selection. The centromeric region of the KIR locus, encoding HLA-C receptors, is highly diverse whereas the telomeric region encoding Bw4-specific KIR3DL1, lacks diversity in Africans. Present in the Ga-Adangbe are high frequencies of Bw4-bearing HLA-B*53:01 and Bw4-lacking HLA-B*35:01, which otherwise are identical. Balancing selection at key residues maintains numerous HLA-B allotypes having and lacking Bw4, and also those of stronger and weaker interaction with LILRB1, a KIR-related receptor. Correspondingly, there is a balance at key residues of KIR3DL1 that modulate its level of cell-surface expression. Thus, capacity to interact with NK cells synergizes with peptide binding diversity to drive HLA-B allele frequency distribution. These features of KIR and HLA are consistent with ongoing co-evolution and selection imposed by a pathogen endemic to West Africa. Because of the prevalence of malaria in the Ga-Adangbe and

Gene-Culture Coevolution in a Social Cetacean: Integrating Acoustic and Genetic Data to Understand Population Structure in the Short-Finned Pilot Whale (Globicephala macrorhynchus)

Science.gov (United States)

Van Cise, Amy

repertoire or dialect. The qualitative correlation between social structure, cultural information transfer, and genetic structure suggest that gene-culture coevolution may be an important mechanism to the evolutionary ecology of short-finned pilot whales. Further research may reveal a similar structure in the transmission of ecological behaviors, such as diet preference, habitat use, or movements. The results of this research underscore the applicability of gene-culture coevolutionary theory to non-human taxa.

Selection on the Major Color Gene Melanocortin-1-Receptor Shaped the Evolution of the Melanocortin System Genes

Directory of Open Access Journals (Sweden)

Linda Dib

2017-12-01

Full Text Available Modular genetic systems and networks have complex evolutionary histories shaped by selection acting on single genes as well as on their integrated function within the network. However, uncovering molecular coevolution requires the detection of coevolving sites in sequences. Detailed knowledge of the functions of each gene in the system is also necessary to identify the selective agents driving coevolution. Using recently developed computational tools, we investigated the effect of positive selection on the coevolution of ten major genes in the melanocortin system, responsible for multiple physiological functions and human diseases. Substitutions driven by positive selection at the melanocortin-1-receptor (MC1R induced more coevolutionary changes on the system than positive selection on other genes in the system. Contrarily, selection on the highly pleiotropic POMC gene, which orchestrates the activation of the different melanocortin receptors, had the lowest coevolutionary influence. MC1R and possibly its main function, melanin pigmentation, seems to have influenced the evolution of the melanocortin system more than functions regulated by MC2-5Rs such as energy homeostasis, glucocorticoid-dependent stress and anti-inflammatory responses. Although replication in other regulatory systems is needed, this suggests that single functional aspects of a genetic network or system can be of higher importance than others in shaping coevolution among the genes that integrate it.

Infection dynamics of the monogenean parasite Gyrodactylus gasterostei on sympatric and allopatric populations of the three-spined stickleback Gasterosteus aculeatus.

Science.gov (United States)

Raeymaekers, Joost A M; Wegner, K Mathias; Huyset, Tine; Volckaert, Filip A M

2011-03-01

Parasites with high host specificity maximally depend on their hosts, which should increase the likelihood of coevolution. However, coevolution requires reciprocal selection exerted by the host and the parasite, and thus a considerable level of parasite virulence. In species of the monogenean ectoparasite genus Gyrodactylus consecutive generations are confronted with a single host, which may constrain the evolution of virulence. Transmission, which is often important in the ecology of Gyrodactylus species, may have the opposite effect, but may also lead to the avoidance of coevolutionary arms races. We investigated the potential outcome of coevolution between Gyrodactylus gasterostei Gläser, 1974 and its host, the three-spined stickleback (Gasterosteus aculeatus L.) by determining the strength of genotype by genotype (GxG) interactions on two levels: within and between sympatric and allopatric host populations. To do so, we compared the parasite's infection dynamics on laboratory-reared sympatric (Belgian) and allopatric (German) hosts. We found that a parasite line successfully infected a range of sympatric host genotypes (represented by families), while it failed to establish on allopatric hosts. Phylogeographic studies suggest that neutral genetic divergence between the host populations cannot explain this dramatic difference. Provided that this result can be generalised towards other parasite lines, we conclude that coevolution in this host-parasite system is more likely to lead to local adaptation on the population level than to GxG interactions within populations.

The Port Service Ecosystem Research Based on the Lotka-Volterra Model

Directory of Open Access Journals (Sweden)

Li Wenjuan

2017-11-01

Full Text Available Under the new normal of China’s economy, the competition among the port enterprises is not only the competition of the core competence of the port, the port industry chain or the port supply chain, but also the competition of the port service ecosystem. In this paper, the concept and characteristics of the port service ecosystem is discussed, a hierarchical model of the port service ecosystem is constructed. As an extended logistic model, Lotka-Volterra model is applied to study the competitive co-evolution and mutually beneficial co-evolution of enterprises in the port service ecosystem. This paper simulates the co-evolution of enterprises in the port service ecosystem by using MATLAB programming. The simulation results show that the breadth of the niche of the enterprises is changing with the change of the competition coefficient and the coefficient of mutual benefit in the port service ecosystem. Based on that, some proposals are put forward to ensure the healthy and orderly development of the port service ecosystem.

Endophytic Epichloë species and their grass hosts: from evolution to applications.

Science.gov (United States)

Saikkonen, Kari; Young, Carolyn A; Helander, Marjo; Schardl, Christopher L

2016-04-01

The closely linked fitness of the Epichloë symbiont and the host grass is presumed to align the coevolution of the species towards specialization and mutually beneficial cooperation. Ecological observations demonstrating that Epichloë-grass symbioses can modulate grassland ecosystems via both above- and belowground ecosystem processes support this. In many cases the detected ecological importance of Epichloë species is directly or indirectly linked to defensive mutualism attributable to alkaloids of fungal-origin. Now, modern genetic and molecular techniques enable the precise studies on evolutionary origin of endophytic Epichloë species, their coevolution with host grasses and identification the genetic variation that explains phenotypic diversity in ecologically relevant characteristics of Epichloë-grass associations. Here we briefly review the most recent findings in these areas of research using the present knowledge of the genetic variation that explains the biosynthetic pathways driving the diversity of alkaloids produced by the endophyte. These findings underscore the importance of genetic interplay between the fungus and the host in shaping their coevolution and ecological role in both natural grass ecosystems, and in the agricultural arena.

Sequence, structure and function relationships in flaviviruses as assessed by evolutive aspects of its conserved non-structural protein domains.

Science.gov (United States)

da Fonseca, Néli José; Lima Afonso, Marcelo Querino; Pedersolli, Natan Gonçalves; de Oliveira, Lucas Carrijo; Andrade, Dhiego Souto; Bleicher, Lucas

2017-10-28

Flaviviruses are responsible for serious diseases such as dengue, yellow fever, and zika fever. Their genomes encode a polyprotein which, after cleavage, results in three structural and seven non-structural proteins. Homologous proteins can be studied by conservation and coevolution analysis as detected in multiple sequence alignments, usually reporting positions which are strictly necessary for the structure and/or function of all members in a protein family or which are involved in a specific sub-class feature requiring the coevolution of residue sets. This study provides a complete conservation and coevolution analysis on all flaviviruses non-structural proteins, with results mapped on all well-annotated available sequences. A literature review on the residues found in the analysis enabled us to compile available information on their roles and distribution among different flaviviruses. Also, we provide the mapping of conserved and coevolved residues for all sequences currently in SwissProt as a supplementary material, so that particularities in different viruses can be easily analyzed. Copyright © 2017 Elsevier Inc. All rights reserved.

The Coevolution of Digital Ecosystems

Science.gov (United States)

SungYong, Um

2016-01-01

Digital ecosystems are one of the most important strategic issues in the current digital economy. Digital ecosystems are dynamic and generative. They evolve as new firms join and as heterogeneous systems are integrated into other systems. These features digital ecosystems determine economic and technological success in the competition among…

The Dynamical Theory of Coevolution

NARCIS (Netherlands)

Dieckmann, Ulf

1997-01-01

A unifying framework is presented for describing the phenotypic coevolutionary dynamics of a general ecological community. We start from an individual-based approach allowing for the interaction of an arbitrary number of species. The adaptive dynamics of species’ trait values are derived from the

Impact of two specialist insect herbivores on reproduction of horse nettle, Solanum carolinense.

Science.gov (United States)

Wise, Michael J; Sacchi, Christopher F

1996-10-01

The frequency of coevolution as a process of strong mutual interaction between a single plant and herbivore species has been questioned in light of more commonly observed, complex relationships between a plant and a suite of herbivore species. Despite recognition of the possibility of diffuse coevolution, relatively few studies have examined ecological responses of plants to herbivores in complex associations. We studied the impact of two specialist herbivores, the horse nettle beetle, Leptinotarsa juncta, and the eggplant flea beetle, Epitrix fuscula, on reproduction of their host, Solanum carolinense. Our study involved field and controlled-environment experimental tests of the impact on sexual and potential asexual reproduction of attack by individuals of the two herbivore species, individually and in combination. Field tests demonstrated that under normal levels of phytophagous insect attack, horse nettle plants experienced a reduction in fruit production of more than 75% compared with plants from which insects were excluded. In controlled-environment experiments using enclosure-exclosure cages, the horse nettle's two principal herbivores, the flea beetle and the horse nettle beetle, caused decreases in sexual reproduction similar to those observed in the field, and a reduction in potential asexual reproduction, represented by root biomass. Attack by each herbivore reduced the numbers of fruits produced, and root growth, when feeding in isolation. When both species were feeding together, fruit production, but not root growth, was lower than when either beetle species fed alone. Ecological interactions between horse nettle and its two primary herbivores necessary for diffuse coevolution to occur were evident from an overall analysis of the statistical interactions between the two herbivores for combined assessment of fruit and vegetative traits. For either of these traits alone, the interactions necessary to promote diffuse coevolution apparently were lacking.

Irreducible Vagueness