Adaptive processes drive ecomorphological convergent evolution in antwrens (Thamnophilidae).

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Bravo, Gustavo A; Remsen, J V; Brumfield, Robb T

2014-10-01

Phylogenetic niche conservatism (PNC) and convergence are contrasting evolutionary patterns that describe phenotypic similarity across independent lineages. Assessing whether and how adaptive processes give origin to these patterns represent a fundamental step toward understanding phenotypic evolution. Phylogenetic model-based approaches offer the opportunity not only to distinguish between PNC and convergence, but also to determine the extent that adaptive processes explain phenotypic similarity. The Myrmotherula complex in the Neotropical family Thamnophilidae is a polyphyletic group of sexually dimorphic small insectivorous forest birds that are relatively homogeneous in size and shape. Here, we integrate a comprehensive species-level molecular phylogeny of the Myrmotherula complex with morphometric and ecological data within a comparative framework to test whether phenotypic similarity is described by a pattern of PNC or convergence, and to identify evolutionary mechanisms underlying body size and shape evolution. We show that antwrens in the Myrmotherula complex represent distantly related clades that exhibit adaptive convergent evolution in body size and divergent evolution in body shape. Phenotypic similarity in the group is primarily driven by their tendency to converge toward smaller body sizes. Differences in body size and shape across lineages are associated to ecological and behavioral factors. © 2014 The Author(s). Evolution © 2014 The Society for the Study of Evolution.

Adaptation and evolution of drug-resistant Mycobacterium tuberculosis

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Bergval, I.L.

2013-01-01

Many studies have been conducted on drug resistance and the evolution of Mycobacterium tuberculosis. Notwithstanding, many molecular mechanisms facilitating the emergence, adaptation and spread of drug-resistant tuberculosis have yet to be discovered. This thesis reports studies of the adaptive

Harmony Search Based Parameter Ensemble Adaptation for Differential Evolution

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Rammohan Mallipeddi

2013-01-01

Full Text Available In differential evolution (DE algorithm, depending on the characteristics of the problem at hand and the available computational resources, different strategies combined with a different set of parameters may be effective. In addition, a single, well-tuned combination of strategies and parameters may not guarantee optimal performance because different strategies combined with different parameter settings can be appropriate during different stages of the evolution. Therefore, various adaptive/self-adaptive techniques have been proposed to adapt the DE strategies and parameters during the course of evolution. In this paper, we propose a new parameter adaptation technique for DE based on ensemble approach and harmony search algorithm (HS. In the proposed method, an ensemble of parameters is randomly sampled which form the initial harmony memory. The parameter ensemble evolves during the course of the optimization process by HS algorithm. Each parameter combination in the harmony memory is evaluated by testing them on the DE population. The performance of the proposed adaptation method is evaluated using two recently proposed strategies (DE/current-to-pbest/bin and DE/current-to-gr_best/bin as basic DE frameworks. Numerical results demonstrate the effectiveness of the proposed adaptation technique compared to the state-of-the-art DE based algorithms on a set of challenging test problems (CEC 2005.

Resilience through adaptation.

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Guus A Ten Broeke

Full Text Available Adaptation of agents through learning or evolution is an important component of the resilience of Complex Adaptive Systems (CAS. Without adaptation, the flexibility of such systems to cope with outside pressures would be much lower. To study the capabilities of CAS to adapt, social simulations with agent-based models (ABMs provide a helpful tool. However, the value of ABMs for studying adaptation depends on the availability of methodologies for sensitivity analysis that can quantify resilience and adaptation in ABMs. In this paper we propose a sensitivity analysis methodology that is based on comparing time-dependent probability density functions of output of ABMs with and without agent adaptation. The differences between the probability density functions are quantified by the so-called earth-mover's distance. We use this sensitivity analysis methodology to quantify the probability of occurrence of critical transitions and other long-term effects of agent adaptation. To test the potential of this new approach, it is used to analyse the resilience of an ABM of adaptive agents competing for a common-pool resource. Adaptation is shown to contribute positively to the resilience of this ABM. If adaptation proceeds sufficiently fast, it may delay or avert the collapse of this system.

Resilience through adaptation.

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Ten Broeke, Guus A; van Voorn, George A K; Ligtenberg, Arend; Molenaar, Jaap

2017-01-01

Adaptation of agents through learning or evolution is an important component of the resilience of Complex Adaptive Systems (CAS). Without adaptation, the flexibility of such systems to cope with outside pressures would be much lower. To study the capabilities of CAS to adapt, social simulations with agent-based models (ABMs) provide a helpful tool. However, the value of ABMs for studying adaptation depends on the availability of methodologies for sensitivity analysis that can quantify resilience and adaptation in ABMs. In this paper we propose a sensitivity analysis methodology that is based on comparing time-dependent probability density functions of output of ABMs with and without agent adaptation. The differences between the probability density functions are quantified by the so-called earth-mover's distance. We use this sensitivity analysis methodology to quantify the probability of occurrence of critical transitions and other long-term effects of agent adaptation. To test the potential of this new approach, it is used to analyse the resilience of an ABM of adaptive agents competing for a common-pool resource. Adaptation is shown to contribute positively to the resilience of this ABM. If adaptation proceeds sufficiently fast, it may delay or avert the collapse of this system.

The adaptive evolution of the mammalian mitochondrial genome

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O'Brien Stephen J

2008-03-01

Full Text Available Abstract Background The mitochondria produce up to 95% of a eukaryotic cell's energy through oxidative phosphorylation. The proteins involved in this vital process are under high functional constraints. However, metabolic requirements vary across species, potentially modifying selective pressures. We evaluate the adaptive evolution of 12 protein-coding mitochondrial genes in 41 placental mammalian species by assessing amino acid sequence variation and exploring the functional implications of observed variation in secondary and tertiary protein structures. Results Wide variation in the properties of amino acids were observed at functionally important regions of cytochrome b in species with more-specialized metabolic requirements (such as adaptation to low energy diet or large body size, such as in elephant, dugong, sloth, and pangolin, and adaptation to unusual oxygen requirements, for example diving in cetaceans, flying in bats, and living at high altitudes in alpacas. Signatures of adaptive variation in the NADH dehydrogenase complex were restricted to the loop regions of the transmembrane units which likely function as protons pumps. Evidence of adaptive variation in the cytochrome c oxidase complex was observed mostly at the interface between the mitochondrial and nuclear-encoded subunits, perhaps evidence of co-evolution. The ATP8 subunit, which has an important role in the assembly of F0, exhibited the highest signal of adaptive variation. ATP6, which has an essential role in rotor performance, showed a high adaptive variation in predicted loop areas. Conclusion Our study provides insight into the adaptive evolution of the mtDNA genome in mammals and its implications for the molecular mechanism of oxidative phosphorylation. We present a framework for future experimental characterization of the impact of specific mutations in the function, physiology, and interactions of the mtDNA encoded proteins involved in oxidative phosphorylation.

Differential Evolution for Many-Particle Adaptive Quantum Metrology

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Lovett, N.B.; Crosnier, C.; Perarnau- Llobet, M.; Sanders, B.

2013-01-01

We devise powerful algorithms based on differential evolution for adaptive many-particle quantum metrology. Our new approach delivers adaptive quantum metrology policies for feedback control that are orders-of-magnitude more efficient and surpass the few-dozen-particle limitation arising in methods

How adaptive learning affects evolution: reviewing theory on the Baldwin effect

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Sznajder, B.; Sabelis, M.W.; Egas, M.

2012-01-01

We review models of the Baldwin effect, i.e., the hypothesis that adaptive learning (i.e., learning to improve fitness) accelerates genetic evolution of the phenotype. Numerous theoretical studies scrutinized the hypothesis that a non-evolving ability of adaptive learning accelerates evolution of

The population ecology of contemporary adaptations: what empirical studies reveal about the conditions that promote adaptive evolution.

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Reznick, D N; Ghalambor, C K

2001-01-01

Under what conditions might organisms be capable of rapid adaptive evolution? We reviewed published studies documenting contemporary adaptations in natural populations and looked for general patterns in the population ecological causes. We found that studies of contemporary adaptation fall into two general settings: (1) colonization of new environments that established newly adapted populations, and (2) local adaptations within the context of a heterogeneous environments and metapopulation structure. Local ecological processes associated with colonizations and introductions included exposure to: (1) a novel host or food resource; (2) a new biophysical environment; (3) a new predator community; and (4) a new coexisting competitor. The new environments that were colonized often had depauperate communities, sometimes because of anthropogenic disturbance. Local adaptation in heterogeneous environments was also often associated with recent anthropogenic changes, such as insecticide and herbicide resistance, or industrial melanism. A common feature of many examples is the combination of directional selection with at least a short-term opportunity for population growth. We suggest that such opportunities for population growth may be a key factor that promotes rapid evolution, since directional selection might otherwise be expected to cause population decline and create the potential for local extinction, which is an ever-present alternative to local adaptation. We also address the large discrepancy between the rate of evolution observed in contemporary studies and the apparent rate of evolution seen in the fossil record.

Adaptive evolution of conserved noncoding elements in mammals.

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Su Yeon Kim

2007-09-01

Full Text Available Conserved noncoding elements (CNCs are an abundant feature of vertebrate genomes. Some CNCs have been shown to act as cis-regulatory modules, but the function of most CNCs remains unclear. To study the evolution of CNCs, we have developed a statistical method called the "shared rates test" to identify CNCs that show significant variation in substitution rates across branches of a phylogenetic tree. We report an application of this method to alignments of 98,910 CNCs from the human, chimpanzee, dog, mouse, and rat genomes. We find that approximately 68% of CNCs evolve according to a null model where, for each CNC, a single parameter models the level of constraint acting throughout the phylogeny linking these five species. The remaining approximately 32% of CNCs show departures from the basic model including speed-ups and slow-downs on particular branches and occasionally multiple rate changes on different branches. We find that a subset of the significant CNCs have evolved significantly faster than the local neutral rate on a particular branch, providing strong evidence for adaptive evolution in these CNCs. The distribution of these signals on the phylogeny suggests that adaptive evolution of CNCs occurs in occasional short bursts of evolution. Our analyses suggest a large set of promising targets for future functional studies of adaptation.

Evolution of adaptation mechanisms: Adaptation energy, stress, and oscillating death.

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Gorban, Alexander N; Tyukina, Tatiana A; Smirnova, Elena V; Pokidysheva, Lyudmila I

2016-09-21

In 1938, Selye proposed the notion of adaptation energy and published 'Experimental evidence supporting the conception of adaptation energy.' Adaptation of an animal to different factors appears as the spending of one resource. Adaptation energy is a hypothetical extensive quantity spent for adaptation. This term causes much debate when one takes it literally, as a physical quantity, i.e. a sort of energy. The controversial points of view impede the systematic use of the notion of adaptation energy despite experimental evidence. Nevertheless, the response to many harmful factors often has general non-specific form and we suggest that the mechanisms of physiological adaptation admit a very general and nonspecific description. We aim to demonstrate that Selye׳s adaptation energy is the cornerstone of the top-down approach to modelling of non-specific adaptation processes. We analyze Selye׳s axioms of adaptation energy together with Goldstone׳s modifications and propose a series of models for interpretation of these axioms. Adaptation energy is considered as an internal coordinate on the 'dominant path' in the model of adaptation. The phenomena of 'oscillating death' and 'oscillating remission' are predicted on the base of the dynamical models of adaptation. Natural selection plays a key role in the evolution of mechanisms of physiological adaptation. We use the fitness optimization approach to study of the distribution of resources for neutralization of harmful factors, during adaptation to a multifactor environment, and analyze the optimal strategies for different systems of factors. Copyright © 2016 Elsevier Ltd. All rights reserved.

Evolution of morphological and climatic adaptations in Veronica L. (Plantaginaceae

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Jian-Cheng Wang

2016-08-01

Full Text Available Perennials and annuals apply different strategies to adapt to the adverse environment, based on ‘tolerance’ and ‘avoidance’, respectively. To understand lifespan evolution and its impact on plant adaptability, we carried out a comparative study of perennials and annuals in the genus Veronica from a phylogenetic perspective. The results showed that ancestors of the genus Veronicawere likely to be perennial plants. Annual life history of Veronica has evolved multiple times and subtrees with more annual species have a higher substitution rate. Annuals can adapt to more xeric habitats than perennials. This indicates that annuals are more drought-resistant than their perennial relatives. Due to adaptation to similar selective pressures, parallel evolution occurs in morphological characters among annual species of Veronica.

Farming System Evolution and Adaptive Capacity: Insights for Adaptation Support

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Jami L. Dixon

2014-02-01

Full Text Available Studies of climate impacts on agriculture and adaptation often provide current or future assessments, ignoring the historical contexts farming systems are situated within. We investigate how historical trends have influenced farming system adaptive capacity in Uganda using data from household surveys, semi-structured interviews, focus-group discussions and observations. By comparing two farming systems, we note three major findings: (1 similar trends in farming system evolution have had differential impacts on the diversity of farming systems; (2 trends have contributed to the erosion of informal social and cultural institutions and an increasing dependence on formal institutions; and (3 trade-offs between components of adaptive capacity are made at the farm-scale, thus influencing farming system adaptive capacity. To identify the actual impacts of future climate change and variability, it is important to recognize the dynamic nature of adaptation. In practice, areas identified for further adaptation support include: shift away from one-size-fits-all approach the identification and integration of appropriate modern farming method; a greater focus on building inclusive formal and informal institutions; and a more nuanced understanding regarding the roles and decision-making processes of influential, but external, actors. More research is needed to understand farm-scale trade-offs and the resulting impacts across spatial and temporal scales.

Adaptive evolution of transcription factor binding sites

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Berg Johannes

2004-10-01

Full Text Available Abstract Background The regulation of a gene depends on the binding of transcription factors to specific sites located in the regulatory region of the gene. The generation of these binding sites and of cooperativity between them are essential building blocks in the evolution of complex regulatory networks. We study a theoretical model for the sequence evolution of binding sites by point mutations. The approach is based on biophysical models for the binding of transcription factors to DNA. Hence we derive empirically grounded fitness landscapes, which enter a population genetics model including mutations, genetic drift, and selection. Results We show that the selection for factor binding generically leads to specific correlations between nucleotide frequencies at different positions of a binding site. We demonstrate the possibility of rapid adaptive evolution generating a new binding site for a given transcription factor by point mutations. The evolutionary time required is estimated in terms of the neutral (background mutation rate, the selection coefficient, and the effective population size. Conclusions The efficiency of binding site formation is seen to depend on two joint conditions: the binding site motif must be short enough and the promoter region must be long enough. These constraints on promoter architecture are indeed seen in eukaryotic systems. Furthermore, we analyse the adaptive evolution of genetic switches and of signal integration through binding cooperativity between different sites. Experimental tests of this picture involving the statistics of polymorphisms and phylogenies of sites are discussed.

Differential Evolution Algorithm with Self-Adaptive Population Resizing Mechanism

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Xu Wang

2013-01-01

Full Text Available A differential evolution (DE algorithm with self-adaptive population resizing mechanism, SapsDE, is proposed to enhance the performance of DE by dynamically choosing one of two mutation strategies and tuning control parameters in a self-adaptive manner. More specifically, more appropriate mutation strategies along with its parameter settings can be determined adaptively according to the previous status at different stages of the evolution process. To verify the performance of SapsDE, 17 benchmark functions with a wide range of dimensions, and diverse complexities are used. Nonparametric statistical procedures were performed for multiple comparisons between the proposed algorithm and five well-known DE variants from the literature. Simulation results show that SapsDE is effective and efficient. It also exhibits much more superiorresultsthan the other five algorithms employed in the comparison in most of the cases.

Quantifying the evolution of individual scientific impact.

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Sinatra, Roberta; Wang, Dashun; Deville, Pierre; Song, Chaoming; Barabási, Albert-László

2016-11-04

Despite the frequent use of numerous quantitative indicators to gauge the professional impact of a scientist, little is known about how scientific impact emerges and evolves in time. Here, we quantify the changes in impact and productivity throughout a career in science, finding that impact, as measured by influential publications, is distributed randomly within a scientist's sequence of publications. This random-impact rule allows us to formulate a stochastic model that uncouples the effects of productivity, individual ability, and luck and unveils the existence of universal patterns governing the emergence of scientific success. The model assigns a unique individual parameter Q to each scientist, which is stable during a career, and it accurately predicts the evolution of a scientist's impact, from the h-index to cumulative citations, and independent recognitions, such as prizes. Copyright © 2016, American Association for the Advancement of Science.

Advances on molecular mechanism of the adaptive evolution of Chiroptera (bats).

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Yunpeng, Liang; Li, Yu

2015-01-01

As the second biggest animal group in mammals, Chiroptera (bats) demonstrates many unique adaptive features in terms of flight, echolocation, auditory acuity, feeding habit, hibernation and immune defense, providing an excellent system for understanding the molecular basis of how organisms adapt to the living environments encountered. In this review, we summarize the researches on the molecular mechanism of the adaptive evolution of Chiroptera, especially the recent researches at the genome levels, suggesting a far more complex evolutionary pattern and functional diversity than previously thought. In the future, along with the increasing numbers of Chiroptera species genomes available, new evolutionary patterns and functional divergence will be revealed, which can promote the further understanding of this animal group and the molecular mechanism of adaptive evolution.

Quantifying long-term evolution of intra-urban spatial interactions

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Sun, Lijun; Jin, Jian Gang; Axhausen, Kay W.; Lee, Der-Horng; Cebrian, Manuel

2015-01-01

Understanding the long-term impact that changes in a city's transportation infrastructure have on its spatial interactions remains a challenge. The difficulty arises from the fact that the real impact may not be revealed in static or aggregated mobility measures, as these are remarkably robust to perturbations. More generally, the lack of longitudinal, cross-sectional data demonstrating the evolution of spatial interactions at a meaningful urban scale also hinders us from evaluating the sensitivity of movement indicators, limiting our capacity to understand the evolution of urban mobility in depth. Using very large mobility records distributed over 3 years, we quantify the impact of the completion of a metro line extension: the Circle Line (CCL) in Singapore. We find that the commonly used movement indicators are almost identical before and after the project was completed. However, in comparing the temporal community structure across years, we do observe significant differences in the spatial reorganization of the affected geographical areas. The completion of CCL enables travellers to re-identify their desired destinations collectively with lower transport cost, making the community structure more consistent. These changes in locality are dynamic and characterized over short timescales, offering us a different approach to identify and analyse the long-term impact of new infrastructures on cities and their evolution dynamics. PMID:25551142

Molecular evolution and thermal adaptation

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Chen, Peiqiu

2011-12-01

In this thesis, we address problems in molecular evolution, thermal adaptation, and the kinetics of adaptation of bacteria and viruses to elevated environmental temperatures. We use a nearly neutral fitness model where the replication speed of an organism is proportional to the copy number of folded proteins. Our model reproduces the distribution of stabilities of natural proteins in excellent agreement with experiment. We find that species with high mutation rates tend to have less stable proteins compared to species with low mutation rate. We found that a broad distribution of protein stabilities observed in the model and in experiment is the key determinant of thermal response for viruses and bacteria. Our results explain most of the earlier experimental observations: striking asymmetry of thermal response curves, the absence of evolutionary trade-off which was expected but not found in experiments, correlation between denaturation temperature for several protein families and the Optimal Growth Temperature (OGT) of their carrier organisms, and proximity of bacterial or viral OGTs to their evolutionary temperatures. Our theory quantitatively and with high accuracy described thermal response curves for 35 bacterial species. The model also addresses the key to adaptation is in weak-link genes (WLG), which encode least thermodynamically stable essential proteins in the proteome. We observe, as in experiment, a two-stage adaptation process. The first stage is a Luria-Delbruck type of selection, whereby rare WLG alleles, whose proteins are more stable than WLG proteins of the majority of the population (either due to standing genetic variation or due to an early acquired mutation), rapidly rise to fixation. The second stage constitutes subsequent slow accumulation of mutations in an adapted population. As adaptation progresses, selection regime changes from positive to neutral: Selection coefficient of beneficial mutations scales as a negative power of number of

Adaptation to Temporally Fluctuating Environments by the Evolution of Maternal Effects.

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Snigdhadip Dey

2016-02-01

Full Text Available All organisms live in temporally fluctuating environments. Theory predicts that the evolution of deterministic maternal effects (i.e., anticipatory maternal effects or transgenerational phenotypic plasticity underlies adaptation to environments that fluctuate in a predictably alternating fashion over maternal-offspring generations. In contrast, randomizing maternal effects (i.e., diversifying and conservative bet-hedging, are expected to evolve in response to unpredictably fluctuating environments. Although maternal effects are common, evidence for their adaptive significance is equivocal since they can easily evolve as a correlated response to maternal selection and may or may not increase the future fitness of offspring. Using the hermaphroditic nematode Caenorhabditis elegans, we here show that the experimental evolution of maternal glycogen provisioning underlies adaptation to a fluctuating normoxia-anoxia hatching environment by increasing embryo survival under anoxia. In strictly alternating environments, we found that hermaphrodites evolved the ability to increase embryo glycogen provisioning when they experienced normoxia and to decrease embryo glycogen provisioning when they experienced anoxia. At odds with existing theory, however, populations facing irregularly fluctuating normoxia-anoxia hatching environments failed to evolve randomizing maternal effects. Instead, adaptation in these populations may have occurred through the evolution of fitness effects that percolate over multiple generations, as they maintained considerably high expected growth rates during experimental evolution despite evolving reduced fecundity and reduced embryo survival under one or two generations of anoxia. We develop theoretical models that explain why adaptation to a wide range of patterns of environmental fluctuations hinges on the existence of deterministic maternal effects, and that such deterministic maternal effects are more likely to contribute to

Epistatic adaptive evolution of human color vision.

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Shozo Yokoyama

2014-12-01

Full Text Available Establishing genotype-phenotype relationship is the key to understand the molecular mechanism of phenotypic adaptation. This initial step may be untangled by analyzing appropriate ancestral molecules, but it is a daunting task to recapitulate the evolution of non-additive (epistatic interactions of amino acids and function of a protein separately. To adapt to the ultraviolet (UV-free retinal environment, the short wavelength-sensitive (SWS1 visual pigment in human (human S1 switched from detecting UV to absorbing blue light during the last 90 million years. Mutagenesis experiments of the UV-sensitive pigment in the Boreoeutherian ancestor show that the blue-sensitivity was achieved by seven mutations. The experimental and quantum chemical analyses show that 4,008 of all 5,040 possible evolutionary trajectories are terminated prematurely by containing a dehydrated nonfunctional pigment. Phylogenetic analysis further suggests that human ancestors achieved the blue-sensitivity gradually and almost exclusively by epistasis. When the final stage of spectral tuning of human S1 was underway 45-30 million years ago, the middle and long wavelength-sensitive (MWS/LWS pigments appeared and so-called trichromatic color vision was established by interprotein epistasis. The adaptive evolution of human S1 differs dramatically from orthologous pigments with a major mutational effect used in achieving blue-sensitivity in a fish and several mammalian species and in regaining UV vision in birds. These observations imply that the mechanisms of epistatic interactions must be understood by studying various orthologues in different species that have adapted to various ecological and physiological environments.

Parameter identification of PEMFC model based on hybrid adaptive differential evolution algorithm

International Nuclear Information System (INIS)

Sun, Zhe; Wang, Ning; Bi, Yunrui; Srinivasan, Dipti

2015-01-01

In this paper, a HADE (hybrid adaptive differential evolution) algorithm is proposed for the identification problem of PEMFC (proton exchange membrane fuel cell). Inspired by biological genetic strategy, a novel adaptive scaling factor and a dynamic crossover probability are presented to improve the adaptive and dynamic performance of differential evolution algorithm. Moreover, two kinds of neighborhood search operations based on the bee colony foraging mechanism are introduced for enhancing local search efficiency. Through testing the benchmark functions, the proposed algorithm exhibits better performance in convergent accuracy and speed. Finally, the HADE algorithm is applied to identify the nonlinear parameters of PEMFC stack model. Through experimental comparison with other identified methods, the PEMFC model based on the HADE algorithm shows better performance. - Highlights: • We propose a hybrid adaptive differential evolution algorithm (HADE). • The search efficiency is enhanced in low and high dimension search space. • The effectiveness is confirmed by testing benchmark functions. • The identification of the PEMFC model is conducted by adopting HADE.

Immune genes undergo more adaptive evolution than non-immune system genes in Daphnia pulex

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McTaggart Seanna J

2012-05-01

Full Text Available Abstract Background Understanding which parts of the genome have been most influenced by adaptive evolution remains an unsolved puzzle. Some evidence suggests that selection has the greatest impact on regions of the genome that interact with other evolving genomes, including loci that are involved in host-parasite co-evolutionary processes. In this study, we used a population genetic approach to test this hypothesis by comparing DNA sequences of 30 putative immune system genes in the crustacean Daphnia pulex with 24 non-immune system genes. Results In support of the hypothesis, results from a multilocus extension of the McDonald-Kreitman (MK test indicate that immune system genes as a class have experienced more adaptive evolution than non-immune system genes. However, not all immune system genes show evidence of adaptive evolution. Additionally, we apply single locus MK tests and calculate population genetic parameters at all loci in order to characterize the mode of selection (directional versus balancing in the genes that show the greatest deviation from neutral evolution. Conclusions Our data are consistent with the hypothesis that immune system genes undergo more adaptive evolution than non-immune system genes, possibly as a result of host-parasite arms races. The results of these analyses highlight several candidate loci undergoing adaptive evolution that could be targeted in future studies.

An Efficient Binary Differential Evolution with Parameter Adaptation

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Dongli Jia

2013-04-01

Full Text Available Differential Evolution (DE has been applied to many scientific and engineering problems for its simplicity and efficiency. However, the standard DE cannot be used in a binary search space directly. This paper proposes an adaptive binary Differential Evolution algorithm, or ABDE, that has a similar framework as the standard DE but with an improved binary mutation strategy in which the best individual participates. To further enhance the search ability, the parameters of the ABDE are slightly disturbed in an adaptive manner. Experiments have been carried out by comparing ABDE with two binary DE variants, normDE and BDE, and the most used binary search technique, GA, on a set of 13 selected benchmark functions and the classical 0-1 knapsack problem. Results show that the ABDE performs better than, or at least comparable to, the other algorithms in terms of search ability, convergence speed, and solution accuracy.

Adaptive evolution of relish, a Drosophila NF-kappaB/IkappaB protein.

OpenAIRE

Begun, D J; Whitley, P

2000-01-01

NF-kappaB and IkappaB proteins have central roles in regulation of inflammation and innate immunity in mammals. Homologues of these proteins also play an important role in regulation of the Drosophila immune response. Here we present a molecular population genetic analysis of Relish, a Drosophila NF-kappaB/IkappaB protein, in Drosophila simulans and D. melanogaster. We find strong evidence for adaptive protein evolution in D. simulans, but not in D. melanogaster. The adaptive evolution appear...

Adaptive evolution of Escherichia coli to Ciprofloxacin in controlled stress environments: emergence of tolerance in spatial and temporal gradients

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Deng, J.; Sanford, R. A.; Dong, Y.; Shechtman, L. A.; Zhou, L.; Alcalde, R.; Werth, C. J.; Fouke, B. W.

2016-12-01

Microorganisms in nature have evolved in response to a variety of environmental stresses, including gradients of temperature, pH, substrate availability and aqueous chemistry. While environmental stresses are considered to be the driving forces of adaptive evolution, the impact and extent of any specific stress needed to drive such changes has not been well characterized. In this study, the antibiotic Ciprofloxacin was used as a stressor and systematically applied to E. coli st. 307 cells via a spatial gradient in a microfluidic pore network and a temporal gradient in batch cultures. The microfluidic device facilitated in vitro real-time tracking of bacterial abundances and dynamic spatial distributions in response to the gradients of both the antibiotic and nutrients. Cells collected from the microfluidic device showed growth on plates containing up to 10-times the original minimum inhibition concentration (MIC). In batch systems, Ciprofloxacin was used to evaluate adaptive responses via temporal gradients, in which the stressor concentration was incrementally increased over time with each transfer of the culture after 24 hours of growth. Responses of E. coli 307 to these stress patterns were measured by quantifying changes in the MIC for Ciprofloxacin. Over a period of 18 days of step-wise concentration increments, bacterial cells were observed to acquire tolerance gradually and eventually adapt to a 28-fold increase in the original MIC. Samples at different stages within the temporal Ciprofloxacin gradient treatment show different extents of resistance. All samples exhibited resistance exceeding the highest exposure stress concentration. In combination with the spatial and temporal gradient systems, this work provides the first comprehensive measure of the dynamic resistance of E. coli in response to Ciprofloxacin concentration gradients. These will provide invaluable insights to understand the effects of antibiotic stresses on bacterial adaptive evolution in

Convergent evolution and adaptation of Pseudomonas aeruginosa within patients with cystic fibrosis.

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Marvig, Rasmus Lykke; Sommer, Lea Mette; Molin, Søren; Johansen, Helle Krogh

2015-01-01

Little is known about how within-host evolution compares between genotypically different strains of the same pathogenic species. We sequenced the whole genomes of 474 longitudinally collected clinical isolates of Pseudomonas aeruginosa sampled from 34 children and young individuals with cystic fibrosis. Our analysis of 36 P. aeruginosa lineages identified convergent molecular evolution in 52 genes. This list of genes suggests a role in host adaptation for remodeling of regulatory networks and central metabolism, acquisition of antibiotic resistance and loss of extracellular virulence factors. Furthermore, we find an ordered succession of mutations in key regulatory networks. Accordingly, mutations in downstream transcriptional regulators were contingent upon mutations in upstream regulators, suggesting that remodeling of regulatory networks might be important in adaptation. The characterization of genes involved in host adaptation may help in predicting bacterial evolution in patients with cystic fibrosis and in the design of future intervention strategies.

Experiments on the role of deleterious mutations as stepping stones in adaptive evolution

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Covert, Arthur W.; Lenski, Richard E.; Wilke, Claus O.; Ofria, Charles

2013-01-01

Many evolutionary studies assume that deleterious mutations necessarily impede adaptive evolution. However, a later mutation that is conditionally beneficial may interact with a deleterious predecessor before it is eliminated, thereby providing access to adaptations that might otherwise be inaccessible. It is unknown whether such sign-epistatic recoveries are inconsequential events or an important factor in evolution, owing to the difficulty of monitoring the effects and fates of all mutations during experiments with biological organisms. Here, we used digital organisms to compare the extent of adaptive evolution in populations when deleterious mutations were disallowed with control populations in which such mutations were allowed. Significantly higher fitness levels were achieved over the long term in the control populations because some of the deleterious mutations served as stepping stones across otherwise impassable fitness valleys. As a consequence, initially deleterious mutations facilitated the evolution of complex, beneficial functions. We also examined the effects of disallowing neutral mutations, of varying the mutation rate, and of sexual recombination. Populations evolving without neutral mutations were able to leverage deleterious and compensatory mutation pairs to overcome, at least partially, the absence of neutral mutations. Substantially raising or lowering the mutation rate reduced or eliminated the long-term benefit of deleterious mutations, but introducing recombination did not. Our work demonstrates that deleterious mutations can play an important role in adaptive evolution under at least some conditions. PMID:23918358

Contemporary evolution during invasion: evidence for differentiation, natural selection, and local adaptation.

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Colautti, Robert I; Lau, Jennifer A

2015-05-01

Biological invasions are 'natural' experiments that can improve our understanding of contemporary evolution. We evaluate evidence for population differentiation, natural selection and adaptive evolution of invading plants and animals at two nested spatial scales: (i) among introduced populations (ii) between native and introduced genotypes. Evolution during invasion is frequently inferred, but rarely confirmed as adaptive. In common garden studies, quantitative trait differentiation is only marginally lower (~3.5%) among introduced relative to native populations, despite genetic bottlenecks and shorter timescales (i.e. millennia vs. decades). However, differentiation between genotypes from the native vs. introduced range is less clear and confounded by nonrandom geographic sampling; simulations suggest this causes a high false-positive discovery rate (>50%) in geographically structured populations. Selection differentials (¦s¦) are stronger in introduced than in native species, although selection gradients (¦β¦) are not, consistent with introduced species experiencing weaker genetic constraints. This could facilitate rapid adaptation, but evidence is limited. For example, rapid phenotypic evolution often manifests as geographical clines, but simulations demonstrate that nonadaptive trait clines can evolve frequently during colonization (~two-thirds of simulations). Additionally, QST-FST studies may often misrepresent the strength and form of natural selection acting during invasion. Instead, classic approaches in evolutionary ecology (e.g. selection analysis, reciprocal transplant, artificial selection) are necessary to determine the frequency of adaptive evolution during invasion and its influence on establishment, spread and impact of invasive species. These studies are rare but crucial for managing biological invasions in the context of global change. © 2015 John Wiley & Sons Ltd.

Adaptive Multiscale Modeling of Geochemical Impacts on Fracture Evolution

Science.gov (United States)

Molins, S.; Trebotich, D.; Steefel, C. I.; Deng, H.

2016-12-01

Understanding fracture evolution is essential for many subsurface energy applications, including subsurface storage, shale gas production, fracking, CO2 sequestration, and geothermal energy extraction. Geochemical processes in particular play a significant role in the evolution of fractures through dissolution-driven widening, fines migration, and/or fracture sealing due to precipitation. One obstacle to understanding and exploiting geochemical fracture evolution is that it is a multiscale process. However, current geochemical modeling of fractures cannot capture this multi-scale nature of geochemical and mechanical impacts on fracture evolution, and is limited to either a continuum or pore-scale representation. Conventional continuum-scale models treat fractures as preferential flow paths, with their permeability evolving as a function (often, a cubic law) of the fracture aperture. This approach has the limitation that it oversimplifies flow within the fracture in its omission of pore scale effects while also assuming well-mixed conditions. More recently, pore-scale models along with advanced characterization techniques have allowed for accurate simulations of flow and reactive transport within the pore space (Molins et al., 2014, 2015). However, these models, even with high performance computing, are currently limited in their ability to treat tractable domain sizes (Steefel et al., 2013). Thus, there is a critical need to develop an adaptive modeling capability that can account for separate properties and processes, emergent and otherwise, in the fracture and the rock matrix at different spatial scales. Here we present an adaptive modeling capability that treats geochemical impacts on fracture evolution within a single multiscale framework. Model development makes use of the high performance simulation capability, Chombo-Crunch, leveraged by high resolution characterization and experiments. The modeling framework is based on the adaptive capability in Chombo

Exaptation in human evolution: how to test adaptive vs exaptive evolutionary hypotheses.

Science.gov (United States)

Pievani, Telmo; Serrelli, Emanuele

2011-01-01

Palaeontologists, Stephen J. Gould and Elisabeth Vrba, introduced the term "ex-aptation" with the aim of improving and enlarging the scientific language available to researchers studying the evolution of any useful character, instead of calling it an "adaptation" by default, coming up with what Gould named an "extended taxonomy of fitness". With the extension to functional co-optations from non-adaptive structures ("spandrels"), the notion of exaptation expanded and revised the neo-Darwinian concept of "pre-adaptation" (which was misleading, for Gould and Vrba, suggesting foreordination). Exaptation is neither a "saltationist" nor an "anti-Darwinian" concept and, since 1982, has been adopted by many researchers in evolutionary and molecular biology, and particularly in human evolution. Exaptation has also been contested. Objections include the "non-operationality objection".We analyze the possible operationalization of this concept in two recent studies, and identify six directions of empirical research, which are necessary to test "adaptive vs. exaptive" evolutionary hypotheses. We then comment on a comprehensive survey of literature (available online), and on the basis of this we make a quantitative and qualitative evaluation of the adoption of the term among scientists who study human evolution. We discuss the epistemic conditions that may have influenced the adoption and appropriate use of exaptation, and comment on the benefits of an "extended taxonomy of fitness" in present and future studies concerning human evolution.

Adapting Digital Libraries to Continual Evolution

Science.gov (United States)

Barkstrom, Bruce R.; Finch, Melinda; Ferebee, Michelle; Mackey, Calvin

2002-01-01

In this paper, we describe five investment streams (data storage infrastructure, knowledge management, data production control, data transport and security, and personnel skill mix) that need to be balanced against short-term operating demands in order to maximize the probability of long-term viability of a digital library. Because of the rapid pace of information technology change, a digital library cannot be a static institution. Rather, it has to become a flexible organization adapted to continuous evolution of its infrastructure.

Increased tolerance towards serine obtained by adaptive laboratory evolution

DEFF Research Database (Denmark)

Mundhada, Hemanshu; Seoane, Jose Miguel; Koza, Anna

2014-01-01

The amino acid serine has previously been identified as one of the top 30 candidates of value added chemicals, making the production of serine from glucose attractive. Production of serine have previously been attempted in E. coli and C. glutamicum, however, titers sufficient for commercial...... by glyA), the conversion of serine to pyruvate (encoded by sdaA, sdaB and tdcG) was also deleted. As expected, the resulting strain turned out to be susceptible to even low concentrations of serine in the media. In order to improve the tolerance of the strain towards serine, adaptive laboratory evolution....... During the evolution experiment, the serine tolerance was increased substantially. Genome re-sequencing was subsequently used to analyze the genotype of a number of selected strains. These results reveal insights towards the adaptation process as well as the mechanism of serine tolerance....

Genetic variation in adaptability and pleiotropy in budding yeast.

Science.gov (United States)

Jerison, Elizabeth R; Kryazhimskiy, Sergey; Mitchell, James Kameron; Bloom, Joshua S; Kruglyak, Leonid; Desai, Michael M

2017-08-17

Evolution can favor organisms that are more adaptable, provided that genetic variation in adaptability exists. Here, we quantify this variation among 230 offspring of a cross between diverged yeast strains. We measure the adaptability of each offspring genotype, defined as its average rate of adaptation in a specific environmental condition, and analyze the heritability, predictability, and genetic basis of this trait. We find that initial genotype strongly affects adaptability and can alter the genetic basis of future evolution. Initial genotype also affects the pleiotropic consequences of adaptation for fitness in a different environment. This genetic variation in adaptability and pleiotropy is largely determined by initial fitness, according to a rule of declining adaptability with increasing initial fitness, but several individual QTLs also have a significant idiosyncratic role. Our results demonstrate that both adaptability and pleiotropy are complex traits, with extensive heritable differences arising from naturally occurring variation.

Evolution of Genetic Variance during Adaptive Radiation.

Science.gov (United States)

Walter, Greg M; Aguirre, J David; Blows, Mark W; Ortiz-Barrientos, Daniel

2018-04-01

Genetic correlations between traits can concentrate genetic variance into fewer phenotypic dimensions that can bias evolutionary trajectories along the axis of greatest genetic variance and away from optimal phenotypes, constraining the rate of evolution. If genetic correlations limit adaptation, rapid adaptive divergence between multiple contrasting environments may be difficult. However, if natural selection increases the frequency of rare alleles after colonization of new environments, an increase in genetic variance in the direction of selection can accelerate adaptive divergence. Here, we explored adaptive divergence of an Australian native wildflower by examining the alignment between divergence in phenotype mean and divergence in genetic variance among four contrasting ecotypes. We found divergence in mean multivariate phenotype along two major axes represented by different combinations of plant architecture and leaf traits. Ecotypes also showed divergence in the level of genetic variance in individual traits and the multivariate distribution of genetic variance among traits. Divergence in multivariate phenotypic mean aligned with divergence in genetic variance, with much of the divergence in phenotype among ecotypes associated with changes in trait combinations containing substantial levels of genetic variance. Overall, our results suggest that natural selection can alter the distribution of genetic variance underlying phenotypic traits, increasing the amount of genetic variance in the direction of natural selection and potentially facilitating rapid adaptive divergence during an adaptive radiation.

Pollinator adaptation and the evolution of floral nectar sugar composition.

Science.gov (United States)

Abrahamczyk, S; Kessler, M; Hanley, D; Karger, D N; Müller, M P J; Knauer, A C; Keller, F; Schwerdtfeger, M; Humphreys, A M

2017-01-01

A long-standing debate concerns whether nectar sugar composition evolves as an adaptation to pollinator dietary requirements or whether it is 'phylogenetically constrained'. Here, we use a modelling approach to evaluate the hypothesis that nectar sucrose proportion (NSP) is an adaptation to pollinators. We analyse ~ 2100 species of asterids, spanning several plant families and pollinator groups (PGs), and show that the hypothesis of adaptation cannot be rejected: NSP evolves towards two optimal values, high NSP for specialist-pollinated and low NSP for generalist-pollinated plants. However, the inferred adaptive process is weak, suggesting that adaptation to PG only provides a partial explanation for how nectar evolves. Additional factors are therefore needed to fully explain nectar evolution, and we suggest that future studies might incorporate floral shape and size and the abiotic environment into the analytical framework. Further, we show that NSP and PG evolution are correlated - in a manner dictated by pollinator behaviour. This contrasts with the view that a plant necessarily has to adapt its nectar composition to ensure pollination but rather suggests that pollinators adapt their foraging behaviour or dietary requirements to the nectar sugar composition presented by the plants. Finally, we document unexpectedly sucrose-poor nectar in some specialized nectarivorous bird-pollinated plants from the Old World, which might represent an overlooked form of pollinator deception. Thus, our broad study provides several new insights into how nectar evolves and we conclude by discussing why maintaining the conceptual dichotomy between adaptation and constraint might be unhelpful for advancing this field. © 2016 European Society For Evolutionary Biology. Journal of Evolutionary Biology © 2016 European Society For Evolutionary Biology.

Extensive X-linked adaptive evolution in central chimpanzees

DEFF Research Database (Denmark)

Hvilsom, Christina; Qian, Yu; Bataillon, Thomas

2012-01-01

on the dominance of beneficial (adaptive) and deleterious mutations. Here we capture and sequence the complete exomes of 12 chimpanzees and present the largest set of protein-coding polymorphism to date. We report extensive adaptive evolution specifically targeting the X chromosome of chimpanzees with as much...... to humans, we find that purifying selection is stronger on the X chromosome than on the autosomes in chimpanzees. We therefore conclude that most adaptive mutations are recessive. We also document dramatically reduced synonymous diversity in the chimpanzee X chromosome relative to autosomes and stronger...... purifying selection than for the human X chromosome. If similar processes were operating in the human-chimpanzee ancestor as in central chimpanzees today, our results therefore provide an explanation for the much-discussed reduction in the human-chimpanzee divergence at the X chromosome....

Trans gene regulation in adaptive evolution: a genetic algorithm model.

Science.gov (United States)

Behera, N; Nanjundiah, V

1997-09-21

This is a continuation of earlier studies on the evolution of infinite populations of haploid genotypes within a genetic algorithm framework. We had previously explored the evolutionary consequences of the existence of indeterminate-"plastic"-loci, where a plastic locus had a finite probability in each generation of functioning (being switched "on") or not functioning (being switched "off"). The relative probabilities of the two outcomes were assigned on a stochastic basis. The present paper examines what happens when the transition probabilities are biased by the presence of regulatory genes. We find that under certain conditions regulatory genes can improve the adaptation of the population and speed up the rate of evolution (on occasion at the cost of lowering the degree of adaptation). Also, the existence of regulatory loci potentiates selection in favour of plasticity. There is a synergistic effect of regulatory genes on plastic alleles: the frequency of such alleles increases when regulatory loci are present. Thus, phenotypic selection alone can be a potentiating factor in a favour of better adaptation. Copyright 1997 Academic Press Limited.

Evolution of Cooperation in Adaptive Social Networks

Science.gov (United States)

Segbroeck, Sven Van; Santos, Francisco C.; Traulsen, Arne; Lenaerts, Tom; Pacheco, Jorge M.

Humans are organized in societies, a phenomenon that would never have been possible without the evolution of cooperative behavior. Several mechanisms that foster this evolution have been unraveled over the years, with population structure as a prominent promoter of cooperation. Modern networks of exchange and cooperation are, however, becoming increasingly volatile, and less and less based on long-term stable structure. Here, we address how this change of paradigm aspects the evolution of cooperation. We discuss analytical and numerical models in which individuals can break social ties and create new ones. Interactions are modeled as two-player dilemmas of cooperation. Once a link between two individuals has formed, the productivity of this link is evaluated. Links can be broken off at different rates. This individual capacity of forming new links or severing inconvenient ones can effectively change the nature of the game. We address random formation of new links and local linking rules as well as different individual capacities to maintain social interactions. We conclude by discussing how adaptive social networks can become an important step towards more realistic models of cultural dynamics.

Exploiting adaptive laboratory evolution of Streptomyces clavuligerus for antibiotic discovery and overproduction.

Directory of Open Access Journals (Sweden)

Pep Charusanti

Full Text Available Adaptation is normally viewed as the enemy of the antibiotic discovery and development process because adaptation among pathogens to antibiotic exposure leads to resistance. We present a method here that, in contrast, exploits the power of adaptation among antibiotic producers to accelerate the discovery of antibiotics. A competition-based adaptive laboratory evolution scheme is presented whereby an antibiotic-producing microorganism is competed against a target pathogen and serially passed over time until the producer evolves the ability to synthesize a chemical entity that inhibits growth of the pathogen. When multiple Streptomyces clavuligerus replicates were adaptively evolved against methicillin-resistant Staphylococcus aureus N315 in this manner, a strain emerged that acquired the ability to constitutively produce holomycin. In contrast, no holomycin could be detected from the unevolved wild-type strain. Moreover, genome re-sequencing revealed that the evolved strain had lost pSCL4, a large 1.8 Mbp plasmid, and acquired several single nucleotide polymorphisms in genes that have been shown to affect secondary metabolite biosynthesis. These results demonstrate that competition-based adaptive laboratory evolution can constitute a platform to create mutants that overproduce known antibiotics and possibly to discover new compounds as well.

Camelid genomes reveal evolution and adaptation to desert environments.

Science.gov (United States)

Wu, Huiguang; Guang, Xuanmin; Al-Fageeh, Mohamed B; Cao, Junwei; Pan, Shengkai; Zhou, Huanmin; Zhang, Li; Abutarboush, Mohammed H; Xing, Yanping; Xie, Zhiyuan; Alshanqeeti, Ali S; Zhang, Yanru; Yao, Qiulin; Al-Shomrani, Badr M; Zhang, Dong; Li, Jiang; Manee, Manee M; Yang, Zili; Yang, Linfeng; Liu, Yiyi; Zhang, Jilin; Altammami, Musaad A; Wang, Shenyuan; Yu, Lili; Zhang, Wenbin; Liu, Sanyang; Ba, La; Liu, Chunxia; Yang, Xukui; Meng, Fanhua; Wang, Shaowei; Li, Lu; Li, Erli; Li, Xueqiong; Wu, Kaifeng; Zhang, Shu; Wang, Junyi; Yin, Ye; Yang, Huanming; Al-Swailem, Abdulaziz M; Wang, Jun

2014-10-21

Bactrian camel (Camelus bactrianus), dromedary (Camelus dromedarius) and alpaca (Vicugna pacos) are economically important livestock. Although the Bactrian camel and dromedary are large, typically arid-desert-adapted mammals, alpacas are adapted to plateaus. Here we present high-quality genome sequences of these three species. Our analysis reveals the demographic history of these species since the Tortonian Stage of the Miocene and uncovers a striking correlation between large fluctuations in population size and geological time boundaries. Comparative genomic analysis reveals complex features related to desert adaptations, including fat and water metabolism, stress responses to heat, aridity, intense ultraviolet radiation and choking dust. Transcriptomic analysis of Bactrian camels further reveals unique osmoregulation, osmoprotection and compensatory mechanisms for water reservation underpinned by high blood glucose levels. We hypothesize that these physiological mechanisms represent kidney evolutionary adaptations to the desert environment. This study advances our understanding of camelid evolution and the adaptation of camels to arid-desert environments.

Numerically-quantified two dimensionality of microstructure evolution accompanying variant selection of FePd

International Nuclear Information System (INIS)

Ueshima, N; Yoshiya, M; Yasuda, H; Fukuda, T; Kakeshita, T

2015-01-01

Through three-dimensional (3D) simulations of microstructure evolution by phase-field modeling (PFM), microstructures have been quantified during their time evolution by an image processing technique with particular attention to the shape of variants in the course of variant selection. It is found that the emerging variants exhibit planar shapes rather than 3D shapes due to the elastic field around the variants arising upon disorder-to-order transition to the L1 0 phase. The two-dimensionality is more pronounced as variant selection proceeds. Although three equivalent variants compete for dominance under an external field, one of the three variants vanishes before final competition occurs between the remaining variants, which can be explained by the elastic strain energy. These numerical analyses provide better understanding of the microstructure evolution in a more quantitative manner, including the small influence of the third variant, and the results obtained confirm that the understanding of variant selection obtained from two-dimensional (2D) simulations by PFM is valid. (paper)

Adaptive CGFs Based on Grammatical Evolution

Directory of Open Access Journals (Sweden)

Jian Yao

2015-01-01

Full Text Available Computer generated forces (CGFs play blue or red units in military simulations for personnel training and weapon systems evaluation. Traditionally, CGFs are controlled through rule-based scripts, despite the doctrine-driven behavior of CGFs being rigid and predictable. Furthermore, CGFs are often tricked by trainees or fail to adapt to new situations (e.g., changes in battle field or update in weapon systems, and, in most cases, the subject matter experts (SMEs review and redesign a large amount of CGF scripts for new scenarios or training tasks, which is both challenging and time-consuming. In an effort to overcome these limitations and move toward more true-to-life scenarios, a study using grammatical evolution (GE to generate adaptive CGFs for air combat simulations has been conducted. Expert knowledge is encoded with modular behavior trees (BTs for compatibility with the operators in genetic algorithm (GA. GE maps CGFs, represented with BTs to binary strings, and uses GA to evolve CGFs with performance feedback from the simulation. Beyond-visual-range air combat experiments between adaptive CGFs and nonadaptive baseline CGFs have been conducted to observe and study this evolutionary process. The experimental results show that the GE is an efficient framework to generate CGFs in BTs formalism and evolve CGFs via GA.

Identification of genes that have undergone adaptive evolution in ...

African Journals Online (AJOL)

Cassava (Manihot esculenta) is a vital food security crop and staple in Africa, yet cassava brown streak disease (CBSD) and cassava mosaic disease result in substantial yield losses. The aim of this study was to identify genes that have undergone positive selection during adaptive evolution, from CBSD resistant, tolerant ...

Molecular evolution of rbcL in three gymnosperm families: identifying adaptive and coevolutionary patterns

LENUS (Irish Health Repository)

Sen, Lin

2011-06-03

Abstract Background The chloroplast-localized ribulose-1, 5-biphosphate carboxylase\\/oxygenase (Rubisco), the primary enzyme responsible for autotrophy, is instrumental in the continual adaptation of plants to variations in the concentrations of CO2. The large subunit (LSU) of Rubisco is encoded by the chloroplast rbcL gene. Although adaptive processes have been previously identified at this gene, characterizing the relationships between the mutational dynamics at the protein level may yield clues on the biological meaning of such adaptive processes. The role of such coevolutionary dynamics in the continual fine-tuning of RbcL remains obscure. Results We used the timescale and phylogenetic analyses to investigate and search for processes of adaptive evolution in rbcL gene in three gymnosperm families, namely Podocarpaceae, Taxaceae and Cephalotaxaceae. To understand the relationships between regions identified as having evolved under adaptive evolution, we performed coevolutionary analyses using the software CAPS. Importantly, adaptive processes were identified at amino acid sites located on the contact regions among the Rubisco subunits and on the interface between Rubisco and its activase. Adaptive amino acid replacements at these regions may have optimized the holoenzyme activity. This hypothesis was pinpointed by evidence originated from our analysis of coevolution that supported the correlated evolution between Rubisco and its activase. Interestingly, the correlated adaptive processes between both these proteins have paralleled the geological variation history of the concentration of atmospheric CO2. Conclusions The gene rbcL has experienced bursts of adaptations in response to the changing concentration of CO2 in the atmosphere. These adaptations have emerged as a result of a continuous dynamic of mutations, many of which may have involved innovation of functional Rubisco features. Analysis of the protein structure and the functional implications of such

Mechanisms of adaptive evolution. Darwinism and Lamarckism restated.

Science.gov (United States)

Aboitiz, F

1992-07-01

This article discusses the conceptual basis of the different mechanisms of adaptive evolution. It is argued that only two such mechanisms may conceivably exist, Lamarckism and Darwinism. Darwinism is the fundamental process generating the diversity of species. Some aspects of the gene-centered approach to Darwinism are questioned, since they do not account for the generation of biological diversity. Diversity in biological design must be explained in relation to the diversity of interactions of organisms (or other higher-level units) with their environment. This aspect is usually overlooked in gene-centered views of evolution. A variant of the gene-selectionist approach has been proposed to account for the spread of cultural traits in human societies. Alternatively, I argue that social evolution is rather driven by what I call pseudo-Lamarckian inheritance. Finally, I argue that Lamarckian and pseudo-Lamarckian inheritance are just special cases of faithful replication which are found in the development of some higher-order units, such as multicellular organisms and human societies.

Evidence for adaptive evolution of low-temperature stress response genes in a Pooideae grass ancestor

DEFF Research Database (Denmark)

Vigeland, Magnus D; Spannagl, Manuel; Asp, Torben

2013-01-01

Adaptation to temperate environments is common in the grass subfamily Pooideae, suggesting an ancestral origin of cold climate adaptation. Here, we investigated substitution rates of genes involved in low-temperature-induced (LTI) stress responses to test the hypothesis that adaptive molecular...... evolution of LTI pathway genes was important for Pooideae evolution. Substitution rates and signatures of positive selection were analyzed using 4330 gene trees including three warm climate-adapted species (maize (Zea mays), sorghum (Sorghum bicolor), and rice (Oryza sativa)) and five temperate Pooideae...... species (Brachypodium distachyon, wheat (Triticum aestivum), barley (Hordeum vulgare), Lolium perenne and Festuca pratensis). Nonsynonymous substitution rate differences between Pooideae and warm habitat-adapted species were elevated in LTI trees compared with all trees. Furthermore, signatures...

Rampant adaptive evolution in regions of proteins with unknown function in Drosophila simulans.

Directory of Open Access Journals (Sweden)

Alisha K Holloway

2007-10-01

Full Text Available Adaptive protein evolution is pervasive in Drosophila. Genomic studies, thus far, have analyzed each protein as a single entity. However, the targets of adaptive events may be localized to particular parts of proteins, such as protein domains or regions involved in protein folding. We compared the population genetic mechanisms driving sequence polymorphism and divergence in defined protein domains and non-domain regions. Interestingly, we find that non-domain regions of proteins are more frequent targets of directional selection. Protein domains are also evolving under directional selection, but appear to be under stronger purifying selection than non-domain regions. Non-domain regions of proteins clearly play a major role in adaptive protein evolution on a genomic scale and merit future investigations of their functional properties.

Adaptive evolution of the vertebrate skeletal muscle sodium channel

Directory of Open Access Journals (Sweden)

Jian Lu

2011-01-01

Full Text Available Tetrodotoxin (TTX is a highly potent neurotoxin that blocks the action potential by selectively binding to voltage-gated sodium channels (Na v. The skeletal muscle Na v (Na v1.4 channels in most pufferfish species and certain North American garter snakes are resistant to TTX, whereas in most mammals they are TTX-sensitive. It still remains unclear as to whether the difference in this sensitivity among the various vertebrate species can be associated with adaptive evolution. In this study, we investigated the adaptive evolution of the vertebrate Na v1.4 channels. By means of the CODEML program of the PAML 4.3 package, the lineages of both garter snakes and pufferfishes were denoted to be under positive selection. The positively selected sites identified in the p-loop regions indicated their involvement in Na v1.4 channel sensitivity to TTX. Most of these sites were located in the intracellular regions of the Na v1.4 channel, thereby implying the possible association of these regions with the regulation of voltage-sensor movement.

Gene expression and adaptive noncoding changes during human evolution.

Science.gov (United States)

Babbitt, Courtney C; Haygood, Ralph; Nielsen, William J; Wray, Gregory A

2017-06-05

Despite evidence for adaptive changes in both gene expression and non-protein-coding, putatively regulatory regions of the genome during human evolution, the relationship between gene expression and adaptive changes in cis-regulatory regions remains unclear. Here we present new measurements of gene expression in five tissues of humans and chimpanzees, and use them to assess this relationship. We then compare our results with previous studies of adaptive noncoding changes, analyzing correlations at the level of gene ontology groups, in order to gain statistical power to detect correlations. Consistent with previous studies, we find little correlation between gene expression and adaptive noncoding changes at the level of individual genes; however, we do find significant correlations at the level of biological function ontology groups. The types of function include processes regulated by specific transcription factors, responses to genetic or chemical perturbations, and differentiation of cell types within the immune system. Among functional categories co-enriched with both differential expression and noncoding adaptation, prominent themes include cancer, particularly epithelial cancers, and neural development and function.

Adaptive evolution and effective population size in wild house mice

Czech Academy of Sciences Publication Activity Database

Phifer-Rixey, M.; Bonhomme, F.; Boursot, P.; Churchill, G. A.; Piálek, Jaroslav; Tucker, P.; Nachman, M.

2012-01-01

Roč. 29, č. 10 (2012), s. 2949-2955 ISSN 0737-4038 R&D Projects: GA ČR GA206/08/0640 Institutional support: RVO:68081766 Keywords : substitution * adaptation * evolution * effective population size * house mouse Subject RIV: EG - Zoology Impact factor: 10.353, year: 2012

Adaptive evolution in locomotor performance: How selective pressures and functional relationships produce diversity.

Science.gov (United States)

Scales, Jeffrey A; Butler, Marguerite A

2016-01-01

Despite the complexity of nature, most comparative studies of phenotypic evolution consider selective pressures in isolation. When competing pressures operate on the same system, it is commonly expected that trade-offs will occur that will limit the evolution of phenotypic diversity, however, it is possible that interactions among selective pressures may promote diversity instead. We explored the evolution of locomotor performance in lizards in relation to possible selective pressures using the Ornstein-Uhlenbeck process. Here, we show that a combination of selection based on foraging mode and predator escape is required to explain variation in performance phenotypes. Surprisingly, habitat use contributed little explanatory power. We find that it is possible to evolve very different abilities in performance which were previously thought to be tightly correlated, supporting a growing literature that explores the many-to-one mapping of morphological design. Although we generally find the expected trade-off between maximal exertion and speed, this relationship surprisingly disappears when species experience selection for both performance types. We conclude that functional integration need not limit adaptive potential, and that an integrative approach considering multiple major influences on a phenotype allows a more complete understanding of adaptation and the evolution of diversity. © 2015 The Author(s). Evolution © 2015 The Society for the Study of Evolution.

The ongoing adaptive evolution of ASPM and Microcephalin is not explained by increased intelligence.

NARCIS (Netherlands)

Mekel-Bobrov, N.; Posthuma, D.; Gilbert, S.L.; Lind, P.; Gosso, M.F.; Luciano, M.; Harris, S.E.; Bates, T.C.; Polderman, T.J.C.; Whalley, L.J.; Fox, H.; Starr, J.M.; Evans, P.D.; Montgomery, GW; Fernandes, C.; Heutink, P.; Martin, N.G.; Boomsma, D.I.; Deary, I.J.; Wright, M.J.; de Geus, E.J.C.; Lahn, B.T.

2007-01-01

Recent studies have made great strides towards identifying putative genetic events underlying the evolution of the human brain and its emergent cognitive capacities. One of the most intriguing findings is the recurrent identification of adaptive evolution in genes associated with primary

Biodiversity, evolution and adaptation of cultivated crops.

Science.gov (United States)

Vigouroux, Yves; Barnaud, Adeline; Scarcelli, Nora; Thuillet, Anne-Céline

2011-05-01

The human diet depends on very few crops. Current diversity in these crops is the result of a long interaction between farmers and cultivated plants, and their environment. Man largely shaped crop biodiversity from the domestication period 12,000 B.P. to the development of improved varieties during the last century. We illustrate this process through a detailed analysis of the domestication and early diffusion of maize. In smallholder agricultural systems, farmers still have a major impact on crop diversity today. We review several examples of the major impact of man on current diversity. Finally, biodiversity is considered to be an asset for adaptation to current environmental changes. We describe the evolution of pearl millet in West Africa, where average rainfall has decreased over the last forty years. Diversity in cultivated varieties has certainly helped this crop to adapt to climate variation. Copyright © 2011 Académie des sciences. Published by Elsevier SAS. All rights reserved.

Parameter extraction of different fuel cell models with transferred adaptive differential evolution

International Nuclear Information System (INIS)

Gong, Wenyin; Yan, Xuesong; Liu, Xiaobo; Cai, Zhihua

2015-01-01

To improve the design and control of FC (fuel cell) models, it is important to extract their unknown parameters. Generally, the parameter extraction problems of FC models can be transformed as nonlinear and multi-variable optimization problems. To extract the parameters of different FC models exactly and fast, in this paper, we propose a transferred adaptive DE (differential evolution) framework, in which the successful parameters of the adaptive DE solving previous problems are properly transferred to solve new optimization problems in the similar problem-domains. Based on this framework, an improved adaptive DE method (TRADE, in short) is presented as an illustration. To verify the performance of our proposal, TRADE is used to extract the unknown parameters of two types of fuel cell models, i.e., PEMFC (proton exchange membrane fuel cell) and SOFC (solid oxide fuel cell). The results of TRADE are also compared with those of other state-of-the-art EAs (evolutionary algorithms). Even though the modification is very simple, the results indicate that TRADE can extract the parameters of both PEMFC and SOFC models exactly and fast. Moreover, the V–I characteristics obtained by TRADE agree well with the simulated and experimental data in all cases for both types of fuel cell models. Also, it improves the performance of the original adaptive DE significantly in terms of both the quality of final solutions and the convergence speed in all cases. Additionally, TRADE is able to provide better results compared with other EAs. - Highlights: • A framework of transferred adaptive differential evolution is proposed. • Based on the framework, an improved differential evolution (TRADE) is presented. • TRADE obtains very promising results to extract the parameters of PEMFC and SOFC models

A Self Adaptive Differential Evolution Algorithm for Global Optimization

Science.gov (United States)

Kumar, Pravesh; Pant, Millie

This paper presents a new Differential Evolution algorithm based on hybridization of adaptive control parameters and trigonometric mutation. First we propose a self adaptive DE named ADE where choice of control parameter F and Cr is not fixed at some constant value but is taken iteratively. The proposed algorithm is further modified by applying trigonometric mutation in it and the corresponding algorithm is named as ATDE. The performance of ATDE is evaluated on the set of 8 benchmark functions and the results are compared with the classical DE algorithm in terms of average fitness function value, number of function evaluations, convergence time and success rate. The numerical result shows the competence of the proposed algorithm.

Genomics of adaptation during experimental evolution of the opportunistic pathogen Pseudomonas aeruginosa.

Directory of Open Access Journals (Sweden)

Alex Wong

2012-09-01

Full Text Available Adaptation is likely to be an important determinant of the success of many pathogens, for example when colonizing a new host species, when challenged by antibiotic treatment, or in governing the establishment and progress of long-term chronic infection. Yet, the genomic basis of adaptation is poorly understood in general, and for pathogens in particular. We investigated the genetics of adaptation to cystic fibrosis-like culture conditions in the presence and absence of fluoroquinolone antibiotics using the opportunistic pathogen Pseudomonas aeruginosa. Whole-genome sequencing of experimentally evolved isolates revealed parallel evolution at a handful of known antibiotic resistance genes. While the level of antibiotic resistance was largely determined by these known resistance genes, the costs of resistance were instead attributable to a number of mutations that were specific to individual experimental isolates. Notably, stereotypical quinolone resistance mutations in DNA gyrase often co-occurred with other mutations that, together, conferred high levels of resistance but no consistent cost of resistance. This result may explain why these mutations are so prevalent in clinical quinolone-resistant isolates. In addition, genes involved in cyclic-di-GMP signalling were repeatedly mutated in populations evolved in viscous culture media, suggesting a shared mechanism of adaptation to this CF-like growth environment. Experimental evolutionary approaches to understanding pathogen adaptation should provide an important complement to studies of the evolution of clinical isolates.

Evolution of plasticity and adaptive responses to climate change along climate gradients.

Science.gov (United States)

Kingsolver, Joel G; Buckley, Lauren B

2017-08-16

The relative contributions of phenotypic plasticity and adaptive evolution to the responses of species to recent and future climate change are poorly understood. We combine recent (1960-2010) climate and phenotypic data with microclimate, heat balance, demographic and evolutionary models to address this issue for a montane butterfly, Colias eriphyle , along an elevational gradient. Our focal phenotype, wing solar absorptivity, responds plastically to developmental (pupal) temperatures and plays a central role in thermoregulatory adaptation in adults. Here, we show that both the phenotypic and adaptive consequences of plasticity vary with elevation. Seasonal changes in weather generate seasonal variation in phenotypic selection on mean and plasticity of absorptivity, especially at lower elevations. In response to climate change in the past 60 years, our models predict evolutionary declines in mean absorptivity (but little change in plasticity) at high elevations, and evolutionary increases in plasticity (but little change in mean) at low elevation. The importance of plasticity depends on the magnitude of seasonal variation in climate relative to interannual variation. Our results suggest that selection and evolution of both trait means and plasticity can contribute to adaptive response to climate change in this system. They also illustrate how plasticity can facilitate rather than retard adaptive evolutionary responses to directional climate change in seasonal environments. © 2017 The Author(s).

Adaptive Laboratory Evolution of Antibiotic Resistance Using Different Selection Regimes Lead to Similar Phenotypes and Genotypes

DEFF Research Database (Denmark)

Jahn, Leonie Johanna; Munck, Christian; Ellabaan, Mostafa M Hashim

2017-01-01

independently of the selection regime. Yet, lineages that underwent evolution under mild selection displayed a growth advantage independently of the acquired level of antibiotic resistance compared to lineages adapted under maximal selection in a drug gradient. Our data suggests that even though different......Antibiotic resistance is a global threat to human health, wherefore it is crucial to study the mechanisms of antibiotic resistance as well as its emergence and dissemination. One way to analyze the acquisition of de novo mutations conferring antibiotic resistance is adaptive laboratory evolution....... However, various evolution methods exist that utilize different population sizes, selection strengths, and bottlenecks. While evolution in increasing drug gradients guarantees high-level antibiotic resistance promising to identify the most potent resistance conferring mutations, other selection regimes...

Adaptive evolution of benzoxazinoids in wild emmer wheat, Triticum dicoccoides, at "Evolution Canyon", Mount Carmel, Israel.

Science.gov (United States)

Ben-Abu, Yuval; Beiles, Avigdor; Flom, Dvir; Nevo, Eviatar

2018-01-01

"Evolution Canyon" (ECI) at Lower Nahal Oren, Mount Carmel, Israel, is an optimal natural microscale model for unraveling evolution-in-action, highlighting the evolutionary processes of biodiversity evolution, adaptation, and incipient sympatric speciation. A major model organism in ECI is the tetraploid wild emmer wheat, Triticum dicoccoides (TD), the progenitor of cultivated emmer and durum wheat. TD displays dramatic interslope adaptive evolutionary divergence on the tropical, savannoid-hot and dry south-facing, "African" slope (AS), and on the temperate, forested, cool and humid, north-facing, "European" slope (ES), separated on average by 250 m. From the perspective of chemical evolution and metabolomics, it is important to unravel interslope divergence in biologically relevant secondary metabolites between the abutting slope populations. Here, in TD we examined hydroxamic acid (Hx), which is a family of secondary cereal metabolites, and plays a major role in defending the plant against fungi, insects and weeds. Our examination revealed that higher concentrations of DIBOA and DIMBOA were found in seedlings growing in the same greenhouse from seeds collected from the cool and humid forested ES, whereas the seedlings of seeds collected from the savannoid AS (both in root and shoot tissues), showed no DIMBOA. Remarkably, only DIBOA appears in both shoots and roots of the AS seedlings. It rises to a peak and then decreases in both organs and in seedlings from both slopes. The DIMBOA, which appears only in the ES seedlings, rises to a peak and decreases in the shoot, but increased and remained in a plateau in the root, till the end of the experiment. The results suggest stronger genetic resistance of defense compounds DIBOA and DIMBOA against biotic stresses (fungi and other pathogens) by ES seedlings. However, AS seedlings responded earlier but were to the same biotic stresses. The genetic difference found in AS seedlings was caused by the main adaptive selection

Adaptive evolution of benzoxazinoids in wild emmer wheat, Triticum dicoccoides, at "Evolution Canyon", Mount Carmel, Israel.

Directory of Open Access Journals (Sweden)

Yuval Ben-Abu

Full Text Available "Evolution Canyon" (ECI at Lower Nahal Oren, Mount Carmel, Israel, is an optimal natural microscale model for unraveling evolution-in-action, highlighting the evolutionary processes of biodiversity evolution, adaptation, and incipient sympatric speciation. A major model organism in ECI is the tetraploid wild emmer wheat, Triticum dicoccoides (TD, the progenitor of cultivated emmer and durum wheat. TD displays dramatic interslope adaptive evolutionary divergence on the tropical, savannoid-hot and dry south-facing, "African" slope (AS, and on the temperate, forested, cool and humid, north-facing, "European" slope (ES, separated on average by 250 m. From the perspective of chemical evolution and metabolomics, it is important to unravel interslope divergence in biologically relevant secondary metabolites between the abutting slope populations. Here, in TD we examined hydroxamic acid (Hx, which is a family of secondary cereal metabolites, and plays a major role in defending the plant against fungi, insects and weeds.Our examination revealed that higher concentrations of DIBOA and DIMBOA were found in seedlings growing in the same greenhouse from seeds collected from the cool and humid forested ES, whereas the seedlings of seeds collected from the savannoid AS (both in root and shoot tissues, showed no DIMBOA. Remarkably, only DIBOA appears in both shoots and roots of the AS seedlings. It rises to a peak and then decreases in both organs and in seedlings from both slopes. The DIMBOA, which appears only in the ES seedlings, rises to a peak and decreases in the shoot, but increased and remained in a plateau in the root, till the end of the experiment.The results suggest stronger genetic resistance of defense compounds DIBOA and DIMBOA against biotic stresses (fungi and other pathogens by ES seedlings. However, AS seedlings responded earlier but were to the same biotic stresses. The genetic difference found in AS seedlings was caused by the main adaptive

Pervasive Adaptive Evolution in Primate Seminal Proteins.

Directory of Open Access Journals (Sweden)

2005-09-01

Full Text Available Seminal fluid proteins show striking effects on reproduction, involving manipulation of female behavior and physiology, mechanisms of sperm competition, and pathogen defense. Strong adaptive pressures are expected for such manifestations of sexual selection and host defense, but the extent of positive selection in seminal fluid proteins from divergent taxa is unknown. We identified adaptive evolution in primate seminal proteins using genomic resources in a tissue-specific study. We found extensive signatures of positive selection when comparing 161 human seminal fluid proteins and 2,858 prostate-expressed genes to those in chimpanzee. Seven of eight outstanding genes yielded statistically significant evidence of positive selection when analyzed in divergent primates. Functional clues were gained through divergent analysis, including several cases of species-specific loss of function in copulatory plug genes, and statistically significant spatial clustering of positively selected sites near the active site of kallikrein 2. This study reveals previously unidentified positive selection in seven primate seminal proteins, and when considered with findings in Drosophila, indicates that extensive positive selection is found in seminal fluid across divergent taxonomic groups.

Adaptive evolution of facial colour patterns in Neotropical primates

OpenAIRE

Santana, Sharlene E.; Lynch Alfaro, Jessica; Alfaro, Michael E.

2012-01-01

The rich diversity of primate faces has interested naturalists for over a century. Researchers have long proposed that social behaviours have shaped the evolution of primate facial diversity. However, the primate face constitutes a unique structure where the diverse and potentially competing functions of communication, ecology and physiology intersect, and the major determinants of facial diversity remain poorly understood. Here, we provide the first evidence for an adaptive role of facial co...

Implications of prion adaptation and evolution paradigm for human neurodegenerative diseases.

Science.gov (United States)

Kabir, M Enamul; Safar, Jiri G

2014-01-01

There is a growing body of evidence indicating that number of human neurodegenerative diseases, including Alzheimer disease, Parkinson disease, fronto-temporal dementias, and amyotrophic lateral sclerosis, propagate in the brain via prion-like intercellular induction of protein misfolding. Prions cause lethal neurodegenerative diseases in humans, the most prevalent being sporadic Creutzfeldt-Jakob disease (sCJD); they self-replicate and spread by converting the cellular form of prion protein (PrP(C)) to a misfolded pathogenic conformer (PrP(Sc)). The extensive phenotypic heterogeneity of human prion diseases is determined by polymorphisms in the prion protein gene, and by prion strain-specific conformation of PrP(Sc). Remarkably, even though informative nucleic acid is absent, prions may undergo rapid adaptation and evolution in cloned cells and upon crossing the species barrier. In the course of our investigation of this process, we isolated distinct populations of PrP(Sc) particles that frequently co-exist in sCJD. The human prion particles replicate independently and undergo competitive selection of those with lower initial conformational stability. Exposed to mutant substrate, the winning PrP(Sc) conformers are subject to further evolution by natural selection of the subpopulation with the highest replication rate due to the lowest stability. Thus, the evolution and adaptation of human prions is enabled by a dynamic collection of distinct populations of particles, whose evolution is governed by the selection of progressively less stable, faster replicating PrP(Sc) conformers. This fundamental biological mechanism may explain the drug resistance that some prions gained after exposure to compounds targeting PrP(Sc). Whether the phenotypic heterogeneity of other neurodegenerative diseases caused by protein misfolding is determined by the spectrum of misfolded conformers (strains) remains to be established. However, the prospect that these conformers may evolve and

APPLICATION OF RESTART COVARIANCE MATRIX ADAPTATION EVOLUTION STRATEGY (RCMA-ES TO GENERATION EXPANSION PLANNING PROBLEM

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K. Karthikeyan

2012-10-01

Full Text Available This paper describes the application of an evolutionary algorithm, Restart Covariance Matrix Adaptation Evolution Strategy (RCMA-ES to the Generation Expansion Planning (GEP problem. RCMA-ES is a class of continuous Evolutionary Algorithm (EA derived from the concept of self-adaptation in evolution strategies, which adapts the covariance matrix of a multivariate normal search distribution. The original GEP problem is modified by incorporating Virtual Mapping Procedure (VMP. The GEP problem of a synthetic test systems for 6-year, 14-year and 24-year planning horizons having five types of candidate units is considered. Two different constraint-handling methods are incorporated and impact of each method has been compared. In addition, comparison and validation has also made with dynamic programming method.

Quantifiably secure power grid operation, management, and evolution :

Energy Technology Data Exchange (ETDEWEB)

Gray, Genetha Anne.; Watson, Jean-Paul; Silva Monroy, Cesar Augusto; Gramacy, Robert B.

2013-09-01

This report summarizes findings and results of the Quantifiably Secure Power Grid Operation, Management, and Evolution LDRD. The focus of the LDRD was to develop decisionsupport technologies to enable rational and quantifiable risk management for two key grid operational timescales: scheduling (day-ahead) and planning (month-to-year-ahead). Risk or resiliency metrics are foundational in this effort. The 2003 Northeast Blackout investigative report stressed the criticality of enforceable metrics for system resiliency the grids ability to satisfy demands subject to perturbation. However, we neither have well-defined risk metrics for addressing the pervasive uncertainties in a renewable energy era, nor decision-support tools for their enforcement, which severely impacts efforts to rationally improve grid security. For day-ahead unit commitment, decision-support tools must account for topological security constraints, loss-of-load (economic) costs, and supply and demand variability especially given high renewables penetration. For long-term planning, transmission and generation expansion must ensure realized demand is satisfied for various projected technological, climate, and growth scenarios. The decision-support tools investigated in this project paid particular attention to tailoriented risk metrics for explicitly addressing high-consequence events. Historically, decisionsupport tools for the grid consider expected cost minimization, largely ignoring risk and instead penalizing loss-of-load through artificial parameters. The technical focus of this work was the development of scalable solvers for enforcing risk metrics. Advanced stochastic programming solvers were developed to address generation and transmission expansion and unit commitment, minimizing cost subject to pre-specified risk thresholds. Particular attention was paid to renewables where security critically depends on production and demand prediction accuracy. To address this

Adaptation and convergent evolution within the Jamesonia-Eriosorus complex in high-elevation biodiverse Andean hotspots.

Science.gov (United States)

Sánchez-Baracaldo, Patricia; Thomas, Gavin H

2014-01-01

The recent uplift of the tropical Andes (since the late Pliocene or early Pleistocene) provided extensive ecological opportunity for evolutionary radiations. We test for phylogenetic and morphological evidence of adaptive radiation and convergent evolution to novel habitats (exposed, high-altitude páramo habitats) in the Andean fern genera Jamesonia and Eriosorus. We construct time-calibrated phylogenies for the Jamesonia-Eriosorus clade. We then use recent phylogenetic comparative methods to test for evolutionary transitions among habitats, associations between habitat and leaf morphology, and ecologically driven variation in the rate of morphological evolution. Páramo species (Jamesonia) display morphological adaptations consistent with convergent evolution in response to the demands of a highly exposed environment but these adaptations are associated with microhabitat use rather than the páramo per se. Species that are associated with exposed microhabitats (including Jamesonia and Eriorsorus) are characterized by many but short pinnae per frond whereas species occupying sheltered microhabitats (primarily Eriosorus) have few but long pinnae per frond. Pinnae length declines more rapidly with altitude in sheltered species. Rates of speciation are significantly higher among páramo than non-páramo lineages supporting the hypothesis of adaptation and divergence in the unique Páramo biodiversity hotspot.

Niche evolution and adaptive radiation: Testing the order of trait divergence

Science.gov (United States)

Ackerly, D.D.; Schwilk, D.W.; Webb, C.O.

2006-01-01

In the course of an adaptive radiation, the evolution of niche parameters is of particular interest for understanding modes of speciation and the consequences for coexistence of related species within communities. We pose a general question: In the course of an evolutionary radiation, do traits related to within-community niche differences (?? niche) evolve before or after differentiation of macrohabitat affinity or climatic tolerances (?? niche)? Here we introduce a new test to address this question, based on a modification of the method of independent contrasts. The divergence order test (DOT) is based on the average age of the nodes on a tree, weighted by the absolute magnitude of the contrast at each node for a particular trait. The comparison of these weighted averages reveals whether large divergences for one trait have occurred earlier or later in the course of diversification, relative to a second trait; significance is determined by bootstrapping from maximum-likelihood ancestral state reconstructions. The method is applied to the evolution of Ceanothus, a woody plant group in California, in which co-occurring species exhibit significant differences in a key leaf trait (specific leaf area) associated with contrasting physiological and life history strategies. Co-occurring species differ more for this trait than expected under a null model of community assembly. This ?? niche difference evolved early in the divergence of two major subclades within Ceanothus, whereas climatic distributions (?? niche traits) diversified later within each of the subclades. However, rapid evolution of climate parameters makes inferences of early divergence events highly uncertain, and differentiation of the ?? niche might have taken place throughout the evolution of the group, without leaving a clear phylogenetic signal. Similar patterns observed in several plant and animal groups suggest that early divergence of ?? niche traits might be a common feature of niche evolution in

Evidence of correlated evolution and adaptive differentiation of stem and leaf functional traits in the herbaceous genus, Helianthus.

Science.gov (United States)

Pilote, Alex J; Donovan, Lisa A

2016-12-01

Patterns of plant stem traits are expected to align with a "fast-slow" plant economic spectrum across taxa. Although broad patterns support such tradeoffs in field studies, tests of hypothesized correlated trait evolution and adaptive differentiation are more robust when taxa relatedness and environment are taken into consideration. Here we test for correlated evolution of stem and leaf traits and their adaptive differentiation across environments in the herbaceous genus, Helianthus. Stem and leaf traits of 14 species of Helianthus (28 populations) were assessed in a common garden greenhouse study. Phylogenetically independent contrasts were used to test for evidence of correlated evolution of stem hydraulic and biomechanical properties, correlated evolution of stem and leaf traits, and adaptive differentiation associated with source habitat environments. Among stem traits, there was evidence for correlated evolution of some hydraulic and biomechanical properties, supporting an expected tradeoff between stem theoretical hydraulic efficiency and resistance to bending stress. Population differentiation for suites of stem and leaf traits was found to be consistent with a "fast-slow" resource-use axis for traits related to water transport and use. Associations of population traits with source habitat characteristics supported repeated evolution of a resource-acquisitive "drought-escape" strategy in arid environments. This study provides evidence of correlated evolution of stem and leaf traits consistent with the fast-slow spectrum of trait combinations related to water transport and use along the stem-to-leaf pathway. Correlations of traits with source habitat characteristics further indicate that the correlated evolution is associated, at least in part, with adaptive differentiation of Helianthus populations among native habitats differing in climate. © 2016 Botanical Society of America.

Genetic evolution, plasticity, and bet-hedging as adaptive responses to temporally autocorrelated fluctuating selection: A quantitative genetic model.

Science.gov (United States)

Tufto, Jarle

2015-08-01

Adaptive responses to autocorrelated environmental fluctuations through evolution in mean reaction norm elevation and slope and an independent component of the phenotypic variance are analyzed using a quantitative genetic model. Analytic approximations expressing the mutual dependencies between all three response modes are derived and solved for the joint evolutionary outcome. Both genetic evolution in reaction norm elevation and plasticity are favored by slow temporal fluctuations, with plasticity, in the absence of microenvironmental variability, being the dominant evolutionary outcome for reasonable parameter values. For fast fluctuations, tracking of the optimal phenotype through genetic evolution and plasticity is limited. If residual fluctuations in the optimal phenotype are large and stabilizing selection is strong, selection then acts to increase the phenotypic variance (bet-hedging adaptive). Otherwise, canalizing selection occurs. If the phenotypic variance increases with plasticity through the effect of microenvironmental variability, this shifts the joint evolutionary balance away from plasticity in favor of genetic evolution. If microenvironmental deviations experienced by each individual at the time of development and selection are correlated, however, more plasticity evolves. The adaptive significance of evolutionary fluctuations in plasticity and the phenotypic variance, transient evolution, and the validity of the analytic approximations are investigated using simulations. © 2015 The Author(s). Evolution © 2015 The Society for the Study of Evolution.

An Adaptive Laboratory Evolution Method to Accelerate Autotrophic Metabolism

DEFF Research Database (Denmark)

Zhang, Tian; Tremblay, Pier-Luc

2018-01-01

Adaptive laboratory evolution (ALE) is an approach enabling the development of novel characteristics in microbial strains via the application of a constant selection pressure. This method is also an efficient tool to acquire insights on molecular mechanisms responsible for specific phenotypes. ALE...... autotrophically and reducing CO2 into acetate more efficiently. Strains developed via this ALE method were also used to gain knowledge on the autotrophic metabolism of S. ovata as well as other acetogenic bacteria....

Adaptive Evolution of CENP-A in Percid Fishes

Directory of Open Access Journals (Sweden)

Harriet N. A. Abbey

2015-07-01

Full Text Available Centromeric protein A (CENP-A is the epigenetic determinant of centromeres. This protein has been shown to be adaptively evolving in a number of animal and plant species. In a previous communication we were able to demonstrate that signs of adaptive evolution were detected in the comparison of CENP-A sequences from three percid fish species. In this study we isolated the CENP-A gene from eight additional species from the Percidae family. With these sequences and those previously obtained, we carried out a more robust statistical analysis of codon specific positive selection in CENP-A coding sequences of eleven percid species. We were able to demonstrate that at least two amino acid positions within the N-terminal tail are under strong positive selection and that one of these positions is potentially a substrate for phosphorylation. While nonsynonymous substitutions were detected in the histone fold domain, these were not statistically supported as resulting from positive selection.

Convergent evolution and adaptation of Pseudomonas aeruginosa within patients with cystic fibrosis

DEFF Research Database (Denmark)

Marvig, Rasmus Lykke; Madsen Sommer, Lea Mette; Molin, Søren

2015-01-01

fibrosis. Our analysis of 36 P. aeruginosa lineages identified convergent molecular evolution in 52 genes. This list of genes suggests a role in host adaptation for remodeling of regulatory networks and central metabolism, acquisition of antibiotic resistance and loss of extracellular virulence factors....... Furthermore, we find an ordered succession of mutations in key regulatory networks. Accordingly, mutations in downstream transcriptional regulators were contingent upon mutations in upstream regulators, suggesting that remodeling of regulatory networks might be important in adaptation. The characterization...

Reproductive isolation and local adaptation quantified for a chromosome inversion in a malaria mosquito.

Science.gov (United States)

Ayala, Diego; Guerrero, Rafael F; Kirkpatrick, Mark

2013-04-01

Chromosome inversions have long been thought to be involved in speciation and local adaptation. We have little quantitative information, however, about the effects that inversion polymorphisms have on reproductive isolation and viability. Here we provide the first estimates from any organism for the total amount of reproductive isolation associated with an inversion segregating in natural populations. We sampled chromosomes from 751 mosquitoes of the malaria vector Anopheles funestus along a 1421 km transect in Cameroon that traverses savannah, highland, and rainforest ecological zones. We then developed a series of population genetic models that account for selection, migration, and assortative mating, and fit the models to the data using likelihood. Results from the best-fit models suggest there is strong local adaptation, with relative viabilities of homozygotes ranging from 25% to 130% compared to heterozygotes. Viabilities vary qualitatively between regions: the inversion is underdominant in the savannah, whereas in the highlands it is overdominant. The inversion is also implicated in strong assortative mating. In the savannah, the two homozygote forms show 92% reproductive isolation, suggesting that this one inversion can generate most of the genetic barriers needed for speciation. © 2012 The Author(s). Evolution© 2012 The Society for the Study of Evolution.

On the adaptivity and complexity embedded into differential evolution

International Nuclear Information System (INIS)

Senkerik, Roman; Pluhacek, Michal; Jasek, Roman; Zelinka, Ivan

2016-01-01

This research deals with the comparison of the two modern approaches for evolutionary algorithms, which are the adaptivity and complex chaotic dynamics. This paper aims on the investigations on the chaos-driven Differential Evolution (DE) concept. This paper is aimed at the embedding of discrete dissipative chaotic systems in the form of chaotic pseudo random number generators for the DE and comparing the influence to the performance with the state of the art adaptive representative jDE. This research is focused mainly on the possible disadvantages and advantages of both compared approaches. Repeated simulations for Lozi map driving chaotic systems were performed on the simple benchmark functions set, which are more close to the real optimization problems. Obtained results are compared with the canonical not-chaotic and not adaptive DE. Results show that with used simple test functions, the performance of ChaosDE is better in the most cases than jDE and Canonical DE, furthermore due to the unique sequencing in CPRNG given by the hidden chaotic dynamics, thus better and faster selection of unique individuals from population, ChaosDE is faster.

On the adaptivity and complexity embedded into differential evolution

Energy Technology Data Exchange (ETDEWEB)

Senkerik, Roman; Pluhacek, Michal; Jasek, Roman [Tomas Bata University in Zlin, Faculty of Applied Informatics, Nam T.G. Masaryka 5555, 760 01 Zlin, Czech Republic, senkerik@fai.utb.cz,pluhacek@fai.utb.cz (Czech Republic); Zelinka, Ivan [Technical University of Ostrava, Faculty of Electrical Engineering and Computer Science, 17. listopadu 15,708 33 Ostrava-Poruba, Czech Republic, ivan.zelinka@vsb.cz (Czech Republic)

2016-06-08

This research deals with the comparison of the two modern approaches for evolutionary algorithms, which are the adaptivity and complex chaotic dynamics. This paper aims on the investigations on the chaos-driven Differential Evolution (DE) concept. This paper is aimed at the embedding of discrete dissipative chaotic systems in the form of chaotic pseudo random number generators for the DE and comparing the influence to the performance with the state of the art adaptive representative jDE. This research is focused mainly on the possible disadvantages and advantages of both compared approaches. Repeated simulations for Lozi map driving chaotic systems were performed on the simple benchmark functions set, which are more close to the real optimization problems. Obtained results are compared with the canonical not-chaotic and not adaptive DE. Results show that with used simple test functions, the performance of ChaosDE is better in the most cases than jDE and Canonical DE, furthermore due to the unique sequencing in CPRNG given by the hidden chaotic dynamics, thus better and faster selection of unique individuals from population, ChaosDE is faster.

On the adaptivity and complexity embedded into differential evolution

Science.gov (United States)

Senkerik, Roman; Pluhacek, Michal; Zelinka, Ivan; Jasek, Roman

2016-06-01

This research deals with the comparison of the two modern approaches for evolutionary algorithms, which are the adaptivity and complex chaotic dynamics. This paper aims on the investigations on the chaos-driven Differential Evolution (DE) concept. This paper is aimed at the embedding of discrete dissipative chaotic systems in the form of chaotic pseudo random number generators for the DE and comparing the influence to the performance with the state of the art adaptive representative jDE. This research is focused mainly on the possible disadvantages and advantages of both compared approaches. Repeated simulations for Lozi map driving chaotic systems were performed on the simple benchmark functions set, which are more close to the real optimization problems. Obtained results are compared with the canonical not-chaotic and not adaptive DE. Results show that with used simple test functions, the performance of ChaosDE is better in the most cases than jDE and Canonical DE, furthermore due to the unique sequencing in CPRNG given by the hidden chaotic dynamics, thus better and faster selection of unique individuals from population, ChaosDE is faster.

Biological adaptations for functional features of language in the face of cultural evolution.

Science.gov (United States)

Christiansen, Morten H; Reali, Florencia; Chater, Nick

2011-04-01

Although there may be no true language universals, it is nonetheless possible to discern several family resemblance patterns across the languages of the world. Recent work on the cultural evolution of language indicates the source of these patterns is unlikely to be an innate universal grammar evolved through biological adaptations for arbitrary linguistic features. Instead, it has been suggested that the patterns of resemblance emerge because language has been shaped by the brain, with individual languages representing different but partially overlapping solutions to the same set of nonlinguistic constraints. Here, we use computational simulations to investigate whether biological adaptation for functional features of language, deriving from cognitive and communicative constraints, may nonetheless be possible alongside rapid cultural evolution. Specifically, we focus on the Baldwin effect as an evolutionary mechanism by which previously learned linguistic features might become innate through natural selection across many generations of language users. The results indicate that cultural evolution of language does not necessarily prevent functional features of language from becoming genetically fixed, thus potentially providing a particularly informative source of constraints on cross-linguistic resemblance patterns.

pSum-SaDE: A Modified p-Median Problem and Self-Adaptive Differential Evolution Algorithm for Text Summarization

Directory of Open Access Journals (Sweden)

Rasim M. Alguliev

2011-01-01

Full Text Available Extractive multidocument summarization is modeled as a modified p-median problem. The problem is formulated with taking into account four basic requirements, namely, relevance, information coverage, diversity, and length limit that should satisfy summaries. To solve the optimization problem a self-adaptive differential evolution algorithm is created. Differential evolution has been proven to be an efficient and robust algorithm for many real optimization problems. However, it still may converge toward local optimum solutions, need to manually adjust the parameters, and finding the best values for the control parameters is a consuming task. In the paper is proposed a self-adaptive scaling factor in original DE to increase the exploration and exploitation ability. This paper has found that self-adaptive differential evolution can efficiently find the best solution in comparison with the canonical differential evolution. We implemented our model on multi-document summarization task. Experiments have shown that the proposed model is competitive on the DUC2006 dataset.

Transient MutS-Based Hypermutation System for Adaptive Evolution of Lactobacillus casei to Low pH.

Science.gov (United States)

Overbeck, Tom J; Welker, Dennis L; Hughes, Joanne E; Steele, James L; Broadbent, Jeff R

2017-10-15

This study explored transient inactivation of the gene encoding the DNA mismatch repair enzyme MutS as a tool for adaptive evolution of Lactobacillus casei MutS deletion derivatives of L. casei 12A and ATCC 334 were constructed and subjected to a 100-day adaptive evolution process to increase lactic acid resistance at low pH. Wild-type parental strains were also subjected to this treatment. At the end of the process, the Δ mutS lesion was repaired in representative L. casei 12A and ATCC 334 Δ mutS mutant isolates. Growth studies in broth at pH 4.0 (titrated with lactic acid) showed that all four adapted strains grew more rapidly, to higher cell densities, and produced significantly more lactic acid than untreated wild-type cells. However, the adapted Δ mutS derivative mutants showed the greatest increases in growth and lactic acid production. Further characterization of the L. casei 12A-adapted Δ mutS derivative revealed that it had a significantly smaller cell volume, a rougher cell surface, and significantly better survival at pH 2.5 than parental L. casei 12A. Genome sequence analysis confirmed that transient mutS inactivation decreased DNA replication fidelity in both L. casei strains, and it identified genetic changes that might contribute to the lactic acid-resistant phenotypes of adapted cells. Targeted inactivation of three genes that had acquired nonsense mutations in the adapted L. casei 12A Δ mutS mutant derivative showed that NADH dehydrogenase ( ndh ), phosphate transport ATP-binding protein PstB ( pstB ), and two-component signal transduction system (TCS) quorum-sensing histidine protein kinase ( hpk ) genes act in combination to increase lactic acid resistance in L. casei 12A. IMPORTANCE Adaptive evolution has been applied to microorganisms to increase industrially desirable phenotypes, including acid resistance. We developed a method to increase the adaptability of Lactobacillus casei 12A and ATCC 334 through transient inactivation of the DNA

Sex speeds adaptation by altering the dynamics of molecular evolution.

Science.gov (United States)

McDonald, Michael J; Rice, Daniel P; Desai, Michael M

2016-03-10

Sex and recombination are pervasive throughout nature despite their substantial costs. Understanding the evolutionary forces that maintain these phenomena is a central challenge in biology. One longstanding hypothesis argues that sex is beneficial because recombination speeds adaptation. Theory has proposed several distinct population genetic mechanisms that could underlie this advantage. For example, sex can promote the fixation of beneficial mutations either by alleviating interference competition (the Fisher-Muller effect) or by separating them from deleterious load (the ruby in the rubbish effect). Previous experiments confirm that sex can increase the rate of adaptation, but these studies did not observe the evolutionary dynamics that drive this effect at the genomic level. Here we present the first, to our knowledge, comparison between the sequence-level dynamics of adaptation in experimental sexual and asexual Saccharomyces cerevisiae populations, which allows us to identify the specific mechanisms by which sex speeds adaptation. We find that sex alters the molecular signatures of evolution by changing the spectrum of mutations that fix, and confirm theoretical predictions that it does so by alleviating clonal interference. We also show that substantially deleterious mutations hitchhike to fixation in adapting asexual populations. In contrast, recombination prevents such mutations from fixing. Our results demonstrate that sex both speeds adaptation and alters its molecular signature by allowing natural selection to more efficiently sort beneficial from deleterious mutations.

Adaptation, validation and application of the chemo-thermal oxidation method to quantify black carbon in soils

International Nuclear Information System (INIS)

Agarwal, Tripti; Bucheli, Thomas D.

2011-01-01

The chemo-thermal oxidation method at 375 o C (CTO-375) has been widely used to quantify black carbon (BC) in sediments. In the present study, CTO-375 was tested and adapted for application to soil, accounting for some matrix specific properties like high organic carbon (≤39%) and carbonate (≤37%) content. Average recoveries of standard reference material SRM-2975 ranged from 25 to 86% for nine representative Swiss and Indian samples, which is similar to literature data for sediments. The adapted method was applied to selected samples of the Swiss soil monitoring network (NABO). BC content exhibited different patterns in three soil profiles while contribution of BC to TOC was found maximum below the topsoil at all three sites, however at different depths (60-130 cm). Six different NABO sites exhibited largely constant BC concentrations over the last 25 years, with short-term (6 months) prevailing over long-term (5 years) temporal fluctuations. - Research highlights: → The CTO-375 method was adapted and validated for BC analysis in soils. → Method validation figures of merit proofed satisfactory. → Application is shown with soil cores and topsoil temporal variability. → BC content can be elevated in subsurface soils. → BC contents in surface soils were largely constant over the last 25 years. - Although widely used also for soils, the chemo-thermal oxidation method at 375 o C to quantify black carbon has never been properly validated for this matrix before.

Quantifying the Evolution of Melt Ponds in the Marginal Ice Zone Using High Resolution Optical Imagery and Neural Networks

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Ortiz, M.; Pinales, J. C.; Graber, H. C.; Wilkinson, J.; Lund, B.

2016-02-01

Melt ponds on sea ice play a significant and complex role on the thermodynamics in the Marginal Ice Zone (MIZ). Ponding reduces the sea ice's ability to reflect sunlight, and in consequence, exacerbates the albedo positive feedback cycle. In order to understand how melt ponds work and their effect on the heat uptake of sea ice, we must quantify ponds through their seasonal evolution first. A semi-supervised neural network three-class learning scheme using a gradient descent with momentum and adaptive learning rate backpropagation function is applied to classify melt ponds/melt areas in the Beaufort Sea region. The network uses high resolution panchromatic satellite images from the MEDEA program, which are collocated with autonomous platform arrays from the Marginal Ice Zone Program, including ice mass-balance buoys, arctic weather stations and wave buoys. The goal of the study is to capture the spatial variation of melt onset and freeze-up of the ponds within the MIZ, and gather ponding statistics such as size and concentration. The innovation of this work comes from training the neural network as the melt ponds evolve over time; making the machine learning algorithm time-dependent, which has not been previously done. We will achieve this by analyzing the image histograms through quantification of the minima and maxima intensity changes as well as linking textural variation information of the imagery. We will compare the evolution of the melt ponds against several different array sites on the sea ice to explore if there are spatial differences among the separated platforms in the MIZ.

Hologenomic adaptations underlying the evolution of sanguivory in the common vampire bat

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Zepeda Mendoza, M. Lisandra; Xiong, Zijun; Escalera-Zamudio, Marina

2018-01-01

Adaptation to specialized diets often requires modifications at both genomic and microbiome levels. We applied a hologenomic approach to the common vampire bat (Desmodus rotundus), one of the only three obligate blood-feeding (sanguivorous) mammals, to study the evolution of its complex dietary...... adaptation. Specifically, we assembled its high-quality reference genome (scaffold N50 = 26.9 Mb, contig N50 = 36.6 kb) and gut metagenome, and compared them against those of insectivorous, frugivorous and carnivorous bats. Our analyses showed a particular common vampire bat genomic landscape regarding...

Adaptive evolution influences the infectious dose of MERS-CoV necessary to achieve severe respiratory disease.

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Douglas, Madeline G; Kocher, Jacob F; Scobey, Trevor; Baric, Ralph S; Cockrell, Adam S

2018-04-01

We recently established a mouse model (288-330 +/+ ) that developed acute respiratory disease resembling human pathology following infection with a high dose (5 × 10 6 PFU) of mouse-adapted MERS-CoV (icMERSma1). Although this high dose conferred fatal respiratory disease in mice, achieving similar pathology at lower viral doses may more closely reflect naturally acquired infections. Through continued adaptive evolution of icMERSma1 we generated a novel mouse-adapted MERS-CoV (maM35c4) capable of achieving severe respiratory disease at doses between 10 3 and 10 5 PFU. Novel mutations were identified in the maM35c4 genome that may be responsible for eliciting etiologies of acute respiratory distress syndrome at 10-1000 fold lower viral doses. Importantly, comparative genetics of the two mouse-adapted MERS strains allowed us to identify specific mutations that remained fixed through an additional 20 cycles of adaptive evolution. Our data indicate that the extent of MERS-CoV adaptation determines the minimal infectious dose required to achieve severe respiratory disease. Copyright © 2017 Elsevier Inc. All rights reserved.

Adaptation and evolution in marine environments. Vol. 2. The impacts of global change on biodiversity

Energy Technology Data Exchange (ETDEWEB)

Verde, Cinzia; Di Prisco, Guido (eds.) [CNR, Napoli (Italy). Inst. of Protein Biochemistry

2013-02-01

Offers a regionally focussed approach. Describes research on adaptive evolution. State-of-the-art content. The second volume of ''Adaptation and Evolution in Marine Environments - The Impacts of Global Change on Biodiversity'' from the series ''From Pole to Pole'' integrates the marine biology contribution of the first tome to the IPY 2007-2009, presenting overviews of organisms (from bacteria and ciliates to higher vertebrates) thriving on polar continental shelves, slopes and deep sea. The speed and extent of warming in the Arctic and in regions of Antarctica (the Peninsula, at the present) are greater than elsewhere. Changes impact several parameters, in particular the extent of sea ice; organisms, ecosystems and communities that became finely adapted to increasing cold in the course of millions of years are now becoming vulnerable, and biodiversity is threatened. Investigating evolutionary adaptations helps to foresee the impact of changes in temperate areas, highlighting the invaluable contribution of polar marine research to present and future outcomes of the IPY in the Earth system scenario.

Evolution of the Marginal Ice Zone: Adaptive Sampling with Autonomous Gliders

Science.gov (United States)

2015-09-30

release; distribution is unlimited. Evolution of the Marginal Ice Zone: Adaptive Sampling with Autonomous Gliders Craig M. Lee, Luc Rainville and Jason I...missions in ice-covered waters , where they provide several unique capabilities. Ice-capable Seagliders can maintain persistent (many months) sampling ...irradiance. Careful calibration casts, including water sampling , were conducted during both the deployment and recovery cruises. An example of a

Evolution dynamics of a model for gene duplication under adaptive conflict

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Ancliff, Mark; Park, Jeong-Man

2014-06-01

We present and solve the dynamics of a model for gene duplication showing escape from adaptive conflict. We use a Crow-Kimura quasispecies model of evolution where the fitness landscape is a function of Hamming distances from two reference sequences, which are assumed to optimize two different gene functions, to describe the dynamics of a mixed population of individuals with single and double copies of a pleiotropic gene. The evolution equations are solved through a spin coherent state path integral, and we find two phases: one is an escape from an adaptive conflict phase, where each copy of a duplicated gene evolves toward subfunctionalization, and the other is a duplication loss of function phase, where one copy maintains its pleiotropic form and the other copy undergoes neutral mutation. The phase is determined by a competition between the fitness benefits of subfunctionalization and the greater mutational load associated with maintaining two gene copies. In the escape phase, we find a dynamics of an initial population of single gene sequences only which escape adaptive conflict through gene duplication and find that there are two time regimes: until a time t* single gene sequences dominate, and after t* double gene sequences outgrow single gene sequences. The time t* is identified as the time necessary for subfunctionalization to evolve and spread throughout the double gene sequences, and we show that there is an optimum mutation rate which minimizes this time scale.

Adaptive Patterns of Mitogenome Evolution Are Associated with the Loss of Shell Scutes in Turtles.

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Escalona, Tibisay; Weadick, Cameron J; Antunes, Agostinho

2017-10-01

The mitochondrial genome encodes several protein components of the oxidative phosphorylation (OXPHOS) pathway and is critical for aerobic respiration. These proteins have evolved adaptively in many taxa, but linking molecular-level patterns with higher-level attributes (e.g., morphology, physiology) remains a challenge. Turtles are a promising system for exploring mitochondrial genome evolution as different species face distinct respiratory challenges and employ multiple strategies for ensuring efficient respiration. One prominent adaptation to a highly aquatic lifestyle in turtles is the secondary loss of keratenized shell scutes (i.e., soft-shells), which is associated with enhanced swimming ability and, in some species, cutaneous respiration. We used codon models to examine patterns of selection on mitochondrial protein-coding genes along the three turtle lineages that independently evolved soft-shells. We found strong evidence for positive selection along the branches leading to the pig-nosed turtle (Carettochelys insculpta) and the softshells clade (Trionychidae), but only weak evidence for the leatherback (Dermochelys coriacea) branch. Positively selected sites were found to be particularly prevalent in OXPHOS Complex I proteins, especially subunit ND2, along both positively selected lineages, consistent with convergent adaptive evolution. Structural analysis showed that many of the identified sites are within key regions or near residues involved in proton transport, indicating that positive selection may have precipitated substantial changes in mitochondrial function. Overall, our study provides evidence that physiological challenges associated with adaptation to a highly aquatic lifestyle have shaped the evolution of the turtle mitochondrial genome in a lineage-specific manner. © The Author 2017. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Chewing on the trees: Constraints and adaptation in the evolution of the primate mandible.

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Meloro, Carlo; Cáceres, Nilton Carlos; Carotenuto, Francesco; Sponchiado, Jonas; Melo, Geruza Leal; Passaro, Federico; Raia, Pasquale

2015-07-01

Chewing on different food types is a demanding biological function. The classic assumption in studying the shape of feeding apparatuses is that animals are what they eat, meaning that adaptation to different food items accounts for most of their interspecific variation. Yet, a growing body of evidence points against this concept. We use the primate mandible as a model structure to investigate the complex interplay among shape, size, diet, and phylogeny. We find a weak but significant impact of diet on mandible shape variation in primates as a whole but not in anthropoids and catarrhines as tested in isolation. These clades mainly exhibit allometric shape changes, which are unrelated to diet. Diet is an important factor in the diversification of strepsirrhines and platyrrhines and a phylogenetic signal is detected in all primate clades. Peaks in morphological disparity occur during the Oligocene (between 37 and 25 Ma) supporting the notion that an adaptive radiation characterized the evolution of South American monkeys. In all primate clades, the evolution of mandible size is faster than its shape pointing to a strong effect of allometry on ecomorphological diversification in this group. © 2015 The Author(s). Evolution © 2015 The Society for the Study of Evolution.

Gene duplication and adaptive evolution of digestive proteases in Drosophila arizonae female reproductive tracts.

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Erin S Kelleher

2007-08-01

Full Text Available It frequently has been postulated that intersexual coevolution between the male ejaculate and the female reproductive tract is a driving force in the rapid evolution of reproductive proteins. The dearth of research on female tracts, however, presents a major obstacle to empirical tests of this hypothesis. Here, we employ a comparative EST approach to identify 241 candidate female reproductive proteins in Drosophila arizonae, a repleta group species in which physiological ejaculate-female coevolution has been documented. Thirty-one of these proteins exhibit elevated amino acid substitution rates, making them candidates for molecular coevolution with the male ejaculate. Strikingly, we also discovered 12 unique digestive proteases whose expression is specific to the D. arizonae lower female reproductive tract. These enzymes belong to classes most commonly found in the gastrointestinal tracts of a diverse array of organisms. We show that these proteases are associated with recent, lineage-specific gene duplications in the Drosophila repleta species group, and exhibit strong signatures of positive selection. Observation of adaptive evolution in several female reproductive tract proteins indicates they are active players in the evolution of reproductive tract interactions. Additionally, pervasive gene duplication, adaptive evolution, and rapid acquisition of a novel digestive function by the female reproductive tract points to a novel coevolutionary mechanism of ejaculate-female interaction.

Adaptive evolution of body size subject to indirect effect in trophic cascade system.

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Wang, Xin; Fan, Meng; Hao, Lina

2017-09-01

Trophic cascades represent a classic example of indirect effect and are wide-spread in nature. Their ecological impact are well established, but the evolutionary consequences have received even less theoretical attention. We theoretically and numerically investigate the trait (i.e., body size of consumer) evolution in response to indirect effect in a trophic cascade system. By applying the quantitative trait evolutionary theory and the adaptive dynamic theory, we formulate and explore two different types of eco-evolutionary resource-consumer-predator trophic cascade model. First, an eco-evolutionary model incorporating the rapid evolution is formulated to investigate the effect of rapid evolution of the consumer's body size, and to explore the impact of density-mediate indirect effect on the population dynamics and trait dynamics. Next, by employing the adaptive dynamic theory, a long-term evolutionary model of consumer body size is formulated to evaluate the effect of long-term evolution on the population dynamics and the effect of trait-mediate indirect effect. Those models admit rich dynamics that has not been observed yet in empirical studies. It is found that, both in the trait-mediated and density-mediated system, the body size of consumer in predator-consumer-resource interaction (indirect effect) evolves smaller than that in consumer-resource and predator-consumer interaction (direct effect). Moreover, in the density-mediated system, we found that the evolution of consumer body size contributes to avoiding consumer extinction (i.e., evolutionary rescue). The trait-mediate and density-mediate effects may produce opposite evolutionary response. This study suggests that the trophic cascade indirect effect affects consumer evolution, highlights a more comprehensive mechanistic understanding of the intricate interplay between ecological and evolutionary force. The modeling approaches provide avenue for study on indirect effects from an evolutionary perspective

A Convergent Differential Evolution Algorithm with Hidden Adaptation Selection for Engineering Optimization

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Zhongbo Hu

2014-01-01

Full Text Available Many improved differential Evolution (DE algorithms have emerged as a very competitive class of evolutionary computation more than a decade ago. However, few improved DE algorithms guarantee global convergence in theory. This paper developed a convergent DE algorithm in theory, which employs a self-adaptation scheme for the parameters and two operators, that is, uniform mutation and hidden adaptation selection (haS operators. The parameter self-adaptation and uniform mutation operator enhance the diversity of populations and guarantee ergodicity. The haS can automatically remove some inferior individuals in the process of the enhancing population diversity. The haS controls the proposed algorithm to break the loop of current generation with a small probability. The breaking probability is a hidden adaptation and proportional to the changes of the number of inferior individuals. The proposed algorithm is tested on ten engineering optimization problems taken from IEEE CEC2011.

Adaptive evolution of cooperation through Darwinian dynamics in Public Goods games.

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Deng, Kuiying; Chu, Tianguang

2011-01-01

The linear or threshold Public Goods game (PGG) is extensively accepted as a paradigmatic model to approach the evolution of cooperation in social dilemmas. Here we explore the significant effect of nonlinearity of the structures of public goods on the evolution of cooperation within the well-mixed population by adopting Darwinian dynamics, which simultaneously consider the evolution of populations and strategies on a continuous adaptive landscape, and extend the concept of evolutionarily stable strategy (ESS) as a coalition of strategies that is both convergent-stable and resistant to invasion. Results show (i) that in the linear PGG contributing nothing is an ESS, which contradicts experimental data, (ii) that in the threshold PGG contributing the threshold value is a fragile ESS, which cannot resist the invasion of contributing nothing, and (iii) that there exists a robust ESS of contributing more than half in the sigmoid PGG if the return rate is relatively high. This work reveals the significant effect of the nonlinearity of the structures of public goods on the evolution of cooperation, and suggests that, compared with the linear or threshold PGG, the sigmoid PGG might be a more proper model for the evolution of cooperation within the well-mixed population.

Evolution of static allometries: adaptive change in allometric slopes of eye span in stalk-eyed flies.

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Voje, Kjetil L; Hansen, Thomas F

2013-02-01

Julian Huxley showed that within-species (static) allometric (power-law) relations can arise from proportional growth regulation with the exponent in the power law equaling the factor of proportionality. Allometric exponents may therefore be hard to change and act as constraints on the independent evolution of traits. In apparent contradiction to this, many empirical studies have concluded that static allometries are evolvable. Many of these studies have been based, however, on a broad definition of allometry that includes any monotonic shape change with size, and do not falsify the hypothesis of constrained narrow-sense allometry. Here, we present the first phylogenetic comparative study of narrow-sense allometric exponents based on a reanalysis of data on eye span and body size in stalk-eyed flies (Diopsidae). Consistent with a role in sexual selection, we found strong evidence that male slopes were tracking "optima" based on sexual dimorphism and relative male trait size. This tracking was slow, however, with estimated times of 2-3 million years for adaptation to exceed ancestral influence on the trait. Our results are therefore consistent with adaptive evolution on million-year time scales, but cannot rule out that static allometry may act as a constraint on eye-span adaptation at shorter time scales. © 2012 The Author(s). Evolution© 2012 The Society for the Study of Evolution.

Adaptive microclimatic structural and expressional dehydrin 1 evolution in wild barley, Hordeum spontaneum, at 'Evolution Canyon', Mount Carmel, Israel.

Science.gov (United States)

Yang, Zujun; Zhang, Tao; Bolshoy, Alexander; Beharav, Alexander; Nevo, Eviatar

2009-05-01

'Evolution Canyon' (ECI) at Lower Nahal Oren, Mount Carmel, Israel, is an optimal natural microscale model for unravelling evolution in action highlighting the twin evolutionary processes of adaptation and speciation. A major model organism in ECI is wild barley, Hordeum spontaneum, the progenitor of cultivated barley, which displays dramatic interslope adaptive and speciational divergence on the 'African' dry slope (AS) and the 'European' humid slope (ES), separated on average by 200 m. Here we examined interslope single nucleotide polymorphism (SNP) sequences and the expression diversity of the drought resistant dehydrin 1 gene (Dhn1) between the opposite slopes. We analysed 47 plants (genotypes), 4-10 individuals in each of seven stations (populations) in an area of 7000 m(2), for Dhn1 sequence diversity located in the 5' upstream flanking region of the gene. We found significant levels of Dhn1 genic diversity represented by 29 haplotypes, derived from 45 SNPs in a total of 708 bp sites. Most of the haplotypes, 25 out of 29 (= 86.2%), were represented by one genotype; hence, unique to one population. Only a single haplotype was common to both slopes. Genetic divergence of sequence and haplotype diversity was generally and significantly different among the populations and slopes. Nucleotide diversity was higher on the AS, whereas haplotype diversity was higher on the ES. Interslope divergence was significantly higher than intraslope divergence. The applied Tajima D rejected neutrality of the SNP diversity. The Dhn1 expression under dehydration indicated interslope divergent expression between AS and ES genotypes, reinforcing Dhn1 associated with drought resistance of wild barley at 'Evolution Canyon'. These results are inexplicable by mutation, gene flow, or chance effects, and support adaptive natural microclimatic selection as the major evolutionary divergent driving force.

Adaptive evolution of a key gene affecting queen and worker traits in the honey bee, Apis mellifera.

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Kent, Clement F; Issa, Amer; Bunting, Alexandra C; Zayed, Amro

2011-12-01

The vitellogenin egg yolk precursor protein represents a well-studied case of social pleiotropy in the model organism Apis mellifera. Vitellogenin is associated with fecundity in queens and plays a major role in controlling division of labour in workers, thereby affecting both individual and colony-level fitness. We studied the molecular evolution of vitellogenin and seven other genes sequenced in a large population panel of Apis mellifera and several closely related species to investigate the role of social pleiotropy on adaptive protein evolution. We found a significant excess of nonsynonymous fixed differences between A. mellifera, A. cerana and A. florea relative to synonymous sites indicating high rates of adaptive evolution at vitellogenin. Indeed, 88% of amino acid changes were fixed by selection in some portions of the gene. Further, vitellogenin exhibited hallmark signatures of selective sweeps in A. mellifera, including a significant skew in the allele frequency spectrum, extreme levels of genetic differentiation and linkage disequilibrium. Finally, replacement polymorphisms in vitellogenin were significantly enriched in parts of the protein involved in binding lipid, establishing a link between the gene's structure, function and effects on fitness. Our case study provides unequivocal evidence of historical and ongoing bouts of adaptive evolution acting on a key socially pleiotropic gene in the honey bee. © 2011 Blackwell Publishing Ltd.

Adaptive evolution of the matrix extracellular phosphoglycoprotein in mammals

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Machado João

2011-11-01

Full Text Available Abstract Background Matrix extracellular phosphoglycoprotein (MEPE belongs to a family of small integrin-binding ligand N-linked glycoproteins (SIBLINGs that play a key role in skeleton development, particularly in mineralization, phosphate regulation and osteogenesis. MEPE associated disorders cause various physiological effects, such as loss of bone mass, tumors and disruption of renal function (hypophosphatemia. The study of this developmental gene from an evolutionary perspective could provide valuable insights on the adaptive diversification of morphological phenotypes in vertebrates. Results Here we studied the adaptive evolution of the MEPE gene in 26 Eutherian mammals and three birds. The comparative genomic analyses revealed a high degree of evolutionary conservation of some coding and non-coding regions of the MEPE gene across mammals indicating a possible regulatory or functional role likely related with mineralization and/or phosphate regulation. However, the majority of the coding region had a fast evolutionary rate, particularly within the largest exon (1467 bp. Rodentia and Scandentia had distinct substitution rates with an increased accumulation of both synonymous and non-synonymous mutations compared with other mammalian lineages. Characteristics of the gene (e.g. biochemical, evolutionary rate, and intronic conservation differed greatly among lineages of the eight mammalian orders. We identified 20 sites with significant positive selection signatures (codon and protein level outside the main regulatory motifs (dentonin and ASARM suggestive of an adaptive role. Conversely, we find three sites under selection in the signal peptide and one in the ASARM motif that were supported by at least one selection model. The MEPE protein tends to accumulate amino acids promoting disorder and potential phosphorylation targets. Conclusion MEPE shows a high number of selection signatures, revealing the crucial role of positive selection in the

Evolution of regulatory networks towards adaptability and stability in a changing environment

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Lee, Deok-Sun

2014-11-01

Diverse biological networks exhibit universal features distinguished from those of random networks, calling much attention to their origins and implications. Here we propose a minimal evolution model of Boolean regulatory networks, which evolve by selectively rewiring links towards enhancing adaptability to a changing environment and stability against dynamical perturbations. We find that sparse and heterogeneous connectivity patterns emerge, which show qualitative agreement with real transcriptional regulatory networks and metabolic networks. The characteristic scaling behavior of stability reflects the balance between robustness and flexibility. The scaling of fluctuation in the perturbation spread shows a dynamic crossover, which is analyzed by investigating separately the stochasticity of internal dynamics and the network structure differences depending on the evolution pathways. Our study delineates how the ambivalent pressure of evolution shapes biological networks, which can be helpful for studying general complex systems interacting with environments.

Dancing to a Different Tune: Adaptive Evolution Fine-Tunes Protein Dynamics

Science.gov (United States)

2015-09-01

efficiency at low temperatures when the enzymes from mesophilic bacteria were evolved to have stabilities as high as their thermophilic homologs. The work...wild-type enzyme . This unfolding temperature is relatively high for a non- thermophilic enzyme ,15 as mesophilic enzymes typically unfold below 60 °C...The work described in this thesis provides a case study exploring the molecular changes underlying adaptive evolution in a key allosteric enzyme . It

Testing for adaptive evolution of the female reproductive protein ZPC in mammals, birds and fishes reveals problems with the M7-M8 likelihood ratio test.

Science.gov (United States)

Berlin, Sofia; Smith, Nick G C

2005-11-10

Adaptive evolution appears to be a common feature of reproductive proteins across a very wide range of organisms. A promising way of addressing the evolutionary forces responsible for this general phenomenon is to test for adaptive evolution in the same gene but among groups of species, which differ in their reproductive biology. One can then test evolutionary hypotheses by asking whether the variation in adaptive evolution is consistent with the variation in reproductive biology. We have attempted to apply this approach to the study of a female reproductive protein, zona pellucida C (ZPC), which has been previously shown by the use of likelihood ratio tests (LRTs) to be under positive selection in mammals. We tested for evidence of adaptive evolution of ZPC in 15 mammalian species, in 11 avian species and in six fish species using three different LRTs (M1a-M2a, M7-M8, and M8a-M8). The only significant findings of adaptive evolution came from the M7-M8 test in mammals and fishes. Since LRTs of adaptive evolution may yield false positives in some situations, we examined the properties of the LRTs by several different simulation methods. When we simulated data to test the robustness of the LRTs, we found that the pattern of evolution in ZPC generates an excess of false positives for the M7-M8 LRT but not for the M1a-M2a or M8a-M8 LRTs. This bias is strong enough to have generated the significant M7-M8 results for mammals and fishes. We conclude that there is no strong evidence for adaptive evolution of ZPC in any of the vertebrate groups we studied, and that the M7-M8 LRT can be biased towards false inference of adaptive evolution by certain patterns of non-adaptive evolution.

Coupling of diversification and pH adaptation during the evolution of terrestrial Thaumarchaeota

Science.gov (United States)

Gubry-Rangin, Cécile; Kratsch, Christina; Williams, Tom A.; McHardy, Alice C.; Embley, T. Martin; Prosser, James I.; Macqueen, Daniel J.

2015-01-01

The Thaumarchaeota is an abundant and ubiquitous phylum of archaea that plays a major role in the global nitrogen cycle. Previous analyses of the ammonia monooxygenase gene amoA suggest that pH is an important driver of niche specialization in these organisms. Although the ecological distribution and ecophysiology of extant Thaumarchaeota have been studied extensively, the evolutionary rise of these prokaryotes to ecological dominance in many habitats remains poorly understood. To characterize processes leading to their diversification, we investigated coevolutionary relationships between amoA, a conserved marker gene for Thaumarchaeota, and soil characteristics, by using deep sequencing and comprehensive environmental data in Bayesian comparative phylogenetics. These analyses reveal a large and rapid increase in diversification rates during early thaumarchaeotal evolution; this finding was verified by independent analyses of 16S rRNA. Our findings suggest that the entire Thaumarchaeota diversification regime was strikingly coupled to pH adaptation but less clearly correlated with several other tested environmental factors. Interestingly, the early radiation event coincided with a period of pH adaptation that enabled the terrestrial Thaumarchaeota ancestor to initially move from neutral to more acidic and alkaline conditions. In contrast to classic evolutionary models, whereby niches become rapidly filled after adaptive radiation, global diversification rates have remained stably high in Thaumarchaeota during the past 400–700 million years, suggesting an ongoing high rate of niche formation or switching for these microbes. Our study highlights the enduring importance of environmental adaptation during thaumarchaeotal evolution and, to our knowledge, is the first to link evolutionary diversification to environmental adaptation in a prokaryotic phylum. PMID:26170282

Analysis of adaptive evolution in Lyssavirus genomes reveals pervasive diversifying selection during species diversification.

Science.gov (United States)

Voloch, Carolina M; Capellão, Renata T; Mello, Beatriz; Schrago, Carlos G

2014-11-19

Lyssavirus is a diverse genus of viruses that infect a variety of mammalian hosts, typically causing encephalitis. The evolution of this lineage, particularly the rabies virus, has been a focus of research because of the extensive occurrence of cross-species transmission, and the distinctive geographical patterns present throughout the diversification of these viruses. Although numerous studies have examined pattern-related questions concerning Lyssavirus evolution, analyses of the evolutionary processes acting on Lyssavirus diversification are scarce. To clarify the relevance of positive natural selection in Lyssavirus diversification, we conducted a comprehensive scan for episodic diversifying selection across all lineages and codon sites of the five coding regions in lyssavirus genomes. Although the genomes of these viruses are generally conserved, the glycoprotein (G), RNA-dependent RNA polymerase (L) and polymerase (P) genes were frequently targets of adaptive evolution during the diversification of the genus. Adaptive evolution is particularly manifest in the glycoprotein gene, which was inferred to have experienced the highest density of positively selected codon sites along branches. Substitutions in the L gene were found to be associated with the early diversification of phylogroups. A comparison between the number of positively selected sites inferred along the branches of RABV population branches and Lyssavirus intespecies branches suggested that the occurrence of positive selection was similar on the five coding regions of the genome in both groups.

Analysis of Adaptive Evolution in Lyssavirus Genomes Reveals Pervasive Diversifying Selection during Species Diversification

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Carolina M. Voloch

2014-11-01

Full Text Available Lyssavirus is a diverse genus of viruses that infect a variety of mammalian hosts, typically causing encephalitis. The evolution of this lineage, particularly the rabies virus, has been a focus of research because of the extensive occurrence of cross-species transmission, and the distinctive geographical patterns present throughout the diversification of these viruses. Although numerous studies have examined pattern-related questions concerning Lyssavirus evolution, analyses of the evolutionary processes acting on Lyssavirus diversification are scarce. To clarify the relevance of positive natural selection in Lyssavirus diversification, we conducted a comprehensive scan for episodic diversifying selection across all lineages and codon sites of the five coding regions in lyssavirus genomes. Although the genomes of these viruses are generally conserved, the glycoprotein (G, RNA-dependent RNA polymerase (L and polymerase (P genes were frequently targets of adaptive evolution during the diversification of the genus. Adaptive evolution is particularly manifest in the glycoprotein gene, which was inferred to have experienced the highest density of positively selected codon sites along branches. Substitutions in the L gene were found to be associated with the early diversification of phylogroups. A comparison between the number of positively selected sites inferred along the branches of RABV population branches and Lyssavirus intespecies branches suggested that the occurrence of positive selection was similar on the five coding regions of the genome in both groups.

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

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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.

Adaptive evolution of the mitochondrial ND6 gene in the domestic horse.

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Ning, T; Xiao, H; Li, J; Hua, S; Zhang, Y P

2010-01-26

Mitochondria play a crucial role in energy metabolism through oxidative phosphorylation. Organisms living at high altitudes are potentially influenced by oxygen deficits and cold temperatures. The severe environmental conditions can impact on metabolism and direct selection of mitochondrial DNA. As a wide-ranging animal, the domestic horse (Equus caballus) has developed various morphological and physiological characteristics for adapting to different altitudes. Thus, this is a good species for studying adaption to high altitudes at a molecular level. We sequenced the complete NADH dehydrogenase 6 gene (ND6) of 509 horses from 24 sampling locations. By comparative analysis of three horse populations living at different altitudes (>2200 m, 1200-1700 m, and horses was found distributed on the selected branches. We conclude that the high-altitude environment has directed adaptive evolution of the mitochondrial ND6 gene in the plateau horse.

Laboratory Evolution to Alternating Substrate Environments Yields Distinct Phenotypic and Genetic Adaptive Strategies

DEFF Research Database (Denmark)

Sandberg, Troy E.; Lloyd, Colton J.; Palsson, Bernhard O.

2017-01-01

conditions and different adaptation strategies depending on the substrates being switched between; in some environments, a persistent "generalist" strain developed, while in another, two "specialist" subpopulations arose that alternated dominance. Diauxic lag phenotype varied across the generalists...... maintain simple, static culturing environments so as to reduce selection pressure complexity. In this study, we investigated the adaptive strategies underlying evolution to fluctuating environments by evolving Escherichia coli to conditions of frequently switching growth substrate. Characterization...... of evolved strains via a number of different data types revealed the various genetic and phenotypic changes implemented in pursuit of growth optimality and how these differed across the different growth substrates and switching protocols. This work not only helps to establish general principles of adaptation...

Adaptive evolution of facial colour patterns in Neotropical primates.

Science.gov (United States)

Santana, Sharlene E; Lynch Alfaro, Jessica; Alfaro, Michael E

2012-06-07

The rich diversity of primate faces has interested naturalists for over a century. Researchers have long proposed that social behaviours have shaped the evolution of primate facial diversity. However, the primate face constitutes a unique structure where the diverse and potentially competing functions of communication, ecology and physiology intersect, and the major determinants of facial diversity remain poorly understood. Here, we provide the first evidence for an adaptive role of facial colour patterns and pigmentation within Neotropical primates. Consistent with the hypothesis that facial patterns function in communication and species recognition, we find that species living in smaller groups and in sympatry with a higher number of congener species have evolved more complex patterns of facial colour. The evolution of facial pigmentation and hair length is linked to ecological factors, and ecogeographical rules related to UV radiation and thermoregulation are met by some facial regions. Our results demonstrate the interaction of behavioural and ecological factors in shaping one of the most outstanding facial diversities of any mammalian lineage.

Natural Selection Causes Adaptive Genetic Resistance in Wild Emmer Wheat against Powdery Mildew at ?Evolution Canyon? Microsite, Mt. Carmel, Israel

OpenAIRE

Yin, Huayan; Ben-Abu, Yuval; Wang, Hongwei; Li, Anfei; Nevo, Eviatar; Kong, Lingrang

2015-01-01

Background ?Evolution Canyon? (ECI) at Lower Nahal Oren, Mount Carmel, Israel, is an optimal natural microscale model for unraveling evolution in action highlighting the basic evolutionary processes of adaptation and speciation. A major model organism in ECI is wild emmer, Triticum dicoccoides, the progenitor of cultivated wheat, which displays dramatic interslope adaptive and speciational divergence on the tropical-xeric ?African? slope (AS) and the temperate-mesic ?European? slope (ES), sep...

Shared human-chimpanzee pattern of perinatal femoral shaft morphology and its implications for the evolution of hominin locomotor adaptations.

Directory of Open Access Journals (Sweden)

Naoki Morimoto

Full Text Available Acquisition of bipedality is a hallmark of human evolution. How bipedality evolved from great ape-like locomotor behaviors, however, is still highly debated. This is mainly because it is difficult to infer locomotor function, and even more so locomotor kinematics, from fossil hominin long bones. Structure-function relationships are complex, as long bone morphology reflects phyletic history, developmental programs, and loading history during an individual's lifetime. Here we discriminate between these factors by investigating the morphology of long bones in fetal and neonate great apes and humans, before the onset of locomotion.Comparative morphometric analysis of the femoral diaphysis indicates that its morphology reflects phyletic relationships between hominoid taxa to a greater extent than taxon-specific locomotor adaptations. Diaphyseal morphology in humans and chimpanzees exhibits several shared-derived features, despite substantial differences in locomotor adaptations. Orangutan and gorilla morphologies are largely similar, and likely represent the primitive hominoid state.These findings are compatible with two possible evolutionary scenarios. Diaphyseal morphology may reflect retained adaptive traits of ancestral taxa, hence human-chimpanzee shared-derived features may be indicative of the locomotor behavior of our last common ancestor. Alternatively, diaphyseal morphology might reflect evolution by genetic drift (neutral evolution rather than selection, and might thus be more informative about phyletic relationships between taxa than about locomotor adaptations. Both scenarios are consistent with the hypothesis that knuckle-walking in chimpanzees and gorillas resulted from convergent evolution, and that the evolution of human bipedality is unrelated to extant great ape locomotor specializations.

On the Adaptive Design Rules of Biochemical Networks in Evolution

Directory of Open Access Journals (Sweden)

Bor-Sen Chen

2007-01-01

Full Text Available Biochemical networks are the backbones of physiological systems of organisms. Therefore, a biochemical network should be sufficiently robust (not sensitive to tolerate genetic mutations and environmental changes in the evolutionary process. In this study, based on the robustness and sensitivity criteria of biochemical networks, the adaptive design rules are developed for natural selection in the evolutionary process. This will provide insights into the robust adaptive mechanism of biochemical networks in the evolutionary process. We find that if a mutated biochemical network satisfies the robustness and sensitivity criteria of natural selection, there is a high probability for the biochemical network to prevail during natural selection in the evolutionary process. Since there are various mutated biochemical networks that can satisfy these criteria but have some differences in phenotype, the biochemical networks increase their diversities in the evolutionary process. The robustness of a biochemical network enables co-option so that new phenotypes can be generated in evolution. The proposed robust adaptive design rules of natural selection gain much insight into the evolutionary mechanism and provide a systematic robust biochemical circuit design method of biochemical networks for biotechnological and therapeutic purposes in the future.

Adaptation to an extraordinary environment by evolution of phenotypic plasticity and genetic assimilation.

Science.gov (United States)

Lande, Russell

2009-07-01

Adaptation to a sudden extreme change in environment, beyond the usual range of background environmental fluctuations, is analysed using a quantitative genetic model of phenotypic plasticity. Generations are discrete, with time lag tau between a critical period for environmental influence on individual development and natural selection on adult phenotypes. The optimum phenotype, and genotypic norms of reaction, are linear functions of the environment. Reaction norm elevation and slope (plasticity) vary among genotypes. Initially, in the average background environment, the character is canalized with minimum genetic and phenotypic variance, and no correlation between reaction norm elevation and slope. The optimal plasticity is proportional to the predictability of environmental fluctuations over time lag tau. During the first generation in the new environment the mean fitness suddenly drops and the mean phenotype jumps towards the new optimum phenotype by plasticity. Subsequent adaptation occurs in two phases. Rapid evolution of increased plasticity allows the mean phenotype to closely approach the new optimum. The new phenotype then undergoes slow genetic assimilation, with reduction in plasticity compensated by genetic evolution of reaction norm elevation in the original environment.

Evolution and Adaptation in Pseudomonas aeruginosa Biofilms Driven by Mismatch Repair System-Deficient Mutators

DEFF Research Database (Denmark)

Luján, Adela M.; Maciá, María D.; Yang, Liang

2011-01-01

, which are rarely eradicated despite intensive antibiotic therapy. Current knowledge indicates that three major adaptive strategies, biofilm development, phenotypic diversification, and mutator phenotypes [driven by a defective mismatch repair system (MRS)], play important roles in P. aeruginosa chronic...... infections, but the relationship between these strategies is still poorly understood. We have used the flow-cell biofilm model system to investigate the impact of the mutS associated mutator phenotype on development, dynamics, diversification and adaptation of P. aeruginosa biofilms. Through competition...... diversification, evidenced by biofilm architecture features and by a wider range and proportion of morphotypic colony variants, respectively. Additionally, morphotypic variants generated in mutator biofilms showed increased competitiveness, providing further evidence for mutator-driven adaptive evolution...

The eunuch phenomenon: adaptive evolution of genital emasculation in sexually dimorphic spiders.

Science.gov (United States)

Kuntner, Matjaž; Agnarsson, Ingi; Li, Daiqin

2015-02-01

Under natural and sexual selection traits often evolve that secure paternity or maternity through self-sacrifice to predators, rivals, offspring, or partners. Emasculation-males removing their genitals-is an unusual example of such behaviours. Known only in insects and spiders, the phenomenon's adaptiveness is difficult to explain, yet its repeated origins and association with sexual size dimorphism (SSD) and sexual cannibalism suggest an adaptive significance. In spiders, emasculation of paired male sperm-transferring organs - secondary genitals - (hereafter, palps), results in 'eunuchs'. This behaviour has been hypothesized to be adaptive because (i) males plug female genitals with their severed palps (plugging hypothesis), (ii) males remove their palps to become better fighters in male-male contests (better-fighter hypothesis), perhaps reaching higher agility due to reduced total body mass (gloves-off hypothesis), and (iii) males achieve prolonged sperm transfer through severed genitals (remote-copulation hypothesis). Prior research has provided evidence in support of these hypotheses in some orb-weaving spiders but these explanations are far from general. Seeking broad macroevolutionary patterns of spider emasculation, we review the known occurrences, weigh the evidence in support of the hypotheses in each known case, and redefine more precisely the particular cases of emasculation depending on its timing in relation to maturation and mating: 'pre-maturation', 'mating', and 'post-mating'. We use a genus-level spider phylogeny to explore emasculation evolution and to investigate potential evolutionary linkage between emasculation, SSD, lesser genital damage (embolic breakage), and sexual cannibalism (females consuming their mates). We find a complex pattern of spider emasculation evolution, all cases confined to Araneoidea: emasculation evolved at least five and up to 11 times, was lost at least four times, and became further modified at least once. We also find

Slowly switching between environments facilitates reverse evolution in small populations

Science.gov (United States)

Tan, Longzhi; Gore, Jeff

2011-03-01

The rate at which a physical process occurs usually changes the behavior of a system. In thermodynamics, the reversibility of a process generally increases when it occurs at an infinitely slow rate. In biological evolution, adaptations to a new environment may be reversed by evolution in the ancestral environment. Such fluctuating environments are ubiquitous in nature, although how the rate of switching affects reverse evolution is unknown. Here we use a computational approach to quantify evolutionary reversibility as a function of the rate of switching between two environments. For small population sizes, which travel on landscapes as random walkers, we find that both genotypic and phenotypic reverse evolution increase at slow switching rates. However, slow switching of environments decreases evolutionary reversibility for a greedy walker, corresponding to large populations (extensive clonal interference). We conclude that the impact of the switching rate for biological evolution is more complicated than other common physical processes, and that a quantitative approach may yield significant insight into reverse evolution.

Adaptive evolution of mitochondrial energy metabolism genes associated with increased energy demand in flying insects.

Science.gov (United States)

Yang, Yunxia; Xu, Shixia; Xu, Junxiao; Guo, Yan; Yang, Guang

2014-01-01

Insects are unique among invertebrates for their ability to fly, which raises intriguing questions about how energy metabolism in insects evolved and changed along with flight. Although physiological studies indicated that energy consumption differs between flying and non-flying insects, the evolution of molecular energy metabolism mechanisms in insects remains largely unexplored. Considering that about 95% of adenosine triphosphate (ATP) is supplied by mitochondria via oxidative phosphorylation, we examined 13 mitochondrial protein-encoding genes to test whether adaptive evolution of energy metabolism-related genes occurred in insects. The analyses demonstrated that mitochondrial DNA protein-encoding genes are subject to positive selection from the last common ancestor of Pterygota, which evolved primitive flight ability. Positive selection was also found in insects with flight ability, whereas no significant sign of selection was found in flightless insects where the wings had degenerated. In addition, significant positive selection was also identified in the last common ancestor of Neoptera, which changed its flight mode from direct to indirect. Interestingly, detection of more positively selected genes in indirect flight rather than direct flight insects suggested a stronger selective pressure in insects having higher energy consumption. In conclusion, mitochondrial protein-encoding genes involved in energy metabolism were targets of adaptive evolution in response to increased energy demands that arose during the evolution of flight ability in insects.

Adaptive evolution of Saccharomyces cerevisiae with enhanced ethanol tolerance for Chinese rice wine fermentation.

Science.gov (United States)

Chen, Shuang; Xu, Yan

2014-08-01

High tolerance towards ethanol is a desirable property for the Saccharomyces cerevisiae strains used in the alcoholic beverage industry. To improve the ethanol tolerance of an industrial Chinese rice wine yeast, a sequential batch fermentation strategy was used to adaptively evolve a chemically mutagenized Chinese rice wine G85 strain. The high level of ethanol produced under Chinese rice wine-like fermentation conditions was used as the selective pressure. After adaptive evolution of approximately 200 generations, mutant G85X-8 was isolated and shown to have markedly increased ethanol tolerance. The evolved strain also showed higher osmotic and temperature tolerances than the parental strain. Laboratory Chinese rice wine fermentation showed that the evolved G85X-8 strain was able to catabolize sugars more completely than the parental G85 strain. A higher level of yeast cell activity was found in the fermentation mash produced by the evolved strain, but the aroma profiles were similar between the evolved and parental strains. The improved ethanol tolerance in the evolved strain might be ascribed to the altered fatty acids composition of the cell membrane and higher intracellular trehalose concentrations. These results suggest that adaptive evolution is an efficient approach for the non-recombinant modification of industrial yeast strains.

Can the experimental evolution programme help us elucidate the genetic basis of adaptation in nature?

DEFF Research Database (Denmark)

Bailey, Susan; Bataillon, Thomas

2015-01-01

and continue to play an important role in shaping adaptive evolution in the natural world. Further to this, experimental evolution studies allow for tests of theories that may be difficult or impossible to test in natural populations for logistical and methodological reasons and can even generate new insights......, suggesting further refinement of existing theories. However, as experimental evolution studies often take place in a very particular set of controlled conditions – that is simple environments, a small range of usually asexual species, relatively short timescales – the question remains as to how applicable...... natural population studies. We finish by making suggestions for future work in particular a need for natural population genomic time series data, as well as the necessity for studies that combine both experimental evolution and natural population approaches....

Quantifying the effect of autonomous adaptation to global river flood projections: application to future flood risk assessments

Science.gov (United States)

Kinoshita, Youhei; Tanoue, Masahiro; Watanabe, Satoshi; Hirabayashi, Yukiko

2018-01-01

This study represents the first attempt to quantify the effects of autonomous adaptation on the projection of global flood hazards and to assess future flood risk by including this effect. A vulnerability scenario, which varies according to the autonomous adaptation effect for conventional disaster mitigation efforts, was developed based on historical vulnerability values derived from flood damage records and a river inundation simulation. Coupled with general circulation model outputs and future socioeconomic scenarios, potential future flood fatalities and economic loss were estimated. By including the effect of autonomous adaptation, our multimodel ensemble estimates projected a 2.0% decrease in potential flood fatalities and an 821% increase in potential economic losses by 2100 under the highest emission scenario together with a large population increase. Vulnerability changes reduced potential flood consequences by 64%-72% in terms of potential fatalities and 28%-42% in terms of potential economic losses by 2100. Although socioeconomic changes made the greatest contribution to the potential increased consequences of future floods, about a half of the increase of potential economic losses was mitigated by autonomous adaptation. There is a clear and positive relationship between the global temperature increase from the pre-industrial level and the estimated mean potential flood economic loss, while there is a negative relationship with potential fatalities due to the autonomous adaptation effect. A bootstrapping analysis suggests a significant increase in potential flood fatalities (+5.7%) without any adaptation if the temperature increases by 1.5 °C-2.0 °C, whereas the increase in potential economic loss (+0.9%) was not significant. Our method enables the effects of autonomous adaptation and additional adaptation efforts on climate-induced hazards to be distinguished, which would be essential for the accurate estimation of the cost of adaptation to

Accelerating Markov chain Monte Carlo simulation by differential evolution with self-adaptive randomized subspace sampling

Energy Technology Data Exchange (ETDEWEB)

Vrugt, Jasper A [Los Alamos National Laboratory; Hyman, James M [Los Alamos National Laboratory; Robinson, Bruce A [Los Alamos National Laboratory; Higdon, Dave [Los Alamos National Laboratory; Ter Braak, Cajo J F [NETHERLANDS; Diks, Cees G H [UNIV OF AMSTERDAM

2008-01-01

Markov chain Monte Carlo (MCMC) methods have found widespread use in many fields of study to estimate the average properties of complex systems, and for posterior inference in a Bayesian framework. Existing theory and experiments prove convergence of well constructed MCMC schemes to the appropriate limiting distribution under a variety of different conditions. In practice, however this convergence is often observed to be disturbingly slow. This is frequently caused by an inappropriate selection of the proposal distribution used to generate trial moves in the Markov Chain. Here we show that significant improvements to the efficiency of MCMC simulation can be made by using a self-adaptive Differential Evolution learning strategy within a population-based evolutionary framework. This scheme, entitled DiffeRential Evolution Adaptive Metropolis or DREAM, runs multiple different chains simultaneously for global exploration, and automatically tunes the scale and orientation of the proposal distribution in randomized subspaces during the search. Ergodicity of the algorithm is proved, and various examples involving nonlinearity, high-dimensionality, and multimodality show that DREAM is generally superior to other adaptive MCMC sampling approaches. The DREAM scheme significantly enhances the applicability of MCMC simulation to complex, multi-modal search problems.

An adaptive left–right eigenvector evolution algorithm for vibration isolation control

International Nuclear Information System (INIS)

Wu, T Y

2009-01-01

The purpose of this research is to investigate the feasibility of utilizing an adaptive left and right eigenvector evolution (ALREE) algorithm for active vibration isolation. As depicted in the previous paper presented by Wu and Wang (2008 Smart Mater. Struct. 17 015048), the structural vibration behavior depends on both the disturbance rejection capability and mode shape distributions, which correspond to the left and right eigenvector distributions of the system, respectively. In this paper, a novel adaptive evolution algorithm is developed for finding the optimal combination of left–right eigenvectors of the vibration isolator, which is an improvement over the simultaneous left–right eigenvector assignment (SLREA) method proposed by Wu and Wang (2008 Smart Mater. Struct. 17 015048). The isolation performance index used in the proposed algorithm is defined by combining the orthogonality index of left eigenvectors and the modal energy ratio index of right eigenvectors. Through the proposed ALREE algorithm, both the left and right eigenvectors evolve such that the isolation performance index decreases, and therefore one can find the optimal combination of left–right eigenvectors of the closed-loop system for vibration isolation purposes. The optimal combination of left–right eigenvectors is then synthesized to determine the feedback gain matrix of the closed-loop system. The result of the active isolation control shows that the proposed method can be utilized to improve the vibration isolation performance compared with the previous approaches

An adapted yield criterion for the evolution of subsequent yield surfaces

Science.gov (United States)

Küsters, N.; Brosius, A.

2017-09-01

In numerical analysis of sheet metal forming processes, the anisotropic material behaviour is often modelled with isotropic work hardening and an average Lankford coefficient. In contrast, experimental observations show an evolution of the Lankford coefficients, which can be associated with a yield surface change due to kinematic and distortional hardening. Commonly, extensive efforts are carried out to describe these phenomena. In this paper an isotropic material model based on the Yld2000-2d criterion is adapted with an evolving yield exponent in order to change the yield surface shape. The yield exponent is linked to the accumulative plastic strain. This change has the effect of a rotating yield surface normal. As the normal is directly related to the Lankford coefficient, the change can be used to model the evolution of the Lankford coefficient during yielding. The paper will focus on the numerical implementation of the adapted material model for the FE-code LS-Dyna, mpi-version R7.1.2-d. A recently introduced identification scheme [1] is used to obtain the parameters for the evolving yield surface and will be briefly described for the proposed model. The suitability for numerical analysis will be discussed for deep drawing processes in general. Efforts for material characterization and modelling will be compared to other common yield surface descriptions. Besides experimental efforts and achieved accuracy, the potential of flexibility in material models and the risk of ambiguity during identification are of major interest in this paper.

Functional evolution of leptin of Ochotona curzoniae in adaptive thermogenesis driven by cold environmental stress.

Directory of Open Access Journals (Sweden)

Jie Yang

Full Text Available BACKGROUND: Environmental stress can accelerate the directional selection and evolutionary rate of specific stress-response proteins to bring about new or altered functions, enhancing an organism's fitness to challenging environments. Plateau pika (Ochotona curzoniae, an endemic and keystone species on Qinghai-Tibetan Plateau, is a high hypoxia and low temperature tolerant mammal with high resting metabolic rate and non-shivering thermogenesis to cope in this harsh plateau environment. Leptin is a key hormone related to how these animals regulate energy homeostasis. Previous molecular evolutionary analysis helped to generate the hypothesis that adaptive evolution of plateau pika leptin may be driven by cold stress. METHODOLOGY/PRINCIPAL FINDINGS: To test the hypothesis, recombinant pika leptin was first purified. The thermogenic characteristics of C57BL/6J mice injected with pika leptin under warm (23±1°C and cold (5±1°C acclimation is investigated. Expression levels of genes regulating adaptive thermogenesis in brown adipose tissue and the hypothalamus are compared between pika leptin and human leptin treatment, suggesting that pika leptin has adaptively and functionally evolved. Our results show that pika leptin regulates energy homeostasis via reduced food intake and increased energy expenditure under both warm and cold conditions. Compared with human leptin, pika leptin demonstrates a superior induced capacity for adaptive thermogenesis, which is reflected in a more enhanced β-oxidation, mitochondrial biogenesis and heat production. Moreover, leptin treatment combined with cold stimulation has a significant synergistic effect on adaptive thermogenesis, more so than is observed with a single cold exposure or single leptin treatment. CONCLUSIONS/SIGNIFICANCE: These findings support the hypothesis that cold stress has driven the functional evolution of plateau pika leptin as an ecological adaptation to the Qinghai-Tibetan Plateau.

Multi-objective optimization of p-xylene oxidation process using an improved self-adaptive differential evolution algorithm

Institute of Scientific and Technical Information of China (English)

Lili Tao; Bin Xu; Zhihua Hu; Weimin Zhong

2017-01-01

The rise in the use of global polyester fiber contributed to strong demand of the Terephthalic acid (TPA). The liquid-phase catalytic oxidation of p-xylene (PX) to TPA is regarded as a critical and efficient chemical process in industry [1]. PX oxidation reaction involves many complex side reactions, among which acetic acid combustion and PX combustion are the most important. As the target product of this oxidation process, the quality and yield of TPA are of great concern. However, the improvement of the qualified product yield can bring about the high energy consumption, which means that the economic objectives of this process cannot be achieved simulta-neously because the two objectives are in conflict with each other. In this paper, an improved self-adaptive multi-objective differential evolution algorithm was proposed to handle the multi-objective optimization prob-lems. The immune concept is introduced to the self-adaptive multi-objective differential evolution algorithm (SADE) to strengthen the local search ability and optimization accuracy. The proposed algorithm is successfully tested on several benchmark test problems, and the performance measures such as convergence and divergence metrics are calculated. Subsequently, the multi-objective optimization of an industrial PX oxidation process is carried out using the proposed immune self-adaptive multi-objective differential evolution algorithm (ISADE). Optimization results indicate that application of ISADE can greatly improve the yield of TPA with low combustion loss without degenerating TA quality.

Evolution and Adaptation of Wild Emmer Wheat Populations to Biotic and Abiotic Stresses.

Science.gov (United States)

Huang, Lin; Raats, Dina; Sela, Hanan; Klymiuk, Valentina; Lidzbarsky, Gabriel; Feng, Lihua; Krugman, Tamar; Fahima, Tzion

2016-08-04

The genetic bottlenecks associated with plant domestication and subsequent selection in man-made agroecosystems have limited the genetic diversity of modern crops and increased their vulnerability to environmental stresses. Wild emmer wheat, the tetraploid progenitor of domesticated wheat, distributed along a wide range of ecogeographical conditions in the Fertile Crescent, has valuable "left behind" adaptive diversity to multiple diseases and environmental stresses. The biotic and abiotic stress responses are conferred by series of genes and quantitative trait loci (QTLs) that control complex resistance pathways. The study of genetic diversity, genomic organization, expression profiles, protein structure and function of biotic and abiotic stress-resistance genes, and QTLs could shed light on the evolutionary history and adaptation mechanisms of wild emmer populations for their natural habitats. The continuous evolution and adaptation of wild emmer to the changing environment provide novel solutions that can contribute to safeguarding food for the rapidly growing human population.

Design of 2-D Recursive Filters Using Self-adaptive Mutation Differential Evolution Algorithm

Directory of Open Access Journals (Sweden)

Lianghong Wu

2011-08-01

Full Text Available This paper investigates a novel approach to the design of two-dimensional recursive digital filters using differential evolution (DE algorithm. The design task is reformulated as a constrained minimization problem and is solved by an Self-adaptive Mutation DE algorithm (SAMDE, which adopts an adaptive mutation operator that combines with the advantages of the DE/rand/1/bin strategy and the DE/best/2/bin strategy. As a result, its convergence performance is improved greatly. Numerical experiment results confirm the conclusion. The proposedSAMDE approach is effectively applied to test a numerical example and is compared with previous design methods. The computational experiments show that the SAMDE approach can obtain better results than previous design methods.

Quantifying camouflage: how to predict detectability from appearance.

Science.gov (United States)

Troscianko, Jolyon; Skelhorn, John; Stevens, Martin

2017-01-06

Quantifying the conspicuousness of objects against particular backgrounds is key to understanding the evolution and adaptive value of animal coloration, and in designing effective camouflage. Quantifying detectability can reveal how colour patterns affect survival, how animals' appearances influence habitat preferences, and how receiver visual systems work. Advances in calibrated digital imaging are enabling the capture of objective visual information, but it remains unclear which methods are best for measuring detectability. Numerous descriptions and models of appearance have been used to infer the detectability of animals, but these models are rarely empirically validated or directly compared to one another. We compared the performance of human 'predators' to a bank of contemporary methods for quantifying the appearance of camouflaged prey. Background matching was assessed using several established methods, including sophisticated feature-based pattern analysis, granularity approaches and a range of luminance and contrast difference measures. Disruptive coloration is a further camouflage strategy where high contrast patterns disrupt they prey's tell-tale outline, making it more difficult to detect. Disruptive camouflage has been studied intensely over the past decade, yet defining and measuring it have proven far more problematic. We assessed how well existing disruptive coloration measures predicted capture times. Additionally, we developed a new method for measuring edge disruption based on an understanding of sensory processing and the way in which false edges are thought to interfere with animal outlines. Our novel measure of disruptive coloration was the best predictor of capture times overall, highlighting the importance of false edges in concealment over and above pattern or luminance matching. The efficacy of our new method for measuring disruptive camouflage together with its biological plausibility and computational efficiency represents a substantial

Light adaptation and the evolution of vertebrate photoreceptors.

Science.gov (United States)

Morshedian, Ala; Fain, Gordon L

2017-07-15

Lamprey are cyclostomes, a group of vertebrates that diverged from lines leading to jawed vertebrates (including mammals) in the late Cambrian, 500 million years ago. It may therefore be possible to infer properties of photoreceptors in early vertebrate progenitors by comparing lamprey to other vertebrates. We show that lamprey rods and cones respond to light much like rods and cones in amphibians and mammals. They operate over a similar range of light intensities and adapt to backgrounds and bleaches nearly identically. These correspondences are pervasive and detailed; they argue for the presence of rods and cones very early in the evolution of vertebrates with properties much like those of rods and cones in existing vertebrate species. The earliest vertebrates were agnathans - fish-like organisms without jaws, which first appeared near the end of the Cambrian radiation. One group of agnathans became cyclostomes, which include lamprey and hagfish. Other agnathans gave rise to jawed vertebrates or gnathostomes, the group including all other existing vertebrate species. Because cyclostomes diverged from other vertebrates 500 million years ago, it may be possible to infer some of the properties of the retina of early vertebrate progenitors by comparing lamprey to other vertebrates. We have previously shown that rods and cones in lamprey respond to light much like photoreceptors in other vertebrates and have a similar sensitivity. We now show that these affinities are even closer. Both rods and cones adapt to background light and to bleaches in a manner almost identical to other vertebrate photoreceptors. The operating range in darkness is nearly the same in lamprey and in amphibian or mammalian rods and cones; moreover background light shifts response-intensity curves downward and to the right over a similar range of ambient intensities. Rods show increment saturation at about the same intensity as mammalian rods, and cones never saturate. Bleaches decrease

Has Human Evolution Stopped?

Directory of Open Access Journals (Sweden)

Alan R. Templeton

2010-07-01

Full Text Available It has been argued that human evolution has stopped because humans now adapt to their environment via cultural evolution and not biological evolution. However, all organisms adapt to their environment, and humans are no exception. Culture defines much of the human environment, so cultural evolution has actually led to adaptive evolution in humans. Examples are given to illustrate the rapid pace of adaptive evolution in response to cultural innovations. These adaptive responses have important implications for infectious diseases, Mendelian genetic diseases, and systemic diseases in current human populations. Moreover, evolution proceeds by mechanisms other than natural selection. The recent growth in human population size has greatly increased the reservoir of mutational variants in the human gene pool, thereby enhancing the potential for human evolution. The increase in human population size coupled with our increased capacity to move across the globe has induced a rapid and ongoing evolutionary shift in how genetic variation is distributed within and among local human populations. In particular, genetic differences between human populations are rapidly diminishing and individual heterozygosity is increasing, with beneficial health effects. Finally, even when cultural evolution eliminates selection on a trait, the trait can still evolve due to natural selection on other traits. Our traits are not isolated, independent units, but rather are integrated into a functional whole, so selection on one trait can cause evolution to occur on another trait, sometimes with mildly maladaptive consequences.

Evolution of Escherichia coli to 42 °C and Subsequent Genetic Engineering Reveals Adaptive Mechanisms and Novel Mutations

DEFF Research Database (Denmark)

Sandberg, Troy E.; Pedersen, Margit; LaCroix, Ryan A.

2014-01-01

Adaptive laboratory evolution (ALE) has emerged as a valuable method by which to investigate microbial adaptation to a desired environment. Here, we performed ALE to 42 °C of ten parallel populations of Escherichia coli K-12 MG1655 grown in glucose minimal media. Tightly controlled experimental c...... targets for additional ameliorating mutations. Overall, the results of this study provide insight into the adaptation process and yield lessons important for the future implementation of ALE as a tool for scientific research and engineering....

The elusive nature of adaptive mitochondrial DNA evolution of an Arctic lineage prone to frequent introgression

DEFF Research Database (Denmark)

Melo-Ferreira, Jose; Vilela, Joana; Fonseca, Miguel M.

2014-01-01

understood. Hares (Lepus spp.) are privileged models to study the impact of natural selection on mitogenomic evolution because 1) species are adapted to contrasting environments, including arctic, with different metabolic pressures, and 2) mtDNA introgression from arctic into temperate species is widespread...

Prolonged Adaptive Evolution of a Defensive Gene in the Solanaceae.

Science.gov (United States)

Rausher, Mark D; Huang, Jie

2016-01-01

Although plants and their natural enemies may coevolve for prolonged periods, little is known about how long individual plant defensive genes are involved in the coevolutionary process. We address this issue by examining patterns of selection on the defensive gene threonine deaminase (TD). Tomato (Solanum lycopersicum) has two copies of this gene. One performs the canonical housekeeping function in amino acid metabolism of catalyzing the first reaction in the conversion of threonine to isoleucine. The second copy functions as an antinutritive defense against lepidopteran herbivores by depleting threonine in the insect gut. Wild tobacco (Nicotiana attenuata) also contains a defensive copy. We show that a single copy of TD underwent two or three duplications near the base of the Solanaceae. One copy retains the housekeeping function, whereas a second copy evolved defensive functions. Positive selection occurred on the branch of the TD2 gene tree subtending the common ancestor of the Nicotianoideae and Solanoideae. It also occurred within the Solanoideae clade but not within the Nicotianoideae clade. Finally, it occurred on most branches leading from the common ancestor to S. lycopersicum. Based on recent calibrations of the Solanaceae phylogeny, TD2 experienced adaptive substitutions for a period of 30-50 My. We suggest that the most likely explanation for this result is fluctuating herbivore abundances: When herbivores are rare, relaxed selection increases the likelihood that slightly disadvantageous mutations will be fixed by drift; when herbivores are common, increased selection causes the evolution of compensatory adaptive mutations. Alternative explanations are also discussed. © The Author 2015. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

CBCT-guided evolutive library for cervical adaptive IMRT.

Science.gov (United States)

Rigaud, Bastien; Simon, Antoine; Gobeli, Maxime; Lafond, Caroline; Leseur, Julie; Barateau, Anais; Jaksic, Nicolas; Castelli, Joël; Williaume, Danièle; Haigron, Pascal; De Crevoisier, Renaud

2018-04-01

In the context of adaptive radiation therapy (ART) for locally advanced cervical carcinoma (LACC), this study proposed an original cone-beam computed tomography (CBCT)-guided "Evolutive library" and evaluated it against four other known radiotherapy (RT) strategies. For 20 patients who underwent intensity-modulated radiation therapy (IMRT) for LACC, three planning CTs [with empty (EB), intermediate (IB), and full (FB) bladder volumes], a CT scan at 20 Gy and bi-weekly CBCTs for 5 weeks were performed. Five RT strategies were simulated for each patient: "Standard RT" was based on one IB planning CT; "internal target volume (ITV)-based RT" was an ITV built from the three planning CTs; "RT with one mid-treatment replanning (MidTtReplan)" corresponded to the standard RT with a replanning at 20 Gy; "Pretreatment library ART" using a planning library based on the three planning CTs; and the "Evolutive library ART", which was the "Pretreatment library ART" strategy enriched by including some CBCT anatomies into the library when the daily clinical target volume (CTV) shape differed from the ones in the library. Two planning target volume (PTV) margins of 7 and 10 mm were evaluated. All the strategies were geometrically compared in terms of the percentage of coverage by the PTV, for the CTV and the organs at risk (OAR) delineated on the CBCT. Inadequate coverage of the CTV and OARs by the PTV was also assessed using deformable image registration. The cumulated dose distributions of each strategy were likewise estimated and compared for one patient. The "Evolutive library ART" strategy involved a number of added CBCTs: 0 for 55%; 1 for 30%; 2 for 5%; and 3 for 10% of patients. Compared with the other four, this strategy provided the highest CTV geometric coverage by the PTV, with a mean (min-max) coverage of 98.5% (96.4-100) for 10 mm margins and 96.2% (93.0-99.7) for 7 mm margins (P < 0.05). Moreover, this strategy significantly decreased the geometric coverage of the bowel

Inventing an arsenal: adaptive evolution and neofunctionalization of snake venom phospholipase A2 genes

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Lynch Vincent J

2007-01-01

Full Text Available Abstract Background Gene duplication followed by functional divergence has long been hypothesized to be the main source of molecular novelty. Convincing examples of neofunctionalization, however, remain rare. Snake venom phospholipase A2 genes are members of large multigene families with many diverse functions, thus they are excellent models to study the emergence of novel functions after gene duplications. Results Here, I show that positive Darwinian selection and neofunctionalization is common in snake venom phospholipase A2 genes. The pattern of gene duplication and positive selection indicates that adaptive molecular evolution occurs immediately after duplication events as novel functions emerge and continues as gene families diversify and are refined. Surprisingly, adaptive evolution of group-I phospholipases in elapids is also associated with speciation events, suggesting adaptation of the phospholipase arsenal to novel prey species after niche shifts. Mapping the location of sites under positive selection onto the crystal structure of phospholipase A2 identified regions evolving under diversifying selection are located on the molecular surface and are likely protein-protein interactions sites essential for toxin functions. Conclusion These data show that increases in genomic complexity (through gene duplications can lead to phenotypic complexity (venom composition and that positive Darwinian selection is a common evolutionary force in snake venoms. Finally, regions identified under selection on the surface of phospholipase A2 enzymes are potential candidate sites for structure based antivenin design.

A Bayesian Network Based Adaptability Design of Product Structures for Function Evolution

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Shaobo Li

2018-03-01

Full Text Available Structure adaptability design is critical for function evolution in product families, in which many structural and functional design factors are intertwined together with manufacturing cost, customer satisfaction, and final market sales. How to achieve a delicate balance among all of these factors to maximize the market performance of the product is too complicated to address based on traditional domain experts’ knowledge or some ad hoc heuristics. Here, we propose a quantitative product evolution design model that is based on Bayesian networks to model the dynamic relationship between customer needs and product structure design. In our model, all of the structural or functional features along with customer satisfaction, manufacturing cost, sale price, market sales, and indirect factors are modeled as random variables denoted as nodes in the Bayesian networks. The structure of the Bayesian model is then determined based on the historical data, which captures the dynamic sophisticated relationship of customer demands of a product, structural design, and market performance. Application of our approach to an electric toothbrush product family evolution design problem shows that our model allows for designers to interrogate with the model and obtain theoretical and decision support for dynamic product feature design process.

Hologenomic adaptations underlying the evolution of sanguivory in the common vampire bat

DEFF Research Database (Denmark)

Zepeda Mendoza, M. Lisandra; Xiong, Zijun; Escalera-Zamudio, Marina

2018-01-01

Adaptation to specialized diets often requires modifications at both genomic and microbiome levels. We applied a hologenomic approach to the common vampire bat (Desmodus rotundus), one of the only three obligate blood-feeding (sanguivorous) mammals, to study the evolution of its complex dietary...... integrated viral elements, a dietary and phylogenetic influence on gut microbiome taxonomic and functional profiles, and that both genetic elements harbour key traits related to the nutritional (for example, vitamin and lipid shortage) and non-nutritional (for example, nitrogen waste and osmotic homeostasis...

Phylogeny and adaptive evolution of the brain-development gene microcephalin (MCPH1 in cetaceans

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Montgomery Stephen H

2011-04-01

Full Text Available Abstract Background Representatives of Cetacea have the greatest absolute brain size among animals, and the largest relative brain size aside from humans. Despite this, genes implicated in the evolution of large brain size in primates have yet to be surveyed in cetaceans. Results We sequenced ~1240 basepairs of the brain development gene microcephalin (MCPH1 in 38 cetacean species. Alignments of these data and a published complete sequence from Tursiops truncatus with primate MCPH1 were utilized in phylogenetic analyses and to estimate ω (rate of nonsynonymous substitution/rate of synonymous substitution using site and branch models of molecular evolution. We also tested the hypothesis that selection on MCPH1 was correlated with brain size in cetaceans using a continuous regression analysis that accounted for phylogenetic history. Our analyses revealed widespread signals of adaptive evolution in the MCPH1 of Cetacea and in other subclades of Mammalia, however, there was not a significant positive association between ω and brain size within Cetacea. Conclusion In conjunction with a recent study of Primates, we find no evidence to support an association between MCPH1 evolution and the evolution of brain size in highly encephalized mammalian species. Our finding of significant positive selection in MCPH1 may be linked to other functions of the gene.

Modeling adaptive and non-adaptive responses to environmental change

DEFF Research Database (Denmark)

Coulson, Tim; Kendall, Bruce E; Barthold, Julia A.

2017-01-01

, with plastic responses being either adaptive or non-adaptive. We develop an approach that links quantitative genetic theory with data-driven structured models to allow prediction of population responses to environmental change via plasticity and adaptive evolution. After introducing general new theory, we...... construct a number of example models to demonstrate that evolutionary responses to environmental change over the short-term will be considerably slower than plastic responses, and that the rate of adaptive evolution to a new environment depends upon whether plastic responses are adaptive or non-adaptive....... Parameterization of the models we develop requires information on genetic and phenotypic variation and demography that will not always be available, meaning that simpler models will often be required to predict responses to environmental change. We consequently develop a method to examine whether the full...

The evolution model of Uppsala in light of the complex adaptive systems approach

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Rennaly Alves da Silva

2013-11-01

Full Text Available The behavioral approach to the internationalization of companies explains that the movements toward external markets occur in accordance with the increasing commitment of resources to mitigate the effects of uncertainty and reduce the perception of risk. Evidence indicates that the theories and practices developed in the domestic market may not be able to explain the reality of companies that operate in international markets. Thus, the Paradigm of Complexity presents itself as a comprehensive alternative to realize the relationships within organizations and markets. Accordingly, the aim of this theoretical paper is to analyze the evolution of the Uppsala Model between years 1975 and 2010 with the understanding of the companies in the process of internationalization as Complex Adaptive Systems, in accordance with the Model Kelly and Allison (1998. Four propositions are presented that show the links between the approaches. The most surprising is the perception that the conceptual evolution of the Uppsala Model seems to accompany the evolution of complexity levels, presented in Model Kelly and Allison.

Global Rebalancing of Cellular Resources by Pleiotropic Point Mutations Illustrates a Multi-scale Mechanism of Adaptive Evolution

DEFF Research Database (Denmark)

Utrilla, José; O'Brien, Edward J.; Chen, Ke

2016-01-01

Pleiotropic regulatory mutations affect diverse cellular processes, posing a challenge to our understanding of genotype-phenotype relationships across multiple biological scales. Adaptive laboratory evolution (ALE) allows for such mutations to be found and characterized in the context of clear se...

Widespread correlations between climatic niche evolution and species diversification in birds.

Science.gov (United States)

Cooney, Christopher R; Seddon, Nathalie; Tobias, Joseph A

2016-07-01

The adaptability of species' climatic niches can influence the dynamics of colonization and gene flow across climatic gradients, potentially increasing the likelihood of speciation or reducing extinction in the face of environmental change. However, previous comparative studies have tested these ideas using geographically, taxonomically and ecologically restricted samples, yielding mixed results, and thus the processes linking climatic niche evolution with diversification remain poorly understood. Focusing on birds, the largest and most widespread class of terrestrial vertebrates, we test whether variation in species diversification among clades is correlated with rates of climatic niche evolution and the extent to which these patterns are modified by underlying gradients in biogeography and species' ecology. We quantified climatic niches, latitudinal distribution and ecological traits for 7657 (˜75%) bird species based on geographical range polygons and then used Bayesian phylogenetic analyses to test whether niche evolution was related to species richness and rates of diversification across genus- and family-level clades. We found that the rate of climatic niche evolution has a positive linear relationship with both species richness and diversification rate at two different taxonomic levels (genus and family). Furthermore, this positive association between labile climatic niches and diversification was detected regardless of variation in clade latitude or key ecological traits. Our findings suggest either that rapid adaptation to unoccupied areas of climatic niche space promotes avian diversification, or that diversification promotes adaptation. Either way, we propose that climatic niche evolution is a fundamental process regulating the link between climate and biodiversity at global scales, irrespective of the geographical and ecological context of speciation and extinction. © 2016 The Authors. Journal of Animal Ecology © 2016 British Ecological Society.

Strong Selection Significantly Increases Epistatic Interactions in the Long-Term Evolution of a Protein.

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Aditi Gupta

2016-03-01

Full Text Available Epistatic interactions between residues determine a protein's adaptability and shape its evolutionary trajectory. When a protein experiences a changed environment, it is under strong selection to find a peak in the new fitness landscape. It has been shown that strong selection increases epistatic interactions as well as the ruggedness of the fitness landscape, but little is known about how the epistatic interactions change under selection in the long-term evolution of a protein. Here we analyze the evolution of epistasis in the protease of the human immunodeficiency virus type 1 (HIV-1 using protease sequences collected for almost a decade from both treated and untreated patients, to understand how epistasis changes and how those changes impact the long-term evolvability of a protein. We use an information-theoretic proxy for epistasis that quantifies the co-variation between sites, and show that positive information is a necessary (but not sufficient condition that detects epistasis in most cases. We analyze the "fossils" of the evolutionary trajectories of the protein contained in the sequence data, and show that epistasis continues to enrich under strong selection, but not for proteins whose environment is unchanged. The increase in epistasis compensates for the information loss due to sequence variability brought about by treatment, and facilitates adaptation in the increasingly rugged fitness landscape of treatment. While epistasis is thought to enhance evolvability via valley-crossing early-on in adaptation, it can hinder adaptation later when the landscape has turned rugged. However, we find no evidence that the HIV-1 protease has reached its potential for evolution after 9 years of adapting to a drug environment that itself is constantly changing. We suggest that the mechanism of encoding new information into pairwise interactions is central to protein evolution not just in HIV-1 protease, but for any protein adapting to a changing

Quantifying environmental adaptation of metabolic pathways in metagenomics

DEFF Research Database (Denmark)

Gianoulis, Tara A; Raes, Jeroen; Patel, Prianka V

2009-01-01

of particular pathways and subnetworks reflects the adaptation of microbial communities across environments and habitats-i.e., how network dynamics relates to environmental features. Previous research has treated environments as discrete, somewhat simplified classes (e.g., terrestrial vs. marine), and searched...... multiple, continuously varying factors defining an environment to the extent of particular microbial pathways present in a geographic site. Moreover, rather than looking only at individual correlations (one-to-one), we adapted canonical correlation analysis and related techniques to define an ensemble...

Evidence for determinism in species diversification and contingency in phenotypic evolution during adaptive radiation.

Science.gov (United States)

Burbrink, Frank T; Chen, Xin; Myers, Edward A; Brandley, Matthew C; Pyron, R Alexander

2012-12-07

Adaptive radiation (AR) theory predicts that groups sharing the same source of ecological opportunity (EO) will experience deterministic species diversification and morphological evolution. Thus, deterministic ecological and morphological evolution should be correlated with deterministic patterns in the tempo and mode of speciation for groups in similar habitats and time periods. We test this hypothesis using well-sampled phylogenies of four squamate groups that colonized the New World (NW) in the Late Oligocene. We use both standard and coalescent models to assess species diversification, as well as likelihood models to examine morphological evolution. All squamate groups show similar early pulses of speciation, as well as diversity-dependent ecological limits on clade size at a continental scale. In contrast, processes of morphological evolution are not easily predictable and do not show similar pulses of early and rapid change. Patterns of morphological and species diversification thus appear uncoupled across these groups. This indicates that the processes that drive diversification and disparification are not mechanistically linked, even among similar groups of taxa experiencing the same sources of EO. It also suggests that processes of phenotypic diversification cannot be predicted solely from the existence of an AR or knowledge of the process of diversification.

Sympathetic nervous system activity measured by skin conductance quantifies the challenge of walking adaptability tasks after stroke.

Science.gov (United States)

Clark, David J; Chatterjee, Sudeshna A; McGuirk, Theresa E; Porges, Eric C; Fox, Emily J; Balasubramanian, Chitralakshmi K

2018-02-01

Walking adaptability tasks are challenging for people with motor impairments. The construct of perceived challenge is typically measured by self-report assessments, which are susceptible to subjective measurement error. The development of an objective physiologically-based measure of challenge may help to improve the ability to assess this important aspect of mobility function. The objective of this study to investigate the use of sympathetic nervous system (SNS) activity measured by skin conductance to gauge the physiological stress response to challenging walking adaptability tasks in people post-stroke. Thirty adults with chronic post-stroke hemiparesis performed a battery of seventeen walking adaptability tasks. SNS activity was measured by skin conductance from the palmar surface of each hand. The primary outcome variable was the percent change in skin conductance level (ΔSCL) between the baseline resting and walking phases of each task. Task difficulty was measured by performance speed and by physical therapist scoring of performance. Walking function and balance confidence were measured by preferred walking speed and the Activities-specific Balance Confidence Scale, respectively. There was a statistically significant negative association between ΔSCL and task performance speed and between ΔSCL and clinical score, indicating that tasks with greater SNS activity had slower performance speed and poorer clinical scores. ΔSCL was significantly greater for low functioning participants versus high functioning participants, particularly during the most challenging walking adaptability tasks. This study supports the use of SNS activity measured by skin conductance as a valuable approach for objectively quantifying the perceived challenge of walking adaptability tasks in people post-stroke. Published by Elsevier B.V.

Comparative genomics reveals insights into avian genome evolution and adaptation

Science.gov (United States)

Zhang, Guojie; Li, Cai; Li, Qiye; Li, Bo; Larkin, Denis M.; Lee, Chul; Storz, Jay F.; Antunes, Agostinho; Greenwold, Matthew J.; Meredith, Robert W.; Ödeen, Anders; Cui, Jie; Zhou, Qi; Xu, Luohao; Pan, Hailin; Wang, Zongji; Jin, Lijun; Zhang, Pei; Hu, Haofu; Yang, Wei; Hu, Jiang; Xiao, Jin; Yang, Zhikai; Liu, Yang; Xie, Qiaolin; Yu, Hao; Lian, Jinmin; Wen, Ping; Zhang, Fang; Li, Hui; Zeng, Yongli; Xiong, Zijun; Liu, Shiping; Zhou, Long; Huang, Zhiyong; An, Na; Wang, Jie; Zheng, Qiumei; Xiong, Yingqi; Wang, Guangbiao; Wang, Bo; Wang, Jingjing; Fan, Yu; da Fonseca, Rute R.; Alfaro-Núñez, Alonzo; Schubert, Mikkel; Orlando, Ludovic; Mourier, Tobias; Howard, Jason T.; Ganapathy, Ganeshkumar; Pfenning, Andreas; Whitney, Osceola; Rivas, Miriam V.; Hara, Erina; Smith, Julia; Farré, Marta; Narayan, Jitendra; Slavov, Gancho; Romanov, Michael N; Borges, Rui; Machado, João Paulo; Khan, Imran; Springer, Mark S.; Gatesy, John; Hoffmann, Federico G.; Opazo, Juan C.; Håstad, Olle; Sawyer, Roger H.; Kim, Heebal; Kim, Kyu-Won; Kim, Hyeon Jeong; Cho, Seoae; Li, Ning; Huang, Yinhua; Bruford, Michael W.; Zhan, Xiangjiang; Dixon, Andrew; Bertelsen, Mads F.; Derryberry, Elizabeth; Warren, Wesley; Wilson, Richard K; Li, Shengbin; Ray, David A.; Green, Richard E.; O’Brien, Stephen J.; Griffin, Darren; Johnson, Warren E.; Haussler, David; Ryder, Oliver A.; Willerslev, Eske; Graves, Gary R.; Alström, Per; Fjeldså, Jon; Mindell, David P.; Edwards, Scott V.; Braun, Edward L.; Rahbek, Carsten; Burt, David W.; Houde, Peter; Zhang, Yong; Yang, Huanming; Wang, Jian; Jarvis, Erich D.; Gilbert, M. Thomas P.; Wang, Jun

2015-01-01

Birds are the most species-rich class of tetrapod vertebrates and have wide relevance across many research fields. We explored bird macroevolution using full genomes from 48 avian species representing all major extant clades. The avian genome is principally characterized by its constrained size, which predominantly arose because of lineage-specific erosion of repetitive elements, large segmental deletions, and gene loss. Avian genomes furthermore show a remarkably high degree of evolutionary stasis at the levels of nucleotide sequence, gene synteny, and chromosomal structure. Despite this pattern of conservation, we detected many non-neutral evolutionary changes in protein-coding genes and noncoding regions. These analyses reveal that pan-avian genomic diversity covaries with adaptations to different lifestyles and convergent evolution of traits. PMID:25504712

Adaptive landscape and functional diversity of Neotropical cichlids: implications for the ecology and evolution of Cichlinae (Cichlidae; Cichliformes).

Science.gov (United States)

Arbour, J H; López-Fernández, H

2014-11-01

Morphological, lineage and ecological diversity can vary substantially even among closely related lineages. Factors that influence morphological diversification, especially in functionally relevant traits, can help to explain the modern distribution of disparity across phylogenies and communities. Multivariate axes of feeding functional morphology from 75 species of Neotropical cichlid and a stepwise-AIC algorithm were used to estimate the adaptive landscape of functional morphospace in Cichlinae. Adaptive landscape complexity and convergence, as well as the functional diversity of Cichlinae, were compared with expectations under null evolutionary models. Neotropical cichlid feeding function varied primarily between traits associated with ram feeding vs. suction feeding/biting and secondarily with oral jaw muscle size and pharyngeal crushing capacity. The number of changes in selective regimes and the amount of convergence between lineages was higher than expected under a null model of evolution, but convergence was not higher than expected under a similarly complex adaptive landscape. Functional disparity was compatible with an adaptive landscape model, whereas the distribution of evolutionary change through morphospace corresponded with a process of evolution towards a single adaptive peak. The continentally distributed Neotropical cichlids have evolved relatively rapidly towards a number of adaptive peaks in functional trait space. Selection in Cichlinae functional morphospace is more complex than expected under null evolutionary models. The complexity of selective constraints in feeding morphology has likely been a significant contributor to the diversity of feeding ecology in this clade. © 2014 European Society For Evolutionary Biology. Journal of Evolutionary Biology © 2014 European Society For Evolutionary Biology.

Evolution of cooperation through adaptive interaction in a spatial prisoner's dilemma game

Science.gov (United States)

Pan, Qiuhui; Liu, Xuesong; Bao, Honglin; Su, Yu; He, Mingfeng

2018-02-01

In this paper, we study the effect of adaptive interaction on the evolution of cooperation in a spatial prisoner's dilemma game. The connections of players are co-evolutionary with cooperation; whether adjacent players can play the prisoner's dilemma game is associated with the strategies they took in the preceding round. If a player defected in the preceding round, his neighbors will refuse to play the prisoner's dilemma game with him in accordance with a certain probability distribution. We use the disconnecting strength to represent this probability. We discuss the evolution of cooperation with different values of temptation to defect, sucker's payoff and disconnecting strength. The simulation results show that cooperation can be significantly enhanced through increasing the value of the disconnecting strength. In addition, the increase in disconnecting strength can improve the cooperators' ability to resist the increase in temptation and the decrease in reward. We study the parameter ranges for three different evolutionary results: cooperators extinction, defectors extinction, cooperator and defector co-existence. Meanwhile, we recruited volunteers and designed a human behavioral experiment to verify the theoretical simulation results. The punishment of disconnection has a positive effect on cooperation. A higher disconnecting strength will enhance cooperation more significantly. Our research findings reveal some significant insights into efficient mechanisms of the evolution of cooperation.

Quantifying and Validating Rapid Floodplain Geomorphic Evolution, a Monitoring and Modelling Case Study

Science.gov (United States)

Scott, R.; Entwistle, N. S.

2017-12-01

Gravel bed rivers and their associated wider systems present an ideal subject for development and improvement of rapid monitoring tools, with features dynamic enough to evolve within relatively short-term timescales. For detecting and quantifying topographical evolution, UAV based remote sensing has manifested as a reliable, low cost, and accurate means of topographic data collection. Here we present some validated methodologies for detection of geomorphic change at resolutions down to 0.05 m, building on the work of Wheaton et al. (2009) and Milan et al. (2007), to generate mesh based and pointcloud comparison data to produce a reliable picture of topographic evolution. Results are presented for the River Glen, Northumberland, UK. Recent channel avulsion and floodplain interaction, resulting in damage to flood defence structures make this site a particularly suitable case for application of geomorphic change detection methods, with the UAV platform at its centre. We compare multi-temporal, high-resolution point clouds derived from SfM processing, cross referenced with aerial LiDAR data, over a 1.5 km reach of the watercourse. Changes detected included bank erosion, bar and splay deposition, vegetation stripping and incipient channel avulsion. Utilisation of the topographic data for numerical modelling, carried out using CAESAR-Lisflood predicted the avulsion of the main channel, resulting in erosion of and potentially complete circumvention of original channel and flood levees. A subsequent UAV survey highlighted topographic change and reconfiguration of the local sedimentary conveyor as we predicted with preliminary modelling. The combined monitoring and modelling approach has allowed probable future geomorphic configurations to be predicted permitting more informed implementation of channel and floodplain management strategies.

Agent-Based Model to Study and Quantify the Evolution Dynamics of Android Malware Infection

Directory of Open Access Journals (Sweden)

Juan Alegre-Sanahuja

2014-01-01

Full Text Available In the last years the number of malware Apps that the users download to their devices has risen. In this paper, we propose an agent-based model to quantify the Android malware infection evolution, modeling the behavior of the users and the different markets where the users may download Apps. The model predicts the number of infected smartphones depending on the type of malware. Additionally, we will estimate the cost that the users should afford when the malware is in their devices. We will be able to analyze which part is more critical: the users, giving indiscriminate permissions to the Apps or not protecting their devices with antivirus software, or the Android platform, due to the vulnerabilities of the Android devices that permit their rooted. We focus on the community of Valencia, Spain, although the obtained results can be extrapolated to other places where the number of Android smartphones remains fairly stable.

Genetic Adaptation to Salt Stress in Experimental Evolution of Desulfovibrio vulgaris Hildenborough

Energy Technology Data Exchange (ETDEWEB)

Zhou, Aifen; Hillesland, Kristina; He, Zhili; Joachimiak, Marcin; Zane, Grant; Dehal, Paramvir; Arkin, Adam; Stahl, David; Wall, Judy; Hazen, Terry; Zhou, Jizhong; Baidoo, Edward; Benke, Peter; Mukhopadhyay, Aindrila

2010-05-17

High salinity is one of the most common environmental stressors. In order to understand how environmental organisms adapt to salty environment, an experiment evolution with sulfate reducing bacteria Desulfovibrio vugaris Hildenborough was conducted. Control lines and salt-stressed lines (6 lines each) grown in minimal medium LS4D or LS4D + 100 mM NaCl were transferred for 1200 generations. The salt tolerance was tested with LS4D supplemented with 250 mM NaCl. Statistical analysis of the growth data suggested that all lines adapted to their evolutionary environment. In addition, the control lines performed better than the ancestor with faster growth rate, higher biomass yield and shorter lag phase under salty environment they did not evolve in. However, the salt-adapted lines performed better than the control lines on measures of growth rate and yield under salty environment, suggesting that the salt?evolved lines acquired mutations specific to having extra salt in LS4D. Growth data and gene transcription data suggested that populations tended to improve till 1000 generations and active mutations tended to be fixed at the stage of 1000 generations. Point mutations and insertion/deletions were identified in isolated colonies from salt-adapted and control lines via whole genome sequencing. Glu, Gln and Ala appears to be the major osmoprotectant in evolved salt-stressed line. Ongoing studies are now characterizing the contribution of specific mutations identified in the salt-evolved D. vulgaris.

Evidence for determinism in species diversification and contingency in phenotypic evolution during adaptive radiation

Science.gov (United States)

Burbrink, Frank T.; Chen, Xin; Myers, Edward A.; Brandley, Matthew C.; Pyron, R. Alexander

2012-01-01

Adaptive radiation (AR) theory predicts that groups sharing the same source of ecological opportunity (EO) will experience deterministic species diversification and morphological evolution. Thus, deterministic ecological and morphological evolution should be correlated with deterministic patterns in the tempo and mode of speciation for groups in similar habitats and time periods. We test this hypothesis using well-sampled phylogenies of four squamate groups that colonized the New World (NW) in the Late Oligocene. We use both standard and coalescent models to assess species diversification, as well as likelihood models to examine morphological evolution. All squamate groups show similar early pulses of speciation, as well as diversity-dependent ecological limits on clade size at a continental scale. In contrast, processes of morphological evolution are not easily predictable and do not show similar pulses of early and rapid change. Patterns of morphological and species diversification thus appear uncoupled across these groups. This indicates that the processes that drive diversification and disparification are not mechanistically linked, even among similar groups of taxa experiencing the same sources of EO. It also suggests that processes of phenotypic diversification cannot be predicted solely from the existence of an AR or knowledge of the process of diversification. PMID:23034709

Resilience through adaptation

NARCIS (Netherlands)

Broeke, ten Guus; Voorn, van George A.K.; Ligtenberg, Arend; Molenaar, Jaap

2017-01-01

Adaptation of agents through learning or evolution is an important component of the resilience of Complex Adaptive Systems (CAS). Without adaptation, the flexibility of such systems to cope with outside pressures would be much lower. To study the capabilities of CAS to adapt, social simulations

Contemporary evolution strategies

CERN Document Server

Bäck, Thomas; Krause, Peter

2013-01-01

Evolution strategies have more than 50 years of history in the field of evolutionary computation. Since the early 1990s, many algorithmic variations of evolution strategies have been developed, characterized by the fact that they use the so-called derandomization concept for strategy parameter adaptation. Most importantly, the covariance matrix adaptation strategy (CMA-ES) and its successors are the key representatives of this group of contemporary evolution strategies. This book provides an overview of the key algorithm developments between 1990 and 2012, including brief descriptions of the a

Evolution, epigenetics and cooperation

Indian Academy of Sciences (India)

Explanations for biological evolution in terms of changes in gene frequencies refer to outcomes rather than process. Integrating epigenetic studies with older evolutionary theories has drawn attention to the ways in which evolution occurs. Adaptation at the level of the gene is givingway to adaptation at the level of the ...

Adaptive Evolution of the Myo6 Gene in Old World Fruit Bats (Family: Pteropodidae)

Science.gov (United States)

Shen, Bin; Han, Xiuqun; Jones, Gareth; Rossiter, Stephen J.; Zhang, Shuyi

2013-01-01

Myosin VI (encoded by the Myo6 gene) is highly expressed in the inner and outer hair cells of the ear, retina, and polarized epithelial cells such as kidney proximal tubule cells and intestinal enterocytes. The Myo6 gene is thought to be involved in a wide range of physiological functions such as hearing, vision, and clathrin-mediated endocytosis. Bats (Chiroptera) represent one of the most fascinating mammal groups for molecular evolutionary studies of the Myo6 gene. A diversity of specialized adaptations occur among different bat lineages, such as echolocation and associated high-frequency hearing in laryngeal echolocating bats, large eyes and a strong dependence on vision in Old World fruit bats (Pteropodidae), and specialized high-carbohydrate but low-nitrogen diets in both Old World and New World fruit bats (Phyllostomidae). To investigate what role(s) the Myo6 gene might fulfill in bats, we sequenced the coding region of the Myo6 gene in 15 bat species and used molecular evolutionary analyses to detect evidence of positive selection in different bat lineages. We also conducted real-time PCR assays to explore the expression levels of Myo6 in a range of tissues from three representative bat species. Molecular evolutionary analyses revealed that the Myo6 gene, which was widely considered as a hearing gene, has undergone adaptive evolution in the Old World fruit bats which lack laryngeal echolocation and associated high-frequency hearing. Real-time PCR showed the highest expression level of the Myo6 gene in the kidney among ten tissues examined in three bat species, indicating an important role for this gene in kidney function. We suggest that Myo6 has undergone adaptive evolution in Old World fruit bats in relation to receptor-mediated endocytosis for the preservation of protein and essential nutrients. PMID:23620821

Rapid and Parallel Adaptive Evolution of the Visual System of Neotropical Midas Cichlid Fishes.

Science.gov (United States)

Torres-Dowdall, Julián; Pierotti, Michele E R; Härer, Andreas; Karagic, Nidal; Woltering, Joost M; Henning, Frederico; Elmer, Kathryn R; Meyer, Axel

2017-10-01

Midas cichlid fish are a Central American species flock containing 13 described species that has been dated to only a few thousand years old, a historical timescale infrequently associated with speciation. Their radiation involved the colonization of several clear water crater lakes from two turbid great lakes. Therefore, Midas cichlids have been subjected to widely varying photic conditions during their radiation. Being a primary signal relay for information from the environment to the organism, the visual system is under continuing selective pressure and a prime organ system for accumulating adaptive changes during speciation, particularly in the case of dramatic shifts in photic conditions. Here, we characterize the full visual system of Midas cichlids at organismal and genetic levels, to determine what types of adaptive changes evolved within the short time span of their radiation. We show that Midas cichlids have a diverse visual system with unexpectedly high intra- and interspecific variation in color vision sensitivity and lens transmittance. Midas cichlid populations in the clear crater lakes have convergently evolved visual sensitivities shifted toward shorter wavelengths compared with the ancestral populations from the turbid great lakes. This divergence in sensitivity is driven by changes in chromophore usage, differential opsin expression, opsin coexpression, and to a lesser degree by opsin coding sequence variation. The visual system of Midas cichlids has the evolutionary capacity to rapidly integrate multiple adaptations to changing light environments. Our data may indicate that, in early stages of divergence, changes in opsin regulation could precede changes in opsin coding sequence evolution. © The Author 2017. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Evolution, epigenetics and cooperation.

Science.gov (United States)

Bateson, Patrick

2014-04-01

Explanations for biological evolution in terms of changes in gene frequencies refer to outcomes rather than process. Integrating epigenetic studies with older evolutionary theories has drawn attention to the ways in which evolution occurs. Adaptation at the level of the gene is givingway to adaptation at the level of the organism and higher-order assemblages of organisms. These ideas impact on the theories of how cooperation might have evolved. Two of the theories, i.e. that cooperating individuals are genetically related or that they cooperate for self-interested reasons, have been accepted for a long time. The idea that adaptation takes place at the level of groups is much more controversial. However, bringing together studies of development with those of evolution is taking away much of the heat in the debate about the evolution of group behaviour.

Coastal wetland adaptation to sea level rise: Quantifying potential for landward migration and coastal squeeze

Science.gov (United States)

Borchert, Sinéad M.; Osland, Michael J.; Enwright, Nicholas M.; Griffith, Kereen

2018-01-01

Coastal wetland ecosystems are expected to migrate landwards in response to rising seas. However, due to differences in topography and coastal urbanization, estuaries vary in their ability to accommodate migration. Low‐lying urban areas can constrain migration and lead to wetland loss (i.e. coastal squeeze), especially where existing wetlands cannot keep pace with rising seas via vertical adjustments. In many estuaries, there is a pressing need to identify landward migration corridors and better quantify the potential for landward migration and coastal squeeze.We quantified and compared the area available for landward migration of tidal saline wetlands and the area where urban development is expected to prevent migration for 39 estuaries along the wetland‐rich USA Gulf of Mexico coast. We did so under three sea level rise scenarios (0.5, 1.0, and 1.5 m by 2100).Within the region, the potential for wetland migration is highest within certain estuaries in Louisiana and southern Florida (e.g. Atchafalaya/Vermilion Bays, Mermentau River, Barataria Bay, and the North and South Ten Thousand Islands estuaries).The potential for coastal squeeze is highest in estuaries containing major metropolitan areas that extend into low‐lying lands. The Charlotte Harbor, Tampa Bay, and Crystal‐Pithlachascotee estuaries (Florida) have the highest amounts of urban land expected to constrain wetland migration. Urban barriers to migration are also high in the Galveston Bay (Texas) and Atchafalaya/Vermilion Bays (Louisiana) estuaries.Synthesis and applications. Coastal wetlands provide many ecosystem services that benefit human health and well‐being, including shoreline protection and fish and wildlife habitat. As the rate of sea level rise accelerates in response to climate change, coastal wetland resources could be lost in areas that lack space for landward migration. Migration corridors are particularly important in highly urbanized estuaries where, due to low‐lying coastal

Adaptive evolution of the venom-targeted vWF protein in opossums that eat pitvipers.

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Sharon A Jansa

Full Text Available The rapid evolution of venom toxin genes is often explained as the result of a biochemical arms race between venomous animals and their prey. However, it is not clear that an arms race analogy is appropriate in this context because there is no published evidence for rapid evolution in genes that might confer toxin resistance among routinely envenomed species. Here we report such evidence from an unusual predator-prey relationship between opossums (Marsupialia: Didelphidae and pitvipers (Serpentes: Crotalinae. In particular, we found high ratios of replacement to silent substitutions in the gene encoding von Willebrand Factor (vWF, a venom-targeted hemostatic blood protein, in a clade of opossums known to eat pitvipers and to be resistant to their hemorrhagic venom. Observed amino-acid substitutions in venom-resistant opossums include changes in net charge and hydrophobicity that are hypothesized to weaken the bond between vWF and one of its toxic snake-venom ligands, the C-type lectin-like protein botrocetin. Our results provide the first example of rapid adaptive evolution in any venom-targeted molecule, and they support the notion that an evolutionary arms race might be driving the rapid evolution of snake venoms. However, in the arms race implied by our results, venomous snakes are prey, and their venom has a correspondingly defensive function in addition to its usual trophic role.

CRISPR-Cas: evolution of an RNA-based adaptive immunity system in prokaryotes.

Science.gov (United States)

Koonin, Eugene V; Makarova, Kira S

2013-05-01

The CRISPR-Cas (clustered regularly interspaced short palindromic repeats, CRISPR-associated genes) is an adaptive immunity system in bacteria and archaea that functions via a distinct self-non-self recognition mechanism that is partially analogous to the mechanism of eukaryotic RNA interference (RNAi). The CRISPR-Cas system incorporates fragments of virus or plasmid DNA into the CRISPR repeat cassettes and employs the processed transcripts of these spacers as guide RNAs to cleave the cognate foreign DNA or RNA. The Cas proteins, however, are not homologous to the proteins involved in RNAi and comprise numerous, highly diverged families. The majority of the Cas proteins contain diverse variants of the RNA recognition motif (RRM), a widespread RNA-binding domain. Despite the fast evolution that is typical of the cas genes, the presence of diverse versions of the RRM in most Cas proteins provides for a simple scenario for the evolution of the three distinct types of CRISPR-cas systems. In addition to several proteins that are directly implicated in the immune response, the cas genes encode a variety of proteins that are homologous to prokaryotic toxins that typically possess nuclease activity. The predicted toxins associated with CRISPR-Cas systems include the essential Cas2 protein, proteins of COG1517 that, in addition to a ligand-binding domain and a helix-turn-helix domain, typically contain different nuclease domains and several other predicted nucleases. The tight association of the CRISPR-Cas immunity systems with predicted toxins that, upon activation, would induce dormancy or cell death suggests that adaptive immunity and dormancy/suicide response are functionally coupled. Such coupling could manifest in the persistence state being induced and potentially providing conditions for more effective action of the immune system or in cell death being triggered when immunity fails.

Evolution of motion uncertainty in rectal cancer: implications for adaptive radiotherapy

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Kleijnen, Jean-Paul J. E.; van Asselen, Bram; Burbach, Johannes P. M.; Intven, Martijn; Philippens, Marielle E. P.; Reerink, Onne; Lagendijk, Jan J. W.; Raaymakers, Bas W.

2016-01-01

Reduction of motion uncertainty by applying adaptive radiotherapy strategies depends largely on the temporal behavior of this motion. To fully optimize adaptive strategies, insight into target motion is needed. The purpose of this study was to analyze stability and evolution in time of motion uncertainty of both the gross tumor volume (GTV) and clinical target volume (CTV) for patients with rectal cancer. We scanned 16 patients daily during one week, on a 1.5 T MRI scanner in treatment position, prior to each radiotherapy fraction. Single slice sagittal cine MRIs were made at the beginning, middle, and end of each scan session, for one minute at 2 Hz temporal resolution. GTV and CTV motion were determined by registering a delineated reference frame to time-points later in time. The 95th percentile of observed motion (dist95%) was taken as a measure of motion. The stability of motion in time was evaluated within each cine-MRI separately. The evolution of motion was investigated between the reference frame and the cine-MRIs of a single scan session and between the reference frame and the cine-MRIs of several days later in the course of treatment. This observed motion was then converted into a PTV-margin estimate. Within a one minute cine-MRI scan, motion was found to be stable and small. Independent of the time-point within the scan session, the average dist95% remains below 3.6 mm and 2.3 mm for CTV and GTV, respectively 90% of the time. We found similar motion over time intervals from 18 min to 4 days. When reducing the time interval from 18 min to 1 min, a large reduction in motion uncertainty is observed. A reduction in motion uncertainty, and thus the PTV-margin estimate, of 71% and 75% for CTV and tumor was observed, respectively. Time intervals of 15 and 30 s yield no further reduction in motion uncertainty compared to a 1 min time interval.

Thermotolerant Yeast Strains Adapted by Laboratory Evolution Show Trade-Off at Ancestral Temperatures and Preadaptation to Other Stresses

DEFF Research Database (Denmark)

Caspeta, Luis; Nielsen, Jens

2015-01-01

adaptive laboratory evolution, we previously isolated seven Saccharomyces cerevisiae strains with improved growth at 40°C. Here, we show that genetic adaptations to high temperature caused a growth trade-off at ancestral temperatures, reduced cellular functions, and improved tolerance of other stresses...... in the ancestral strain. The latter is an advantageous attribute for acquiring thermotolerance and correlates with the reduction of yeast functions associated with loss of respiration capacity. This trait caused glycerol overproduction that was associated with the growth trade-off at ancestral temperatures....... In combination with altered sterol composition of cellular membranes, glycerol overproduction was also associated with yeast osmotolerance and improved tolerance of high concentrations of glucose and ethanol. Our study shows that thermal adaptation of yeast is suitable for improving yeast resistance...

On the contrast between Germanic and Romance negated quantifiers

OpenAIRE

Robert Cirillo

2009-01-01

Universal quantifiers can be stranded in the manner described by Sportiche (1988), Giusti (1990) and Shlonsky (1991) in both the Romance and Germanic languages, but a negated universal quantifier can only be stranded in the Germanic languages. The goal of this paper is to show that this contrast between the Romance and the Germanic languages can be explained if one adapts the theory of sentential negation in Zeijlstra (2004) to constituent (quantifier) negation. According to Zeijlstra’s theor...

HyCAW: Hydrological Climate change Adaptation Wizard

Science.gov (United States)

Bagli, Stefano; Mazzoli, Paolo; Broccoli, Davide; Luzzi, Valerio

2016-04-01

Changes in temporal and total water availability due to hydrologic and climate change requires an efficient use of resources through the selection of the best adaptation options. HyCAW provides a novel service to users willing or needing to adapt to hydrological change, by turning available scientific information into a user friendly online wizard that lets to: • Evaluate the monthly reduction of water availability induced by climate change; • Select the best adaptation options and visualize the benefits in terms of water balance and cost reduction; • Quantify potential of water saving by improving of water use efficiency. The tool entails knowledge of the intra-annual distribution of available surface and groundwater flows at a site under present and future (climate change) scenarios. This information is extracted from long term scenario simulation by E-HYPE (European hydrological predictions for the environment) model from Swedish Meteorological and Hydrological Institute, to quantify the expected evolution in water availability (e.g. percent reduction of soil infiltration and aquifer recharge; relative seasonal shift of runoff from summer to winter in mountain areas; etc.). Users are requested to provide in input their actual water supply on a monthly basis, both from surface and groundwater sources. Appropriate decision trees and an embedded precompiled database of Water saving technology for different sectors (household, agriculture, industrial, tourisms) lead them to interactively identify good practices for water saving/recycling/harvesting that they may implement in their specific context. Thanks to this service, users are not required to have a detailed understanding neither of data nor of hydrological processes, but may benefit of scientific analysis directly for practical adaptation in a simple and user friendly way, effectively improving their adaptation capacity. The tool is being developed under a collaborative FP7 funded project called SWITCH

Adaptive evolution of the spike gene of SARS coronavirus: changes in positively selected sites in different epidemic groups

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He Shao-Heng

2006-10-01

Full Text Available Abstract Background It is believed that animal-to-human transmission of severe acute respiratory syndrome (SARS coronavirus (CoV is the cause of the SARS outbreak worldwide. The spike (S protein is one of the best characterized proteins of SARS-CoV, which plays a key role in SARS-CoV overcoming species barrier and accomplishing interspecies transmission from animals to humans, suggesting that it may be the major target of selective pressure. However, the process of adaptive evolution of S protein and the exact positively selected sites associated with this process remain unknown. Results By investigating the adaptive evolution of S protein, we identified twelve amino acid sites (75, 239, 244, 311, 479, 609, 613, 743, 765, 778, 1148, and 1163 in the S protein under positive selective pressure. Based on phylogenetic tree and epidemiological investigation, SARS outbreak was divided into three epidemic groups: 02–04 interspecies, 03-early-mid, and 03-late epidemic groups in the present study. Positive selection was detected in the first two groups, which represent the course of SARS-CoV interspecies transmission and of viral adaptation to human host, respectively. In contrast, purifying selection was detected in 03-late group. These indicate that S protein experiences variable positive selective pressures before reaching stabilization. A total of 25 sites in 02–04 interspecies epidemic group and 16 sites in 03-early-mid epidemic group were identified under positive selection. The identified sites were different between these two groups except for site 239, which suggests that positively selected sites are changeable between groups. Moreover, it was showed that a larger proportion (24% of positively selected sites was located in receptor-binding domain (RBD than in heptad repeat (HR1-HR2 region in 02–04 interspecies epidemic group (p = 0.0208, and a greater percentage (25% of these sites occurred in HR1–HR2 region than in RBD in 03-early

Convergent evolution and mimicry of protein linear motifs in host-pathogen interactions.

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Chemes, Lucía Beatriz; de Prat-Gay, Gonzalo; Sánchez, Ignacio Enrique

2015-06-01

Pathogen linear motif mimics are highly evolvable elements that facilitate rewiring of host protein interaction networks. Host linear motifs and pathogen mimics differ in sequence, leading to thermodynamic and structural differences in the resulting protein-protein interactions. Moreover, the functional output of a mimic depends on the motif and domain repertoire of the pathogen protein. Regulatory evolution mediated by linear motifs can be understood by measuring evolutionary rates, quantifying positive and negative selection and performing phylogenetic reconstructions of linear motif natural history. Convergent evolution of linear motif mimics is widespread among unrelated proteins from viral, prokaryotic and eukaryotic pathogens and can also take place within individual protein phylogenies. Statistics, biochemistry and laboratory models of infection link pathogen linear motifs to phenotypic traits such as tropism, virulence and oncogenicity. In vitro evolution experiments and analysis of natural sequences suggest that changes in linear motif composition underlie pathogen adaptation to a changing environment. Copyright © 2015 Elsevier Ltd. All rights reserved.

Convergent adaptive evolution in marginal environments: unloading transposable elements as a common strategy among mangrove genomes.

Science.gov (United States)

Lyu, Haomin; He, Ziwen; Wu, Chung-I; Shi, Suhua

2018-01-01

Several clades of mangrove trees independently invade the interface between land and sea at the margin of woody plant distribution. As phenotypic convergence among mangroves is common, the possibility of convergent adaptation in their genomes is quite intriguing. To study this molecular convergence, we sequenced multiple mangrove genomes. In this study, we focused on the evolution of transposable elements (TEs) in relation to the genome size evolution. TEs, generally considered genomic parasites, are the most common components of woody plant genomes. Analyzing the long terminal repeat-retrotransposon (LTR-RT) type of TE, we estimated their death rates by counting solo-LTRs and truncated elements. We found that all lineages of mangroves massively and convergently reduce TE loads in comparison to their nonmangrove relatives; as a consequence, genome size reduction happens independently in all six mangrove lineages; TE load reduction in mangroves can be attributed to the paucity of young elements; the rarity of young LTR-RTs is a consequence of fewer births rather than access death. In conclusion, mangrove genomes employ a convergent strategy of TE load reduction by suppressing element origination in their independent adaptation to a new environment. © 2017 The Authors. New Phytologist © 2017 New Phytologist Trust.

The Hitchhiker’s Guide to Adaptive Dynamics

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Jacob Johansson

2013-06-01

Full Text Available Adaptive dynamics is a mathematical framework for studying evolution. It extends evolutionary game theory to account for more realistic ecological dynamics and it can incorporate both frequency- and density-dependent selection. This is a practical guide to adaptive dynamics that aims to illustrate how the methodology can be applied to the study of specific systems. The theory is presented in detail for a single, monomorphic, asexually reproducing population. We explain the necessary terminology to understand the basic arguments in models based on adaptive dynamics, including invasion fitness, the selection gradient, pairwise invasibility plots (PIP, evolutionarily singular strategies, and the canonical equation. The presentation is supported with a worked-out example of evolution of arrival times in migratory birds. We show how the adaptive dynamics methodology can be extended to study evolution in polymorphic populations using trait evolution plots (TEPs. We give an overview of literature that generalises adaptive dynamics techniques to other scenarios, such as sexual, diploid populations, and spatially-structured populations. We conclude by discussing how adaptive dynamics relates to evolutionary game theory and how adaptive-dynamics techniques can be used in speciation research.

Molecular evolution of the hyperthermophilic archaea of the Pyrococcus genus: analysis of adaptation to different environmental conditions

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Afonnikov Dmitry A

2009-12-01

Full Text Available Abstract Background Prokaryotic microorganisms are able to survive and proliferate in severe environmental conditions. The increasing number of complete sequences of prokaryotic genomes has provided the basis for studying the molecular mechanisms of their adaptation at the genomic level. We apply here a computer-based approach to compare the genomes and proteomes from P. furiosus, P. horikoshii, and P. abyssi to identify features of their molecular evolution related to adaptation strategy to diverse environmental conditions. Results Phylogenetic analysis of rRNA genes from 26 Pyrococcus strains suggested that the divergence of P. furiosus, P. horikoshii and P. abyssi might have occurred from ancestral deep-sea organisms. It was demonstrated that the function of genes that have been subject to positive Darwinian selection is closely related to abiotic and biotic conditions to which archaea managed to become adapted. Divergence of the P. furiosus archaea might have been due to loss of some genes involved in cell motility or signal transduction, and/or to evolution under positive selection of the genes for translation machinery. In the course of P. horikoshii divergence, positive selection was found to operate mainly on the transcription machinery; divergence of P. abyssi was related with positive selection for the genes mainly involved in inorganic ion transport. Analysis of radical amino acid replacement rate in evolving P. furiosus, P. horikoshii and P. abyssi showed that the fixation rate was higher for radical substitutions relative to the volume of amino acid side-chain. Conclusions The current results give due credit to the important role of hydrostatic pressure as a cause of variability in the P. furiosus, P. horikoshii and P. abyssi genomes evolving in different habitats. Nevertheless, adaptation to pressure does not appear to be the sole factor ensuring adaptation to environment. For example, at the stage of the divergence of P

Computational Strategies for Dissecting the High-Dimensional Complexity of Adaptive Immune Repertoires

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Enkelejda Miho

2018-02-01

Full Text Available The adaptive immune system recognizes antigens via an immense array of antigen-binding antibodies and T-cell receptors, the immune repertoire. The interrogation of immune repertoires is of high relevance for understanding the adaptive immune response in disease and infection (e.g., autoimmunity, cancer, HIV. Adaptive immune receptor repertoire sequencing (AIRR-seq has driven the quantitative and molecular-level profiling of immune repertoires, thereby revealing the high-dimensional complexity of the immune receptor sequence landscape. Several methods for the computational and statistical analysis of large-scale AIRR-seq data have been developed to resolve immune repertoire complexity and to understand the dynamics of adaptive immunity. Here, we review the current research on (i diversity, (ii clustering and network, (iii phylogenetic, and (iv machine learning methods applied to dissect, quantify, and compare the architecture, evolution, and specificity of immune repertoires. We summarize outstanding questions in computational immunology and propose future directions for systems immunology toward coupling AIRR-seq with the computational discovery of immunotherapeutics, vaccines, and immunodiagnostics.

Within-host evolution of Pseudomonas aeruginosa reveals adaptation toward iron acquisition from hemoglobin

DEFF Research Database (Denmark)

Marvig, Rasmus Lykke; Pedersen, Søren Damkiær; Khademi, Seyed Mohammad Hossein

2014-01-01

the within-host evolution of the transmissible P. aeruginosa DK2 lineage. We found positive selection for promoter mutations leading to increased expression of the phu system. By mimicking conditions of the CF airways in vitro, we experimentally demonstrate that increased expression of phuR confers a growth...... advantage in the presence of hemoglobin, thus suggesting that P. aeruginosa evolves toward iron acquisition from hemoglobin. To rule out that this adaptive trait is specific to the DK2 lineage, we inspected the genomes of additional P. aeruginosa lineages isolated from CF airways and found similar adaptive...... might therefore be a promising strategy for the treatment of P. aeruginosa infections in CF patients. IMPORTANCE Most bacterial pathogens depend on scavenging iron within their hosts, which makes the battle for iron between pathogens and hosts a hallmark of infection. Accordingly, the ability...

The ALICE-HMPID Detector Control System: Its evolution towards an expert and adaptive system

Science.gov (United States)

De Cataldo, G.; Franco, A.; Pastore, C.; Sgura, I.; Volpe, G.

2011-05-01

The High Momentum Particle IDentification (HMPID) detector is a proximity focusing Ring Imaging Cherenkov (RICH) for charged hadron identification. The HMPID is based on liquid C 6F 14 as the radiator medium and on a 10 m 2 CsI coated, pad segmented photocathode of MWPCs for UV Cherenkov photon detection. To ensure full remote control, the HMPID is equipped with a detector control system (DCS) responding to industrial standards for robustness and reliability. It has been implemented using PVSS as Slow Control And Data Acquisition (SCADA) environment, Programmable Logic Controller as control devices and Finite State Machines for modular and automatic command execution. In the perspective of reducing human presence at the experiment site, this paper focuses on DCS evolution towards an expert and adaptive control system, providing, respectively, automatic error recovery and stable detector performance. HAL9000, the first prototype of the HMPID expert system, is then presented. Finally an analysis of the possible application of the adaptive features is provided.

The ALICE-HMPID Detector Control System: Its evolution towards an expert and adaptive system

International Nuclear Information System (INIS)

De Cataldo, G.; Franco, A.; Pastore, C.; Sgura, I.; Volpe, G.

2011-01-01

The High Momentum Particle IDentification (HMPID) detector is a proximity focusing Ring Imaging Cherenkov (RICH) for charged hadron identification. The HMPID is based on liquid C 6 F 14 as the radiator medium and on a 10 m 2 CsI coated, pad segmented photocathode of MWPCs for UV Cherenkov photon detection. To ensure full remote control, the HMPID is equipped with a detector control system (DCS) responding to industrial standards for robustness and reliability. It has been implemented using PVSS as Slow Control And Data Acquisition (SCADA) environment, Programmable Logic Controller as control devices and Finite State Machines for modular and automatic command execution. In the perspective of reducing human presence at the experiment site, this paper focuses on DCS evolution towards an expert and adaptive control system, providing, respectively, automatic error recovery and stable detector performance. HAL9000, the first prototype of the HMPID expert system, is then presented. Finally an analysis of the possible application of the adaptive features is provided.

Evolution and adaptation in Pseudomonas aeruginosa biofilms driven by mismatch repair system-deficient mutators.

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Adela M Luján

Full Text Available Pseudomonas aeruginosa is an important opportunistic pathogen causing chronic airway infections, especially in cystic fibrosis (CF patients. The majority of the CF patients acquire P. aeruginosa during early childhood, and most of them develop chronic infections resulting in severe lung disease, which are rarely eradicated despite intensive antibiotic therapy. Current knowledge indicates that three major adaptive strategies, biofilm development, phenotypic diversification, and mutator phenotypes [driven by a defective mismatch repair system (MRS], play important roles in P. aeruginosa chronic infections, but the relationship between these strategies is still poorly understood. We have used the flow-cell biofilm model system to investigate the impact of the mutS associated mutator phenotype on development, dynamics, diversification and adaptation of P. aeruginosa biofilms. Through competition experiments we demonstrate for the first time that P. aeruginosa MRS-deficient mutators had enhanced adaptability over wild-type strains when grown in structured biofilms but not as planktonic cells. This advantage was associated with enhanced micro-colony development and increased rates of phenotypic diversification, evidenced by biofilm architecture features and by a wider range and proportion of morphotypic colony variants, respectively. Additionally, morphotypic variants generated in mutator biofilms showed increased competitiveness, providing further evidence for mutator-driven adaptive evolution in the biofilm mode of growth. This work helps to understand the basis for the specific high proportion and role of mutators in chronic infections, where P. aeruginosa develops in biofilm communities.

Adaptive evolution of defense ability leads to diversification of prey species.

Science.gov (United States)

Zu, Jian; Wang, Jinliang; Du, Jianqiang

2014-06-01

In this paper, by using the adaptive dynamics approach, we investigate how the adaptive evolution of defense ability promotes the diversity of prey species in an initial one-prey-two-predator community. We assume that the prey species can evolve to a safer strategy such that it can reduce the predation risk, but a prey with a high defense ability for one predator may have a low defense ability for the other and vice versa. First, by using the method of critical function analysis, we find that if the trade-off is convex in the vicinity of the evolutionarily singular strategy, then this singular strategy is a continuously stable strategy. However, if the trade-off is weakly concave near the singular strategy and the competition between the two predators is relatively weak, then the singular strategy may be an evolutionary branching point. Second, we find that after the branching has occurred in the prey strategy, if the trade-off curve is globally concave, then the prey species might eventually evolve into two specialists, each caught by only one predator species. However, if the trade-off curve is convex-concave-convex, the prey species might eventually branch into two partial specialists, each being caught by both of the two predators and they can stably coexist on the much longer evolutionary timescale.

A Self-Adaptive Evolutionary Approach to the Evolution of Aesthetic Maps for a RTS Game

OpenAIRE

Lara-Cabrera, Raúl; Cotta, Carlos; Fernández-Leiva, Antonio J.

2014-01-01

Procedural content generation (PCG) is a research eld on the rise,with numerous papers devoted to this topic. This paper presents a PCG method based on a self-adaptive evolution strategy for the automatic generation of maps for the real-time strategy (RTS) game PlanetWars. These maps are generated in order to ful ll the aesthetic preferences of the user, as implied by her assessment of a collection of maps used as training set. A topological approach is used for the characterization of th...

Testing Biological Hypotheses with Embodied Robots: Adaptations, Accidents, and By-Products in the Evolution of Vertebrates

OpenAIRE

Roberts, Sonia F.; Hirokawa, Jonathan; Rosenblum, Hannah G.; Sakhtah, Hassan; Gutierrez, Andres A.; Porter, Marianne E.; Long, John H.

2014-01-01

Evolutionary robotics allows biologists to test hypotheses about extinct animals. In our case, we modeled some of the first vertebrates, jawless fishes, in order to study the evolution of the trait after which vertebrates are named: vertebrae. We tested the hypothesis that vertebrae are an adaptation for enhanced feeding and fleeing performance. We created a population of autonomous embodied robots, Preyro, in which the number of vertebrae, N, were free to evolve. In addition, two other trait...

GNBP domain of Anopheles darlingi: are polymorphic inversions and gene variation related to adaptive evolution?

Science.gov (United States)

Bridi, L C; Rafael, M S

2016-02-01

Anopheles darlingi is the main malaria vector in humans in South America. In the Amazon basin, it lives along the banks of rivers and lakes, which responds to the annual hydrological cycle (dry season and rainy season). In these breeding sites, the larvae of this mosquito feed on decomposing organic and microorganisms, which can be pathogenic and trigger the activation of innate immune system pathways, such as proteins Gram-negative binding protein (GNBP). Such environmental changes affect the occurrence of polymorphic inversions especially at the heterozygote frequency, which confer adaptative advantage compared to homozygous inversions. We mapped the GNBP probe to the An. darlingi 2Rd inversion by fluorescent in situ hybridization (FISH), which was a good indicator of the GNBP immune response related to the chromosomal polymorphic inversions and adaptative evolution. To better understand the evolutionary relations and time of divergence of the GNBP of An. darlingi, we compared it with nine other mosquito GNBPs. The results of the phylogenetic analysis of the GNBP sequence between the species of mosquitoes demonstrated three clades. Clade I and II included the GNBPB5 sequence, and clade III the sequence of GNBPB1. Most of these sequences of GNBP analyzed were homologous with that of subfamily B, including that of An. gambiae (87 %), therefore suggesting that GNBP of An. darling belongs to subfamily B. This work helps us understand the role of inversion polymorphism in evolution of An. darlingi.

The sources of adaptive variation.

Science.gov (United States)

Charlesworth, Deborah; Barton, Nicholas H; Charlesworth, Brian

2017-05-31

The role of natural selection in the evolution of adaptive phenotypes has undergone constant probing by evolutionary biologists, employing both theoretical and empirical approaches. As Darwin noted, natural selection can act together with other processes, including random changes in the frequencies of phenotypic differences that are not under strong selection, and changes in the environment, which may reflect evolutionary changes in the organisms themselves. As understanding of genetics developed after 1900, the new genetic discoveries were incorporated into evolutionary biology. The resulting general principles were summarized by Julian Huxley in his 1942 book Evolution: the modern synthesis Here, we examine how recent advances in genetics, developmental biology and molecular biology, including epigenetics, relate to today's understanding of the evolution of adaptations. We illustrate how careful genetic studies have repeatedly shown that apparently puzzling results in a wide diversity of organisms involve processes that are consistent with neo-Darwinism. They do not support important roles in adaptation for processes such as directed mutation or the inheritance of acquired characters, and therefore no radical revision of our understanding of the mechanism of adaptive evolution is needed. © 2017 The Author(s).

Development Of An Efficient Glycerol Utilizing Saccharomyces Cerevisiae Strain Via Adaptive Laboratory Evolution

DEFF Research Database (Denmark)

Strucko, Tomas; Zirngibl, Katharina; Tharwat Tolba Mohamed, Elsayed

2015-01-01

that popular wild-type laboratory yeast strains, commonly applied in metabolic engineering studies, did not grow or grew very slowly in glycerol medium.In this work, an adaptive laboratory evolution approach to obtain S. cerevisiae strains with an improved ability to grow on glycerol was applied. A broad array...... of evolved strains, which exhibited a significant increase in the specific growth rate and a higher glycerol consumption rate, were isolated. The best performing strains were further analyzed by classical genetics and whole genome re-sequencing in order to understand the molecular basis of glycerol...

Optimal Decision Fusion for Urban Land-Use/Land-Cover Classification Based on Adaptive Differential Evolution Using Hyperspectral and LiDAR Data

Directory of Open Access Journals (Sweden)

Yanfei Zhong

2017-08-01

Full Text Available Hyperspectral images and light detection and ranging (LiDAR data have, respectively, the high spectral resolution and accurate elevation information required for urban land-use/land-cover (LULC classification. To combine the respective advantages of hyperspectral and LiDAR data, this paper proposes an optimal decision fusion method based on adaptive differential evolution, namely ODF-ADE, for urban LULC classification. In the ODF-ADE framework the normalized difference vegetation index (NDVI, gray-level co-occurrence matrix (GLCM and digital surface model (DSM are extracted to form the feature map. The three different classifiers of the maximum likelihood classifier (MLC, support vector machine (SVM and multinomial logistic regression (MLR are used to classify the extracted features. To find the optimal weights for the different classification maps, weighted voting is used to obtain the classification result and the weights of each classification map are optimized by the differential evolution algorithm which uses a self-adaptive strategy to obtain the parameter adaptively. The final classification map is obtained after post-processing based on conditional random fields (CRF. The experimental results confirm that the proposed algorithm is very effective in urban LULC classification.

Quantifying quantum coherence with quantum Fisher information.

Science.gov (United States)

Feng, X N; Wei, L F

2017-11-14

Quantum coherence is one of the old but always important concepts in quantum mechanics, and now it has been regarded as a necessary resource for quantum information processing and quantum metrology. However, the question of how to quantify the quantum coherence has just been paid the attention recently (see, e.g., Baumgratz et al. PRL, 113. 140401 (2014)). In this paper we verify that the well-known quantum Fisher information (QFI) can be utilized to quantify the quantum coherence, as it satisfies the monotonicity under the typical incoherent operations and the convexity under the mixing of the quantum states. Differing from most of the pure axiomatic methods, quantifying quantum coherence by QFI could be experimentally testable, as the bound of the QFI is practically measurable. The validity of our proposal is specifically demonstrated with the typical phase-damping and depolarizing evolution processes of a generic single-qubit state, and also by comparing it with the other quantifying methods proposed previously.

Experimental Evolution of UV-C Radiation Tolerance: Emergence of Adaptive and Non-Adaptive Traits in Escherichia coli Under Differing Flux Regimes

Science.gov (United States)

Moffet, A.; Okansinski, A.; Sloan, C.; Grace, J. M.; Paulino-Lima, I. G.; Gentry, D.; Rothschild, L. J.; Camps, M.

2014-12-01

High-energy ultraviolet (UV-C) radiation is a significant challenge to life in environments such as high altitude areas, the early Earth, the Martian surface, and space. As UV-C exposure is both a selection pressure and a mutagen, adaptation dynamics in such environments include a high rate of change in both tolerance-related and non-tolerance-related genes, as well changes in linkages between the resulting traits. Determining the relationship between the intensity and duration of the UV-C exposure, mutation rate, and emergence of UV-C resistance will inform our understanding of both the emergence of radiation-related extremophily in natural environments and the optimal strategies for generating artificial extremophiles. In this study, we iteratively exposed an Escherichia colistrain to UV-C radiation of two different fluxes, 3.3 J/m^2/s for 6 seconds and 0.5 J/m^2/s for 40 seconds, with the same overall fluence of 20 J/m^2. After each iteration, cells from each exposure regime were assayed for increased UV-C tolerance as an adaptive trait. The exposed cells carried a plasmid bearing a TEM beta-lactamase gene, which in the absence of antibiotic treatment is a neutral reporter for mutagenesis. Sequencing of this gene allowed us to determine the baseline mutation frequency for each flux. As an additional readout for adaptation, the presence of extended-spectrum beta-lactamase mutations was tested by plating UV-exposed cultures in cefotaxime plates. We observed an increase of approximately one-million-fold in UV-C tolerance over seven iterations; no significant difference between the two fluxes was found. Future work will focus on identifying the genomic changes responsible for the change in UV-C tolerance; determining the mechanisms of the emerged UV-C tolerance; and performing competition experiments between the iteration strains to quantify fitness tradeoffs resulting from UV-C adaptation.

Trickle-down evolution: an approach to getting major evolutionary adaptive changes into textbooks and curricula.

Science.gov (United States)

Padian, Kevin

2008-08-01

Although contemporary high school and college textbooks of biology generally cover the principles and data of microevolution (genetic and populational change) and speciation rather well, coverage of what is known of the major changes in evolution (macroevolution), and how the evidence is understood is generally poor to nonexistent. It is critical to improve this because acceptance of evolution by the American public rests on the understanding of how we know what we know about the emergence of major new taxonomic groups, and about their adaptations, behaviors, and ecologies in geologic time. An efficient approach to this problem is to improve the illustrations in college textbooks to show the consilience of different lines of fossil, morphological, and molecular evidence mapped on phylogenies. Such "evograms" will markedly improve traditional illustrations of phylogenies, "menageries," and "companatomies." If "evograms" are installed at the college level, the basic principles and evidence of macroevolution will be more likely taught in K-12, thus providing an essential missing piece in biological education.

Macroscopic description of complex adaptive networks coevolving with dynamic node states

Science.gov (United States)

Wiedermann, Marc; Donges, Jonathan F.; Heitzig, Jobst; Lucht, Wolfgang; Kurths, Jürgen

2015-05-01

In many real-world complex systems, the time evolution of the network's structure and the dynamic state of its nodes are closely entangled. Here we study opinion formation and imitation on an adaptive complex network which is dependent on the individual dynamic state of each node and vice versa to model the coevolution of renewable resources with the dynamics of harvesting agents on a social network. The adaptive voter model is coupled to a set of identical logistic growth models and we mainly find that, in such systems, the rate of interactions between nodes as well as the adaptive rewiring probability are crucial parameters for controlling the sustainability of the system's equilibrium state. We derive a macroscopic description of the system in terms of ordinary differential equations which provides a general framework to model and quantify the influence of single node dynamics on the macroscopic state of the network. The thus obtained framework is applicable to many fields of study, such as epidemic spreading, opinion formation, or socioecological modeling.

Computational identification of adaptive mutants using the VERT system

Directory of Open Access Journals (Sweden)

Winkler James

2012-04-01

Full Text Available Background Evolutionary dynamics of microbial organisms can now be visualized using the Visualizing Evolution in Real Time (VERT system, in which several isogenic strains expressing different fluorescent proteins compete during adaptive evolution and are tracked using fluorescent cell sorting to construct a population history over time. Mutations conferring enhanced growth rates can be detected by observing changes in the fluorescent population proportions. Results Using data obtained from several VERT experiments, we construct a hidden Markov-derived model to detect these adaptive events in VERT experiments without external intervention beyond initial training. Analysis of annotated data revealed that the model achieves consensus with human annotation for 85-93% of the data points when detecting adaptive events. A method to determine the optimal time point to isolate adaptive mutants is also introduced. Conclusions The developed model offers a new way to monitor adaptive evolution experiments without the need for external intervention, thereby simplifying adaptive evolution efforts relying on population tracking. Future efforts to construct a fully automated system to isolate adaptive mutants may find the algorithm a useful tool.

Micro-droplet based directed evolution outperforms conventional laboratory evolution

DEFF Research Database (Denmark)

Sjostrom, Staffan L.; Huang, Mingtao; Nielsen, Jens

2014-01-01

We present droplet adaptive laboratory evolution (DrALE), a directed evolution method used to improve industrial enzyme producing microorganisms for e.g. feedstock digestion. DrALE is based linking a desired phenotype to growth rate allowing only desired cells to proliferate. Single cells are con...... a whole-genome mutated library of yeast cells for α-amylase activity....

Evolution of vertebrate adaptive immunity: immune cells and tissues, and AID/APOBEC cytidine deaminases.

Science.gov (United States)

Hirano, Masayuki

2015-08-01

All surviving jawed vertebrate representatives achieve diversity in immunoglobulin-based B and T cell receptors for antigen recognition through recombinatorial rearrangement of V(D)J segments. However, the extant jawless vertebrates, lampreys and hagfish, instead generate three types of variable lymphocyte receptors (VLRs) through a template-mediated combinatorial assembly of different leucine-rich repeat (LRR) sequences. The clonally diverse VLRB receptors are expressed by B-like lymphocytes, while the VLRA and VLRC receptors are expressed by lymphocyte lineages that resemble αβ and γδ T lymphocytes, respectively. These findings suggest that three basic types of lymphocytes, one B-like and two T-like, are an essential feature of vertebrate adaptive immunity. Around 500 million years ago, a common ancestor of jawed and jawless vertebrates evolved a genetic program for the development of prototypic lymphoid cells as a foundation for an adaptive immune system. This acquisition preceded the convergent evolution of alternative types of clonally diverse receptors for antigens in all vertebrates, as reviewed in this article. © 2015 WILEY Periodicals, Inc.

[The motive force of evolution based on the principle of organismal adjustment evolution.].

Science.gov (United States)

Cao, Jia-Shu

2010-08-01

From the analysis of the existing problems of the prevalent theories of evolution, this paper discussed the motive force of evolution based on the knowledge of the principle of organismal adjustment evolution to get a new understanding of the evolution mechanism. In the guide of Schrodinger's theory - "life feeds on negative entropy", the author proposed that "negative entropy flow" actually includes material flow, energy flow and information flow, and the "negative entropy flow" is the motive force for living and development. By modifying my own theory of principle of organismal adjustment evolution (not adaptation evolution), a new theory of "regulation system of organismal adjustment evolution involved in DNA, RNA and protein interacting with environment" is proposed. According to the view that phylogenetic development is the "integral" of individual development, the difference of negative entropy flow between organisms and environment is considered to be a motive force for evolution, which is a new understanding of the mechanism of evolution. Based on such understanding, evolution is regarded as "a changing process that one subsystem passes all or part of its genetic information to the next generation in a larger system, and during the adaptation process produces some new elements, stops some old ones, and thereby lasts in the larger system". Some other controversial questions related to evolution are also discussed.

Pathogenic adaptation of intracellular bacteria by rewiring a cis-regulatory input function.

Science.gov (United States)

Osborne, Suzanne E; Walthers, Don; Tomljenovic, Ana M; Mulder, David T; Silphaduang, Uma; Duong, Nancy; Lowden, Michael J; Wickham, Mark E; Waller, Ross F; Kenney, Linda J; Coombes, Brian K

2009-03-10

The acquisition of DNA by horizontal gene transfer enables bacteria to adapt to previously unexploited ecological niches. Although horizontal gene transfer and mutation of protein-coding sequences are well-recognized forms of pathogen evolution, the evolutionary significance of cis-regulatory mutations in creating phenotypic diversity through altered transcriptional outputs is not known. We show the significance of regulatory mutation for pathogen evolution by mapping and then rewiring a cis-regulatory module controlling a gene required for murine typhoid. Acquisition of a binding site for the Salmonella pathogenicity island-2 regulator, SsrB, enabled the srfN gene, ancestral to the Salmonella genus, to play a role in pathoadaptation of S. typhimurium to a host animal. We identified the evolved cis-regulatory module and quantified the fitness gain that this regulatory output accrues for the bacterium using competitive infections of host animals. Our findings highlight a mechanism of pathogen evolution involving regulatory mutation that is selected because of the fitness advantage the new regulatory output provides the incipient clones.

Comparative and functional genomics of the Lactococcus lactis taxon; insights into evolution and niche adaptation.

Science.gov (United States)

Kelleher, Philip; Bottacini, Francesca; Mahony, Jennifer; Kilcawley, Kieran N; van Sinderen, Douwe

2017-03-29

Lactococcus lactis is among the most widely studied lactic acid bacterial species due to its long history of safe use and economic importance to the dairy industry, where it is exploited as a starter culture in cheese production. In the current study, we report on the complete sequencing of 16 L. lactis subsp. lactis and L. lactis subsp. cremoris genomes. The chromosomal features of these 16 L. lactis strains in conjunction with 14 completely sequenced, publicly available lactococcal chromosomes were assessed with particular emphasis on discerning the L. lactis subspecies division, evolution and niche adaptation. The deduced pan-genome of L. lactis was found to be closed, indicating that the representative data sets employed for this analysis are sufficient to fully describe the genetic diversity of the taxon. Niche adaptation appears to play a significant role in governing the genetic content of each L. lactis subspecies, while (differential) genome decay and redundancy in the dairy niche is also highlighted.

Adaptive grid based multi-objective Cauchy differential evolution for stochastic dynamic economic emission dispatch with wind power uncertainty.

Science.gov (United States)

Zhang, Huifeng; Lei, Xiaohui; Wang, Chao; Yue, Dong; Xie, Xiangpeng

2017-01-01

Since wind power is integrated into the thermal power operation system, dynamic economic emission dispatch (DEED) has become a new challenge due to its uncertain characteristics. This paper proposes an adaptive grid based multi-objective Cauchy differential evolution (AGB-MOCDE) for solving stochastic DEED with wind power uncertainty. To properly deal with wind power uncertainty, some scenarios are generated to simulate those possible situations by dividing the uncertainty domain into different intervals, the probability of each interval can be calculated using the cumulative distribution function, and a stochastic DEED model can be formulated under different scenarios. For enhancing the optimization efficiency, Cauchy mutation operation is utilized to improve differential evolution by adjusting the population diversity during the population evolution process, and an adaptive grid is constructed for retaining diversity distribution of Pareto front. With consideration of large number of generated scenarios, the reduction mechanism is carried out to decrease the scenarios number with covariance relationships, which can greatly decrease the computational complexity. Moreover, the constraint-handling technique is also utilized to deal with the system load balance while considering transmission loss among thermal units and wind farms, all the constraint limits can be satisfied under the permitted accuracy. After the proposed method is simulated on three test systems, the obtained results reveal that in comparison with other alternatives, the proposed AGB-MOCDE can optimize the DEED problem while handling all constraint limits, and the optimal scheme of stochastic DEED can decrease the conservation of interval optimization, which can provide a more valuable optimal scheme for real-world applications.

Quantifying Functional Reuse from Object Oriented Requirements Specifications

NARCIS (Netherlands)

Condori-Fernandez, Nelly; Condori-Fernández, N.; Pastor, O; Daneva, Maia; Abran, A.; Castro, J.; Quer, C.; Carvallo, J. B.; Fernandes da Silva, L.

2008-01-01

Software reuse is essential in improving efficiency and productivity in the software development process. This paper analyses reuse within requirements engineering phase by taking and adapting a standard functional size measurement method, COSMIC FFP. Our proposal attempts to quantify reusability

Fitness declines towards range limits and local adaptation to climate affect dispersal evolution during climate‐induced range shifts

DEFF Research Database (Denmark)

Hargreaves, Anna; Bailey, Susan; Laird, Robert

2015-01-01

Dispersal ability will largely determine whether species track their climatic niches during climate change, a process especially important for populations at contracting (low-latitude/low-elevation) range limits that otherwise risk extinction. We investigate whether dispersal evolution....... We simulate a species distributed continuously along a temperature gradient using a spatially explicit, individual-based model. We compare range-wide dispersal evolution during climate stability vs. directional climate change, with uniform fitness vs. fitness that declines towards range limits (RLs...... at contracting range limits is facilitated by two processes that potentially enable edge populations to experience and adjust to the effects of climate deterioration before they cause extinction: (i) climate-induced fitness declines towards range limits and (ii) local adaptation to a shifting climate gradient...

Comparative Transcriptome Analysis Reveals Adaptive Evolution of Notopterygium incisum and Notopterygium franchetii, Two High-Alpine Herbal Species Endemic to China

Directory of Open Access Journals (Sweden)

Yun Jia

2017-07-01

Full Text Available The extreme conditions (e.g., cold, low oxygen, and strong ultraviolet radiation of the high mountains provide an ideal natural laboratory for studies on speciation and the adaptive evolution of organisms. Up to now, few genome/transcriptome-based studies have been carried out on how plants adapt to conditions at extremely high altitudes. Notopterygium incisum and Notopterygium franchetii (Notopterygium, Apiaceae are two endangered high-alpine herbal plants endemic to China. To explore the molecular genetic mechanisms of adaptation to high altitudes, we performed high-throughput RNA sequencing (RNA-seq to characterize the transcriptomes of the two species. In total, more than 130 million sequence reads, 81,446 and 63,153 unigenes with total lengths of 86,924,837 and 62,615,693 bp, were generated for the two herbal species, respectively. OrthoMCL analysis identified 6375 single-copy orthologous genes between N. incisum and N. franchetii. In total, 381 positively-selected candidate genes were identified for both plants by using estimations of the non-synonymous to synonymous substitution rate. At least 18 of these genes potentially participate in RNA splicing, DNA repair, glutathione metabolism and the plant–pathogen interaction pathway, which were further enriched in various functional gene categories possibly responsible for environment adaptation in high mountains. Meanwhile, we detected various transcription factors that regulated the material and energy metabolism in N. incisum and N. franchetii, which probably play vital roles in the tolerance to stress in surroundings. In addition, 60 primer pairs based on orthologous microsatellite-containing sequences between the both Notopterygium species were determined. Finally, 17 polymorphic microsatellite markers (SSR were successfully characterized for the two endangered species. Based on these candidate orthologous and SSR markers, we detected that the adaptive evolution and species divergence

Adaptive Evolution of Signaling Partners

Science.gov (United States)

Urano, Daisuke; Dong, Taoran; Bennetzen, Jeffrey L.; Jones, Alan M.

2015-01-01

Proteins that interact coevolve their structures. When mutation disrupts the interaction, compensation by the partner occurs to restore interaction otherwise counterselection occurs. We show in this study how a destabilizing mutation in one protein is compensated by a stabilizing mutation in its protein partner and their coevolving path. The pathway in this case and likely a general principle of coevolution is that the compensatory change must tolerate both the original and derived structures with equivalence in function and activity. Evolution of the structure of signaling elements in a network is constrained by specific protein pair interactions, by requisite conformational changes, and by catalytic activity. The heterotrimeric G protein-coupled signaling is a paragon of this protein interaction/function complexity and our deep understanding of this pathway in diverse organisms lends itself to evolutionary study. Regulators of G protein Signaling (RGS) proteins accelerate the intrinsic GTP hydrolysis rate of the Gα subunit of the heterotrimeric G protein complex. An important RGS-contact site is a hydroxyl-bearing residue on the switch I region of Gα subunits in animals and most plants, such as Arabidopsis. The exception is the grasses (e.g., rice, maize, sugarcane, millets); these plants have Gα subunits that replaced the critical hydroxyl-bearing threonine with a destabilizing asparagine shown to disrupt interaction between Arabidopsis RGS protein (AtRGS1) and the grass Gα subunit. With one known exception (Setaria italica), grasses do not encode RGS genes. One parsimonious deduction is that the RGS gene was lost in the ancestor to the grasses and then recently acquired horizontally in the lineage S. italica from a nongrass monocot. Like all investigated grasses, S. italica has the Gα subunit with the destabilizing asparagine residue in the protein interface but, unlike other known grass genomes, still encodes an expressed RGS gene, SiRGS1. SiRGS1

Directed evolution of adaptive traits

Science.gov (United States)

As a species, switchgrass is adapted to an amazingly broad range of environments, spanning hardiness zones ranging from HZ3 to HZ9 (Canada to Mexico), from the mid-grass prairie to the Atlantic Seaboard, from sandy soils to heavy clay soils, from acid to alkaline soils, and from wetland to dryland h...

Morphogenesis in bat wings: linking development, evolution and ecology.

Science.gov (United States)

Adams, Rick A

2008-01-01

The evolution of powered flight in mammals required specific developmental shifts from an ancestral limb morphology to one adapted for flight. Through studies of comparative morphogenesis, investigators have quantified points and rates of divergence providing important insights into how wings evolved in mammals. Herein I compare growth,development and skeletogenesis of forelimbs between bats and the more ancestral state provided by the rat (Rattus norvegicus)and quantify growth trajectories that illustrate morphological divergence both developmentally and evolutionarily. In addition, I discuss how wing shape is controlled during morphogenesis by applying multivariate analyses of wing bones and wing membranes and discuss how flight dynamics are stabilized during flight ontogeny. Further, I discuss the development of flight in bats in relation to the ontogenetic niche and how juveniles effect populational foraging patterns. In addition, I provide a hypothetical ontogenetic landscape model that predicts how and when selection is most intense during juvenile morphogenesis and test this model with data from a population of the little brown bat, Myotis lucifugus. (c) 2007 S. Karger AG, Basel

Molecular evolution of the odorant and gustatory receptor genes in lepidopteran insects: implications for their adaptation and speciation.

Science.gov (United States)

Engsontia, Patamarerk; Sangket, Unitsa; Chotigeat, Wilaiwan; Satasook, Chutamas

2014-08-01

Lepidoptera (comprised of butterflies and moths) is one of the largest groups of insects, including more than 160,000 described species. Chemoreception plays important roles in the adaptation of these species to a wide range of niches, e.g., plant hosts, egg-laying sites, and mates. This study investigated the molecular evolution of the lepidopteran odorant (Or) and gustatory receptor (Gr) genes using recently identified genes from Bombyx mori, Danaus plexippus, Heliconius melpomene, Plutella xylostella, Heliothis virescens, Manduca sexta, Cydia pomonella, and Spodoptera littoralis. A limited number of cases of large lineage-specific gene expansion are observed (except in the P. xylostella lineage), possibly due to selection against tandem gene duplication. There has been strong purifying selection during the evolution of both lepidopteran odorant and gustatory genes, as shown by the low ω values estimated through CodeML analysis, ranging from 0.0093 to 0.3926. However, purifying selection has been relaxed on some amino acid sites in these receptors, leading to sequence divergence, which is a precursor of positive selection on these sequences. Signatures of positive selection were detected only in a few loci from the lineage-specific analysis. Estimation of gene gains and losses suggests that the common ancestor of the Lepidoptera had fewer Or genes compared to extant species and an even more reduced number of Gr genes, particularly within the bitter receptor clade. Multiple gene gains and a few gene losses occurred during the evolution of Lepidoptera. Gene family expansion may be associated with the adaptation of lepidopteran species to plant hosts, especially after angiosperm radiation. Phylogenetic analysis of the moth sex pheromone receptor genes suggested that chromosomal translocations have occurred several times. New sex pheromone receptors have arisen through tandem gene duplication. Positive selection was detected at some amino acid sites predicted to be

Whole-Genome Scans Provide Evidence of Adaptive Evolution in Malawian Plasmodium falciparum Isolates

DEFF Research Database (Denmark)

Ocholla, Harold; Preston, Mark D; Mipando, Mwapatsa

2014-01-01

BACKGROUND:  Selection by host immunity and antimalarial drugs has driven extensive adaptive evolution in Plasmodium falciparum and continues to produce ever-changing landscapes of genetic variation. METHODS:  We performed whole-genome sequencing of 69 P. falciparum isolates from Malawi and used......, an area of high malaria transmission. Allele frequency-based tests provided evidence of recent population growth in Malawi and detected potential targets of host immunity and candidate vaccine antigens. Comparison of the sequence variation between isolates from Malawi and those from 5 geographically...... dispersed countries (Kenya, Burkina Faso, Mali, Cambodia, and Thailand) detected population genetic differences between Africa and Asia, within Southeast Asia, and within Africa. Haplotype-based tests of selection to sequence data from all 6 populations identified signals of directional selection at known...

New Computational Model Based on Finite Element Method to Quantify Damage Evolution Due to External Sulfate Attack on Self-Compacting Concretes

KAUST Repository

Khelifa, Mohammed Rissel

2012-12-27

Abstract: This work combines experimental and numerical investigations to study the mechanical degradation of self-compacting concrete under accelerated aging conditions. Four different experimental treatments are tested among them constant immersion and immersion-drying protocols allow an efficient external sulfate attack of the material. Significant damage is observed due to interfacial ettringite. A predictive analysis is then adopted to quantify the relationship between ettringite growth and mechanical damage evolution during aging. Typical 3D microstructures representing the cement paste-aggregate structures are generated using Monte Carlo scheme. These images are converted into a finite element model to predict the mechanical performance under different criteria of damage kinetics. The effect of ettringite is then associated to the development of an interphase of lower mechanical properties. Our results show that the observed time evolution of Young\\'s modulus is best described by a linear increase of the interphase content. Our model results indicate also that the interphase regions grow at maximum stress regions rather than exclusively at interfaces. Finally, constant immersion predicts a rate of damage growth five times lower than that of immersion-drying protocol. © 2012 Computer-Aided Civil and Infrastructure Engineering.

New Computational Model Based on Finite Element Method to Quantify Damage Evolution Due to External Sulfate Attack on Self-Compacting Concretes

KAUST Repository

Khelifa, Mohammed Rissel; Guessasma, Sofiane

2012-01-01

Abstract: This work combines experimental and numerical investigations to study the mechanical degradation of self-compacting concrete under accelerated aging conditions. Four different experimental treatments are tested among them constant immersion and immersion-drying protocols allow an efficient external sulfate attack of the material. Significant damage is observed due to interfacial ettringite. A predictive analysis is then adopted to quantify the relationship between ettringite growth and mechanical damage evolution during aging. Typical 3D microstructures representing the cement paste-aggregate structures are generated using Monte Carlo scheme. These images are converted into a finite element model to predict the mechanical performance under different criteria of damage kinetics. The effect of ettringite is then associated to the development of an interphase of lower mechanical properties. Our results show that the observed time evolution of Young's modulus is best described by a linear increase of the interphase content. Our model results indicate also that the interphase regions grow at maximum stress regions rather than exclusively at interfaces. Finally, constant immersion predicts a rate of damage growth five times lower than that of immersion-drying protocol. © 2012 Computer-Aided Civil and Infrastructure Engineering.

Functional genetic divergence in high CO2 adapted Emiliania huxleyi populations.

Science.gov (United States)

Lohbeck, Kai T; Riebesell, Ulf; Collins, Sinéad; Reusch, Thorsten B H

2013-07-01

Predicting the impacts of environmental change on marine organisms, food webs, and biogeochemical cycles presently relies almost exclusively on short-term physiological studies, while the possibility of adaptive evolution is often ignored. Here, we assess adaptive evolution in the coccolithophore Emiliania huxleyi, a well-established model species in biological oceanography, in response to ocean acidification. We previously demonstrated that this globally important marine phytoplankton species adapts within 500 generations to elevated CO2 . After 750 and 1000 generations, no further fitness increase occurred, and we observed phenotypic convergence between replicate populations. We then exposed adapted populations to two novel environments to investigate whether or not the underlying basis for high CO2 -adaptation involves functional genetic divergence, assuming that different novel mutations become apparent via divergent pleiotropic effects. The novel environment "high light" did not reveal such genetic divergence whereas growth in a low-salinity environment revealed strong pleiotropic effects in high CO2 adapted populations, indicating divergent genetic bases for adaptation to high CO2 . This suggests that pleiotropy plays an important role in adaptation of natural E. huxleyi populations to ocean acidification. Our study highlights the potential mutual benefits for oceanography and evolutionary biology of using ecologically important marine phytoplankton for microbial evolution experiments. © 2012 The Author(s). Evolution © 2012 The Society for the Study of Evolution.

A new paradigma on the plant evolution: from a natural evolution to an artificial evolution?

Science.gov (United States)

Bennici, Andrea

2005-01-01

After evidencing the great importance of plants for animals and humans in consequence of the photosynthesis, several considerations on plant evolution are made. One of the peculiar characteristics of the plant is the sessile property, due especially to the cell wall. This factor, principally, strengthened by the photosynthetic process, determined the particular developmental pattern of the plant, which is characterized by the continuous formation of new organs. The plant immobility, although negative for its survival, has been, in great part, overcome by the acquisition of the capacity of adaptation (plasticity) to the environmental stresses and changes, and the establishment of more adapted genotypes. This capacity to react to the external signals induced Trewavas to speak of "plant intelligence". The plant movement incapacity and the evolution of the sexual reproduction system were strongly correlated. In this context, the evolution of the flower in the Angiosperms has been particularly important to allow the male gamete to fertilize the immobile female gamete. Moreover, the formation of fruit and seed greatly improved the dispersal and conservation of the progeny in the environment. With the flower, mechanisms to favour the outcrossing among different individuals appeared, which are essential to increase the genetic variability and, then, the plant evolution itself. Although the Angiosperms seem highly evolved, the plant evolution is not surely finished, because many reported morpho-physiological processes may be still considered susceptible of further improvement. In the last years the relationships among humans, plants and environment are becoming closer and closer. This is due to the use of the DNA recombinant techniques with the aim to modify artificially plant characters. Therefore, the risk of a plant evolution strongly directed towards practical or commercial objectives, or "an artificial evolution", may be hypothesized.

Quantifying climate risk - the starting point

International Nuclear Information System (INIS)

Fairweather, Helen; Luo, Qunying; Liu, De Li; Wiles, Perry

2007-01-01

Full text: All natural systems have evolved to their current state as a result inter alia of the climate in which they developed. Similarly, man-made systems (such as agricultural production) have developed to suit the climate experienced over the last 100 or so years. The capacity of different systems to adapt to changes in climate that are outside those that have been experienced previously is largely unknown. This results in considerable uncertainty when predicting climate change impacts. However, it is possible to quantify the relative probabilities of a range of potential impacts of climate change. Quantifying current climate risks is an effective starting point for analysing the probable impacts of future climate change and guiding the selection of appropriate adaptation strategies. For a farming system to be viable within the current climate, its profitability must be sustained and, therefore, possible adaptation strategies need to be tested for continued viability in a changed climate. The methodology outlined in this paper examines historical patterns of key climate variables (rainfall and temperature) across the season and their influence on the productivity of wheat growing in NSW. This analysis is used to identify the time of year that the system is most vulnerable to climate variation, within the constraints of the current climate. Wheat yield is used as a measure of productivity, which is also assumed to be a surrogate for profitability. A time series of wheat yields is sorted into ascending order and categorised into five percentile groupings (i.e. 20th, 40th, 60th and 80th percentiles) for each shire across NSW (-100 years). Five time series of climate data (which are aggregated daily data from the years in each percentile) are analysed to determine the period that provides the greatest climate risk to the production system. Once this period has been determined, this risk is quantified in terms of the degree of separation of the time series

The king cobra genome reveals dynamic gene evolution and adaptation in the snake venom system.

Science.gov (United States)

Vonk, Freek J; Casewell, Nicholas R; Henkel, Christiaan V; Heimberg, Alysha M; Jansen, Hans J; McCleary, Ryan J R; Kerkkamp, Harald M E; Vos, Rutger A; Guerreiro, Isabel; Calvete, Juan J; Wüster, Wolfgang; Woods, Anthony E; Logan, Jessica M; Harrison, Robert A; Castoe, Todd A; de Koning, A P Jason; Pollock, David D; Yandell, Mark; Calderon, Diego; Renjifo, Camila; Currier, Rachel B; Salgado, David; Pla, Davinia; Sanz, Libia; Hyder, Asad S; Ribeiro, José M C; Arntzen, Jan W; van den Thillart, Guido E E J M; Boetzer, Marten; Pirovano, Walter; Dirks, Ron P; Spaink, Herman P; Duboule, Denis; McGlinn, Edwina; Kini, R Manjunatha; Richardson, Michael K

2013-12-17

Snakes are limbless predators, and many species use venom to help overpower relatively large, agile prey. Snake venoms are complex protein mixtures encoded by several multilocus gene families that function synergistically to cause incapacitation. To examine venom evolution, we sequenced and interrogated the genome of a venomous snake, the king cobra (Ophiophagus hannah), and compared it, together with our unique transcriptome, microRNA, and proteome datasets from this species, with data from other vertebrates. In contrast to the platypus, the only other venomous vertebrate with a sequenced genome, we find that snake toxin genes evolve through several distinct co-option mechanisms and exhibit surprisingly variable levels of gene duplication and directional selection that correlate with their functional importance in prey capture. The enigmatic accessory venom gland shows a very different pattern of toxin gene expression from the main venom gland and seems to have recruited toxin-like lectin genes repeatedly for new nontoxic functions. In addition, tissue-specific microRNA analyses suggested the co-option of core genetic regulatory components of the venom secretory system from a pancreatic origin. Although the king cobra is limbless, we recovered coding sequences for all Hox genes involved in amniote limb development, with the exception of Hoxd12. Our results provide a unique view of the origin and evolution of snake venom and reveal multiple genome-level adaptive responses to natural selection in this complex biological weapon system. More generally, they provide insight into mechanisms of protein evolution under strong selection.

Venom Evolution

Indian Academy of Sciences (India)

IAS Admin

Therefore, the platypus sequence was studied to quantify the role of gene duplication in the evolution of venom. ... Platypus venom is present only in males and is used for asserting dominance over com- petitors during the ... Certain toxin gene families are known to re- peatedly evolve through gene duplications. The rapidly ...

Adaptive evolution of simian immunodeficiency viruses isolated from two conventional progressor macaques with neuroaids

Energy Technology Data Exchange (ETDEWEB)

Foley, Brian T [Los Alamos National Laboratory; Korber, Bette T [Los Alamos National Laboratory

2008-01-01

Simian immunodeficiency virus infection of macaques may result in neuroAIDS, a feature more commonly observed in macaques with rapid progressive disease than in those with conventional disease. This is the first report of two conventional progressors (H631 and H636) with encephalitis in rhesus macaques inoculated with a derivative of SIVsmES43-3. Phylogenetic analyses of viruses isolated from the cerebral spinal fluid (CSF) and plasma from both animals demonstrated tissue compartmentalization. Additionally, virus from the central nervous system (CNS) was able to infect primary macaque monocyte-derived macrophages more efficiently than virus from plasma. Conversely, virus isolated from plasma was able to replicate better in peripheral blood mononuclear cells than virus from CNS. We speculate that these viruses were under different selective pressures in their separate compartments. Furthermore, these viruses appear to have undergone adaptive evolution to preferentially replicate in their respective cell targets. Analysis of the number of potential N-linked glycosylation sites (PNGS) in gp160 showed that there was a statistically significant loss of PNGS in viruses isolated from CNS in both macaques compared to SIVsmE543-3. Moreover, virus isolated from the brain in H631, had statistically significant loss of PNGS compared to virus isolated from CSF and plasma of the same animal. It is possible that the brain isolate may have adapted to decrease the number of PNGS given that humoral immune selection pressure is less likely to be encountered in the brain. These viruses provide a relevant model to study the adaptations required for SIV to induce encephalitis.

Two Case Studies to Quantify Resilience across Food-Energy-Water Systems: the Columbia River Treaty and Adaptation in Yakima River Basin Irrigation Systems

Science.gov (United States)

Malek, K.; Adam, J. C.; Richey, A.; Rushi, B. R.; Stockle, C.; Yoder, J.; Barik, M.; Lee, S. Y.; Rajagopalan, K.; Brady, M.; Barber, M. E.; Boll, J.; Padowski, J.

2017-12-01

The U.S. Pacific Northwest (PNW) plays a significant role in meeting agricultural and hydroelectric demands nationwide. Climatic and anthropogenic stressors, however, potentially threaten the productivity, resilience, and environmental health of the region. Our objective is to understand how resilience of each Food-Energy-Water (FEW) sector, and the combined Nexus, respond to exogenous perturbations and the extent to which technological and institutional advances can buffer these perturbations. In the process of taking information from complex integrated models and assessing resilience across FEW sectors, we start with two case studies: 1) Columbia River Treaty (CRT) with Canada that determines how multiple reservoirs in the Columbia River basin (CRB) are operated, and 2) climate change adaptation actions in the Yakima River basin (YRB). We discuss these case studies in terms of the similarities and contrasts related to FEW sectors and management complexities. Both the CRB and YBP systems are highly sensitive to climate change (they are both snowmelt-dominant) and already experience water conflict. The CRT is currently undergoing renegotiation; a new CRT will need to consider a much more comprehensive approach, e.g., treating environmental flows explicitly. The YRB also already experiences significant water conflict and thus the comprehensive Yakima Basin Integrated Plan (YBIP) is being pursued. We apply a new modeling framework that mechanistically captures the interactions between the FEW sectors to quantify the impacts of CRT and YBIP planning (as well as adaptation decisions taken by individuals, e.g., irrigators) on resilience in each sector. Proposed modification to the CRT may relieve impacts to multiple sectors. However, in the YRB, irrigators' actions to adapt to climate change (through investing in more efficient irrigation technology) could reduce downstream water availability for other users. Developing a process to quantify resilience to perturbations

Hidden Randomness between Fitness Landscapes Limits Reverse Evolution

Science.gov (United States)

Tan, Longzhi; Serene, Stephen; Xiao Chao, Hui; Gore, Jeff

2012-02-01

Natural populations must constantly adapt to the ever-changing environment. A fundamental question in evolutionary biology is whether adaptations can be reversed by returning the population to its ancestral environment. Traditionally, reverse evolution is defined as restoring an ancestral phenotype (physical characteristics such as body size), and the classic Dollo's Law has hypothesized the impossibility of reversing complex adaptations. However, this ``law'' remains ambiguous unless reverse evolution can be studied at the level of genotypes (the underlying genome sequence). We measured the fitness landscapes of a bacterial antibiotic-resistance gene and analyzed the reversibility of evolution as a global, statistical feature of the landscapes. In both experiments and simulations, we find that an adaptation's reversibility declines as the number of mutations it involves increases, suggesting a probabilistic form of Dollo's Law at the molecular level. We also show computationally that slowly switching between environments facilitates reverse evolution in small populations, where clonal interference is negligible or moderate. This is an analogy to thermodynamics, where the reversibility of a physical process is maximized when conditions are modified infinitely slowly.

Quantifying the relevance of adaptive thermal comfort models in moderate thermal climate zones

Energy Technology Data Exchange (ETDEWEB)

Hoof, Joost van; Hensen, Jan L.M. [Faculty of Architecture, Building and Planning, Technische Universiteit Eindhoven, Vertigo 6.18, P.O. Box 513, 5600 MB Eindhoven (Netherlands)

2007-01-15

Standards governing thermal comfort evaluation are on a constant cycle of revision and public review. One of the main topics being discussed in the latest round was the introduction of an adaptive thermal comfort model, which now forms an optional part of ASHRAE Standard 55. Also on a national level, adaptive thermal comfort guidelines come into being, such as in the Netherlands. This paper discusses two implementations of the adaptive comfort model in terms of usability and energy use for moderate maritime climate zones by means of literature study, a case study comprising temperature measurements, and building performance simulation. It is concluded that for moderate climate zones the adaptive model is only applicable during summer months, and can reduce energy for naturally conditioned buildings. However, the adaptive thermal comfort model has very limited application potential for such climates. Additionally we suggest a temperature parameter with a gradual course to replace the mean monthly outdoor air temperature to avoid step changes in optimum comfort temperatures. (author)

Opposition-Based Adaptive Fireworks Algorithm

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Chibing Gong

2016-07-01

Full Text Available A fireworks algorithm (FWA is a recent swarm intelligence algorithm that is inspired by observing fireworks explosions. An adaptive fireworks algorithm (AFWA proposes additional adaptive amplitudes to improve the performance of the enhanced fireworks algorithm (EFWA. The purpose of this paper is to add opposition-based learning (OBL to AFWA with the goal of further boosting performance and achieving global optimization. Twelve benchmark functions are tested in use of an opposition-based adaptive fireworks algorithm (OAFWA. The final results conclude that OAFWA significantly outperformed EFWA and AFWA in terms of solution accuracy. Additionally, OAFWA was compared with a bat algorithm (BA, differential evolution (DE, self-adapting control parameters in differential evolution (jDE, a firefly algorithm (FA, and a standard particle swarm optimization 2011 (SPSO2011 algorithm. The research results indicate that OAFWA ranks the highest of the six algorithms for both solution accuracy and runtime cost.

Darwinian evolution on a chip.

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Brian M Paegel

2008-04-01

Full Text Available Computer control of Darwinian evolution has been demonstrated by propagating a population of RNA enzymes in a microfluidic device. The RNA population was challenged to catalyze the ligation of an oligonucleotide substrate under conditions of progressively lower substrate concentrations. A microchip-based serial dilution circuit automated an exponential growth phase followed by a 10-fold dilution, which was repeated for 500 log-growth iterations. Evolution was observed in real time as the population adapted and achieved progressively faster growth rates over time. The final evolved enzyme contained a set of 11 mutations that conferred a 90-fold improvement in substrate utilization, coinciding with the applied selective pressure. This system reduces evolution to a microfluidic algorithm, allowing the experimenter to observe and manipulate adaptation.

Quantifying selection in evolving populations using time-resolved genetic data

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Illingworth, Christopher J. R.; Mustonen, Ville

2013-01-01

Methods which uncover the molecular basis of the adaptive evolution of a population address some important biological questions. For example, the problem of identifying genetic variants which underlie drug resistance, a question of importance for the treatment of pathogens, and of cancer, can be understood as a matter of inferring selection. One difficulty in the inference of variants under positive selection is the potential complexity of the underlying evolutionary dynamics, which may involve an interplay between several contributing processes, including mutation, recombination and genetic drift. A source of progress may be found in modern sequencing technologies, which confer an increasing ability to gather information about evolving populations, granting a window into these complex processes. One particularly interesting development is the ability to follow evolution as it happens, by whole-genome sequencing of an evolving population at multiple time points. We here discuss how to use time-resolved sequence data to draw inferences about the evolutionary dynamics of a population under study. We begin by reviewing our earlier analysis of a yeast selection experiment, in which we used a deterministic evolutionary framework to identify alleles under selection for heat tolerance, and to quantify the selection acting upon them. Considering further the use of advanced intercross lines to measure selection, we here extend this framework to cover scenarios of simultaneous recombination and selection, and of two driver alleles with multiple linked neutral, or passenger, alleles, where the driver pair evolves under an epistatic fitness landscape. We conclude by discussing the limitations of the approach presented and outlining future challenges for such methodologies.

A Cultural Evolution Approach to Digital Media.

Science.gov (United States)

Acerbi, Alberto

2016-01-01

Digital media have today an enormous diffusion, and their influence on the behavior of a vast part of the human population can hardly be underestimated. In this review I propose that cultural evolution theory, including both a sophisticated view of human behavior and a methodological attitude to modeling and quantitative analysis, provides a useful framework to study the effects and the developments of media in the digital age. I will first give a general presentation of the cultural evolution framework, and I will then introduce this more specific research program with two illustrative topics. The first topic concerns how cultural transmission biases, that is, simple heuristics such as "copy prestigious individuals" or "copy the majority," operate in the novel context of digital media. The existence of transmission biases is generally justified with their adaptivity in small-scale societies. How do they operate in an environment where, for example, prestigious individuals possess not-relevant skills, or popularity is explicitly quantified and advertised? The second aspect relates to fidelity of cultural transmission. Digitally-mediated interactions support cheap and immediate high-fidelity transmission, in opposition, for example, to oral traditions. How does this change the content that is more likely to spread? Overall, I suggest the usefulness of a "long view" to our contemporary digital environment, contextualized in cognitive science and cultural evolution theory, and I discuss how this perspective could help us to understand what is genuinely new and what is not.

A cultural evolution approach to digital media

Directory of Open Access Journals (Sweden)

Alberto Acerbi

2016-12-01

Full Text Available Digital media have today an enormous diffusion, and their influence on the behaviour of a vast part of the human population can hardly be underestimated. In this review I propose that cultural evolution theory, including both a sophisticated view of human behaviour and a methodological attitude to modelling and quantitative analysis, provides a useful framework to study the effects and the developments of media in the digital age. I will first give a general presentation of the cultural evolution framework, and I will then introduce this more specific research program with two illustrative topics.The first topic concerns how cultural transmission biases, that is, simple heuristics such as copy prestigious individuals or copy the majority, operate in the novel context of digital media. The existence of transmission biases is generally justified with their adaptivity in small-scale societies. How do they operate in an environment where, for example, prestigious individuals possess not-relevant skills, or popularity is explicitly quantified and advertised?The second aspect relates to fidelity of cultural transmission. Digitally-mediated interactions support cheap and immediate high-fidelity transmission, in opposition, for example, to oral traditions. How does this change the content that is more likely to spread? Overall, I suggest the usefulness of a long view to our contemporary digital environment, contextualised in cognitive science and cultural evolution theory, and I discuss how this perspective could help us to understand what is genuinely new and what is not.

A Cultural Evolution Approach to Digital Media

Science.gov (United States)

Acerbi, Alberto

2016-01-01

Digital media have today an enormous diffusion, and their influence on the behavior of a vast part of the human population can hardly be underestimated. In this review I propose that cultural evolution theory, including both a sophisticated view of human behavior and a methodological attitude to modeling and quantitative analysis, provides a useful framework to study the effects and the developments of media in the digital age. I will first give a general presentation of the cultural evolution framework, and I will then introduce this more specific research program with two illustrative topics. The first topic concerns how cultural transmission biases, that is, simple heuristics such as “copy prestigious individuals” or “copy the majority,” operate in the novel context of digital media. The existence of transmission biases is generally justified with their adaptivity in small-scale societies. How do they operate in an environment where, for example, prestigious individuals possess not-relevant skills, or popularity is explicitly quantified and advertised? The second aspect relates to fidelity of cultural transmission. Digitally-mediated interactions support cheap and immediate high-fidelity transmission, in opposition, for example, to oral traditions. How does this change the content that is more likely to spread? Overall, I suggest the usefulness of a “long view” to our contemporary digital environment, contextualized in cognitive science and cultural evolution theory, and I discuss how this perspective could help us to understand what is genuinely new and what is not. PMID:28018200

Qualitative and quantitative assessment of step size adaptation rules

DEFF Research Database (Denmark)

Krause, Oswin; Glasmachers, Tobias; Igel, Christian

2017-01-01

We present a comparison of step size adaptation methods for evolution strategies, covering recent developments in the field. Following recent work by Hansen et al. we formulate a concise list of performance criteria: a) fast convergence of the mean, b) near-optimal fixed point of the normalized s...... that cumulative step size adaptation (CSA) and twopoint adaptation (TPA) provide reliable estimates of the optimal step size. We further find that removing the evolution path of CSA still leads to a reliable algorithm without the computational requirements of CSA.......We present a comparison of step size adaptation methods for evolution strategies, covering recent developments in the field. Following recent work by Hansen et al. we formulate a concise list of performance criteria: a) fast convergence of the mean, b) near-optimal fixed point of the normalized...

Cooperative Learning Groups and the Evolution of Human Adaptability : (Another Reason) Why Hermits Are Rare in Tonga and Elsewhere.

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Bell, Adrian Viliami; Hernandez, Daniel

2017-03-01

Understanding the prevalence of adaptive culture in part requires understanding the dynamics of learning. Here we explore the adaptive value of social learning in groups and how formal social groups function as effective mediums of information exchange. We discuss the education literature on Cooperative Learning Groups (CLGs), which outlines the potential of group learning for enhancing learning outcomes. Four qualities appear essential for CLGs to enhance learning: (1) extended conversations, (2) regular interactions, (3) gathering of experts, and (4) incentives for sharing knowledge. We analyze these four qualities within the context of a small-scale agricultural society using data we collected in 2010 and 2012. Through an analysis of surveys, interviews, and observations in the Tongan islands, we describe the role CLGs likely plays in facilitating individuals' learning of adaptive information. Our analysis of group affiliation, membership, and topics of conversation suggest that the first three CLG qualities reflect conditions for adaptive learning in groups. We utilize ethnographic anecdotes to suggest the fourth quality is also conducive to adaptive group learning. Using an evolutionary model, we further explore the scope for CLGs outside the Tongan socioecological context. Model analysis shows that environmental volatility and migration rates among human groups mediate the scope for CLGs. We call for wider attention to how group structure facilitates learning in informal settings, which may be key to assessing the contribution of groups to the evolution of complex, adaptive culture.

How Large Asexual Populations Adapt

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Desai, Michael

2007-03-01

We often think of beneficial mutations as being rare, and of adaptation as a sequence of selected substitutions: a beneficial mutation occurs, spreads through a population in a selective sweep, then later another beneficial mutation occurs, and so on. This simple picture is the basis for much of our intuition about adaptive evolution, and underlies a number of practical techniques for analyzing sequence data. Yet many large and mostly asexual populations -- including a wide variety of unicellular organisms and viruses -- live in a very different world. In these populations, beneficial mutations are common, and frequently interfere or cooperate with one another as they all attempt to sweep simultaneously. This radically changes the way these populations adapt: rather than an orderly sequence of selective sweeps, evolution is a constant swarm of competing and interfering mutations. I will describe some aspects of these dynamics, including why large asexual populations cannot evolve very quickly and the character of the diversity they maintain. I will explain how this changes our expectations of sequence data, how sex can help a population adapt, and the potential role of ``mutator'' phenotypes with abnormally high mutation rates. Finally, I will discuss comparisons of these predictions with evolution experiments in laboratory yeast populations.

Evolution of increased adult longevity in Drosophila melanogaster populations selected for adaptation to larval crowding.

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Shenoi, V N; Ali, S Z; Prasad, N G

2016-02-01

In holometabolous animals such as Drosophila melanogaster, larval crowding can affect a wide range of larval and adult traits. Adults emerging from high larval density cultures have smaller body size and increased mean life span compared to flies emerging from low larval density cultures. Therefore, adaptation to larval crowding could potentially affect adult longevity as a correlated response. We addressed this issue by studying a set of large, outbred populations of D. melanogaster, experimentally evolved for adaptation to larval crowding for 83 generations. We assayed longevity of adult flies from both selected (MCUs) and control populations (MBs) after growing them at different larval densities. We found that MCUs have evolved increased mean longevity compared to MBs at all larval densities. The interaction between selection regime and larval density was not significant, indicating that the density dependence of mean longevity had not evolved in the MCU populations. The increase in longevity in MCUs can be partially attributed to their lower rates of ageing. It is also noteworthy that reaction norm of dry body weight, a trait probably under direct selection in our populations, has indeed evolved in MCU populations. To the best of our knowledge, this is the first report of the evolution of adult longevity as a correlated response of adaptation to larval crowding. © 2015 European Society For Evolutionary Biology. Journal of Evolutionary Biology © 2015 European Society For Evolutionary Biology.

Evolution of opercle shape in cichlid fishes from Lake Tanganyika - adaptive trait interactions in extant and extinct species flocks.

Science.gov (United States)

Wilson, Laura A B; Colombo, Marco; Sánchez-Villagra, Marcelo R; Salzburger, Walter

2015-11-20

Phenotype-environment correlations and the evolution of trait interactions in adaptive radiations have been widely studied to gain insight into the dynamics underpinning rapid species diversification. In this study we explore the phenotype-environment correlation and evolution of operculum shape in cichlid fishes using an outline-based geometric morphometric approach combined with stable isotope indicators of macrohabitat and trophic niche. We then apply our method to a sample of extinct saurichthyid fishes, a highly diverse and near globally distributed group of actinopterygians occurring throughout the Triassic, to assess the utility of extant data to inform our understanding of ecomorphological evolution in extinct species flocks. A series of comparative methods were used to analyze shape data for 54 extant species of cichlids (N = 416), and 6 extinct species of saurichthyids (N = 44). Results provide evidence for a relationship between operculum shape and feeding ecology, a concentration in shape evolution towards present along with evidence for convergence in form, and significant correlation between the major axes of shape change and measures of gut length and body elongation. The operculum is one of few features that can be compared in extant and extinct groups, enabling reconstruction of phenotype-environment interactions and modes of evolutionary diversification in deep time.

Nutrient-dependent/pheromone-controlled adaptive evolution: a model

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James Vaughn Kohl

2013-06-01

Full Text Available Background: The prenatal migration of gonadotropin-releasing hormone (GnRH neurosecretory neurons allows nutrients and human pheromones to alter GnRH pulsatility, which modulates the concurrent maturation of the neuroendocrine, reproductive, and central nervous systems, thus influencing the development of ingestive behavior, reproductive sexual behavior, and other behaviors. Methods: This model details how chemical ecology drives adaptive evolution via: (1 ecological niche construction, (2 social niche construction, (3 neurogenic niche construction, and (4 socio-cognitive niche construction. This model exemplifies the epigenetic effects of olfactory/pheromonal conditioning, which alters genetically predisposed, nutrient-dependent, hormone-driven mammalian behavior and choices for pheromones that control reproduction via their effects on luteinizing hormone (LH and systems biology. Results: Nutrients are metabolized to pheromones that condition behavior in the same way that food odors condition behavior associated with food preferences. The epigenetic effects of olfactory/pheromonal input calibrate and standardize molecular mechanisms for genetically predisposed receptor-mediated changes in intracellular signaling and stochastic gene expression in GnRH neurosecretory neurons of brain tissue. For example, glucose and pheromones alter the hypothalamic secretion of GnRH and LH. A form of GnRH associated with sexual orientation in yeasts links control of the feedback loops and developmental processes required for nutrient acquisition, movement, reproduction, and the diversification of species from microbes to man. Conclusion: An environmental drive evolved from that of nutrient ingestion in unicellular organisms to that of pheromone-controlled socialization in insects. In mammals, food odors and pheromones cause changes in hormones such as LH, which has developmental affects on pheromone-controlled sexual behavior in nutrient-dependent reproductively

A Gene Gravity Model for the Evolution of Cancer Genomes: A Study of 3,000 Cancer Genomes across 9 Cancer Types

Science.gov (United States)

Lin, Chen-Ching; Zhao, Junfei; Jia, Peilin; Li, Wen-Hsiung; Zhao, Zhongming

2015-01-01

Cancer development and progression result from somatic evolution by an accumulation of genomic alterations. The effects of those alterations on the fitness of somatic cells lead to evolutionary adaptations such as increased cell proliferation, angiogenesis, and altered anticancer drug responses. However, there are few general mathematical models to quantitatively examine how perturbations of a single gene shape subsequent evolution of the cancer genome. In this study, we proposed the gene gravity model to study the evolution of cancer genomes by incorporating the genome-wide transcription and somatic mutation profiles of ~3,000 tumors across 9 cancer types from The Cancer Genome Atlas into a broad gene network. We found that somatic mutations of a cancer driver gene may drive cancer genome evolution by inducing mutations in other genes. This functional consequence is often generated by the combined effect of genetic and epigenetic (e.g., chromatin regulation) alterations. By quantifying cancer genome evolution using the gene gravity model, we identified six putative cancer genes (AHNAK, COL11A1, DDX3X, FAT4, STAG2, and SYNE1). The tumor genomes harboring the nonsynonymous somatic mutations in these genes had a higher mutation density at the genome level compared to the wild-type groups. Furthermore, we provided statistical evidence that hypermutation of cancer driver genes on inactive X chromosomes is a general feature in female cancer genomes. In summary, this study sheds light on the functional consequences and evolutionary characteristics of somatic mutations during tumorigenesis by propelling adaptive cancer genome evolution, which would provide new perspectives for cancer research and therapeutics. PMID:26352260

The purpose of adaptation.

Science.gov (United States)

Gardner, Andy

2017-10-06

A central feature of Darwin's theory of natural selection is that it explains the purpose of biological adaptation. Here, I: emphasize the scientific importance of understanding what adaptations are for, in terms of facilitating the derivation of empirically testable predictions; discuss the population genetical basis for Darwin's theory of the purpose of adaptation, with reference to Fisher's 'fundamental theorem of natural selection'; and show that a deeper understanding of the purpose of adaptation is achieved in the context of social evolution, with reference to inclusive fitness and superorganisms.

Use of Adaptive Laboratory Evolution To Discover Key Mutations Enabling Rapid Growth of Escherichia coli K-12 MG1655 on Glucose Minimal Medium

DEFF Research Database (Denmark)

LaCroix, Ryan A.; Sandberg, Troy E.; O'Brien, Edward J.

2015-01-01

Adaptive laboratory evolution (ALE) has emerged as an effective tool for scientific discovery and addressing biotechnological needs. Much of ALE's utility is derived from reproducibly obtained fitness increases. Identifying causal genetic changes and their combinatorial effects is challenging...

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)

On the contrast between Germanic and Romance negated quantifiers

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Robert Cirillo

2009-01-01

Full Text Available Universal quantifiers can be stranded in the manner described by Sportiche (1988, Giusti (1990 and Shlonsky (1991 in both the Romance and Germanic languages, but a negated universal quantifier can only be stranded in the Germanic languages. The goal of this paper is to show that this contrast between the Romance and the Germanic languages can be explained if one adapts the theory of sentential negation in Zeijlstra (2004 to constituent (quantifier negation. According to Zeijlstra’s theory, a negation marker in the Romance languages is the head of a NegP that dominates vP, whereas in the Germanic languages a negation marker is a maximal projection that occupies the specifier position of a verbal phrase. I will show that the non-occurrence of stranded negated quantifiers in the Romance languages follows from the fact that negation markers in the Romance languages are highly positioned syntactic heads.

Adaptive Differential Evolution Approach for Constrained Economic Power Dispatch with Prohibited Operating Zones

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Abdellatif HAMOUDA

2011-12-01

Full Text Available Economic power dispatch (EPD is one of the main tools for optimal operation and planning of modern power systems. To solve effectively the EPD problem, most of the conventional calculus methods rely on the assumption that the fuel cost characteristic of a generating unit is a continuous and convex function, resulting in inaccurate dispatch. This paper presents the design and application of efficient adaptive differential evolution (ADE algorithm for the solution of the economic power dispatch problem, where the non-convex characteristics of the generators, such us prohibited operating zones and ramp rate limits of the practical generator operation are considered. The 26 bus benchmark test system with 6 units having prohibited operating zones and ramp rate limits was used for testing and validation purposes. The results obtained demonstrate the effectiveness of the proposed method for solving the non-convex economic dispatch problem.

Evolution of phenotypic clusters through competition and local adaptation along an environmental gradient.

Science.gov (United States)

Leimar, Olof; Doebeli, Michael; Dieckmann, Ulf

2008-04-01

We have analyzed the evolution of a quantitative trait in populations that are spatially extended along an environmental gradient, with gene flow between nearby locations. In the absence of competition, there is stabilizing selection toward a locally best-adapted trait that changes gradually along the gradient. According to traditional ideas, gradual spatial variation in environmental conditions is expected to lead to gradual variation in the evolved trait. A contrasting possibility is that the trait distribution instead breaks up into discrete clusters. Doebeli and Dieckmann (2003) argued that competition acting locally in trait space and geographical space can promote such clustering. We have investigated this possibility using deterministic population dynamics for asexual populations, analyzing our model numerically and through an analytical approximation. We examined how the evolution of clusters is affected by the shape of competition kernels, by the presence of Allee effects, and by the strength of gene flow along the gradient. For certain parameter ranges clustering was a robust outcome, and for other ranges there was no clustering. Our analysis shows that the shape of competition kernels is important for clustering: the sign structure of the Fourier transform of a competition kernel determines whether the kernel promotes clustering. Also, we found that Allee effects promote clustering, whereas gene flow can have a counteracting influence. In line with earlier findings, we could demonstrate that phenotypic clustering was favored by gradients of intermediate slope.

Evolutionary Medicine and Future of Humanity: Will Evolution Have the Final Word?

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Maciej Henneberg

2013-06-01

Full Text Available Evolutionary medicine in its classical form assumes that since cultural evolution is faster than biological evolution, ailments of modern people are a result of mismatch between adaptations to the past environments and current situations. A core principle is that we, humans, having evolved for millions of years in a specific natural environment (environment of evolutionary adaptation EEA are biologically adapted to this past environment and the ancient lifestyle. This adaptation to the past produces major mismatch of our bodies with the present, highly anthropic and thus “artificial” living conditions. This article provides two areas of possible future evolution, diet and physical activity levels which have been dramatically altered in industrialised societies. Consequently, micro-evolution is an on-going process.

The many shades of prion strain adaptation.

Science.gov (United States)

Baskakov, Ilia V

2014-01-01

In several recent studies transmissible prion disease was induced in animals by inoculation with recombinant prion protein amyloid fibrils produced in vitro. Serial transmission of amyloid fibrils gave rise to a new class of prion strains of synthetic origin. Gradual transformation of disease phenotypes and PrP(Sc) properties was observed during serial transmission of synthetic prions, a process that resembled the phenomenon of prion strain adaptation. The current article discusses the remarkable parallels between phenomena of prion strain adaptation that accompanies cross-species transmission and the evolution of synthetic prions occurring within the same host. Two alternative mechanisms underlying prion strain adaptation and synthetic strain evolution are discussed. The current article highlights the complexity of the prion transmission barrier and strain adaptation and proposes that the phenomenon of prion adaptation is more common than previously thought.

Time in Redox Adaptation Processes: From Evolution to Hormesis

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Mireille M. J. P. E. Sthijns

2016-09-01

Full Text Available Life on Earth has to adapt to the ever changing environment. For example, due to introduction of oxygen in the atmosphere, an antioxidant network evolved to cope with the exposure to oxygen. The adaptive mechanisms of the antioxidant network, specifically the glutathione (GSH system, are reviewed with a special focus on the time. The quickest adaptive response to oxidative stress is direct enzyme modification, increasing the GSH levels or activating the GSH-dependent protective enzymes. After several hours, a hormetic response is seen at the transcriptional level by up-regulating Nrf2-mediated expression of enzymes involved in GSH synthesis. In the long run, adaptations occur at the epigenetic and genomic level; for example, the ability to synthesize GSH by phototrophic bacteria. Apparently, in an adaptive hormetic response not only the dose or the compound, but also time, should be considered. This is essential for targeted interventions aimed to prevent diseases by successfully coping with changes in the environment e.g., oxidative stress.

The king cobra genome reveals dynamic gene evolution and adaptation in the snake venom system

Science.gov (United States)

Vonk, Freek J.; Casewell, Nicholas R.; Henkel, Christiaan V.; Heimberg, Alysha M.; Jansen, Hans J.; McCleary, Ryan J. R.; Kerkkamp, Harald M. E.; Vos, Rutger A.; Guerreiro, Isabel; Calvete, Juan J.; Wüster, Wolfgang; Woods, Anthony E.; Logan, Jessica M.; Harrison, Robert A.; Castoe, Todd A.; de Koning, A. P. Jason; Pollock, David D.; Yandell, Mark; Calderon, Diego; Renjifo, Camila; Currier, Rachel B.; Salgado, David; Pla, Davinia; Sanz, Libia; Hyder, Asad S.; Ribeiro, José M. C.; Arntzen, Jan W.; van den Thillart, Guido E. E. J. M.; Boetzer, Marten; Pirovano, Walter; Dirks, Ron P.; Spaink, Herman P.; Duboule, Denis; McGlinn, Edwina; Kini, R. Manjunatha; Richardson, Michael K.

2013-01-01

Snakes are limbless predators, and many species use venom to help overpower relatively large, agile prey. Snake venoms are complex protein mixtures encoded by several multilocus gene families that function synergistically to cause incapacitation. To examine venom evolution, we sequenced and interrogated the genome of a venomous snake, the king cobra (Ophiophagus hannah), and compared it, together with our unique transcriptome, microRNA, and proteome datasets from this species, with data from other vertebrates. In contrast to the platypus, the only other venomous vertebrate with a sequenced genome, we find that snake toxin genes evolve through several distinct co-option mechanisms and exhibit surprisingly variable levels of gene duplication and directional selection that correlate with their functional importance in prey capture. The enigmatic accessory venom gland shows a very different pattern of toxin gene expression from the main venom gland and seems to have recruited toxin-like lectin genes repeatedly for new nontoxic functions. In addition, tissue-specific microRNA analyses suggested the co-option of core genetic regulatory components of the venom secretory system from a pancreatic origin. Although the king cobra is limbless, we recovered coding sequences for all Hox genes involved in amniote limb development, with the exception of Hoxd12. Our results provide a unique view of the origin and evolution of snake venom and reveal multiple genome-level adaptive responses to natural selection in this complex biological weapon system. More generally, they provide insight into mechanisms of protein evolution under strong selection. PMID:24297900

Genome-wide signatures of complex introgression and adaptive evolution in the big cats

Science.gov (United States)

Figueiró, Henrique V.; Li, Gang; Trindade, Fernanda J.; Assis, Juliana; Pais, Fabiano; Fernandes, Gabriel; Santos, Sarah H. D.; Hughes, Graham M.; Komissarov, Aleksey; Antunes, Agostinho; Trinca, Cristine S.; Rodrigues, Maíra R.; Linderoth, Tyler; Bi, Ke; Silveira, Leandro; Azevedo, Fernando C. C.; Kantek, Daniel; Ramalho, Emiliano; Brassaloti, Ricardo A.; Villela, Priscilla M. S.; Nunes, Adauto L. V.; Teixeira, Rodrigo H. F.; Morato, Ronaldo G.; Loska, Damian; Saragüeta, Patricia; Gabaldón, Toni; Teeling, Emma C.; O’Brien, Stephen J.; Nielsen, Rasmus; Coutinho, Luiz L.; Oliveira, Guilherme; Murphy, William J.; Eizirik, Eduardo

2017-01-01

The great cats of the genus Panthera comprise a recent radiation whose evolutionary history is poorly understood. Their rapid diversification poses challenges to resolving their phylogeny while offering opportunities to investigate the historical dynamics of adaptive divergence. We report the sequence, de novo assembly, and annotation of the jaguar (Panthera onca) genome, a novel genome sequence for the leopard (Panthera pardus), and comparative analyses encompassing all living Panthera species. Demographic reconstructions indicated that all of these species have experienced variable episodes of population decline during the Pleistocene, ultimately leading to small effective sizes in present-day genomes. We observed pervasive genealogical discordance across Panthera genomes, caused by both incomplete lineage sorting and complex patterns of historical interspecific hybridization. We identified multiple signatures of species-specific positive selection, affecting genes involved in craniofacial and limb development, protein metabolism, hypoxia, reproduction, pigmentation, and sensory perception. There was remarkable concordance in pathways enriched in genomic segments implicated in interspecies introgression and in positive selection, suggesting that these processes were connected. We tested this hypothesis by developing exome capture probes targeting ~19,000 Panthera genes and applying them to 30 wild-caught jaguars. We found at least two genes (DOCK3 and COL4A5, both related to optic nerve development) bearing significant signatures of interspecies introgression and within-species positive selection. These findings indicate that post-speciation admixture has contributed genetic material that facilitated the adaptive evolution of big cat lineages. PMID:28776029

Adaptive evolution of the symbiotic gene NORK is not correlated with shifts of rhizobial specificity in the genus Medicago

Directory of Open Access Journals (Sweden)

Ronfort Joëlle

2007-11-01

Full Text Available Abstract Background The NODULATION RECEPTOR KINASE (NORK gene encodes a Leucine-Rich Repeat (LRR-containing receptor-like protein and controls the infection by symbiotic rhizobia and endomycorrhizal fungi in Legumes. The occurrence of numerous amino acid changes driven by directional selection has been reported in this gene, using a limited number of messenger RNA sequences, but the functional reason of these changes remains obscure. The Medicago genus, where changes in rhizobial associations have been previously examined, is a good model to test whether the evolution of NORK is influenced by rhizobial interactions. Results We sequenced a region of 3610 nucleotides (encoding a 392 amino acid-long region of the NORK protein in 32 Medicago species. We confirm that positive selection in NORK has occurred within the Medicago genus and find that the amino acid positions targeted by selection occur in sites outside of solvent-exposed regions in LRRs, and other sites in the N-terminal region of the protein. We tested if branches of the Medicago phylogeny where changes of rhizobial symbionts occurred displayed accelerated rates of amino acid substitutions. Only one branch out of five tested, leading to M. noeana, displays such a pattern. Among other branches, the most likely for having undergone positive selection is not associated with documented shift of rhizobial specificity. Conclusion Adaptive changes in the sequence of the NORK receptor have involved the LRRs, but targeted different sites than in most previous studies of LRR proteins evolution. The fact that positive selection in NORK tends not to be associated to changes in rhizobial specificity indicates that this gene was probably not involved in evolving rhizobial preferences. Other explanations (e.g. coevolutionary arms race must be tested to explain the adaptive evolution of NORK.

Quantifying the Variability of CH4 Emissions from Pan-Arctic Lakes with Lake Biogeochemical and Landscape Evolution Models

Science.gov (United States)

Tan, Z.; Zhuang, Q.

2014-12-01

Recent studies in the arctic and subarctic show that CH4 emissions from pan-arctic lakes are playing much more significant roles in the regional carbon cycling than previously estimated. Permafrost thawing due to pronounced warming at northern high latitudes affects lake morphology, changing its CH4 emissions. Thermokarst can enlarge the extent of artic lakes, exposing stable ancient carbon buried in the permafrost zone for degradation and changing a previously known carbon sink to a large carbon source. In some areas, the thawing of subarctic discontinuous and isolated permafrost can diminish thermokarst lakes. To date, few models have considered these important hydrological and biogeochemical processes to provide adequate estimation of CH4 emissions from these lakes. To fill this gap, we have developed a process-based climate-sensitive lake biogeochemical model and a landscape evolution model, which have been applied to quantify the state and variability of CH4 emissions from this freshwater system. Site-level experiments show the models are capable to capture the spatial and temporal variability of CH4 emissions from lakes across Siberia and Alaska. With the lake biogeochemical model solely, we estimate that the magnitude of CH4 emissions from lakes is 13.2 Tg yr-1 in the north of 60 ºN at present, which is on the same order of CH4 emissions from northern high-latitude wetlands. The maximum increment is 11.8 Tg CH4 yr-1 by the end of the 21st century when the worst warming scenario is assumed. We expect the landscape evolution model will improve the existing estimates.

The genetic basis of local adaptation for pathogenic fungi in agricultural ecosystems.

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Croll, Daniel; McDonald, Bruce A

2017-04-01

Local adaptation plays a key role in the evolutionary trajectory of host-pathogen interactions. However, the genetic architecture of local adaptation in host-pathogen systems is poorly understood. Fungal plant pathogens in agricultural ecosystems provide highly tractable models to quantify phenotypes and map traits to corresponding genomic loci. The outcome of crop-pathogen interactions is thought to be governed largely by gene-for-gene interactions. However, recent studies showed that virulence can be governed by quantitative trait loci and that many abiotic factors contribute to the outcome of the interaction. After introducing concepts of local adaptation and presenting examples from wild plant pathosystems, we focus this review on a major pathogen of wheat, Zymoseptoria tritici, to show how a multitude of traits can affect local adaptation. Zymoseptoria tritici adapted to different thermal environments across its distribution range, indicating that thermal adaptation may limit effective dispersal to different climates. The application of fungicides led to the rapid evolution of multiple, independent resistant populations. The degree of colony melanization showed strong pleiotropic effects with other traits, including trade-offs with colony growth rates and fungicide sensitivity. The success of the pathogen on its host can be assessed quantitatively by counting pathogen reproductive structures and measuring host damage based on necrotic lesions. Interestingly, these two traits can be weakly correlated and depend both on host and pathogen genotypes. Quantitative trait mapping studies showed that the genetic architecture of locally adapted traits varies from single loci with large effects to many loci with small individual effects. We discuss how local adaptation could hinder or accelerate the development of epidemics in agricultural ecosystems. © 2016 John Wiley & Sons Ltd.

Convergent evolution and divergent selection: lizards at the White Sands ecotone.

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Rosenblum, Erica Bree

2006-01-01

Ecological transition zones, where organismal phenotypes result from a delicate balance between selection and migration, highlight the interplay of local adaptation and gene flow. Here, I study the response of an entire species assemblage to natural selection across a common ecotone. Three lizard species, distributed along a dramatic environmental gradient in substrate color, display convergent adaptation of blanched coloration on the gypsum dunes of White Sands National Monument. I investigate the role of gene flow in modulating phenotypic response to selection by quantifying color variation and genetic variation across the ecotone. I find species differences in degree of background matching and in genetic connectivity of populations across the ecotone. Differences among species in phenotypic response to selection scale precisely to levels of genetic isolation. Species with higher levels of gene flow across the ecotone exhibit less dramatic responses to selection. Results also reveal a strong signal of ecologically mediated divergence for White Sands lizards. For all species, phenotypic variation is better explained by habitat similarity than genetic similarity. Convergent evolution of blanched coloration at White Sands clearly reflects the action of strong divergent selection; however, adaptive response appears to be modulated by gene flow and demographic history and can be predicted by divergence-with-gene-flow models.

[Stress-induced cellular adaptive mutagenesis].

Science.gov (United States)

Zhu, Linjiang; Li, Qi

2014-04-01

The adaptive mutations exist widely in the evolution of cells, such as antibiotic resistance mutations of pathogenic bacteria, adaptive evolution of industrial strains, and cancerization of human somatic cells. However, how these adaptive mutations are generated is still controversial. Based on the mutational analysis models under the nonlethal selection conditions, stress-induced cellular adaptive mutagenesis is proposed as a new evolutionary viewpoint. The hypothetic pathway of stress-induced mutagenesis involves several intracellular physiological responses, including DNA damages caused by accumulation of intracellular toxic chemicals, limitation of DNA MMR (mismatch repair) activity, upregulation of general stress response and activation of SOS response. These responses directly affect the accuracy of DNA replication from a high-fidelity manner to an error-prone one. The state changes of cell physiology significantly increase intracellular mutation rate and recombination activity. In addition, gene transcription under stress condition increases the instability of genome in response to DNA damage, resulting in transcription-associated DNA mutagenesis. In this review, we summarize these two molecular mechanisms of stress-induced mutagenesis and transcription-associated DNA mutagenesis to help better understand the mechanisms of adaptive mutagenesis.

Monitoring adaptive genetic responses to environmental change

DEFF Research Database (Denmark)

Hansen, M.M.; Olivieri, I.; Waller, D.M.

2012-01-01

Widespread environmental changes including climate change, selective harvesting and landscape alterations now greatly affect selection regimes for most organisms. How animals and plants can adapt to these altered environments via contemporary evolution is thus of strong interest. We discuss how...... for selection and establishing clear links between genetic and environmental change. We then review a few exemplary studies that explore adaptive responses to climate change in Drosophila, selective responses to hunting and fishing, and contemporary evolution in Daphnia using resurrected resting eggs. We...

Quantifying nutrient export and deposition with a dynamic landscape evolution model for the lake Bolsena watershed, Italy

Science.gov (United States)

Pelorosso, Raffaele; Temme, Arnoud; Gobattoni, Federica; Leone, Antonio

2010-05-01

other hand, recent researches have been improving landscape evolution simulation models.. One such model, LAPSUS (LandscApe ProcesS modelling at mUlti-dimensions and Scales, Schoorl et al.,2002; Temme et al., 2009) has been applied to the Lake Bolsena watershed in Lazio, Italy. LAPSUS takes into account erosion as a naturally occurring process in landscape evolution and shapes landscapes by both erosion and deposition allowing interactions at different spatial and temporal resolutions and extents. An integrated approach to quantify nutrient export and deposition at catchment scale is presented and discussed here coupling such a dynamic landscape evolution model (LAPSUS) with the characteristic transport equations for nutrients.

Epistasis increases the rate of conditionally neutral substitution in an adapting population.

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Draghi, Jeremy A; Parsons, Todd L; Plotkin, Joshua B

2011-04-01

Kimura observed that the rate of neutral substitution should equal the neutral mutation rate. This classic result is central to our understanding of molecular evolution, and it continues to influence phylogenetics, genomics, and the interpretation of evolution experiments. By demonstrating that neutral mutations substitute at a rate independent of population size and selection at linked sites, Kimura provided an influential justification for the idea of a molecular clock and emphasized the importance of genetic drift in shaping molecular evolution. But when epistasis among sites is common, as numerous empirical studies suggest, do neutral mutations substitute according to Kimura's expectation? Here we study simulated, asexual populations of RNA molecules, and we observe that conditionally neutral mutations--i.e., mutations that do not alter the fitness of the individual in which they arise, but that may alter the fitness effects of subsequent mutations--substitute much more often than expected while a population is adapting. We quantify these effects using a simple population-genetic model that elucidates how the substitution rate at conditionally neutral sites depends on the population size, mutation rate, strength of selection, and prevalence of epistasis. We discuss the implications of these results for our understanding of the molecular clock, and for the interpretation of molecular variation in laboratory and natural populations.

Predicting adaptive phenotypes from multilocus genotypes in Sitka spruce (Picea sitchensis) using random forest.

Science.gov (United States)

Holliday, Jason A; Wang, Tongli; Aitken, Sally

2012-09-01

Climate is the primary driver of the distribution of tree species worldwide, and the potential for adaptive evolution will be an important factor determining the response of forests to anthropogenic climate change. Although association mapping has the potential to improve our understanding of the genomic underpinnings of climatically relevant traits, the utility of adaptive polymorphisms uncovered by such studies would be greatly enhanced by the development of integrated models that account for the phenotypic effects of multiple single-nucleotide polymorphisms (SNPs) and their interactions simultaneously. We previously reported the results of association mapping in the widespread conifer Sitka spruce (Picea sitchensis). In the current study we used the recursive partitioning algorithm 'Random Forest' to identify optimized combinations of SNPs to predict adaptive phenotypes. After adjusting for population structure, we were able to explain 37% and 30% of the phenotypic variation, respectively, in two locally adaptive traits--autumn budset timing and cold hardiness. For each trait, the leading five SNPs captured much of the phenotypic variation. To determine the role of epistasis in shaping these phenotypes, we also used a novel approach to quantify the strength and direction of pairwise interactions between SNPs and found such interactions to be common. Our results demonstrate the power of Random Forest to identify subsets of markers that are most important to climatic adaptation, and suggest that interactions among these loci may be widespread.

Protein domain evolution is associated with reproductive diversification and adaptive radiation in the genus Eucalyptus.

Science.gov (United States)

Kersting, Anna R; Mizrachi, Eshchar; Bornberg-Bauer, Erich; Myburg, Alexander A

2015-06-01

Eucalyptus is a pivotal genus within the rosid order Myrtales with distinct geographic history and adaptations. Comparative analysis of protein domain evolution in the newly sequenced Eucalyptus grandis genome and other rosid lineages sheds light on the adaptive mechanisms integral to the success of this genus of woody perennials. We reconstructed the ancestral domain content to elucidate the gain, loss and expansion of protein domains and domain arrangements in Eucalyptus in the context of rosid phylogeny. We used functional gene ontology (GO) annotation of genes to investigate the possible biological and evolutionary consequences of protein domain expansion. We found that protein modulation within the angiosperms occurred primarily on the level of expansion of certain domains and arrangements. Using RNA-Seq data from E. grandis, we showed that domain expansions have contributed to tissue-specific expression of tandemly duplicated genes. Our results indicate that tandem duplication of genes, a key feature of the Eucalyptus genome, has played an important role in the expansion of domains, particularly in proteins related to the specialization of reproduction and biotic and abiotic interactions affecting root and floral biology, and that tissue-specific expression of proteins with expanded domains has facilitated subfunctionalization in domain families. © 2014 University of Pretoria New Phytologist © 2014 New Phytologist Trust.

Information-theoretic metamodel of organizational evolution

Science.gov (United States)

Sepulveda, Alfredo

2011-12-01

Social organizations are abstractly modeled by holarchies---self-similar connected networks---and intelligent complex adaptive multiagent systems---large networks of autonomous reasoning agents interacting via scaled processes. However, little is known of how information shapes evolution in such organizations, a gap that can lead to misleading analytics. The research problem addressed in this study was the ineffective manner in which classical model-predict-control methods used in business analytics attempt to define organization evolution. The purpose of the study was to construct an effective metamodel for organization evolution based on a proposed complex adaptive structure---the info-holarchy. Theoretical foundations of this study were holarchies, complex adaptive systems, evolutionary theory, and quantum mechanics, among other recently developed physical and information theories. Research questions addressed how information evolution patterns gleamed from the study's inductive metamodel more aptly explained volatility in organization. In this study, a hybrid grounded theory based on abstract inductive extensions of information theories was utilized as the research methodology. An overarching heuristic metamodel was framed from the theoretical analysis of the properties of these extension theories and applied to business, neural, and computational entities. This metamodel resulted in the synthesis of a metaphor for, and generalization of organization evolution, serving as the recommended and appropriate analytical tool to view business dynamics for future applications. This study may manifest positive social change through a fundamental understanding of complexity in business from general information theories, resulting in more effective management.

Dual phase evolution

CERN Document Server

Green, David G; Abbass, Hussein A

2014-01-01

This book explains how dual phase evolution operates in all these settings and provides a detailed treatment of the subject. The authors discuss the theoretical foundations for the theory, how it relates to other phase transition phenomena and its advantages in evolutionary computation and complex adaptive systems. The book provides methods and techniques to use this concept for problem solving. Dual phase evolution concerns systems that evolve via repeated phase shifts in the connectivity of their elements. It occurs in vast range of settings, including natural systems (species evolution, landscape ecology, geomorphology), socio-economic systems (social networks) and in artificial systems (annealing, evolutionary computing).

Carbon source utilization patterns of Bacillus simplex ecotypes do not reflect their adaptation to ecologically divergent slopes in 'Evolution Canyon', Israel.

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Sikorski, Johannes; Pukall, Rüdiger; Stackebrandt, Erko

2008-10-01

The 'Evolution Canyons' I and II in Israel are model habitats to study adaptation and speciation of bacteria in the environment. These canyons represent similar ecological replicates, separated by 40 km, with a strongly sun-exposed and hot 'African' south-facing slope (SFS) vs. a cooler and mesic-lush 'European' north-facing slope (NFS). Previously, among 131 Bacillus simplex isolates, distinct genetic lineages (ecotypes), each specific for either SFS or NFS, were identified, suggesting a temperature-driven slope-specific adaptation. Here, we asked whether the ecological heterogeneity of SFS vs. NFS also affected carbon utilization abilities, as determined using the Biolog assay. Contrary to expectation, a correlation between substrate utilization patterns and the ecological origin of strains was not found. Rather, the patterns split according to the two major phylogenetic lineages each of which contain SFS and NFS ecotypes. We conclude that traits related to the general energy metabolism, as far as assessed here, are neither shaped by the major abiotic features of 'Evolution Canyon', namely solar radiation, temperature, and drought, nor by the soil characteristics. We further conclude that some traits diverge rather neutrally from each other, whereas other, more environmentally related traits are shaped by natural selection and show evolutionary convergence.

Urban Evolution: The Role of Water

Directory of Open Access Journals (Sweden)

Sujay S. Kaushal

2015-07-01

Full Text Available The structure, function, and services of urban ecosystems evolve over time scales from seconds to centuries as Earth’s population grows, infrastructure ages, and sociopolitical values alter them. In order to systematically study changes over time, the concept of “urban evolution” was proposed. It allows urban planning, management, and restoration to move beyond reactive management to predictive management based on past observations of consistent patterns. Here, we define and review a glossary of core concepts for studying urban evolution, which includes the mechanisms of urban selective pressure and urban adaptation. Urban selective pressure is an environmental or societal driver contributing to urban adaptation. Urban adaptation is the sequential process by which an urban structure, function, or services becomes more fitted to its changing environment or human choices. The role of water is vital to driving urban evolution as demonstrated by historical changes in drainage, sewage flows, hydrologic pulses, and long-term chemistry. In the current paper, we show how hydrologic traits evolve across successive generations of urban ecosystems via shifts in selective pressures and adaptations over time. We explore multiple empirical examples including evolving: (1 urban drainage from stream burial to stormwater management; (2 sewage flows and water quality in response to wastewater treatment; (3 amplification of hydrologic pulses due to the interaction between urbanization and climate variability; and (4 salinization and alkalinization of fresh water due to human inputs and accelerated weathering. Finally, we propose a new conceptual model for the evolution of urban waters from the Industrial Revolution to the present day based on empirical trends and historical information. Ultimately, we propose that water itself is a critical driver of urban evolution that forces urban adaptation, which transforms the structure, function, and services of urban

Resource-adaptive cognitive processes

CERN Document Server

Crocker, Matthew W

2010-01-01

This book investigates the adaptation of cognitive processes to limited resources. The central topics of this book are heuristics considered as results of the adaptation to resource limitations, through natural evolution in the case of humans, or through artificial construction in the case of computational systems; the construction and analysis of resource control in cognitive processes; and an analysis of resource-adaptivity within the paradigm of concurrent computation. The editors integrated the results of a collaborative 5-year research project that involved over 50 scientists. After a mot

Practical splitting methods for the adaptive integration of nonlinear evolution equations. Part I: Construction of optimized schemes and pairs of schemes

KAUST Repository

Auzinger, Winfried; Hofstä tter, Harald; Ketcheson, David I.; Koch, Othmar

2016-01-01

We present a number of new contributions to the topic of constructing efficient higher-order splitting methods for the numerical integration of evolution equations. Particular schemes are constructed via setup and solution of polynomial systems for the splitting coefficients. To this end we use and modify a recent approach for generating these systems for a large class of splittings. In particular, various types of pairs of schemes intended for use in adaptive integrators are constructed.

Practical splitting methods for the adaptive integration of nonlinear evolution equations. Part I: Construction of optimized schemes and pairs of schemes

KAUST Repository

Auzinger, Winfried

2016-07-28

We present a number of new contributions to the topic of constructing efficient higher-order splitting methods for the numerical integration of evolution equations. Particular schemes are constructed via setup and solution of polynomial systems for the splitting coefficients. To this end we use and modify a recent approach for generating these systems for a large class of splittings. In particular, various types of pairs of schemes intended for use in adaptive integrators are constructed.

The geography of sex-specific selection, local adaptation, and sexual dimorphism.

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Connallon, Tim

2015-09-01

Local adaptation and sexual dimorphism are iconic evolutionary scenarios of intraspecific adaptive differentiation in the face of gene flow. Although theory has traditionally considered local adaptation and sexual dimorphism as conceptually distinct processes, emerging data suggest that they often act concurrently during evolutionary diversification. Here, I merge theories of local adaptation in space and sex-specific adaptation over time, and show that their confluence yields several new predictions about the roles of context-specific selection, migration, and genetic correlations, in adaptive diversification. I specifically revisit two influential predictions from classical studies of clinal adaptation and sexual dimorphism: (1) that local adaptation should decrease with distance from the species' range center and (2) that opposing directional selection between the sexes (sexual antagonism) should inevitably accompany the evolution of sexual dimorphism. I show that both predictions can break down under clinally varying selection. First, the geography of local adaptation can be sexually dimorphic, with locations of relatively high local adaptation differing profoundly between the sexes. Second, the intensity of sexual antagonism varies across the species' range, with subpopulations near the range center representing hotspots for antagonistic selection. The results highlight the context-dependent roles of migration versus sexual conflict as primary constraints to adaptive diversification. © 2015 The Author(s). Evolution © 2015 The Society for the Study of Evolution.

Natural selection causes adaptive genetic resistance in wild emmer wheat against powdery mildew at "Evolution Canyon" microsite, Mt. Carmel, Israel.

Science.gov (United States)

Yin, Huayan; Ben-Abu, Yuval; Wang, Hongwei; Li, Anfei; Nevo, Eviatar; Kong, Lingrang

2015-01-01

"Evolution Canyon" (ECI) at Lower Nahal Oren, Mount Carmel, Israel, is an optimal natural microscale model for unraveling evolution in action highlighting the basic evolutionary processes of adaptation and speciation. A major model organism in ECI is wild emmer, Triticum dicoccoides, the progenitor of cultivated wheat, which displays dramatic interslope adaptive and speciational divergence on the tropical-xeric "African" slope (AS) and the temperate-mesic "European" slope (ES), separated on average by 250 m. We examined 278 single sequence repeats (SSRs) and the phenotype diversity of the resistance to powdery mildew between the opposite slopes. Furthermore, 18 phenotypes on the AS and 20 phenotypes on the ES, were inoculated by both Bgt E09 and a mixture of powdery mildew races. In the experiment of genetic diversity, very little polymorphism was identified intra-slope in the accessions from both the AS or ES. By contrast, 148 pairs of SSR primers (53.23%) amplified polymorphic products between the phenotypes of AS and ES. There are some differences between the two wild emmer wheat genomes and the inter-slope SSR polymorphic products between genome A and B. Interestingly, all wild emmer types growing on the south-facing slope (SFS=AS) were susceptible to a composite of Blumeria graminis, while the ones growing on the north-facing slope (NFS=ES) were highly resistant to Blumeria graminis at both seedling and adult stages. Remarkable inter-slope evolutionary divergent processes occur in wild emmer wheat, T. dicoccoides at EC I, despite the shot average distance of 250 meters. The AS, a dry and hot slope, did not develop resistance to powdery mildew, whereas the ES, a cool and humid slope, did develop resistance since the disease stress was strong there. This is a remarkable demonstration in host-pathogen interaction on how resistance develops when stress causes an adaptive result at a micro-scale distance.

What kind of memory has evolution wrought? Introductory article for the special issue of memory: adaptive memory: the emergence and nature of proximate mechanisms.

Science.gov (United States)

Otgaar, Henry; Howe, Mark L

2014-01-01

It is without question that our memory system evolved through a process of natural selection. However, basic research into the evolutionary foundations of memory has begun in earnest only recently. This is quite peculiar as the majority, perhaps even all, of memory research relates to whether memory is adaptive or not. In this Special Issue of Memory we have assembled a variety of papers that represent the cutting edge in research on the evolution of memory. These papers are centred on issues about the ultimate and proximate explanations of memory, the development of the adaptive functions of memory, as well as the positive consequences that arise from the current evolutionary form that our memory has taken. In this introductory article we briefly outline these different areas and indicate why they are vital for a more complete theory of memory. Further we argue that, by adopting a more applied stance in the area of the evolution of memory, one of the many future directions in this field could be a new branch of psychology that addresses questions in evolutionary legal psychology.

Adaptive evolution of sexual systems in pedunculate barnacles

DEFF Research Database (Denmark)

Yusa, Yoichi; Yoshikawa, Mai; Kitaura, Jun

2012-01-01

(androdioecy), and coexistence of dwarf males and females (dioecy). Here, we report the first phylogenetically controlled test of the hypothesis that the ultimate cause of the diverse sexual systems and presence of dwarf males in this group is limited mating opportunities for non-dwarf individuals, owing...... to mating in small groups. Within the pedunculate barnacle phylogeny, dwarf males and females have evolved repeatedly. Females are more likely to evolve in androdioecious than hermaphroditic populations, suggesting that evolution of dwarf males has preceded that of females in pedunculates. Both dwarf males...... and females are associated with a higher proportion of solitary individuals in the population, corroborating the hypothesis that limited mating opportunities have favoured evolution of these diverse sexual systems, which have puzzled biologists since Darwin....

Selection towards different adaptive optima drove the early diversification of locomotor phenotypes in the radiation of Neotropical geophagine cichlids.

Science.gov (United States)

Astudillo-Clavijo, Viviana; Arbour, Jessica H; López-Fernández, Hernán

2015-05-01

Simpson envisaged a conceptual model of adaptive radiation in which lineages diversify into "adaptive zones" within a macroevolutionary adaptive landscape. However, only a handful of studies have empirically investigated this adaptive landscape and its consequences for our interpretation of the underlying mechanisms of phenotypic evolution. In fish radiations the evolution of locomotor phenotypes may represent an important dimension of ecomorphological diversification given the implications of locomotion for feeding and habitat use. Neotropical geophagine cichlids represent a newly identified adaptive radiation and provide a useful system for studying patterns of locomotor diversification and the implications of selective constraints on phenotypic divergence in general. We use multivariate ordination, models of phenotypic evolution and posterior predictive approaches to investigate the macroevolutionary adaptive landscape and test for evidence of early divergence of locomotor phenotypes in Geophagini. The evolution of locomotor phenotypes was characterized by selection towards at least two distinct adaptive peaks and the early divergence of modern morphological disparity. One adaptive peak included the benthic and epibenthic invertivores and was characterized by fishes with deep, laterally compressed bodies that optimize precise, slow-swimming manoeuvres. The second adaptive peak resulted from a shift in adaptive optima in the species-rich ram-feeding/rheophilic Crenicichla-Teleocichla clade and was characterized by species with streamlined bodies that optimize fast starts and rapid manoeuvres. Evolutionary models and posterior predictive approaches favoured an early shift to a new adaptive peak over decreasing rates of evolution as the underlying process driving the early divergence of locomotor phenotypes. The influence of multiple adaptive peaks on the divergence of locomotor phenotypes in Geophagini is compatible with the expectations of an ecologically driven

Convergent evolution of the genomes of marine mammals

Science.gov (United States)

Foote, Andrew D.; Liu, Yue; Thomas, Gregg W.C.; Vinař, Tomáš; Alföldi, Jessica; Deng, Jixin; Dugan, Shannon; van Elk, Cornelis E.; Hunter, Margaret; Joshi, Vandita; Khan, Ziad; Kovar, Christie; Lee, Sandra L.; Lindblad-Toh, Kerstin; Mancia, Annalaura; Nielsen, Rasmus; Qin, Xiang; Qu, Jiaxin; Raney, Brian J.; Vijay, Nagarjun; Wolf, Jochen B. W.; Hahn, Matthew W.; Muzny, Donna M.; Worley, Kim C.; Gilbert, M. Thomas P.; Gibbs, Richard A.

2015-01-01

Marine mammals from different mammalian orders share several phenotypic traits adapted to the aquatic environment and therefore represent a classic example of convergent evolution. To investigate convergent evolution at the genomic level, we sequenced and performed de novo assembly of the genomes of three species of marine mammals (the killer whale, walrus and manatee) from three mammalian orders that share independently evolved phenotypic adaptations to a marine existence. Our comparative genomic analyses found that convergent amino acid substitutions were widespread throughout the genome and that a subset of these substitutions were in genes evolving under positive selection and putatively associated with a marine phenotype. However, we found higher levels of convergent amino acid substitutions in a control set of terrestrial sister taxa to the marine mammals. Our results suggest that, whereas convergent molecular evolution is relatively common, adaptive molecular convergence linked to phenotypic convergence is comparatively rare.

Adaptation hypothesis of biological efficiency of ionizing radiation

International Nuclear Information System (INIS)

Kudritskij, Yu.K.; Georgievskij, A.B.; Karpov, V.I.

1992-01-01

Adaptation hypothesis of biological efficiency of ionizing radiation is based on acknowledgement of invariance of fundamental laws and principles of biology related to unity of biota and media, evolution and adaptation for radiobiology. The basic arguments for adaptation hypothesis validity, its correspondence to the requirements imposed on scientific hypothes are presented

Ready or Not: Microbial Adaptive Responses in Dynamic Symbiosis Environments.

Science.gov (United States)

Cao, Mengyi; Goodrich-Blair, Heidi

2017-08-01

In mutually beneficial and pathogenic symbiotic associations, microbes must adapt to the host environment for optimal fitness. Both within an individual host and during transmission between hosts, microbes are exposed to temporal and spatial variation in environmental conditions. The phenomenon of phenotypic variation, in which different subpopulations of cells express distinctive and potentially adaptive characteristics, can contribute to microbial adaptation to a lifestyle that includes rapidly changing environments. The environments experienced by a symbiotic microbe during its life history can be erratic or predictable, and each can impact the evolution of adaptive responses. In particular, the predictability of a rhythmic or cyclical series of environments may promote the evolution of signal transduction cascades that allow preadaptive responses to environments that are likely to be encountered in the future, a phenomenon known as adaptive prediction. In this review, we summarize environmental variations known to occur in some well-studied models of symbiosis and how these may contribute to the evolution of microbial population heterogeneity and anticipatory behavior. We provide details about the symbiosis between Xenorhabdus bacteria and Steinernema nematodes as a model to investigate the concept of environmental adaptation and adaptive prediction in a microbial symbiosis. Copyright © 2017 American Society for Microbiology.

Hydrological responses of a watershed to historical land use evolution and future land use scenarios under climate change conditions

Directory of Open Access Journals (Sweden)

R. Quilbé

2008-01-01

Full Text Available Watershed runoff is closely related to land use but this influence is difficult to quantify. This study focused on the Chaudière River watershed (Québec, Canada and had two objectives: (i to quantify the influence of historical agricultural land use evolution on watershed runoff; and (ii to assess the effect of future land use evolution scenarios under climate change conditions (CC. To achieve this, we used the integrated modeling system GIBSI. Past land use evolution was constructed using satellite images that were integrated into GIBSI. The general trend was an increase of agricultural land in the 80's, a slight decrease in the beginning of the 90's and a steady state over the last ten years. Simulations showed strong correlations between land use evolution and water discharge at the watershed outlet. For the prospective approach, we first assessed the effect of CC and then defined two opposite land use evolution scenarios for the horizon 2025 based on two different trends: agriculture intensification and sustainable development. Simulations led to a wide range of results depending on the climatologic models and gas emission scenarios considered, varying from a decrease to an increase of annual and monthly water discharge. In this context, the two land use scenarios induced opposite effects on water discharge and low flow sequences, especially during the growing season. However, due to the large uncertainty linked to CC simulations, it is difficult to conclude that one land use scenario provides a better adaptation to CC than another. Nevertheless, this study shows that land use is a key factor that has to be taken into account when predicting potential future hydrological responses of a watershed.

An index for quantifying flocking behavior.

Science.gov (United States)

Quera, Vicenç; Herrando, Salvador; Beltran, Francesc S; Salas, Laura; Miñano, Meritxell

2007-12-01

One of the classic research topics in adaptive behavior is the collective displacement of groups of organisms such as flocks of birds, schools of fish, herds of mammals, and crowds of people. However, most agent-based simulations of group behavior do not provide a quantitative index for determining the point at which the flock emerges. An index was developed of the aggregation of moving individuals in a flock and an example was provided of how it can be used to quantify the degree to which a group of moving individuals actually forms a flock.

The evolution of opsins and color vision: connecting genotype to a complex phenotype

Directory of Open Access Journals (Sweden)

Natasha I Bloch

2016-09-01

Full Text Available Dissecting the genetic basis of adaptive traits is key to our understanding of evolutionary processes. A major and essential step in the study of evolutionary genetics is drawing link between genotype and phenotype, which depends on the difficult process of defining the phenotype at different levels, from functional to organismal. Visual pigments are a key component of the visual system and their evolution could also provide important clues on the evolution of visual sensory system in response to sexual and natural selection. As a system in which genotype can be linked to phenotype, I will use visual pigments and color vision, particularly in birds, as a case of a complex phenotype. I aim to emphasize the difficulties in drawing the genotype-phenotype relationship for complex phenotypes and to highlight the challenges of doing so for color vision. The use of vision-based receiver models to quantify animal colors and patterns is increasingly important in many fields of evolutionary research, spanning studies of mate choice, predation, camouflage and sensory ecology. Given these models impact on evolution and ecology, it is important to provide other researchers with the opportunity to better understand animal vision and the corresponding advantages and limitations of these models.

Landscape Evolution Modelling-LAPSUS

Energy Technology Data Exchange (ETDEWEB)

Baartman, J. E. M.; Temme, A. J. A. M.; Schoorl, J. M.; Claessens, L.; Viveen, W.; Gorp, W. van; Veldkamp, A.

2009-07-01

Landscape evolution modelling can make the consequences of landscape evolution hypotheses explicit and theoretically allows for their falsification and improvement. ideally, landscape evolution models (LEMs) combine the results of all relevant landscape forming processes into an ever-adapting digital landscape (e.g. DEM). These processes may act on different spatial and temporal scales. LAPSUS is such a LEM. Processes that have in different studies been included in LAPSUS are water erosion and deposition, landslide activity, creep, solidification, weathering, tectonics and tillage. Process descriptions are as simple and generic as possible, ensuring wide applicability. (Author) 25 refs.

Landscape Evolution Modelling-LAPSUS

International Nuclear Information System (INIS)

Baartman, J. E. M.; Temme, A. J. A. M.; Schoorl, J. M.; Claessens, L.; Viveen, W.; Gorp, W. van; Veldkamp, A.

2009-01-01

Landscape evolution modelling can make the consequences of landscape evolution hypotheses explicit and theoretically allows for their falsification and improvement. ideally, landscape evolution models (LEMs) combine the results of all relevant landscape forming processes into an ever-adapting digital landscape (e.g. DEM). These processes may act on different spatial and temporal scales. LAPSUS is such a LEM. Processes that have in different studies been included in LAPSUS are water erosion and deposition, landslide activity, creep, solidification, weathering, tectonics and tillage. Process descriptions are as simple and generic as possible, ensuring wide applicability. (Author) 25 refs.

Evolution of social learning does not explain the origin of human cumulative culture.

Science.gov (United States)

Enquist, Magnus; Ghirlanda, Stefano

2007-05-07

Because culture requires transmission of information between individuals, thinking about the origin of culture has mainly focused on the genetic evolution of abilities for social learning. Current theory considers how social learning affects the adaptiveness of a single cultural trait, yet human culture consists of the accumulation of very many traits. Here we introduce a new modeling strategy that tracks the adaptive value of many cultural traits, showing that genetic evolution favors only limited social learning owing to the accumulation of maladaptive as well as adaptive culture. We further show that culture can be adaptive, and refined social learning can evolve, if individuals can identify and discard maladaptive culture. This suggests that the evolution of such "adaptive filtering" mechanisms may have been crucial for the birth of human culture.

Adaptive mutation: has the unicorn landed?

Science.gov (United States)

Foster, P L

1998-04-01

Reversion of an episomal Lac- allele during lactose selection has been studied as a model for adaptive mutation. Although recent results show that the mutations that arise during selection are not "adaptive" in the original sense, the mutagenic mechanism that produces these mutations may nonetheless be of evolutionary significance. In addition, a transient mutational state induced in a subpopulation of starving cells could provide a species with a mechanism for adaptive evolution.

Adaptive mutation: has the unicorn landed?

Science.gov (United States)

Foster, P L

1998-01-01

Reversion of an episomal Lac- allele during lactose selection has been studied as a model for adaptive mutation. Although recent results show that the mutations that arise during selection are not "adaptive" in the original sense, the mutagenic mechanism that produces these mutations may nonetheless be of evolutionary significance. In addition, a transient mutational state induced in a subpopulation of starving cells could provide a species with a mechanism for adaptive evolution. PMID:9560365

Lifetime monogamy and the evolution of eusociality

DEFF Research Database (Denmark)

Boomsma, Jacobus J

2009-01-01

and termites is thus analogous to the evolution of multicellularity. Focusing on lifetime monogamy as a universal precondition for the evolution of obligate eusociality simplifies the theory and may help to resolve controversies about levels of selection and targets of adaptation. The monogamy window...... underlines that cooperative breeding and eusociality are different domains of social evolution, characterized by different sectors of parameter space for Hamilton's rule....

Morpho morphometrics: Shared ancestry and selection drive the evolution of wing size and shape in Morpho butterflies.

Science.gov (United States)

Chazot, Nicolas; Panara, Stephen; Zilbermann, Nicolas; Blandin, Patrick; Le Poul, Yann; Cornette, Raphaël; Elias, Marianne; Debat, Vincent

2016-01-01

Butterfly wings harbor highly diverse phenotypes and are involved in many functions. Wing size and shape result from interactions between adaptive processes, phylogenetic history, and developmental constraints, which are complex to disentangle. Here, we focus on the genus Morpho (Nymphalidae: Satyrinae, 30 species), which presents a high diversity of sizes, shapes, and color patterns. First, we generate a comprehensive molecular phylogeny of these 30 species. Next, using 911 collection specimens, we quantify the variation of wing size and shape across species, to assess the importance of shared ancestry, microhabitat use, and sexual selection in the evolution of the wings. While accounting for phylogenetic and allometric effects, we detect a significant difference in wing shape but not size among microhabitats. Fore and hindwings covary at the individual and species levels, and the covariation differs among microhabitats. However, the microhabitat structure in covariation disappears when phylogenetic relationships are taken into account. Our results demonstrate that microhabitat has driven wing shape evolution, although it has not strongly affected forewing and hindwing integration. We also found that sexual dimorphism of forewing shape and color pattern are coupled, suggesting a common selective force. © 2015 The Author(s). Evolution © 2015 The Society for the Study of Evolution.

Polyploidy can drive rapid adaptation in yeast

Science.gov (United States)

Selmecki, Anna M.; Maruvka, Yosef E.; Richmond, Phillip A.; Guillet, Marie; Shoresh, Noam; Sorenson, Amber L.; de, Subhajyoti; Kishony, Roy; Michor, Franziska; Dowell, Robin; Pellman, David

2015-03-01

Polyploidy is observed across the tree of life, yet its influence on evolution remains incompletely understood. Polyploidy, usually whole-genome duplication, is proposed to alter the rate of evolutionary adaptation. This could occur through complex effects on the frequency or fitness of beneficial mutations. For example, in diverse cell types and organisms, immediately after a whole-genome duplication, newly formed polyploids missegregate chromosomes and undergo genetic instability. The instability following whole-genome duplications is thought to provide adaptive mutations in microorganisms and can promote tumorigenesis in mammalian cells. Polyploidy may also affect adaptation independently of beneficial mutations through ploidy-specific changes in cell physiology. Here we perform in vitro evolution experiments to test directly whether polyploidy can accelerate evolutionary adaptation. Compared with haploids and diploids, tetraploids undergo significantly faster adaptation. Mathematical modelling suggests that rapid adaptation of tetraploids is driven by higher rates of beneficial mutations with stronger fitness effects, which is supported by whole-genome sequencing and phenotypic analyses of evolved clones. Chromosome aneuploidy, concerted chromosome loss, and point mutations all provide large fitness gains. We identify several mutations whose beneficial effects are manifest specifically in the tetraploid strains. Together, these results provide direct quantitative evidence that in some environments polyploidy can accelerate evolutionary adaptation.

Emergent explosive synchronization in adaptive complex networks

Science.gov (United States)

Avalos-Gaytán, Vanesa; Almendral, Juan A.; Leyva, I.; Battiston, F.; Nicosia, V.; Latora, V.; Boccaletti, S.

2018-04-01

Adaptation plays a fundamental role in shaping the structure of a complex network and improving its functional fitting. Even when increasing the level of synchronization in a biological system is considered as the main driving force for adaptation, there is evidence of negative effects induced by excessive synchronization. This indicates that coherence alone cannot be enough to explain all the structural features observed in many real-world networks. In this work, we propose an adaptive network model where the dynamical evolution of the node states toward synchronization is coupled with an evolution of the link weights based on an anti-Hebbian adaptive rule, which accounts for the presence of inhibitory effects in the system. We found that the emergent networks spontaneously develop the structural conditions to sustain explosive synchronization. Our results can enlighten the shaping mechanisms at the heart of the structural and dynamical organization of some relevant biological systems, namely, brain networks, for which the emergence of explosive synchronization has been observed.

A case study of evolutionary computation of biochemical adaptation

International Nuclear Information System (INIS)

François, Paul; Siggia, Eric D

2008-01-01

Simulations of evolution have a long history, but their relation to biology is questioned because of the perceived contingency of evolution. Here we provide an example of a biological process, adaptation, where simulations are argued to approach closer to biology. Adaptation is a common feature of sensory systems, and a plausible component of other biochemical networks because it rescales upstream signals to facilitate downstream processing. We create random gene networks numerically, by linking genes with interactions that model transcription, phosphorylation and protein–protein association. We define a fitness function for adaptation in terms of two functional metrics, and show that any reasonable combination of them will yield the same adaptive networks after repeated rounds of mutation and selection. Convergence to these networks is driven by positive selection and thus fast. There is always a path in parameter space of continuously improving fitness that leads to perfect adaptation, implying that the actual mutation rates we use in the simulation do not bias the results. Our results imply a kinetic view of evolution, i.e., it favors gene networks that can be learned quickly from the random examples supplied by mutation. This formulation allows for deductive predictions of the networks realized in nature

Thermotolerant Yeast Strains Adapted by Laboratory Evolution Show Trade-Off at Ancestral Temperatures and Preadaptation to Other Stresses.

Science.gov (United States)

Caspeta, Luis; Nielsen, Jens

2015-07-21

A major challenge for the production of ethanol from biomass-derived feedstocks is to develop yeasts that can sustain growth under the variety of inhibitory conditions present in the production process, e.g., high osmolality, high ethanol titers, and/or elevated temperatures (≥ 40 °C). Using adaptive laboratory evolution, we previously isolated seven Saccharomyces cerevisiae strains with improved growth at 40 °C. Here, we show that genetic adaptations to high temperature caused a growth trade-off at ancestral temperatures, reduced cellular functions, and improved tolerance of other stresses. Thermotolerant yeast strains showed horizontal displacement of their thermal reaction norms to higher temperatures. Hence, their optimal and maximum growth temperatures increased by about 3 °C, whereas they showed a growth trade-off at temperatures below 34 °C. Computational analysis of the physical properties of proteins showed that the lethal temperature for yeast is around 49 °C, as a large fraction of the yeast proteins denature above this temperature. Our analysis also indicated that the number of functions involved in controlling the growth rate decreased in the thermotolerant strains compared with the number in the ancestral strain. The latter is an advantageous attribute for acquiring thermotolerance and correlates with the reduction of yeast functions associated with loss of respiration capacity. This trait caused glycerol overproduction that was associated with the growth trade-off at ancestral temperatures. In combination with altered sterol composition of cellular membranes, glycerol overproduction was also associated with yeast osmotolerance and improved tolerance of high concentrations of glucose and ethanol. Our study shows that thermal adaptation of yeast is suitable for improving yeast resistance to inhibitory conditions found in industrial ethanol production processes. Yeast thermotolerance can significantly reduce the production costs of biomass

On the feedback error compensation for adaptive modulation and coding scheme

KAUST Repository

Choi, Seyeong

2011-11-25

In this paper, we consider the effect of feedback error on the performance of the joint adaptive modulation and diversity combining (AMDC) scheme which was previously studied with an assumption of perfect feedback channels. We quantify the performance of two joint AMDC schemes in the presence of feedback error, in terms of the average spectral efficiency, the average number of combined paths, and the average bit error rate. The benefit of feedback error compensation with adaptive combining is also quantified. Selected numerical examples are presented and discussed to illustrate the effectiveness of the proposed feedback error compensation strategy with adaptive combining. Copyright (c) 2011 John Wiley & Sons, Ltd.

Detecting consistent patterns of directional adaptation using differential selection codon models.

Science.gov (United States)

Parto, Sahar; Lartillot, Nicolas

2017-06-23

Phylogenetic codon models are often used to characterize the selective regimes acting on protein-coding sequences. Recent methodological developments have led to models explicitly accounting for the interplay between mutation and selection, by modeling the amino acid fitness landscape along the sequence. However, thus far, most of these models have assumed that the fitness landscape is constant over time. Fluctuations of the fitness landscape may often be random or depend on complex and unknown factors. However, some organisms may be subject to systematic changes in selective pressure, resulting in reproducible molecular adaptations across independent lineages subject to similar conditions. Here, we introduce a codon-based differential selection model, which aims to detect and quantify the fine-grained consistent patterns of adaptation at the protein-coding level, as a function of external conditions experienced by the organism under investigation. The model parameterizes the global mutational pressure, as well as the site- and condition-specific amino acid selective preferences. This phylogenetic model is implemented in a Bayesian MCMC framework. After validation with simulations, we applied our method to a dataset of HIV sequences from patients with known HLA genetic background. Our differential selection model detects and characterizes differentially selected coding positions specifically associated with two different HLA alleles. Our differential selection model is able to identify consistent molecular adaptations as a function of repeated changes in the environment of the organism. These models can be applied to many other problems, ranging from viral adaptation to evolution of life-history strategies in plants or animals.

Adaptive evolution of the Hox gene family for development in bats and dolphins.

Directory of Open Access Journals (Sweden)

Lu Liang

Full Text Available Bats and cetaceans (i.e., whales, dolphins, porpoises are two kinds of mammals with unique locomotive styles and occupy novel niches. Bats are the only mammals capable of sustained flight in the sky, while cetaceans have returned to the aquatic environment and are specialized for swimming. Associated with these novel adaptations to their environment, various development changes have occurred to their body plans and associated structures. Given the importance of Hox genes in many aspects of embryonic development, we conducted an analysis of the coding regions of all Hox gene family members from bats (represented by Pteropus vampyrus, Pteropus alecto, Myotis lucifugus and Myotis davidii and cetaceans (represented by Tursiops truncatus for adaptive evolution using the available draft genome sequences. Differences in the selective pressures acting on many Hox genes in bats and cetaceans were found compared to other mammals. Positive selection, however, was not found to act on any of the Hox genes in the common ancestor of bats and only upon Hoxb9 in cetaceans. PCR amplification data from additional bat and cetacean species, and application of the branch-site test 2, showed that the Hoxb2 gene within bats had significant evidence of positive selection. Thus, our study, with genomic and newly sequenced Hox genes, identifies two candidate Hox genes that may be closely linked with developmental changes in bats and cetaceans, such as those associated with the pancreatic, neuronal, thymus shape and forelimb. In addition, the difference in our results from the genome-wide scan and newly sequenced data reveals that great care must be taken in interpreting results from draft genome data from a limited number of species, and deep genetic sampling of a particular clade is a powerful tool for generating complementary data to address this limitation.

Incorporating information on predicted solvent accessibility to the co-evolution-based study of protein interactions.

Science.gov (United States)

Ochoa, David; García-Gutiérrez, Ponciano; Juan, David; Valencia, Alfonso; Pazos, Florencio

2013-01-27

A widespread family of methods for studying and predicting protein interactions using sequence information is based on co-evolution, quantified as similarity of phylogenetic trees. Part of the co-evolution observed between interacting proteins could be due to co-adaptation caused by inter-protein contacts. In this case, the co-evolution is expected to be more evident when evaluated on the surface of the proteins or the internal layers close to it. In this work we study the effect of incorporating information on predicted solvent accessibility to three methods for predicting protein interactions based on similarity of phylogenetic trees. We evaluate the performance of these methods in predicting different types of protein associations when trees based on positions with different characteristics of predicted accessibility are used as input. We found that predicted accessibility improves the results of two recent versions of the mirrortree methodology in predicting direct binary physical interactions, while it neither improves these methods, nor the original mirrortree method, in predicting other types of interactions. That improvement comes at no cost in terms of applicability since accessibility can be predicted for any sequence. We also found that predictions of protein-protein interactions are improved when multiple sequence alignments with a richer representation of sequences (including paralogs) are incorporated in the accessibility prediction.

Natural selection causes adaptive genetic resistance in wild emmer wheat against powdery mildew at "Evolution Canyon" microsite, Mt. Carmel, Israel.

Directory of Open Access Journals (Sweden)

Huayan Yin

Full Text Available "Evolution Canyon" (ECI at Lower Nahal Oren, Mount Carmel, Israel, is an optimal natural microscale model for unraveling evolution in action highlighting the basic evolutionary processes of adaptation and speciation. A major model organism in ECI is wild emmer, Triticum dicoccoides, the progenitor of cultivated wheat, which displays dramatic interslope adaptive and speciational divergence on the tropical-xeric "African" slope (AS and the temperate-mesic "European" slope (ES, separated on average by 250 m.We examined 278 single sequence repeats (SSRs and the phenotype diversity of the resistance to powdery mildew between the opposite slopes. Furthermore, 18 phenotypes on the AS and 20 phenotypes on the ES, were inoculated by both Bgt E09 and a mixture of powdery mildew races.In the experiment of genetic diversity, very little polymorphism was identified intra-slope in the accessions from both the AS or ES. By contrast, 148 pairs of SSR primers (53.23% amplified polymorphic products between the phenotypes of AS and ES. There are some differences between the two wild emmer wheat genomes and the inter-slope SSR polymorphic products between genome A and B. Interestingly, all wild emmer types growing on the south-facing slope (SFS=AS were susceptible to a composite of Blumeria graminis, while the ones growing on the north-facing slope (NFS=ES were highly resistant to Blumeria graminis at both seedling and adult stages.Remarkable inter-slope evolutionary divergent processes occur in wild emmer wheat, T. dicoccoides at EC I, despite the shot average distance of 250 meters. The AS, a dry and hot slope, did not develop resistance to powdery mildew, whereas the ES, a cool and humid slope, did develop resistance since the disease stress was strong there. This is a remarkable demonstration in host-pathogen interaction on how resistance develops when stress causes an adaptive result at a micro-scale distance.

Epigenetics and brain evolution.

Science.gov (United States)

Keverne, Eric B

2011-04-01

Fundamental aspects of mammalian brain evolution occurred in the context of viviparity and placentation brought about by the epigenetic regulation of imprinted genes. Since the fetal placenta hormonally primes the maternal brain, two genomes in one individual are transgenerationally co-adapted to ensure maternal care and nurturing. Advanced aspects of neocortical brain evolution has shown very few genetic changes between monkeys and humans. Although these lineages diverged at approximately the same time as the rat and mouse (20 million years ago), synonymous sequence divergence between the rat and mouse is double that when comparing monkey with human sequences. Paradoxically, encephalization of rat and mouse are remarkably similar, while comparison of the human and monkey shows the human cortex to be three times the size of the monkey. This suggests an element of genetic stability between the brains of monkey and man with a greater emphasis on epigenetics providing adaptable variability.

Evolution of Scale Worms

DEFF Research Database (Denmark)

Gonzalez, Brett Christopher

) caves, and the interstitium, recovering six monophyletic clades within Aphroditiformia: Acoetidae, Aphroditidae, Eulepethidae, Iphionidae, Polynoidae, and Sigalionidae (inclusive of the former ‘Pisionidae’ and ‘Pholoidae’), respectively. Tracing of morphological character evolution showed a high degree...... of adaptability and convergent evolution between relatively closely related scale worms. While some morphological and behavioral modifications in cave polynoids reflected troglomorphism, other modifications like eye loss were found to stem from a common ancestor inhabiting the deep sea, further corroborating...... the deep sea ancestry of scale worm cave fauna. In conclusion, while morphological characterization across Aphroditiformia appears deceptively easy due to the presence of elytra, convergent evolution during multiple early radiations across wide ranging habitats have confounded our ability to reconstruct...

Adaptive evolution of threonine deaminase in plant defense against insect herbivores

Energy Technology Data Exchange (ETDEWEB)

Gonzales-Vigil, Eliana; Bianchetti, Christopher M.; Phillips, Jr., George N.; Howe, Gregg A. (MSU); (UW)

2011-11-07

Gene duplication is a major source of plant chemical diversity that mediates plant-herbivore interactions. There is little direct evidence, however, that novel chemical traits arising from gene duplication reduce herbivory. Higher plants use threonine deaminase (TD) to catalyze the dehydration of threonine (Thr) to {alpha}-ketobutyrate and ammonia as the committed step in the biosynthesis of isoleucine (Ile). Cultivated tomato and related Solanum species contain a duplicated TD paralog (TD2) that is coexpressed with a suite of genes involved in herbivore resistance. Analysis of TD2-deficient tomato lines showed that TD2 has a defensive function related to Thr catabolism in the gut of lepidopteran herbivores. During herbivory, the regulatory domain of TD2 is removed by proteolysis to generate a truncated protein (pTD2) that efficiently degrades Thr without being inhibited by Ile. We show that this proteolytic activation step occurs in the gut of lepidopteran but not coleopteran herbivores, and is catalyzed by a chymotrypsin-like protease of insect origin. Analysis of purified recombinant enzymes showed that TD2 is remarkably more resistant to proteolysis and high temperature than the ancestral TD1 isoform. The crystal structure of pTD2 provided evidence that electrostatic interactions constitute a stabilizing feature associated with adaptation of TD2 to the extreme environment of the lepidopteran gut. These findings demonstrate a role for gene duplication in the evolution of a plant defense that targets and co-opts herbivore digestive physiology.

A new paradigm of quantifying ecosystem stress through chemical signatures

Energy Technology Data Exchange (ETDEWEB)

Kravitz, Ben [Atmospheric Sciences and Global Change Division, Pacific Northwest National Laboratory, P.O. Box 999, MSIN K9-30 Richland Washington 99352 USA; Guenther, Alex B. [Department of Earth System Science, University of California Irvine, 3200 Croul Hall Street Irvine California 92697 USA; Gu, Lianhong [Environmental Sciences Division, Oak Ridge National Laboratory, Oak Ridge Tennessee 37831 USA; Karl, Thomas [Institute of Atmospheric and Crysopheric Sciences, University of Innsbruck, Innrain 52f A-6020 Innsbruck Austria; Kaser, Lisa [National Center for Atmospheric Research, P.O. Box 3000 Boulder Colorado 80307 USA; Pallardy, Stephen G. [Department of Forestry, University of Missouri, 203 Anheuser-Busch Natural Resources Building Columbia Missouri 65211 USA; Peñuelas, Josep [CREAF, Cerdanyola del Vallès 08193 Catalonia Spain; Global Ecology Unit CREAF-CSIC-UAB, CSIC, Cerdanyola del Vallès 08193 Catalonia Spain; Potosnak, Mark J. [Department of Environmental Science and Studies, DePaul University, McGowan South, Suite 203 Chicago Illinois 60604 USA; Seco, Roger [Department of Earth System Science, University of California Irvine, 3200 Croul Hall Street Irvine California 92697 USA

2016-11-01

Stress-induced emissions of biogenic volatile organic compounds (VOCs) from terrestrial ecosystems may be one of the dominant sources of VOC emissions world-wide. Understanding the ecosystem stress response could reveal how ecosystems will respond and adapt to climate change and, in turn, quantify changes in the atmospheric burden of VOC oxidants and secondary organic aerosols. Here we argue, based on preliminary evidence from several opportunistic measurement sources, that chemical signatures of stress can be identified and quantified at the ecosystem scale. We also outline future endeavors that we see as next steps toward uncovering quantitative signatures of stress, including new advances in both VOC data collection and analysis of "big data."

Emigrating Beyond Earth Human Adaptation and Space Colonization

CERN Document Server

Smith, Cameron M

2012-01-01

For four million years humankind has been actively expanding geographically and in doing so has adapted to a wide variety of hostile environments. Now we are looking towards the ultimate adaptation - the colonization of space. Emigrating Beyond Earth illustrates that this is not a technocratic endeavor, but a natural continuation of human evolution; a journey not just for the engineer and rocket scientist, but for everyman. Based on the most current understanding of our universe, human adaptation and evolution, the authors explain why space colonization must be planned as an adaptation to, rather than the conquest of, space. Emigrating Beyond Earth argues that space colonization is an insurance policy for our species, and that it isn't about rockets and robots, it's about humans doing what we've been doing for four million years: finding new places and new ways to live. Applying a unique anthropological approach, the authors outline a framework for continued human space exploration and offer a glimpse of a po...

Linearized Flux Evolution (LiFE): A technique for rapidly adapting fluxes from full-physics radiative transfer models

Science.gov (United States)

Robinson, Tyler D.; Crisp, David

2018-05-01

Solar and thermal radiation are critical aspects of planetary climate, with gradients in radiative energy fluxes driving heating and cooling. Climate models require that radiative transfer tools be versatile, computationally efficient, and accurate. Here, we describe a technique that uses an accurate full-physics radiative transfer model to generate a set of atmospheric radiative quantities which can be used to linearly adapt radiative flux profiles to changes in the atmospheric and surface state-the Linearized Flux Evolution (LiFE) approach. These radiative quantities describe how each model layer in a plane-parallel atmosphere reflects and transmits light, as well as how the layer generates diffuse radiation by thermal emission and by scattering light from the direct solar beam. By computing derivatives of these layer radiative properties with respect to dynamic elements of the atmospheric state, we can then efficiently adapt the flux profiles computed by the full-physics model to new atmospheric states. We validate the LiFE approach, and then apply this approach to Mars, Earth, and Venus, demonstrating the information contained in the layer radiative properties and their derivatives, as well as how the LiFE approach can be used to determine the thermal structure of radiative and radiative-convective equilibrium states in one-dimensional atmospheric models.

Putative adaptive inter-slope divergence of transposon frequency in fruit flies (Drosophila melanogaster) at "Evolution Canyon", Mount Carmel, Israel.

Science.gov (United States)

Beiles, Avigdor; Raz, Shmuel; Ben-Abu, Yuval; Nevo, Eviatar

2015-10-14

The current analysis of transposon elements (TE) in Drosophila melanogaster at Evolution Canyon, (EC), Israel, is based on data and analysis done by our collaborators (Drs. J. Gonzalez, J. Martinez and W. Makalowski, this issue). They estimated the frequencies of 28 TEs (transposon elements) in fruit flies (D. melanogaster) from the ecologically tropic, hot, and dry south-facing slope (SFS) or "African" slope (AS) of EC and compared it with the TE frequencies on the temperate-cool and humid north-facing slope (NFS) or "European" slope (ES), separated, on average, by 250 m. The flies were sampled from two stations on each slope. We received their results, including the frequencies of each TE on each slope, and the probabilities of the statistical analyses (G-tests) of each TE separately. We continued the analysis of the inter-slope differences of the frequencies of the TEs, and based our different conclusions on that analysis and on the difference between micro (=EC) and macro (2000 km.) comparisons [Gonzalez et al. 2015 doi: 10.1186/s13062-015-0075-4 ]. Our collaborators based all their conclusions on the non-significant results of each of the individual tests of the 28 TEs. We analysed also the distribution of the TE differences between the slopes, based on their results. Thirteen TEs were more frequent on the SFS, 11 were more frequent on the NFS, and four had equal frequencies. Because of the equalizing effect of the ongoing migration, only small and temporary differences between the slopes (0 - 0.06) were regarded by us as random fluctuations (drift). Three TEs were intermediate (0.08-0.09) and await additional research. The 11 TEs with large frequency differences (0.12 - 0.22) were regarded by us as putative adaptive TEs, because the equalizing power of ongoing migration will eliminate random large differences. Five of them were higher on the SFS and six were higher on the NFS. Gaps in the distribution of the differences distinguished between the large and

Teaching Adaptability of Object-Oriented Programming Language Curriculum

Science.gov (United States)

Zhu, Xiao-dong

2012-01-01

The evolution of object-oriented programming languages includes update of their own versions, update of development environments, and reform of new languages upon old languages. In this paper, the evolution analysis of object-oriented programming languages is presented in term of the characters and development. The notion of adaptive teaching upon…

Biological evolution: Some genetic considerations

African Journals Online (AJOL)

Mohammad Saad Zaghloul Salem

2013-12-08

Dec 8, 2013 ... cept of evolution, viz. genetic memory and evolutionary variations, genomic adaptations to stress .... or codons, along the transcript without giving attention to whether they are ... They do not affect the genome in a straightfor-.

Brain evolution and development: adaptation, allometry and constraint

Science.gov (United States)

Barton, Robert A.

2016-01-01

Phenotypic traits are products of two processes: evolution and development. But how do these processes combine to produce integrated phenotypes? Comparative studies identify consistent patterns of covariation, or allometries, between brain and body size, and between brain components, indicating the presence of significant constraints limiting independent evolution of separate parts. These constraints are poorly understood, but in principle could be either developmental or functional. The developmental constraints hypothesis suggests that individual components (brain and body size, or individual brain components) tend to evolve together because natural selection operates on relatively simple developmental mechanisms that affect the growth of all parts in a concerted manner. The functional constraints hypothesis suggests that correlated change reflects the action of selection on distributed functional systems connecting the different sub-components, predicting more complex patterns of mosaic change at the level of the functional systems and more complex genetic and developmental mechanisms. These hypotheses are not mutually exclusive but make different predictions. We review recent genetic and neurodevelopmental evidence, concluding that functional rather than developmental constraints are the main cause of the observed patterns. PMID:27629025

Rethinking the evolution of specialization: A model for the evolution of phenotypic heterogeneity.

Science.gov (United States)

Rubin, Ilan N; Doebeli, Michael

2017-12-21

Phenotypic heterogeneity refers to genetically identical individuals that express different phenotypes, even when in the same environment. Traditionally, "bet-hedging" in fluctuating environments is offered as the explanation for the evolution of phenotypic heterogeneity. However, there are an increasing number of examples of microbial populations that display phenotypic heterogeneity in stable environments. Here we present an evolutionary model of phenotypic heterogeneity of microbial metabolism and a resultant theory for the evolution of phenotypic versus genetic specialization. We use two-dimensional adaptive dynamics to track the evolution of the population phenotype distribution of the expression of two metabolic processes with a concave trade-off. Rather than assume a Gaussian phenotype distribution, we use a Beta distribution that is capable of describing genotypes that manifest as individuals with two distinct phenotypes. Doing so, we find that environmental variation is not a necessary condition for the evolution of phenotypic heterogeneity, which can evolve as a form of specialization in a stable environment. There are two competing pressures driving the evolution of specialization: directional selection toward the evolution of phenotypic heterogeneity and disruptive selection toward genetically determined specialists. Because of the lack of a singular point in the two-dimensional adaptive dynamics and the fact that directional selection is a first order process, while disruptive selection is of second order, the evolution of phenotypic heterogeneity dominates and often precludes speciation. We find that branching, and therefore genetic specialization, occurs mainly under two conditions: the presence of a cost to maintaining a high phenotypic variance or when the effect of mutations is large. A cost to high phenotypic variance dampens the strength of selection toward phenotypic heterogeneity and, when sufficiently large, introduces a singular point into

Hyphenated hydrology: Multidisciplinary evolution of water resource science

Science.gov (United States)

McCurley, K. 4553; Jawitz, J. W.

2016-12-01

Hydrology has advanced considerably as a scientific discipline since its recognized inception in the mid-20th century. While hydrology may have evolved from the singular viewpoint of a more rigid physical or engineering science, modern water resource related questions have forced adaptation toward a deliberate interdisciplinary context. Over the past few decades, many of the eventual manifestations of this evolution have been foreseen by prominent expert hydrologists, though their narrative descriptions were not substantially quantified. This study addresses that gap by directly measuring and inspecting the words that hydrologists use to define and describe their research endeavors. We analyzed 16,591 journal article titles from 1965-2015 in Water Resources Research, through which the scientific dialogue and its time-sensitive progression emerges. Word frequency and term concurrence reveal the dynamic timing of the lateral movement of hydrology across multiple disciplines and a deepening of scientific discourse with respect to traditional hydrologic questions. This study concludes that formerly exotic disciplines are increasingly modifying hydrology, prompting new insights as well as inspiring unconventional perspectives on old questions.

Microorganism and filamentous fungi drive evolution of plant synapses.

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Baluška, František; Mancuso, Stefano

2013-01-01

In the course of plant evolution, there is an obvious trend toward an increased complexity of plant bodies, as well as an increased sophistication of plant behavior and communication. Phenotypic plasticity of plants is based on the polar auxin transport machinery that is directly linked with plant sensory systems impinging on plant behavior and adaptive responses. Similar to the emergence and evolution of eukaryotic cells, evolution of land plants was also shaped and driven by infective and symbiotic microorganisms. These microorganisms are the driving force behind the evolution of plant synapses and other neuronal aspects of higher plants; this is especially pronounced in the root apices. Plant synapses allow synaptic cell-cell communication and coordination in plants, as well as sensory-motor integration in root apices searching for water and mineral nutrition. These neuronal aspects of higher plants are closely linked with their unique ability to adapt to environmental changes.

MONTE CARLO SIMULATIONS OF GLOBULAR CLUSTER EVOLUTION. V. BINARY STELLAR EVOLUTION

International Nuclear Information System (INIS)

Chatterjee, Sourav; Umbreit, Stefan; Rasio, Frederic A.; Fregeau, John M.

2010-01-01

We study the dynamical evolution of globular clusters containing primordial binaries, including full single and binary stellar evolution using our Monte Carlo cluster evolution code updated with an adaptation of the single and binary stellar evolution codes SSE and BSE from Hurley et al. We describe the modifications that we have made to the code. We present several test calculations and comparisons with existing studies to illustrate the validity of the code. We show that our code finds very good agreement with direct N-body simulations including primordial binaries and stellar evolution. We find significant differences in the evolution of the global properties of the simulated clusters using stellar evolution compared with simulations without any stellar evolution. In particular, we find that the mass loss from the stellar evolution acts as a significant energy production channel simply by reducing the total gravitational binding energy and can significantly prolong the initial core contraction phase before reaching the binary-burning quasi-steady state of the cluster evolution. We simulate a large grid of models varying the initial cluster mass, binary fraction, and concentration parameter, and we compare properties of the simulated clusters with those of the observed Galactic globular clusters (GGCs). We find that simply including stellar evolution in our simulations and assuming the typical initial cluster half-mass radius is approximately a few pc independent of mass, our simulated cluster properties agree well with the observed GGC properties such as the core radius and the ratio of the core radius to the half-mass radius. We explore in some detail qualitatively different clusters in different phases of their evolution and construct synthetic Hertzsprung-Russell diagrams for these clusters.

Event-driven Adaptation in COP

Directory of Open Access Journals (Sweden)

Pierpaolo Degano

2016-06-01

Full Text Available Context-Oriented Programming languages provide us with primitive constructs to adapt program behaviour depending on the evolution of their operational environment, namely the context. In previous work we proposed ML_CoDa, a context-oriented language with two-components: a declarative constituent for programming the context and a functional one for computing. This paper describes an extension of ML_CoDa to deal with adaptation to unpredictable context changes notified by asynchronous events.

Evidence for adaptive radiation from a phylogenetic study of plant defenses

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Agrawal, Anurag A.; Fishbein, Mark; Halitschke, Rayko; Hastings, Amy P.; Rabosky, Daniel L.; Rasmann, Sergio

2009-01-01

One signature of adaptive radiation is a high level of trait change early during the diversification process and a plateau toward the end of the radiation. Although the study of the tempo of evolution has historically been the domain of paleontologists, recently developed phylogenetic tools allow for the rigorous examination of trait evolution in a tremendous diversity of organisms. Enemy-driven adaptive radiation was a key prediction of Ehrlich and Raven's coevolutionary hypothesis [Ehrlich PR, Raven PH (1964) Evolution 18:586–608], yet has remained largely untested. Here we examine patterns of trait evolution in 51 North American milkweed species (Asclepias), using maximum likelihood methods. We study 7 traits of the milkweeds, ranging from seed size and foliar physiological traits to defense traits (cardenolides, latex, and trichomes) previously shown to impact herbivores, including the monarch butterfly. We compare the fit of simple random-walk models of trait evolution to models that incorporate stabilizing selection (Ornstein-Ulenbeck process), as well as time-varying rates of trait evolution. Early bursts of trait evolution were implicated for 2 traits, while stabilizing selection was implicated for several others. We further modeled the relationship between trait change and species diversification while allowing rates of trait evolution to vary during the radiation. Species-rich lineages underwent a proportionately greater decline in latex and cardenolides relative to species-poor lineages, and the rate of trait change was most rapid early in the radiation. An interpretation of this result is that reduced investment in defensive traits accelerated diversification, and disproportionately so, early in the adaptive radiation of milkweeds. PMID:19805160

Quantifying the Effects of Gas-Rich Flyby Encounters on Galaxy Evolution

Science.gov (United States)

Dumas, Julie; Holley-Bockelmann, Kelly; Lang, Meagan

2017-01-01

Recent work has shown that flyby encounters may be a common event in a galaxy's lifetime. Galaxy flybys are a one-time encounter when two halos interpenetrate, but unlike a galaxy merger, the two halos later detach. Relatively little work has been done to assess how flybys affect galaxy evolution. We present preliminary results of a suite of high-resolution hydrodynamical + N-body simulations of gas-rich flyby encounters, concentrating on Milky Way-like primaries. We track the bulk changes in structure, star formation history, kinematics, and morphology over a broad span of flyby encounters.

Evaluation of uncertainty of adaptive radiation therapy

International Nuclear Information System (INIS)

Garcia Molla, R.; Gomez Martin, C.; Vidueira, L.; Juan-Senabre, X.; Garcia Gomez, R.

2013-01-01

This work is part of tests to perform to its acceptance in the clinical practice. The uncertainties of adaptive radiation, and which will separate the study, can be divided into two large parts: dosimetry in the CBCT and RDI. At each stage, their uncertainties are quantified and a level of action from which it would be reasonable to adapt the plan may be obtained with the total. (Author)

Rapid evolution in insect pests: the importance of space and time in population genomics studies.

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Pélissié, Benjamin; Crossley, Michael S; Cohen, Zachary Paul; Schoville, Sean D

2018-04-01

Pest species in agroecosystems often exhibit patterns of rapid evolution to environmental and human-imposed selection pressures. Although the role of adaptive processes is well accepted, few insect pests have been studied in detail and most research has focused on selection at insecticide resistance candidate genes. Emerging genomic datasets provide opportunities to detect and quantify selection in insect pest populations, and address long-standing questions about mechanisms underlying rapid evolutionary change. We examine the strengths of recent studies that stratify population samples both in space (along environmental gradients and comparing ancestral vs. derived populations) and in time (using chronological sampling, museum specimens and comparative phylogenomics), resulting in critical insights on evolutionary processes, and providing new directions for studying pests in agroecosystems. Copyright © 2018 Elsevier Inc. All rights reserved.

Prospects for the study of evolution in the deep biosphere.

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Biddle, Jennifer F; Sylvan, Jason B; Brazelton, William J; Tully, Benjamin J; Edwards, Katrina J; Moyer, Craig L; Heidelberg, John F; Nelson, William C

2011-01-01

Since the days of Darwin, scientists have used the framework of the theory of evolution to explore the interconnectedness of life on Earth and adaptation of organisms to the ever-changing environment. The advent of molecular biology has advanced and accelerated the study of evolution by allowing direct examination of the genetic material that ultimately determines the phenotypes upon which selection acts. The study of evolution has been furthered through examination of microbial evolution, with large population numbers, short generation times, and easily extractable DNA. Such work has spawned the study of microbial biogeography, with the realization that concepts developed in population genetics may be applicable to microbial genomes (Martiny et al., 2006; Manhes and Velicer, 2011). Microbial biogeography and adaptation has been examined in many different environments. Here we argue that the deep biosphere is a unique environment for the study of evolution and list specific factors that can be considered and where the studies may be performed. This publication is the result of the NSF-funded Center for Dark Energy Biosphere Investigations (C-DEBI) theme team on Evolution (www.darkenergybiosphere.org).

Boussinesq evolution equations

DEFF Research Database (Denmark)

Bredmose, Henrik; Schaffer, H.; Madsen, Per A.

2004-01-01

This paper deals with the possibility of using methods and ideas from time domain Boussinesq formulations in the corresponding frequency domain formulations. We term such frequency domain models "evolution equations". First, we demonstrate that the numerical efficiency of the deterministic...... Boussinesq evolution equations of Madsen and Sorensen [Madsen, P.A., Sorensen, O.R., 1993. Bound waves and triad interactions in shallow water. Ocean Eng. 20 359-388] can be improved by using Fast Fourier Transforms to evaluate the nonlinear terms. For a practical example of irregular waves propagating over...... a submerged bar, it is demonstrated that evolution equations utilising FFT can be solved around 100 times faster than the corresponding time domain model. Use of FFT provides an efficient bridge between the frequency domain and the time domain. We utilise this by adapting the surface roller model for wave...

Mapping the evolution of scientific fields.

Science.gov (United States)

Herrera, Mark; Roberts, David C; Gulbahce, Natali

2010-05-04

Despite the apparent cross-disciplinary interactions among scientific fields, a formal description of their evolution is lacking. Here we describe a novel approach to study the dynamics and evolution of scientific fields using a network-based analysis. We build an idea network consisting of American Physical Society Physics and Astronomy Classification Scheme (PACS) numbers as nodes representing scientific concepts. Two PACS numbers are linked if there exist publications that reference them simultaneously. We locate scientific fields using a community finding algorithm, and describe the time evolution of these fields over the course of 1985-2006. The communities we identify map to known scientific fields, and their age depends on their size and activity. We expect our approach to quantifying the evolution of ideas to be relevant for making predictions about the future of science and thus help to guide its development.

Evolution and adaptation of the pandemic A/H1N1 2009 influenza virus

Directory of Open Access Journals (Sweden)

Ducatez MF

2011-07-01

Full Text Available Mariette F Ducatez, Thomas P Fabrizio, Richard J WebbyDepartment of Infectious Diseases, St Jude Children's Research Hospital, Memphis, TN, USAAbstract: The emergence of the 2009 H1N1 pandemic influenza virus [A(H1N1pdm09] has provided the public health community with many challenges, but also the scientific community with an opportunity to monitor closely its evolution through the processes of drift and shift. To date, and despite having circulated in humans for nearly two years, little antigenic variation has been observed in the A(H1N1pdm09 viruses. However, as the A(H1N1pdm09 virus continues to circulate and the immunologic pressure within the human population increases, future antigenic change is almost a certainty. Several coinfections of A(H1N1pdm09 and seasonal A(H1N1 or A(H3N2 viruses have been observed, but no reassortant viruses have been described in humans, suggesting a lack of fitness of reassortant viruses or a lack of opportunities for interaction of different viral lineages. In contrast, multiple reassortment events have been detected in swine populations between A(H1N1 pdm09 and other endemic swine viruses. Somewhat surprisingly, many of the well characterized influenza virus virulence markers appear to have limited impact on the phenotype of the A(H1N1pdm09 viruses when they have been introduced into mutant viruses in laboratory settings. As such, it is unclear what the evolutionary path of the pandemic virus will be, but the monitoring of any changes in the circulating viruses will remain a global public and animal health priority.Keywords: influenza, pandemic, evolution, adaptation

Thermodynamic evolution far from equilibrium

Science.gov (United States)

Khantuleva, Tatiana A.

2018-05-01

The presented model of thermodynamic evolution of an open system far from equilibrium is based on the modern results of nonequilibrium statistical mechanics, the nonlocal theory of nonequilibrium transport developed by the author and the Speed Gradient principle introduced in the theory of adaptive control. Transition to a description of the system internal structure evolution at the mesoscopic level allows a new insight at the stability problem of non-equilibrium processes. The new model is used in a number of specific tasks.

Evolutionary adaptations to dietary changes.

Science.gov (United States)

Luca, F; Perry, G H; Di Rienzo, A

2010-08-21

Through cultural innovation and changes in habitat and ecology, there have been a number of major dietary shifts in human evolution, including meat eating, cooking, and those associated with plant and animal domestication. The identification of signatures of adaptations to such dietary changes in the genome of extant primates (including humans) may shed light not only on the evolutionary history of our species, but also on the mechanisms that underlie common metabolic diseases in modern human populations. In this review, we provide a brief overview of the major dietary shifts that occurred during hominin evolution, and we discuss the methods and approaches used to identify signals of natural selection in patterns of sequence variation. We then review the results of studies aimed at detecting the genetic loci that played a major role in dietary adaptations and conclude by outlining the potential of future studies in this area.

Can Evolution Supply What Ecology Demands?

Science.gov (United States)

Kokko, Hanna; Chaturvedi, Anurag; Croll, Daniel; Fischer, Martin C; Guillaume, Frédéric; Karrenberg, Sophie; Kerr, Ben; Rolshausen, Gregor; Stapley, Jessica

2017-03-01

A simplistic view of the adaptive process pictures a hillside along which a population can climb: when ecological 'demands' change, evolution 'supplies' the variation needed for the population to climb to a new peak. Evolutionary ecologists point out that this simplistic view can be incomplete because the fitness landscape changes dynamically as the population evolves. Geneticists meanwhile have identified complexities relating to the nature of genetic variation and its architecture, and the importance of epigenetic variation is under debate. In this review, we highlight how complexity in both ecological 'demands' and the evolutionary 'supply' influences organisms' ability to climb fitness landscapes that themselves change dynamically as evolution proceeds, and encourage new synthetic effort across research disciplines towards ecologically realistic studies of adaptation. Copyright © 2016 Elsevier Ltd. All rights reserved.

Faster-X evolution: Theory and evidence from Drosophila.

Science.gov (United States)

Charlesworth, Brian; Campos, José L; Jackson, Benjamin C

2018-02-12

A faster rate of adaptive evolution of X-linked genes compared with autosomal genes can be caused by the fixation of recessive or partially recessive advantageous mutations, due to the full expression of X-linked mutations in hemizygous males. Other processes, including recombination rate and mutation rate differences between X chromosomes and autosomes, may also cause faster evolution of X-linked genes. We review population genetics theory concerning the expected relative values of variability and rates of evolution of X-linked and autosomal DNA sequences. The theoretical predictions are compared with data from population genomic studies of several species of Drosophila. We conclude that there is evidence for adaptive faster-X evolution of several classes of functionally significant nucleotides. We also find evidence for potential differences in mutation rates between X-linked and autosomal genes, due to differences in mutational bias towards GC to AT mutations. Many aspects of the data are consistent with the male hemizygosity model, although not all possible confounding factors can be excluded. © 2018 John Wiley & Sons Ltd.

Gene duplication, modularity and adaptation in the evolution of the aflatoxin gene cluster

Directory of Open Access Journals (Sweden)

Jakobek Judy L

2007-07-01

Full Text Available Abstract Background The biosynthesis of aflatoxin (AF involves over 20 enzymatic reactions in a complex polyketide pathway that converts acetate and malonate to the intermediates sterigmatocystin (ST and O-methylsterigmatocystin (OMST, the respective penultimate and ultimate precursors of AF. Although these precursors are chemically and structurally very similar, their accumulation differs at the species level for Aspergilli. Notable examples are A. nidulans that synthesizes only ST, A. flavus that makes predominantly AF, and A. parasiticus that generally produces either AF or OMST. Whether these differences are important in the evolutionary/ecological processes of species adaptation and diversification is unknown. Equally unknown are the specific genomic mechanisms responsible for ordering and clustering of genes in the AF pathway of Aspergillus. Results To elucidate the mechanisms that have driven formation of these clusters, we performed systematic searches of aflatoxin cluster homologs across five Aspergillus genomes. We found a high level of gene duplication and identified seven modules consisting of highly correlated gene pairs (aflA/aflB, aflR/aflS, aflX/aflY, aflF/aflE, aflT/aflQ, aflC/aflW, and aflG/aflL. With the exception of A. nomius, contrasts of mean Ka/Ks values across all cluster genes showed significant differences in selective pressure between section Flavi and non-section Flavi species. A. nomius mean Ka/Ks values were more similar to partial clusters in A. fumigatus and A. terreus. Overall, mean Ka/Ks values were significantly higher for section Flavi than for non-section Flavi species. Conclusion Our results implicate several genomic mechanisms in the evolution of ST, OMST and AF cluster genes. Gene modules may arise from duplications of a single gene, whereby the function of the pre-duplication gene is retained in the copy (aflF/aflE or the copies may partition the ancestral function (aflA/aflB. In some gene modules, the

Quantitative adaptation analytics for assessing dynamic systems of systems: LDRD Final Report

Energy Technology Data Exchange (ETDEWEB)

Gauthier, John H. [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States). System Readiness & Sustainment Technologies (6133, M/S 1188); Miner, Nadine E. [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States). Military & Energy Systems Analysis (6114, M/S 1188); Wilson, Michael L. [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States). Resilience and Regulatory Effects (6921, M/S 1138); Le, Hai D. [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States). System Readiness & Sustainment Technologies (6133, M/S 1188); Kao, Gio K. [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States). Networked System Survivability & Assurance (5629, M/S 0671); Melander, Darryl J. [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States). Software Systems R& D (9525, M/S 1188); Longsine, Dennis Earl [Sandia National Laboratories, Unknown, Unknown; Vander Meer, Jr., Robert C. [SAIC, Inc., Albuquerque, NM (United States)

2015-01-01

Our society is increasingly reliant on systems and interoperating collections of systems, known as systems of systems (SoS). These SoS are often subject to changing missions (e.g., nation- building, arms-control treaties), threats (e.g., asymmetric warfare, terrorism), natural environments (e.g., climate, weather, natural disasters) and budgets. How well can SoS adapt to these types of dynamic conditions? This report details the results of a three year Laboratory Directed Research and Development (LDRD) project aimed at developing metrics and methodologies for quantifying the adaptability of systems and SoS. Work products include: derivation of a set of adaptability metrics, a method for combining the metrics into a system of systems adaptability index (SoSAI) used to compare adaptability of SoS designs, development of a prototype dynamic SoS (proto-dSoS) simulation environment which provides the ability to investigate the validity of the adaptability metric set, and two test cases that evaluate the usefulness of a subset of the adaptability metrics and SoSAI for distinguishing good from poor adaptability in a SoS. Intellectual property results include three patents pending: A Method For Quantifying Relative System Adaptability, Method for Evaluating System Performance, and A Method for Determining Systems Re-Tasking.

A stochastic approach for quantifying immigrant integration: the Spanish test case

Science.gov (United States)

Agliari, Elena; Barra, Adriano; Contucci, Pierluigi; Sandell, Richard; Vernia, Cecilia

2014-10-01

We apply stochastic process theory to the analysis of immigrant integration. Using a unique and detailed data set from Spain, we study the relationship between local immigrant density and two social and two economic immigration quantifiers for the period 1999-2010. As opposed to the classic time-series approach, by letting immigrant density play the role of ‘time’ and the quantifier the role of ‘space,’ it becomes possible to analyse the behavior of the quantifiers by means of continuous time random walks. Two classes of results are then obtained. First, we show that social integration quantifiers evolve following diffusion law, while the evolution of economic quantifiers exhibits ballistic dynamics. Second, we make predictions of best- and worst-case scenarios taking into account large local fluctuations. Our stochastic process approach to integration lends itself to interesting forecasting scenarios which, in the hands of policy makers, have the potential to improve political responses to integration problems. For instance, estimating the standard first-passage time and maximum-span walk reveals local differences in integration performance for different immigration scenarios. Thus, by recognizing the importance of local fluctuations around national means, this research constitutes an important tool to assess the impact of immigration phenomena on municipal budgets and to set up solid multi-ethnic plans at the municipal level as immigration pressures build.

A stochastic approach for quantifying immigrant integration: the Spanish test case

International Nuclear Information System (INIS)

Agliari, Elena; Barra, Adriano; Contucci, Pierluigi; Sandell, Richard; Vernia, Cecilia

2014-01-01

We apply stochastic process theory to the analysis of immigrant integration. Using a unique and detailed data set from Spain, we study the relationship between local immigrant density and two social and two economic immigration quantifiers for the period 1999–2010. As opposed to the classic time-series approach, by letting immigrant density play the role of ‘time’ and the quantifier the role of ‘space,’ it becomes possible to analyse the behavior of the quantifiers by means of continuous time random walks. Two classes of results are then obtained. First, we show that social integration quantifiers evolve following diffusion law, while the evolution of economic quantifiers exhibits ballistic dynamics. Second, we make predictions of best- and worst-case scenarios taking into account large local fluctuations. Our stochastic process approach to integration lends itself to interesting forecasting scenarios which, in the hands of policy makers, have the potential to improve political responses to integration problems. For instance, estimating the standard first-passage time and maximum-span walk reveals local differences in integration performance for different immigration scenarios. Thus, by recognizing the importance of local fluctuations around national means, this research constitutes an important tool to assess the impact of immigration phenomena on municipal budgets and to set up solid multi-ethnic plans at the municipal level as immigration pressures build. (paper)

Multi-objective differential evolution with adaptive Cauchy mutation for short-term multi-objective optimal hydro-thermal scheduling

Energy Technology Data Exchange (ETDEWEB)

Qin Hui [College of Hydropower and Information Engineering, Huazhong University of Science and Technology, Wuhan 430074 (China); Zhou Jianzhong, E-mail: jz.zhou@hust.edu.c [College of Hydropower and Information Engineering, Huazhong University of Science and Technology, Wuhan 430074 (China); Lu Youlin; Wang Ying; Zhang Yongchuan [College of Hydropower and Information Engineering, Huazhong University of Science and Technology, Wuhan 430074 (China)

2010-04-15

A new multi-objective optimization method based on differential evolution with adaptive Cauchy mutation (MODE-ACM) is presented to solve short-term multi-objective optimal hydro-thermal scheduling (MOOHS) problem. Besides fuel cost, the pollutant gas emission is also optimized as an objective. The water transport delay between connected reservoirs and the effect of valve-point loading of thermal units are also taken into account in the presented problem formulation. The proposed algorithm adopts an elitist archive to retain non-dominated solutions obtained during the evolutionary process. It modifies the DE's operators to make it suit for multi-objective optimization (MOO) problems and improve its performance. Furthermore, to avoid premature convergence, an adaptive Cauchy mutation is proposed to preserve the diversity of population. An effective constraints handling method is utilized to handle the complex equality and inequality constraints. The effectiveness of the proposed algorithm is tested on a hydro-thermal system consisting of four cascaded hydro plants and three thermal units. The results obtained by MODE-ACM are compared with several previous studies. It is found that the results obtained by MODE-ACM are superior in terms of fuel cost as well as emission output, consuming a shorter time. Thus it can be a viable alternative to generate optimal trade-offs for short-term MOOHS problem.

Reconstructing the ups and downs of primate brain evolution: implications for adaptive hypotheses and Homo floresiensis

Directory of Open Access Journals (Sweden)

Barton Robert A

2010-01-01

Full Text Available Abstract Background Brain size is a key adaptive trait. It is often assumed that increasing brain size was a general evolutionary trend in primates, yet recent fossil discoveries have documented brain size decreases in some lineages, raising the question of how general a trend there was for brains to increase in mass over evolutionary time. We present the first systematic phylogenetic analysis designed to answer this question. Results We performed ancestral state reconstructions of three traits (absolute brain mass, absolute body mass, relative brain mass using 37 extant and 23 extinct primate species and three approaches to ancestral state reconstruction: parsimony, maximum likelihood and Bayesian Markov-chain Monte Carlo. Both absolute and relative brain mass generally increased over evolutionary time, but body mass did not. Nevertheless both absolute and relative brain mass decreased along several branches. Applying these results to the contentious case of Homo floresiensis, we find a number of scenarios under which the proposed evolution of Homo floresiensis' small brain appears to be consistent with patterns observed along other lineages, dependent on body mass and phylogenetic position. Conclusions Our results confirm that brain expansion began early in primate evolution and show that increases occurred in all major clades. Only in terms of an increase in absolute mass does the human lineage appear particularly striking, with both the rate of proportional change in mass and relative brain size having episodes of greater expansion elsewhere on the primate phylogeny. However, decreases in brain mass also occurred along branches in all major clades, and we conclude that, while selection has acted to enlarge primate brains, in some lineages this trend has been reversed. Further analyses of the phylogenetic position of Homo floresiensis and better body mass estimates are required to confirm the plausibility of the evolution of its small brain

Analytic models for the evolution of semilocal string networks

International Nuclear Information System (INIS)

Nunes, A. S.; Martins, C. J. A. P.; Avgoustidis, A.; Urrestilla, J.

2011-01-01

We revisit previously developed analytic models for defect evolution and adapt them appropriately for the study of semilocal string networks. We thus confirm the expectation (based on numerical simulations) that linear scaling evolution is the attractor solution for a broad range of model parameters. We discuss in detail the evolution of individual semilocal segments, focusing on the phenomenology of segment growth, and also provide a preliminary comparison with existing numerical simulations.

Ecological adaptations and commensal evolution of the Polynoidae (Polychaeta) in the Southwest Indian Ocean Ridge: A phylogenetic approach

Science.gov (United States)

Serpetti, Natalia; Taylor, M. L.; Brennan, D.; Green, D. H.; Rogers, A. D.; Paterson, G. L. J.; Narayanaswamy, B. E.

2017-03-01

The polychaete family polynoid is very large and includes a high diversity of behaviours, including numerous examples of commensal species. The comparison between free-living and commensal behaviours and the evolution of the relationships between commensal species and their hosts are valuable case studies of ecological adaptations. Deep-sea species of Polynoidae were sampled at four seamounts in the Southwest Indian Ridge and twenty specimens from seven species were selected to be analysed. Among them, there were free-living species, living within the three-dimensional framework of cold-water coral reefs, on coral rubble and on mobile sediments, and commensal species, associated with octocorals, hydrocorals (stylasterids), antipatharians and echinoderms (holothurian and ophiuroids). We analysed two mitochondrial (COI, 16S) and two nuclear (18S, 28S) ribosomal genetic markers and their combined sequences were compared with other Genbank sequences to assess the taxonomic relationships within the species under study, and the potential role of hosts in speciation processes. Most basal species of the sub-family Polynoinae are obligate symbionts showing specific morphological adaptations. Obligate and facultative commensal species and free-living species have evolved a number of times, although, according to our results, the obligate coral commensal species appear to be monophyletic.

Correlated evolution of thermal niches and functional physiology in tropical freshwater fishes.

Science.gov (United States)

Culumber, Zachary W; Tobler, Michael

2018-05-01

The role of ecology in phenotypic and species diversification is widely documented. Nonetheless, numerous nonadaptive processes can shape realized niches and phenotypic variation in natural populations, complicating inferences about adaptive evolution at macroevolutionary scales. We tested for evolved differences in thermal tolerances and their association with the realized thermal niche (including metrics describing diurnal and seasonal patterns of temperature extremes and variability) across a genus of tropical freshwater fishes reared in a standardized environment. There was limited evolution along the thermal niche axis associated with variation in maximum temperature and in upper thermal limits. In contrast, there was considerable diversification along the first major axis of the thermal niche associated with minimum temperatures and in lower thermal limits. Across our adaptive landscape analyses, 70% of species exhibited evidence of divergence in thermal niches. Most importantly, the first two major axes of thermal niche variation were significantly correlated with variation in lower thermal limits. Our results indicate adaptation to divergent thermal niches and adaptive evolution of related functional traits, and highlight the importance of divergence in lower thermal limits for the evolution of tropical biodiversity. © 2018 European Society For Evolutionary Biology. Journal of Evolutionary Biology © 2018 European Society For Evolutionary Biology.

Adaptive laboratory evolution of ethanologenic Zymomonas mobilis strain tolerant to furfural and acetic acid inhibitors.

Science.gov (United States)

Shui, Zong-Xia; Qin, Han; Wu, Bo; Ruan, Zhi-yong; Wang, Lu-shang; Tan, Fu-Rong; Wang, Jing-Li; Tang, Xiao-Yu; Dai, Li-Chun; Hu, Guo-Quan; He, Ming-Xiong

2015-07-01

Furfural and acetic acid from lignocellulosic hydrolysates are the prevalent inhibitors to Zymomonas mobilis during cellulosic ethanol production. Developing a strain tolerant to furfural or acetic acid inhibitors is difficul by using rational engineering strategies due to poor understanding of their underlying molecular mechanisms. In this study, strategy of adaptive laboratory evolution (ALE) was used for development of a furfural and acetic acid-tolerant strain. After three round evolution, four evolved mutants (ZMA7-2, ZMA7-3, ZMF3-2, and ZMF3-3) that showed higher growth capacity were successfully obtained via ALE method. Based on the results of profiling of cell growth, glucose utilization, ethanol yield, and activity of key enzymes, two desired strains, ZMA7-2 and ZMF3-3, were achieved, which showed higher tolerance under 7 g/l acetic acid and 3 g/l furfural stress condition. Especially, it is the first report of Z. mobilis strain that could tolerate higher furfural. The best strain, Z. mobilis ZMF3-3, has showed 94.84% theoretical ethanol yield under 3-g/l furfural stress condition, and the theoretical ethanol yield of ZM4 is only 9.89%. Our study also demonstrated that ALE method might also be used as a powerful metabolic engineering tool for metabolic engineering in Z. mobilis. Furthermore, the two best strains could be used as novel host for further metabolic engineering in cellulosic ethanol or future biorefinery. Importantly, the two strains may also be used as novel-tolerant model organisms for the genetic mechanism on the "omics" level, which will provide some useful information for inverse metabolic engineering.

Constrained pattern of viral evolution in acute and early HCV infection limits viral plasticity.

Directory of Open Access Journals (Sweden)

Katja Pfafferott

2011-02-01

Full Text Available Cellular immune responses during acute Hepatitis C virus (HCV and HIV infection are a known correlate of infection outcome. Viral adaptation to these responses via mutation(s within CD8+ T-cell epitopes allows these viruses to subvert host immune control. This study examined HCV evolution in 21 HCV genotype 1-infected subjects to characterise the level of viral adaptation during acute and early HCV infection. Of the total mutations observed 25% were within described CD8+ T-cell epitopes or at viral adaptation sites. Most mutations were maintained into the chronic phase of HCV infection (75%. The lack of reversion of adaptations and high proportion of silent substitutions suggests that HCV has structural and functional limitations that constrain evolution. These results were compared to the pattern of viral evolution observed in 98 subjects during a similar phase in HIV infection from a previous study. In contrast to HCV, evolution during acute HIV infection is marked by high levels of amino acid change relative to silent substitutions, including a higher proportion of adaptations, likely reflecting strong and continued CD8+ T-cell pressure combined with greater plasticity of the virus. Understanding viral escape dynamics for these two viruses is important for effective T cell vaccine design.

Population differences in host use by a seed-beetle: local adaptation, phenotypic plasticity and maternal effects.

Science.gov (United States)

Amarillo-Suárez, Angela R; Fox, Charles W

2006-11-01

For insects that develop inside discrete hosts, both host size and host quality constrain offspring growth, influencing the evolution of body size and life history traits. Using a two-generation common garden experiment, we quantified the contribution of maternal and rearing hosts to differences in growth and life history traits between populations of the seed-feeding beetle Stator limbatus that use a large-seeded host, Acacia greggii, and a small-seeded host, Pseudosamanea guachapele. Populations differed genetically for all traits when beetles were raised in a common garden. Contrary to expectations from the local adaptation hypothesis, beetles from all populations were larger, developed faster and had higher survivorship when reared on seeds of A. greggii (the larger host), irrespective of their native host. We observed two host plant-mediated maternal effects: offspring matured sooner, regardless of their rearing host, when their mothers were reared on P. guachapele (this was not caused by an effect of rearing host on egg size), and females laid larger eggs on P. guachapele. This is the first study to document plasticity by S. limbatus in response to P. guachapele, suggesting that plasticity is an ancestral trait in S. limbatus that likely plays an important role in diet expansion. Although differences between populations in growth and life history traits are likely adaptations to their host plants, host-associated maternal effects, partly mediated by maternal egg size plasticity, influence growth and life history traits and likely play an important role in the evolution of the breadth of S. limbatus' diet. More generally, phenotypic plasticity mediates the fitness consequences of using novel hosts, likely facilitating colonization of new hosts, but also buffering herbivores from selection post-colonization. Plasticity in response to novel versus normal hosts varied among our study populations such that disentangling the historical role of plasticity in

Ultra Linear Low-loss Varactors & Circuits for Adaptive RF Systems

NARCIS (Netherlands)

Huang, C.

2010-01-01

With the evolution of wireless communication, varactors can play an important role in enabling adaptive transceivers as well as phase-diversity systems. This thesis presents various varactor diode-based circuit topologies that facilitate RF adaptivity. The proposed varactor configurations can act as

Adaptive value of sex in microbial pathogens.

Science.gov (United States)

Michod, Richard E; Bernstein, Harris; Nedelcu, Aurora M

2008-05-01

Explaining the adaptive value of sex is one of the great outstanding problems in biology. The challenge comes from the difficulty in identifying the benefits provided by sex, which must outweigh the substantial costs of sex. Here, we consider the adaptive value of sex in viruses, bacteria and fungi, and particularly the information available on the adaptive role of sex in pathogenic microorganisms. Our general theme is that the varied aspects of sex in pathogens illustrate the varied issues surrounding the evolution of sex generally. These include, the benefits of sex (in the short- and long-term), as well as the costs of sex (both to the host and to the pathogen). For the benefits of sex (that is, its adaptive value), we consider three hypotheses: (i) sex provides for effective and efficient recombinational repair of DNA damages, (ii) sex provides DNA for food, and (iii) sex produces variation and reduces genetic associations among alleles under selection. Although the evolution of sex in microbial pathogens illustrates these general issues, our paper is not a general review of theories for the evolution of sex in all organisms. Rather, we focus on the adaptive value of sex in microbial pathogens and conclude that in terms of short-term benefits, the DNA repair hypothesis has the most support and is the most generally applicable hypothesis in this group. In particular, recombinational repair of DNA damages may substantially benefit pathogens when challenged by the oxidative defenses of the host. However, in the long-term, sex may help get rid of mutations, increase the rate of adaptation of the population, and, in pathogens, may infrequently create new infective strains. An additional general issue about sex illustrated by pathogens is that some of the most interesting consequences of sex are not necessarily the reasons for which sex evolved. For example, antibiotic resistance may be transferred by bacterial sex, but this transfer is probably not the reason sex

Adaptive simplification and the evolution of gecko locomotion: Morphological and biomechanical consequences of losing adhesion

Science.gov (United States)

Higham, Timothy E.; Birn-Jeffery, Aleksandra V.; Collins, Clint E.; Hulsey, C. Darrin; Russell, Anthony P.

2015-01-01

Innovations permit the diversification of lineages, but they may also impose functional constraints on behaviors such as locomotion. Thus, it is not surprising that secondary simplification of novel locomotory traits has occurred several times among vertebrates and could potentially lead to exceptional divergence when constraints are relaxed. For example, the gecko adhesive system is a remarkable innovation that permits locomotion on surfaces unavailable to other animals, but has been lost or simplified in species that have reverted to a terrestrial lifestyle. We examined the functional and morphological consequences of this adaptive simplification in the Pachydactylus radiation of geckos, which exhibits multiple unambiguous losses or bouts of simplification of the adhesive system. We found that the rates of morphological and 3D locomotor kinematic evolution are elevated in those species that have simplified or lost adhesive capabilities. This finding suggests that the constraints associated with adhesion have been circumvented, permitting these species to either run faster or burrow. The association between a terrestrial lifestyle and the loss/reduction of adhesion suggests a direct link between morphology, biomechanics, and ecology. PMID:25548182

An Adaptive Fuzzy-Based System to Simulate, Quantify and Compensate Color Blindness

OpenAIRE

Lee, Jinmi; Santos, Wellington Pinheiro dos

2017-01-01

About 8% of the male population of the world are affected by a determined type of color vision disturbance, which varies from the partial to complete reduction of the ability to distinguish certain colors. A considerable amount of color blind people are able to live all life long without knowing they have color vision disabilities and abnormalities. Nowadays the evolution of information technology and computer science, specifically image processing techniques and computer graphics, can be fun...

Prospects for the study of evolution in the deep biosphere

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Jennifer F Biddle

2012-01-01

Full Text Available Since the days of Darwin, scientists have used the framework of the theory of evolution to explore the interconnectedness of life on Earth and adaptation of organisms to the ever-changing environment. The advent of molecular biology has advanced and accelerated the study of evolution by allowing direct examination of the genetic material that ultimately determines the phenotypes upon which selection acts. The study of evolution has been furthered through examination of microbial evolution, with large population numbers, short generation times and easily extractable DNA. Such work has spawned the study of microbial biogeography, with the realization that concepts developed in population genetics may be applicable to microbial genomes (Manhes et al. 2011, Martiny et al. 2006. Microbial biogeography and adaptation has been examined in many different environments. Here we argue that the deep biosphere is a unique environment for the study of evolution and list specific factors that can be considered and where the studies may be performed. This publication is the result of the NSF-funded Center for Dark Energy Biosphere Investigations (C-DEBI theme team on Evolution (www.darkenergybiosphere.org.

Prospects for the Study of Evolution in the Deep Biosphere

Science.gov (United States)

Biddle, Jennifer F.; Sylvan, Jason B.; Brazelton, William J.; Tully, Benjamin J.; Edwards, Katrina J.; Moyer, Craig L.; Heidelberg, John F.; Nelson, William C.

2012-01-01

Since the days of Darwin, scientists have used the framework of the theory of evolution to explore the interconnectedness of life on Earth and adaptation of organisms to the ever-changing environment. The advent of molecular biology has advanced and accelerated the study of evolution by allowing direct examination of the genetic material that ultimately determines the phenotypes upon which selection acts. The study of evolution has been furthered through examination of microbial evolution, with large population numbers, short generation times, and easily extractable DNA. Such work has spawned the study of microbial biogeography, with the realization that concepts developed in population genetics may be applicable to microbial genomes (Martiny et al., 2006; Manhes and Velicer, 2011). Microbial biogeography and adaptation has been examined in many different environments. Here we argue that the deep biosphere is a unique environment for the study of evolution and list specific factors that can be considered and where the studies may be performed. This publication is the result of the NSF-funded Center for Dark Energy Biosphere Investigations (C-DEBI) theme team on Evolution (www.darkenergybiosphere.org). PMID:22319515

Adapting to Population Growth: The Evolutionary Alternative to Malthus

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Axel Kristinsson

2016-06-01

Full Text Available A long-standing debate on the dynamics of population growth in human history has become polarized between a Malthusian stance and a Boserupian one. The former tends to view population growth as limited by carrying capacity, dependent on environment and technology, whereas the latter sees population growth itself as a major inducement to social, economic and technological developments. In this paper the authors experiment with approaching this debate by using recent developments in evolutionary theory. According to these, evolutionary principles, as expounded by Charles Darwin and subsequent evolutionary scientists, apply not only to biological evolution but also to social or cultural evolution. Here, the role of genes is taken over by culture and, since culture is much more pliable than our DNA, evolution speeds up. As the only organisms on Earth whose evolution relies as heavily on culture as on genes, humans have become extremely adaptable. Their hyper-adaptability suggest that humans, through their cultural evolution, have managed increasingly to adapt to their own growing population, thus succeeding in accommodating ever-growing numbers. This hypothesis fits the Boserupian approach to population very well but less so the Malthusian one, perhaps indicating a gradual shift from a Malthusian regime to a Boserupian one in human history. The hypothesis is discussed and examined through four case studies: The beginning of farming around Göbekli Tepe in southeast Turkey, the productive farming systems of Tiwanaku in South America, the population crisis of late medieval and early modern Iceland, and the ‘collapse’ of Rapa Nui (Easter Island.

Evolving Personalized Content for Super Mario Bros Using Grammatical Evolution

DEFF Research Database (Denmark)

Shaker, Noor; Yannakakis, Georgios N.; Togelius, Julian

2012-01-01

-adapted content by employing an adaptation mechanism as a fitness function in grammatical evolution to optimize the player experience of three emotional states: engagement, frustration and challenge. The fitness functions used are models of player experience constructed in our previous work from crowd...

The evolution of sex is favoured during adaptation to new environments.

Science.gov (United States)

Becks, Lutz; Agrawal, Aneil F

2012-01-01

Both theory and experiments have demonstrated that sex can facilitate adaptation, potentially yielding a group-level advantage to sex. However, it is unclear whether this process can help solve the more difficult problem of the maintenance of sex within populations. Using experimental populations of the facultatively sexual rotifer Brachionus calyciflorus, we show that rates of sex evolve to higher levels during adaptation but then decline as fitness plateaus. To assess the fitness consequences of genetic mixing, we directly compare the fitnesses of sexually and asexually derived genotypes that naturally occur in our experimental populations. Sexually derived genotypes are more fit than asexually derived genotypes when adaptive pressures are strong, but this pattern reverses as the pace of adaptation slows, matching the pattern of evolutionary change in the rate of sex. These fitness assays test the net effect of sex but cannot be used to disentangle whether selection on sex arises because highly sexual lineages become associated with different allele combinations or with different allele frequencies than less sexual lineages (i.e., "short-" or "long-term" effects, respectively). We infer which of these mechanisms provides an advantage to sex by performing additional manipulations to obtain fitness distributions of sexual and asexual progeny arrays from unbiased parents (rather than from naturally occurring, and thereby evolutionarily biased, parents). We find evidence that sex breaks down adaptive gene combinations, resulting in lower average fitness of sexual progeny (i.e., a short-term disadvantage to sex). As predicted by theory, the advantage to sex arises because sexually derived progeny are more variable in fitness, allowing for faster adaptation. This "long-term advantage" builds over multiple generations, eventually resulting in higher fitness of sexual types.

Psychosocial adaptation: an evolutionary concept analysis exploring a common multidisciplinary language.

Science.gov (United States)

Londono, Yenly; McMillan, Diana E

2015-11-01

To provide the first known concept analysis of psychosocial adaptation, exploring its evolution from the concept adaptation. We also determine how psychosocial adaptation is conceptualized across nursing, health, sociobehavioural and education disciplines. Psychosocial adaptation is an important conceptual term that is poorly defined in nursing and other health, sociobehavioural and education disciplines. A thorough understanding of the concept's application in nursing and across disciplines can help to clarify its meaning, facilitate a more effective common language between disciplines and inform future psychosocial adaptation research. Rodger's evolutionary view guided this concept analysis. Peer-reviewed English and Spanish manuscripts published between 2011-2013 were retrieved from the following databases: CINAHL, Psych INFO, PubMed, Scopus and LILACS. Eighty-nine articles related to psychosocial adaptation were included in the analysis. Findings identify key attributes, antecedents and consequences associated with the use of the concept. Findings were compared vis-a-vis reported characteristics of adaptation. The attributes characterizing psychosocial adaptation are: change, process, continuity, interaction and influence. In psychosocial adaptation, new life conditions serve as antecedents, while consequences are good or bad outcomes. Important features of the evolution of this concept include its broad appropriation across the reviewed disciplines. The attributes of psychosocial adaptation, have some similarities to those of general adaptation. Both concepts include an aspect of change, but unlike adaptation, psychosocial adaptation has branched away from biological descriptors, such as homeostasis and tends to focus on relational characteristics, such as interaction and influences. © 2015 John Wiley & Sons Ltd.

Mapping the evolution of scientific ideas

Energy Technology Data Exchange (ETDEWEB)

Roberts, David C [Los Alamos National Laboratory; Herrera, Mark [UNIV OF MARYLAND; Gulbahce, Natali [NORTHEASTERN UNIV

2008-01-01

The importance of interdisciplinary research is ever increasing as challenging world problems require expertise across diverse fields. Despite the apparent conceptual boundaries of scientific fields, a formal description for their evolution is lacking. Here we describe a novel approach to study the dynamics and evolution of scientific ideas and fields using a network-based analysis. We build a idea network consisting of American Physical Society Pacs numbers as nodes representing scientific concepts. Two Pacs numbers are linked in the network if there exist publications that reference them simultaneously. We locate scientific fields using an overlapping community finding algorithm and describe the time evolution of these fields using a community evolution method over the course of 1985-2006. We find that the communities we find map to scientific fields, the lifetime of these fields strongly depends on their size, impact and activity, and longest living communities are least volatile. The described approach to quantify the evolution of ideas is expected to be relevant in making predictions about the future of science and how to guide its development.

Nudging Evolution?

OpenAIRE

Katharine N. Farrell; Andreas Thiel

2013-01-01

This Special Feature, "Nudging Evolution? Critical Exploration of the Potential and Limitations of the Concept of Institutional Fit for the Study and Adaptive Management of Social-Ecological Systems," aims to contribute toward the development of social theory and social research methods for the study of social-ecological system dynamics. Our objective is to help strengthen the academic discourse concerning if, and if so, how, to what extent, and in what concrete ways the concept of institut...

Quantifier spreading in child eye movements: A case of the Russian quantifier kazhdyj ‘every'

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Irina A. Sekerina

2017-07-01

Full Text Available Extensive cross-linguistic work has documented that children up to the age of 9–10 make errors when performing a sentence-picture verification task that pairs spoken sentences with the universal quantifier 'every 'and pictures with entities in partial one-to-one correspondence. These errors stem from children’s difficulties in restricting the domain of a universal quantifier to the appropriate noun phrase and are referred in the literature as 'quantifier-spreading '('q'-spreading. We adapted the task to be performed in conjunction with eye-movement recordings using the Visual World Paradigm. Russian-speaking 5-to-6-year-old children ('N '= 31 listened to sentences like 'Kazhdyj alligator lezhit v vanne '‘Every alligator is lying in a bathtub’ and viewed pictures with three alligators, each in a bathtub, and two extra empty bathtubs. Non-spreader children ('N '= 12 were adult-like in their accuracy whereas 'q'-spreading ones ('N '= 19 were only 43% correct in interpreting such sentences compared to the control sentences. Eye movements of 'q'-spreading children revealed that more looks to the extra containers (two empty bathtubs correlated with higher error rates reflecting the processing pattern of 'q'-spreading. In contrast, more looks to the distractors in control sentences did not lead to errors in interpretation. We argue that 'q'-spreading errors are caused by interference from the extra entities in the visual context, and our results support the processing difficulty account of acquisition of quantification. Interference results in cognitive overload as children have to integrate multiple sources of information, i.e., visual context with salient extra entities and the spoken sentence in which these entities are mentioned in real-time processing.   This article is part of the special collection: Acquisition of Quantification

Bioavailability of Metal Ions and Evolutionary Adaptation

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Rolando P. Hong Enriquez

2012-10-01

Full Text Available The evolution of life on earth has been a long process that began nearly 3,5 x 109 years ago. In their initial moments, evolution was mainly influenced by anaerobic environments; with the rise of O2 and the corresponding change in bioavailability of metal ions, new mechanisms of survival were created. Here we review the relationships between ancient atmospheric conditions, metal ion bioavailability and adaptation of metals homeostasis during early evolution. A general picture linking geochemistry, biochemistry and homeostasis is supported by the reviewed literature and is further illustrated in this report using simple database searches.

HOMFLYPT polynomial is the best quantifier for topological cascades of vortex knots

Science.gov (United States)

Ricca, Renzo L.; Liu, Xin

2018-02-01

In this paper we derive and compare numerical sequences obtained by adapted polynomials such as HOMFLYPT, Jones and Alexander-Conway for the topological cascade of vortex torus knots and links that progressively untie by a single reconnection event at a time. Two cases are considered: the alternate sequence of knots and co-oriented links (with positive crossings) and the sequence of two-component links with oppositely oriented components (negative crossings). New recurrence equations are derived and sequences of numerical values are computed. In all cases the adapted HOMFLYPT polynomial proves to be the best quantifier for the topological cascade of torus knots and links.

A Theoretical Approach to Norm Ecosystems: Two Adaptive Architectures of Indirect Reciprocity Show Different Paths to the Evolution of Cooperation

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Satoshi Uchida

2018-02-01

Full Text Available Indirect reciprocity is one of the basic mechanisms to sustain mutual cooperation, by which beneficial acts are returned, not by the recipient, but by third parties. This mechanism relies on the ability of individuals to know the past actions of others, and to assess those actions. There are many different systems of assessing others, which can be interpreted as rudimentary social norms (i.e., views on what is “good” or “bad”. In this paper, impacts of different adaptive architectures, i.e., ways for individuals to adapt to environments, on indirect reciprocity are investigated. We examine two representative architectures: one based on replicator dynamics and the other on genetic algorithm. Different from the replicator dynamics, the genetic algorithm requires describing the mixture of all possible norms in the norm space under consideration. Therefore, we also propose an analytic method to study norm ecosystems in which all possible second order social norms potentially exist and compete. The analysis reveals that the different adaptive architectures show different paths to the evolution of cooperation. Especially we find that so called Stern-Judging, one of the best studied norms in the literature, exhibits distinct behaviors in both architectures. On one hand, in the replicator dynamics, Stern-Judging remains alive and gets a majority steadily when the population reaches a cooperative state. On the other hand, in the genetic algorithm, it gets a majority only temporarily and becomes extinct in the end.

A Theoretical Approach to Norm Ecosystems: Two Adaptive Architectures of Indirect Reciprocity Show Different Paths to the Evolution of Cooperation

Science.gov (United States)

Uchida, Satoshi; Yamamoto, Hitoshi; Okada, Isamu; Sasaki, Tatsuya

2018-02-01

Indirect reciprocity is one of the basic mechanisms to sustain mutual cooperation, by which beneficial acts are returned, not by the recipient, but by third parties. This mechanism relies on the ability of individuals to know the past actions of others, and to assess those actions. There are many different systems of assessing others, which can be interpreted as rudimentary social norms (i.e., views on what is “good” or “bad”). In this paper, impacts of different adaptive architectures, i.e., ways for individuals to adapt to environments, on indirect reciprocity are investigated. We examine two representative architectures: one based on replicator dynamics and the other on genetic algorithm. Different from the replicator dynamics, the genetic algorithm requires describing the mixture of all possible norms in the norm space under consideration. Therefore, we also propose an analytic method to study norm ecosystems in which all possible second order social norms potentially exist and compete. The analysis reveals that the different adaptive architectures show different paths to the evolution of cooperation. Especially we find that so called Stern-Judging, one of the best studied norms in the literature, exhibits distinct behaviors in both architectures. On one hand, in the replicator dynamics, Stern-Judging remains alive and gets a majority steadily when the population reaches a cooperative state. On the other hand, in the genetic algorithm, it gets a majority only temporarily and becomes extinct in the end.

Art as A Playground for Evolution

DEFF Research Database (Denmark)

Beloff, Laura

2016-01-01

Art works which engage with the topic of human enhancement and evolution have begun appearing parallel to increased awareness about anthropogenic changes to our environment and acceleration of the speed of technological developments that impact us and our biological environment. The article...... and related topics is proposed as play activity for adults, which simultaneously experiments directly with ideas concerning evolution and human development. The author proposes that these kinds of experimental art projects support our mental adaptation to evolutionary changes....

Evolution of female carotenoid coloration by sexual constraint in Carduelis finches

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Cardoso Gonçalo C

2010-03-01

Full Text Available Abstract Background Females often express the same ornaments as males to a similar or lesser degree. Female ornaments can be adaptive, but little is known regarding their origins and mode of evolution. Current utility does not imply evolutionary causation, and therefore it is possible that female ornamentation evolved due to selection on females, as a correlated response to selection on males (sexual constraint, or a combination of both. We tested these ideas simulating simple models for the evolution of male and female correlated traits, and compared their predictions against the coloration of finches in the genus Carduelis. Results For carotenoid-based ornamental coloration, a model of sexual constraint on females fits the Carduelis data well. The two alternative models (sexual constraint on males, and mutual constraint were rejected as causing the similarities in carotenoid coloration between males and females. For melanin coloration, the correlation between the sexes was weaker, indicating that males and females evolved independently to a greater extent. Conclusions This indicates that sexual constraint on females was an important mechanism for the evolution of ornamental carotenoid coloration in females, but less so for melanin coloration. This does not mean that female carotenoid coloration is non-adaptive or maladaptive, because sexual dichromatism could evolve if it were maladaptive. It suggests, however, that most evolution of female carotenoid coloration was male-driven and, when adaptive, may not be an adaptation stricto sensu.

Transformation and diversification in early mammal evolution.

Science.gov (United States)

Luo, Zhe-Xi

2007-12-13

Evolution of the earliest mammals shows successive episodes of diversification. Lineage-splitting in Mesozoic mammals is coupled with many independent evolutionary experiments and ecological specializations. Classic scenarios of mammalian morphological evolution tend to posit an orderly acquisition of key evolutionary innovations leading to adaptive diversification, but newly discovered fossils show that evolution of such key characters as the middle ear and the tribosphenic teeth is far more labile among Mesozoic mammals. Successive diversifications of Mesozoic mammal groups multiplied the opportunities for many dead-end lineages to iteratively evolve developmental homoplasies and convergent ecological specializations, parallel to those in modern mammal groups.

Mixed integer evolution strategies for parameter optimization.

Science.gov (United States)

Li, Rui; Emmerich, Michael T M; Eggermont, Jeroen; Bäck, Thomas; Schütz, M; Dijkstra, J; Reiber, J H C

2013-01-01

Evolution strategies (ESs) are powerful probabilistic search and optimization algorithms gleaned from biological evolution theory. They have been successfully applied to a wide range of real world applications. The modern ESs are mainly designed for solving continuous parameter optimization problems. Their ability to adapt the parameters of the multivariate normal distribution used for mutation during the optimization run makes them well suited for this domain. In this article we describe and study mixed integer evolution strategies (MIES), which are natural extensions of ES for mixed integer optimization problems. MIES can deal with parameter vectors consisting not only of continuous variables but also with nominal discrete and integer variables. Following the design principles of the canonical evolution strategies, they use specialized mutation operators tailored for the aforementioned mixed parameter classes. For each type of variable, the choice of mutation operators is governed by a natural metric for this variable type, maximal entropy, and symmetry considerations. All distributions used for mutation can be controlled in their shape by means of scaling parameters, allowing self-adaptation to be implemented. After introducing and motivating the conceptual design of the MIES, we study the optimality of the self-adaptation of step sizes and mutation rates on a generalized (weighted) sphere model. Moreover, we prove global convergence of the MIES on a very general class of problems. The remainder of the article is devoted to performance studies on artificial landscapes (barrier functions and mixed integer NK landscapes), and a case study in the optimization of medical image analysis systems. In addition, we show that with proper constraint handling techniques, MIES can also be applied to classical mixed integer nonlinear programming problems.

Academic Preparation in Biology and Advocacy for Teaching Evolution: Biology versus Non-Biology Teachers

Science.gov (United States)

Nehm, Ross H.; Kim, Sun Young; Sheppard, Keith

2009-01-01

Despite considerable focus on evolution knowledge-belief relationships, little research has targeted populations with strong content backgrounds, such as undergraduate degrees in biology. This study (1) measured precertified biology and non-biology teachers' (n = 167) knowledge of evolution and the nature of science; (2) quantified teacher…

Evolution of agricultural production of Zaire before and after 1960

Directory of Open Access Journals (Sweden)

Sabiti, K.

1991-01-01

Full Text Available This study presents the evolution of agricultural production of Zaire before and after 1960 with the help of variable quantifies of products, the cultured area and the exported quantifies of products. A comparative analysis of quantifies of studied products shows that after 1960, the agricultural production of basis foodstuffs of the Zairian population has fallen of the order of 91 % in comparison with the first period. This study shows that the system of peasantry introduced in 1936 by the INEAC, the rationalization of cultural methods connected to the governmental explain the agricultural expansion of Zaire before 1960.

Adaptation and evolution of deep-sea scale worms (Annelida: Polynoidae): insights from transcriptome comparison with a shallow-water species

Science.gov (United States)

Zhang, Yanjie; Sun, Jin; Chen, Chong; Watanabe, Hiromi K.; Feng, Dong; Zhang, Yu; Chiu, Jill M.Y.; Qian, Pei-Yuan; Qiu, Jian-Wen

2017-01-01

Polynoid scale worms (Polynoidae, Annelida) invaded deep-sea chemosynthesis-based ecosystems approximately 60 million years ago, but little is known about their genetic adaptation to the extreme deep-sea environment. In this study, we reported the first two transcriptomes of deep-sea polynoids (Branchipolynoe pettiboneae, Lepidonotopodium sp.) and compared them with the transcriptome of a shallow-water polynoid (Harmothoe imbricata). We determined codon and amino acid usage, positive selected genes, highly expressed genes and putative duplicated genes. Transcriptome assembly produced 98,806 to 225,709 contigs in the three species. There were more positively charged amino acids (i.e., histidine and arginine) and less negatively charged amino acids (i.e., aspartic acid and glutamic acid) in the deep-sea species. There were 120 genes showing clear evidence of positive selection. Among the 10% most highly expressed genes, there were more hemoglobin genes with high expression levels in both deep-sea species. The duplicated genes related to DNA recombination and metabolism, and gene expression were only enriched in deep-sea species. Deep-sea scale worms adopted two strategies of adaptation to hypoxia in the chemosynthesis-based habitats (i.e., rapid evolution of tetra-domain hemoglobin in Branchipolynoe or high expression of single-domain hemoglobin in Lepidonotopodium sp.). PMID:28397791

Quantifying the relevance of adaptive thermal comfort models in moderate thermal climate zones

NARCIS (Netherlands)

Hoof, van J.; Hensen, J.L.M.

2007-01-01

Standards governing thermal comfort evaluation are on a constant cycle of revision and public review. One of the main topics being discussed in the latest round was the introduction of an adaptive thermal comfort model, which now forms an optional part of ASHRAE Standard 55. Also on a national

A brief history of adaptation: conceptual evolution across the IPCC reports (1990-2014)

International Nuclear Information System (INIS)

Simonet, Guillaume

2015-01-01

In the past decade, work on the concepts of vulnerability, resilience and adaptation became central in climate change literature. At the same time a growing number of studies have focussed on the influence of cognitive factors on decision-making processes, such as interpreting elusive concepts such as adaptation. Comprehension of adaptation has evolved considerably since its recognition as a response to climate change in the 90's by the Intergovernmental Panel on Climate Change (IPCC). Currently protecting systems from weather events (the 'adjustment adaptation' approach) is still the prevailing view in climate policies. Nevertheless, a shift toward a 'transformation adaptation' approach is being observed. This position would take better account of the complexity of existing systems and allow reexamining their mechanisms (institutional, technical, financial). This paper aims to analyze conceptual advances on adaptation across the five IPCC reports from 1990 to 2014. This contribution attempts to show that the prominence given to adaptation in the latest report (2014) reflects the cognitive difficulty of conceiving this concept, responds to the growing demand to facilitate its operationalization and confirms its relevance for a better understanding of the underlying complexity of climate change and the global environmental change issue. Pursuing reflection on the adaptation concept should certainly contribute to the emergence of a promising and interdisciplinary field of research

From dinosaurs to modern bird diversity: extending the time scale of adaptive radiation.

Directory of Open Access Journals (Sweden)

Daniel Moen

2014-05-01

Full Text Available What explains why some groups of organisms, like birds, are so species rich? And what explains their extraordinary ecological diversity, ranging from large, flightless birds to small migratory species that fly thousand of kilometers every year? These and similar questions have spurred great interest in adaptive radiation, the diversification of ecological traits in a rapidly speciating group of organisms. Although the initial formulation of modern concepts of adaptive radiation arose from consideration of the fossil record, rigorous attempts to identify adaptive radiation in the fossil record are still uncommon. Moreover, most studies of adaptive radiation concern groups that are less than 50 million years old. Thus, it is unclear how important adaptive radiation is over temporal scales that span much larger portions of the history of life. In this issue, Benson et al. test the idea of a "deep-time" adaptive radiation in dinosaurs, compiling and using one of the most comprehensive phylogenetic and body-size datasets for fossils. Using recent phylogenetic statistical methods, they find that in most clades of dinosaurs there is a strong signal of an "early burst" in body-size evolution, a predicted pattern of adaptive radiation in which rapid trait evolution happens early in a group's history and then slows down. They also find that body-size evolution did not slow down in the lineage leading to birds, hinting at why birds survived to the present day and diversified. This paper represents one of the most convincing attempts at understanding deep-time adaptive radiations.

From dinosaurs to modern bird diversity: extending the time scale of adaptive radiation.

Science.gov (United States)

Moen, Daniel; Morlon, Hélène

2014-05-01

What explains why some groups of organisms, like birds, are so species rich? And what explains their extraordinary ecological diversity, ranging from large, flightless birds to small migratory species that fly thousand of kilometers every year? These and similar questions have spurred great interest in adaptive radiation, the diversification of ecological traits in a rapidly speciating group of organisms. Although the initial formulation of modern concepts of adaptive radiation arose from consideration of the fossil record, rigorous attempts to identify adaptive radiation in the fossil record are still uncommon. Moreover, most studies of adaptive radiation concern groups that are less than 50 million years old. Thus, it is unclear how important adaptive radiation is over temporal scales that span much larger portions of the history of life. In this issue, Benson et al. test the idea of a "deep-time" adaptive radiation in dinosaurs, compiling and using one of the most comprehensive phylogenetic and body-size datasets for fossils. Using recent phylogenetic statistical methods, they find that in most clades of dinosaurs there is a strong signal of an "early burst" in body-size evolution, a predicted pattern of adaptive radiation in which rapid trait evolution happens early in a group's history and then slows down. They also find that body-size evolution did not slow down in the lineage leading to birds, hinting at why birds survived to the present day and diversified. This paper represents one of the most convincing attempts at understanding deep-time adaptive radiations.

Quantifying Matter

CERN Document Server

Angelo, Joseph A

2011-01-01

Quantifying Matter explains how scientists learned to measure matter and quantify some of its most fascinating and useful properties. It presents many of the most important intellectual achievements and technical developments that led to the scientific interpretation of substance. Complete with full-color photographs, this exciting new volume describes the basic characteristics and properties of matter. Chapters include:. -Exploring the Nature of Matter. -The Origin of Matter. -The Search for Substance. -Quantifying Matter During the Scientific Revolution. -Understanding Matter's Electromagnet

Mechanisms and impact of genetic recombination in the evolution of Streptococcus pneumoniae.

Science.gov (United States)

Chaguza, Chrispin; Cornick, Jennifer E; Everett, Dean B

2015-01-01

Streptococcus pneumoniae (the pneumococcus) is a highly recombinogenic bacterium responsible for a high burden of human disease globally. Genetic recombination, a process in which exogenous DNA is acquired and incorporated into its genome, is a key evolutionary mechanism employed by the pneumococcus to rapidly adapt to selective pressures. The rate at which the pneumococcus acquires genetic variation through recombination is much higher than the rate at which the organism acquires variation through spontaneous mutations. This higher rate of variation allows the pneumococcus to circumvent the host innate and adaptive immune responses, escape clinical interventions, including antibiotic therapy and vaccine introduction. The rapid influx of whole genome sequence (WGS) data and the advent of novel analysis methods and powerful computational tools for population genetics and evolution studies has transformed our understanding of how genetic recombination drives pneumococcal adaptation and evolution. Here we discuss how genetic recombination has impacted upon the evolution of the pneumococcus.

Experimental evolution in biofilm populations

Science.gov (United States)

Steenackers, Hans P.; Parijs, Ilse; Foster, Kevin R.; Vanderleyden, Jozef

2016-01-01

Biofilms are a major form of microbial life in which cells form dense surface associated communities that can persist for many generations. The long-life of biofilm communities means that they can be strongly shaped by evolutionary processes. Here, we review the experimental study of evolution in biofilm communities. We first provide an overview of the different experimental models used to study biofilm evolution and their associated advantages and disadvantages. We then illustrate the vast amount of diversification observed during biofilm evolution, and we discuss (i) potential ecological and evolutionary processes behind the observed diversification, (ii) recent insights into the genetics of adaptive diversification, (iii) the striking degree of parallelism between evolution experiments and real-life biofilms and (iv) potential consequences of diversification. In the second part, we discuss the insights provided by evolution experiments in how biofilm growth and structure can promote cooperative phenotypes. Overall, our analysis points to an important role of biofilm diversification and cooperation in bacterial survival and productivity. Deeper understanding of both processes is of key importance to design improved antimicrobial strategies and diagnostic techniques. PMID:26895713

The adaptation to climate change

International Nuclear Information System (INIS)

Van Gameren, Valentine; Weikmans, Romain; Zaccai, Edwin

2014-01-01

The authors address the issue of adaptation to climate change. They first address the physical aspects related to this issue: scenarios of temperature evolution, main possible impacts. Then, they address the social impacts related to climate risks, and the adaptation strategies which aim at reducing the exposure and vulnerability of human societies, or at increasing their resilience. Some examples of losses of human lives and of economic damages due to recent catastrophes related to climate change are evoked. The authors address the international framework, the emergence of an international regime on climate, the quite recent emergence of adaptation within international negotiations in 2001, the emergence of the idea of a support to developing countries. National and local policies are presented in the next chapter (in the European Union, the Netherlands which are faced with the issue of sea level rise, programs in developing countries) and their limitations are also outlined. The next chapter addresses the adaptation actions performed by private actors (enterprises, households, associations, civil society, and so on) with example of vulnerability, and adaptation opportunities and possibilities in some specific sectors. The last chapter presents a typology of actions of adaptation, indicators of adaptation to climate change, and examples of mistaken adaptation

Adaptation to seasonality and the winter freeze

Directory of Open Access Journals (Sweden)

Jill Christine Preston

2013-06-01

Full Text Available Flowering plants initially diversified during the Mesozoic era at least 140 million years ago in regions of the world where temperate seasonal environments were not encountered. Since then several cooling events resulted in the contraction of warm and wet environments and the establishment of novel temperate zones in both hemispheres. In response, less than half of modern angiosperm families have members that evolved specific adaptations to cold seasonal climates, including cold acclimation, freezing tolerance, endodormancy, and vernalization responsiveness. Despite compelling evidence for multiple independent origins, the level of genetic constraint on the evolution of adaptations to seasonal cold is not well understood. However, the recent increase in molecular genetic studies examining the response of model and crop species to seasonal cold offers new insight into the evolutionary lability of these traits. This insight has major implications for our understanding of complex trait evolution, and the potential role of local adaptation in response to past and future climate change. In this review, we discuss the biochemical, morphological, and developmental basis of adaptations to seasonal cold, and synthesize recent literature on the genetic basis of these traits in a phylogenomic context. We find evidence for multiple genetic links between distinct physiological responses to cold, possibly reinforcing the coordinated expression of these traits. Furthermore, repeated recruitment of the same or similar ancestral pathways suggests that land plants might be somewhat pre-adapted to dealing with temperature stress, perhaps making inducible cold traits relatively easy to evolve.

Adaptation of Enterococcus faecalis to daptomycin reveals an ordered progression to resistance.

Science.gov (United States)

Miller, Corwin; Kong, Jiayi; Tran, Truc T; Arias, Cesar A; Saxer, Gerda; Shamoo, Yousif

2013-11-01

With increasing numbers of hospital-acquired antibiotic resistant infections each year and staggering health care costs, there is a clear need for new antimicrobial agents, as well as novel strategies to extend their clinical efficacy. While genomic studies have provided a wealth of information about the alleles associated with adaptation to antibiotics, they do not provide essential information about the relative importance of genomic changes, their order of appearance, or potential epistatic relationships between adaptive changes. Here we used quantitative experimental evolution of a single polymorphic population in continuous culture with whole-genome sequencing and allelic frequency measurements to study daptomycin (DAP) resistance in the vancomycin-resistant clinical pathogen Enterococcus faecalis S613. Importantly, we sustained both planktonic and nonplanktonic (i.e., biofilm) populations in coculture as the concentration of antibiotic was raised, facilitating the development of more ecological complexity than is typically observed in laboratory evolution. Quantitative experimental evolution revealed a clear order and hierarchy of genetic changes leading to resistance, the signaling and metabolic pathways responsible, and the relative importance of these mutations to the evolution of DAP resistance. Despite the relative simplicity of this ex vivo approach compared to the ecological complexity of the human body, we showed that experimental evolution allows for rapid identification of clinically relevant adaptive molecular pathways and new targets for drug design in pathogens.

Cell-Gazing Into the Future: What Genes, Homo heidelbergensis, and Punishment Tell Us About Our Adaptive Capacity

Directory of Open Access Journals (Sweden)

Jeffrey Andrews

2013-02-01

Full Text Available If we wish to understand how our species can adapt to the coming tide of environmental change, then understanding how we have adapted throughout the course of evolution is vital. Evolutionary biologists have been exploring these questions in the last forty years, establishing a solid record of evidence that conventional, individual-based models of natural selection are insufficient in explaining social evolution. More recently, this work has supported a growing consensus that our evolution, in which we have expressed extra-ordinary adaptive capacities, can best be explained by “Multi-level Selection”, a theory that includes the influence of both genes and culture to support unique adaptive capacities premised on pro-social behaviours and group selection, not individual-level competition for survival. Applying this scholarship to contemporary concerns about adapting to environmental change may be quite fruitful for identifying sources of vulnerability and adaptive capacity, thereby informing efforts to enhance the likelihood for sustainable futures. Doing so, however, requires that we bridge the gap between evolutionary biology, and the social sciences study of sustainability.

Molecular adaptation during adaptive radiation in the Hawaiian endemic genus Schiedea.

Directory of Open Access Journals (Sweden)

Maxim V Kapralov

2006-12-01

Full Text Available "Explosive" adaptive radiations on islands remain one of the most puzzling evolutionary phenomena. The rate of phenotypic and ecological adaptations is extremely fast during such events, suggesting that many genes may be under fairly strong selection. However, no evidence for adaptation at the level of protein coding genes was found, so it has been suggested that selection may work mainly on regulatory elements. Here we report the first evidence that positive selection does operate at the level of protein coding genes during rapid adaptive radiations. We studied molecular adaptation in Hawaiian endemic plant genus Schiedea (Caryophyllaceae, which includes closely related species with a striking range of morphological and ecological forms, varying from rainforest vines to woody shrubs growing in desert-like conditions on cliffs. Given the remarkable difference in photosynthetic performance between Schiedea species from different habitats, we focused on the "photosynthetic" Rubisco enzyme, the efficiency of which is known to be a limiting step in plant photosynthesis.We demonstrate that the chloroplast rbcL gene, encoding the large subunit of Rubisco enzyme, evolved under strong positive selection in Schiedea. Adaptive amino acid changes occurred in functionally important regions of Rubisco that interact with Rubisco activase, a chaperone which promotes and maintains the catalytic activity of Rubisco. Interestingly, positive selection acting on the rbcL might have caused favorable cytotypes to spread across several Schiedea species.We report the first evidence for adaptive changes at the DNA and protein sequence level that may have been associated with the evolution of photosynthetic performance and colonization of new habitats during a recent adaptive radiation in an island plant genus. This illustrates how small changes at the molecular level may change ecological species performance and helps us to understand the molecular bases of extremely

Overcoming Deception in Evolution of Cognitive Behaviors

DEFF Research Database (Denmark)

Lehman, Joel; Miikkulainen, Risto

2014-01-01

When scaling neuroevolution to complex behaviors, cognitive capabilities such as learning, communication, and memory become increasingly important. However, successfully evolving such cognitive abilities remains difficult. This paper argues that a main cause for such difficulty is deception, i.......e. evolution converges to a behavior unrelated to the desired solution. More specifically, cognitive behaviors often require accumulating neural structure that provides no immediate fitness benefit, and evolution often thus converges to non-cognitive solutions. To investigate this hypothesis, a common...... evolutionary robotics T-Maze domain is adapted in three separate ways to require agents to communicate, remember, and learn. Indicative of deception, evolution driven by objective-based fitness often converges upon simple non- cognitive behaviors. In contrast, evolution driven to explore novel behaviors, i...

Optimality models in the age of experimental evolution and genomics.

Science.gov (United States)

Bull, J J; Wang, I-N

2010-09-01

Optimality models have been used to predict evolution of many properties of organisms. They typically neglect genetic details, whether by necessity or design. This omission is a common source of criticism, and although this limitation of optimality is widely acknowledged, it has mostly been defended rather than evaluated for its impact. Experimental adaptation of model organisms provides a new arena for testing optimality models and for simultaneously integrating genetics. First, an experimental context with a well-researched organism allows dissection of the evolutionary process to identify causes of model failure--whether the model is wrong about genetics or selection. Second, optimality models provide a meaningful context for the process and mechanics of evolution, and thus may be used to elicit realistic genetic bases of adaptation--an especially useful augmentation to well-researched genetic systems. A few studies of microbes have begun to pioneer this new direction. Incompatibility between the assumed and actual genetics has been demonstrated to be the cause of model failure in some cases. More interestingly, evolution at the phenotypic level has sometimes matched prediction even though the adaptive mutations defy mechanisms established by decades of classic genetic studies. Integration of experimental evolutionary tests with genetics heralds a new wave for optimality models and their extensions that does not merely emphasize the forces driving evolution.

Adaptive Divergence in Experimental Populations of Pseudomonas fluorescens. IV. Genetic Constraints Guide Evolutionary Trajectories in a Parallel Adaptive Radiation

OpenAIRE

McDonald, Michael J.; Gehrig, Stefanie M.; Meintjes, Peter L.; Zhang, Xue-Xian; Rainey, Paul B.

2009-01-01

The capacity for phenotypic evolution is dependent upon complex webs of functional interactions that connect genotype and phenotype. Wrinkly spreader (WS) genotypes arise repeatedly during the course of a model Pseudomonas adaptive radiation. Previous work showed that the evolution of WS variation was explained in part by spontaneous mutations in wspF, a component of the Wsp-signaling module, but also drew attention to the existence of unknown mutational causes. Here, we identify two new muta...

Meiosis evolves: adaptation to external and internal environments.

Science.gov (United States)

Bomblies, Kirsten; Higgins, James D; Yant, Levi

2015-10-01

306 I. 306 II. 307 III. 312 IV. 317 V. 318 319 References 319 SUMMARY: Meiosis is essential for the fertility of most eukaryotes and its structures and progression are conserved across kingdoms. Yet many of its core proteins show evidence of rapid or adaptive evolution. What drives the evolution of meiosis proteins? How can constrained meiotic processes be modified in response to challenges without compromising their essential functions? In surveying the literature, we found evidence of two especially potent challenges to meiotic chromosome segregation that probably necessitate adaptive evolutionary responses: whole-genome duplication and abiotic environment, especially temperature. Evolutionary solutions to both kinds of challenge are likely to involve modification of homologous recombination and synapsis, probably via adjustments of core structural components important in meiosis I. Synthesizing these findings with broader patterns of meiosis gene evolution suggests that the structural components of meiosis coevolve as adaptive modules that may change in primary sequence and function while maintaining three-dimensional structures and protein interactions. The often sharp divergence of these genes among species probably reflects periodic modification of entire multiprotein complexes driven by genomic or environmental changes. We suggest that the pressures that cause meiosis to evolve to maintain fertility may cause pleiotropic alterations of global crossover rates. We highlight several important areas for future research. © 2015 The Authors. New Phytologist © 2015 New Phytologist Trust.

The Semiosic Evolution of Education

Science.gov (United States)

Olteanu, Alin

2014-01-01

The recent development of biosemiotics has revealed the achievement of knowledge and the development of science to be the results of the semiosis of all life forms, including those commonly regarded as cultural constructs. Education is thus a semiosic structure to which evolution itself has adapted, while learning is the semiotic phenomenon that…

Collaborative Adaptation Planning for Water Security: Preliminary Lessons, Challenges, and the Way Forward for Maipo Basin Adaptation Plan, Chile

Science.gov (United States)

Vicuna, S.; Scott, C. A.; Bonelli, S.; Bustos, E.; Meza, F. J.

2014-12-01

The Maipo basin holds 40% of Chile's total population and almost half of the country's Gross Domestic Product. The basin is located in the semiarid central region of the country and, aside from the typical pressures of growth in developing country basins, the Maipo river faces climate change impacts associated with a reduction in total runoff and changes in its seasonality. Surface water is the main water source for human settlements and economic activities including agriculture. In 2012 we started a research project to create a climate variability and climate change adaptation plan for the basin. The pillars of the plan are co-produced by researchers and a Scenario Building Team (SBT) with membership of relevant water and land use stakeholders (including from civil society, public and private sectors) in the basin. Following similar experiences in other regions in the world that have faced the challenges of dealing with long term planning under uncertainty, the project has divided the task of developing the plan into a series of interconnected elements. A critical first component is to work on the desired vision(s) of the basin for the future. In this regards, the "water security" concept has been chosen as a framework that accommodates all objectives of the SBT members. Understanding and quantifying the uncertainties that could affect the future water security of the basin is another critical aspect of the plan. Near and long term climate scenarios are one dimension of these uncertainties that are combined with base development uncertainties such as urban growth scenarios. A third component constructs the models/tools that allows the assessment of impacts on water security that could arise under these scenarios. The final critical component relates to the development of the adaptation measures that could avoid the negative impacts and/or capture the potential opportunities. After two years in the development of the adaptation plan a series of results has been

Mapping the evolution of scientific ideas

Energy Technology Data Exchange (ETDEWEB)

Roberts, David [Los Alamos National Laboratory; Herrera, Mark [UNIV OF MARYLAND; Gulbahce, Natali [UNIV OF BOSTON

2009-01-01

Despite the apparent conceptual boundaries of scientific fields, a formal description for their evolution is lacking. Here we describe a novel approach to study the dynamics and evolution of scientific fields using a network-based analysis. We build an idea network consisting of American Physical Society PACS numbers as nodes representing scientific concepts. Two PACS numbers are linked if there exist publications that reference them simultaneously. We locate scientific fields using Cfinder, an overlapping community finding algorithm, and describe the time evolution of these fields using a community evolution method over the course of 1985-2006. The communities we identify map to known scientific fields, and their age strongly depends on t.heir size, impact and activity. Our analysis further suggests that communities that redefine themselves by merging and creating new groups of ideas tend to have more fitness as measured by the impact per paper, and hence communities with a higher fitness tend to be short-lived. The described approach to quantify the evolution of ideas may be relevant in making predictions about the future of science and how to guide its development.

Horizontal Gene Transfer Contributes to the Evolution of Arthropod Herbivory.

Science.gov (United States)

Wybouw, Nicky; Pauchet, Yannick; Heckel, David G; Van Leeuwen, Thomas

2016-06-27

Within animals, evolutionary transition toward herbivory is severely limited by the hostile characteristics of plants. Arthropods have nonetheless counteracted many nutritional and defensive barriers imposed by plants and are currently considered as the most successful animal herbivores in terrestrial ecosystems. We gather a body of evidence showing that genomes of various plant feeding insects and mites possess genes whose presence can only be explained by horizontal gene transfer (HGT). HGT is the asexual transmission of genetic information between reproductively isolated species. Although HGT is known to have great adaptive significance in prokaryotes, its impact on eukaryotic evolution remains obscure. Here, we show that laterally transferred genes into arthropods underpin many adaptations to phytophagy, including efficient assimilation and detoxification of plant produced metabolites. Horizontally acquired genes and the traits they encode often functionally diversify within arthropod recipients, enabling the colonization of more host plant species and organs. We demonstrate that HGT can drive metazoan evolution by uncovering its prominent role in the adaptations of arthropods to exploit plants. © The Author 2016. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

Multilocus genetics to reconstruct aeromonad evolution

Directory of Open Access Journals (Sweden)

Roger Frédéric

2012-04-01

Full Text Available Abstract Background Aeromonas spp. are versatile bacteria that exhibit a wide variety of lifestyles. In an attempt to improve the understanding of human aeromonosis, we investigated whether clinical isolates displayed specific characteristics in terms of genetic diversity, population structure and mode of evolution among Aeromonas spp. A collection of 195 Aeromonas isolates from human, animal and environmental sources was therefore genotyped using multilocus sequence analysis (MLSA based on the dnaK, gltA, gyrB, radA, rpoB, tsf and zipA genes. Results The MLSA showed a high level of genetic diversity among the population, and multilocus-based phylogenetic analysis (MLPA revealed 3 major clades: the A. veronii, A. hydrophila and A. caviae clades, among the eleven clades detected. Lower genetic diversity was observed within the A. caviae clade as well as among clinical isolates compared to environmental isolates. Clonal complexes, each of which included a limited number of strains, mainly corresponded to host-associated subsclusters of strains, i.e., a fish-associated subset within A. salmonicida and 11 human-associated subsets, 9 of which included only disease-associated strains. The population structure was shown to be clonal, with modes of evolution that involved mutations in general and recombination events locally. Recombination was detected in 5 genes in the MLSA scheme and concerned approximately 50% of the STs. Therefore, these recombination events could explain the observed phylogenetic incongruities and low robustness. However, the MLPA globally confirmed the current systematics of the genus Aeromonas. Conclusions Evolution in the genus Aeromonas has resulted in exceptionally high genetic diversity. Emerging from this diversity, subsets of strains appeared to be host adapted and/or “disease specialized” while the A. caviae clade displayed an atypical tempo of evolution among aeromonads. Considering that A. salmonicida has been

Evolution of body shape in differently coloured sympatric congeners and allopatric populations of Lake Malawi's rock-dwelling cichlids.

Science.gov (United States)

Husemann, M; Tobler, M; McCauley, C; Ding, B; Danley, P D

2014-05-01

The cichlid fishes of Lake Malawi represent one of the most diverse adaptive radiations of vertebrates known. Among the rock-dwelling cichlids (mbuna), closely related sympatric congeners possess similar trophic morphologies (i.e. cranial and jaw structures), defend overlapping or adjacent territories, but can be easily distinguished based on male nuptial coloration. The apparent morphological similarity of congeners, however, leads to an ecological conundrum: theory predicts that ecological competition should lead to competitive exclusion. Hence, we hypothesized that slight, yet significant, ecological differences accompanied the divergence in sexual signals and that the divergence of ecological and sexual traits is correlated. To evaluate this hypothesis, we quantified body shape, a trait of known ecological importance, in populations of Maylandia zebra, a barred, widespread mbuna, and several sympatric nonbarred congeners. We found that the barred populations differ in body shape from their nonbarred sympatric congeners and that the direction of shape differences was consistent across all barred vs. nonbarred comparisons. Barred populations are generally deeper bodied which may be an adaptation to the structurally complex habitat they prefer, whereas the nonbarred species have a more fusiform body shape, which may be adaptive in their more open microhabitat. Furthermore, M. zebra populations sympatric with nonbarred congeners differ from populations where the nonbarred phenotype is absent and occupy less morphospace, indicating potential ecological character displacement. Mitochondrial DNA as well as published AFLP data indicated that the nonbarred populations are not monophyletic and therefore may have evolved multiple times independently. Overall our data suggest that the evolution of coloration and body shape may be coupled as a result of correlational selection. We hypothesize that correlated evolution of sexually selected and ecological traits may have

Quantifying the Number of Independent Organelle DNA Insertions in Genome Evolution and Human Health.

Science.gov (United States)

Hazkani-Covo, Einat; Martin, William F

2017-05-01

Fragments of organelle genomes are often found as insertions in nuclear DNA. These fragments of mitochondrial DNA (numts) and plastid DNA (nupts) are ubiquitous components of eukaryotic genomes. They are, however, often edited out during the genome assembly process, leading to systematic underestimation of their frequency. Numts and nupts, once inserted, can become further fragmented through subsequent insertion of mobile elements or other recombinational events that disrupt the continuity of the inserted sequence relative to the genuine organelle DNA copy. Because numts and nupts are typically identified through sequence comparison tools such as BLAST, disruption of insertions into smaller fragments can lead to systematic overestimation of numt and nupt frequencies. Accurate identification of numts and nupts is important, however, both for better understanding of their role during evolution, and for monitoring their increasingly evident role in human disease. Human populations are polymorphic for 141 numt loci, five numts are causal to genetic disease, and cancer genomic studies are revealing an abundance of numts associated with tumor progression. Here, we report investigation of salient parameters involved in obtaining accurate estimates of numt and nupt numbers in genome sequence data. Numts and nupts from 44 sequenced eukaryotic genomes reveal lineage-specific differences in the number, relative age and frequency of insertional events as well as lineage-specific dynamics of their postinsertional fragmentation. Our findings outline the main technical parameters influencing accurate identification and frequency estimation of numts in genomic studies pertinent to both evolution and human health. © The Author 2017. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

TH-A-BRF-02: BEST IN PHYSICS (JOINT IMAGING-THERAPY) - Modeling Tumor Evolution for Adaptive Radiation Therapy

International Nuclear Information System (INIS)

Liu, Y; Lee, CG; Chan, TCY; Cho, YB; Islam, MK

2014-01-01

Purpose: To develop mathematical models of tumor geometry changes under radiotherapy that may support future adaptive paradigms. Methods: A total of 29 cervical patients were scanned using MRI, once for planning and weekly thereafter for treatment monitoring. Using the tumor volumes contoured by a radiologist, three mathematical models were investigated based on the assumption of a stochastic process of tumor evolution. The “weekly MRI” model predicts tumor geometry for the following week from the last two consecutive MRI scans, based on the voxel transition probability. The other two models use only the first pair of consecutive MRI scans, and the transition probabilities were estimated via tumor type classified from the entire data set. The classification is based on either measuring the tumor volume (the “weekly volume” model), or implementing an auxiliary “Markov chain” model. These models were compared to a constant volume approach that represents the current clinical practice, using various model parameters; e.g., the threshold probability β converts the probability map into a tumor shape (larger threshold implies smaller tumor). Model performance was measured using volume conformity index (VCI), i.e., the union of the actual target and modeled target volume squared divided by product of these two volumes. Results: The “weekly MRI” model outperforms the constant volume model by 26% on average, and by 103% for the worst 10% of cases in terms of VCI under a wide range of β. The “weekly volume” and “Markov chain” models outperform the constant volume model by 20% and 16% on average, respectively. They also perform better than the “weekly MRI” model when β is large. Conclusion: It has been demonstrated that mathematical models can be developed to predict tumor geometry changes for cervical cancer undergoing radiotherapy. The models can potentially support adaptive radiotherapy paradigm by reducing normal tissue dose. This research

TH-A-BRF-02: BEST IN PHYSICS (JOINT IMAGING-THERAPY) - Modeling Tumor Evolution for Adaptive Radiation Therapy

Energy Technology Data Exchange (ETDEWEB)

Liu, Y; Lee, CG [University of Toronto, Toronto, ON (Canada); Chan, TCY [University of Toronto, Toronto, ON (Canada); Techna Institute for the Advancement of Technology for Health, Toronto, ON (Canada); Cho, YB; Islam, MK [University of Toronto, Toronto, ON (Canada); Princess Margaret Hospital, Toronto, ON (Canada); Ontario Consortium for Adaptive Interventions in Radiation Oncology (OCAIRO) (Canada)

2014-06-15

Purpose: To develop mathematical models of tumor geometry changes under radiotherapy that may support future adaptive paradigms. Methods: A total of 29 cervical patients were scanned using MRI, once for planning and weekly thereafter for treatment monitoring. Using the tumor volumes contoured by a radiologist, three mathematical models were investigated based on the assumption of a stochastic process of tumor evolution. The “weekly MRI” model predicts tumor geometry for the following week from the last two consecutive MRI scans, based on the voxel transition probability. The other two models use only the first pair of consecutive MRI scans, and the transition probabilities were estimated via tumor type classified from the entire data set. The classification is based on either measuring the tumor volume (the “weekly volume” model), or implementing an auxiliary “Markov chain” model. These models were compared to a constant volume approach that represents the current clinical practice, using various model parameters; e.g., the threshold probability β converts the probability map into a tumor shape (larger threshold implies smaller tumor). Model performance was measured using volume conformity index (VCI), i.e., the union of the actual target and modeled target volume squared divided by product of these two volumes. Results: The “weekly MRI” model outperforms the constant volume model by 26% on average, and by 103% for the worst 10% of cases in terms of VCI under a wide range of β. The “weekly volume” and “Markov chain” models outperform the constant volume model by 20% and 16% on average, respectively. They also perform better than the “weekly MRI” model when β is large. Conclusion: It has been demonstrated that mathematical models can be developed to predict tumor geometry changes for cervical cancer undergoing radiotherapy. The models can potentially support adaptive radiotherapy paradigm by reducing normal tissue dose. This research

Adaptive response to DNA-damaging agents in natural Saccharomyces cerevisiae populations from "Evolution Canyon", Mt. Carmel, Israel.

Directory of Open Access Journals (Sweden)

Gabriel A Lidzbarsky

2009-06-01

Full Text Available Natural populations of most organisms, especially unicellular microorganisms, are constantly exposed to harsh environmental factors which affect their growth. UV radiation is one of the most important physical parameters which influences yeast growth in nature. Here we used 46 natural strains of Saccharomyces cerevisiae isolated from several natural populations at the "Evolution Canyon" microsite (Nahal Oren, Mt. Carmel, Israel. The opposing slopes of this canyon share the same geology, soil, and macroclimate, but they differ in microclimatic conditions. The interslope differences in solar radiation (200%-800% more on the "African" slope caused the development of two distinct biomes. The south-facing slope is sunnier and has xeric, savannoid "African" environment while the north-facing slope is represented by temperate, "European" forested environment. Here we studied the phenotypic response of the S. cerevisiae strains to UVA and UVC radiations and to methyl methanesulfonate (MMS in order to evaluate the interslope effect on the strains' ability to withstand DNA-damaging agents.We exposed our strains to the different DNA-damaging agents and measured survival by counting colony forming units. The strains from the "African" slope were more resilient to both UVA and MMS than the strains from the "European" slope. In contrast, we found that there was almost no difference between strains (with similar ploidy from the opposite slopes, in their sensitivity to UVC radiation. These results suggest that the "African" strains are more adapted to higher solar radiation than the "European" strains. We also found that the tetraploids strains were more tolerant to all DNA-damaging agents than their neighboring diploid strains, which suggest that high ploidy level might be a mechanism of adaptation to high solar radiation.Our results and the results of parallel studies with several other organisms, suggest that natural selection appears to select, at a

Constructing carbon offsets: The obstacles to quantifying emission reductions

International Nuclear Information System (INIS)

Millard-Ball, Adam; Ortolano, Leonard

2010-01-01

The existing literature generally ascribes the virtual absence of the transport sector from the Clean Development Mechanism (CDM) to the inherent complexity of quantifying emission reductions from mobile sources. We use archival analysis and interviews with CDM decision-makers and experts to identify two additional groups of explanations. First, we show the significance of aspects of the CDM's historical evolution, such as the order in which methodologies were considered and the assignment of expert desk reviewers. Second, we highlight inconsistencies in the treatment of uncertainty across sectors. In contrast to transport methodologies, other sectors are characterized by a narrow focus on sources of measurement uncertainty and a neglect of economic effects ('market leakages'). We do not argue that the rejection of transport methodologies was unjustified, but rather than many of the same problems are inherent in other sectors. Thus, the case of transport sheds light on fundamental problems in quantifying emission reductions under the CDM. We argue that a key theoretical attraction of the CDM-equalization of marginal abatement costs across all sectors-has been difficult to achieve in practice.

Evidence for Adaptation to the Tibetan Plateau Inferred from Tibetan Loach Transcriptomes.

Science.gov (United States)

Wang, Ying; Yang, Liandong; Zhou, Kun; Zhang, Yanping; Song, Zhaobin; He, Shunping

2015-10-09

Triplophysa fishes are the primary component of the fish fauna on the Tibetan Plateau and are well adapted to the high-altitude environment. Despite the importance of Triplophysa fishes on the plateau, the genetic mechanisms of the adaptations of these fishes to this high-altitude environment remain poorly understood. In this study, we generated the transcriptome sequences for three Triplophysa fishes, that is, Triplophysa siluroides, Triplophysa scleroptera, and Triplophysa dalaica, and used these and the previously available transcriptome and genome sequences from fishes living at low altitudes to identify potential genetic mechanisms for the high-altitude adaptations in Triplophysa fishes. An analysis of 2,269 orthologous genes among cave fish (Astyanax mexicanus), zebrafish (Danio rerio), large-scale loach (Paramisgurnus dabryanus), and Triplophysa fishes revealed that each of the terminal branches of the Triplophysa fishes had a significantly higher ratio of nonsynonymous to synonymous substitutions than that of the branches of the fishes from low altitudes, which provided consistent evidence for genome-wide rapid evolution in the Triplophysa genus. Many of the GO (Gene Ontology) categories associated with energy metabolism and hypoxia response exhibited accelerated evolution in the Triplophysa fishes compared with the large-scale loach. The genes that exhibited signs of positive selection and rapid evolution in the Triplophysa fishes were also significantly enriched in energy metabolism and hypoxia response categories. Our analysis identified widespread Triplophysa-specific nonsynonymous mutations in the fast evolving genes and positively selected genes. Moreover, we detected significant evidence of positive selection in the HIF (hypoxia-inducible factor)-1A and HIF-2B genes in Triplophysa fishes and found that the Triplophysa-specific nonsynonymous mutations in the HIF-1A and HIF-2B genes were associated with functional changes. Overall, our study provides

Evolutions in food marketing, quantifying the impact, and policy implications.

Science.gov (United States)

Cairns, Georgina

2013-03-01

A case study on interactive digital marketing examined the adequacy of extant policy controls and their underpinning paradigms to constrain the effects of this rapidly emerging practice. Findings were interactive digital marketing is expanding the strategies available to promote products, brands and consumer behaviours. It facilitates relational marketing; the collection of personal data for marketing; integration of the marketing mix, and provides a platform for consumers to engage in the co-creation of marketing communications. The paradigmatic logic of current policies to constrain youth-oriented food marketing does not address the interactive nature of digital marketing. The evidence base on the effects of HFSS marketing and policy interventions is based on conceptualizations of marketing as a force promoting transactions rather than interactions. Digital technologies are generating rich consumer data. Interactive digital technologies increase the complexity of the task of quantifying the impact of marketing. The rapidity of its uptake also increases urgency of need to identify appropriate effects measures. Independent analysis of commercial consumer data (appropriately transformed to protect commercial confidentiality and personal privacy) would provide evidence sources for policy on the impacts of commercial food and beverage marketing and policy controls. Copyright © 2012 Elsevier Ltd. All rights reserved.

Adaptation dynamics of the quasispecies model

Indian Academy of Sciences (India)

We study the adaptation dynamics of an initially maladapted population evolving via the elementary processes of mutation and selection. The evolution occurs on rugged fitness landscapes which are defined on the multi-dimensional genotypic space and have many local peaks separated by low fitness valleys. We mainly ...

The evolution of cooperation by the Hankshaw effect.

Science.gov (United States)

Hammarlund, Sarah P; Connelly, Brian D; Dickinson, Katherine J; Kerr, Benjamin

2016-06-01

The evolution of cooperation-costly behavior that benefits others-faces one clear obstacle. Namely, cooperators are always at a competitive disadvantage relative to defectors, individuals that reap the benefits, but evade the cost of cooperation. One solution to this problem involves genetic hitchhiking, where the allele encoding cooperation becomes linked to a beneficial mutation, allowing cooperation to rise in abundance. Here, we explore hitchhiking in the context of adaptation to a stressful environment by cooperators and defectors with spatially limited dispersal. Under such conditions, clustered cooperators reach higher local densities, thereby experiencing more mutational opportunities than defectors. Thus, the allele encoding cooperation has a greater probability of hitchhiking with alleles conferring stress adaptation. We label this probabilistic enhancement the "Hankshaw effect" after the character Sissy Hankshaw, whose anomalously large thumbs made her a singularly effective hitchhiker. Using an agent-based model, we reveal a broad set of conditions that allow the evolution of cooperation through this effect. Additionally, we show that spite, a costly behavior that harms others, can evolve by the Hankshaw effect. While in an unchanging environment these costly social behaviors have transient success, in a dynamic environment, cooperation and spite can persist indefinitely. © 2016 The Author(s). Evolution © 2016 The Society for the Study of Evolution.

Molecular evolution of the primate antiviral restriction factor tetherin.

Directory of Open Access Journals (Sweden)

Jun Liu

Full Text Available BACKGROUND: Tetherin is a recently identified antiviral restriction factor that restricts HIV-1 particle release in the absence of the HIV-1 viral protein U (Vpu. It is reminiscent of APOBEC3G and TRIM5a that also antagonize HIV. APOBEC3G and TRIM5a have been demonstrated to evolve under pervasive positive selection throughout primate evolution, supporting the red-queen hypothesis. Therefore, one naturally presumes that Tetherin also evolves under pervasive positive selection throughout primate evolution and supports the red-queen hypothesis. Here, we performed a detailed evolutionary analysis to address this presumption. METHODOLOGY/PRINCIPAL FINDINGS: Results of non-synonymous and synonymous substitution rates reveal that Tetherin as a whole experiences neutral evolution rather than pervasive positive selection throughout primate evolution, as well as in non-primate mammal evolution. Sliding-window analyses show that the regions of the primate Tetherin that interact with viral proteins are under positive selection or relaxed purifying selection. In particular, the sites identified under positive selection generally focus on these regions, indicating that the main selective pressure acting on the primate Tetherin comes from virus infection. The branch-site model detected positive selection acting on the ancestral branch of the New World Monkey lineage, suggesting an episodic adaptive evolution. The positive selection was also found in duplicated Tetherins in ruminants. Moreover, there is no bias in the alterations of amino acids in the evolution of the primate Tetherin, implying that the primate Tetherin may retain broad spectrum of antiviral activity by maintaining structure stability. CONCLUSIONS/SIGNIFICANCE: These results conclude that the molecular evolution of Tetherin may be attributed to the host-virus arms race, supporting the Red Queen hypothesis, and Tetherin may be in an intermediate stage in transition from neutral to pervasive

Quantifiers and working memory

NARCIS (Netherlands)

Szymanik, J.; Zajenkowski, M.

2010-01-01

The paper presents a study examining the role of working memory in quantifier verification. We created situations similar to the span task to compare numerical quantifiers of low and high rank, parity quantifiers and proportional quantifiers. The results enrich and support the data obtained

Quantifiers and working memory

NARCIS (Netherlands)

Szymanik, J.; Zajenkowski, M.

2009-01-01

The paper presents a study examining the role of working memory in quantifier verification. We created situations similar to the span task to compare numerical quantifiers of low and high rank, parity quantifiers and proportional quantifiers. The results enrich and support the data obtained

Adaptive divergence in the monkey flower Mimulus guttatus is maintained by a chromosomal inversion.

Science.gov (United States)

Twyford, Alex D; Friedman, Jannice

2015-06-01

Organisms exhibit an incredible diversity of life history strategies as adaptive responses to environmental variation. The establishment of novel life history strategies involves multilocus polymorphisms, which will be challenging to establish in the face of gene flow and recombination. Theory predicts that adaptive allelic combinations may be maintained and spread if they occur in genomic regions of reduced recombination, such as chromosomal inversion polymorphisms, yet empirical support for this prediction is lacking. Here, we use genomic data to investigate the evolution of divergent adaptive ecotypes of the yellow monkey flower Mimulus guttatus. We show that a large chromosomal inversion polymorphism is the major region of divergence between geographically widespread annual and perennial ecotypes. In contrast, ∼40,000 single nucleotide polymorphisms in collinear regions of the genome show no signal of life history, revealing genomic patterns of diversity have been shaped by localized homogenizing gene flow and large-scale Pleistocene range expansion. Our results provide evidence for an inversion capturing and protecting loci involved in local adaptation, while also explaining how adaptive divergence can occur with gene flow. © 2015 The Author(s). Evolution published by Wiley Periodicals, Inc. on behalf of The Society for the Study of Evolution.

Mechanisms by Which Phenotypic Plasticity Affects Adaptive Divergence and Ecological Speciation.

Science.gov (United States)

Nonaka, Etsuko; Svanbäck, Richard; Thibert-Plante, Xavier; Englund, Göran; Brännström, Åke

2015-11-01

Phenotypic plasticity is the ability of one genotype to produce different phenotypes depending on environmental conditions. Several conceptual models emphasize the role of plasticity in promoting reproductive isolation and, ultimately, speciation in populations that forage on two or more resources. These models predict that plasticity plays a critical role in the early stages of speciation, prior to genetic divergence, by facilitating fast phenotypic divergence. The ability to plastically express alternative phenotypes may, however, interfere with the early phase of the formation of reproductive barriers, especially in the absence of geographic barriers. Here, we quantitatively investigate mechanisms under which plasticity can influence progress toward adaptive genetic diversification and ecological speciation. We use a stochastic, individual-based model of a predator-prey system incorporating sexual reproduction and mate choice in the predator. Our results show that evolving plasticity promotes the evolution of reproductive isolation under diversifying environments when individuals are able to correctly select a more profitable habitat with respect to their phenotypes (i.e., adaptive habitat choice) and to assortatively mate with relatively similar phenotypes. On the other hand, plasticity facilitates the evolution of plastic generalists when individuals have a limited capacity for adaptive habitat choice. We conclude that plasticity can accelerate the evolution of a reproductive barrier toward adaptive diversification and ecological speciation through enhanced phenotypic differentiation between diverging phenotypes.

Differences in the Concept of Fitness Between Artificial Evolution and Natural Selection

OpenAIRE

Adami, Christoph; Bryson, David M.; Ofria, Charles; Pennock, Robert T.; Lichocki, Pawel; Keller, Laurent; Floreano, Dario

2012-01-01

Evolutionary algorithms were proposed to automatically find solutions to computational problems, much like evolution discovers new adaptive traits. Lately, they have been used to address challenging questions about the evolution of modularity, the genetic code, communication, division of labor and cooperation. Evolutionary algorithms are increasingly popular in biological studies, because they give precise control over the experimental conditions and allow the study of evolution at unpreceden...

Five Misunderstandings About Cultural Evolution.

Science.gov (United States)

Henrich, Joseph; Boyd, Robert; Richerson, Peter J

2008-06-01

Recent debates about memetics have revealed some widespread misunderstandings about Darwinian approaches to cultural evolution. Drawing from these debates, this paper disputes five common claims: (1) mental representations are rarely discrete, and therefore models that assume discrete, gene-like particles (i.e., replicators) are useless; (2) replicators are necessary for cumulative, adaptive evolution; (3) content-dependent psychological biases are the only important processes that affect the spread of cultural representations; (4) the "cultural fitness" of a mental representation can be inferred from its successful transmission; and (5) selective forces only matter if the sources of variation are random. We close by sketching the outlines of a unified evolutionary science of culture.

Comparative Analysis of Transcriptomes in Rhizophoraceae Provides Insights into the Origin and Adaptive Evolution of Mangrove Plants in Intertidal Environments

Directory of Open Access Journals (Sweden)

Wuxia Guo

2017-05-01

Full Text Available Mangroves are woody plants that grow at the interface between land and sea in tropical and subtropical latitudes, where they exist in conditions of high salinity, extreme tides, strong winds, high temperatures, and muddy, anaerobic soils. Rhizophoraceae is a key mangrove family, with highly developed morphological and physiological adaptations to extreme conditions. It is an ideal system for the study of the origin and adaptive evolution of mangrove plants. In this study, we characterized and comprehensively compared the transcriptomes of four mangrove species, from all four mangrove genera, as well as their closest terrestrial relative in Rhizophoraceae, using RNA-Seq. We obtained 41,936–48,845 unigenes with N50 values of 982–1,185 bp and 61.42–69.48% annotated for the five species in Rhizophoraceae. Orthology annotations of Gene Ontology, Kyoto Encyclopedia of Genes and Genomes, and Clusters of Orthologous Groups revealed overall similarities in the transcriptome profiles among the five species, whereas enrichment analysis identified remarkable genomic characteristics that are conserved across the four mangrove species but differ from their terrestrial relative. Based on 1,816 identified orthologs, phylogeny analysis and divergence time estimation revealed a single origin for mangrove species in Rhizophoraceae, which diverged from the terrestrial lineage ~56.4 million years ago (Mya, suggesting that the transgression during the Paleocene–Eocene Thermal Maximum may have been responsible for the entry of the mangrove lineage of Rhizophoraceae into intertidal environments. Evidence showed that the ancestor of Rhizophoraceae may have experienced a whole genome duplication event ~74.6 Mya, which may have increased the adaptability and survival chances of Rhizophoraceae during and following the Cretaceous–Tertiary extinction. The analysis of positive selection identified 10 positively selected genes from the ancestor branch of

Adaptive pathways and coupled infrastructure: seven centuries of adaptation to water risk and the production of vulnerability in Mexico City

Directory of Open Access Journals (Sweden)

Beth Tellman

2018-03-01

Full Text Available Infrastructure development is central to the processes that abate and produce vulnerabilities in cities. Urban actors, especially those with power and authority, perceive and interpret vulnerability and decide when and how to adapt. When city managers use infrastructure to reduce urban risk in the complex, interconnected city system, new fragilities are introduced because of inherent system feedbacks. We trace the interactions between system dynamics and decision-making processes over 700 years of Mexico City's adaptations to water risks, focusing on the decision cycles of public infrastructure providers (in this case, government authorities. We bring together two lenses in examining this history: robustness-vulnerability trade-offs to explain the evolution of systemic risk dynamics mediated by feedback control, and adaptation pathways to focus on the evolution of decision cycles that motivate significant infrastructure investments. Drawing from historical accounts, archeological evidence, and original research on water, engineering, and cultural history, we examine adaptation pathways of humans settlement, water supply, and flood risk. Mexico City's history reveals insights that expand the theory of coupled infrastructure and lessons salient to contemporary urban risk management: (1 adapting by spatially externalizing risks can backfire: as cities expand, such risks become endogenous; (2 over time, adaptation pathways initiated to address specific risks may begin to intersect, creating complex trade-offs in risk management; and (3 city authorities are agents of risk production: even in the face of new exogenous risks (climate change, acknowledging and managing risks produced endogenously may prove more adaptive. History demonstrates that the very best solutions today may present critical challenges for tomorrow, and that collectively people have far more agency in and influence over the complex systems we live in than is often acknowledged.

Multiple wall-reflection effect in adaptive-array differential-phase reflectometry on QUEST

International Nuclear Information System (INIS)

Idei, H.; Fujisawa, A.; Nagashima, Y.; Onchi, T.; Hanada, K.; Zushi, H.; Mishra, K.; Hamasaki, M.; Hayashi, Y.; Yamamoto, M.K.

2016-01-01

A phased array antenna and Software-Defined Radio (SDR) heterodyne-detection systems have been developed for adaptive array approaches in reflectometry on the QUEST. In the QUEST device considered as a large oversized cavity, standing wave (multiple wall-reflection) effect was significantly observed with distorted amplitude and phase evolution even if the adaptive array analyses were applied. The distorted fields were analyzed by Fast Fourier Transform (FFT) in wavenumber domain to treat separately the components with and without wall reflections. The differential phase evolution was properly obtained from the distorted field evolution by the FFT procedures. A frequency derivative method has been proposed to overcome the multiple-wall reflection effect, and SDR super-heterodyned components with small frequency difference for the derivative method were correctly obtained using the FFT analysis

Hydrogen evolution on nano-particulate transition metal sulfides

DEFF Research Database (Denmark)

Bonde, Jacob Lindner; Moses, Poul Georg; Jaramillo, Thomas F.

2008-01-01

The hydrogen evolution reaction (HER) on carbon supported MoS2 nanoparticles is investigated and compared to findings with previously published work on Au(111) supported MoS2. An investigation into MoS2 oxidation is presented and used to quantify the surface concentration of MoS2. Other metal sul...

Sensory exploitation and cultural transmission: the late emergence of iconic representations in human evolution.

Science.gov (United States)

Verpooten, Jan; Nelissen, Mark

2010-09-01

Iconic representations (i.e., figurative imagery and realistic art) only started to appear consistently some 45,000 years ago, although humans have been anatomically modern since 200,000-160,000 years ago. What explains this? Some authors have suggested a neurocognitive change took place, leading to a creative explosion, although this has been contested. Here, we examine the hypothesis that demographic changes caused cultural "cumulative adaptive evolution" and as such the emergence of modern symbolic behavior. This approach usefully explains the evolution of utilitarian skills and tools, and the creation of symbols to identify groups. However, it does not equally effectively explain the evolution of behaviors that may not be directly adaptive, such as the production of iconic representations like figurines and rock art. In order to shed light on their emergence, we propose to combine the above-mentioned cultural hypothesis with the concept of sensory exploitation. The concept essentially states that behavioral traits (in this case iconic art production) which exploit pre-existing sensory sensitivities will evolve if not hindered by costs (i.e., natural selection). In this view, iconic art traditions are evolved by piggy-backing on cumulative adaptive evolution. Since it is to date uncertain whether art has served any adaptive function in human evolution, parsimony demands paying more attention to the primary and a functional mechanism of sensory exploitation as opposed to mechanisms of models based exclusively on secondary benefits (such as Miller's, for instance, in which art is proposed to evolve as a sexual display of fitness).

Adaptive Laboratory Evolution Of Escherichia Coli Reveals Arduous Resistance Development To A Combination Of Three Novel Antimicrobial Compounds And To The Short Amp P9-4

DEFF Research Database (Denmark)

Citterio, Linda; Franzyk, Henrik; Gram, Lone

2015-01-01

Antimicrobial peptides (AMPs) were for long considered as promising new antimicrobials since resistance was not expected. However, adaptive evolution experiments have demonstrated that bacteria may indeed develop resistance also to AMPs. However, we and others hypothesize that the risk...... of resistance development decreases when two or more compounds are combined as compared to single-drug treatments. The purpose of this study was to determine if resistance could develop in Escherichia coli ATCC 25922 to the peptidomimetic HF-1002 2 and the AMPs novicidin and P9-4. The mentioned compounds were...... adaptation to 32 x MIC. This shows that resistance to novicidin and HF-1002 2, administered alone, developed more easily than it occurred in lineages exposed to the combination of three drugs. This result further supports combinatorial treatment as a way to circumvent resistance development. Surprisingly...

A Cretaceous origin for fire adaptations in the Cape flora.

Science.gov (United States)

He, Tianhua; Lamont, Byron B; Manning, John

2016-10-05

Fire has had a profound effect on the evolution of worldwide biotas. The Cape Floristic Region is one of the world's most species-rich regions, yet it is highly prone to recurrent fires and fire-adapted species contribute strongly to the overall flora. It is hypothesized that the current fire regimes in the Cape could be as old as 6-8 million years (My), while indirect evidence indicates that the onset of fire could have reached 18 million years ago (Ma). Here, we trace the origin of fire-dependent traits in two monocot families that are significant elements in the fire-prone Cape flora. Our analysis shows that fire-stimulated flowering originated in the Cape Haemodoraceae 81 Ma, while fire-stimulated germination arose in the African Restionaceae at least 70 Ma, implying that wildfires have been a significant force in the evolution of the Cape flora at least 60 My earlier than previous estimates. Our results provide strong evidence for the presence of fire adaptations in the Cape from the Cretaceous, leading to the extraordinary persistence of a fire-adapted flora in this biodiversity hotspot, and giving support to the hypothesis that Cretaceous fire was a global phenomenon that shaped the evolution of terrestrial floras.

An incoherent feedforward loop facilitates adaptive tuning of gene expression.

Science.gov (United States)

Hong, Jungeui; Brandt, Nathan; Abdul-Rahman, Farah; Yang, Ally; Hughes, Tim; Gresham, David

2018-04-05

We studied adaptive evolution of gene expression using long-term experimental evolution of Saccharomyces cerevisiae in ammonium-limited chemostats. We found repeated selection for non-synonymous variation in the DNA binding domain of the transcriptional activator, GAT1, which functions with the repressor, DAL80 in an incoherent type-1 feedforward loop (I1-FFL) to control expression of the high affinity ammonium transporter gene, MEP2. Missense mutations in the DNA binding domain of GAT1 reduce its binding to the GATAA consensus sequence. However, we show experimentally, and using mathematical modeling, that decreases in GAT1 binding result in increased expression of MEP2 as a consequence of properties of I1-FFLs. Our results show that I1-FFLs, one of the most commonly occurring network motifs in transcriptional networks, can facilitate adaptive tuning of gene expression through modulation of transcription factor binding affinities. Our findings highlight the importance of gene regulatory architectures in the evolution of gene expression. © 2018, Hong et al.

Evolutionary online behaviour learning and adaptation in real robots.

Science.gov (United States)

Silva, Fernando; Correia, Luís; Christensen, Anders Lyhne

2017-07-01

Online evolution of behavioural control on real robots is an open-ended approach to autonomous learning and adaptation: robots have the potential to automatically learn new tasks and to adapt to changes in environmental conditions, or to failures in sensors and/or actuators. However, studies have so far almost exclusively been carried out in simulation because evolution in real hardware has required several days or weeks to produce capable robots. In this article, we successfully evolve neural network-based controllers in real robotic hardware to solve two single-robot tasks and one collective robotics task. Controllers are evolved either from random solutions or from solutions pre-evolved in simulation. In all cases, capable solutions are found in a timely manner (1 h or less). Results show that more accurate simulations may lead to higher-performing controllers, and that completing the optimization process in real robots is meaningful, even if solutions found in simulation differ from solutions in reality. We furthermore demonstrate for the first time the adaptive capabilities of online evolution in real robotic hardware, including robots able to overcome faults injected in the motors of multiple units simultaneously, and to modify their behaviour in response to changes in the task requirements. We conclude by assessing the contribution of each algorithmic component on the performance of the underlying evolutionary algorithm.

Quantifying the effectiveness of conservation measures to control the spread of anthropogenic hybridization in stream salmonids: a climate adaptation case study

Science.gov (United States)

Al-Chokhachy, Robert K.; Muhlfeld, Clint C.; Boyer, Matthew; Jones, Leslie A.; Steed, Amber; Kershner, Jeffrey L.

2014-01-01

Quantifying the effectiveness of management actions to mitigate the effects of changing climatic conditions (i.e., climate adaptation) can be difficult, yet critical for conservation. We used population genetic data from 1984 to 2011 to assess the degree to which ambient climatic conditions and targeted suppression of sources of nonnative Rainbow Trout Oncorhynchus mykiss have influenced the spread of introgressive hybridization in native populations of Westslope Cutthroat Trout O. clarkii lewisi. We found rapid expansion in the spatial distribution and proportion of nonnative genetic admixture in hybridized populations from 1984 to 2004, but minimal change since 2004. The spread of hybridization was negatively correlated with the number of streamflow events in May that exceeded the 75th percentile of historic flows (r = −0.98) and positively correlated with August stream temperatures (r = 0.89). Concomitantly, suppression data showed a 60% decline in catch per unit effort for fish with a high proportion of Rainbow Trout admixture, rendering some uncertainty as to the relative strength of factors controlling the spread of hybridization. Our results illustrate the importance of initiating management actions to mitigate the potential effects of climate change, even where data describing the effectiveness of such actions are initially limited but the risks are severe.

Host-Specific Parvovirus Evolution in Nature Is Recapitulated by In Vitro Adaptation to Different Carnivore Species

Science.gov (United States)

Allison, Andrew B.; Kohler, Dennis J.; Ortega, Alicia; Hoover, Elizabeth A.; Grove, Daniel M.; Holmes, Edward C.; Parrish, Colin R.

2014-01-01

Canine parvovirus (CPV) emerged as a new pandemic pathogen of dogs in the 1970s and is closely related to feline panleukopenia virus (FPV), a parvovirus of cats and related carnivores. Although both viruses have wide host ranges, analysis of viral sequences recovered from different wild carnivore species, as shown here, demonstrated that >95% were derived from CPV-like viruses, suggesting that CPV is dominant in sylvatic cycles. Many viral sequences showed host-specific mutations in their capsid proteins, which were often close to sites known to control binding to the transferrin receptor (TfR), the host receptor for these carnivore parvoviruses, and which exhibited frequent parallel evolution. To further examine the process of host adaptation, we passaged parvoviruses with alternative backgrounds in cells from different carnivore hosts. Specific mutations were selected in several viruses and these differed depending on both the background of the virus and the host cells in which they were passaged. Strikingly, these in vitro mutations recapitulated many specific changes seen in viruses from natural populations, strongly suggesting they are host adaptive, and which were shown to result in fitness advantages over their parental virus. Comparison of the sequences of the transferrin receptors of the different carnivore species demonstrated that many mutations occurred in and around the apical domain where the virus binds, indicating that viral variants were likely selected through their fit to receptor structures. Some of the viruses accumulated high levels of variation upon passage in alternative hosts, while others could infect multiple different hosts with no or only a few additional mutations. Overall, these studies demonstrate that the evolutionary history of a virus, including how long it has been circulating and in which hosts, as well as its phylogenetic background, has a profound effect on determining viral host range. PMID:25375184

Host-specific parvovirus evolution in nature is recapitulated by in vitro adaptation to different carnivore species.

Directory of Open Access Journals (Sweden)

Andrew B Allison

2014-11-01

Full Text Available Canine parvovirus (CPV emerged as a new pandemic pathogen of dogs in the 1970s and is closely related to feline panleukopenia virus (FPV, a parvovirus of cats and related carnivores. Although both viruses have wide host ranges, analysis of viral sequences recovered from different wild carnivore species, as shown here, demonstrated that>95% were derived from CPV-like viruses, suggesting that CPV is dominant in sylvatic cycles. Many viral sequences showed host-specific mutations in their capsid proteins, which were often close to sites known to control binding to the transferrin receptor (TfR, the host receptor for these carnivore parvoviruses, and which exhibited frequent parallel evolution. To further examine the process of host adaptation, we passaged parvoviruses with alternative backgrounds in cells from different carnivore hosts. Specific mutations were selected in several viruses and these differed depending on both the background of the virus and the host cells in which they were passaged. Strikingly, these in vitro mutations recapitulated many specific changes seen in viruses from natural populations, strongly suggesting they are host adaptive, and which were shown to result in fitness advantages over their parental virus. Comparison of the sequences of the transferrin receptors of the different carnivore species demonstrated that many mutations occurred in and around the apical domain where the virus binds, indicating that viral variants were likely selected through their fit to receptor structures. Some of the viruses accumulated high levels of variation upon passage in alternative hosts, while others could infect multiple different hosts with no or only a few additional mutations. Overall, these studies demonstrate that the evolutionary history of a virus, including how long it has been circulating and in which hosts, as well as its phylogenetic background, has a profound effect on determining viral host range.

Ontology evolution in physics

OpenAIRE

Chan, Michael

2013-01-01

With the advent of reasoning problems in dynamic environments, there is an increasing need for automated reasoning systems to automatically adapt to unexpected changes in representations. In particular, the automation of the evolution of their ontologies needs to be enhanced without substantially sacrificing expressivity in the underlying representation. Revision of beliefs is not enough, as adding to or removing from beliefs does not change the underlying formal language. Gene...

Morphological evolution, ecological diversification and climate change in rodents.

Science.gov (United States)

Renaud, Sabrina; Michaux, Jacques; Schmidt, Daniela N; Aguilar, Jean-Pierre; Mein, Pierre; Auffray, Jean-Christophe

2005-03-22

Among rodents, the lineage from Progonomys hispanicus to Stephanomys documents a case of increasing size and dental specialization during an approximately 9 Myr time-interval. On the contrary, some contemporaneous generalist lineages like Apodemus show a limited morphological evolution. Dental shape can be related to diet and can be used to assess the ecological changes along the lineages. Consequently, size and shape of the first upper molar were measured in order to quantify the patterns of morphological evolution along both lineages and compare them to environmental trends. Climatic changes do not have a direct influence on evolution, but they open new ecological opportunities by changing vegetation and allow the evolution of a specialist like Stephanomys. On the other hand, environmental changes are not dramatic enough to destroy the habitat of a long-term generalist like Apodemus. Hence, our results exemplify a case of an influence of climate on the evolution of specialist species, although a generalist species may persist without change.

Localizing recent adaptive evolution in the human genome

DEFF Research Database (Denmark)

Williamson, Scott H; Hubisz, Melissa J; Clark, Andrew G

2007-01-01

, clusters of olfactory receptors, genes involved in nervous system development and function, immune system genes, and heat shock genes. We also observe consistent evidence of selective sweeps in centromeric regions. In general, we find that recent adaptation is strikingly pervasive in the human genome......-nucleotide polymorphism ascertainment, while also providing fine-scale estimates of the position of the selected site, we analyzed a genomic dataset of 1.2 million human single-nucleotide polymorphisms genotyped in African-American, European-American, and Chinese samples. We identify 101 regions of the human genome...

Evolution before genes

Directory of Open Access Journals (Sweden)

Vasas Vera

2012-01-01

Full Text Available Abstract Background Our current understanding of evolution is so tightly linked to template-dependent replication of DNA and RNA molecules that the old idea from Oparin of a self-reproducing 'garbage bag' ('coacervate' of chemicals that predated fully-fledged cell-like entities seems to be farfetched to most scientists today. However, this is exactly the kind of scheme we propose for how Darwinian evolution could have occurred prior to template replication. Results We cannot confirm previous claims that autocatalytic sets of organic polymer molecules could undergo evolution in any interesting sense by themselves. While we and others have previously imagined inhibition would result in selectability, we found that it produced multiple attractors in an autocatalytic set that cannot be selected for. Instead, we discovered that if general conditions are satisfied, the accumulation of adaptations in chemical reaction networks can occur. These conditions are the existence of rare reactions producing viable cores (analogous to a genotype, that sustains a molecular periphery (analogous to a phenotype. Conclusions We conclude that only when a chemical reaction network consists of many such viable cores, can it be evolvable. When many cores are enclosed in a compartment there is competition between cores within the same compartment, and when there are many compartments, there is between-compartment competition due to the phenotypic effects of cores and their periphery at the compartment level. Acquisition of cores by rare chemical events, and loss of cores at division, allows macromutation, limited heredity and selectability, thus explaining how a poor man's natural selection could have operated prior to genetic templates. This is the only demonstration to date of a mechanism by which pre-template accumulation of adaptation could occur. Reviewers This article was reviewed by William Martin and Eugene Koonin.

Global analysis of genes involved in freshwater adaptation in threespine sticklebacks (Gasterosteus aculeatus).

Science.gov (United States)

DeFaveri, Jacquelin; Shikano, Takahito; Shimada, Yukinori; Goto, Akira; Merilä, Juha

2011-06-01

Examples of parallel evolution of phenotypic traits have been repeatedly demonstrated in threespine sticklebacks (Gasterosteus aculeatus) across their global distribution. Using these as a model, we performed a targeted genome scan--focusing on physiologically important genes potentially related to freshwater adaptation--to identify genetic signatures of parallel physiological evolution on a global scale. To this end, 50 microsatellite loci, including 26 loci within or close to (directional selection were detected in 24 loci, including 17 physiologically important genes, in at least one location. Although no loci showed consistent signatures of selection in all divergent population pairs, several outliers were common in multiple locations. In particular, seven physiologically important genes, as well as reference ectodysplasin gene (EDA), showed signatures of selection in three or more locations. Hence, although these results give some evidence for consistent parallel molecular evolution in response to freshwater colonization, they suggest that different evolutionary pathways may underlie physiological adaptation to freshwater habitats within the global distribution of the threespine stickleback. © 2011 The Author(s). Evolution© 2011 The Society for the Study of Evolution.

Adaptive Evolution of Phosphorus Metabolism in Prochlorococcus

DEFF Research Database (Denmark)

Casey, John R; Mardinoglu, Adil; Nielsen, Jens

2016-01-01

Inorganic phosphorus is scarce in the eastern Mediterranean Sea, where the high-light-adapted ecotype HLI of the marine picocyanobacterium Prochlorococcus marinus thrives. Physiological and regulatory control of phosphorus acquisition and partitioning has been observed in HLI both in culture...... and in the field; however, the optimization of phosphorus metabolism and associated gains for its phosphorus-limited-growth (PLG) phenotype have not been studied. Here, we reconstructed a genome-scale metabolic network of the HLI axenic strain MED4 (iJC568), consisting of 568 metabolic genes in relation to 794...... through drastic depletion of phosphorus-containing biomass components but also through network-wide reductions in phosphate-reaction participation and the loss of a key enzyme, succinate dehydrogenase. These alterations occur despite the stringency of having relatively few pathway redundancies...

Metadata to Support Data Warehouse Evolution

Science.gov (United States)

Solodovnikova, Darja

The focus of this chapter is metadata necessary to support data warehouse evolution. We present the data warehouse framework that is able to track evolution process and adapt data warehouse schemata and data extraction, transformation, and loading (ETL) processes. We discuss the significant part of the framework, the metadata repository that stores information about the data warehouse, logical and physical schemata and their versions. We propose the physical implementation of multiversion data warehouse in a relational DBMS. For each modification of a data warehouse schema, we outline the changes that need to be made to the repository metadata and in the database.

Evolution and adaptation of Pseudomonas aeruginosa in cystic fibrosis airways

DEFF Research Database (Denmark)

Madsen Sommer, Lea Mette

of natural environments, the primary obstacle is re-sampling of the samepopulation over time, especially if the population is small.Nevertheless, it has been accomplished: Chronic airway infections of cystic fibrosis (CF) patients have offered a unique view into the adaptationand evolution of Pseudomonas...... to the CF airways. From this analysis we found common clonal lineages among the patients, evidence of patient-to-patient transmission, historic contingencies, and convergent evolution of 52 candidate pathoadaptive genes. By further genome sequencing 26 P. aeruginosa isolates from four Italian CF patients...

High selection pressure promotes increase in cumulative adaptive culture.

Directory of Open Access Journals (Sweden)

Carolin Vegvari

Full Text Available The evolution of cumulative adaptive culture has received widespread interest in recent years, especially the factors promoting its occurrence. Current evolutionary models suggest that an increase in population size may lead to an increase in cultural complexity via a higher rate of cultural transmission and innovation. However, relatively little attention has been paid to the role of natural selection in the evolution of cultural complexity. Here we use an agent-based simulation model to demonstrate that high selection pressure in the form of resource pressure promotes the accumulation of adaptive culture in spite of small population sizes and high innovation costs. We argue that the interaction of demography and selection is important, and that neither can be considered in isolation. We predict that an increase in cultural complexity is most likely to occur under conditions of population pressure relative to resource availability. Our model may help to explain why culture change can occur without major environmental change. We suggest that understanding the interaction between shifting selective pressures and demography is essential for explaining the evolution of cultural complexity.

Enhancer Evolution across 20 Mammalian Species

Science.gov (United States)

Villar, Diego; Berthelot, Camille; Aldridge, Sarah; Rayner, Tim F.; Lukk, Margus; Pignatelli, Miguel; Park, Thomas J.; Deaville, Robert; Erichsen, Jonathan T.; Jasinska, Anna J.; Turner, James M.A.; Bertelsen, Mads F.; Murchison, Elizabeth P.; Flicek, Paul; Odom, Duncan T.

2015-01-01

Summary The mammalian radiation has corresponded with rapid changes in noncoding regions of the genome, but we lack a comprehensive understanding of regulatory evolution in mammals. Here, we track the evolution of promoters and enhancers active in liver across 20 mammalian species from six diverse orders by profiling genomic enrichment of H3K27 acetylation and H3K4 trimethylation. We report that rapid evolution of enhancers is a universal feature of mammalian genomes. Most of the recently evolved enhancers arise from ancestral DNA exaptation, rather than lineage-specific expansions of repeat elements. In contrast, almost all liver promoters are partially or fully conserved across these species. Our data further reveal that recently evolved enhancers can be associated with genes under positive selection, demonstrating the power of this approach for annotating regulatory adaptations in genomic sequences. These results provide important insight into the functional genetics underpinning mammalian regulatory evolution. PMID:25635462

The edge of neutral evolution in social dilemmas

Energy Technology Data Exchange (ETDEWEB)

Cremer, Jonas; Frey, Erwin [Arnold Sommerfeld Center for Theoretical Physics and Center for NanoScience, Department of Physics, Ludwig-Maximilians-Universitaet Muenchen, Theresienstrasse 37, D-80333 Muenchen (Germany); Reichenbach, Tobias [Howard Hughes Medical Institute and Laboratory of Sensory Neuroscience, Rockefeller University, 1230 York Avenue, New York, NY 10065 (United States)], E-mail: jonas.cremer@physik.uni-muenchen.de

2009-09-15

The functioning of animal as well as human societies fundamentally relies on cooperation. Yet, defection is often favorable for the selfish individual, and social dilemmas arise. Selection by individuals' fitness, usually the basic driving force of evolution, quickly eliminates cooperators. However, evolution is also governed by fluctuations that can be of greater importance than fitness differences, and can render evolution effectively neutral. Here, we investigate the effects of selection versus fluctuations in social dilemmas. By studying the mean extinction times of cooperators and defectors, a variable sensitive to fluctuations, we are able to identify and quantify an emerging 'edge of neutral evolution' that delineates regimes of neutral and Darwinian evolution. Our results reveal that cooperation is significantly maintained in the neutral regimes. In contrast, the classical predictions of evolutionary game theory, where defectors beat cooperators, are recovered in the Darwinian regimes. Our studies demonstrate that fluctuations can provide a surprisingly simple way to partly resolve social dilemmas. Our methods are generally applicable to estimate the role of random drift in evolutionary dynamics.

The edge of neutral evolution in social dilemmas

International Nuclear Information System (INIS)

Cremer, Jonas; Frey, Erwin; Reichenbach, Tobias

2009-01-01

The functioning of animal as well as human societies fundamentally relies on cooperation. Yet, defection is often favorable for the selfish individual, and social dilemmas arise. Selection by individuals' fitness, usually the basic driving force of evolution, quickly eliminates cooperators. However, evolution is also governed by fluctuations that can be of greater importance than fitness differences, and can render evolution effectively neutral. Here, we investigate the effects of selection versus fluctuations in social dilemmas. By studying the mean extinction times of cooperators and defectors, a variable sensitive to fluctuations, we are able to identify and quantify an emerging 'edge of neutral evolution' that delineates regimes of neutral and Darwinian evolution. Our results reveal that cooperation is significantly maintained in the neutral regimes. In contrast, the classical predictions of evolutionary game theory, where defectors beat cooperators, are recovered in the Darwinian regimes. Our studies demonstrate that fluctuations can provide a surprisingly simple way to partly resolve social dilemmas. Our methods are generally applicable to estimate the role of random drift in evolutionary dynamics.

Adapting adaptation: the English eco-town initiative as governance process

Directory of Open Access Journals (Sweden)

Daniel Tomozeiu

2014-06-01

Full Text Available Climate change adaptation and mitigation have become key policy drivers in the UK under its Climate Change Act of 2008. At the same time, urbanization has been high on the agenda, given the pressing need for substantial additional housing, particularly in southeast England. These twin policy objectives were brought together in the UK government's 'eco-town' initiative for England launched in 2007, which has since resulted in four eco-town projects currently under development. We critically analyze the eco-town initiative's policy evolution and early planning phase from a multilevel governance perspective by focusing on the following two interrelated aspects: (1 the evolving governance structures and resulting dynamics arising from the development of the eco-town initiative at UK governmental level, and the subsequent partial devolution to local stakeholders, including local authorities and nongovernmental actors, under the new 'localism' agenda; and (2 the effect of these governance dynamics on the conceptual and practical approach to adaptation through the emerging eco-town projects. As such, we problematize the impact of multilevel governance relations, and competing governance strategies and leadership, on shaping eco-town and related adaptation strategies and practice.

Adaptive radiation versus 'radiation' and 'explosive diversification': why conceptual distinctions are fundamental to understanding evolution.

Science.gov (United States)

Givnish, Thomas J

2015-07-01

Adaptive radiation is the rise of a diversity of ecological roles and role-specific adaptations within a lineage. Recently, some researchers have begun to use 'adaptive radiation' or 'radiation' as synonymous with 'explosive species diversification'. This essay aims to clarify distinctions between these concepts, and the related ideas of geographic speciation, sexual selection, key innovations, key landscapes and ecological keys. Several examples are given to demonstrate that adaptive radiation and explosive diversification are not the same phenomenon, and that focusing on explosive diversification and the analysis of phylogenetic topology ignores much of the rich biology associated with adaptive radiation, and risks generating confusion about the nature of the evolutionary forces driving species diversification. Some 'radiations' involve bursts of geographic speciation or sexual selection, rather than adaptive diversification; some adaptive radiations have little or no effect on speciation, or even a negative effect. Many classic examples of 'adaptive radiation' appear to involve effects driven partly by geographic speciation, species' dispersal abilities, and the nature of extrinsic dispersal barriers; partly by sexual selection; and partly by adaptive radiation in the classical sense, including the origin of traits and invasion of adaptive zones that result in decreased diversification rates but add to overall diversity. © 2015 The Author. New Phytologist © 2015 New Phytologist Trust.

Anatomy of an adaptive radiation: Blepharoneura fruit flies

Science.gov (United States)

Insect herbivores have often been linked to the ecological theory of adaptive radiation, which postulates that divergent selection on phenotypes in different habitats or environments results in the evolution of reproductive barriers between populations and subsequent speciation. An expected result o...

Low-energy impact of adaptive cylindrical piezoelectric-composite shells

Energy Technology Data Exchange (ETDEWEB)

Saravanos, D.A. [University of Patras (United Kingdom). Dept. of Mechanical Engineering and Aeronautics; Christoforou, A.P. [Kuwait Univ. (Kuwait). Dept. of Mechanical Engineering

2002-04-01

A theoretical framework for analyzing low-energy impacts of laminated shells with active and sensory piezoelectric layers is presented, including impactor dynamics and contact law. The formulation encompasses a coupled piezoelectric shell theory mixing first order shear displacement assumptions and layerwise variation of electric potential. An exact in-plane Ritz solution for the impact of open cylindrical piezoelectric-composite shells is developed and solved numerically using an explicit time integration scheme. The active impact control problem of adaptive cylindrical shells with distributed curved piezoelectric actuators is addressed. The cases of optimized state feedback controllers and output feedback controllers using piezoelectric sensors are analyzed. Numerical results quantify the impact response of cylindrical shells of various curvatures including the signal of curved piezoelectric sensors. Additional numerical studies quantify the impact response of adaptive cylindrical panels and investigate the feasibility of actively reducing the impact force. (author)

Adaptive dynamics on an environmental gradient that changes over a geological time-scale.

Science.gov (United States)

Fortelius, Mikael; Geritz, Stefan; Gyllenberg, Mats; Toivonen, Jaakko

2015-07-07

The standard adaptive dynamics framework assumes two timescales, i.e. fast population dynamics and slow evolutionary dynamics. We further assume a third timescale, which is even slower than the evolutionary timescale. We call this the geological timescale and we assume that slow climatic change occurs within this timescale. We study the evolution of our model population over this very slow geological timescale with bifurcation plots of the standard adaptive dynamics framework. The bifurcation parameter being varied describes the abiotic environment that changes over the geological timescale. We construct evolutionary trees over the geological timescale and observe both gradual phenotypic evolution and punctuated branching events. We concur with the established notion that branching of a monomorphic population on an environmental gradient only happens when the gradient is not too shallow and not too steep. However, we show that evolution within the habitat can produce polymorphic populations that inhabit steep gradients. What is necessary is that the environmental gradient at some point in time is such that the initial branching of the monomorphic population can occur. We also find that phenotypes adapted to environments in the middle of the existing environmental range are more likely to branch than phenotypes adapted to extreme environments. Copyright © 2015 Elsevier Ltd. All rights reserved.

DyKOSMap: A framework for mapping adaptation between biomedical knowledge organization systems.

Science.gov (United States)

Dos Reis, Julio Cesar; Pruski, Cédric; Da Silveira, Marcos; Reynaud-Delaître, Chantal

2015-06-01

Knowledge Organization Systems (KOS) and their associated mappings play a central role in several decision support systems. However, by virtue of knowledge evolution, KOS entities are modified over time, impacting mappings and potentially turning them invalid. This requires semi-automatic methods to maintain such semantic correspondences up-to-date at KOS evolution time. We define a complete and original framework based on formal heuristics that drives the adaptation of KOS mappings. Our approach takes into account the definition of established mappings, the evolution of KOS and the possible changes that can be applied to mappings. This study experimentally evaluates the proposed heuristics and the entire framework on realistic case studies borrowed from the biomedical domain, using official mappings between several biomedical KOSs. We demonstrate the overall performance of the approach over biomedical datasets of different characteristics and sizes. Our findings reveal the effectiveness in terms of precision, recall and F-measure of the suggested heuristics and methods defining the framework to adapt mappings affected by KOS evolution. The obtained results contribute and improve the quality of mappings over time. The proposed framework can adapt mappings largely automatically, facilitating thus the maintenance task. The implemented algorithms and tools support and minimize the work of users in charge of KOS mapping maintenance. Copyright © 2015 Elsevier Inc. All rights reserved.

Complex inheritance of larval adaptation in Plutella xylostella to a novel host plant

NARCIS (Netherlands)

Henniges-Janssen, K.; Reineke, A.; Heckel, D.G.; Groot, A.T.

2011-01-01

Studying the genetics of host shifts and range expansions in phytophagous insects contributes to our understanding of the evolution of host plant adaptation. We investigated the recent host range expansion to pea, in the pea-adapted strain (P-strain) of the crucifer-specialist diamondback moth,

An Enhanced Jaya Algorithm with a Two Group Adaption

Directory of Open Access Journals (Sweden)

Chibing Gong

2017-01-01

Full Text Available This paper proposes a novel performance enhanced Jaya algorithm with a two group adaption (E-Jaya. Two improvements are presented in E-Jaya. First, instead of using the best and the worst values in Jaya algorithm, EJaya separates all candidates into two groups: the better and the worse groups based on their fitness values, then the mean of the better group and the mean of the worse group are used. Second, in order to add non algorithm-specific parameters in E-Jaya, a novel adaptive method of dividing the two groups has been developed. Finally, twelve benchmark functions with different dimensionality, such as 40, 60, and 100, were evaluated using the proposed EJaya algorithm. The results show that E-Jaya significantly outperformed Jaya algorithm in terms of the solution accuracy. Additionally, E-Jaya was also compared with a differential evolution (DE, a self-adapting control parameters in differential evolution (jDE, a firefly algorithm (FA, and a standard particle swarm optimization 2011 (SPSO2011 algorithm. E-Jaya algorithm outperforms all the algorithms.

Survival and evolution of a large multidrug resistance plasmid in new clinical bacterial hosts

DEFF Research Database (Denmark)

Porse, Andreas; Schønning, Kristian; Munck, Christian

2016-01-01

Large conjugative plasmids are important drivers of bacterial evolution and contribute significantly to the dissemination of antibiotic resistance. Although plasmid borne multidrug resistance is recognized as one of the main challenges in modern medicine, the adaptive forces shaping the evolution...

Physicochemical evolution and positive selection of the ...

Indian Academy of Sciences (India)

2010-04-08

Apr 8, 2010 ... It is not clear whether matK evolves under Darwinian selection. In this study, the gymnosperm Taxaceae, Cephalotaxaceae and Pinaceae were used to illustrate the physicochemical evolution, molecular adaptation and evolutionary dynamics of gene divergence in matKs. matK sequences were amplified ...

Genome Evolution in the Genus Sorghum (Poaceae)

OpenAIRE

PRICE, H. JAMES; DILLON, SALLY L.; HODNETT, GEORGE; ROONEY, WILLIAM L.; ROSS, LARRY; JOHNSTON, J. SPENCER

2005-01-01

• Background and Aims The roles of variation in DNA content in plant evolution and adaptation remain a major biological enigma. Chromosome number and 2C DNA content were determined for 21 of the 25 species of the genus Sorghum and analysed from a phylogenetic perspective.

Host imprints on bacterial genomes--rapid, divergent evolution in individual patients.

Directory of Open Access Journals (Sweden)

Jaroslaw Zdziarski

Full Text Available Bacteria lose or gain genetic material and through selection, new variants become fixed in the population. Here we provide the first, genome-wide example of a single bacterial strain's evolution in different deliberately colonized patients and the surprising insight that hosts appear to personalize their microflora. By first obtaining the complete genome sequence of the prototype asymptomatic bacteriuria strain E. coli 83972 and then resequencing its descendants after therapeutic bladder colonization of different patients, we identified 34 mutations, which affected metabolic and virulence-related genes. Further transcriptome and proteome analysis proved that these genome changes altered bacterial gene expression resulting in unique adaptation patterns in each patient. Our results provide evidence that, in addition to stochastic events, adaptive bacterial evolution is driven by individual host environments. Ongoing loss of gene function supports the hypothesis that evolution towards commensalism rather than virulence is favored during asymptomatic bladder colonization.

Quantifying China's regional economic complexity

Science.gov (United States)

Gao, Jian; Zhou, Tao

2018-02-01

China has experienced an outstanding economic expansion during the past decades, however, literature on non-monetary metrics that reveal the status of China's regional economic development are still lacking. In this paper, we fill this gap by quantifying the economic complexity of China's provinces through analyzing 25 years' firm data. First, we estimate the regional economic complexity index (ECI), and show that the overall time evolution of provinces' ECI is relatively stable and slow. Then, after linking ECI to the economic development and the income inequality, we find that the explanatory power of ECI is positive for the former but negative for the latter. Next, we compare different measures of economic diversity and explore their relationships with monetary macroeconomic indicators. Results show that the ECI index and the non-linear iteration based Fitness index are comparative, and they both have stronger explanatory power than other benchmark measures. Further multivariate regressions suggest the robustness of our results after controlling other socioeconomic factors. Our work moves forward a step towards better understanding China's regional economic development and non-monetary macroeconomic indicators.

Plastid phylogenomics and adaptive evolution of Gaultheria series Trichophyllae (Ericaceae), a clade from sky islands of the Himalaya-Hengduan Mountains.

Science.gov (United States)

Zhang, Ming-Ying; Fritsch, Peter W; Ma, Peng-Fei; Wang, Hong; Lu, Lu; Li, De-Zhu

2017-05-01

Gaultheria series Trichophyllae Airy Shaw is an angiosperm clade of high-alpine shrublets endemic to the Himalaya-Hengduan Mountains and characterized by recent species divergence and convergent character evolution that has until recently caused much confusion in species circumscription. Although multiple DNA sequence regions have been employed previously, phylogenetic relationships among species in the group have remained largely unresolved. Here we examined the effectiveness of the plastid genome for improving phylogenetic resolution within the G. series Trichophyllae clade. Plastid genomes of 31 samples representing all 19 recognized species of the series and three outgroup species were sequenced with Illumina Sequencing technology. Maximum likelihood (ML), maximum parsimony (MP) and Bayesian inference (BI) phylogenetic analyses were performed with various datasets, i.e., that from the whole plastid genome, coding regions, noncoding regions, large single-copy region (LSC) and inverted-repeat region a (IRa). The partitioned whole plastid genome with inverted-repeat region b (IRb) excluded was also analyzed with ML and BI. Tree topologies based on the whole plastid genome, noncoding regions, and LSC region datasets across all analyses, and that based on the partitioned dataset with ML and BI analyses, are identical and generally strongly supported. Gaultheria series Trichophyllae form a clade with three species and one variety that is sister to a clade of the remaining 16 species; the latter comprises seven main subclades. Interspecific relationships within the series are strongly supported except for those based on the coding-region and IRa-region datasets. Eight divergence hotspot regions, each possessing >5% percent variable sites, were screened across the whole plastid genome of the 28 individuals sampled in the series. Results of morphological character evolution reconstruction diagnose several clades, and a hypothesis of adaptive evolution for plant habit is

Functional genomics of physiological plasticity and local adaptation in killifish.

Science.gov (United States)

Whitehead, Andrew; Galvez, Fernando; Zhang, Shujun; Williams, Larissa M; Oleksiak, Marjorie F

2011-01-01

Evolutionary solutions to the physiological challenges of life in highly variable habitats can span the continuum from evolution of a cosmopolitan plastic phenotype to the evolution of locally adapted phenotypes. Killifish (Fundulus sp.) have evolved both highly plastic and locally adapted phenotypes within different selective contexts, providing a comparative system in which to explore the genomic underpinnings of physiological plasticity and adaptive variation. Importantly, extensive variation exists among populations and species for tolerance to a variety of stressors, and we exploit this variation in comparative studies to yield insights into the genomic basis of evolved phenotypic variation. Notably, species of Fundulus occupy the continuum of osmotic habitats from freshwater to marine and populations within Fundulus heteroclitus span far greater variation in pollution tolerance than across all species of fish. Here, we explore how transcriptome regulation underpins extreme physiological plasticity on osmotic shock and how genomic and transcriptomic variation is associated with locally evolved pollution tolerance. We show that F. heteroclitus quickly acclimate to extreme osmotic shock by mounting a dramatic rapid transcriptomic response including an early crisis control phase followed by a tissue remodeling phase involving many regulatory pathways. We also show that convergent evolution of locally adapted pollution tolerance involves complex patterns of gene expression and genome sequence variation, which is confounded with body-weight dependence for some genes. Similarly, exploiting the natural phenotypic variation associated with other established and emerging model organisms is likely to greatly accelerate the pace of discovery of the genomic basis of phenotypic variation.

Adaptability and stability of carotenoids in maize cultivars

Directory of Open Access Journals (Sweden)

Sara de Almeida Rios

2009-01-01

Full Text Available The purpose of this study was to investigate the adaptability and stability of carotenoids in maize cultivars inthe 2004/2005 growing season. Total carotenoids (TC, total carotenoids with provitamin A activity (Pro VA (μg g-1 andgrain yield (kg ha-1 were quantified in 10 cultivars at five locations. The chemical analyses were conducted in a laboratoryof the EMBRAPA/CNPMS, in Sete Lagoas, Minas Gerais. The methodologies of Eberhart and Russell (1966, Lin and Binns(1988 and Rocha et al. (2005 were used to analyze adaptability and stability. In general, the linear regression modelproposed by Eberhart and Russell (1966 failed to fit the Pro VA contents in the evaluated cultivars satisfactorily. However,with regard to the TC levels, all different analysis methodologies of adaptability and stability rated hybrid BRS 2020 as anideal genotype with general adaptability.

Role of pleiotropy during adaptation of TEM-1 β-lactamase to two novel antibiotics

NARCIS (Netherlands)

Schenk, M.F.; Witte, Sariette; Salverda, M.L.M.; Koopmanschap, Bertha; Krug, Joachim; Visser, de J.A.G.M.

2015-01-01

Pleiotropy is a key feature of the genotype-phenotype map, and its form and extent have many evolutionary implications, including for the dynamics of adaptation and the evolution of specialization. Similarly, pleiotropic effects of antibiotic resistance mutations may affect the evolution of

Analytical evaluation of adaptive-modulation-based opportunistic cognitive radio in nakagami-m fading channels

KAUST Repository

Chen, Yunfei; Alouini, Mohamed-Slim; Tang, Liang; Khan, Fahdahmed

2012-01-01

The performance of adaptive modulation for cognitive radio with opportunistic access is analyzed by considering the effects of spectrum sensing, primary user (PU) traffic, and time delay for Nakagami- m fading channels. Both the adaptive continuous rate scheme and the adaptive discrete rate scheme are considered. Numerical examples are presented to quantify the effects of spectrum sensing, PU traffic, and time delay for different system parameters. © 1967-2012 IEEE.