Inferring fitness landscapes and selection on phenotypic states from single-cell genealogical data

PubMed Central

Kussell, Edo

2017-01-01

Recent advances in single-cell time-lapse microscopy have revealed non-genetic heterogeneity and temporal fluctuations of cellular phenotypes. While different phenotypic traits such as abundance of growth-related proteins in single cells may have differential effects on the reproductive success of cells, rigorous experimental quantification of this process has remained elusive due to the complexity of single cell physiology within the context of a proliferating population. We introduce and apply a practical empirical method to quantify the fitness landscapes of arbitrary phenotypic traits, using genealogical data in the form of population lineage trees which can include phenotypic data of various kinds. Our inference methodology for fitness landscapes determines how reproductivity is correlated to cellular phenotypes, and provides a natural generalization of bulk growth rate measures for single-cell histories. Using this technique, we quantify the strength of selection acting on different cellular phenotypic traits within populations, which allows us to determine whether a change in population growth is caused by individual cells’ response, selection within a population, or by a mixture of these two processes. By applying these methods to single-cell time-lapse data of growing bacterial populations that express a resistance-conferring protein under antibiotic stress, we show how the distributions, fitness landscapes, and selection strength of single-cell phenotypes are affected by the drug. Our work provides a unified and practical framework for quantitative measurements of fitness landscapes and selection strength for any statistical quantities definable on lineages, and thus elucidates the adaptive significance of phenotypic states in time series data. The method is applicable in diverse fields, from single cell biology to stem cell differentiation and viral evolution. PMID:28267748

Exploiting the Adaptation Dynamics to Predict the Distribution of Beneficial Fitness Effects

PubMed Central

2016-01-01

Adaptation of asexual populations is driven by beneficial mutations and therefore the dynamics of this process, besides other factors, depends on the distribution of beneficial fitness effects. It is known that on uncorrelated fitness landscapes, this distribution can only be of three types: truncated, exponential and power law. We performed extensive stochastic simulations to study the adaptation dynamics on rugged fitness landscapes, and identified two quantities that can be used to distinguish the underlying distribution of beneficial fitness effects. The first quantity studied here is the fitness difference between successive mutations that spread in the population, which is found to decrease in the case of truncated distributions, remains nearly a constant for exponentially decaying distributions and increases when the fitness distribution decays as a power law. The second quantity of interest, namely, the rate of change of fitness with time also shows quantitatively different behaviour for different beneficial fitness distributions. The patterns displayed by the two aforementioned quantities are found to hold good for both low and high mutation rates. We discuss how these patterns can be exploited to determine the distribution of beneficial fitness effects in microbial experiments. PMID:26990188

Correlation of fitness landscapes from three orthologous TIM barrels originates from sequence and structure constraints

PubMed Central

Chan, Yvonne H.; Venev, Sergey V.; Zeldovich, Konstantin B.; Matthews, C. Robert

2017-01-01

Sequence divergence of orthologous proteins enables adaptation to environmental stresses and promotes evolution of novel functions. Limits on evolution imposed by constraints on sequence and structure were explored using a model TIM barrel protein, indole-3-glycerol phosphate synthase (IGPS). Fitness effects of point mutations in three phylogenetically divergent IGPS proteins during adaptation to temperature stress were probed by auxotrophic complementation of yeast with prokaryotic, thermophilic IGPS. Analysis of beneficial mutations pointed to an unexpected, long-range allosteric pathway towards the active site of the protein. Significant correlations between the fitness landscapes of distant orthologues implicate both sequence and structure as primary forces in defining the TIM barrel fitness landscape and suggest that fitness landscapes can be translocated in sequence space. Exploration of fitness landscapes in the context of a protein fold provides a strategy for elucidating the sequence-structure-fitness relationships in other common motifs. PMID:28262665

Inclusion of the fitness sharing technique in an evolutionary algorithm to analyze the fitness landscape of the genetic code adaptability.

PubMed

Santos, José; Monteagudo, Ángel

2017-03-27

The canonical code, although prevailing in complex genomes, is not universal. It was shown the canonical genetic code superior robustness compared to random codes, but it is not clearly determined how it evolved towards its current form. The error minimization theory considers the minimization of point mutation adverse effect as the main selection factor in the evolution of the code. We have used simulated evolution in a computer to search for optimized codes, which helps to obtain information about the optimization level of the canonical code in its evolution. A genetic algorithm searches for efficient codes in a fitness landscape that corresponds with the adaptability of possible hypothetical genetic codes. The lower the effects of errors or mutations in the codon bases of a hypothetical code, the more efficient or optimal is that code. The inclusion of the fitness sharing technique in the evolutionary algorithm allows the extent to which the canonical genetic code is in an area corresponding to a deep local minimum to be easily determined, even in the high dimensional spaces considered. The analyses show that the canonical code is not in a deep local minimum and that the fitness landscape is not a multimodal fitness landscape with deep and separated peaks. Moreover, the canonical code is clearly far away from the areas of higher fitness in the landscape. Given the non-presence of deep local minima in the landscape, although the code could evolve and different forces could shape its structure, the fitness landscape nature considered in the error minimization theory does not explain why the canonical code ended its evolution in a location which is not an area of a localized deep minimum of the huge fitness landscape.

Adaptation in Tunably Rugged Fitness Landscapes: The Rough Mount Fuji Model

PubMed Central

Neidhart, Johannes; Szendro, Ivan G.; Krug, Joachim

2014-01-01

Much of the current theory of adaptation is based on Gillespie’s mutational landscape model (MLM), which assumes that the fitness values of genotypes linked by single mutational steps are independent random variables. On the other hand, a growing body of empirical evidence shows that real fitness landscapes, while possessing a considerable amount of ruggedness, are smoother than predicted by the MLM. In the present article we propose and analyze a simple fitness landscape model with tunable ruggedness based on the rough Mount Fuji (RMF) model originally introduced by Aita et al. in the context of protein evolution. We provide a comprehensive collection of results pertaining to the topographical structure of RMF landscapes, including explicit formulas for the expected number of local fitness maxima, the location of the global peak, and the fitness correlation function. The statistics of single and multiple adaptive steps on the RMF landscape are explored mainly through simulations, and the results are compared to the known behavior in the MLM model. Finally, we show that the RMF model can explain the large number of second-step mutations observed on a highly fit first-step background in a recent evolution experiment with a microvirid bacteriophage. PMID:25123507

Decision making on fitness landscapes

NASA Astrophysics Data System (ADS)

Arthur, R.; Sibani, P.

2017-04-01

We discuss fitness landscapes and how they can be modified to account for co-evolution. We are interested in using the landscape as a way to model rational decision making in a toy economic system. We develop a model very similar to the Tangled Nature Model of Christensen et al. that we call the Tangled Decision Model. This is a natural setting for our discussion of co-evolutionary fitness landscapes. We use a Monte Carlo step to simulate decision making and investigate two different decision making procedures.

Modeling Evolution on Nearly Neutral Network Fitness Landscapes

NASA Astrophysics Data System (ADS)

Yakushkina, Tatiana; Saakian, David B.

2017-08-01

To describe virus evolution, it is necessary to define a fitness landscape. In this article, we consider the microscopic models with the advanced version of neutral network fitness landscapes. In this problem setting, we suppose a fitness difference between one-point mutation neighbors to be small. We construct a modification of the Wright-Fisher model, which is related to ordinary infinite population models with nearly neutral network fitness landscape at the large population limit. From the microscopic models in the realistic sequence space, we derive two versions of nearly neutral network models: with sinks and without sinks. We claim that the suggested model describes the evolutionary dynamics of RNA viruses better than the traditional Wright-Fisher model with few sequences.

Shifting fitness landscapes in response to altered environments

PubMed Central

Jensen, Jeffrey D.; Bolon, Daniel N. A.

2013-01-01

The role of adaptation in molecular evolution has been contentious for decades. Here, we shed light on the adaptive potential in Saccharomyces cerevisiae by presenting systematic fitness measurements for all possible point mutations in a region of Hsp90 under four environmental conditions. Under elevated salinity, we observe numerous beneficial mutations with growth advantages up to 7% relative to the wild type. All of these beneficial mutations were observed to be associated with high costs of adaptation. We thus demonstrate that an essential protein can harbor adaptive potential upon an environmental challenge, and report a remarkable fit of the data to a version of Fisher's geometric model that focuses on the fitness trade-offs between mutations in different environments. PMID:24299404

Evolution at ‘Sutures’ and ‘Centers’: Recombination Can Aid Adaptation of Spatially Structured Populations on Rugged Fitness Landscapes

PubMed Central

Cooper, Jacob D.; Kerr, Benjamin

2016-01-01

Epistatic interactions among genes can give rise to rugged fitness landscapes, in which multiple “peaks” of high-fitness allele combinations are separated by “valleys” of low-fitness genotypes. How populations traverse rugged fitness landscapes is a long-standing question in evolutionary biology. Sexual reproduction may affect how a population moves within a rugged fitness landscape. Sex may generate new high-fitness genotypes by recombination, but it may also destroy high-fitness genotypes by shuffling the genes of a fit parent with a genetically distinct mate, creating low-fitness offspring. Either of these opposing aspects of sex require genotypic diversity in the population. Spatially structured populations may harbor more diversity than well-mixed populations, potentially amplifying both positive and negative effects of sex. On the other hand, spatial structure leads to clumping in which mating is more likely to occur between like types, diminishing the effects of recombination. In this study, we use computer simulations to investigate the combined effects of recombination and spatial structure on adaptation in rugged fitness landscapes. We find that spatially restricted mating and offspring dispersal may allow multiple genotypes inhabiting suboptimal peaks to coexist, and recombination at the “sutures” between the clusters of these genotypes can create genetically novel offspring. Sometimes such an offspring genotype inhabits a new peak on the fitness landscape. In such a case, spatially restricted mating allows this fledgling subpopulation to avoid recombination with distinct genotypes, as mates are more likely to be the same genotype. Such population “centers” can allow nascent peaks to establish despite recombination. Spatial structure may therefore allow an evolving population to enjoy the creative side of sexual recombination while avoiding its destructive side. PMID:27973606

Adaptation to elevated CO2 in different biodiversity contexts

PubMed Central

Kleynhans, Elizabeth J.; Otto, Sarah P.; Reich, Peter B.; Vellend, Mark

2016-01-01

In the absence of migration, species persistence depends on adaption to a changing environment, but whether and how adaptation to global change is altered by community diversity is not understood. Community diversity may prevent, enhance or alter how species adapt to changing conditions by influencing population sizes, genetic diversity and/or the fitness landscape experienced by focal species. We tested the impact of community diversity on adaptation by performing a reciprocal transplant experiment on grasses that evolved for 14 years under ambient and elevated CO2, in communities of low or high species richness. Using biomass as a fitness proxy, we find evidence for local adaptation to elevated CO2, but only for plants assayed in a community of similar diversity to the one experienced during the period of selection. Our results indicate that the biological community shapes the very nature of the fitness landscape within which species evolve in response to elevated CO2. PMID:27510545

Inferring Microbial Fitness Landscapes

DTIC Science & Technology

2016-02-25

infer from data the determinants of microbial evolution with sufficient resolution that we can quantify 1. REPORT DATE (DD-MM-YYYY) 4. TITLE AND...Distribution Unlimited UU UU UU UU 25-02-2016 1-Oct-2012 30-Sep-2015 Final Report: Inferring Microbial Fitness Landscapes The views, opinions and/or findings...Triangle Park, NC 27709-2211 evolution, fitness landscapes, epistasis, microbial populations REPORT DOCUMENTATION PAGE 11. SPONSOR/MONITOR’S REPORT

Exploring the fitness landscape of poliovirus

NASA Astrophysics Data System (ADS)

Bianco, Simone; Acevedo, Ashely; Andino, Raul; Tang, Chao

2012-02-01

RNA viruses are known to display extraordinary adaptation capabilities to different environments, due to high mutation rates. Their very dynamical evolution is captured by the quasispecies concept, according to which the viral population forms a swarm of genetic variants linked through mutation, which cooperatively interact at a functional level and collectively contribute to the characteristics of the population. The description of the viral fitness landscape becomes paramount towards a more thorough understanding of the virus evolution and spread. The high mutation rate, together with the cooperative nature of the quasispecies, makes it particularly challenging to explore its fitness landscape. I will present an investigation of the dynamical properties of poliovirus fitness landscape, through both the adoption of new experimental techniques and theoretical models.

Can Evolution Supply What Ecology Demands?

PubMed

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.

Role of Utility and Inference in the Evolution of Functional Information

PubMed Central

Sharov, Alexei A.

2009-01-01

Functional information means an encoded network of functions in living organisms from molecular signaling pathways to an organism’s behavior. It is represented by two components: code and an interpretation system, which together form a self-sustaining semantic closure. Semantic closure allows some freedom between components because small variations of the code are still interpretable. The interpretation system consists of inference rules that control the correspondence between the code and the function (phenotype) and determines the shape of the fitness landscape. The utility factor operates at multiple time scales: short-term selection drives evolution towards higher survival and reproduction rate within a given fitness landscape, and long-term selection favors those fitness landscapes that support adaptability and lead to evolutionary expansion of certain lineages. Inference rules make short-term selection possible by shaping the fitness landscape and defining possible directions of evolution, but they are under control of the long-term selection of lineages. Communication normally occurs within a set of agents with compatible interpretation systems, which I call communication system. Functional information cannot be directly transferred between communication systems with incompatible inference rules. Each biological species is a genetic communication system that carries unique functional information together with inference rules that determine evolutionary directions and constraints. This view of the relation between utility and inference can resolve the conflict between realism/positivism and pragmatism. Realism overemphasizes the role of inference in evolution of human knowledge because it assumes that logic is embedded in reality. Pragmatism substitutes usefulness for truth and therefore ignores the advantage of inference. The proposed concept of evolutionary pragmatism rejects the idea that logic is embedded in reality; instead, inference rules are constructed within each communication system to represent reality and they evolve towards higher adaptability on a long time scale. PMID:20160960

Genetic algorithm dynamics on a rugged landscape

NASA Astrophysics Data System (ADS)

Bornholdt, Stefan

1998-04-01

The genetic algorithm is an optimization procedure motivated by biological evolution and is successfully applied to optimization problems in different areas. A statistical mechanics model for its dynamics is proposed based on the parent-child fitness correlation of the genetic operators, making it applicable to general fitness landscapes. It is compared to a recent model based on a maximum entropy ansatz. Finally it is applied to modeling the dynamics of a genetic algorithm on the rugged fitness landscape of the NK model.

Assessments of habitat preferences and quality depend on spatial scale and metrics of fitness

USGS Publications Warehouse

Chalfoun, A.D.; Martin, T.E.

2007-01-01

1. Identifying the habitat features that influence habitat selection and enhance fitness is critical for effective management. Ecological theory predicts that habitat choices should be adaptive, such that fitness is enhanced in preferred habitats. However, studies often report mismatches between habitat preferences and fitness consequences across a wide variety of taxa based on a single spatial scale and/or a single fitness component. 2. We examined whether habitat preferences of a declining shrub steppe songbird, the Brewer's sparrow Spizella breweri, were adaptive when multiple reproductive fitness components and spatial scales (landscape, territory and nest patch) were considered. 3. We found that birds settled earlier and in higher densities, together suggesting preference, in landscapes with greater shrub cover and height. Yet nest success was not higher in these landscapes; nest success was primarily determined by nest predation rates. Thus landscape preferences did not match nest predation risk. Instead, nestling mass and the number of nesting attempts per pair increased in preferred landscapes, raising the possibility that landscapes were chosen on the basis of food availability rather than safe nest sites. 4. At smaller spatial scales (territory and nest patch), birds preferred different habitat features (i.e. density of potential nest shrubs) that reduced nest predation risk and allowed greater season-long reproductive success. 5. Synthesis and applications. Habitat preferences reflect the integration of multiple environmental factors across multiple spatial scales, and individuals may have more than one option for optimizing fitness via habitat selection strategies. Assessments of habitat quality for management prescriptions should ideally include analysis of diverse fitness consequences across multiple ecologically relevant spatial scales. ?? 2007 The Authors.

Adaptation to elevated CO 2 in different biodiversity contexts

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kleynhans, Elizabeth J.; Otto, Sarah P.; Reich, Peter B.

In the absence of migration, species persistence depends on adaption to a changing environment, but whether and how adaptation to global change is altered by community diversity is not understood. Community diversity may prevent, enhance or alter how species adapt to changing conditions by influencing population sizes, genetic diversity and/or the fitness landscape experienced by focal species. For this study, we tested the impact of community diversity on adaptation by performing a reciprocal transplant experiment on grasses that evolved for 14 years under ambient and elevated CO 2, in communities of low or high species richness. Using biomass as amore » fitness proxy, we find evidence for local adaptation to elevated CO 2, but only for plants assayed in a community of similar diversity to the one experienced during the period of selection. Our results indicate that the biological community shapes the very nature of the fitness landscape within which species evolve in response to elevated CO 2.« less

Evolution of Boolean networks under selection for a robust response to external inputs yields an extensive neutral space

NASA Astrophysics Data System (ADS)

Szejka, Agnes; Drossel, Barbara

2010-02-01

We study the evolution of Boolean networks as model systems for gene regulation. Inspired by biological networks, we select simultaneously for robust attractors and for the ability to respond to external inputs by changing the attractor. Mutations change the connections between the nodes and the update functions. In order to investigate the influence of the type of update functions, we perform our simulations with canalizing as well as with threshold functions. We compare the properties of the fitness landscapes that result for different versions of the selection criterion and the update functions. We find that for all studied cases the fitness landscape has a plateau with maximum fitness resulting in the fact that structurally very different networks are able to fulfill the same task and are connected by neutral paths in network (“genotype”) space. We find furthermore a connection between the attractor length and the mutational robustness, and an extremely long memory of the initial evolutionary stage.

Adaptation to elevated CO 2 in different biodiversity contexts

DOE PAGES

Kleynhans, Elizabeth J.; Otto, Sarah P.; Reich, Peter B.; ...

2016-08-11

In the absence of migration, species persistence depends on adaption to a changing environment, but whether and how adaptation to global change is altered by community diversity is not understood. Community diversity may prevent, enhance or alter how species adapt to changing conditions by influencing population sizes, genetic diversity and/or the fitness landscape experienced by focal species. For this study, we tested the impact of community diversity on adaptation by performing a reciprocal transplant experiment on grasses that evolved for 14 years under ambient and elevated CO 2, in communities of low or high species richness. Using biomass as amore » fitness proxy, we find evidence for local adaptation to elevated CO 2, but only for plants assayed in a community of similar diversity to the one experienced during the period of selection. Our results indicate that the biological community shapes the very nature of the fitness landscape within which species evolve in response to elevated CO 2.« less

Fitness landscape of the human immunodeficiency virus envelope protein that is targeted by antibodies

PubMed Central

Louie, Raymond H. Y.; Kaczorowski, Kevin J.; Chakraborty, Arup K.; McKay, Matthew R.

2018-01-01

HIV is a highly mutable virus, and over 30 years after its discovery, a vaccine or cure is still not available. The isolation of broadly neutralizing antibodies (bnAbs) from HIV-infected patients has led to renewed hope for a prophylactic vaccine capable of combating the scourge of HIV. A major challenge is the design of immunogens and vaccination protocols that can elicit bnAbs that target regions of the virus’s spike proteins where the likelihood of mutational escape is low due to the high fitness cost of mutations. Related challenges include the choice of combinations of bnAbs for therapy. An accurate representation of viral fitness as a function of its protein sequences (a fitness landscape), with explicit accounting of the effects of coupling between mutations, could help address these challenges. We describe a computational approach that has allowed us to infer a fitness landscape for gp160, the HIV polyprotein that comprises the viral spike that is targeted by antibodies. We validate the inferred landscape through comparisons with experimental fitness measurements, and various other metrics. We show that an effective antibody that prevents immune escape must selectively bind to high escape cost residues that are surrounded by those where mutations incur a low fitness cost, motivating future applications of our landscape for immunogen design. PMID:29311326

Advanced fitness landscape analysis and the performance of memetic algorithms.

PubMed

Merz, Peter

2004-01-01

Memetic algorithms (MAs) have demonstrated very effective in combinatorial optimization. This paper offers explanations as to why this is so by investigating the performance of MAs in terms of efficiency and effectiveness. A special class of MAs is used to discuss efficiency and effectiveness for local search and evolutionary meta-search. It is shown that the efficiency of MAs can be increased drastically with the use of domain knowledge. However, effectiveness highly depends on the structure of the problem. As is well-known, identifying this structure is made easier with the notion of fitness landscapes: the local properties of the fitness landscape strongly influence the effectiveness of the local search while the global properties strongly influence the effectiveness of the evolutionary meta-search. This paper also introduces new techniques for analyzing the fitness landscapes of combinatorial problems; these techniques focus on the investigation of random walks in the fitness landscape starting at locally optimal solutions as well as on the escape from the basins of attractions of current local optima. It is shown for NK-landscapes and landscapes of the unconstrained binary quadratic programming problem (BQP) that a random walk to another local optimum can be used to explain the efficiency of recombination in comparison to mutation. Moreover, the paper shows that other aspects like the size of the basins of attractions of local optima are important for the efficiency of MAs and a local search escape analysis is proposed. These simple analysis techniques have several advantages over previously proposed statistical measures and provide valuable insight into the behaviour of MAs on different kinds of landscapes.

Genotypic Complexity of Fisher’s Geometric Model

PubMed Central

Hwang, Sungmin; Park, Su-Chan; Krug, Joachim

2017-01-01

Fisher’s geometric model was originally introduced to argue that complex adaptations must occur in small steps because of pleiotropic constraints. When supplemented with the assumption of additivity of mutational effects on phenotypic traits, it provides a simple mechanism for the emergence of genotypic epistasis from the nonlinear mapping of phenotypes to fitness. Of particular interest is the occurrence of reciprocal sign epistasis, which is a necessary condition for multipeaked genotypic fitness landscapes. Here we compute the probability that a pair of randomly chosen mutations interacts sign epistatically, which is found to decrease with increasing phenotypic dimension n, and varies nonmonotonically with the distance from the phenotypic optimum. We then derive expressions for the mean number of fitness maxima in genotypic landscapes comprised of all combinations of L random mutations. This number increases exponentially with L, and the corresponding growth rate is used as a measure of the complexity of the landscape. The dependence of the complexity on the model parameters is found to be surprisingly rich, and three distinct phases characterized by different landscape structures are identified. Our analysis shows that the phenotypic dimension, which is often referred to as phenotypic complexity, does not generally correlate with the complexity of fitness landscapes and that even organisms with a single phenotypic trait can have complex landscapes. Our results further inform the interpretation of experiments where the parameters of Fisher’s model have been inferred from data, and help to elucidate which features of empirical fitness landscapes can be described by this model. PMID:28450460

Evolution of canalizing Boolean networks

NASA Astrophysics Data System (ADS)

Szejka, A.; Drossel, B.

2007-04-01

Boolean networks with canalizing functions are used to model gene regulatory networks. In order to learn how such networks may behave under evolutionary forces, we simulate the evolution of a single Boolean network by means of an adaptive walk, which allows us to explore the fitness landscape. Mutations change the connections and the functions of the nodes. Our fitness criterion is the robustness of the dynamical attractors against small perturbations. We find that with this fitness criterion the global maximum is always reached and that there is a huge neutral space of 100% fitness. Furthermore, in spite of having such a high degree of robustness, the evolved networks still share many features with “chaotic” networks.

Eigen model with general fitness functions and degradation rates

NASA Astrophysics Data System (ADS)

Hu, Chin-Kun; Saakian, David B.

2006-03-01

We present an exact solution of Eigen's quasispecies model with a general degradation rate and fitness functions, including a square root decrease of fitness with increasing Hamming distance from the wild type. The found behavior of the model with a degradation rate is analogous to a viral quasi-species under attack by the immune system of the host. Our exact solutions also revise the known results of neutral networks in quasispecies theory. To explain the existence of mutants with large Hamming distances from the wild type, we propose three different modifications of the Eigen model: mutation landscape, multiple adjacent mutations, and frequency-dependent fitness in which the steady state solution shows a multi-center behavior.

The Influence of Higher-Order Epistasis on Biological Fitness Landscape Topography

NASA Astrophysics Data System (ADS)

Weinreich, Daniel M.; Lan, Yinghong; Jaffe, Jacob; Heckendorn, Robert B.

2018-07-01

The effect of a mutation on the organism often depends on what other mutations are already present in its genome. Geneticists refer to such mutational interactions as epistasis. Pairwise epistatic effects have been recognized for over a century, and their evolutionary implications have received theoretical attention for nearly as long. However, pairwise epistatic interactions themselves can vary with genomic background. This is called higher-order epistasis, and its consequences for evolution are much less well understood. Here, we assess the influence that higher-order epistasis has on the topography of 16 published, biological fitness landscapes. We find that on average, their effects on fitness landscape declines with order, and suggest that notable exceptions to this trend may deserve experimental scrutiny. We conclude by highlighting opportunities for further theoretical and experimental work dissecting the influence that epistasis of all orders has on fitness landscape topography and on the efficiency of evolution by natural selection.

The Influence of Higher-Order Epistasis on Biological Fitness Landscape Topography

NASA Astrophysics Data System (ADS)

Weinreich, Daniel M.; Lan, Yinghong; Jaffe, Jacob; Heckendorn, Robert B.

2018-02-01

The effect of a mutation on the organism often depends on what other mutations are already present in its genome. Geneticists refer to such mutational interactions as epistasis. Pairwise epistatic effects have been recognized for over a century, and their evolutionary implications have received theoretical attention for nearly as long. However, pairwise epistatic interactions themselves can vary with genomic background. This is called higher-order epistasis, and its consequences for evolution are much less well understood. Here, we assess the influence that higher-order epistasis has on the topography of 16 published, biological fitness landscapes. We find that on average, their effects on fitness landscape declines with order, and suggest that notable exceptions to this trend may deserve experimental scrutiny. We conclude by highlighting opportunities for further theoretical and experimental work dissecting the influence that epistasis of all orders has on fitness landscape topography and on the efficiency of evolution by natural selection.

Linking habitat selection to fitness-related traits in herbivores: the role of the energy landscape

Treesearch

Ryan A. Long; R. T. Bowyer; Warren P. Porter; Paul Mathewson; Kevin L. Monteith; Scott L. Findholt; Brian L. Dick; John G. Kie

2016-01-01

Animals may partially overcome environmental constraints on fitness by behaviorally adjusting their exposure to costs and supplies of energy. Few studies, however, have linked spatiotemporal variation in the energy landscape to behaviorally mediated measures of performance that ostensibly influence individual fitness. We hypothesized that strength of selection by North...

Punctuated equilibrium and shock waves in molecular models of biological evolution.

PubMed

Saakian, David B; Ghazaryan, Makar H; Hu, Chin-Kun

2014-08-01

We consider the dynamics in infinite population evolution models with a general symmetric fitness landscape. We find shock waves, i.e., discontinuous transitions in the mean fitness, in evolution dynamics even with smooth fitness landscapes, which means that the search for the optimal evolution trajectory is more complicated. These shock waves appear in the case of positive epistasis and can be used to represent punctuated equilibria in biological evolution during long geological time scales. We find exact analytical solutions for discontinuous dynamics at the large-genome-length limit and derive optimal mutation rates for a fixed fitness landscape to send the population from the initial configuration to some final configuration in the fastest way.

Monotonicity of fitness landscapes and mutation rate control.

PubMed

Belavkin, Roman V; Channon, Alastair; Aston, Elizabeth; Aston, John; Krašovec, Rok; Knight, Christopher G

2016-12-01

A common view in evolutionary biology is that mutation rates are minimised. However, studies in combinatorial optimisation and search have shown a clear advantage of using variable mutation rates as a control parameter to optimise the performance of evolutionary algorithms. Much biological theory in this area is based on Ronald Fisher's work, who used Euclidean geometry to study the relation between mutation size and expected fitness of the offspring in infinite phenotypic spaces. Here we reconsider this theory based on the alternative geometry of discrete and finite spaces of DNA sequences. First, we consider the geometric case of fitness being isomorphic to distance from an optimum, and show how problems of optimal mutation rate control can be solved exactly or approximately depending on additional constraints of the problem. Then we consider the general case of fitness communicating only partial information about the distance. We define weak monotonicity of fitness landscapes and prove that this property holds in all landscapes that are continuous and open at the optimum. This theoretical result motivates our hypothesis that optimal mutation rate functions in such landscapes will increase when fitness decreases in some neighbourhood of an optimum, resembling the control functions derived in the geometric case. We test this hypothesis experimentally by analysing approximately optimal mutation rate control functions in 115 complete landscapes of binding scores between DNA sequences and transcription factors. Our findings support the hypothesis and find that the increase of mutation rate is more rapid in landscapes that are less monotonic (more rugged). We discuss the relevance of these findings to living organisms.

Limits of neutral drift: lessons from the in vitro evolution of two ribozymes.

PubMed

Petrie, Katherine L; Joyce, Gerald F

2014-10-01

The relative contributions of adaptive selection and neutral drift to genetic change are unknown but likely depend on the inherent abundance of functional genotypes in sequence space and how accessible those genotypes are to one another. To better understand the relative roles of selection and drift in evolution, local fitness landscapes for two different RNA ligase ribozymes were examined using a continuous in vitro evolution system under conditions that foster the capacity for neutral drift to mediate genetic change. The exploration of sequence space was accelerated by increasing the mutation rate using mutagenic nucleotide analogs. Drift was encouraged by carrying out evolution within millions of separate compartments to exploit the founder effect. Deep sequencing of individuals from the evolved populations revealed that the distribution of genotypes did not escape the starting local fitness peak, remaining clustered around the sequence used to initiate evolution. This is consistent with a fitness landscape where high-fitness genotypes are sparse and well isolated, and suggests, at least in this context, that neutral drift alone is not a primary driver of genetic change. Neutral drift does, however, provide a repository of genetic variation upon which adaptive selection can act.

Phenotypic plasticity despite source-sink population dynamics in a long-lived perennial plant.

PubMed

Anderson, Jill T; Sparks, Jed P; Geber, Monica A

2010-11-01

• Species that exhibit adaptive plasticity alter their phenotypes in response to environmental conditions, thereby maximizing fitness in heterogeneous landscapes. However, under demographic source-sink dynamics, selection should favor traits that enhance fitness in the source habitat at the expense of fitness in the marginal habitat. Consistent with source-sink dynamics, the perennial blueberry, Vaccinium elliottii (Ericaceae), shows substantially higher fitness and population sizes in dry upland forests than in flood-prone bottomland forests, and asymmetrical gene flow occurs from upland populations into bottomland populations. Here, we examined whether this species expresses plasticity to these distinct environments despite source-sink dynamics. • We assessed phenotypic responses to a complex environmental gradient in the field and to water stress in the glasshouse. • Contrary to expectations, V. elliottii exhibited a high degree of plasticity in foliar and root traits (specific leaf area, carbon isotope ratios, foliar nitrogen content, root : shoot ratio, root porosity and root architecture). • We propose that plasticity can be maintained in source-sink systems if it is favored within the source habitat and/or a phylogenetic artifact that is not costly. Additionally, plasticity could be advantageous if habitat-based differences in fitness result from incipient niche expansion. Our results illuminate the importance of evaluating phenotypic traits and fitness components across heterogeneous landscapes. © The Authors (2010). Journal compilation © New Phytologist Trust (2010).

Clustering and phase transitions on a neutral landscape

NASA Astrophysics Data System (ADS)

Scott, Adam D.; King, Dawn M.; Marić, Nevena; Bahar, Sonya

2013-06-01

Recent computational studies have shown that speciation can occur under neutral conditions, i.e., when the simulated organisms all have identical fitness. These works bear comparison with mathematical studies of clustering on neutral landscapes in the context of branching and coalescing random walks. Here, we show that sympatric clustering/speciation can occur on a neutral landscape whose dimensions specify only the simulated organisms’ phenotypes. We demonstrate that clustering occurs not only in the case of assortative mating, but also in the case of asexual fission; it is not observed in the control case of random mating. We find that the population size and the number of clusters undergo a second-order non-equilibrium phase transition as the maximum mutation size is varied.

Machine learning landscapes and predictions for patient outcomes

NASA Astrophysics Data System (ADS)

Das, Ritankar; Wales, David J.

2017-07-01

The theory and computational tools developed to interpret and explore energy landscapes in molecular science are applied to the landscapes defined by local minima for neural networks. These machine learning landscapes correspond to fits of training data, where the inputs are vital signs and laboratory measurements for a database of patients, and the objective is to predict a clinical outcome. In this contribution, we test the predictions obtained by fitting to single measurements, and then to combinations of between 2 and 10 different patient medical data items. The effect of including measurements over different time intervals from the 48 h period in question is analysed, and the most recent values are found to be the most important. We also compare results obtained for neural networks as a function of the number of hidden nodes, and for different values of a regularization parameter. The predictions are compared with an alternative convex fitting function, and a strong correlation is observed. The dependence of these results on the patients randomly selected for training and testing decreases systematically with the size of the database available. The machine learning landscapes defined by neural network fits in this investigation have single-funnel character, which probably explains why it is relatively straightforward to obtain the global minimum solution, or a fit that behaves similarly to this optimal parameterization.

Fisher's geometrical model emerges as a property of complex integrated phenotypic networks.

PubMed

Martin, Guillaume

2014-05-01

Models relating phenotype space to fitness (phenotype-fitness landscapes) have seen important developments recently. They can roughly be divided into mechanistic models (e.g., metabolic networks) and more heuristic models like Fisher's geometrical model. Each has its own drawbacks, but both yield testable predictions on how the context (genomic background or environment) affects the distribution of mutation effects on fitness and thus adaptation. Both have received some empirical validation. This article aims at bridging the gap between these approaches. A derivation of the Fisher model "from first principles" is proposed, where the basic assumptions emerge from a more general model, inspired by mechanistic networks. I start from a general phenotypic network relating unspecified phenotypic traits and fitness. A limited set of qualitative assumptions is then imposed, mostly corresponding to known features of phenotypic networks: a large set of traits is pleiotropically affected by mutations and determines a much smaller set of traits under optimizing selection. Otherwise, the model remains fairly general regarding the phenotypic processes involved or the distribution of mutation effects affecting the network. A statistical treatment and a local approximation close to a fitness optimum yield a landscape that is effectively the isotropic Fisher model or its extension with a single dominant phenotypic direction. The fit of the resulting alternative distributions is illustrated in an empirical data set. These results bear implications on the validity of Fisher's model's assumptions and on which features of mutation fitness effects may vary (or not) across genomic or environmental contexts.

Landscape genetics as a tool for conservation planning: predicting the effects of landscape change on gene flow.

PubMed

van Strien, Maarten J; Keller, Daniela; Holderegger, Rolf; Ghazoul, Jaboury; Kienast, Felix; Bolliger, Janine

2014-03-01

For conservation managers, it is important to know whether landscape changes lead to increasing or decreasing gene flow. Although the discipline of landscape genetics assesses the influence of landscape elements on gene flow, no studies have yet used landscape-genetic models to predict gene flow resulting from landscape change. A species that has already been severely affected by landscape change is the large marsh grasshopper (Stethophyma grossum), which inhabits moist areas in fragmented agricultural landscapes in Switzerland. From transects drawn between all population pairs within maximum dispersal distance (< 3 km), we calculated several measures of landscape composition as well as some measures of habitat configuration. Additionally, a complete sampling of all populations in our study area allowed incorporating measures of population topology. These measures together with the landscape metrics formed the predictor variables in linear models with gene flow as response variable (F(ST) and mean pairwise assignment probability). With a modified leave-one-out cross-validation approach, we selected the model with the highest predictive accuracy. With this model, we predicted gene flow under several landscape-change scenarios, which simulated construction, rezoning or restoration projects, and the establishment of a new population. For some landscape-change scenarios, significant increase or decrease in gene flow was predicted, while for others little change was forecast. Furthermore, we found that the measures of population topology strongly increase model fit in landscape genetic analysis. This study demonstrates the use of predictive landscape-genetic models in conservation and landscape planning.

Determination of ubiquitin fitness landscapes under different chemical stresses in a classroom setting.

PubMed

Mavor, David; Barlow, Kyle; Thompson, Samuel; Barad, Benjamin A; Bonny, Alain R; Cario, Clinton L; Gaskins, Garrett; Liu, Zairan; Deming, Laura; Axen, Seth D; Caceres, Elena; Chen, Weilin; Cuesta, Adolfo; Gate, Rachel E; Green, Evan M; Hulce, Kaitlin R; Ji, Weiyue; Kenner, Lillian R; Mensa, Bruk; Morinishi, Leanna S; Moss, Steven M; Mravic, Marco; Muir, Ryan K; Niekamp, Stefan; Nnadi, Chimno I; Palovcak, Eugene; Poss, Erin M; Ross, Tyler D; Salcedo, Eugenia C; See, Stephanie K; Subramaniam, Meena; Wong, Allison W; Li, Jennifer; Thorn, Kurt S; Conchúir, Shane Ó; Roscoe, Benjamin P; Chow, Eric D; DeRisi, Joseph L; Kortemme, Tanja; Bolon, Daniel N; Fraser, James S

2016-04-25

Ubiquitin is essential for eukaryotic life and varies in only 3 amino acid positions between yeast and humans. However, recent deep sequencing studies indicate that ubiquitin is highly tolerant to single mutations. We hypothesized that this tolerance would be reduced by chemically induced physiologic perturbations. To test this hypothesis, a class of first year UCSF graduate students employed deep mutational scanning to determine the fitness landscape of all possible single residue mutations in the presence of five different small molecule perturbations. These perturbations uncover 'shared sensitized positions' localized to areas around the hydrophobic patch and the C-terminus. In addition, we identified perturbation specific effects such as a sensitization of His68 in HU and a tolerance to mutation at Lys63 in DTT. Our data show how chemical stresses can reduce buffering effects in the ubiquitin proteasome system. Finally, this study demonstrates the potential of lab-based interdisciplinary graduate curriculum.

Adaptation in protein fitness landscapes is facilitated by indirect paths

PubMed Central

Wu, Nicholas C; Dai, Lei; Olson, C Anders; Lloyd-Smith, James O; Sun, Ren

2016-01-01

The structure of fitness landscapes is critical for understanding adaptive protein evolution. Previous empirical studies on fitness landscapes were confined to either the neighborhood around the wild type sequence, involving mostly single and double mutants, or a combinatorially complete subgraph involving only two amino acids at each site. In reality, the dimensionality of protein sequence space is higher (20L) and there may be higher-order interactions among more than two sites. Here we experimentally characterized the fitness landscape of four sites in protein GB1, containing 204 = 160,000 variants. We found that while reciprocal sign epistasis blocked many direct paths of adaptation, such evolutionary traps could be circumvented by indirect paths through genotype space involving gain and subsequent loss of mutations. These indirect paths alleviate the constraint on adaptive protein evolution, suggesting that the heretofore neglected dimensions of sequence space may change our views on how proteins evolve. DOI: http://dx.doi.org/10.7554/eLife.16965.001 PMID:27391790

Defining the landscape of adaptive genetic diversity.

PubMed

Eckert, Andrew J; Dyer, Rodney J

2012-06-01

Whether they are used to describe fitness, genome architecture or the spatial distribution of environmental variables, the concept of a landscape has figured prominently in our collective reasoning. The tradition of landscapes in evolutionary biology is one of fitness mapped onto axes defined by phenotypes or molecular sequence states. The characteristics of these landscapes depend on natural selection, which is structured across both genomic and environmental landscapes, and thus, the bridge among differing uses of the landscape concept (i.e. metaphorically or literally) is that of an adaptive phenotype and its distribution across geographical landscapes in relation to selective pressures. One of the ultimate goals of evolutionary biology should thus be to construct fitness landscapes in geographical space. Natural plant populations are ideal systems with which to explore the feasibility of attaining this goal, because much is known about the quantitative genetic architecture of complex traits for many different plant species. What is less known are the molecular components of this architecture. In this issue of Molecular Ecology, Parchman et al. (2012) pioneer one of the first truly genome-wide association studies in a tree that moves us closer to this form of mechanistic understanding for an adaptive phenotype in natural populations of lodgepole pine (Pinus contorta Dougl. ex Loud.). © 2012 Blackwell Publishing Ltd.

Does habitat fragmentation affect temperature-related life-history traits? A laboratory test with a woodland butterfly

PubMed Central

Karlsson, Bengt; Van Dyck, Hans

2005-01-01

Habitat fragmentation may change local climatic conditions leading to altered selection regimes for life-history traits in small ectotherms, including several insects. We investigated temperature-related performance in terms of fitness among populations of the woodland butterfly Pararge aegeria (L.) originating from populations of a closed, continuous woodland landscape versus populations of an open, highly fragmented agricultural landscape in central Belgium. Female fecundity and longevity were evaluated in a temperature-gradient experiment. As predicted, females of woodland landscape origin reached higher maximum daily fecundity and lifetime number of eggs than did agricultural landscape females at low ambient temperatures, but this reversed at high ambient temperature. Egg weight decreased with temperature, and eggs of woodland butterflies were smaller. Contrary to what is generally assumed, remaining thorax mass was a better predictor of lifetime reproductive output than was abdomen mass. Since we used the F2 generation from wild-caught females reared under common garden conditions, the observed effects are likely to rely on intrinsic, heritable variation. Our results suggest that differential selection regimes associated with different landscapes intervene by intraspecific variation in the response of a butterfly to variation in ambient temperature, and may thus be helpful when making predictions of future impacts on how wild populations respond to environmental conditions under a global change scenario, with increasing temperatures and fragmented landscapes. PMID:16024390

Determination of the Ubiquitin Fitness Landscape under Seventeen Chemical Conditions in a Classroom Setting

ERIC Educational Resources Information Center

Mavor, David Carl

2017-01-01

Ubiquitin is essential for eukaryotic life and varies in only 3 amino acid positions between yeast and humans. However, recent deep sequencing studies indicate that ubiquitin is highly tolerant to single mutations. We hypothesized that this tolerance would be reduced by chemically induced physiologic perturbations. To test this hypothesis, a class…

Universality Classes of Interaction Structures for NK Fitness Landscapes

NASA Astrophysics Data System (ADS)

Hwang, Sungmin; Schmiegelt, Benjamin; Ferretti, Luca; Krug, Joachim

2018-07-01

Kauffman's NK-model is a paradigmatic example of a class of stochastic models of genotypic fitness landscapes that aim to capture generic features of epistatic interactions in multilocus systems. Genotypes are represented as sequences of L binary loci. The fitness assigned to a genotype is a sum of contributions, each of which is a random function defined on a subset of k ≤ L loci. These subsets or neighborhoods determine the genetic interactions of the model. Whereas earlier work on the NK model suggested that most of its properties are robust with regard to the choice of neighborhoods, recent work has revealed an important and sometimes counter-intuitive influence of the interaction structure on the properties of NK fitness landscapes. Here we review these developments and present new results concerning the number of local fitness maxima and the statistics of selectively accessible (that is, fitness-monotonic) mutational pathways. In particular, we develop a unified framework for computing the exponential growth rate of the expected number of local fitness maxima as a function of L, and identify two different universality classes of interaction structures that display different asymptotics of this quantity for large k. Moreover, we show that the probability that the fitness landscape can be traversed along an accessible path decreases exponentially in L for a large class of interaction structures that we characterize as locally bounded. Finally, we discuss the impact of the NK interaction structures on the dynamics of evolution using adaptive walk models.

Universality Classes of Interaction Structures for NK Fitness Landscapes

NASA Astrophysics Data System (ADS)

Hwang, Sungmin; Schmiegelt, Benjamin; Ferretti, Luca; Krug, Joachim

2018-02-01

Kauffman's NK-model is a paradigmatic example of a class of stochastic models of genotypic fitness landscapes that aim to capture generic features of epistatic interactions in multilocus systems. Genotypes are represented as sequences of L binary loci. The fitness assigned to a genotype is a sum of contributions, each of which is a random function defined on a subset of k ≤ L loci. These subsets or neighborhoods determine the genetic interactions of the model. Whereas earlier work on the NK model suggested that most of its properties are robust with regard to the choice of neighborhoods, recent work has revealed an important and sometimes counter-intuitive influence of the interaction structure on the properties of NK fitness landscapes. Here we review these developments and present new results concerning the number of local fitness maxima and the statistics of selectively accessible (that is, fitness-monotonic) mutational pathways. In particular, we develop a unified framework for computing the exponential growth rate of the expected number of local fitness maxima as a function of L, and identify two different universality classes of interaction structures that display different asymptotics of this quantity for large k. Moreover, we show that the probability that the fitness landscape can be traversed along an accessible path decreases exponentially in L for a large class of interaction structures that we characterize as locally bounded. Finally, we discuss the impact of the NK interaction structures on the dynamics of evolution using adaptive walk models.

The Origins of Order: Self-Organization and Selection in Evolution

NASA Astrophysics Data System (ADS)

Kauffman, Stuart A.

The following sections are included: * Introduction * Fitness Landscapes in Sequence Space * The NK Model of Rugged Fitness Landscapes * The NK Model of Random Epistatic Interactions * The Rank Order Statistics on K = N - 1 Random Landscapes * The number of local optima is very large * The expected fraction of fitter 1-mutant neighbors dwindles by 1/2 on each improvement step * Walks to local optima are short and vary as a logarithmic function of N * The expected time to reach an optimum is proportional to the dimensionality of the space * The ratio of accepted to tried mutations scales as lnN/N * Any genotype can only climb to a small fraction of the local optima * A small fraction of the genotypes can climb to any one optimum * Conflicting constraints cause a "complexity catastrophe": as complexity increase accessible adaptive peaks fall toward the mean fitness * The "Tunable" NK Family of Correlated Landscapes * Other Combinatorial Optimization Problems and Their Landscapes * Summary * References

Exploration of Multi-State Conformational Dynamics and Underlying Global Functional Landscape of Maltose Binding Protein

PubMed Central

Wang, Yong; Tang, Chun; Wang, Erkang; Wang, Jin

2012-01-01

An increasing number of biological machines have been revealed to have more than two macroscopic states. Quantifying the underlying multiple-basin functional landscape is essential for understanding their functions. However, the present models seem to be insufficient to describe such multiple-state systems. To meet this challenge, we have developed a coarse grained triple-basin structure-based model with implicit ligand. Based on our model, the constructed functional landscape is sufficiently sampled by the brute-force molecular dynamics simulation. We explored maltose-binding protein (MBP) which undergoes large-scale domain motion between open, apo-closed (partially closed) and holo-closed (fully closed) states responding to ligand binding. We revealed an underlying mechanism whereby major induced fit and minor population shift pathways co-exist by quantitative flux analysis. We found that the hinge regions play an important role in the functional dynamics as well as that increases in its flexibility promote population shifts. This finding provides a theoretical explanation of the mechanistic discrepancies in PBP protein family. We also found a functional “backtracking” behavior that favors conformational change. We further explored the underlying folding landscape in response to ligand binding. Consistent with earlier experimental findings, the presence of ligand increases the cooperativity and stability of MBP. This work provides the first study to explore the folding dynamics and functional dynamics under the same theoretical framework using our triple-basin functional model. PMID:22532792

Intrinsically Disordered Energy Landscapes

PubMed Central

Chebaro, Yassmine; Ballard, Andrew J.; Chakraborty, Debayan; Wales, David J.

2015-01-01

Analysis of an intrinsically disordered protein (IDP) reveals an underlying multifunnel structure for the energy landscape. We suggest that such ‘intrinsically disordered’ landscapes, with a number of very different competing low-energy structures, are likely to characterise IDPs, and provide a useful way to address their properties. In particular, IDPs are present in many cellular protein interaction networks, and several questions arise regarding how they bind to partners. Are conformations resembling the bound structure selected for binding, or does further folding occur on binding the partner in a induced-fit fashion? We focus on the p53 upregulated modulator of apoptosis (PUMA) protein, which adopts an -helical conformation when bound to its partner, and is involved in the activation of apoptosis. Recent experimental evidence shows that folding is not necessary for binding, and supports an induced-fit mechanism. Using a variety of computational approaches we deduce the molecular mechanism behind the instability of the PUMA peptide as a helix in isolation. We find significant barriers between partially folded states and the helix. Our results show that the favoured conformations are molten-globule like, stabilised by charged and hydrophobic contacts, with structures resembling the bound state relatively unpopulated in equilibrium. PMID:25999294

Relationships between avian richness and landscape structure at multiple scales using multiple landscapes

USGS Publications Warehouse

Mitchell, M.S.; Rutzmoser, S.H.; Wigley, T.B.; Loehle, C.; Gerwin, J.A.; Keyser, P.D.; Lancia, R.A.; Perry, R.W.; Reynolds, C.J.; Thill, R.E.; Weih, R.; White, D.; Wood, P.B.

2006-01-01

Little is known about factors that structure biodiversity on landscape scales, yet current land management protocols, such as forest certification programs, place an increasing emphasis on managing for sustainable biodiversity at landscape scales. We used a replicated landscape study to evaluate relationships between forest structure and avian diversity at both stand and landscape-levels. We used data on bird communities collected under comparable sampling protocols on four managed forests located across the Southeastern US to develop logistic regression models describing relationships between habitat factors and the distribution of overall richness and richness of selected guilds. Landscape models generated for eight of nine guilds showed a strong relationship between richness and both availability and configuration of landscape features. Diversity of topographic features and heterogeneity of forest structure were primary determinants of avian species richness. Forest heterogeneity, in both age and forest type, were strongly and positively associated with overall avian richness and richness for most guilds. Road density was associated positively but weakly with avian richness. Landscape variables dominated all models generated, but no consistent patterns in metrics or scale were evident. Model fit was strong for neotropical migrants and relatively weak for short-distance migrants and resident species. Our models provide a tool that will allow managers to evaluate and demonstrate quantitatively how management practices affect avian diversity on landscapes.

Combinatorial vector fields and the valley structure of fitness landscapes.

PubMed

Stadler, Bärbel M R; Stadler, Peter F

2010-12-01

Adaptive (downhill) walks are a computationally convenient way of analyzing the geometric structure of fitness landscapes. Their inherently stochastic nature has limited their mathematical analysis, however. Here we develop a framework that interprets adaptive walks as deterministic trajectories in combinatorial vector fields and in return associate these combinatorial vector fields with weights that measure their steepness across the landscape. We show that the combinatorial vector fields and their weights have a product structure that is governed by the neutrality of the landscape. This product structure makes practical computations feasible. The framework presented here also provides an alternative, and mathematically more convenient, way of defining notions of valleys, saddle points, and barriers in landscape. As an application, we propose a refined approximation for transition rates between macrostates that are associated with the valleys of the landscape.

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

PubMed

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.

Quantifying the Role of Population Subdivision in Evolution on Rugged Fitness Landscapes

PubMed Central

Bitbol, Anne-Florence; Schwab, David J.

2014-01-01

Natural selection drives populations towards higher fitness, but crossing fitness valleys or plateaus may facilitate progress up a rugged fitness landscape involving epistasis. We investigate quantitatively the effect of subdividing an asexual population on the time it takes to cross a fitness valley or plateau. We focus on a generic and minimal model that includes only population subdivision into equivalent demes connected by global migration, and does not require significant size changes of the demes, environmental heterogeneity or specific geographic structure. We determine the optimal speedup of valley or plateau crossing that can be gained by subdivision, if the process is driven by the deme that crosses fastest. We show that isolated demes have to be in the sequential fixation regime for subdivision to significantly accelerate crossing. Using Markov chain theory, we obtain analytical expressions for the conditions under which optimal speedup is achieved: valley or plateau crossing by the subdivided population is then as fast as that of its fastest deme. We verify our analytical predictions through stochastic simulations. We demonstrate that subdivision can substantially accelerate the crossing of fitness valleys and plateaus in a wide range of parameters extending beyond the optimal window. We study the effect of varying the degree of subdivision of a population, and investigate the trade-off between the magnitude of the optimal speedup and the width of the parameter range over which it occurs. Our results, obtained for fitness valleys and plateaus, also hold for weakly beneficial intermediate mutations. Finally, we extend our work to the case of a population connected by migration to one or several smaller islands. Our results demonstrate that subdivision with migration alone can significantly accelerate the crossing of fitness valleys and plateaus, and shed light onto the quantitative conditions necessary for this to occur. PMID:25122220

Thermodynamical interpretation of an adaptive walk on a Mt. Fuji-type fitness landscape: Einstein relation-like formula holds in a stochastic evolution.

PubMed

Aita, Takuyo; Husimi, Yuzuru

2003-11-21

We have theoretically studied the statistical properties of adaptive walks (or hill-climbing) on a Mt. Fuji-type fitness landscape in the multi-dimensional sequence space through mathematical analysis and computer simulation. The adaptive walk is characterized by the "mutation distance" d as the step-width of the walker and the "population size" N as the number of randomly generated d-fold point mutants to be screened. In addition to the fitness W, we introduced the following quantities analogous to thermodynamical concepts: "free fitness" G(W) is identical with W+T x S(W), where T is the "evolutionary temperature" T infinity square root of d/lnN and S(W) is the entropy as a function of W, and the "evolutionary force" X is identical with d(G(W)/T)/dW, that is caused by the mutation and selection pressure. It is known that a single adaptive walker rapidly climbs on the fitness landscape up to the stationary state where a "mutation-selection-random drift balance" is kept. In our interpretation, the walker tends to the maximal free fitness state, driven by the evolutionary force X. Our major findings are as follows: First, near the stationary point W*, the "climbing rate" J as the expected fitness change per generation is described by J approximately L x X with L approximately V/2, where V is the variance of fitness distribution on a local landscape. This simple relationship is analogous to the well-known Einstein relation in Brownian motion. Second, the "biological information gain" (DeltaG/T) through adaptive walk can be described by combining the Shannon's information gain (DeltaS) and the "fitness information gain" (DeltaW/T).

Spin models inferred from patient-derived viral sequence data faithfully describe HIV fitness landscapes

NASA Astrophysics Data System (ADS)

Shekhar, Karthik; Ruberman, Claire F.; Ferguson, Andrew L.; Barton, John P.; Kardar, Mehran; Chakraborty, Arup K.

2013-12-01

Mutational escape from vaccine-induced immune responses has thwarted the development of a successful vaccine against AIDS, whose causative agent is HIV, a highly mutable virus. Knowing the virus' fitness as a function of its proteomic sequence can enable rational design of potent vaccines, as this information can focus vaccine-induced immune responses to target mutational vulnerabilities of the virus. Spin models have been proposed as a means to infer intrinsic fitness landscapes of HIV proteins from patient-derived viral protein sequences. These sequences are the product of nonequilibrium viral evolution driven by patient-specific immune responses and are subject to phylogenetic constraints. How can such sequence data allow inference of intrinsic fitness landscapes? We combined computer simulations and variational theory á la Feynman to show that, in most circumstances, spin models inferred from patient-derived viral sequences reflect the correct rank order of the fitness of mutant viral strains. Our findings are relevant for diverse viruses.

Determination of ubiquitin fitness landscapes under different chemical stresses in a classroom setting

PubMed Central

Mavor, David; Barlow, Kyle; Thompson, Samuel; Barad, Benjamin A; Bonny, Alain R; Cario, Clinton L; Gaskins, Garrett; Liu, Zairan; Deming, Laura; Axen, Seth D; Caceres, Elena; Chen, Weilin; Cuesta, Adolfo; Gate, Rachel E; Green, Evan M; Hulce, Kaitlin R; Ji, Weiyue; Kenner, Lillian R; Mensa, Bruk; Morinishi, Leanna S; Moss, Steven M; Mravic, Marco; Muir, Ryan K; Niekamp, Stefan; Nnadi, Chimno I; Palovcak, Eugene; Poss, Erin M; Ross, Tyler D; Salcedo, Eugenia C; See, Stephanie K; Subramaniam, Meena; Wong, Allison W; Li, Jennifer; Thorn, Kurt S; Conchúir, Shane Ó; Roscoe, Benjamin P; Chow, Eric D; DeRisi, Joseph L; Kortemme, Tanja; Bolon, Daniel N; Fraser, James S

2016-01-01

Ubiquitin is essential for eukaryotic life and varies in only 3 amino acid positions between yeast and humans. However, recent deep sequencing studies indicate that ubiquitin is highly tolerant to single mutations. We hypothesized that this tolerance would be reduced by chemically induced physiologic perturbations. To test this hypothesis, a class of first year UCSF graduate students employed deep mutational scanning to determine the fitness landscape of all possible single residue mutations in the presence of five different small molecule perturbations. These perturbations uncover 'shared sensitized positions' localized to areas around the hydrophobic patch and the C-terminus. In addition, we identified perturbation specific effects such as a sensitization of His68 in HU and a tolerance to mutation at Lys63 in DTT. Our data show how chemical stresses can reduce buffering effects in the ubiquitin proteasome system. Finally, this study demonstrates the potential of lab-based interdisciplinary graduate curriculum. DOI: http://dx.doi.org/10.7554/eLife.15802.001 PMID:27111525

Real time forecasting of near-future evolution.

PubMed

Gerrish, Philip J; Sniegowski, Paul D

2012-09-07

A metaphor for adaptation that informs much evolutionary thinking today is that of mountain climbing, where horizontal displacement represents change in genotype, and vertical displacement represents change in fitness. If it were known a priori what the 'fitness landscape' looked like, that is, how the myriad possible genotypes mapped onto fitness, then the possible paths up the fitness mountain could each be assigned a probability, thus providing a dynamical theory with long-term predictive power. Such detailed genotype-fitness data, however, are rarely available and are subject to change with each change in the organism or in the environment. Here, we take a very different approach that depends only on fitness or phenotype-fitness data obtained in real time and requires no a priori information about the fitness landscape. Our general statistical model of adaptive evolution builds on classical theory and gives reasonable predictions of fitness and phenotype evolution many generations into the future.

Legislative Framework for Landscape Planning in Latvia

NASA Astrophysics Data System (ADS)

Nitavska, Natalija; Zigmunde, Daiga

2017-10-01

With the adoption and the ratification of the European Landscape Convention a legally justified need for a clear landscape policy was grounded in the European countries. It includes the elaboration of the new and the improvement of the existing legislative documents on landscape planning, protection and management. The aim of the particular study is to analyse the existing legislative documents in Latvia influencing landscape planning on different scales / and the implementation of the European Landscape Convention. The study emphasizes the complex structure of the Latvian legislative framework affected by the distribution of the normative documents under the various ministries. Therefore, the main problem is unclear responsibility levels and organizational system for solving the issues regarding landscape planning, protection and management. Thus the various discussions between the involved disciplines and responsible institutions are arising. Two groups of the legislative documents influencing the implementation of the landscape policy in Latvia are detected within the study. The first group is strategic documents determining main landscape planning principles and directions at European, national, regional and professional or sectoral level. The second group is operational documents providing a set of actions for the landscape planning, protection and management at the local or the municipality level. The study concludes that operational documents developed by the municipalities are in high importance because of their direct influence on the landscape planning in Latvia. This often leads to the different landscape planning requirements included in the normative documents of the neighbouring municipalities, although the spatial and ecological borders of the visual landscape do not fit with the formal borders of the municipalities. Thus, it is essential to develop the common principles and actions that would be incumbent on all municipalities to provide the landscape integrity and to protect its values according to the main principles defined in the European Landscape Convention.

Computational design of hepatitis C vaccines using empirical fitness landscapes and population dynamics

NASA Astrophysics Data System (ADS)

Hart, Gregory; Ferguson, Andrew

Hepatitis C virus (HCV) afflicts 170 million people and kills 350,000 annually. Vaccination offers the most realistic and cost effective hope of controlling this epidemic. Despite 25 years of research, no vaccine is available. A major obstacle is the virus' extreme genetic variability and rapid mutational escape from immune pressure. Improvements in the vaccine design process are urgently needed. Coupling data mining and maximum entropy inference, we have developed a computational approach to translate sequence databases into empirical fitness landscapes. These landscapes explicitly connect viral genotype to phenotypic fitness and reveal vulnerable targets that can be exploited to rationally design vaccines. These landscapes represent the mutational ''playing field'' over which the virus evolves. We have integrated them with agent-based models of the viral mutational and host immune response, establishing a data-driven multi-scale immune simulator. We have used this simulator to perform in silico screening of HCV immunogens to rationally design vaccines to both cripple viral fitness and block escape. By systematically identifying a small number of promising vaccine candidates, these models can accelerate the search for a vaccine by massively reducing the experimental search space.

THE EVOLUTION OF CANALIZATION AND THE BREAKING OF VON BAER'S LAWS: MODELING THE EVOLUTION OF DEVELOPMENT WITH EPISTASIS.

PubMed

Rice, Sean H

1998-06-01

Evolution can change the developmental processes underlying a character without changing the average expression of the character itself. This sort of change must occur in both the evolution of canalization, in which a character becomes increasingly buffered against genetic or developmental variation, and in the phenomenon of closely related species that show similar adult phenotypes but different underlying developmental patterns. To study such phenomena, I develop a model that follows evolution on a surface representing adult phenotype as a function of underlying developmental characters. A contour on such a "phenotype landscape" is a set of states of developmental characters that produce the same adult phenotype. Epistasis induces curvature of this surface, and degree of canalization is represented by the slope along a contour. I first discuss the geometric properties of phenotype landscapes, relating epistasis to canalization. I then impose a fitness function on the phenotype and model evolution of developmental characters as a function of the fitness function and the local geometry of the surface. This model shows how canalization evolves as a population approaches an optimum phenotype. It further shows that under some circumstances, "decanalization" can occur, in which the expression of adult phenotype becomes increasingly sensitive to developmental variation. This process can cause very similar populations to diverge from one another developmentally even when their adult phenotypes experience identical selection regimes. © 1998 The Society for the Study of Evolution.

Fragmentation of nest and foraging habitat affects time budgets of solitary bees, their fitness and pollination services, depending on traits: Results from an individual-based model

PubMed Central

Settele, Josef; Dormann, Carsten F.

2018-01-01

Solitary bees are important but declining wild pollinators. During daily foraging in agricultural landscapes, they encounter a mosaic of patches with nest and foraging habitat and unsuitable matrix. It is insufficiently clear how spatial allocation of nesting and foraging resources and foraging traits of bees affect their daily foraging performance. We investigated potential brood cell construction (as proxy of fitness), number of visited flowers, foraging habitat visitation and foraging distance (pollination proxies) with the model SOLBEE (simulating pollen transport by solitary bees, tested and validated in an earlier study), for landscapes varying in landscape fragmentation and spatial allocation of nesting and foraging resources. Simulated bees varied in body size and nesting preference. We aimed to understand effects of landscape fragmentation and bee traits on bee fitness and the pollination services bees provide, as well as interactions between them, and the general consequences it has to our understanding of the system. This broad scope gives multiple key results. 1) Body size determines fitness more than landscape fragmentation, with large bees building fewer brood cells. High pollen requirements for large bees and the related high time budgets for visiting many flowers may not compensate for faster flight speeds and short handling times on flowers, giving them overall a disadvantage compared to small bees. 2) Nest preference does affect distribution of bees over the landscape, with cavity-nesting bees being restricted to nesting along field edges, which inevitably leads to performance reductions. Fragmentation mitigates this for cavity-nesting bees through increased edge habitat. 3) Landscape fragmentation alone had a relatively small effect on all responses. Instead, the local ratio of nest to foraging habitat affected bee fitness positively through reduced local competition. The spatial coverage of pollination increases steeply in response to this ratio for all bee sizes. The nest to foraging habitat ratio, a strong habitat proxy incorporating fragmentation could be a promising and practical measure for comparing landscape suitability for pollinators. 4) The number of flower visits was hardly affected by resource allocation, but predominantly by bee size. 5) In landscapes with the highest visitation coverage, bees flew least far, suggesting that these pollination proxies are subject to a trade-off between either longer pollen transport distances or a better pollination coverage, linked to how nests are distributed over the landscape rather than being affected by bee size. PMID:29444076

Fragmentation of nest and foraging habitat affects time budgets of solitary bees, their fitness and pollination services, depending on traits: Results from an individual-based model.

PubMed

Everaars, Jeroen; Settele, Josef; Dormann, Carsten F

2018-01-01

Solitary bees are important but declining wild pollinators. During daily foraging in agricultural landscapes, they encounter a mosaic of patches with nest and foraging habitat and unsuitable matrix. It is insufficiently clear how spatial allocation of nesting and foraging resources and foraging traits of bees affect their daily foraging performance. We investigated potential brood cell construction (as proxy of fitness), number of visited flowers, foraging habitat visitation and foraging distance (pollination proxies) with the model SOLBEE (simulating pollen transport by solitary bees, tested and validated in an earlier study), for landscapes varying in landscape fragmentation and spatial allocation of nesting and foraging resources. Simulated bees varied in body size and nesting preference. We aimed to understand effects of landscape fragmentation and bee traits on bee fitness and the pollination services bees provide, as well as interactions between them, and the general consequences it has to our understanding of the system. This broad scope gives multiple key results. 1) Body size determines fitness more than landscape fragmentation, with large bees building fewer brood cells. High pollen requirements for large bees and the related high time budgets for visiting many flowers may not compensate for faster flight speeds and short handling times on flowers, giving them overall a disadvantage compared to small bees. 2) Nest preference does affect distribution of bees over the landscape, with cavity-nesting bees being restricted to nesting along field edges, which inevitably leads to performance reductions. Fragmentation mitigates this for cavity-nesting bees through increased edge habitat. 3) Landscape fragmentation alone had a relatively small effect on all responses. Instead, the local ratio of nest to foraging habitat affected bee fitness positively through reduced local competition. The spatial coverage of pollination increases steeply in response to this ratio for all bee sizes. The nest to foraging habitat ratio, a strong habitat proxy incorporating fragmentation could be a promising and practical measure for comparing landscape suitability for pollinators. 4) The number of flower visits was hardly affected by resource allocation, but predominantly by bee size. 5) In landscapes with the highest visitation coverage, bees flew least far, suggesting that these pollination proxies are subject to a trade-off between either longer pollen transport distances or a better pollination coverage, linked to how nests are distributed over the landscape rather than being affected by bee size.

Dynamics of habitat selection in birds: adaptive response to nest predation depends on multiple factors.

PubMed

Devries, J H; Clark, R G; Armstrong, L M

2018-05-01

According to theory, habitat selection by organisms should reflect underlying habitat-specific fitness consequences and, in birds, reproductive success has a strong impact on population growth in many species. Understanding processes affecting habitat selection also is critically important for guiding conservation initiatives. Northern pintails (Anas acuta) are migratory, temperate-nesting birds that breed in greatest concentrations in the prairies of North America and their population remains below conservation goals. Habitat loss and changing land use practices may have decoupled formerly reliable fitness cues with respect to nest habitat choices. We used data from 62 waterfowl nesting study sites across prairie Canada (1997-2009) to examine nest survival, a primary fitness metric, at multiple scales, in combination with estimates of habitat selection (i.e., nests versus random points), to test for evidence of adaptive habitat choices. We used the same habitat covariates in both analyses. Pintail nest survival varied with nest initiation date, nest habitat, pintail breeding pair density, landscape composition and annual moisture. Selection of nesting habitat reflected patterns in nest survival in some cases, indicating adaptive selection, but strength of habitat selection varied seasonally and depended on population density and landscape composition. Adaptive selection was most evident late in the breeding season, at low breeding densities and in cropland-dominated landscapes. Strikingly, at high breeding density, habitat choice appears to become maladaptive relative to nest predation. At larger spatial scales, the relative availability of habitats with low versus high nest survival, and changing land use practices, may limit the reproductive potential of pintails.

Topographic and fire weather controls of fire refugia in forested ecosystems of northwestern North America

USGS Publications Warehouse

Krawchuk, Meg A.; Haire, Sandra L.; Coop, Jonathan D.; Parisien, Marc-Andre; Whitman, Ellen; Chong, Geneva W.; Miller, Carol

2016-01-01

for seven study fires that burned in conifer-dominated forested landscapes of the Western Cordillera of Canada between 2001 and 2014. We fit nine models, each for distinct levels of fire weather and terrain ruggedness. Our framework revealed that the predictability and abundance of fire refugia varied among these environmental settings. We observed highest predictability under moderate fire weather conditions and moderate terrain ruggedness (ROC-AUC = 0.77), and lowest predictability in flatter landscapes and under high fire weather conditions (ROC-AUC = 0.63–0.68). Catchment slope, local aspect, relative position, topographic wetness, topographic convergence, and local slope all contributed to discriminating where refugia occur but the relative importance of these topographic controls differed among environments. Our framework allows us to characterize the predictability of contemporary fire refugia across multiple environmental settings and provides important insights for ecosystem resilience, wildfire management, conservation planning, and climate change adaptation.

Graphical analysis of evolutionary trade-off in sylvatic Trypanosoma cruzi transmission modes.

PubMed

Kribs-Zaleta, Christopher M

2014-07-21

The notion of evolutionary trade-off (one attribute increasing at the expense of another) is central to the evolution of traits, well-studied especially in life-history theory, where a framework first developed by Levins illustrates how internal (genetics) and external (fitness landscapes) forces interact to shape an organism׳s ongoing adaptation. This manuscript extends this framework to the context of vector-borne pathogens, with the example of Trypanosoma cruzi (the etiological agent of Chagas׳ disease) adapting via trade-off among three different infection routes to hosts-stercorarian, vertical, and oral-in response to an epidemiological landscape that involves both hosts and vectors (where, in particular, parasite evolution depends not on parasite density but on relative host and vector densities). Using a fitness measure derived from an invasion reproductive number, this study analyzes several different trade-off scenarios in cycles involving raccoons or woodrats, including a proper three-way trade-off (two independent parameters). Results indicate that selection favors oral transmission to raccoons but classical stercorarian transmission to woodrats even under the same predation rate, with vertical (congenital) transmission favored only when aligned with dominant oral transmission or (at trace levels) under a weak (convex) trade-off. Copyright © 2014 Elsevier Ltd. All rights reserved.

Individual dispersal, landscape connectivity and ecological networks.

PubMed

Baguette, Michel; Blanchet, Simon; Legrand, Delphine; Stevens, Virginie M; Turlure, Camille

2013-05-01

Connectivity is classically considered an emergent property of landscapes encapsulating individuals' flows across space. However, its operational use requires a precise understanding of why and how organisms disperse. Such movements, and hence landscape connectivity, will obviously vary according to both organism properties and landscape features. We review whether landscape connectivity estimates could gain in both precision and generality by incorporating three fundamental outcomes of dispersal theory. Firstly, dispersal is a multi-causal process; its restriction to an 'escape reaction' to environmental unsuitability is an oversimplification, as dispersing individuals can leave excellent quality habitat patches or stay in poor-quality habitats according to the relative costs and benefits of dispersal and philopatry. Secondly, species, populations and individuals do not always react similarly to those cues that trigger dispersal, which sometimes results in contrasting dispersal strategies. Finally, dispersal is a major component of fitness and is thus under strong selective pressures, which could generate rapid adaptations of dispersal strategies. Such evolutionary responses will entail spatiotemporal variation in landscape connectivity. We thus strongly recommend the use of genetic tools to: (i) assess gene flow intensity and direction among populations in a given landscape; and (ii) accurately estimate landscape features impacting gene flow, and hence landscape connectivity. Such approaches will provide the basic data for planning corridors or stepping stones aiming at (re)connecting local populations of a given species in a given landscape. This strategy is clearly species- and landscape-specific. But we suggest that the ecological network in a given landscape could be designed by stacking up such linkages designed for several species living in different ecosystems. This procedure relies on the use of umbrella species that are representative of other species living in the same ecosystem. © 2012 The Authors. Biological Reviews © 2012 Cambridge Philosophical Society.

Quantifying functional connectivity: The role of breeding habitat, abundance, and landscape features on range-wide gene flow in sage-grouse

Treesearch

Jeffrey R. Row; Kevin E. Doherty; Todd B. Cross; Michael K. Schwartz; Sara Oyler-McCance; Dave E. Naugle; Steven T. Knick; Bradley C. Fedy

2018-01-01

Functional connectivity, quantified using landscape genetics, can inform conservation through the identification of factors linking genetic structure to landscape mechanisms. We used breeding habitat metrics, landscape attributes and indices of grouse abundance, to compare fit between structural connectivity and genetic differentiation within five long‐established Sage...

Bacterial growth laws reflect the evolutionary importance of energy efficiency.

PubMed

Maitra, Arijit; Dill, Ken A

2015-01-13

We are interested in the balance of energy and protein synthesis in bacterial growth. How has evolution optimized this balance? We describe an analytical model that leverages extensive literature data on growth laws to infer the underlying fitness landscape and to draw inferences about what evolution has optimized in Escherichia coli. Is E. coli optimized for growth speed, energy efficiency, or some other property? Experimental data show that at its replication speed limit, E. coli produces about four mass equivalents of nonribosomal proteins for every mass equivalent of ribosomes. This ratio can be explained if the cell's fitness function is the the energy efficiency of cells under fast growth conditions, indicating a tradeoff between the high energy costs of ribosomes under fast growth and the high energy costs of turning over nonribosomal proteins under slow growth. This model gives insight into some of the complex nonlinear relationships between energy utilization and ribosomal and nonribosomal production as a function of cell growth conditions.

Repeated holdout Cross-Validation of Model to Estimate Risk of Lyme Disease by Landscape Attributes

EPA Science Inventory

We previously modeled Lyme disease (LD) risk at the landscape scale; here we evaluate the model's overall goodness-of-fit using holdout validation. Landscapes were characterized within road-bounded analysis units (AU). Observed LD cases (obsLD) were ascertained per AU. Data were ...

A General Model for Estimating Macroevolutionary Landscapes.

PubMed

Boucher, Florian C; Démery, Vincent; Conti, Elena; Harmon, Luke J; Uyeda, Josef

2018-03-01

The evolution of quantitative characters over long timescales is often studied using stochastic diffusion models. The current toolbox available to students of macroevolution is however limited to two main models: Brownian motion and the Ornstein-Uhlenbeck process, plus some of their extensions. Here, we present a very general model for inferring the dynamics of quantitative characters evolving under both random diffusion and deterministic forces of any possible shape and strength, which can accommodate interesting evolutionary scenarios like directional trends, disruptive selection, or macroevolutionary landscapes with multiple peaks. This model is based on a general partial differential equation widely used in statistical mechanics: the Fokker-Planck equation, also known in population genetics as the Kolmogorov forward equation. We thus call the model FPK, for Fokker-Planck-Kolmogorov. We first explain how this model can be used to describe macroevolutionary landscapes over which quantitative traits evolve and, more importantly, we detail how it can be fitted to empirical data. Using simulations, we show that the model has good behavior both in terms of discrimination from alternative models and in terms of parameter inference. We provide R code to fit the model to empirical data using either maximum-likelihood or Bayesian estimation, and illustrate the use of this code with two empirical examples of body mass evolution in mammals. FPK should greatly expand the set of macroevolutionary scenarios that can be studied since it opens the way to estimating macroevolutionary landscapes of any conceivable shape. [Adaptation; bounds; diffusion; FPK model; macroevolution; maximum-likelihood estimation; MCMC methods; phylogenetic comparative data; selection.].

Riding across the selection landscape: fitness consequences of annual variation in reproductive characteristics

PubMed Central

Tremblay, Raymond L.; Ackerman, James D.; Pérez, Maria-Eglée

2010-01-01

Evolutionary models estimating phenotypic selection in character size usually assume that the character is invariant across reproductive bouts. We show that variation in the size of reproductive traits may be large over multiple events and can influence fitness in organisms where these traits are produced anew each season. With data from populations of two orchid species, Caladenia valida and Tolumnia variegata, we used Bayesian statistics to investigate the effect on the distribution in fitness of individuals when the fitness landscape is not flat and when characters vary across reproductive bouts. Inconsistency in character size across reproductive periods within an individual increases the uncertainty of mean fitness and, consequently, the uncertainty in individual fitness. The trajectory of selection is likely to be muddled as a consequence of variation in morphology of individuals across reproductive bouts. The frequency and amplitude of such changes will certainly affect the dynamics between selection and genetic drift. PMID:20047875

VisIt: An End-User Tool for Visualizing and Analyzing Very Large Data

DOE Office of Scientific and Technical Information (OSTI.GOV)

Childs, Hank; Brugger, Eric; Whitlock, Brad

2012-11-01

VisIt is a popular open source tool for visualizing and analyzing big data. It owes its success to its foci of increasing data understanding, large data support, and providing a robust and usable product, as well as its underlying design that fits today's supercomputing landscape. This report, which draws heavily from an earlier publication at the SciDAC Conference in 2011 describes the VisIt project and its accomplishments.

A pivot mutation impedes reverse evolution across an adaptive landscape for drug resistance in Plasmodium vivax.

PubMed

Ogbunugafor, C Brandon; Hartl, Daniel

2016-01-25

The study of reverse evolution from resistant to susceptible phenotypes can reveal constraints on biological evolution, a topic for which evolutionary theory has relatively few general principles. The public health catastrophe of antimicrobial resistance in malaria has brought these constraints on evolution into a practical realm, with one proposed solution: withdrawing anti-malarial medication use in high resistance settings, built on the assumption that reverse evolution occurs readily enough that populations of pathogens may revert to their susceptible states. While past studies have suggested limits to reverse evolution, there have been few attempts to properly dissect its mechanistic constraints. Growth rates were determined from empirical data on the growth and resistance from a set of combinatorially complete set of mutants of a resistance protein (dihydrofolate reductase) in Plasmodium vivax, to construct reverse evolution trajectories. The fitness effects of individual mutations were calculated as a function of drug environment, revealing the magnitude of epistatic interactions between mutations and genetic backgrounds. Evolution across the landscape was simulated in two settings: starting from the population fixed for the quadruple mutant, and from a polymorphic population evenly distributed between double mutants. A single mutation of large effect (S117N) serves as a pivot point for evolution to high resistance regions of the landscape. Through epistatic interactions with other mutations, this pivot creates an epistatic ratchet against reverse evolution towards the wild type ancestor, even in environments where the wild type is the most fit of all genotypes. This pivot mutation underlies the directional bias in evolution across the landscape, where evolution towards the ancestor is precluded across all examined drug concentrations from various starting points in the landscape. The presence of pivot mutations can dictate dynamics of evolution across adaptive landscape through epistatic interactions within a protein, leaving a population trapped on local fitness peaks in an adaptive landscape, unable to locate ancestral genotypes. This irreversibility suggests that the structure of an adaptive landscape for a resistance protein should be understood before considering resistance management strategies. This proposed mechanism for constraints on reverse evolution corroborates evidence from the field indicating that phenotypic reversal often occurs via compensatory mutation at sites independent of those associated with the forward evolution of resistance. Because of this, molecular methods that identify resistance patterns via single SNPs in resistance-associated markers might be missing signals for resistance and compensatory mutation throughout the genome. In these settings, whole genome sequencing efforts should be used to identify resistance patterns, and will likely reveal a more complicated genomic signature for resistance and susceptibility, especially in settings where anti-malarial medications have been used intermittently. Lastly, the findings suggest that, given their role in dictating the dynamics of evolution across the landscape, pivot mutations might serve as future targets for therapy.

Genomics meets applied ecology: Characterizing habitat quality for sloths in a tropical agroecosystem.

PubMed

Fountain, Emily D; Kang, Jung Koo; Tempel, Douglas J; Palsbøll, Per J; Pauli, Jonathan N; Zachariah Peery, M

2018-01-01

Understanding how habitat quality in heterogeneous landscapes governs the distribution and fitness of individuals is a fundamental aspect of ecology. While mean individual fitness is generally considered a key to assessing habitat quality, a comprehensive understanding of habitat quality in heterogeneous landscapes requires estimates of dispersal rates among habitat types. The increasing accessibility of genomic approaches, combined with field-based demographic methods, provides novel opportunities for incorporating dispersal estimation into assessments of habitat quality. In this study, we integrated genomic kinship approaches with field-based estimates of fitness components and approximate Bayesian computation (ABC) procedures to estimate habitat-specific dispersal rates and characterize habitat quality in two-toed sloths (Choloepus hoffmanni) occurring in a Costa Rican agricultural ecosystem. Field-based observations indicated that birth and survival rates were similar in a sparsely shaded cacao farm and adjacent cattle pasture-forest mosaic. Sloth density was threefold higher in pasture compared with cacao, whereas home range size and overlap were greater in cacao compared with pasture. Dispersal rates were similar between the two habitats, as estimated using ABC procedures applied to the spatial distribution of pairs of related individuals identified using 3,431 single nucleotide polymorphism and 11 microsatellite locus genotypes. Our results indicate that crops produced under a sparse overstorey can, in some cases, constitute lower-quality habitat than pasture-forest mosaics for sloths, perhaps because of differences in food resources or predator communities. Finally, our study demonstrates that integrating field-based demographic approaches with genomic methods can provide a powerful means for characterizing habitat quality for animal populations occurring in heterogeneous landscapes. © 2017 John Wiley & Sons Ltd.

Revealing evolutionary pathways by fitness landscape reconstruction.

PubMed

Kogenaru, Manjunatha; de Vos, Marjon G J; Tans, Sander J

2009-01-01

The concept of epistasis has since long been used to denote non-additive fitness effects of genetic changes and has played a central role in understanding the evolution of biological systems. Owing to an array of novel experimental methodologies, it has become possible to experimentally determine epistatic interactions as well as more elaborate genotype-fitness maps. These data have opened up the investigation of a host of long-standing questions in evolutionary biology, such as the ruggedness of fitness landscapes and the accessibility of mutational trajectories, the evolution of sex, and the origin of robustness and modularity. Here we review this recent and timely marriage between systems biology and evolutionary biology, which holds the promise to understand evolutionary dynamics in a more mechanistic and predictive manner.

Landscape Simplification Constrains Adult Size in a Native Ground-Nesting Bee

PubMed Central

Renauld, Miles; Hutchinson, Alena; Loeb, Gregory; Poveda, Katja; Connelly, Heather

2016-01-01

Bees provide critical pollination services to 87% of angiosperm plants; however, the reliability of these services may become threatened as bee populations decline. Agricultural intensification, resulting in the simplification of environments at the landscape scale, greatly changes the quality and quantity of resources available for female bees to provision their offspring. These changes may alter or constrain the tradeoffs in maternal investment allocation between offspring size, number and sex required to maximize fitness. Here we investigate the relationship between landscape scale agricultural intensification and the size and number of individuals within a wild ground nesting bee species, Andrena nasonii. We show that agricultural intensification at the landscape scale was associated with a reduction in the average size of field collected A. nasonii adults in highly agricultural landscapes but not with the number of individuals collected. Small females carried significantly smaller (40%) pollen loads than large females, which is likely to have consequences for subsequent offspring production and fitness. Thus, landscape simplification is likely to constrain allocation of resources to offspring through a reduction in the overall quantity, quality and distribution of resources. PMID:26943127

Landscape Simplification Constrains Adult Size in a Native Ground-Nesting Bee.

PubMed

Renauld, Miles; Hutchinson, Alena; Loeb, Gregory; Poveda, Katja; Connelly, Heather

2016-01-01

Bees provide critical pollination services to 87% of angiosperm plants; however, the reliability of these services may become threatened as bee populations decline. Agricultural intensification, resulting in the simplification of environments at the landscape scale, greatly changes the quality and quantity of resources available for female bees to provision their offspring. These changes may alter or constrain the tradeoffs in maternal investment allocation between offspring size, number and sex required to maximize fitness. Here we investigate the relationship between landscape scale agricultural intensification and the size and number of individuals within a wild ground nesting bee species, Andrena nasonii. We show that agricultural intensification at the landscape scale was associated with a reduction in the average size of field collected A. nasonii adults in highly agricultural landscapes but not with the number of individuals collected. Small females carried significantly smaller (40%) pollen loads than large females, which is likely to have consequences for subsequent offspring production and fitness. Thus, landscape simplification is likely to constrain allocation of resources to offspring through a reduction in the overall quantity, quality and distribution of resources.

FOUNDRY LANDSCAPE LOOKING NORTHWEST FROM MALLEABLE STOCK YARD CRANE SHOWING ...

Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

FOUNDRY LANDSCAPE LOOKING NORTHWEST FROM MALLEABLE STOCK YARD CRANE SHOWING THE MALLEABLE ANNEALING BUILDING AND THE BRASS FOUNDRY. - Stockham Pipe & Fittings Company, 4000 Tenth Avenue North, Birmingham, Jefferson County, AL

FOUNDRY LANDSCAPE LOOKING SOUTHWEST FROM MALLEABLE STOCK YARD CRANE SHOWING ...

Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

FOUNDRY LANDSCAPE LOOKING SOUTHWEST FROM MALLEABLE STOCK YARD CRANE SHOWING CRANE RAILS, GREY IRON CUPOLA AND EMISSION RECOVERY SYSTEM. - Stockham Pipe & Fittings Company, 4000 Tenth Avenue North, Birmingham, Jefferson County, AL

FOUNDRY LANDSCAPE LOOKING WESTSOUTHWEST FROM MALLEABLE STOCK YARD CRANE SHOWING ...

Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

FOUNDRY LANDSCAPE LOOKING WEST-SOUTHWEST FROM MALLEABLE STOCK YARD CRANE SHOWING SHED ROOF OF OLD MALLEABLE CUPOLA CHARGER. - Stockham Pipe & Fittings Company, 4000 Tenth Avenue North, Birmingham, Jefferson County, AL

Fitness landscape transformation through a single amino acid change in the rho terminator.

PubMed

Freddolino, Peter L; Goodarzi, Hani; Tavazoie, Saeed

2012-05-01

Regulatory networks allow organisms to match adaptive behavior to the complex and dynamic contingencies of their native habitats. Upon a sudden transition to a novel environment, the mismatch between the native behavior and the new niche provides selective pressure for adaptive evolution through mutations in elements that control gene expression. In the case of core components of cellular regulation and metabolism, with broad control over diverse biological processes, such mutations may have substantial pleiotropic consequences. Through extensive phenotypic analyses, we have characterized the systems-level consequences of one such mutation (rho*) in the global transcriptional terminator Rho of Escherichia coli. We find that a single amino acid change in Rho results in a massive change in the fitness landscape of the cell, with widely discrepant fitness consequences of identical single locus perturbations in rho* versus rho(WT) backgrounds. Our observations reveal the extent to which a single regulatory mutation can transform the entire fitness landscape of the cell, causing a massive change in the interpretation of individual mutations and altering the evolutionary trajectories which may be accessible to a bacterial population.

Adaptive evolutionary walks require neutral intermediates in RNA fitness landscapes.

PubMed

Rendel, Mark D

2011-01-01

In RNA fitness landscapes with interconnected networks of neutral mutations, neutral precursor mutations can play an important role in facilitating the accessibility of epistatic adaptive mutant combinations. I use an exhaustively surveyed fitness landscape model based on short sequence RNA genotypes (and their secondary structure phenotypes) to calculate the minimum rate at which mutants initially appearing as neutral are incorporated into an adaptive evolutionary walk. I show first, that incorporating neutral mutations significantly increases the number of point mutations in a given evolutionary walk when compared to estimates from previous adaptive walk models. Second, that incorporating neutral mutants into such a walk significantly increases the final fitness encountered on that walk - indeed evolutionary walks including neutral steps often reach the global optimum in this model. Third, and perhaps most importantly, evolutionary paths of this kind are often extremely winding in their nature and have the potential to undergo multiple mutations at a given sequence position within a single walk; the potential of these winding paths to mislead phylogenetic reconstruction is briefly considered. Copyright © 2010 Elsevier Inc. All rights reserved.

RATES OF FITNESS DECLINE AND REBOUND SUGGEST PERVASIVE EPISTASIS

PubMed Central

Perfeito, L; Sousa, A; Bataillon, T; Gordo, I

2014-01-01

Unraveling the factors that determine the rate of adaptation is a major question in evolutionary biology. One key parameter is the effect of a new mutation on fitness, which invariably depends on the environment and genetic background. The fate of a mutation also depends on population size, which determines the amount of drift it will experience. Here, we manipulate both population size and genotype composition and follow adaptation of 23 distinct Escherichia coli genotypes. These have previously accumulated mutations under intense genetic drift and encompass a substantial fitness variation. A simple rule is uncovered: the net fitness change is negatively correlated with the fitness of the genotype in which new mutations appear—a signature of epistasis. We find that Fisher's geometrical model can account for the observed patterns of fitness change and infer the parameters of this model that best fit the data, using Approximate Bayesian Computation. We estimate a genomic mutation rate of 0.01 per generation for fitness altering mutations, albeit with a large confidence interval, a mean fitness effect of mutations of −0.01, and an effective number of traits nine in mutS− E. coli. This framework can be extended to confront a broader range of models with data and test different classes of fitness landscape models. PMID:24372601

Greenhouse warming and landscape care

Treesearch

Kevin T. Smith

2009-01-01

Climate change is one of the few truly planetary processes that influence the assessments and actions of governments and of everyday citizens. Principles and practices of ecological landscaping fit well with concern about hte effects of climate change.

Limiting factors and landscape connectivity: the American marten in the Rocky Mountains

Treesearch

S. A. Cushman; M. G. Raphael; L. F. Ruggiero; A. S. Shirk; T. N. Wasserman; E. C. O' Doherty

2011-01-01

In mobile animals, movement behavior can maximize fitness by optimizing access to critical resources and minimizing risk of predation. We sought to evaluate several hypotheses regarding the effects of landscape structure on American marten foraging path selection in a landscape experiencing forest perforation by patchcut logging. We hypothesized that in the uncut pre-...

Transcription as a source of genome instability

PubMed Central

Kim, Nayun; Jinks-Robertson, Sue

2012-01-01

Alterations in genome sequence and structure contribute to somatic disease, affect the fitness of subsequent generations and drive evolutionary processes. The critical roles of highly accurate replication and efficient repair in maintaining overall genome integrity are well known, but the more localized stability costs associated with transcribing DNA into RNA molecules are less appreciated. Here we review the diverse ways that the essential process of transcription alters the underlying DNA template and thereby modifies the genetic landscape. PMID:22330764

FOUNDRY LANDSCAPE LOOKING WESTNORTHWEST FROM MALLEABLE STOCK YARD CRANE, SHOWING ...

Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

FOUNDRY LANDSCAPE LOOKING WEST-NORTHWEST FROM MALLEABLE STOCK YARD CRANE, SHOWING CRANE MOTOR AND MALLEABLE CUPOLAS WITH OPEN TOPS AND EMISSION RECOVERY DUCTS. - Stockham Pipe & Fittings Company, 4000 Tenth Avenue North, Birmingham, Jefferson County, AL

Disease Risk in a Dynamic Environment: The Spread of Tick-Borne Pathogens in Minnesota, USA

PubMed Central

Robinson, Stacie J.; Neitzel, David F.; Moen, Ronald A.; Craft, Meggan E.; Hamilton, Karin E.; Johnson, Lucinda B.; Mulla, David J.; Munderloh, Ulrike G.; Redig, Patrick T.; Smith, Kirk E.; Turner, Clarence L.; Umber, Jamie K.; Pelican, Katharine M.

2015-01-01

As humans and climate change alter the landscape, novel disease risk scenarios emerge. Understanding the complexities of pathogen emergence and subsequent spread as shaped by landscape heterogeneity is crucial to understanding disease emergence, pinpointing high-risk areas, and mitigating emerging disease threats in a dynamic environment. Tick-borne diseases present an important public health concern and incidence of many of these diseases are increasing in the United States. The complex epidemiology of tick-borne diseases includes strong ties with environmental factors that influence host availability, vector abundance, and pathogen transmission. Here, we used 16 years of case data from the Minnesota Department of Health to report spatial and temporal trends in Lyme disease (LD), human anaplasmosis, and babesiosis. We then used a spatial regression framework to evaluate the impact of landscape and climate factors on the spread of LD. Finally, we use the fitted model, and landscape and climate datasets projected under varying climate change scenarios, to predict future changes in tick-borne pathogen risk. Both forested habitat and temperature were important drivers of LD spread in Minnesota. Dramatic changes in future temperature regimes and forest communities predict rising risk of tick-borne disease. PMID:25281302

Disease risk in a dynamic environment: the spread of tick-borne pathogens in Minnesota, USA.

PubMed

Robinson, Stacie J; Neitzel, David F; Moen, Ronald A; Craft, Meggan E; Hamilton, Karin E; Johnson, Lucinda B; Mulla, David J; Munderloh, Ulrike G; Redig, Patrick T; Smith, Kirk E; Turner, Clarence L; Umber, Jamie K; Pelican, Katharine M

2015-03-01

As humans and climate change alter the landscape, novel disease risk scenarios emerge. Understanding the complexities of pathogen emergence and subsequent spread as shaped by landscape heterogeneity is crucial to understanding disease emergence, pinpointing high-risk areas, and mitigating emerging disease threats in a dynamic environment. Tick-borne diseases present an important public health concern and incidence of many of these diseases are increasing in the United States. The complex epidemiology of tick-borne diseases includes strong ties with environmental factors that influence host availability, vector abundance, and pathogen transmission. Here, we used 16 years of case data from the Minnesota Department of Health to report spatial and temporal trends in Lyme disease (LD), human anaplasmosis, and babesiosis. We then used a spatial regression framework to evaluate the impact of landscape and climate factors on the spread of LD. Finally, we use the fitted model, and landscape and climate datasets projected under varying climate change scenarios, to predict future changes in tick-borne pathogen risk. Both forested habitat and temperature were important drivers of LD spread in Minnesota. Dramatic changes in future temperature regimes and forest communities predict rising risk of tick-borne disease.

Adaptive landscapes: Top-down and bottom-up perspectives

NASA Astrophysics Data System (ADS)

Kerr, Benjamin

Sewall Wright introduced the metaphor of the adaptive landscape, a map from genotype to fitness, more than 80 years ago to help describe his view of adaptive evolution. This metaphor has been immensely popular and has been used in a variety of incarnations. However, a systematic study of the genotype-fitness map presents significant problems. The space of possible genotypes is vast, and the mapping is likely dependent on both environment and the composition of genotypes in a population. In this talk, I will discuss some of these problems and present experimental strategies for uncovering features of adaptive landscapes. In particular, I will discuss how population structure can be used as an experimental variable to elucidate landscape topography and how a combination of experimental evolution and genetic engineering can reveal important landscape features in changing environments. I will also present some potential applications of this work to the problem of antibiotic resistance and potential implications for evolutionary rescue in the face of global climate change. For some of these topics, the classic notion of the adaptive landscape must itself be adapted; however, I propose that there are fruitful ways to continue to apply this metaphor.

Direct Calculation of Protein Fitness Landscapes through Computational Protein Design

PubMed Central

Au, Loretta; Green, David F.

2016-01-01

Naturally selected amino-acid sequences or experimentally derived ones are often the basis for understanding how protein three-dimensional conformation and function are determined by primary structure. Such sequences for a protein family comprise only a small fraction of all possible variants, however, representing the fitness landscape with limited scope. Explicitly sampling and characterizing alternative, unexplored protein sequences would directly identify fundamental reasons for sequence robustness (or variability), and we demonstrate that computational methods offer an efficient mechanism toward this end, on a large scale. The dead-end elimination and A∗ search algorithms were used here to find all low-energy single mutant variants, and corresponding structures of a G-protein heterotrimer, to measure changes in structural stability and binding interactions to define a protein fitness landscape. We established consistency between these algorithms with known biophysical and evolutionary trends for amino-acid substitutions, and could thus recapitulate known protein side-chain interactions and predict novel ones. PMID:26745411

Percolation on fitness landscapes: effects of correlation, phenotype, and incompatibilities

PubMed Central

Gravner, Janko; Pitman, Damien; Gavrilets, Sergey

2009-01-01

We study how correlations in the random fitness assignment may affect the structure of fitness landscapes, in three classes of fitness models. The first is a phenotype space in which individuals are characterized by a large number n of continuously varying traits. In a simple model of random fitness assignment, viable phenotypes are likely to form a giant connected cluster percolating throughout the phenotype space provided the viability probability is larger than 1/2n. The second model explicitly describes genotype-to-phenotype and phenotype-to-fitness maps, allows for neutrality at both phenotype and fitness levels, and results in a fitness landscape with tunable correlation length. Here, phenotypic neutrality and correlation between fitnesses can reduce the percolation threshold, and correlations at the point of phase transition between local and global are most conducive to the formation of the giant cluster. In the third class of models, particular combinations of alleles or values of phenotypic characters are “incompatible” in the sense that the resulting genotypes or phenotypes have zero fitness. This setting can be viewed as a generalization of the canonical Bateson-Dobzhansky-Muller model of speciation and is related to K- SAT problems, prominent in computer science. We analyze the conditions for the existence of viable genotypes, their number, as well as the structure and the number of connected clusters of viable genotypes. We show that analysis based on expected values can easily lead to wrong conclusions, especially when fitness correlations are strong. We focus on pairwise incompatibilities between diallelic loci, but we also address multiple alleles, complex incompatibilities, and continuous phenotype spaces. In the case of diallelic loci, the number of clusters is stochastically bounded and each cluster contains a very large sub-cube. Finally, we demonstrate that the discrete NK model shares some signature properties of models with high correlations. PMID:17692873

A phase transition induces chaos in a predator-prey ecosystem with a dynamic fitness landscape.

PubMed

Gilpin, William; Feldman, Marcus W

2017-07-01

In many ecosystems, natural selection can occur quickly enough to influence the population dynamics and thus future selection. This suggests the importance of extending classical population dynamics models to include such eco-evolutionary processes. Here, we describe a predator-prey model in which the prey population growth depends on a prey density-dependent fitness landscape. We show that this two-species ecosystem is capable of exhibiting chaos even in the absence of external environmental variation or noise, and that the onset of chaotic dynamics is the result of the fitness landscape reversibly alternating between epochs of stabilizing and disruptive selection. We draw an analogy between the fitness function and the free energy in statistical mechanics, allowing us to use the physical theory of first-order phase transitions to understand the onset of rapid cycling in the chaotic predator-prey dynamics. We use quantitative techniques to study the relevance of our model to observational studies of complex ecosystems, finding that the evolution-driven chaotic dynamics confer community stability at the "edge of chaos" while creating a wide distribution of opportunities for speciation during epochs of disruptive selection-a potential observable signature of chaotic eco-evolutionary dynamics in experimental studies.

On Cellular Darwinism: Mitochondria.

PubMed

Bull, Larry

2016-01-01

The significant role of mitochondria within cells is becoming increasingly clear. This letter uses the NKCS model of coupled fitness landscapes to explore aspects of organelle-nucleus coevolution. The phenomenon of mitochondrial diversity is allowed to emerge under a simple intracellular evolutionary process, including varying the relative rate of evolution by the organelle. It is shown how the conditions for the maintenance of more than one genetic variant of mitochondria are similar to those previously suggested as needed for the original symbiotic origins of the relationship using the NKCS model.

Classifying the health of Connecticut streams using benthic macroinvertebrates with implications for water management.

PubMed

Bellucci, Christopher J; Becker, Mary E; Beauchene, Mike; Dunbar, Lee

2013-06-01

Bioassessments have formed the foundation of many water quality monitoring programs throughout the United States. Like many state water quality programs, Connecticut has developed a relational database containing information about species richness, species composition, relative abundance, and feeding relationships among macroinvertebrates present in stream and river systems. Geographic Information Systems can provide estimates of landscape condition and watershed characteristics and when combined with measurements of stream biology, provide a useful visual display of information that is useful in a management context. The objective of our study was to estimate the stream health for all wadeable stream kilometers in Connecticut using a combination of macroinvertebrate metrics and landscape variables. We developed and evaluated models using an information theoretic approach to predict stream health as measured by macroinvertebrate multimetric index (MMI) and identified the best fitting model as a three variable model, including percent impervious land cover, a wetlands metric, and catchment slope that best fit the MMI scores (adj-R (2) = 0.56, SE = 11.73). We then provide examples of how modeling can augment existing programs to support water management policies under the Federal Clean Water Act such as stream assessments and anti-degradation.

Evolutionary genetics of maternal effects

PubMed Central

Wolf, Jason B.; Wade, Michael J.

2016-01-01

Maternal genetic effects (MGEs), where genes expressed by mothers affect the phenotype of their offspring, are important sources of phenotypic diversity in a myriad of organisms. We use a single‐locus model to examine how MGEs contribute patterns of heritable and nonheritable variation and influence evolutionary dynamics in randomly mating and inbreeding populations. We elucidate the influence of MGEs by examining the offspring genotype‐phenotype relationship, which determines how MGEs affect evolutionary dynamics in response to selection on offspring phenotypes. This approach reveals important results that are not apparent from classic quantitative genetic treatments of MGEs. We show that additive and dominance MGEs make different contributions to evolutionary dynamics and patterns of variation, which are differentially affected by inbreeding. Dominance MGEs make the offspring genotype‐phenotype relationship frequency dependent, resulting in the appearance of negative frequency‐dependent selection, while additive MGEs contribute a component of parent‐of‐origin dependent variation. Inbreeding amplifies the contribution of MGEs to the additive genetic variance and, therefore enhances their evolutionary response. Considering evolutionary dynamics of allele frequency change on an adaptive landscape, we show that this landscape differs from the mean fitness surface, and therefore, under some condition, fitness peaks can exist but not be “available” to the evolving population. PMID:26969266

The Contribution of Vegetation and Landscape Configuration for Predicting Environmental Change Impacts on Iberian Birds

PubMed Central

Triviño, Maria; Thuiller, Wilfried; Cabeza, Mar; Hickler, Thomas; Araújo, Miguel B.

2011-01-01

Although climate is known to be one of the key factors determining animal species distributions amongst others, projections of global change impacts on their distributions often rely on bioclimatic envelope models. Vegetation structure and landscape configuration are also key determinants of distributions, but they are rarely considered in such assessments. We explore the consequences of using simulated vegetation structure and composition as well as its associated landscape configuration in models projecting global change effects on Iberian bird species distributions. Both present-day and future distributions were modelled for 168 bird species using two ensemble forecasting methods: Random Forests (RF) and Boosted Regression Trees (BRT). For each species, several models were created, differing in the predictor variables used (climate, vegetation, and landscape configuration). Discrimination ability of each model in the present-day was then tested with four commonly used evaluation methods (AUC, TSS, specificity and sensitivity). The different sets of predictor variables yielded similar spatial patterns for well-modelled species, but the future projections diverged for poorly-modelled species. Models using all predictor variables were not significantly better than models fitted with climate variables alone for ca. 50% of the cases. Moreover, models fitted with climate data were always better than models fitted with landscape configuration variables, and vegetation variables were found to correlate with bird species distributions in 26–40% of the cases with BRT, and in 1–18% of the cases with RF. We conclude that improvements from including vegetation and its landscape configuration variables in comparison with climate only variables might not always be as great as expected for future projections of Iberian bird species. PMID:22216263

Shifts in reproductive assurance strategies and inbreeding costs associated with habitat fragmentation in Central American mahogany

PubMed Central

Breed, Martin F; Gardner, Michael G; Ottewell, Kym M; Navarro, Carlos M; Lowe, Andrew J

2012-01-01

The influence of habitat fragmentation on mating patterns and progeny fitness in trees is critical for understanding the long-term impact of contemporary landscape change on the sustainability of biodiversity. We examined the relationship between mating patterns, using microsatellites, and fitness of progeny, in a common garden trial, for the insect-pollinated big-leaf mahogany, Swietenia macrophylla King, sourced from forests and isolated trees in 16 populations across Central America. As expected, isolated trees had disrupted mating patterns and reduced fitness. However, for dry provenances, fitness was negatively related to correlated paternity, while for mesic provenances, fitness was correlated positively with outcrossing rate and negatively with correlated paternity. Poorer performance of mesic provenances is likely because of reduced effective pollen donor density due to poorer environmental suitability and greater disturbance history. Our results demonstrate a differential shift in reproductive assurance and inbreeding costs in mahogany, driven by exploitation history and contemporary landscape context. PMID:22381041

Error catastrophe and phase transition in the empirical fitness landscape of HIV

NASA Astrophysics Data System (ADS)

Hart, Gregory R.; Ferguson, Andrew L.

2015-03-01

We have translated clinical sequence databases of the p6 HIV protein into an empirical fitness landscape quantifying viral replicative capacity as a function of the amino acid sequence. We show that the viral population resides close to a phase transition in sequence space corresponding to an "error catastrophe" beyond which there is lethal accumulation of mutations. Our model predicts that the phase transition may be induced by drug therapies that elevate the mutation rate, or by forcing mutations at particular amino acids. Applying immune pressure to any combination of killer T-cell targets cannot induce the transition, providing a rationale for why the viral protein can exist close to the error catastrophe without sustaining fatal fitness penalties due to adaptive immunity.

Evolution and Extinction Dynamics in Rugged Fitness Landscapes

NASA Astrophysics Data System (ADS)

Sibani, Paolo; Brandt, Michael; Alstrøm, Preben

After an introductory section summarizing the paleontological data and some of their theoretical descriptions, we describe the "reset" model and its (in part analytically soluble) mean field version, which have been briefly introduced in Letters.1,2 Macroevolution is considered as a problem of stochastic dynamics in a system with many competing agents. Evolutionary events (speciations and extinctions) are triggered by fitness records found by random exploration of the agents' fitness landscapes. As a consequence, the average fitness in the system increases logarithmically with time, while the rate of extinction steadily decreases. This non-stationary dynamics is studied by numerical simulations and, in a simpler mean field version, analytically. We also consider the effect of externally added "mass" extinctions. The predictions for various quantities of paleontological interest (life-time distribution, distribution of event sizes and behavior of the rate of extinction) are robust and in good agreement with available data.

δ-exceedance records and random adaptive walks

NASA Astrophysics Data System (ADS)

Park, Su-Chan; Krug, Joachim

2016-08-01

We study a modified record process where the kth record in a series of independent and identically distributed random variables is defined recursively through the condition {Y}k\\gt {Y}k-1-{δ }k-1 with a deterministic sequence {δ }k\\gt 0 called the handicap. For constant {δ }k\\equiv δ and exponentially distributed random variables it has been shown in previous work that the process displays a phase transition as a function of δ between a normal phase where the mean record value increases indefinitely and a stationary phase where the mean record value remains bounded and a finite fraction of all entries are records (Park et al 2015 Phys. Rev. E 91 042707). Here we explore the behavior for general probability distributions and decreasing and increasing sequences {δ }k, focusing in particular on the case when {δ }k matches the typical spacing between subsequent records in the underlying simple record process without handicap. We find that a continuous phase transition occurs only in the exponential case, but a novel kind of first order transition emerges when {δ }k is increasing. The problem is partly motivated by the dynamics of evolutionary adaptation in biological fitness landscapes, where {δ }k corresponds to the change of the deterministic fitness component after k mutational steps. The results for the record process are used to compute the mean number of steps that a population performs in such a landscape before being trapped at a local fitness maximum.

A phase transition induces chaos in a predator-prey ecosystem with a dynamic fitness landscape

PubMed Central

2017-01-01

In many ecosystems, natural selection can occur quickly enough to influence the population dynamics and thus future selection. This suggests the importance of extending classical population dynamics models to include such eco-evolutionary processes. Here, we describe a predator-prey model in which the prey population growth depends on a prey density-dependent fitness landscape. We show that this two-species ecosystem is capable of exhibiting chaos even in the absence of external environmental variation or noise, and that the onset of chaotic dynamics is the result of the fitness landscape reversibly alternating between epochs of stabilizing and disruptive selection. We draw an analogy between the fitness function and the free energy in statistical mechanics, allowing us to use the physical theory of first-order phase transitions to understand the onset of rapid cycling in the chaotic predator-prey dynamics. We use quantitative techniques to study the relevance of our model to observational studies of complex ecosystems, finding that the evolution-driven chaotic dynamics confer community stability at the “edge of chaos” while creating a wide distribution of opportunities for speciation during epochs of disruptive selection—a potential observable signature of chaotic eco-evolutionary dynamics in experimental studies. PMID:28678792

Influence of network topology on cooperative problem-solving systems.

PubMed

Fontanari, José F; Rodrigues, Francisco A

2016-09-01

The idea of a collective intelligence behind the complex natural structures built by organisms suggests that the organization of social networks is selected so as to optimize problem-solving competence at the group level. Here we study the influence of the social network topology on the performance of a group of agents whose task is to locate the global maxima of NK fitness landscapes. Agents cooperate by broadcasting messages informing on their fitness and use this information to imitate the fittest agent in their influence networks. In the case those messages convey accurate information on the proximity of the solution (i.e., for smooth fitness landscapes), we find that high connectivity as well as centralization boosts the group performance. For rugged landscapes, however, these characteristics are beneficial for small groups only. For large groups, it is advantageous to slow down the information transmission through the network to avoid local maximum traps. Long-range links and modularity have marginal effects on the performance of the group, except for a very narrow region of the model parameters.

Genotype to Phenotype Mapping of the E. coli lac Promoter

NASA Astrophysics Data System (ADS)

Otwinowski, Jakub; Nemenman, Ilya

2014-03-01

Genotype-to-phenotype maps and the related fitness landscapes that include epistatic interactions are difficult to measure because of their high dimensional structure. Here we construct such a map using the recently collected corpora of high-throughput sequence data from the 75 base pairs long mutagenized E. coli lac promoter region, where each sequence is associated with induced transcriptional activity measured by a fluorescent reporter. We find that the additive (non-epistatic) contributions of individual mutations account for about two-thirds of the explainable phenotype variance, while pairwise epistasis explains about 7% of the variance for the full mutagenized sequence and about 15% for the subsequence associated with protein binding sites. Surprisingly, there is no evidence for third order epistatic contributions, and our inferred fitness landscape is essentially single peaked, with a small amount of antagonistic epistasis. We identify transcription factor (CRP) and RNA polymerase binding sites in the promotor region and their interactions. We conclude with a cautionary note that inferred properties of fitness landscapes may be severely influenced by biases in the sequence data. Funded in part by HFSP and James S. McDonnell Foundation.

In silico modelling of directed evolution: Implications for experimental design and stepwise evolution.

PubMed

Wedge, David C; Rowe, William; Kell, Douglas B; Knowles, Joshua

2009-03-07

We model the process of directed evolution (DE) in silico using genetic algorithms. Making use of the NK fitness landscape model, we analyse the effects of mutation rate, crossover and selection pressure on the performance of DE. A range of values of K, the epistatic interaction of the landscape, are considered, and high- and low-throughput modes of evolution are compared. Our findings suggest that for runs of or around ten generations' duration-as is typical in DE-there is little difference between the way in which DE needs to be configured in the high- and low-throughput regimes, nor across different degrees of landscape epistasis. In all cases, a high selection pressure (but not an extreme one) combined with a moderately high mutation rate works best, while crossover provides some benefit but only on the less rugged landscapes. These genetic algorithms were also compared with a "model-based approach" from the literature, which uses sequential fixing of the problem parameters based on fitting a linear model. Overall, we find that purely evolutionary techniques fare better than do model-based approaches across all but the smoothest landscapes.

Adaptation of Bird Communities to Farmland Abandonment in a Mountain Landscape

PubMed Central

Guilherme, João Lopes; Miguel Pereira, Henrique

2013-01-01

Widespread farmland abandonment has led to significant landscape transformations of many European mountain areas. These semi-natural multi-habitat landscapes are important reservoirs of biodiversity and their abandonment has important conservation implications. In multi-habitat landscapes the adaptation of communities depends on the differential affinity of the species to the available habitats. We use nested species-area relationships (SAR) to model species richness patterns of bird communities across scales in a mountain landscape, in NW Portugal. We compare the performance of the classic-SAR and the countryside-SAR (i.e. multi-habitat) models at the landscape scale, and compare species similarity decay (SSD) at the regional scale. We find a considerable overlap of bird communities in the different land-uses (farmland, shrubland and oak forest) at the landscape scale. Analysis of the classic and countryside SAR show that specialist species are strongly related to their favourite habitat. Farmland and shrubland have higher regional SSD compared to oak forests. However, this is due to the opportunistic use of farmlands by generalist birds. Forest specialists display significant regional turnover in oak forest. Overall, the countryside-SAR model had a better fit to the data showing that habitat composition determines species richness across scales. Finally, we use the countryside-SAR model to forecast bird diversity under four scenarios of land-use change. Farmland abandonment scenarios show little impact on bird diversity as the model predicts that the complete loss of farmland is less dramatic, in terms of species diversity loss, than the disappearance of native Galicio-Portuguese oak forest. The affinities of species to non-preferred habitats suggest that bird communities can adapt to land-use changes derived from farmland abandonment. Based on model predictions we argue that rewilding may be a suitable management option for many European mountain areas. PMID:24023892

Genome-Enabled Modeling of Biogeochemical Processes Predicts Metabolic Dependencies that Connect the Relative Fitness of Microbial Functional Guilds

NASA Astrophysics Data System (ADS)

Brodie, E.; King, E.; Molins, S.; Karaoz, U.; Steefel, C. I.; Banfield, J. F.; Beller, H. R.; Anantharaman, K.; Ligocki, T. J.; Trebotich, D.

2015-12-01

Pore-scale processes mediated by microorganisms underlie a range of critical ecosystem services, regulating carbon stability, nutrient flux, and the purification of water. Advances in cultivation-independent approaches now provide us with the ability to reconstruct thousands of genomes from microbial populations from which functional roles may be assigned. With this capability to reveal microbial metabolic potential, the next step is to put these microbes back where they belong to interact with their natural environment, i.e. the pore scale. At this scale, microorganisms communicate, cooperate and compete across their fitness landscapes with communities emerging that feedback on the physical and chemical properties of their environment, ultimately altering the fitness landscape and selecting for new microbial communities with new properties and so on. We have developed a trait-based model of microbial activity that simulates coupled functional guilds that are parameterized with unique combinations of traits that govern fitness under dynamic conditions. Using a reactive transport framework, we simulate the thermodynamics of coupled electron donor-acceptor reactions to predict energy available for cellular maintenance, respiration, biomass development, and enzyme production. From metagenomics, we directly estimate some trait values related to growth and identify the linkage of key traits associated with respiration and fermentation, macromolecule depolymerizing enzymes, and other key functions such as nitrogen fixation. Our simulations were carried out to explore abiotic controls on community emergence such as seasonally fluctuating water table regimes across floodplain organic matter hotspots. Simulations and metagenomic/metatranscriptomic observations highlighted the many dependencies connecting the relative fitness of functional guilds and the importance of chemolithoautotrophic lifestyles. Using an X-Ray microCT-derived soil microaggregate physical model combined with genome-enabled reactive flow and transport we simulated the importance of pore network properties including connectivity in regulating metabolic interdependencies between microbial functional guilds.

Beyond the conventional: meeting the challenges of landscape governance within the European Landscape Convention?

PubMed

Scott, Alister

2011-10-01

Academics and policy makers seeking to deconstruct landscape face major challenges conceptually, methodologically and institutionally. The meaning(s), identity(ies) and management of landscape are controversial and contested. The European Landscape Convention provides an opportunity for action and change set within new governance agendas addressing interdisciplinarity and spatial planning. This paper critically reviews the complex web of conceptual and methodological frameworks that characterise landscape planning and management and then focuses on emerging landscape governance in Scotland within a mixed method approach involving policy analyses, semi-structured interviews and best practice case studies. Using Dower's (2008) criteria from the Articles of the European Landscape Convention, the results show that whilst some progress has been made in landscape policy and practice, largely through the actions of key individuals and champions, there are significant institutional hurdles and resource limitations to overcome. The need to mainstream positive landscape outcomes requires a significant culture change where a one-size-fits-all approach does not work. Copyright © 2011 Elsevier Ltd. All rights reserved.

Floral Resource Competition Between Honey Bees and Wild Bees: Is There Clear Evidence and Can We Guide Management and Conservation?

PubMed

Wojcik, Victoria A; Morandin, Lora A; Davies Adams, Laurie; Rourke, Kelly E

2018-06-05

Supporting managed honey bees by pasturing in natural landscapes has come under review due to concerns that honey bees could negatively impact the survival of wild bees through competition for floral resources. Critique and assessment of the existing body of published literature against our criteria focussing on studies that can support best management resulted in 19 experimental papers. Indirect measures of competition examining foraging patterns and behavior yielded equivocal results. Direct measures of reproduction and growth were investigated in only seven studies, with six indicating negative impacts to wild bees from the presence of managed honey bees. Three of these studies examined fitness impacts to BombusLatreille and all three indicated reduced growth or reduced reproductive output. Because there is a severe lack of literature, yet potential that honey bee presence could negatively impact wild bees, exemplified with bumble bee studies, we advocate for further research into the fitness impacts of competition between managed and wild pollinators. Conservative approaches should be taken with respect to pasturing honey bees on natural lands with sensitive bumble bee populations. Correspondingly, forage opportunities for honey bees in managed, agricultural landscapes, should be increased in an effort to reduce potential pressure and infringement on wild bee populations in natural areas.

Empirical fitness models for hepatitis C virus immunogen design

NASA Astrophysics Data System (ADS)

Hart, Gregory R.; Ferguson, Andrew L.

2015-12-01

Hepatitis C virus (HCV) afflicts 170 million people worldwide, 2%-3% of the global population, and kills 350 000 each year. Prophylactic vaccination offers the most realistic and cost effective hope of controlling this epidemic in the developing world where expensive drug therapies are not available. Despite 20 years of research, the high mutability of the virus and lack of knowledge of what constitutes effective immune responses have impeded development of an effective vaccine. Coupling data mining of sequence databases with spin glass models from statistical physics, we have developed a computational approach to translate clinical sequence databases into empirical fitness landscapes quantifying the replicative capacity of the virus as a function of its amino acid sequence. These landscapes explicitly connect viral genotype to phenotypic fitness, and reveal vulnerable immunological targets within the viral proteome that can be exploited to rationally design vaccine immunogens. We have recovered the empirical fitness landscape for the HCV RNA-dependent RNA polymerase (protein NS5B) responsible for viral genome replication, and validated the predictions of our model by demonstrating excellent accord with experimental measurements and clinical observations. We have used our landscapes to perform exhaustive in silico screening of 16.8 million T-cell immunogen candidates to identify 86 optimal formulations. By reducing the search space of immunogen candidates by over five orders of magnitude, our approach can offer valuable savings in time, expense, and labor for experimental vaccine development and accelerate the search for a HCV vaccine. Abbreviations: HCV—hepatitis C virus, HLA—human leukocyte antigen, CTL—cytotoxic T lymphocyte, NS5B—nonstructural protein 5B, MSA—multiple sequence alignment, PEG-IFN—pegylated interferon.

Adaptive Evolution under Extreme Genetic Drift in Oxidatively Stressed Caenorhabditis elegans

PubMed Central

Christy, Stephen F; Wernick, Riana I; Lue, Michael J; Velasco, Griselda; Howe, Dana K; Denver, Dee R

2017-01-01

Abstract A mutation-accumulation (MA) experiment with Caenorhabditis elegans nematodes was conducted in which replicate, independently evolving lines were initiated from a low-fitness mitochondrial electron transport chain mutant, gas-1. The original intent of the study was to assess the effect of electron transport chain dysfunction involving elevated reactive oxygen species production on patterns of spontaneous germline mutation. In contrast to results of standard MA experiments, gas-1 MA lines evolved slightly higher mean fitness alongside reduced among-line genetic variance compared with their ancestor. Likewise, the gas-1 MA lines experienced partial recovery to wildtype reactive oxygen species levels. Whole-genome sequencing and analysis revealed that the molecular spectrum but not the overall rate of nuclear DNA mutation differed from wildtype patterns. Further analysis revealed an enrichment of mutations in loci that occur in a gas-1-centric region of the C. elegans interactome, and could be classified into a small number of functional-genomic categories. Characterization of a backcrossed four-mutation set isolated from one gas-1 MA line revealed this combination to be beneficial on both gas-1 mutant and wildtype genetic backgrounds. Our combined results suggest that selection favoring beneficial mutations can be powerful even under unfavorable population genetic conditions, and agree with fitness landscape theory predicting an inverse relationship between population fitness and the likelihood of adaptation. PMID:29069345

Modelling the Evolution of Social Structure

PubMed Central

Sutcliffe, A. G.; Dunbar, R. I. M.; Wang, D.

2016-01-01

Although simple social structures are more common in animal societies, some taxa (mainly mammals) have complex, multi-level social systems, in which the levels reflect differential association. We develop a simulation model to explore the conditions under which multi-level social systems of this kind evolve. Our model focuses on the evolutionary trade-offs between foraging and social interaction, and explores the impact of alternative strategies for distributing social interaction, with fitness criteria for wellbeing, alliance formation, risk, stress and access to food resources that reward social strategies differentially. The results suggest that multi-level social structures characterised by a few strong relationships, more medium ties and large numbers of weak ties emerge only in a small part of the overall fitness landscape, namely where there are significant fitness benefits from wellbeing and alliance formation and there are high levels of social interaction. In contrast, ‘favour-the-few’ strategies are more competitive under a wide range of fitness conditions, including those producing homogeneous, single-level societies of the kind found in many birds and mammals. The simulations suggest that the development of complex, multi-level social structures of the kind found in many primates (including humans) depends on a capacity for high investment in social time, preferential social interaction strategies, high mortality risk and/or differential reproduction. These conditions are characteristic of only a few mammalian taxa. PMID:27427758

Panmictic and Clonal Evolution on a Single Patchy Resource Produces Polymorphic Foraging Guilds

PubMed Central

Getz, Wayne M.; Salter, Richard; Lyons, Andrew J.; Sippl-Swezey, Nicolas

2015-01-01

We develop a stochastic, agent-based model to study how genetic traits and experiential changes in the state of agents and available resources influence individuals’ foraging and movement behaviors. These behaviors are manifest as decisions on when to stay and exploit a current resource patch or move to a particular neighboring patch, based on information of the resource qualities of the patches and the anticipated level of intraspecific competition within patches. We use a genetic algorithm approach and an individual’s biomass as a fitness surrogate to explore the foraging strategy diversity of evolving guilds under clonal versus hermaphroditic sexual reproduction. We first present the resource exploitation processes, movement on cellular arrays, and genetic algorithm components of the model. We then discuss their implementation on the Nova software platform. This platform seamlessly combines the dynamical systems modeling of consumer-resource interactions with agent-based modeling of individuals moving over a landscapes, using an architecture that lays transparent the following four hierarchical simulation levels: 1.) within-patch consumer-resource dynamics, 2.) within-generation movement and competition mitigation processes, 3.) across-generation evolutionary processes, and 4.) multiple runs to generate the statistics needed for comparative analyses. The focus of our analysis is on the question of how the biomass production efficiency and the diversity of guilds of foraging strategy types, exploiting resources over a patchy landscape, evolve under clonal versus random hermaphroditic sexual reproduction. Our results indicate greater biomass production efficiency under clonal reproduction only at higher population densities, and demonstrate that polymorphisms evolve and are maintained under random mating systems. The latter result questions the notion that some type of associative mating structure is needed to maintain genetic polymorphisms among individuals exploiting a common patchy resource on an otherwise spatially homogeneous landscape. PMID:26274613

HIV-1 epitopes presented by MHC class I types associated with superior immune containment of viremia have highly constrained fitness landscapes.

PubMed

Gorin, Aleksandr M; Du, Yushen; Liu, Franklin Y; Zhang, Tian-Hao; Ng, Hwee L; Hofmann, Christian; Cumberland, William G; Sun, Ren; Yang, Otto O

2017-08-01

Certain Major Histocompatibility-I (MHC-I) types are associated with superior immune containment of HIV-1 infection by CD8+ cytotoxic T lymphocytes (CTLs), but the mechanisms mediating this containment are difficult to elucidate in vivo. Here we provide controlled assessments of fitness landscapes and CTL-imposed constraints for immunodominant epitopes presented by two protective (B*57 and B*27) and one non-protective (A*02) MHC-I types. Libraries of HIV-1 with saturation mutagenesis of CTL epitopes are propagated with and without CTL selective pressure to define the fitness landscapes for epitope mutation and escape from CTLs via deep sequencing. Immunodominant B*57- and B*27- present epitopes are highly limited in options for fit mutations, with most viable variants recognizable by CTLs, whereas an immunodominant A*02 epitope-presented is highly permissive for mutation, with many options for CTL evasion without loss of viability. Generally, options for evasion overlap considerably between CTL clones despite highly distinct T cell receptors. Finally, patterns of variant recognition suggest population-wide CTL selection for the A*02-presented epitope. Overall, these findings indicate that these protective MHC-I types yield CTL targeting of highly constrained epitopes, and underscore the importance of blocking public escape pathways for CTL-based interventions against HIV-1.

A Systematic Survey of an Intragenic Epistatic Landscape

PubMed Central

Bank, Claudia; Hietpas, Ryan T.; Jensen, Jeffrey D.; Bolon, Daniel N.A.

2015-01-01

Mutations are the source of evolutionary variation. The interactions of multiple mutations can have important effects on fitness and evolutionary trajectories. We have recently described the distribution of fitness effects of all single mutations for a nine-amino-acid region of yeast Hsp90 (Hsp82) implicated in substrate binding. Here, we report and discuss the distribution of intragenic epistatic effects within this region in seven Hsp90 point mutant backgrounds of neutral to slightly deleterious effect, resulting in an analysis of more than 1,000 double mutants. We find negative epistasis between substitutions to be common, and positive epistasis to be rare—resulting in a pattern that indicates a drastic change in the distribution of fitness effects one step away from the wild type. This can be well explained by a concave relationship between phenotype and genotype (i.e., a concave shape of the local fitness landscape), suggesting mutational robustness intrinsic to the local sequence space. Structural analyses indicate that, in this region, epistatic effects are most pronounced when a solvent-inaccessible position is involved in the interaction. In contrast, all 18 observations of positive epistasis involved at least one mutation at a solvent-exposed position. By combining the analysis of evolutionary and biophysical properties of an epistatic landscape, these results contribute to a more detailed understanding of the complexity of protein evolution. PMID:25371431

Exploring Connectivity in Sequence Space of Functional RNA

NASA Technical Reports Server (NTRS)

Wei, Chenyu; Pohorille, Andrzej; Popovic, Milena; Ditzler, Mark

2017-01-01

Emergence of replicable genetic molecules was one of the marking points in the origin of life, evolution of which can be conceptualized as a walk through the space of all possible sequences. A theoretical concept of fitness landscape helps to understand evolutionary processes through assigning a value of fitness to each genotype. Then, evolution of a phenotype is viewed as a series of consecutive, single-point mutations. Natural selection biases evolution toward peaks of high fitness and away from valleys of low fitness. whereas neutral drift occurs in the sequence space without direction as mutations are introduced at random. Large networks of neutral or near-neutral mutations on a fitness landscape, especially for sufficiently long genomes, are possible or even inevitable. Their detection in experiments, however, has been elusive. Although a few near-neutral evolutionary pathways have been found, recent experimental evidence indicates landscapes consist of largely isolated islands. The generality of these results, however, is not clear, as the genome length or the fraction of functional molecules in the genotypic space might have been insufficient for the emergence of large, neutral networks. Thorough investigation on the structure of the fitness landscape is essential to understand the mechanisms of evolution of early genomes. RNA molecules are commonly assumed to play the pivotal role in the origin of genetic systems. They are widely believed to be early, if not the earliest, genetic and catalytic molecules, with abundant biochemical activities as aptamers and ribozymes, i.e. RNA molecules capable, respectively, to bind small molecules or catalyze chemical reactions. Here, we present results of our recent studies on the structure of the sequence space of RNA ligase ribozymes selected through in vitro evolution. Several hundred thousands of sequences active to a different degree were obtained by way of deep sequencing. Analysis of these sequences revealed several large clusters defined such that every sequence in a cluster can be reached from any other sequence in the same cluster through a series of single point mutations. Sequences in a single cluster appear to adopt more than one secondary structure. The mechanism of refolding within a single cluster was examined. To shed light on possible evolutionary paths in the space of ribozymes, the connectivity between clusters was investigated. The effect of length of RNA molecules on the structure of the fitness landscape and possible evolutionary paths was examined by way of comparing functional sequences of 20 and 80 nucleobases in length. It was found that sequences of different lengths shared secondary structure motifs that were presumed responsible for catalytic activity, with increasing complexity and global structural rearrangements emerging in longer molecules.

Can spatial statistical river temperature models be transferred between catchments?

NASA Astrophysics Data System (ADS)

Jackson, Faye L.; Fryer, Robert J.; Hannah, David M.; Malcolm, Iain A.

2017-09-01

There has been increasing use of spatial statistical models to understand and predict river temperature (Tw) from landscape covariates. However, it is not financially or logistically feasible to monitor all rivers and the transferability of such models has not been explored. This paper uses Tw data from four river catchments collected in August 2015 to assess how well spatial regression models predict the maximum 7-day rolling mean of daily maximum Tw (Twmax) within and between catchments. Models were fitted for each catchment separately using (1) landscape covariates only (LS models) and (2) landscape covariates and an air temperature (Ta) metric (LS_Ta models). All the LS models included upstream catchment area and three included a river network smoother (RNS) that accounted for unexplained spatial structure. The LS models transferred reasonably to other catchments, at least when predicting relative levels of Twmax. However, the predictions were biased when mean Twmax differed between catchments. The RNS was needed to characterise and predict finer-scale spatially correlated variation. Because the RNS was unique to each catchment and thus non-transferable, predictions were better within catchments than between catchments. A single model fitted to all catchments found no interactions between the landscape covariates and catchment, suggesting that the landscape relationships were transferable. The LS_Ta models transferred less well, with particularly poor performance when the relationship with the Ta metric was physically implausible or required extrapolation outside the range of the data. A single model fitted to all catchments found catchment-specific relationships between Twmax and the Ta metric, indicating that the Ta metric was not transferable. These findings improve our understanding of the transferability of spatial statistical river temperature models and provide a foundation for developing new approaches for predicting Tw at unmonitored locations across multiple catchments and larger spatial scales.

Motion of a Janus particle very near a wall

NASA Astrophysics Data System (ADS)

Rashidi, Aidin; Wirth, Christopher L.

2017-12-01

This article describes the simulated Brownian motion of a sphere comprising hemispheres of unequal zeta potential (i.e., "Janus" particle) very near a wall. The simulation tool was developed and used to assist in the methodology development for applying Total Internal Reflection Microscopy (TIRM) to anisotropic particles. Simulations of the trajectory of a Janus sphere with cap density matching that of the base particle very near a boundary were used to construct 3D potential energy landscapes that were subsequently used to infer particle and solution properties, as would be done in a TIRM measurement. Results showed that the potential energy landscape of a Janus sphere has a transition region at the location of the boundary between the two Janus halves, which depended on the relative zeta potential magnitude. The potential energy landscape was fit to accurately obtain the zeta potential of each hemisphere, particle size, minimum potential energy position and electrolyte concentration, or Debye length. We also determined the appropriate orientation bin size and regimes over which the potential energy landscape should be fit to obtain system properties. Our simulations showed that an experiment may require more than 106 observations to obtain a suitable potential energy landscape as a consequence of the multivariable nature of observations for an anisotropic particle. These results illustrate important considerations for conducting TIRM for anisotropic particles.

Fitness landscapes, heuristics and technological paradigms: A critique on random search models in evolutionary economics

NASA Astrophysics Data System (ADS)

Frenken, Koen

2001-06-01

The biological evolution of complex organisms, in which the functioning of genes is interdependent, has been analyzed as "hill-climbing" on NK fitness landscapes through random mutation and natural selection. In evolutionary economics, NK fitness landscapes have been used to simulate the evolution of complex technological systems containing elements that are interdependent in their functioning. In these models, economic agents randomly search for new technological design by trial-and-error and run the risk of ending up in sub-optimal solutions due to interdependencies between the elements in a complex system. These models of random search are legitimate for reasons of modeling simplicity, but remain limited as these models ignore the fact that agents can apply heuristics. A specific heuristic is one that sequentially optimises functions according to their ranking by users of the system. To model this heuristic, a generalized NK-model is developed. In this model, core elements that influence many functions can be distinguished from peripheral elements that affect few functions. The concept of paradigmatic search can then be analytically defined as search that leaves core elements in tact while concentrating on improving functions by mutation of peripheral elements.

Predation-related costs and benefits of conspecific attraction in songbirds--an agent-based approach.

PubMed

Szymkowiak, Jakub; Kuczyński, Lechosław

2015-01-01

Songbirds that follow a conspecific attraction strategy in the habitat selection process prefer to settle in habitat patches already occupied by other individuals. This largely affects the patterns of their spatio-temporal distribution and leads to clustered breeding. Although making informed settlement decisions is expected to be beneficial for individuals, such territory clusters may potentially provide additional fitness benefits (e.g., through the dilution effect) or costs (e.g., possibly facilitating nest localization if predators respond functionally to prey distribution). Thus, we hypothesized that the fitness consequences of following a conspecific attraction strategy may largely depend on the composition of the predator community. We developed an agent-based model in which we simulated the settling behavior of birds that use a conspecific attraction strategy and breed in a multi-predator landscape with predators that exhibited different foraging strategies. Moreover, we investigated whether Bayesian updating of prior settlement decisions according to the perceived predation risk may improve the fitness of birds that rely on conspecific cues. Our results provide evidence that the fitness consequences of conspecific attraction are predation-related. We found that in landscapes dominated by predators able to respond functionally to prey distribution, clustered breeding led to fitness costs. However, this cost could be reduced if birds performed Bayesian updating of prior settlement decisions and perceived nesting with too many neighbors as a threat. Our results did not support the hypothesis that in landscapes dominated by incidental predators, clustered breeding as a byproduct of conspecific attraction provides fitness benefits through the dilution effect. We suggest that this may be due to the spatial scale of songbirds' aggregative behavior. In general, we provide evidence that when considering the fitness consequences of conspecific attraction for songbirds, one should expect a trade-off between the benefits of making informed decisions and the costs of clustering.

Predation-Related Costs and Benefits of Conspecific Attraction in Songbirds—An Agent-Based Approach

PubMed Central

Szymkowiak, Jakub; Kuczyński, Lechosław

2015-01-01

Songbirds that follow a conspecific attraction strategy in the habitat selection process prefer to settle in habitat patches already occupied by other individuals. This largely affects the patterns of their spatio-temporal distribution and leads to clustered breeding. Although making informed settlement decisions is expected to be beneficial for individuals, such territory clusters may potentially provide additional fitness benefits (e.g., through the dilution effect) or costs (e.g., possibly facilitating nest localization if predators respond functionally to prey distribution). Thus, we hypothesized that the fitness consequences of following a conspecific attraction strategy may largely depend on the composition of the predator community. We developed an agent-based model in which we simulated the settling behavior of birds that use a conspecific attraction strategy and breed in a multi-predator landscape with predators that exhibited different foraging strategies. Moreover, we investigated whether Bayesian updating of prior settlement decisions according to the perceived predation risk may improve the fitness of birds that rely on conspecific cues. Our results provide evidence that the fitness consequences of conspecific attraction are predation-related. We found that in landscapes dominated by predators able to respond functionally to prey distribution, clustered breeding led to fitness costs. However, this cost could be reduced if birds performed Bayesian updating of prior settlement decisions and perceived nesting with too many neighbors as a threat. Our results did not support the hypothesis that in landscapes dominated by incidental predators, clustered breeding as a byproduct of conspecific attraction provides fitness benefits through the dilution effect. We suggest that this may be due to the spatial scale of songbirds’ aggregative behavior. In general, we provide evidence that when considering the fitness consequences of conspecific attraction for songbirds, one should expect a trade-off between the benefits of making informed decisions and the costs of clustering. PMID:25790479

Rational evolutionary design: the theory of in vitro protein evolution.

PubMed

Voigt, C A; Kauffman, S; Wang, Z G

2000-01-01

Directed evolution uses a combination of powerful search techniques to generate proteins with improved properties. Part of the success is due to the stochastic element of random mutagenesis; improvements can be made without a detailed description of the complex interactions that constitute function or stability. However, optimization is not a conglomeration of random processes. Rather, it requires both knowledge of the system that is being optimized and a logical series of techniques that best explores the pathways of evolution (Eigen et al., 1988). The weighing of parameters associated with mutation, recombination, and screening to achieve the maximum fitness improvement is the beginning of rational evolutionary design. The optimal mutation rate is strongly influenced by the finite number of mutants that can be screened. A smooth fitness landscape implies that many mutations can be accumulated without disrupting the fitness. This has the effect of lowering the required library size to sample a higher mutation rate. As the sequence ascends the fitness landscape, the optimal mutation rate decreases as the probability of discovering improved mutations also decreases. Highly coupled regions require that many mutations be simultaneously made to generate a positive mutant. Therefore, positive mutations are discovered at uncoupled positions as the fitness of the parent increases. The benefit of recombination is twofold: it combines good mutations and searches more sequence space in a meaningful way. Recombination is most beneficial when the number of mutants that can be screened is limited and the landscape is of an intermediate ruggedness. The structure of schema in proteins leads to the conclusion that many cut points are required. The number of parents and their sequence identity are determined by the balance between exploration and exploitation. Many disparate parents can explore more space, but at the risk of losing information. The required screening effort is related to the number of uphill paths, which decreases more rapidly for rugged landscapes. Noise in the fitness measurements causes a dramatic increase in the required mutant library size, thus implying a smaller optimal mutation rate. Because of strict limitations on the number of mutants that can be screened, there is motivation to optimize the content of the mutant library. By restricting mutations to regions of the gene that are expected to show improvement, a greater return can be made with the same number of mutants. Initial studies with subtilisin E have shown that structurally tolerant positions tend to be where positive activity mutants are made during directed evolution. Mutant fitness information is produced by the screening step that has the potential to provide insight into the structure of the fitness landscape, thus aiding the setting of experimental parameters. By analyzing the mutant fitness distribution and targeting specific regions of the sequence, in vitro evolution can be accelerated. However, when expediting the search, there is a trade-off between rapid improvement and the quality of the long-term solution. The benefit of neutrality has yet to be captured with in vitro protein evolution. Neutral theory predicts the punctuated emergence of novel structure and function, however, with current methods, the required time scale is not feasible. Utilizing neutral evolution to accelerate the discovery of new functional and structural solutions requires a theory that predicts the behavior of mutational pathways between networks. Because the transition from neutral to adaptive evolution requires a multi-mutational switch, increasing the mutation rate decreases the time required for a punctuated change to occur. By limiting the search to the less coupled region of the sequence (smooth portion of the fitness landscape), the required larger mutation rate can be tolerated. Advances in directed evolution will be achieved when the driving forces behind such proce

Crossing fitness canyons by a finite population

NASA Astrophysics Data System (ADS)

Saakian, David B.; Bratus, Alexander S.; Hu, Chin-Kun

2017-06-01

We consider the Wright-Fisher model of the finite population evolution on a fitness landscape defined in the sequence space by a path of nearly neutral mutations. We study a specific structure of the fitness landscape: One of the intermediate mutations on the mutation path results in either a large fitness value (climbing up a fitness hill) or a low fitness value (crossing a fitness canyon), the rest of the mutations besides the last one are neutral, and the last sequence has much higher fitness than any intermediate sequence. We derive analytical formulas for the first arrival time of the mutant with two point mutations. For the first arrival problem for the further mutants in the case of canyon crossing, we analytically deduce how the mean first arrival time scales with the population size and fitness difference. The location of the canyon on the path of sequences has a crucial role. If the canyon is at the beginning of the path, then it significantly prolongs the first arrival time; otherwise it just slightly changes it. Furthermore, the fitness hill at the beginning of the path strongly prolongs the arrival time period; however, the hill located near the end of the path shortens it. We optimize the first arrival time by applying a nonzero selection to the intermediate sequences. We extend our results and provide a scaling for the valley crossing time via the depth of the canyon and population size in the case of a fitness canyon at the first position. Our approach is useful for understanding some complex evolution systems, e.g., the evolution of cancer.

Visualisation of Lines of Best Fit

ERIC Educational Resources Information Center

Rudziewicz, Michael; Bossé, Michael J.; Marland, Eric S.; Rhoads, Gregory S.

2017-01-01

Humans possess a remarkable ability to recognise both simple patterns such as shapes and handwriting and very complex patterns such as faces and landscapes. To investigate one small aspect of human pattern recognition, in this study participants position lines of "best fit" to two-dimensional scatter plots of data. The study investigates…

Neuronal boost to evolutionary dynamics.

PubMed

de Vladar, Harold P; Szathmáry, Eörs

2015-12-06

Standard evolutionary dynamics is limited by the constraints of the genetic system. A central message of evolutionary neurodynamics is that evolutionary dynamics in the brain can happen in a neuronal niche in real time, despite the fact that neurons do not reproduce. We show that Hebbian learning and structural synaptic plasticity broaden the capacity for informational replication and guided variability provided a neuronally plausible mechanism of replication is in place. The synergy between learning and selection is more efficient than the equivalent search by mutation selection. We also consider asymmetric landscapes and show that the learning weights become correlated with the fitness gradient. That is, the neuronal complexes learn the local properties of the fitness landscape, resulting in the generation of variability directed towards the direction of fitness increase, as if mutations in a genetic pool were drawn such that they would increase reproductive success. Evolution might thus be more efficient within evolved brains than among organisms out in the wild.

Geospatial Analysis of Atmospheric Haze Effect by Source and Sink Landscape

NASA Astrophysics Data System (ADS)

Yu, T.; Xu, K.; Yuan, Z.

2017-09-01

Based on geospatial analysis model, this paper analyzes the relationship between the landscape patterns of source and sink in urban areas and atmospheric haze pollution. Firstly, the classification result and aerosol optical thickness (AOD) of Wuhan are divided into a number of square grids with the side length of 6 km, and the category level landscape indices (PLAND, PD, COHESION, LPI, FRAC_MN) and AOD of each grid are calculated. Then the source and sink landscapes of atmospheric haze pollution are selected based on the analysis of the correlation between landscape indices and AOD. Next, to make the following analysis more efficient, the indices selected before should be determined through the correlation coefficient between them. Finally, due to the spatial dependency and spatial heterogeneity of the data used in this paper, spatial autoregressive model and geo-weighted regression model are used to analyze atmospheric haze effect by source and sink landscape from the global and local level. The results show that the source landscape of atmospheric haze pollution is the building, and the sink landscapes are shrub and woodland. PLAND, PD and COHESION are suitable for describing the atmospheric haze effect by source and sink landscape. Comparing these models, the fitting effect of SLM, SEM and GWR is significantly better than that of OLS model. The SLM model is superior to the SEM model in this paper. Although the fitting effect of GWR model is more unsuited than that of SLM, the influence degree of influencing factors on atmospheric haze of different geography can be expressed clearer. Through the analysis results of these models, following conclusions can be summarized: Reducing the proportion of source landscape area and increasing the degree of fragmentation could cut down aerosol optical thickness; And distributing the source and sink landscape evenly and interspersedly could effectively reduce aerosol optical thickness which represents atmospheric haze pollution; For Wuhan City, the method of adjusting the built-up area slightly and planning the non-built-up areas reasonably can be taken to reduce atmospheric haze pollution.

Linear algebra of the permutation invariant Crow-Kimura model of prebiotic evolution.

PubMed

Bratus, Alexander S; Novozhilov, Artem S; Semenov, Yuri S

2014-10-01

A particular case of the famous quasispecies model - the Crow-Kimura model with a permutation invariant fitness landscape - is investigated. Using the fact that the mutation matrix in the case of a permutation invariant fitness landscape has a special tridiagonal form, a change of the basis is suggested such that in the new coordinates a number of analytical results can be obtained. In particular, using the eigenvectors of the mutation matrix as the new basis, we show that the quasispecies distribution approaches a binomial one and give simple estimates for the speed of convergence. Another consequence of the suggested approach is a parametric solution to the system of equations determining the quasispecies. Using this parametric solution we show that our approach leads to exact asymptotic results in some cases, which are not covered by the existing methods. In particular, we are able to present not only the limit behavior of the leading eigenvalue (mean population fitness), but also the exact formulas for the limit quasispecies eigenvector for special cases. For instance, this eigenvector has a geometric distribution in the case of the classical single peaked fitness landscape. On the biological side, we propose a mathematical definition, based on the closeness of the quasispecies to the binomial distribution, which can be used as an operational definition of the notorious error threshold. Using this definition, we suggest two approximate formulas to estimate the critical mutation rate after which the quasispecies delocalization occurs. Copyright © 2014 Elsevier Inc. All rights reserved.

Impact of centrality on cooperative processes

NASA Astrophysics Data System (ADS)

Reia, Sandro M.; Herrmann, Sebastian; Fontanari, José F.

2017-02-01

The solution of today's complex problems requires the grouping of task forces whose members are usually connected remotely over long physical distances and different time zones. Hence, understanding the effects of imposed communication patterns (i.e., who can communicate with whom) on group performance is important. Here we use an agent-based model to explore the influence of the betweenness centrality of the nodes on the time the group requires to find the global maxima of NK-fitness landscapes. The agents cooperate by broadcasting messages, informing on their fitness to their neighbors, and use this information to copy the more successful agents in their neighborhood. We find that for easy tasks (smooth landscapes), the topology of the communication network has no effect on the performance of the group, and that the more central nodes are the most likely to find the global maximum first. For difficult tasks (rugged landscapes), however, we find a positive correlation between the variance of the betweenness among the network nodes and the group performance. For these tasks, the performances of individual nodes are strongly influenced by the agents' dispositions to cooperate and by the particular realizations of the rugged landscapes.

Hyperspace geography: visualizing fitness landscapes beyond 4D.

PubMed

Wiles, Janet; Tonkes, Bradley

2006-01-01

Human perception is finely tuned to extract structure about the 4D world of time and space as well as properties such as color and texture. Developing intuitions about spatial structure beyond 4D requires exploiting other perceptual and cognitive abilities. One of the most natural ways to explore complex spaces is for a user to actively navigate through them, using local explorations and global summaries to develop intuitions about structure, and then testing the developing ideas by further exploration. This article provides a brief overview of a technique for visualizing surfaces defined over moderate-dimensional binary spaces, by recursively unfolding them onto a 2D hypergraph. We briefly summarize the uses of a freely available Web-based visualization tool, Hyperspace Graph Paper (HSGP), for exploring fitness landscapes and search algorithms in evolutionary computation. HSGP provides a way for a user to actively explore a landscape, from simple tasks such as mapping the neighborhood structure of different points, to seeing global properties such as the size and distribution of basins of attraction or how different search algorithms interact with landscape structure. It has been most useful for exploring recursive and repetitive landscapes, and its strength is that it allows intuitions to be developed through active navigation by the user, and exploits the visual system's ability to detect pattern and texture. The technique is most effective when applied to continuous functions over Boolean variables using 4 to 16 dimensions.

EVALUATING EFFECTS OF LOW QUALITY HABITATS ON REGIONAL GROWTH IN PEOMYCUS LEUCOPUS: INSIGHTS FROM FIELD-PARAMETERIZED SPATIAL MATRIX MODELS.

EPA Science Inventory

Due to complex population dynamics and source-sink metapopulation processes, animal fitness sometimes varies across landscapes in ways that cannot be deduced from simple density patterns. In this study, we examine spatial patterns in fitness using a combination of intensive fiel...

Modelling and estimating pollen movement in oilseed rape (Brassica napus) at the landscape scale using genetic markers.

PubMed

Devaux, C; Lavigne, C; Austerlitz, F; Klein, E K

2007-02-01

Understanding patterns of pollen movement at the landscape scale is important for establishing management rules following the release of genetically modified (GM) crops. We use here a mating model adapted to cultivated species to estimate dispersal kernels from the genotypes of the progenies of male-sterile plants positioned at different sampling sites within a 10 x 10-km oilseed rape production area. Half of the pollen clouds sampled by the male-sterile plants originated from uncharacterized pollen sources that could consist of both large volunteer and feral populations, and fields within and outside the study area. The geometric dispersal kernel was the most appropriate to predict pollen movement in the study area. It predicted a much larger proportion of long-distance pollination than previously fitted dispersal kernels. This best-fitting mating model underestimated the level of differentiation among pollen clouds but could predict its spatial structure. The estimation method was validated on simulated genotypic data, and proved to provide good estimates of both the shape of the dispersal kernel and the rate and composition of pollen issued from uncharacterized pollen sources. The best dispersal kernel fitted here, the geometric kernel, should now be integrated into models that aim at predicting gene flow at the landscape level, in particular between GM and non-GM crops.

The topology of evolutionary novelty and innovation in macroevolution

PubMed Central

2017-01-01

Sewall Wright's fitness landscape introduced the concept of evolutionary spaces in 1932. George Gaylord Simpson modified this to an adaptive, phenotypic landscape in 1944 and since then evolutionary spaces have played an important role in evolutionary theory through fitness and adaptive landscapes, phenotypic and functional trait spaces, morphospaces and related concepts. Although the topology of such spaces is highly variable, from locally Euclidean to pre-topological, evolutionary change has often been interpreted as a search through a pre-existing space of possibilities, with novelty arising by accessing previously inaccessible or difficult to reach regions of a space. Here I discuss the nature of evolutionary novelty and innovation within the context of evolutionary spaces, and argue that the primacy of search as a conceptual metaphor ignores the generation of new spaces as well as other changes that have played important evolutionary roles. This article is part of the themed issue ‘Process and pattern in innovations from cells to societies’. PMID:29061895

Population size effects in evolutionary dynamics on neutral networks and toy landscapes

NASA Astrophysics Data System (ADS)

Sumedha; Martin, Olivier C.; Peliti, Luca

2007-05-01

We study the dynamics of a population subject to selective pressures, evolving either on RNA neutral networks or on toy fitness landscapes. We discuss the spread and the neutrality of the population in the steady state. Different limits arise depending on whether selection or random drift is dominant. In the presence of strong drift we show that the observables depend mainly on Mμ, M being the population size and μ the mutation rate, while corrections to this scaling go as 1/M: such corrections can be quite large in the presence of selection if there are barriers in the fitness landscape. Also we find that the convergence to the large-Mμ limit is linear in 1/Mμ. Finally we introduce a protocol that minimizes drift; then observables scale like 1/M rather than 1/(Mμ), allowing one to determine the large-M limit more quickly when μ is small; furthermore the genotypic diversity increases from O(lnM) to O(M).

The potential and flux landscape theory of evolution.

PubMed

Zhang, Feng; Xu, Li; Zhang, Kun; Wang, Erkang; Wang, Jin

2012-08-14

We established the potential and flux landscape theory for evolution. We found explicitly the conventional Wright's gradient adaptive landscape based on the mean fitness is inadequate to describe the general evolutionary dynamics. We show the intrinsic potential as being Lyapunov function(monotonically decreasing in time) does exist and can define the adaptive landscape for general evolution dynamics for studying global stability. The driving force determining the dynamics can be decomposed into gradient of potential landscape and curl probability flux. Non-zero flux causes detailed balance breaking and measures how far the evolution from equilibrium state. The gradient of intrinsic potential and curl flux are perpendicular to each other in zero fluctuation limit resembling electric and magnetic forces on electrons. We quantified intrinsic energy, entropy and free energy of evolution and constructed non-equilibrium thermodynamics. The intrinsic non-equilibrium free energy is a Lyapunov function. Both intrinsic potential and free energy can be used to quantify the global stability and robustness of evolution. We investigated an example of three allele evolutionary dynamics with frequency dependent selection (detailed balance broken). We uncovered the underlying single, triple, and limit cycle attractor landscapes. We found quantitative criterions for stability through landscape topography. We also quantified evolution pathways and found paths do not follow potential gradient and are irreversible due to non-zero flux. We generalized the original Fisher's fundamental theorem to the general (i.e., frequency dependent selection) regime of evolution by linking the adaptive rate with not only genetic variance related to the potential but also the flux. We show there is an optimum potential where curl flux resulting from biotic interactions of individuals within a species or between species can sustain an endless evolution even if the physical environment is unchanged. We offer a theoretical basis for explaining the corresponding Red Queen hypothesis proposed by Van Valen. Our work provides a theoretical foundation for evolutionary dynamics.

Energy landscapes for a machine learning application to series data

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ballard, Andrew J.; Stevenson, Jacob D.; Das, Ritankar

2016-03-28

Methods developed to explore and characterise potential energy landscapes are applied to the corresponding landscapes obtained from optimisation of a cost function in machine learning. We consider neural network predictions for the outcome of local geometry optimisation in a triatomic cluster, where four distinct local minima exist. The accuracy of the predictions is compared for fits using data from single and multiple points in the series of atomic configurations resulting from local geometry optimisation and for alternative neural networks. The machine learning solution landscapes are visualised using disconnectivity graphs, and signatures in the effective heat capacity are analysed in termsmore » of distributions of local minima and their properties.« less

Imfit: A Fast, Flexible Program for Astronomical Image Fitting

NASA Astrophysics Data System (ADS)

Erwin, Peter

2014-08-01

Imift is an open-source astronomical image-fitting program specialized for galaxies but potentially useful for other sources, which is fast, flexible, and highly extensible. Its object-oriented design allows new types of image components (2D surface-brightness functions) to be easily written and added to the program. Image functions provided with Imfit include Sersic, exponential, and Gaussian galaxy decompositions along with Core-Sersic and broken-exponential profiles, elliptical rings, and three components that perform line-of-sight integration through 3D luminosity-density models of disks and rings seen at arbitrary inclinations. Available minimization algorithms include Levenberg-Marquardt, Nelder-Mead simplex, and Differential Evolution, allowing trade-offs between speed and decreased sensitivity to local minima in the fit landscape. Minimization can be done using the standard chi^2 statistic (using either data or model values to estimate per-pixel Gaussian errors, or else user-supplied error images) or the Cash statistic; the latter is particularly appropriate for cases of Poisson data in the low-count regime. The C++ source code for Imfit is available under the GNU Public License.

A mathematical model of marine bacteriophage evolution.

PubMed

Pagliarini, Silvia; Korobeinikov, Andrei

2018-03-01

To explore how particularities of a host cell-virus system, and in particular host cell replication, affect viral evolution, in this paper we formulate a mathematical model of marine bacteriophage evolution. The intrinsic simplicity of real-life phage-bacteria systems, and in particular aquatic systems, for which the assumption of homogeneous mixing is well justified, allows for a reasonably simple model. The model constructed in this paper is based upon the Beretta-Kuang model of bacteria-phage interaction in an aquatic environment (Beretta & Kuang 1998 Math. Biosci. 149 , 57-76. (doi:10.1016/S0025-5564(97)10015-3)). Compared to the original Beretta-Kuang model, the model assumes the existence of a multitude of viral variants which correspond to continuously distributed phenotypes. It is noteworthy that the model is mechanistic (at least as far as the Beretta-Kuang model is mechanistic). Moreover, this model does not include any explicit law or mechanism of evolution; instead it is assumed, in agreement with the principles of Darwinian evolution, that evolution in this system can occur as a result of random mutations and natural selection. Simulations with a simplistic linear fitness landscape (which is chosen for the convenience of demonstration only and is not related to any real-life system) show that a pulse-type travelling wave moving towards increasing Darwinian fitness appears in the phenotype space. This implies that the overall fitness of a viral quasi-species steadily increases with time. That is, the simulations demonstrate that for an uneven fitness landscape random mutations combined with a mechanism of natural selection (for this particular system this is given by the conspecific competition for the resource) lead to the Darwinian evolution. It is noteworthy that in this system the speed of propagation of this wave (and hence the rate of evolution) is not constant but varies, depending on the current viral fitness and the abundance of susceptible bacteria. A specific feature of the original Beretta-Kuang model is that this model exhibits a supercritical Hopf bifurcation, leading to the loss of stability and the rise of self-sustained oscillations in the system. This phenomenon corresponds to the paradox of enrichment in the system. It is remarkable that under the conditions that ensure the bifurcation in the Beretta-Kuang model, the viral evolution model formulated in this paper also exhibits a rise in self-sustained oscillations of the abundance of all interacting populations. The propagation of the travelling wave, however, remains stable under these conditions. The only visible impact of the oscillations on viral evolution is a lower speed of the evolution.

Fitness-valley crossing with generalized parent-offspring transmission.

PubMed

Osmond, Matthew M; Otto, Sarah P

2015-11-01

Simple and ubiquitous gene interactions create rugged fitness landscapes composed of coadapted gene complexes separated by "valleys" of low fitness. Crossing such fitness valleys allows a population to escape suboptimal local fitness peaks to become better adapted. This is the premise of Sewall Wright's shifting balance process. Here we generalize the theory of fitness-valley crossing in the two-locus, bi-allelic case by allowing bias in parent-offspring transmission. This generalization extends the existing mathematical framework to genetic systems with segregation distortion and uniparental inheritance. Our results are also flexible enough to provide insight into shifts between alternate stable states in cultural systems with "transmission valleys". Using a semi-deterministic analysis and a stochastic diffusion approximation, we focus on the limiting step in valley crossing: the first appearance of the genotype on the new fitness peak whose lineage will eventually fix. We then apply our results to specific cases of segregation distortion, uniparental inheritance, and cultural transmission. Segregation distortion favouring mutant alleles facilitates crossing most when recombination and mutation are rare, i.e., scenarios where crossing is otherwise unlikely. Interactions with more mutable genes (e.g., uniparental inherited cytoplasmic elements) substantially reduce crossing times. Despite component traits being passed on poorly in the previous cultural background, small advantages in the transmission of a new combination of cultural traits can greatly facilitate a cultural transition. While peak shifts are unlikely under many of the common assumptions of population genetic theory, relaxing some of these assumptions can promote fitness-valley crossing. Copyright © 2015 Elsevier Inc. All rights reserved.

The Fitness Consequences of Aneuploidy Are Driven by Condition-Dependent Gene Effects

PubMed Central

Sunshine, Anna B.; Payen, Celia; Ong, Giang T.; Liachko, Ivan; Tan, Kean Ming; Dunham, Maitreya J.

2015-01-01

Aneuploidy is a hallmark of tumor cells, and yet the precise relationship between aneuploidy and a cell’s proliferative ability, or cellular fitness, has remained elusive. In this study, we have combined a detailed analysis of aneuploid clones isolated from laboratory-evolved populations of Saccharomyces cerevisiae with a systematic, genome-wide screen for the fitness effects of telomeric amplifications to address the relationship between aneuploidy and cellular fitness. We found that aneuploid clones rise to high population frequencies in nutrient-limited evolution experiments and show increased fitness relative to wild type. Direct competition experiments confirmed that three out of four aneuploid events isolated from evolved populations were themselves sufficient to improve fitness. To expand the scope beyond this small number of exemplars, we created a genome-wide collection of >1,800 diploid yeast strains, each containing a different telomeric amplicon (Tamp), ranging in size from 0.4 to 1,000 kb. Using pooled competition experiments in nutrient-limited chemostats followed by high-throughput sequencing of strain-identifying barcodes, we determined the fitness effects of these >1,800 Tamps under three different conditions. Our data revealed that the fitness landscape explored by telomeric amplifications is much broader than that explored by single-gene amplifications. As also observed in the evolved clones, we found the fitness effects of most Tamps to be condition specific, with a minority showing common effects in all three conditions. By integrating our data with previous work that examined the fitness effects of single-gene amplifications genome-wide, we found that a small number of genes within each Tamp are centrally responsible for each Tamp’s fitness effects. Our genome-wide Tamp screen confirmed that telomeric amplifications identified in laboratory-evolved populations generally increased fitness. Our results show that Tamps are mutations that produce large, typically condition-dependent changes in fitness that are important drivers of increased fitness in asexually evolving populations. PMID:26011532

Determining the numbers of a landscape architect species (Tapirus terrestris), using footprints.

PubMed

Moreira, Danielle O; Alibhai, Sky K; Jewell, Zoe C; da Cunha, Cristina J; Seibert, Jardel B; Gatti, Andressa

2018-01-01

As a landscape architect and a major seed disperser, the lowland tapir ( Tapirus terrestris ) is an important indicator of the ecological health of certain habitats. Therefore, reliable data regarding tapir populations are fundamental in understanding ecosystem dynamics, including those associated with the Atlantic Forest in Brazil. Currently, many population monitoring studies use invasive tagging with radio or satellite/Global Positioning System (GPS) collars. These techniques can be costly and unreliable, and the immobilization required carries physiological risks that are undesirable particularly for threatened and elusive species such as the lowland tapir. We collected data from one of the last regions with a viable population of lowland tapir in the south-eastern Atlantic Forest, Brazil, using a new non-invasive method for identifying species, the footprint identification technique (FIT). We identified the minimum number of tapirs in the study area and, in addition, we observed that they have overlapping ranges. Four hundred and forty footprints from 46 trails collected from six locations in the study area in a landscape known to contain tapir were analyzed, and 29 individuals were identified from these footprints. We demonstrate a practical application of FIT for lowland tapir censusing. Our study shows that FIT is an effective method for the identification of individuals of a threatened species, even when they lack visible natural markings on their bodies. FIT offers several benefits over other methods, especially for tapir management. As a non-invasive method, it can be used to census or monitor species, giving rapid feedback to managers of protected areas.

Determining the numbers of a landscape architect species (Tapirus terrestris), using footprints

PubMed Central

da Cunha, Cristina J.

2018-01-01

Background As a landscape architect and a major seed disperser, the lowland tapir (Tapirus terrestris) is an important indicator of the ecological health of certain habitats. Therefore, reliable data regarding tapir populations are fundamental in understanding ecosystem dynamics, including those associated with the Atlantic Forest in Brazil. Currently, many population monitoring studies use invasive tagging with radio or satellite/Global Positioning System (GPS) collars. These techniques can be costly and unreliable, and the immobilization required carries physiological risks that are undesirable particularly for threatened and elusive species such as the lowland tapir. Methods We collected data from one of the last regions with a viable population of lowland tapir in the south-eastern Atlantic Forest, Brazil, using a new non-invasive method for identifying species, the footprint identification technique (FIT). Results We identified the minimum number of tapirs in the study area and, in addition, we observed that they have overlapping ranges. Four hundred and forty footprints from 46 trails collected from six locations in the study area in a landscape known to contain tapir were analyzed, and 29 individuals were identified from these footprints. Discussion We demonstrate a practical application of FIT for lowland tapir censusing. Our study shows that FIT is an effective method for the identification of individuals of a threatened species, even when they lack visible natural markings on their bodies. FIT offers several benefits over other methods, especially for tapir management. As a non-invasive method, it can be used to census or monitor species, giving rapid feedback to managers of protected areas. PMID:29610711

Fitness in animals correlates with proximity to discontinuities in body mass distributions.

USGS Publications Warehouse

Angeler, David G.; Allen, Craig R.; Vila-Gispert, Anna; Almeida, David

2014-01-01

Discontinuous structure in landscapes may cause discontinuous, aggregated species body-mass patterns, reflecting the scales of structure available to animal communities within a landscape. Empirical analyses have shown that the location of species within body mass aggregations, which reflect this scale-specific organization, is non-random with regard to several ecological phenomena, including species extinctions. The propensity of declining species to have body masses proximate to discontinuities suggests that transition zones between scaling regimes ultimately decreases the ecological fitness for some species. We test this proposition using vulnerable and unthreatened fish species in Mediterranean streams with differing levels of human impact. We show that the proximity to discontinuities in body mass aggregations (“distance-to-edge”) of more vs. less fit individuals within vulnerable and unthreatened populations differs. Specifically, regression analysis between the scaled mass index, a proxy of animal fitness, and distance-to-edge reveals negative and positive relationships for vulnerable and unthreatened species, respectively. That is, fitness is higher close to discontinuities in vulnerable populations and toward the center of body mass aggregation groups in unthreatened populations. Our results demonstrate the suitability of the discontinuity framework for scrutinizing non-random patterns of environmental impact in populations. Further exploration of the usefulness of this method across other ecosystems and organism groups is warranted.

Neuronal boost to evolutionary dynamics

PubMed Central

de Vladar, Harold P.; Szathmáry, Eörs

2015-01-01

Standard evolutionary dynamics is limited by the constraints of the genetic system. A central message of evolutionary neurodynamics is that evolutionary dynamics in the brain can happen in a neuronal niche in real time, despite the fact that neurons do not reproduce. We show that Hebbian learning and structural synaptic plasticity broaden the capacity for informational replication and guided variability provided a neuronally plausible mechanism of replication is in place. The synergy between learning and selection is more efficient than the equivalent search by mutation selection. We also consider asymmetric landscapes and show that the learning weights become correlated with the fitness gradient. That is, the neuronal complexes learn the local properties of the fitness landscape, resulting in the generation of variability directed towards the direction of fitness increase, as if mutations in a genetic pool were drawn such that they would increase reproductive success. Evolution might thus be more efficient within evolved brains than among organisms out in the wild. PMID:26640653

Evaluation of a landscape evolution model to simulate stream piracies: Insights from multivariable numerical tests using the example of the Meuse basin, France

NASA Astrophysics Data System (ADS)

Benaïchouche, Abed; Stab, Olivier; Tessier, Bruno; Cojan, Isabelle

2016-01-01

In landscapes dominated by fluvial erosion, the landscape morphology is closely related to the hydrographic network system. In this paper, we investigate the hydrographic network reorganization caused by a headward piracy mechanism between two drainage basins in France, the Meuse and the Moselle. Several piracies occurred in the Meuse basin during the past one million years, and the basin's current characteristics are favorable to new piracies by the Moselle river network. This study evaluates the consequences over the next several million years of a relative lowering of the Moselle River (and thus of its basin) with respect to the Meuse River. The problem is addressed with a numerical modeling approach (landscape evolution model, hereafter LEM) that requires empirical determinations of parameters and threshold values. Classically, fitting of the parameters is based on analysis of the relationship between the slope and the drainage area and is conducted under the hypothesis of equilibrium. Application of this conventional approach to the capture issue yields incomplete results that have been consolidated by a parametric sensitivity analysis. The LEM equations give a six-dimensional parameter space that was explored with over 15,000 simulations using the landscape evolution model GOLEM. The results demonstrate that stream piracies occur in only four locations in the studied reach near the city of Toul. The locations are mainly controlled by the local topography and are model-independent. Nevertheless, the chronology of the captures depends on two parameters: the river concavity (given by the fluvial advection equation) and the hillslope erosion factor. Thus, the simulations lead to three different scenarios that are explained by a phenomenon of exclusion or a string of events.

Soil Production and Erosion Rates and Processes in Mountainous Landscapes

NASA Astrophysics Data System (ADS)

Heimsath, A. M.; DiBiase, R. A.; Whipple, K. X.

2012-12-01

We focus here on high-relief, steeply sloped landscapes from the Nepal Himalaya to the San Gabriels of California that are typically thought to be at a critical threshold of soil cover. Observations reveal that, instead, there are significant areas mantled with soil that fit the conceptual framework of a physically mobile layer derived from the underlying parent material with some locally-derived organic content. The extent and persistence of such soils depends on the long-term balance between soil production and erosion despite the perceived discrepancy between high erosion and low soil production rates. We present cosmogenic Be-10-derived soil production and erosion rates that show that soil production increases with catchment-averaged erosion, suggesting a feedback that enhances soil-cover persistence, even in threshold landscapes. Soil production rates do decline systematically with increasing soil thickness, but hint at the potential for separate soil production functions for different erosional regimes. We also show that a process transistion to landslide-dominated erosion results in thinner, patchier soils and rockier topography, but find that there is no sudden transition to bedrock landscapes. Our landslide modeling is combined with a detailed quantification of bedrock exposure for these steep, mountainous landscapes. We also draw an important conclusion connecting the physical processes producing and transporting soil and the chemical processes weathering the parent material by measuring parent material strength across three different field settings. We observe that parent material strength increases with overlying soil thickness and, therefore, the weathered extent of the saprolite. Soil production rates, thus, decrease with increasing parent material competence. These observation highlight the importance of quantifying hillslope hydrologic processes where such multi-facted measurements are made.

Variation in the post-mating fitness landscape in fruit flies.

PubMed

Fricke, C; Chapman, T

2017-07-01

Sperm competition is pervasive and fundamental to determining a male's overall fitness. Sperm traits and seminal fluid proteins (Sfps) are key factors. However, studies of sperm competition may often exclude females that fail to remate during a defined period. Hence, the resulting data sets contain fewer data from the potentially fittest males that have most success in preventing female remating. It is also important to consider a male's reproductive success before entering sperm competition, which is a major contributor to fitness. The exclusion of these data can both hinder our understanding of the complete fitness landscapes of competing males and lessen our ability to assess the contribution of different determinants of reproductive success to male fitness. We addressed this here, using the Drosophila melanogaster model system, by (i) capturing a comprehensive range of intermating intervals that define the fitness of interacting wild-type males and (ii) analysing outcomes of sperm competition using selection analyses. We conducted additional tests using males lacking the sex peptide (SP) ejaculate component vs. genetically matched (SP + ) controls. This allowed us to assess the comprehensive fitness effects of this important Sfp on sperm competition. The results showed a signature of positive, linear selection in wild-type and SP + control males on the length of the intermating interval and on male sperm competition defence. However, the fitness surface for males lacking SP was distinct, with local fitness peaks depending on contrasting combinations of remating intervals and offspring numbers. The results suggest that there are alternative routes to success in sperm competition and provide an explanation for the maintenance of variation in sperm competition traits. © 2017 The Authors. Journal of Evolutionary Biology published by John Wiley & Sons Ltd on behalf of European Society for Evolutionary Biology.

The response to selection in Glycoside Hydrolase Family 13 structures: A comparative quantitative genetics approach.

PubMed

Hleap, Jose Sergio; Blouin, Christian

2018-01-01

The Glycoside Hydrolase Family 13 (GH13) is both evolutionarily diverse and relevant to many industrial applications. Its members hydrolyze starch into smaller carbohydrates and members of the family have been bioengineered to improve catalytic function under industrial environments. We introduce a framework to analyze the response to selection of GH13 protein structures given some phylogenetic and simulated dynamic information. We find that the TIM-barrel (a conserved protein fold consisting of eight α-helices and eight parallel β-strands that alternate along the peptide backbone, common to all amylases) is not selectable since it is under purifying selection. We also show a method to rank important residues with higher inferred response to selection. These residues can be altered to effect change in properties. In this work, we define fitness as inferred thermodynamic stability. We show that under the developed framework, residues 112Y, 122K, 124D, 125W, and 126P are good candidates to increase the stability of the truncated α-amylase protein from Geobacillus thermoleovorans (PDB code: 4E2O; α-1,4-glucan-4-glucanohydrolase; EC 3.2.1.1). Overall, this paper demonstrates the feasibility of a framework for the analysis of protein structures for any other fitness landscape.

The response to selection in Glycoside Hydrolase Family 13 structures: A comparative quantitative genetics approach

PubMed Central

2018-01-01

The Glycoside Hydrolase Family 13 (GH13) is both evolutionarily diverse and relevant to many industrial applications. Its members hydrolyze starch into smaller carbohydrates and members of the family have been bioengineered to improve catalytic function under industrial environments. We introduce a framework to analyze the response to selection of GH13 protein structures given some phylogenetic and simulated dynamic information. We find that the TIM-barrel (a conserved protein fold consisting of eight α-helices and eight parallel β-strands that alternate along the peptide backbone, common to all amylases) is not selectable since it is under purifying selection. We also show a method to rank important residues with higher inferred response to selection. These residues can be altered to effect change in properties. In this work, we define fitness as inferred thermodynamic stability. We show that under the developed framework, residues 112Y, 122K, 124D, 125W, and 126P are good candidates to increase the stability of the truncated α-amylase protein from Geobacillus thermoleovorans (PDB code: 4E2O; α-1,4-glucan-4-glucanohydrolase; EC 3.2.1.1). Overall, this paper demonstrates the feasibility of a framework for the analysis of protein structures for any other fitness landscape. PMID:29698417

Patent landscape of countermeasures against smallpox and estimation of grant attraction capability through patent landscape data.

PubMed

Mayburd, Anatoly L; Kedia, Govind; Evans, Haydn W; Kaslival, Pritesh C

2010-11-01

The study was concerned with countermeasures against a possible smallpox outbreak. In the process of assessment 18 landscaping sectors were defined and described, the advantages and drawbacks of the corresponding countermeasures being reviewed. The data of the previously published influenza landscape were revisited. The current economic climate of deficit cutting (austerity) also puts emphasis on the optimization of capital investment. We used the materials of the landscape to define and analyze metrics of capital placement optimization. Value score was obtained by fitting patent landscape internals to the sale price of individual patents. Success score was obtained as a product of a-priori parameters that measure likelihood of emergence of a marketable product in a technological sector. Both scores were combined in a qualitative metric. Our methodology defined weight as a product of the sector size by the success score. We hypothesized - based on the material of two landscapes- that a life cycle of a technology begins in IP space with a high patent quality low volume "bud" of low weight, reaches maximum weight and then weight falls again when the technology becomes outdated. The weight and the annual dynamic of weight can serve a measure of investment risk and return. In this report we modeled investment by issue of government grants or purchase of patents by government. In the smallpox landscape the number of patents purchased by government agencies was the highest in the sectors with the highest weight and the trend was confirmed by the count of NIH grants issued in support of the technological sectors. In the influenza landscape only grant issue count was statistically meaningful and the trend was also confirmed. To better fit the grant support levels, the weight expression was optimized by using training coefficients. We propose to use value scores for evaluation of individual patent publications/company portfolios and to use weights for assessment of technological sectors. Such a combination of automated analytical tools may lead to optimized allocation of capital and is intended to support the decisions taken by human experts.

Assessing habitat quality of farm-dwelling house sparrows in different agricultural landscapes.

PubMed

von Post, Maria; Borgström, Pernilla; Smith, Henrik G; Olsson, Ola

2012-04-01

Having historically been abundant throughout Europe, the house sparrow (Passer domesticus) has in recent decades suffered severe population declines in many urban and rural areas. The decline in rural environments is believed to be caused by agricultural intensification, which has resulted in landscape simplification. We used giving-up densities (GUDs) of house sparrows feeding in artificial food patches placed in farmlands of southern Sweden to determine habitat quality during the breeding season at two different spatial scales: the landscape and the patch scale. At the landscape scale, GUDs were lower on farms in homogeneous landscapes dominated by crop production compared to more heterogeneous landscapes with mixed farming or animal husbandry. At the patch level, feeding patches with a higher predation risk (caused by fitting a wall to the patch to obstruct vigilance) had higher GUDs. In addition, GUDs were positively related to population size, which strongly implies that GUDs reflect habitat quality. However, the increase followed different patterns in homogeneous and heterogeneous landscapes, indicating differing population limiting mechanisms in these two environments. We found no effect of the interaction between patch type and landscape type, suggesting that predation risk was similar in both landscape types. Thus, our study suggests that simplified landscapes constitute a poorer feeding environment for house sparrows during breeding, that the population-regulating mechanisms in the landscapes differ, but that predation risk is the same across the landscape types.

The Frequency of Fitness Peak Shifts Is Increased at Expanding Range Margins Due to Mutation Surfing

PubMed Central

Burton, Olivia J.; Travis, Justin M. J.

2008-01-01

Dynamic species' ranges, those that are either invasive or shifting in response to environmental change, are the focus of much recent interest in ecology, evolution, and genetics. Understanding how range expansions can shape evolutionary trajectories requires the consideration of nonneutral variability and genetic architecture, yet the majority of empirical and theoretical work to date has explored patterns of neutral variability. Here we use forward computer simulations of population growth, dispersal, and mutation to explore how range-shifting dynamics can influence evolution on rugged fitness landscapes. We employ a two-locus model, incorporating sign epistasis, and find that there is an increased likelihood of fitness peak shifts during a period of range expansion. Maladapted valley genotypes can accumulate at an expanding range front through a phenomenon called mutation surfing, which increases the likelihood that a mutation leading to a higher peak will occur. Our results indicate that most peak shifts occur close to the expanding front. We also demonstrate that periods of range shifting are especially important for peak shifting in species with narrow geographic distributions. Our results imply that trajectories on rugged fitness landscapes can be modified substantially when ranges are dynamic. PMID:18505864

Compensatory mutations cause excess of antagonistic epistasis in RNA secondary structure folding.

PubMed

Wilke, Claus O; Lenski, Richard E; Adami, Christoph

2003-02-05

The rate at which fitness declines as an organism's genome accumulates random mutations is an important variable in several evolutionary theories. At an intuitive level, it might seem natural that random mutations should tend to interact synergistically, such that the rate of mean fitness decline accelerates as the number of random mutations is increased. However, in a number of recent studies, a prevalence of antagonistic epistasis (the tendency of multiple mutations to have a mitigating rather than reinforcing effect) has been observed. We studied in silico the net amount and form of epistatic interactions in RNA secondary structure folding by measuring the fraction of neutral mutants as a function of mutational distance d. We found a clear prevalence of antagonistic epistasis in RNA secondary structure folding. By relating the fraction of neutral mutants at distance d to the average neutrality at distance d, we showed that this prevalence derives from the existence of many compensatory mutations at larger mutational distances. Our findings imply that the average direction of epistasis in simple fitness landscapes is directly related to the density with which fitness peaks are distributed in these landscapes.

Compensatory mutations cause excess of antagonistic epistasis in RNA secondary structure folding

PubMed Central

Wilke, Claus O; Lenski, Richard E; Adami, Christoph

2003-01-01

Background The rate at which fitness declines as an organism's genome accumulates random mutations is an important variable in several evolutionary theories. At an intuitive level, it might seem natural that random mutations should tend to interact synergistically, such that the rate of mean fitness decline accelerates as the number of random mutations is increased. However, in a number of recent studies, a prevalence of antagonistic epistasis (the tendency of multiple mutations to have a mitigating rather than reinforcing effect) has been observed. Results We studied in silico the net amount and form of epistatic interactions in RNA secondary structure folding by measuring the fraction of neutral mutants as a function of mutational distance d. We found a clear prevalence of antagonistic epistasis in RNA secondary structure folding. By relating the fraction of neutral mutants at distance d to the average neutrality at distance d, we showed that this prevalence derives from the existence of many compensatory mutations at larger mutational distances. Conclusions Our findings imply that the average direction of epistasis in simple fitness landscapes is directly related to the density with which fitness peaks are distributed in these landscapes. PMID:12590655

Kernel Method Based Human Model for Enhancing Interactive Evolutionary Optimization

PubMed Central

Zhao, Qiangfu; Liu, Yong

2015-01-01

A fitness landscape presents the relationship between individual and its reproductive success in evolutionary computation (EC). However, discrete and approximate landscape in an original search space may not support enough and accurate information for EC search, especially in interactive EC (IEC). The fitness landscape of human subjective evaluation in IEC is very difficult and impossible to model, even with a hypothesis of what its definition might be. In this paper, we propose a method to establish a human model in projected high dimensional search space by kernel classification for enhancing IEC search. Because bivalent logic is a simplest perceptual paradigm, the human model is established by considering this paradigm principle. In feature space, we design a linear classifier as a human model to obtain user preference knowledge, which cannot be supported linearly in original discrete search space. The human model is established by this method for predicting potential perceptual knowledge of human. With the human model, we design an evolution control method to enhance IEC search. From experimental evaluation results with a pseudo-IEC user, our proposed model and method can enhance IEC search significantly. PMID:25879050

Influences of landscape heterogeneity on home-range sizes of brown bears

USGS Publications Warehouse

Mangipane, Lindsey S.; Belant, Jerrold L.; Hiller, Tim L.; Colvin, Michael E.; Gustine, David; Mangipane, Buck A.; Hilderbrand, Grant V.

2018-01-01

Animal space use is influenced by many factors and can affect individual survival and fitness. Under optimal foraging theory, individuals use landscapes to optimize high-quality resources while minimizing the amount of energy used to acquire them. The spatial resource variability hypothesis states that as patchiness of resources increases, individuals use larger areas to obtain the resources necessary to meet energetic requirements. Additionally, under the temporal resource variability hypothesis, seasonal variation in available resources can reduce distances moved while providing a variety of food sources. Our objective was to determine if seasonal home ranges of brown bears (Ursus arctos) were influenced by temporal availability and spatial distribution of resources and whether individual reproductive status, sex, or size (i.e., body mass) mediated space use. To test our hypotheses, we radio collared brown bears (n = 32 [9 male, 23 female]) in 2014–2016 and used 18 a prioriselected linear models to evaluate seasonal utilization distributions (UD) in relation to our hypotheses. Our top-ranked model by AICc, supported the spatial resource variability hypothesis and included percentage of like adjacency (PLADJ) of all cover types (P < 0.01), reproductive class (P > 0.17 for males, solitary females, and females with dependent young), and body mass (kg; P = 0.66). Based on this model, for every percentage increase in PLADJ, UD area was predicted to increase 1.16 times for all sex and reproductive classes. Our results suggest that landscape heterogeneity influences brown bear space use; however, we found that bears used larger areas when landscape homogeneity increased, presumably to gain a diversity of food resources. Our results did not support the temporal resource variability hypothesis, suggesting that the spatial distribution of food was more important than seasonal availability in relation to brown bear home range size.

Urban landscape architecture design under the view of sustainable development

NASA Astrophysics Data System (ADS)

Chen, WeiLin

2017-08-01

The concept of sustainable development in modern city landscape design advocates landscape architecture, which is the main development direction in the field of landscape design. They are also effective measures to promote the sustainable development of city garden. Based on this, combined with the connotation of sustainable development and sustainable design, this paper analyzes and discusses the design of urban landscape under the concept of sustainable development.

[Effects of sampling plot number on tree species distribution prediction under climate change].

PubMed

Liang, Yu; He, Hong-Shi; Wu, Zhi-Wei; Li, Xiao-Na; Luo, Xu

2013-05-01

Based on the neutral landscapes under different degrees of landscape fragmentation, this paper studied the effects of sampling plot number on the prediction of tree species distribution at landscape scale under climate change. The tree species distribution was predicted by the coupled modeling approach which linked an ecosystem process model with a forest landscape model, and three contingent scenarios and one reference scenario of sampling plot numbers were assumed. The differences between the three scenarios and the reference scenario under different degrees of landscape fragmentation were tested. The results indicated that the effects of sampling plot number on the prediction of tree species distribution depended on the tree species life history attributes. For the generalist species, the prediction of their distribution at landscape scale needed more plots. Except for the extreme specialist, landscape fragmentation degree also affected the effects of sampling plot number on the prediction. With the increase of simulation period, the effects of sampling plot number on the prediction of tree species distribution at landscape scale could be changed. For generalist species, more plots are needed for the long-term simulation.

How do the effects of mutations add up?

NASA Astrophysics Data System (ADS)

Velenich, Andrea; Dai, Mingjie; Gore, Jeff

2011-03-01

Genetic mutations affect the fitness of any organism and provide the variability necessary for natural selection to occur. Given the fitness of a wild type organism and the fitness of mutants A and B which differ from the wild type by a single mutation, predicting the fitness of the double mutant AB is a fundamental problem with broad implications in many fields, from evolutionary theory to medicine. Analysis of millions of double gene knockouts in yeast reveals that, on average, the fitness of AB is the product of the fitness of A and the fitness of B. However, most pairs of mutations deviate from this mean behavior in a way that challenges existing theoretical models. We propose a natural generalization of the geometric Fisher's model which accommodates the experimentally observed features and allows us to characterize the fitness landscape of yeast.

Experimental evidence of reorganizing landscape under changing climatic forcing

NASA Astrophysics Data System (ADS)

Singh, A.; Tejedor, A.; Zaliapin, I. V.; Reinhardt, L.; Foufoula-Georgiou, E.

2015-12-01

Quantification of the dynamics of landscape reorganization under changing climatic forcing is important to understand geomorphic transport laws under transient conditions, assess response of landscapes to external perturbations for future predictive modeling, and for interpreting past climate from stratigraphic record. For such an analysis, however, real landscape observations are limited. To this end, a series of controlled laboratory experiments on evolving landscape were conducted at the St. Anthony Falls laboratory at the University of Minnesota. High resolution elevation data at a temporal resolution of 5 mins and spatial resolution of 0.5 mm were collected as the landscape approached steady state (constant uplift and precipitation rate) and in the transient state (under the same uplift and 5 times precipitation rate). Our results reveal rapid topographic re-organization under a five-fold increase in precipitation with the fluvial regime encroaching into the previously debris dominated regime, widening and aggradation of channels and valleys, and accelerated erosion happening at hillslope scales. To better understand the initiation of the observed reorganization, we perform a connectivity and clustering analysis of the erosional and depositional events, showing strikingly different spatial patterns on landscape evolution under steady-state (SS) and transient-state (TS), even when the time under SS is renormalized to match the total volume of eroded and deposited sediment in TS. Our results suggest a regime shift in the behavior of transport processes on the landscape at the intermediate scales i.e., from supply-limited to transport-limited.

Forest landscape restoration: increasing the positive impacts of forest restoration or simply the area under tree cover?

Treesearch

Stephanie Mansourian; John A. Stanturf; Mercy Afua Adutwumwaa Derkyi; Vera Lex Engel

2017-01-01

Restoring forest landscapes is critical in the face of continued global forest loss and degradation. In this article, weexplore some challenges underlying the delivery of global commitments to restore forest landscapes. We propose that threefundamental questions need to be resolved upfront for the effective implementation of Forest Landscape...

HIV-1 Env C2-V4 Diversification in a Slow-Progressor Infant Reveals a Flat but Rugged Fitness Landscape

PubMed Central

Smith, S. Abigail; Wood, Charles; West, John T.

2013-01-01

Human immunodeficiency virus type-1 (HIV-1) fitness has been associated with virus entry, a process mediated by the envelope glycoprotein (Env). We previously described Env genetic diversification in a Zambian, subtype C infected, slow-progressor child (1157i) in parallel with an evolving neutralizing antibody response. Because of the role the Variable-3 loop (V3) plays in transmission, cell tropism, neutralization sensitivity, and fitness, longitudinally isolated 1157i C2-V4 alleles were cloned into HIV-1NL4-3-eGFP and -DsRed2 infectious molecular clones. The fluorescent reporters allowed for dual-infection competitions between all patient-derived C2-V4 chimeras to quantify the effect of V3 diversification and selection on fitness. ‘Winners’ and ‘losers’ were readily discriminated among the C2-V4 alleles. Exceptional sensitivity for detection of subtle fitness differences was revealed through analysis of two alleles differing in a single synonymous amino acid. However, when the outcomes of N = 33 competitions were averaged for each chimera, the aggregate analysis showed that despite increasing diversification and divergence with time, natural selection of C2-V4 sequences in this individual did not appear to be producing a ‘survival of the fittest’ evolutionary pattern. Rather, we detected a relatively flat fitness landscape consistent with mutational robustness. Fitness outcomes were then correlated with individual components of the entry process. Env incorporation into particles correlated best with fitness, suggesting a role for Env avidity, as opposed to receptor/coreceptor affinity, in defining fitness. Nevertheless, biochemical analyses did not identify any step in HIV-1 entry as a dominant determinant of fitness. Our results lead us to conclude that multiple aspects of entry contribute to maintaining adequate HIV-1 fitness, and there is no surrogate analysis for determining fitness. The capacity for subtle polymorphisms in Env to nevertheless significantly impact viral fitness suggests fitness is best defined by head-to-head competition. PMID:23638182

Estimates of connectivity reveal non-equilibrium epiphyte occurrence patterns almost 180 years after habitat decline.

PubMed

Johansson, Victor; Snäll, Tord; Ranius, Thomas

2013-06-01

Habitat loss is a major cause of species decline and extinction. Immediately after habitat loss, species occurrences are not in equilibrium with the new landscape and more closely reflect the previous landscape structure. Species with slow colonisation-extinction dynamics may display long time-lags before reaching a new equilibrium. We investigated the importance of connectivity to current and historical dispersal sources with the aim of explaining the occurrence pattern of epiphytic lichens with different traits among 104 old oaks. We used oak survey data collected from 1830 and 2009 for a Swedish landscape where oak densities declined drastically shortly after 1830. We fitted a commonly used connectivity measure and estimated the confidence interval for the spatial scale parameter. Small differences in the spatial scale parameter resulted in large differences in model fit. Connectivity to trees in 1830 better explained the occurrence of three of the four species compared to the connectivity in 2009. The explanatory power of the historical landscape structure was highest for the species with traits that may result in a low colonisation rate--both a narrow niche (here few suitable trees) and large dispersal propagules. The results suggest that oak-dependent epiphytic lichens have not reached equilibrium with the spatial landscape structure 180 years after the drastic decline in habitat. For the long-term persistence of epiphytes associated with old trees, conservation efforts should focus on (1) protecting and restoring stands where specialised species with large dispersal propagules (i.e. with low colonisation rates) occur today and (2) promoting tree regeneration in their near vicinity.

Experimental evidence of dynamic re-organization of evolving landscapes under changing climatic forcing

NASA Astrophysics Data System (ADS)

Singh, Arvind; Tejedor, Alejandro; Zaliapin, Ilya; Reinhardt, Liam; Foufoula-Georgiou, Efi

2015-04-01

The aim of this study is to better understand the dynamic re-organization of an evolving landscape under a scenario of changing climatic forcing for improving our knowledge of geomorphic transport laws under transient conditions and developing predictive models of landscape response to external perturbations. Real landscape observations for long-term analysis are limited and to this end a high resolution controlled laboratory experiment was conducted at the St. Anthony Falls laboratory at the University of Minnesota. Elevation data were collected at temporal resolution of 5 mins and spatial resolution of 0.5 mm as the landscape approached steady state (constant uplift and precipitation rate) and in the transient state (under the same uplift and 5x precipitation). The results reveal rapid topographic re-organization under a five-fold precipitation increase with the fluvial regime expanding into the previously debris dominated regime, accelerated erosion happening at hillslope scales, and rivers shifting from an erosion-limited to a transport-limited regime. From a connectivity and clustering analysis of the erosional and depositional events, we demonstrate the strikingly different spatial patterns of landscape evolution under steady-state (SS) and transient-state (TS), even when the time under SS is "stretched" compared to that under TS such as to match the total volume and PDF of erosional and depositional amounts. We quantify the spatial coupling of hillslopes and channels and demonstrate that hillslopes lead and channels follow in re-organizing the whole landscape under such an amplified precipitation regime.

OncoSimulR: genetic simulation with arbitrary epistasis and mutator genes in asexual populations.

PubMed

Diaz-Uriarte, Ramon

2017-06-15

OncoSimulR implements forward-time genetic simulations of biallelic loci in asexual populations with special focus on cancer progression. Fitness can be defined as an arbitrary function of genetic interactions between multiple genes or modules of genes, including epistasis, restrictions in the order of accumulation of mutations, and order effects. Mutation rates can differ among genes, and can be affected by (anti)mutator genes. Also available are sampling from simulations (including single-cell sampling), plotting the genealogical relationships of clones and generating and plotting fitness landscapes. Implemented in R and C ++, freely available from BioConductor for Linux, Mac and Windows under the GNU GPL license. Version 2.5.9 or higher available from: http://www.bioconductor.org/packages/devel/bioc/html/OncoSimulR.html . GitHub repository at: https://github.com/rdiaz02/OncoSimul. ramon.diaz@iib.uam.es. Supplementary data are available at Bioinformatics online. © The Author 2017. Published by Oxford University Press.

Patent law for the dermatologist.

PubMed

Mei, Dan Feng; Liu, Josephine

2013-12-01

An exciting discovery in the laboratory may translate to a commercial product. How does the patent system fit into the picture? We first discuss the circumstances under which an invention is granted a patent. What is the purpose of a patent and what are the functions of the patent system? Who can apply for a patent? What makes an invention patentable? A patent does not automatically grant a right to make or sell a product. This is because multiple patents can cover a single pharmaceutical product. Understanding the patent landscape covering a product of interest is key to evaluating the risk of infringing another's exclusivity rights. We use a hypothetical example relating to skin cancer to guide a discussion of patent law.

A Smoluchowski model of crystallization dynamics of small colloidal clusters

NASA Astrophysics Data System (ADS)

Beltran-Villegas, Daniel J.; Sehgal, Ray M.; Maroudas, Dimitrios; Ford, David M.; Bevan, Michael A.

2011-10-01

We investigate the dynamics of colloidal crystallization in a 32-particle system at a fixed value of interparticle depletion attraction that produces coexisting fluid and solid phases. Free energy landscapes (FELs) and diffusivity landscapes (DLs) are obtained as coefficients of 1D Smoluchowski equations using as order parameters either the radius of gyration or the average crystallinity. FELs and DLs are estimated by fitting the Smoluchowski equations to Brownian dynamics (BD) simulations using either linear fits to locally initiated trajectories or global fits to unbiased trajectories using Bayesian inference. The resulting FELs are compared to Monte Carlo Umbrella Sampling results. The accuracy of the FELs and DLs for modeling colloidal crystallization dynamics is evaluated by comparing mean first-passage times from BD simulations with analytical predictions using the FEL and DL models. While the 1D models accurately capture dynamics near the free energy minimum fluid and crystal configurations, predictions near the transition region are not quantitatively accurate. A preliminary investigation of ensemble averaged 2D order parameter trajectories suggests that 2D models are required to capture crystallization dynamics in the transition region.

Forecasting climate change impacts on plant populations over large spatial extents

DOE PAGES

Tredennick, Andrew T.; Hooten, Mevin B.; Aldridge, Cameron L.; ...

2016-10-24

Plant population models are powerful tools for predicting climate change impacts in one location, but are difficult to apply at landscape scales. Here, we overcome this limitation by taking advantage of two recent advances: remotely sensed, species-specific estimates of plant cover and statistical models developed for spatiotemporal dynamics of animal populations. Using computationally efficient model reparameterizations, we fit a spatiotemporal population model to a 28-year time series of sagebrush (Artemisia spp.) percent cover over a 2.5 × 5 km landscape in southwestern Wyoming while formally accounting for spatial autocorrelation. We include interannual variation in precipitation and temperature as covariates inmore » the model to investigate how climate affects the cover of sagebrush. We then use the model to forecast the future abundance of sagebrush at the landscape scale under projected climate change, generating spatially explicit estimates of sagebrush population trajectories that have, until now, been impossible to produce at this scale. Our broadscale and long-term predictions are rooted in small-scale and short-term population dynamics and provide an alternative to predictions offered by species distribution models that do not include population dynamics. Finally, our approach, which combines several existing techniques in a novel way, demonstrates the use of remote sensing data to model population responses to environmental change that play out at spatial scales far greater than the traditional field study plot.« less

Forecasting climate change impacts on plant populations over large spatial extents

DOE Office of Scientific and Technical Information (OSTI.GOV)

Tredennick, Andrew T.; Hooten, Mevin B.; Aldridge, Cameron L.

Plant population models are powerful tools for predicting climate change impacts in one location, but are difficult to apply at landscape scales. Here, we overcome this limitation by taking advantage of two recent advances: remotely sensed, species-specific estimates of plant cover and statistical models developed for spatiotemporal dynamics of animal populations. Using computationally efficient model reparameterizations, we fit a spatiotemporal population model to a 28-year time series of sagebrush (Artemisia spp.) percent cover over a 2.5 × 5 km landscape in southwestern Wyoming while formally accounting for spatial autocorrelation. We include interannual variation in precipitation and temperature as covariates inmore » the model to investigate how climate affects the cover of sagebrush. We then use the model to forecast the future abundance of sagebrush at the landscape scale under projected climate change, generating spatially explicit estimates of sagebrush population trajectories that have, until now, been impossible to produce at this scale. Our broadscale and long-term predictions are rooted in small-scale and short-term population dynamics and provide an alternative to predictions offered by species distribution models that do not include population dynamics. Finally, our approach, which combines several existing techniques in a novel way, demonstrates the use of remote sensing data to model population responses to environmental change that play out at spatial scales far greater than the traditional field study plot.« less

Forecasting climate change impacts on plant populations over large spatial extents

USGS Publications Warehouse

Tredennick, Andrew T.; Hooten, Mevin B.; Aldridge, Cameron L.; Homer, Collin G.; Kleinhesselink, Andrew R.; Adler, Peter B.

2016-01-01

Plant population models are powerful tools for predicting climate change impacts in one location, but are difficult to apply at landscape scales. We overcome this limitation by taking advantage of two recent advances: remotely sensed, species-specific estimates of plant cover and statistical models developed for spatiotemporal dynamics of animal populations. Using computationally efficient model reparameterizations, we fit a spatiotemporal population model to a 28-year time series of sagebrush (Artemisia spp.) percent cover over a 2.5 × 5 km landscape in southwestern Wyoming while formally accounting for spatial autocorrelation. We include interannual variation in precipitation and temperature as covariates in the model to investigate how climate affects the cover of sagebrush. We then use the model to forecast the future abundance of sagebrush at the landscape scale under projected climate change, generating spatially explicit estimates of sagebrush population trajectories that have, until now, been impossible to produce at this scale. Our broadscale and long-term predictions are rooted in small-scale and short-term population dynamics and provide an alternative to predictions offered by species distribution models that do not include population dynamics. Our approach, which combines several existing techniques in a novel way, demonstrates the use of remote sensing data to model population responses to environmental change that play out at spatial scales far greater than the traditional field study plot.

Evolutionary dynamics from a variational principle.

PubMed

Klimek, Peter; Thurner, Stefan; Hanel, Rudolf

2010-07-01

We demonstrate with a thought experiment that fitness-based population dynamical approaches to evolution are not able to make quantitative, falsifiable predictions about the long-term behavior of some evolutionary systems. A key characteristic of evolutionary systems is the ongoing endogenous production of new species. These novel entities change the conditions for already existing species. Even Darwin's Demon, a hypothetical entity with exact knowledge of the abundance of all species and their fitness functions at a given time, could not prestate the impact of these novelties on established populations. We argue that fitness is always a posteriori knowledge--it measures but does not explain why a species has reproductive success or not. To overcome these conceptual limitations, a variational principle is proposed in a spin-model-like setup of evolutionary systems. We derive a functional which is minimized under the most general evolutionary formulation of a dynamical system, i.e., evolutionary trajectories causally emerge as a minimization of a functional. This functional allows the derivation of analytic solutions of the asymptotic diversity for stochastic evolutionary systems within a mean-field approximation. We test these approximations by numerical simulations of the corresponding model and find good agreement in the position of phase transitions in diversity curves. The model is further able to reproduce stylized facts of timeseries from several man-made and natural evolutionary systems. Light will be thrown on how species and their fitness landscapes dynamically coevolve.

A Model with Darwinian Dynamics on a Rugged Landscape

NASA Astrophysics Data System (ADS)

Brotto, Tommaso; Bunin, Guy; Kurchan, Jorge

2017-02-01

We discuss the population dynamics with selection and random diffusion, keeping the total population constant, in a fitness landscape associated with Constraint Satisfaction, a paradigm for difficult optimization problems. We obtain a phase diagram in terms of the size of the population and the diffusion rate, with a glass phase inside which the dynamics keeps searching for better configurations, and outside which deleterious `mutations' spoil the performance. The phase diagram is analogous to that of dense active matter in terms of temperature and drive.

Landscape Planning of Schoolyards

NASA Astrophysics Data System (ADS)

Kopeva, A.; Khrapko, O.; Ivanova, O.

2017-11-01

The optimal landscape architecture planning of schoolyards allows for creation of favorable conditions for children personal development and physical fitness. The key principles of schoolyard landscape planning, same as for other areas intended for children, are as follows: establishment of a favorable microclimate, safety, aesthetic and educational environment. Green spaces play an essential role in this respect as they are essential to sanitary, hygienic, structural, and spatial planning performing decorative, artistic, cognitive, and educational functions in these areas. Various types of landscape plantings are used in school areas: borders, lawns, beds, vines, ornamental arrangements, and various potted plants. Children’s safety is the key principle when selecting a landscape design type and the plants’ range. Any allergenic, poisonous, thorny, strong-smelling or life-threatening plants are excluded. Plants on school grounds can serve as visual aids for studies. Drought-resistant, attractive, colorful, abundantly blooming plants with variable leaf texture are preferred. Ornamental trees and shrubs as well as perennials and annuals provide a broad plant range for school grounds.

Geographic Information System Tools for Conservation Planning: User's Manual

USGS Publications Warehouse

Fox, Timothy J.; Rohweder, Jason J.; Kenow, K.P.; Korschgen, C.E.; DeHaan, H.C.

2003-01-01

Public and private land managers desire better ways to incorporate landscape, species, and habitat relations into their conservation planning processes. We present three tools, developed for the Environmental Systems Research Institute?s ArcView 3.x platform, applicable to many types of wildlife conservation management and planning efforts. These tools provide managers and planners with the ability to rapidly assess landscape attributes and link these attributes with species-habitat information. To use the tools, the user provides a detailed land cover spatial database and develops a matrix to identify species-habitat relations for the landscape of interest. The tools are applicable to any taxa or suite of taxa for which the required data are available. The user also has the ability to interactively make polygon-specific changes to the landscape and re-examine species-habitat relations. The development of these tools has given resource managers the means to evaluate the merits of proposed landscape management scenarios and to choose the scenario that best fits the goals of the managed area.

Trade-offs between enzyme fitness and solubility illuminated by deep mutational scanning

PubMed Central

Bacik, John-Paul; Wrenbeck, Emily E.; Michalczyk, Ryszard; Whitehead, Timothy A.

2017-01-01

Proteins are marginally stable, and an understanding of the sequence determinants for improved protein solubility is highly desired. For enzymes, it is well known that many mutations that increase protein solubility decrease catalytic activity. These competing effects frustrate efforts to design and engineer stable, active enzymes without laborious high-throughput activity screens. To address the trade-off between enzyme solubility and activity, we performed deep mutational scanning using two different screens/selections that purport to gauge protein solubility for two full-length enzymes. We assayed a TEM-1 beta-lactamase variant and levoglucosan kinase (LGK) using yeast surface display (YSD) screening and a twin-arginine translocation pathway selection. We then compared these scans with published experimental fitness landscapes. Results from the YSD screen could explain 37% of the variance in the fitness landscapes for one enzyme. Five percent to 10% of all single missense mutations improve solubility, matching theoretical predictions of global protein stability. For a given solubility-enhancing mutation, the probability that it would retain wild-type fitness was correlated with evolutionary conservation and distance to active site, and anticorrelated with contact number. Hybrid classification models were developed that could predict solubility-enhancing mutations that maintain wild-type fitness with an accuracy of 90%. The downside of using such classification models is the removal of rare mutations that improve both fitness and solubility. To reveal the biophysical basis of enhanced protein solubility and function, we determined the crystallographic structure of one such LGK mutant. Beyond fundamental insights into trade-offs between stability and activity, these results have potential biotechnological applications. PMID:28196882

Self-organization and information in biosystems: a case study.

PubMed

Haken, Hermann

2018-05-01

Eigen's original molecular evolution equations are extended in two ways. (1) By an additional nonlinear autocatalytic term leading to new stability features, their dependence on the relative size of fitness parameters and on initial conditions is discussed in detail. (2) By adding noise terms that represent the spontaneous generation of molecules by mutations of substrate molecules, these terms are taken care of by both Langevin and Fokker-Planck equations. The steady-state solution of the latter provides us with a potential landscape giving a bird's eye view on all stable states (attractors). Two different types of evolutionary processes are suggested: (a) in a fixed attractor landscape and (b) caused by a changed landscape caused by changed fitness parameters. This may be related to Gould's concept of punctuated equilibria. External signals in the form of additional molecules may generate a new initial state within a specific basin of attraction. The corresponding attractor is then reached by self-organization. This approach allows me to define pragmatic information as signals causing a specific reaction of the receiver and to use equations equivalent to (1) as model of (human) pattern recognition as substantiated by the synergetic computer.

Computational design of hepatitis C vaccines using maximum entropy models and population dynamics

NASA Astrophysics Data System (ADS)

Hart, Gregory; Ferguson, Andrew

Hepatitis C virus (HCV) afflicts 170 million people and kills 350,000 annually. Vaccination offers the most realistic and cost effective hope of controlling this epidemic. Despite 20 years of research, no vaccine is available. A major obstacle is the virus' extreme genetic variability and rapid mutational escape from immune pressure. Improvements in the vaccine design process are urgently needed. Coupling data mining with spin glass models and maximum entropy inference, we have developed a computational approach to translate sequence databases into empirical fitness landscapes. These landscapes explicitly connect viral genotype to phenotypic fitness and reveal vulnerable targets that can be exploited to rationally design immunogens. Viewing these landscapes as the mutational ''playing field'' over which the virus is constrained to evolve, we have integrated them with agent-based models of the viral mutational and host immune response dynamics, establishing a data-driven immune simulator of HCV infection. We have employed this simulator to perform in silico screening of HCV immunogens. By systematically identifying a small number of promising vaccine candidates, these models can accelerate the search for a vaccine by massively reducing the experimental search space.

Evolutionary advantage via common action of recombination and neutrality

NASA Astrophysics Data System (ADS)

Saakian, David B.; Hu, Chin-Kun

2013-11-01

We investigate evolution models with recombination and neutrality. We consider the Crow-Kimura (parallel) mutation-selection model with the neutral fitness landscape, in which there is a central peak with high fitness A, and some of 1-point mutants have the same high fitness A, while the fitness of other sequences is 0. We find that the effect of recombination and neutrality depends on the concrete version of both neutrality and recombination. We consider three versions of neutrality: (a) all the nearest neighbor sequences of the peak sequence have the same high fitness A; (b) all the l-point mutations in a piece of genome of length l≥1 are neutral; (c) the neutral sequences are randomly distributed among the nearest neighbors of the peak sequences. We also consider three versions of recombination: (I) the simple horizontal gene transfer (HGT) of one nucleotide; (II) the exchange of a piece of genome of length l, HGT-l; (III) two-point crossover recombination (2CR). For the case of (a), the 2CR gives a rather strong contribution to the mean fitness, much stronger than that of HGT for a large genome length L. For the random distribution of neutral sequences there is a critical degree of neutrality νc, and for μ<μc and (μc-μ) is not large, the 2CR suppresses the mean fitness while HGT increases it; for ν much larger than νc, the 2CR and HGT-l increase the mean fitness larger than that of the HGT. We also consider the recombination in the case of smooth fitness landscapes. The recombination gives some advantage in the evolutionary dynamics, where recombination distinguishes clearly the mean-field-like evolutionary factors from the fluctuation-like ones. By contrast, mutations affect the mean-field-like and fluctuation-like factors similarly. Consequently, recombination can accelerate the non-mean-field (fluctuation) type dynamics without considerably affecting the mean-field-like factors.

From Product to Place-Spatializing governance in a commodified landscape.

PubMed

van Oosten, Cora; Moeliono, Moira; Wiersum, Freerk

2018-07-01

This article analyzes the potential for landscape governance in large-scale commodity landscapes in Indonesia. It conceptualizes landscape governance as the spatialization of governance, which entails the interplay between natural-spatial conditions of place, public-private actor constellations, and policy responses. The article presents the case of a commodified oil palm landscape in West Kalimantan, where a potentially new type of landscape governance is emerging out of the experimental activities of an ecologically responsible commercial enterprise. It describes the development of a multifunctional concession as a process of productive bricolage involving the creative combination of different land uses within a single productive space. It also describes how such a multifunctional concession does not fit into existing policies, which are sectorally defined and embedded in sticky institutional frames. The formation of new public-private institutional arrangements needed for the development of multifunctional concessions is a difficult process, as it requires an alignment of contrasting discourses and an integration of sectorally-defined policy frames. If successful, it might facilitate the transition from multifunctional concessions to multifunctional landscapes. Such a fundamental change in land use and production relations however requires intensive stakeholder engagement and policy dialog. Indonesia's continuous decentralization process offers opportunities for this, as it increasingly provides institutional space at the landscape level, for public and private actors to explore common concerns, and craft public-private arrangements specific to the landscape.

Improving estimation of kinetic parameters in dynamic force spectroscopy using cluster analysis

NASA Astrophysics Data System (ADS)

Yen, Chi-Fu; Sivasankar, Sanjeevi

2018-03-01

Dynamic Force Spectroscopy (DFS) is a widely used technique to characterize the dissociation kinetics and interaction energy landscape of receptor-ligand complexes with single-molecule resolution. In an Atomic Force Microscope (AFM)-based DFS experiment, receptor-ligand complexes, sandwiched between an AFM tip and substrate, are ruptured at different stress rates by varying the speed at which the AFM-tip and substrate are pulled away from each other. The rupture events are grouped according to their pulling speeds, and the mean force and loading rate of each group are calculated. These data are subsequently fit to established models, and energy landscape parameters such as the intrinsic off-rate (koff) and the width of the potential energy barrier (xβ) are extracted. However, due to large uncertainties in determining mean forces and loading rates of the groups, errors in the estimated koff and xβ can be substantial. Here, we demonstrate that the accuracy of fitted parameters in a DFS experiment can be dramatically improved by sorting rupture events into groups using cluster analysis instead of sorting them according to their pulling speeds. We test different clustering algorithms including Gaussian mixture, logistic regression, and K-means clustering, under conditions that closely mimic DFS experiments. Using Monte Carlo simulations, we benchmark the performance of these clustering algorithms over a wide range of koff and xβ, under different levels of thermal noise, and as a function of both the number of unbinding events and the number of pulling speeds. Our results demonstrate that cluster analysis, particularly K-means clustering, is very effective in improving the accuracy of parameter estimation, particularly when the number of unbinding events are limited and not well separated into distinct groups. Cluster analysis is easy to implement, and our performance benchmarks serve as a guide in choosing an appropriate method for DFS data analysis.

Landscape metrics, scales of resolution

Treesearch

Samuel A. Cushman; Kevin McGarigal

2008-01-01

Effective implementation of the "multiple path" approach to managing green landscapes depends fundamentally on rigorous quantification of the composition and structure of the landscapes of concern at present, modelling landscape structure trajectories under alternative management paths, and monitoring landscape structure into the future to confirm...

Inferring genetic interactions from comparative fitness data

PubMed Central

2017-01-01

Darwinian fitness is a central concept in evolutionary biology. In practice, however, it is hardly possible to measure fitness for all genotypes in a natural population. Here, we present quantitative tools to make inferences about epistatic gene interactions when the fitness landscape is only incompletely determined due to imprecise measurements or missing observations. We demonstrate that genetic interactions can often be inferred from fitness rank orders, where all genotypes are ordered according to fitness, and even from partial fitness orders. We provide a complete characterization of rank orders that imply higher order epistasis. Our theory applies to all common types of gene interactions and facilitates comprehensive investigations of diverse genetic interactions. We analyzed various genetic systems comprising HIV-1, the malaria-causing parasite Plasmodium vivax, the fungus Aspergillus niger, and the TEM-family of β-lactamase associated with antibiotic resistance. For all systems, our approach revealed higher order interactions among mutations. PMID:29260711

Inferring genetic interactions from comparative fitness data.

PubMed

Crona, Kristina; Gavryushkin, Alex; Greene, Devin; Beerenwinkel, Niko

2017-12-20

Darwinian fitness is a central concept in evolutionary biology. In practice, however, it is hardly possible to measure fitness for all genotypes in a natural population. Here, we present quantitative tools to make inferences about epistatic gene interactions when the fitness landscape is only incompletely determined due to imprecise measurements or missing observations. We demonstrate that genetic interactions can often be inferred from fitness rank orders, where all genotypes are ordered according to fitness, and even from partial fitness orders. We provide a complete characterization of rank orders that imply higher order epistasis. Our theory applies to all common types of gene interactions and facilitates comprehensive investigations of diverse genetic interactions. We analyzed various genetic systems comprising HIV-1, the malaria-causing parasite Plasmodium vivax , the fungus Aspergillus niger , and the TEM-family of β-lactamase associated with antibiotic resistance. For all systems, our approach revealed higher order interactions among mutations.

Evolution of complex dynamics

NASA Astrophysics Data System (ADS)

Wilds, Roy; Kauffman, Stuart A.; Glass, Leon

2008-09-01

We study the evolution of complex dynamics in a model of a genetic regulatory network. The fitness is associated with the topological entropy in a class of piecewise linear equations, and the mutations are associated with changes in the logical structure of the network. We compare hill climbing evolution, in which only mutations that increase the fitness are allowed, with neutral evolution, in which mutations that leave the fitness unchanged are allowed. The simple structure of the fitness landscape enables us to estimate analytically the rates of hill climbing and neutral evolution. In this model, allowing neutral mutations accelerates the rate of evolutionary advancement for low mutation frequencies. These results are applicable to evolution in natural and technological systems.

Energy landscape analysis of neuroimaging data

NASA Astrophysics Data System (ADS)

Ezaki, Takahiro; Watanabe, Takamitsu; Ohzeki, Masayuki; Masuda, Naoki

2017-05-01

Computational neuroscience models have been used for understanding neural dynamics in the brain and how they may be altered when physiological or other conditions change. We review and develop a data-driven approach to neuroimaging data called the energy landscape analysis. The methods are rooted in statistical physics theory, in particular the Ising model, also known as the (pairwise) maximum entropy model and Boltzmann machine. The methods have been applied to fitting electrophysiological data in neuroscience for a decade, but their use in neuroimaging data is still in its infancy. We first review the methods and discuss some algorithms and technical aspects. Then, we apply the methods to functional magnetic resonance imaging data recorded from healthy individuals to inspect the relationship between the accuracy of fitting, the size of the brain system to be analysed and the data length. This article is part of the themed issue `Mathematical methods in medicine: neuroscience, cardiology and pathology'.

Stream fish colonization but not persistence varies regionally across a large North American river basin

USGS Publications Warehouse

Wheeler, Kit; Wengerd, Seth J.; Walsh, Stephen J.; Martin, Zachary P.; Jelks, Howard L.; Freeman, Mary C.

2018-01-01

Many species have distributions that span distinctly different physiographic regions, and effective conservation of such taxa will require a full accounting of all factors that potentially influence populations. Ecologists recognize effects of physiographic differences in topography, geology and climate on local habitat configurations, and thus the relevance of landscape heterogeneity to species distributions and abundances. However, research is lacking that examines how physiography affects the processes underlying metapopulation dynamics. We used data describing occupancy dynamics of stream fishes to evaluate evidence that physiography influences rates at which individual taxa persist in or colonize stream reaches under different flow conditions. Using periodic survey data from a stream fish assemblage in a large river basin that encompasses multiple physiographic regions, we fit multi-species dynamic occupancy models. Our modeling results suggested that stream fish colonization but not persistence was strongly governed by physiography, with estimated colonization rates considerably higher in Coastal Plain streams than in Piedmont and Blue Ridge systems. Like colonization, persistence was positively related to an index of stream flow magnitude, but the relationship between flow and persistence did not depend on physiography. Understanding the relative importance of colonization and persistence, and how one or both processes may change across the landscape, is critical information for the conservation of broadly distributed taxa, and conservation strategies explicitly accounting for spatial variation in these processes are likely to be more successful for such taxa.

Atomic Force Microscope Studies of the Fusion of Floating Lipid Bilayers

PubMed Central

Abdulreda, Midhat H.; Moy, Vincent T.

2007-01-01

This study investigated the fusion of apposing floating bilayers of egg L-α-phosphatidylcholine (egg PC) or 1,2-dimyristoyl-sn-glycero-3-phosphocholine. Atomic force microscope measurements of fusion forces under different compression rates were acquired to reveal the energy landscape of the fusion process under varied lipid composition and temperature. Between compression rates of ∼1000 and ∼100,000 pN/s, applied forces in the range from ∼100 to ∼500 pN resulted in fusion of floating bilayers. Our atomic force microscope measurements indicated that one main energy barrier dominated the fusion process. The acquired dynamic force spectra were fit with a simple model based on the transition state theory with the assumption that the fusion activation potential is linear. A significant shift in the energy landscape was observed when bilayer fluidity and composition were modified, respectively, by temperature and different cholesterol concentrations (15% ≤ chol ≤ 25%). Such modifications resulted in a more than twofold increase in the width of the fusion energy barrier for egg PC and 1,2-dimyristoyl-sn-glycero-3-phosphocholine floating bilayers. The addition of 25% cholesterol to egg PC bilayers increased the activation energy by ∼1.0 kBT compared with that of bilayers with egg PC alone. These results reveal that widening of the energy barrier and consequently reduction in its slope facilitated membrane fusion. PMID:17400691

Atomic force microscope studies of the fusion of floating lipid bilayers.

PubMed

Abdulreda, Midhat H; Moy, Vincent T

2007-06-15

This study investigated the fusion of apposing floating bilayers of egg L-alpha-phosphatidylcholine (egg PC) or 1,2-dimyristoyl-sn-glycero-3-phosphocholine. Atomic force microscope measurements of fusion forces under different compression rates were acquired to reveal the energy landscape of the fusion process under varied lipid composition and temperature. Between compression rates of approximately 1000 and approximately 100,000 pN/s, applied forces in the range from approximately 100 to approximately 500 pN resulted in fusion of floating bilayers. Our atomic force microscope measurements indicated that one main energy barrier dominated the fusion process. The acquired dynamic force spectra were fit with a simple model based on the transition state theory with the assumption that the fusion activation potential is linear. A significant shift in the energy landscape was observed when bilayer fluidity and composition were modified, respectively, by temperature and different cholesterol concentrations (15% < or = chol < or = 25%). Such modifications resulted in a more than twofold increase in the width of the fusion energy barrier for egg PC and 1,2-dimyristoyl-sn-glycero-3-phosphocholine floating bilayers. The addition of 25% cholesterol to egg PC bilayers increased the activation energy by approximately 1.0 k(B)T compared with that of bilayers with egg PC alone. These results reveal that widening of the energy barrier and consequently reduction in its slope facilitated membrane fusion.

Which DEM is best for analyzing fluvial landscape development in mountainous terrains?

NASA Astrophysics Data System (ADS)

Boulton, Sarah J.; Stokes, Martin

2018-06-01

Regional studies of fluvial landforms and long-term (Quaternary) landscape development in remote mountain landscapes routinely use satellite-derived DEM data sets. The SRTM and ASTER DEMs are the most commonly utilised because of their longer availability, free cost, and ease of access. However, rapid technological developments mean that newer and higher resolution DEM data sets such as ALOS World 3D (AW3D) and TanDEM-X are being released to the scientific community. Geomorphologists are thus faced with an increasingly problematic challenge of selecting an appropriate DEM for their landscape analyses. Here, we test the application of four medium resolution DEM products (30 m = SRTM, ASTER, AW3D; 12 m = TanDEM-X) for qualitative and quantitative analysis of a fluvial mountain landscape using the Dades River catchment (High Atlas Mountains, Morocco). This landscape comprises significant DEM remote sensing challenges, notably a high mountain relief, steep slopes, and a deeply incised high sinuosity drainage network with narrow canyon/gorge reaches. Our goal was to see which DEM produced the most representative best fit drainage network and meaningful quantification. To achieve this, we used ArcGIS and Stream Profiler platforms to generate catchment hillshade and slope rasters and to extract drainage network, channel long profile and channel slope, and area data. TanDEM-X produces the clearest landscape representation but with channel routing errors in localised high relief areas. Thirty-metre DEMs are smoother and less detailed, but the AW3D shows the closest fit to the real drainage network configuration. The TanDEM-X elevation values are the closest to field-derived GPS measurements. Long profiles exhibit similar shapes but with minor differences in length, elevation, and the degree of noise/smoothing, with AW3D producing the best representation. Slope-area plots display similarly positioned slope-break knickpoints with modest differences in steepness and concavity indices, but again best represented by AW3D. Collectively, our study shows that despite the higher effective resolution of TanDEM-X (12 m), the AW3D (30 m) data performs strongly across all analyses suggesting that it currently offers the greatest potential for regional mountain geomorphological analyses.

Predicting Landscape-Genetic Consequences of Habitat Loss, Fragmentation and Mobility for Multiple Species of Woodland Birds

PubMed Central

Amos, J. Nevil; Bennett, Andrew F.; Mac Nally, Ralph; Newell, Graeme; Pavlova, Alexandra; Radford, James Q.; Thomson, James R.; White, Matt; Sunnucks, Paul

2012-01-01

Inference concerning the impact of habitat fragmentation on dispersal and gene flow is a key theme in landscape genetics. Recently, the ability of established approaches to identify reliably the differential effects of landscape structure (e.g. land-cover composition, remnant vegetation configuration and extent) on the mobility of organisms has been questioned. More explicit methods of predicting and testing for such effects must move beyond post hoc explanations for single landscapes and species. Here, we document a process for making a priori predictions, using existing spatial and ecological data and expert opinion, of the effects of landscape structure on genetic structure of multiple species across replicated landscape blocks. We compare the results of two common methods for estimating the influence of landscape structure on effective distance: least-cost path analysis and isolation-by-resistance. We present a series of alternative models of genetic connectivity in the study area, represented by different landscape resistance surfaces for calculating effective distance, and identify appropriate null models. The process is applied to ten species of sympatric woodland-dependant birds. For each species, we rank a priori the expectation of fit of genetic response to the models according to the expected response of birds to loss of structural connectivity and landscape-scale tree-cover. These rankings (our hypotheses) are presented for testing with empirical genetic data in a subsequent contribution. We propose that this replicated landscape, multi-species approach offers a robust method for identifying the likely effects of landscape fragmentation on dispersal. PMID:22363508

Impact of Climate Variability and Landscape Patterns on Water Budget and Nutrient Loads in a Peri-urban Watershed: A Coupled Analysis Using Process-based Hydrological Model and Landscape Indices.

PubMed

Li, Chongwei; Zhang, Yajuan; Kharel, Gehendra; Zou, Chris B

2018-06-01

Nutrient discharge into peri-urban streams and reservoirs constitutes a significant pressure on environmental management, but quantitative assessment of non-point source pollution under climate variability in fast changing peri-urban watersheds is challenging. Soil and Water Assessment Tool (SWAT) was used to simulate water budget and nutrient loads for landscape patterns representing a 30-year progression of urbanization in a peri-urban watershed near Tianjin metropolis, China. A suite of landscape pattern indices was related to nitrogen (N) and phosphorous (P) loads under dry and wet climate using CANOCO redundancy analysis. The calibrated SWAT model was adequate to simulate runoff and nutrient loads for this peri-urban watershed, with Nash-Sutcliffe coefficient (NSE) and coefficient of determination (R 2 ) > 0.70 and percentage bias (PBIAS) between -7 and +18 for calibration and validation periods. With the progression of urbanization, forest remained the main "sink" landscape while cultivated and urban lands remained the main "source" landscapes with the role of orchard and grassland being uncertain and changing with time. Compared to 1984, the landscape use pattern in 2013 increased nutrient discharge by 10%. Nutrient loads modelled under wet climate were 3-4 times higher than that under dry climate for the same landscape pattern. Results indicate that climate change could impose a far greater impact on runoff and nutrient discharge in a peri-urban watershed than landscape pattern change.

Impact of Climate Variability and Landscape Patterns on Water Budget and Nutrient Loads in a Peri-urban Watershed: A Coupled Analysis Using Process-based Hydrological Model and Landscape Indices

NASA Astrophysics Data System (ADS)

Li, Chongwei; Zhang, Yajuan; Kharel, Gehendra; Zou, Chris B.

2018-06-01

Nutrient discharge into peri-urban streams and reservoirs constitutes a significant pressure on environmental management, but quantitative assessment of non-point source pollution under climate variability in fast changing peri-urban watersheds is challenging. Soil and Water Assessment Tool (SWAT) was used to simulate water budget and nutrient loads for landscape patterns representing a 30-year progression of urbanization in a peri-urban watershed near Tianjin metropolis, China. A suite of landscape pattern indices was related to nitrogen (N) and phosphorous (P) loads under dry and wet climate using CANOCO redundancy analysis. The calibrated SWAT model was adequate to simulate runoff and nutrient loads for this peri-urban watershed, with Nash-Sutcliffe coefficient (NSE) and coefficient of determination ( R 2) > 0.70 and percentage bias (PBIAS) between -7 and +18 for calibration and validation periods. With the progression of urbanization, forest remained the main "sink" landscape while cultivated and urban lands remained the main "source" landscapes with the role of orchard and grassland being uncertain and changing with time. Compared to 1984, the landscape use pattern in 2013 increased nutrient discharge by 10%. Nutrient loads modelled under wet climate were 3-4 times higher than that under dry climate for the same landscape pattern. Results indicate that climate change could impose a far greater impact on runoff and nutrient discharge in a peri-urban watershed than landscape pattern change.

Inferring Causalities in Landscape Genetics: An Extension of Wright's Causal Modeling to Distance Matrices.

PubMed

Fourtune, Lisa; Prunier, Jérôme G; Paz-Vinas, Ivan; Loot, Géraldine; Veyssière, Charlotte; Blanchet, Simon

2018-04-01

Identifying landscape features that affect functional connectivity among populations is a major challenge in fundamental and applied sciences. Landscape genetics combines landscape and genetic data to address this issue, with the main objective of disentangling direct and indirect relationships among an intricate set of variables. Causal modeling has strong potential to address the complex nature of landscape genetic data sets. However, this statistical approach was not initially developed to address the pairwise distance matrices commonly used in landscape genetics. Here, we aimed to extend the applicability of two causal modeling methods-that is, maximum-likelihood path analysis and the directional separation test-by developing statistical approaches aimed at handling distance matrices and improving functional connectivity inference. Using simulations, we showed that these approaches greatly improved the robustness of the absolute (using a frequentist approach) and relative (using an information-theoretic approach) fits of the tested models. We used an empirical data set combining genetic information on a freshwater fish species (Gobio occitaniae) and detailed landscape descriptors to demonstrate the usefulness of causal modeling to identify functional connectivity in wild populations. Specifically, we demonstrated how direct and indirect relationships involving altitude, temperature, and oxygen concentration influenced within- and between-population genetic diversity of G. occitaniae.

Fire-mediated disruptive selection can explain the reseeder-resprouter dichotomy in Mediterranean-type vegetation.

PubMed

Altwegg, Res; De Klerk, Helen M; Midgley, Guy F

2015-02-01

Crown fire is a key selective pressure in Mediterranean-type plant communities. Adaptive responses to fire regimes involve trade-offs between investment for persistence (fire survival and resprouting) and reproduction (fire mortality, fast growth to reproductive maturity, and reseeding) as investments that enhance adult survival lower growth and reproductive rates. Southern hemisphere Mediterranean-type ecosystems are dominated by species with either endogenous regeneration from adult resprouting or fire-triggered seedling recruitment. Specifically, on nutrient-poor soils, these are either resprouting or reseeding life histories, with few intermediate forms, despite the fact that the transition between strategies is evolutionarily labile. How did this strong dichotomy evolve? We address this question by developing a stochastic demographic model to assess determinants of relative fitness of reseeders, resprouters and hypothetical intermediate forms. The model was parameterised using published demographic data from South African protea species and run over various relevant fire regime parameters facets. At intermediate fire return intervals, trade-offs between investment in growth versus fire resilience can cause fitness to peak at either of the extremes of the reseeder-resprouter continuum, especially when assuming realistic non-linear shapes for these trade-offs. Under these circumstances, the fitness landscape exhibits a saddle which could lead to disruptive selection. The fitness gradient between the peaks was shallow, which may explain why this life-history trait is phylogenetically labile. Resprouters had maximum fitness at shorter fire-return intervals than reseeders. The model suggests that a strong dichotomy in fire survival strategy depends on a non-linear trade-off between growth and fire persistence traits.

Spatial analysis of instream nitrogen loads and factors controlling nitrogen delivery to streams in the southeastern United States using spatially referenced regression on watershed attributes (SPARROW) and regional classification frameworks

USGS Publications Warehouse

Hoos, A.B.; McMahon, G.

2009-01-01

Understanding how nitrogen transport across the landscape varies with landscape characteristics is important for developing sound nitrogen management policies. We used a spatially referenced regression analysis (SPARROW) to examine landscape characteristics influencing delivery of nitrogen from sources in a watershed to stream channels. Modelled landscape delivery ratio varies widely (by a factor of 4) among watersheds in the southeastern United States - higher in the western part (Tennessee, Alabama, and Mississippi) than in the eastern part, and the average value for the region is lower compared to other parts of the nation. When we model landscape delivery ratio as a continuous function of local-scale landscape characteristics, we estimate a spatial pattern that varies as a function of soil and climate characteristics but exhibits spatial structure in residuals (observed load minus predicted load). The spatial pattern of modelled landscape delivery ratio and the spatial pattern of residuals coincide spatially with Level III ecoregions and also with hydrologic landscape regions. Subsequent incorporation into the model of these frameworks as regional scale variables improves estimation of landscape delivery ratio, evidenced by reduced spatial bias in residuals, and suggests that cross-scale processes affect nitrogen attenuation on the landscape. The model-fitted coefficient values are logically consistent with the hypothesis that broad-scale classifications of hydrologic response help to explain differential rates of nitrogen attenuation, controlling for local-scale landscape characteristics. Negative model coefficients for hydrologic landscape regions where the primary flow path is shallow ground water suggest that a lower fraction of nitrogen mass will be delivered to streams; this relation is reversed for regions where the primary flow path is overland flow.

Spatial analysis of instream nitrogen loads and factors controlling nitrogen delivery to streams in the southeastern United States using spatially referenced regression on watershed attributes (SPARROW) and regional classification frameworks

USGS Publications Warehouse

Hoos, Anne B.; McMahon, Gerard

2009-01-01

Understanding how nitrogen transport across the landscape varies with landscape characteristics is important for developing sound nitrogen management policies. We used a spatially referenced regression analysis (SPARROW) to examine landscape characteristics influencing delivery of nitrogen from sources in a watershed to stream channels. Modelled landscape delivery ratio varies widely (by a factor of 4) among watersheds in the southeastern United States—higher in the western part (Tennessee, Alabama, and Mississippi) than in the eastern part, and the average value for the region is lower compared to other parts of the nation. When we model landscape delivery ratio as a continuous function of local-scale landscape characteristics, we estimate a spatial pattern that varies as a function of soil and climate characteristics but exhibits spatial structure in residuals (observed load minus predicted load). The spatial pattern of modelled landscape delivery ratio and the spatial pattern of residuals coincide spatially with Level III ecoregions and also with hydrologic landscape regions. Subsequent incorporation into the model of these frameworks as regional scale variables improves estimation of landscape delivery ratio, evidenced by reduced spatial bias in residuals, and suggests that cross-scale processes affect nitrogen attenuation on the landscape. The model-fitted coefficient values are logically consistent with the hypothesis that broad-scale classifications of hydrologic response help to explain differential rates of nitrogen attenuation, controlling for local-scale landscape characteristics. Negative model coefficients for hydrologic landscape regions where the primary flow path is shallow ground water suggest that a lower fraction of nitrogen mass will be delivered to streams; this relation is reversed for regions where the primary flow path is overland flow.

Landscape co-evolution and river discharge.

NASA Astrophysics Data System (ADS)

van der Velde, Ype; Temme, Arnaud

2015-04-01

Fresh water is crucial for society and ecosystems. However, our ability to secure fresh water resources under climatic and anthropogenic change is impaired by the complexity of interactions between human society, ecosystems, soils, and topography. These interactions cause landscape properties to co-evolve, continuously changing the flow paths of water through the landscape. These co-evolution driven flow path changes and their effect on river runoff are, to-date, poorly understood. In this presentation we introduce a spatially distributed landscape evolution model that incorporates growing vegetation and its effect on evapotranspiration, interception, infiltration, soil permeability, groundwater-surface water exchange and erosion. This landscape scale (10km2) model is calibrated to evolve towards well known empirical organising principles such as the Budyko curve and Hacks law under different climate conditions. To understand how positive and negative feedbacks within the model structure form complex landscape patterns of forests and peat bogs that resemble observed landscapes under humid and boreal climates, we analysed the effects of individual processes on the spatial distribution of vegetation and river peak and mean flows. Our results show that especially river peak flows and droughts decrease with increasing evolution of the landscape, which is a result that has direct implications for flood management.

Electrical transport measurements of thin film samples under high hydrostatic pressure

NASA Astrophysics Data System (ADS)

Zabaleta, J.; Parks, S. C.; Baum, B.; Teker, A.; Syassen, K.; Mannhart, J.

2017-03-01

We present a method to perform electrical measurements of epitaxial films and heterostructures a few nanometers thick under high hydrostatic pressures in a diamond anvil cell (DAC). Hydrostatic pressure offers the possibility to tune the rich landscape of properties shown by epitaxial heterostructures, systems in which the combination of different materials, performed with atomic precision, can give rise to properties not present in their individual constituents. Measuring electrical conductivity under hydrostatic pressure in these systems requires a robust method that can address all the challenges: the preparation of the sample with side length and thickness that fits in the DAC setup, a contacting method compatible with liquid media, a gasket insulation that resists high forces, as well as an accurate procedure to place the sample in the pressure chamber. We prove the robustness of the method described by measuring the resistance of a two dimensional electron system buried at the interface between two insulating oxides under hydrostatic conditions up to ˜5 GPa. The setup remains intact until ˜10 GPa, where large pressure gradients affect the two dimensional conductivity.

Electrical transport measurements of thin film samples under high hydrostatic pressure.

PubMed

Zabaleta, J; Parks, S C; Baum, B; Teker, A; Syassen, K; Mannhart, J

2017-03-01

We present a method to perform electrical measurements of epitaxial films and heterostructures a few nanometers thick under high hydrostatic pressures in a diamond anvil cell (DAC). Hydrostatic pressure offers the possibility to tune the rich landscape of properties shown by epitaxial heterostructures, systems in which the combination of different materials, performed with atomic precision, can give rise to properties not present in their individual constituents. Measuring electrical conductivity under hydrostatic pressure in these systems requires a robust method that can address all the challenges: the preparation of the sample with side length and thickness that fits in the DAC setup, a contacting method compatible with liquid media, a gasket insulation that resists high forces, as well as an accurate procedure to place the sample in the pressure chamber. We prove the robustness of the method described by measuring the resistance of a two dimensional electron system buried at the interface between two insulating oxides under hydrostatic conditions up to ∼5 GPa. The setup remains intact until ∼10 GPa, where large pressure gradients affect the two dimensional conductivity.

Intraspecific competition reduces niche width in experimental populations

PubMed Central

Parent, Christine E; Agashe, Deepa; Bolnick, Daniel I

2014-01-01

Intraspecific competition is believed to drive niche expansion, because otherwise suboptimal resources can provide a refuge from competition for preferred resources. Competitive niche expansion is well supported by empirical observations, experiments, and theory, and is often invoked to explain phenotypic diversification within populations, some forms of speciation, and adaptive radiation. However, some foraging models predict the opposite outcome, and it therefore remains unclear whether competition will promote or inhibit niche expansion. We conducted experiments to test whether competition changes the fitness landscape to favor niche expansion, and if competition indeed drives niche expansion as expected. Using Tribolium castaneum flour beetles fed either wheat (their ancestral resource), corn (a novel resource) or mixtures of both resources, we show that fitness is maximized on a mixed diet. Next, we show that at higher population density, the optimal diet shifts toward greater use of corn, favoring niche expansion. In stark contrast, when beetles were given a choice of resources, we found that competition caused niche contraction onto the ancestral resource. This presents a puzzling mismatch between how competition alters the fitness landscape, versus competition's effects on resource use. We discuss several explanations for this mismatch, highlighting potential reasons why optimality models might be misleading. PMID:25505525

Towards a mechanistic foundation of evolutionary theory.

PubMed

Doebeli, Michael; Ispolatov, Yaroslav; Simon, Burt

2017-02-15

Most evolutionary thinking is based on the notion of fitness and related ideas such as fitness landscapes and evolutionary optima. Nevertheless, it is often unclear what fitness actually is, and its meaning often depends on the context. Here we argue that fitness should not be a basal ingredient in verbal or mathematical descriptions of evolution. Instead, we propose that evolutionary birth-death processes, in which individuals give birth and die at ever-changing rates, should be the basis of evolutionary theory, because such processes capture the fundamental events that generate evolutionary dynamics. In evolutionary birth-death processes, fitness is at best a derived quantity, and owing to the potential complexity of such processes, there is no guarantee that there is a simple scalar, such as fitness, that would describe long-term evolutionary outcomes. We discuss how evolutionary birth-death processes can provide useful perspectives on a number of central issues in evolution.

Historical range of variability in landscape structure: a simulation study in Oregon, USA.

Treesearch

Etsuko Nonaka; Thomas A. Spies

2005-01-01

We estimated the historical range of variability (HRV) of forest landscape structure under natural disturbance regimes at the scale of a physiographic province (Oregon Coast Range, 2 million ha) and evaluated the similarity to HRV of current and future landscapes under alternative management scenarios. We used a stochastic fire simulation model to simulate...

Loss surface of XOR artificial neural networks

NASA Astrophysics Data System (ADS)

Mehta, Dhagash; Zhao, Xiaojun; Bernal, Edgar A.; Wales, David J.

2018-05-01

Training an artificial neural network involves an optimization process over the landscape defined by the cost (loss) as a function of the network parameters. We explore these landscapes using optimization tools developed for potential energy landscapes in molecular science. The number of local minima and transition states (saddle points of index one), as well as the ratio of transition states to minima, grow rapidly with the number of nodes in the network. There is also a strong dependence on the regularization parameter, with the landscape becoming more convex (fewer minima) as the regularization term increases. We demonstrate that in our formulation, stationary points for networks with Nh hidden nodes, including the minimal network required to fit the XOR data, are also stationary points for networks with Nh+1 hidden nodes when all the weights involving the additional node are zero. Hence, smaller networks trained on XOR data are embedded in the landscapes of larger networks. Our results clarify certain aspects of the classification and sensitivity (to perturbations in the input data) of minima and saddle points for this system, and may provide insight into dropout and network compression.

Multivariate landscape trajectory analysis: An example using simulation modeling of American marten habitat change under four timber harvest scenarios

Treesearch

Samuel A. Cushman; Kevin McGarigal

2007-01-01

Integrating temporal variabilily into spatial analyses is one of the abiding challenges in landscape ecology. In this chapter we use landscape trajectory analysis to assess changes in landscape patterns over time. Landscape trajectory analysis is an approach to quantify changes in landscape structure over time. There are three key concepts which underlie the...

Adaptation and Coevolution on an Emergent Global Competitive Landscape

NASA Astrophysics Data System (ADS)

Fellman, Philip Vos; Post, Jonathan Vos; Wright, Roxana; Dasari, Usha

Notions of Darwinian selection have been implicit in economic theory for at least sixty years. Richard Nelson and Sidney Winter have argued that while evolutionary thinking was prevalent in prewar economics, the postwar Neoclassical school became almost entirely preoccupied with equilibrium conditions and their mathematical conditions. One of the problems with the economic interpretation of firm selection through competition has been a weak grasp on an incomplete scientific paradigm. As I.F. Price notes: "The biological metaphor has long lurked in the background of management theory largely because the message of 'survival of the fittest' (usually wrongly attributed to Charles Darwin rather than Herbert Spencer) provides a seemingly natural model for market competition (e.g. Alchian 1950, Merrell 1984, Henderson 1989, Moore 1993), without seriously challenging the underlying paradigms of what an organisation is." [1] In this paper we examine the application of dynamic fitness landscape models to economic theory, particularly the theory of technology substitution, drawing on recent work by Kauffman, Arthur, McKelvey, Nelson and Winter, and Windrum and Birchenhall. In particular we use Professor Post's early work with John Holland on the genetic algorithm to explain some of the key differences between static and dynamic approaches to economic modeling.

Agroforestry landscapes and global change: landscape ecology tools for management and conservation

Treesearch

Guillermo Martinez Pastur; Emilie Andrieu; Louis R. Iverson; Pablo Luis Peri

2012-01-01

Forest ecosystems are impacted by multiple uses under the influence of global drivers, and where landscape ecology tools may substantially facilitate the management and conservation of the agroforestry ecosystems. The use of landscape ecology tools was described in the eight papers of the present special issue, including changes in forested landscapes due to...

Developing approaches for linear mixed modeling in landscape genetics through landscape-directed dispersal simulations

USGS Publications Warehouse

Row, Jeffrey R.; Knick, Steven T.; Oyler-McCance, Sara J.; Lougheed, Stephen C.; Fedy, Bradley C.

2017-01-01

Dispersal can impact population dynamics and geographic variation, and thus, genetic approaches that can establish which landscape factors influence population connectivity have ecological and evolutionary importance. Mixed models that account for the error structure of pairwise datasets are increasingly used to compare models relating genetic differentiation to pairwise measures of landscape resistance. A model selection framework based on information criteria metrics or explained variance may help disentangle the ecological and landscape factors influencing genetic structure, yet there are currently no consensus for the best protocols. Here, we develop landscape-directed simulations and test a series of replicates that emulate independent empirical datasets of two species with different life history characteristics (greater sage-grouse; eastern foxsnake). We determined that in our simulated scenarios, AIC and BIC were the best model selection indices and that marginal R2 values were biased toward more complex models. The model coefficients for landscape variables generally reflected the underlying dispersal model with confidence intervals that did not overlap with zero across the entire model set. When we controlled for geographic distance, variables not in the underlying dispersal models (i.e., nontrue) typically overlapped zero. Our study helps establish methods for using linear mixed models to identify the features underlying patterns of dispersal across a variety of landscapes.

Equivalence between Step Selection Functions and Biased Correlated Random Walks for Statistical Inference on Animal Movement.

PubMed

Duchesne, Thierry; Fortin, Daniel; Rivest, Louis-Paul

2015-01-01

Animal movement has a fundamental impact on population and community structure and dynamics. Biased correlated random walks (BCRW) and step selection functions (SSF) are commonly used to study movements. Because no studies have contrasted the parameters and the statistical properties of their estimators for models constructed under these two Lagrangian approaches, it remains unclear whether or not they allow for similar inference. First, we used the Weak Law of Large Numbers to demonstrate that the log-likelihood function for estimating the parameters of BCRW models can be approximated by the log-likelihood of SSFs. Second, we illustrated the link between the two approaches by fitting BCRW with maximum likelihood and with SSF to simulated movement data in virtual environments and to the trajectory of bison (Bison bison L.) trails in natural landscapes. Using simulated and empirical data, we found that the parameters of a BCRW estimated directly from maximum likelihood and by fitting an SSF were remarkably similar. Movement analysis is increasingly used as a tool for understanding the influence of landscape properties on animal distribution. In the rapidly developing field of movement ecology, management and conservation biologists must decide which method they should implement to accurately assess the determinants of animal movement. We showed that BCRW and SSF can provide similar insights into the environmental features influencing animal movements. Both techniques have advantages. BCRW has already been extended to allow for multi-state modeling. Unlike BCRW, however, SSF can be estimated using most statistical packages, it can simultaneously evaluate habitat selection and movement biases, and can easily integrate a large number of movement taxes at multiple scales. SSF thus offers a simple, yet effective, statistical technique to identify movement taxis.

Emergent reorganization of an evolving experimental landscape under changing climatic forcing

NASA Astrophysics Data System (ADS)

Singh, A.; Tejedor, A.; Zaliapin, I. V.; Reinhardt, L.; Foufoula-Georgiou, E.

2014-12-01

Understanding landscape re-organization under changing climatic forcing is fundamental to advancing our understanding of geomorphic transport laws under transient conditions, developing predictive models of landscape response to external perturbations, and interpreting the stratigraphic record for past climates by incorporating possible regime shifts. Real landscape observations for long-term analysis are limited and to this end a high resolution controlled laboratory experiment was conducted at the St. Anthony Falls laboratory at the University of Minnesota. Elevation data were collected at temporal resolution of 5 mins and spatial resolution of 0.5 mm as the landscape approached steady state (for a constant uplift and precipitation rate) and in the transient state (under the same uplift and 5x precipitation). The results reveal rapid topographic re-organization under a five-fold precipitation increase with the fluvial regime expanding into previously debris dominated regime, accelerated erosion happening at hillslope scales, and rivers shifting from an erosion-limited to a transport-limited regime. By studying the space-time structure of the individual erosional and depositional events in terms of their size, location, clustering, and total volume we report complex space-time patterns of change which are scale-dependent and bounded by the river network topology. At the same time, the river network topology itself adjusts at smaller scales, with new channels added to accommodate increased hillslope erosional transport, further adjusting the landscape. Some new ideas related to landscape variability and entropy evolution at different scales during steady and transient states and the possibility of analyzing the self-organization with Optimal Mass Transport (OMT) metrics to infer possible underlying "optimality" principles governing the re-organization will also be presented.

Epigenetic Inheritance across the Landscape.

PubMed

Whipple, Amy V; Holeski, Liza M

2016-01-01

The study of epigenomic variation at the landscape-level in plants may add important insight to studies of adaptive variation. A major goal of landscape genomic studies is to identify genomic regions contributing to adaptive variation across the landscape. Heritable variation in epigenetic marks, resulting in transgenerational plasticity, can influence fitness-related traits. Epigenetic marks are influenced by the genome, the environment, and their interaction, and can be inherited independently of the genome. Thus, epigenomic variation likely influences the heritability of many adaptive traits, but the extent of this influence remains largely unknown. Here, we summarize the relevance of epigenetic inheritance to ecological and evolutionary processes, and review the literature on landscape-level patterns of epigenetic variation. Landscape-level patterns of epigenomic variation in plants generally show greater levels of isolation by distance and isolation by environment then is found for the genome, but the causes of these patterns are not yet clear. Linkage between the environment and epigenomic variation has been clearly shown within a single generation, but demonstrating transgenerational inheritance requires more complex breeding and/or experimental designs. Transgenerational epigenetic variation may alter the interpretation of landscape genomic studies that rely upon phenotypic analyses, but should have less influence on landscape genomic approaches that rely upon outlier analyses or genome-environment associations. We suggest that multi-generation common garden experiments conducted across multiple environments will allow researchers to understand which parts of the epigenome are inherited, as well as to parse out the relative contribution of heritable epigenetic variation to the phenotype.

Epigenetic Inheritance across the Landscape

PubMed Central

Whipple, Amy V.; Holeski, Liza M.

2016-01-01

The study of epigenomic variation at the landscape-level in plants may add important insight to studies of adaptive variation. A major goal of landscape genomic studies is to identify genomic regions contributing to adaptive variation across the landscape. Heritable variation in epigenetic marks, resulting in transgenerational plasticity, can influence fitness-related traits. Epigenetic marks are influenced by the genome, the environment, and their interaction, and can be inherited independently of the genome. Thus, epigenomic variation likely influences the heritability of many adaptive traits, but the extent of this influence remains largely unknown. Here, we summarize the relevance of epigenetic inheritance to ecological and evolutionary processes, and review the literature on landscape-level patterns of epigenetic variation. Landscape-level patterns of epigenomic variation in plants generally show greater levels of isolation by distance and isolation by environment then is found for the genome, but the causes of these patterns are not yet clear. Linkage between the environment and epigenomic variation has been clearly shown within a single generation, but demonstrating transgenerational inheritance requires more complex breeding and/or experimental designs. Transgenerational epigenetic variation may alter the interpretation of landscape genomic studies that rely upon phenotypic analyses, but should have less influence on landscape genomic approaches that rely upon outlier analyses or genome–environment associations. We suggest that multi-generation common garden experiments conducted across multiple environments will allow researchers to understand which parts of the epigenome are inherited, as well as to parse out the relative contribution of heritable epigenetic variation to the phenotype. PMID:27826318

Functional connectivity in replicated urban landscapes in the land snail (Cornu aspersum).

PubMed

Balbi, Manon; Ernoult, Aude; Poli, Pedro; Madec, Luc; Guiller, Annie; Martin, Marie-Claire; Nabucet, Jean; Beaujouan, Véronique; Petit, Eric J

2018-03-01

Urban areas are highly fragmented and thereby exert strong constraints on individual dispersal. Despite this, some species manage to persist in urban areas, such as the garden snail, Cornu aspersum, which is common in cityscapes despite its low mobility. Using landscape genetic approaches, we combined study area replication and multiscale analysis to determine how landscape composition, configuration and connectivity influence snail dispersal across urban areas. At the overall landscape scale, areas with a high percentage of roads decreased genetic differentiation between populations. At the population scale, genetic differentiation was positively linked with building surface, the proportion of borders where wooded patches and roads appeared side by side and the proportion of borders combining wooded patches and other impervious areas. Analyses based on pairwise genetic distances validated the isolation-by-distance and isolation-by-resistance models for this land snail, with an equal fit to least-cost paths and circuit-theory-based models. Each of the 12 landscapes analysed separately yielded specific relations to environmental features, whereas analyses integrating all replicates highlighted general common effects. Our results suggest that urban transport infrastructures facilitate passive snail dispersal. At a local scale, corresponding to active dispersal, unfavourable habitats (wooded and impervious areas) isolate populations. This work upholds the use of replicated landscapes to increase the generalizability of landscape genetics results and shows how multiscale analyses provide insight into scale-dependent processes. © 2018 John Wiley & Sons Ltd.

Visualizing phylogenetic tree landscapes.

PubMed

Wilgenbusch, James C; Huang, Wen; Gallivan, Kyle A

2017-02-02

Genomic-scale sequence alignments are increasingly used to infer phylogenies in order to better understand the processes and patterns of evolution. Different partitions within these new alignments (e.g., genes, codon positions, and structural features) often favor hundreds if not thousands of competing phylogenies. Summarizing and comparing phylogenies obtained from multi-source data sets using current consensus tree methods discards valuable information and can disguise potential methodological problems. Discovery of efficient and accurate dimensionality reduction methods used to display at once in 2- or 3- dimensions the relationship among these competing phylogenies will help practitioners diagnose the limits of current evolutionary models and potential problems with phylogenetic reconstruction methods when analyzing large multi-source data sets. We introduce several dimensionality reduction methods to visualize in 2- and 3-dimensions the relationship among competing phylogenies obtained from gene partitions found in three mid- to large-size mitochondrial genome alignments. We test the performance of these dimensionality reduction methods by applying several goodness-of-fit measures. The intrinsic dimensionality of each data set is also estimated to determine whether projections in 2- and 3-dimensions can be expected to reveal meaningful relationships among trees from different data partitions. Several new approaches to aid in the comparison of different phylogenetic landscapes are presented. Curvilinear Components Analysis (CCA) and a stochastic gradient decent (SGD) optimization method give the best representation of the original tree-to-tree distance matrix for each of the three- mitochondrial genome alignments and greatly outperformed the method currently used to visualize tree landscapes. The CCA + SGD method converged at least as fast as previously applied methods for visualizing tree landscapes. We demonstrate for all three mtDNA alignments that 3D projections significantly increase the fit between the tree-to-tree distances and can facilitate the interpretation of the relationship among phylogenetic trees. We demonstrate that the choice of dimensionality reduction method can significantly influence the spatial relationship among a large set of competing phylogenetic trees. We highlight the importance of selecting a dimensionality reduction method to visualize large multi-locus phylogenetic landscapes and demonstrate that 3D projections of mitochondrial tree landscapes better capture the relationship among the trees being compared.

Navigating the Interface Between Landscape Genetics and Landscape Genomics.

PubMed

Storfer, Andrew; Patton, Austin; Fraik, Alexandra K

2018-01-01

As next-generation sequencing data become increasingly available for non-model organisms, a shift has occurred in the focus of studies of the geographic distribution of genetic variation. Whereas landscape genetics studies primarily focus on testing the effects of landscape variables on gene flow and genetic population structure, landscape genomics studies focus on detecting candidate genes under selection that indicate possible local adaptation. Navigating the transition between landscape genomics and landscape genetics can be challenging. The number of molecular markers analyzed has shifted from what used to be a few dozen loci to thousands of loci and even full genomes. Although genome scale data can be separated into sets of neutral loci for analyses of gene flow and population structure and putative loci under selection for inference of local adaptation, there are inherent differences in the questions that are addressed in the two study frameworks. We discuss these differences and their implications for study design, marker choice and downstream analysis methods. Similar to the rapid proliferation of analysis methods in the early development of landscape genetics, new analytical methods for detection of selection in landscape genomics studies are burgeoning. We focus on genome scan methods for detection of selection, and in particular, outlier differentiation methods and genetic-environment association tests because they are the most widely used. Use of genome scan methods requires an understanding of the potential mismatches between the biology of a species and assumptions inherent in analytical methods used, which can lead to high false positive rates of detected loci under selection. Key to choosing appropriate genome scan methods is an understanding of the underlying demographic structure of study populations, and such data can be obtained using neutral loci from the generated genome-wide data or prior knowledge of a species' phylogeographic history. To this end, we summarize recent simulation studies that test the power and accuracy of genome scan methods under a variety of demographic scenarios and sampling designs. We conclude with a discussion of additional considerations for future method development, and a summary of methods that show promise for landscape genomics studies but are not yet widely used.

Navigating the Interface Between Landscape Genetics and Landscape Genomics

PubMed Central

Storfer, Andrew; Patton, Austin; Fraik, Alexandra K.

2018-01-01

As next-generation sequencing data become increasingly available for non-model organisms, a shift has occurred in the focus of studies of the geographic distribution of genetic variation. Whereas landscape genetics studies primarily focus on testing the effects of landscape variables on gene flow and genetic population structure, landscape genomics studies focus on detecting candidate genes under selection that indicate possible local adaptation. Navigating the transition between landscape genomics and landscape genetics can be challenging. The number of molecular markers analyzed has shifted from what used to be a few dozen loci to thousands of loci and even full genomes. Although genome scale data can be separated into sets of neutral loci for analyses of gene flow and population structure and putative loci under selection for inference of local adaptation, there are inherent differences in the questions that are addressed in the two study frameworks. We discuss these differences and their implications for study design, marker choice and downstream analysis methods. Similar to the rapid proliferation of analysis methods in the early development of landscape genetics, new analytical methods for detection of selection in landscape genomics studies are burgeoning. We focus on genome scan methods for detection of selection, and in particular, outlier differentiation methods and genetic-environment association tests because they are the most widely used. Use of genome scan methods requires an understanding of the potential mismatches between the biology of a species and assumptions inherent in analytical methods used, which can lead to high false positive rates of detected loci under selection. Key to choosing appropriate genome scan methods is an understanding of the underlying demographic structure of study populations, and such data can be obtained using neutral loci from the generated genome-wide data or prior knowledge of a species' phylogeographic history. To this end, we summarize recent simulation studies that test the power and accuracy of genome scan methods under a variety of demographic scenarios and sampling designs. We conclude with a discussion of additional considerations for future method development, and a summary of methods that show promise for landscape genomics studies but are not yet widely used. PMID:29593776

Landscape characteristics influencing the genetic structure of greater sage-grouse within the stronghold of their range: a holistic modeling approach

USGS Publications Warehouse

Row, Jeff R; Oyler-McCance, Sara J.; Fike, Jennifer; O'Donnell, Michael; Doherty, Kevin E.; Aldridge, Cameron L.; Bowen, Zachary H.; Fedy, Brad C.

2015-01-01

Given the significance of animal dispersal to population dynamics and geographic variability, understanding how dispersal is impacted by landscape patterns has major ecological and conservation importance. Speaking to the importance of dispersal, the use of linear mixed models to compare genetic differentiation with pairwise resistance derived from landscape resistance surfaces has presented new opportunities to disentangle the menagerie of factors behind effective dispersal across a given landscape. Here, we combine these approaches with novel resistance surface parameterization to determine how the distribution of high- and low-quality seasonal habitat and individual landscape components shape patterns of gene flow for the greater sage-grouse (Centrocercus urophasianus) across Wyoming. We found that pairwise resistance derived from the distribution of low-quality nesting and winter, but not summer, seasonal habitat had the strongest correlation with genetic differentiation. Although the patterns were not as strong as with habitat distribution, multivariate models with sagebrush cover and landscape ruggedness or forest cover and ruggedness similarly had a much stronger fit with genetic differentiation than an undifferentiated landscape. In most cases, landscape resistance surfaces transformed with 17.33-km-diameter moving windows were preferred, suggesting small-scale differences in habitat were unimportant at this large spatial extent. Despite the emergence of these overall patterns, there were differences in the selection of top models depending on the model selection criteria, suggesting research into the most appropriate criteria for landscape genetics is required. Overall, our results highlight the importance of differences in seasonal habitat preferences to patterns of gene flow and suggest the combination of habitat suitability modeling and linear mixed models with our resistance parameterization is a powerful approach to discerning the effects of landscape on gene flow.

Scale-dependent erosional patterns in steady-state and transient-state landscapes.

PubMed

Tejedor, Alejandro; Singh, Arvind; Zaliapin, Ilya; Densmore, Alexander L; Foufoula-Georgiou, Efi

2017-09-01

Landscape topography is the expression of the dynamic equilibrium between external forcings (for example, climate and tectonics) and the underlying lithology. The magnitude and spatial arrangement of erosional and depositional fluxes dictate the evolution of landforms during both statistical steady state (SS) and transient state (TS) of major landscape reorganization. For SS landscapes, the common expectation is that any point of the landscape has an equal chance to erode below or above the landscape median erosion rate. We show that this is not the case. Afforded by a unique experimental landscape that provided a detailed space-time recording of erosional fluxes and by defining the so-called E50-area curve, we reveal for the first time that there exists a hierarchical pattern of erosion. Specifically, hillslopes and fluvial channels erode more rapidly than the landscape median erosion rate, whereas intervening parts of the landscape in terms of upstream contributing areas (colluvial regime) erode more slowly. We explain this apparent paradox by documenting the dynamic nature of SS landscapes-landscape locations may transition from being a hillslope to being a valley and then to being a fluvial channel due to ridge migration, channel piracy, and small-scale landscape dynamics through time. Under TS conditions caused by increased precipitation, we show that the E50-area curve drastically changes shape during landscape reorganization. Scale-dependent erosional patterns, as observed in this study, suggest benchmarks in evaluating numerical models and interpreting the variability of sampled erosional rates in field landscapes.

Sensitivity of resource selection and connectivity models to landscape definition

Treesearch

Katherine A. Zeller; Kevin McGarigal; Samuel A. Cushman; Paul Beier; T. Winston Vickers; Walter M. Boyce

2017-01-01

Context: The definition of the geospatial landscape is the underlying basis for species-habitat models, yet sensitivity of habitat use inference, predicted probability surfaces, and connectivity models to landscape definition has received little attention. Objectives: We evaluated the sensitivity of resource selection and connectivity models to four landscape...

The Role of River Morphodynamic Disturbance and Groundwater Hydrology As Driving Factors of Riparian Landscape Patterns in Mediterranean Rivers.

PubMed

Rivaes, Rui; Pinheiro, António N; Egger, Gregory; Ferreira, Teresa

2017-01-01

Fluvial disturbances, especially floods and droughts, are the main drivers of the successional patterns of riparian vegetation. Those disturbances control the riparian landscape dynamics through the direct interaction between flow and vegetation. The main aim of this work is to investigate the specific paths by which fluvial disturbances, distributed by its components of groundwater hydrology (grndh) and morphodynamic disturbance (mrphd), drive riparian landscape patterns as characterized by the location (position in the river corridor) and shape (physical form of the patch) of vegetation patches in Mediterranean rivers. Specifically, this work assesses how the different components of fluvial disturbances affect these features in general and particularly in each succession phase of riparian vegetation. grndh and mrphd were defined by time and intensity weighted indexes calculated, respectively, from the mean annual water table elevations and the annual maximum instantaneous discharge shear stresses of the previous decade. The interactions between riparian landscape features and fluvial disturbances were assessed by confirmatory factor analysis using structural equation modeling. Two hypothetical models for patch location and shape were conceptualized and tested against empirical data collected from 220 patches at four different study sites. Both models were successfully fitted, meaning that they adequately depicted the relationships between the variables. Furthermore, the models achieved a good adjustment for the observed data, based on the evaluation of several approximate fit indexes. The patch location model explained approximately 80% of the patch location variability, demonstrating that the location of the riparian patches is primarily driven by grndh, while the mrphd had very little effect on this feature. In a multigroup analysis regarding the succession phases of riparian vegetation, the fitted model explained more than 68% of the variance of the data, confirming the results of the general model. The patch shape model explained nearly 13% of the patch shape variability, in which the disturbances came to have less influence on driving this feature. However, grndh continues to be the primary driver of riparian vegetation between the two disturbance factors, despite the proportional increase of the mrphd effect to approximately a third of the grndh effect.

The Role of River Morphodynamic Disturbance and Groundwater Hydrology As Driving Factors of Riparian Landscape Patterns in Mediterranean Rivers

PubMed Central

Rivaes, Rui; Pinheiro, António N.; Egger, Gregory; Ferreira, Teresa

2017-01-01

Fluvial disturbances, especially floods and droughts, are the main drivers of the successional patterns of riparian vegetation. Those disturbances control the riparian landscape dynamics through the direct interaction between flow and vegetation. The main aim of this work is to investigate the specific paths by which fluvial disturbances, distributed by its components of groundwater hydrology (grndh) and morphodynamic disturbance (mrphd), drive riparian landscape patterns as characterized by the location (position in the river corridor) and shape (physical form of the patch) of vegetation patches in Mediterranean rivers. Specifically, this work assesses how the different components of fluvial disturbances affect these features in general and particularly in each succession phase of riparian vegetation. grndh and mrphd were defined by time and intensity weighted indexes calculated, respectively, from the mean annual water table elevations and the annual maximum instantaneous discharge shear stresses of the previous decade. The interactions between riparian landscape features and fluvial disturbances were assessed by confirmatory factor analysis using structural equation modeling. Two hypothetical models for patch location and shape were conceptualized and tested against empirical data collected from 220 patches at four different study sites. Both models were successfully fitted, meaning that they adequately depicted the relationships between the variables. Furthermore, the models achieved a good adjustment for the observed data, based on the evaluation of several approximate fit indexes. The patch location model explained approximately 80% of the patch location variability, demonstrating that the location of the riparian patches is primarily driven by grndh, while the mrphd had very little effect on this feature. In a multigroup analysis regarding the succession phases of riparian vegetation, the fitted model explained more than 68% of the variance of the data, confirming the results of the general model. The patch shape model explained nearly 13% of the patch shape variability, in which the disturbances came to have less influence on driving this feature. However, grndh continues to be the primary driver of riparian vegetation between the two disturbance factors, despite the proportional increase of the mrphd effect to approximately a third of the grndh effect. PMID:28979278

Understanding the Spatial Distribution and Quantity of Soil Organic Carbon in Depressional Landscapes of Minnesota

NASA Astrophysics Data System (ADS)

Wu, A.; Bell, J. C.; Nater, E. A.

2012-12-01

Human disturbance has dramatically affected organic carbon cycling in soils. The Des Moines Lobe region of Minnesota is a young glaciated region with closed depressions and a deranged drainage network. Native prairie and forests in this region were nearly all converted to cropland following European settlement circa 1840s. It has generally been assumed that intensive tillage intensifies soil erosion and increases the rate of oxidation of soil organic carbon (SOC) and the subsequent release of carbon dioxide (CO2) to the atmosphere. However, more recent studies suggest that tillage simply redistributes sediments and SOC to concave and low-lying areas, and that dynamic replacement of SOC at erosional sites and burial of SOC in poorly-aerated depressional wetlands may serve as a soil carbon sink in this region. The spatial distribution of SOC in these depressional landscapes following tillage and subsequent erosion/deposition is not well understood. We aim to understand the distribution of SOC in relation to topographic controls at the landscape scale and to quantify SOC contents at the regional extent. While spatial distribution of SOC can be modeled by terrain analysis, topographic characteristics used to predict soil properties including SOC have been mostly limited to local neighborhoods (i.e. attributes calculated using three by three cell-sized windows in gridded datasets). Relevant topographic characteristics in the upslope contributing area (UCA) were rarely applied in soil-landscape models, possibly due to technical complexity. Our objectives in this study were: 1. To develop variables that represent UCA terrain attributes for soil-landscape modeling, 2. to predict SOC distribution and mass contents from the best-fit spatial SOC models with model validation for use in this depressional landscape region, and 3. to interpret SOC processes under the impact of agriculture-induced erosion and deposition since the settlement in this region. We took soil samples by soil horizon to a depth of 1m in transects following hillslope positions at our study site at Lake Rebecca Park Reserve. A mass-preserving spline function was applied to provide the mean SOC values (%) in 25cm increments to 1m deep from horizon-based field data in order to model SOC in fixed depths. Local neighborhood terrain attributes, including elevation, slope steepness, slope length, specific catchment area, profile curvature, plan curvature, topographic wetness index and stream power index, were developed from a LiDAR-based 1-m digital elevation model. Gridded UCA datasets for each sampling site were carefully queried and investigated. Mean and standard deviation of the terrain attributes within the UCA were extracted as representative variables for the UCA terrain attributes. We applied both local and upslope terrain attributes as predictor variables for spatial SOC modeling using regression and principle component regression analyses. Performance and validation of the SOC models were investigated. Intending to apply the best-fit SOC model at the regional scale, we validated the models using SOC data from soil samples taken in thirteen counties with similar Des Moines Lobe till landscapes in south-central Minnesota. The spatial distribution of SOC was mapped and the overall SOC mass (kg/m3) was estimated for this region of Minnesota.

Uncovering the Nutritional Landscape of Food

PubMed Central

Kim, Seunghyeon; Sung, Jaeyun; Foo, Mathias; Jin, Yong-Su; Kim, Pan-Jun

2015-01-01

Recent progresses in data-driven analysis methods, including network-based approaches, are revolutionizing many classical disciplines. These techniques can also be applied to food and nutrition, which must be studied to design healthy diets. Using nutritional information from over 1,000 raw foods, we systematically evaluated the nutrient composition of each food in regards to satisfying daily nutritional requirements. The nutrient balance of a food was quantified and termed nutritional fitness; this measure was based on the food’s frequency of occurrence in nutritionally adequate food combinations. Nutritional fitness offers a way to prioritize recommendable foods within a global network of foods, in which foods are connected based on the similarities of their nutrient compositions. We identified a number of key nutrients, such as choline and α-linolenic acid, whose levels in foods can critically affect the nutritional fitness of the foods. Analogously, pairs of nutrients can have the same effect. In fact, two nutrients can synergistically affect the nutritional fitness, although the individual nutrients alone may not have an impact. This result, involving the tendency among nutrients to exhibit correlations in their abundances across foods, implies a hidden layer of complexity when exploring for foods whose balance of nutrients within pairs holistically helps meet nutritional requirements. Interestingly, foods with high nutritional fitness successfully maintain this nutrient balance. This effect expands our scope to a diverse repertoire of nutrient-nutrient correlations, which are integrated under a common network framework that yields unexpected yet coherent associations between nutrients. Our nutrient-profiling approach combined with a network-based analysis provides a more unbiased, global view of the relationships between foods and nutrients, and can be extended towards nutritional policies, food marketing, and personalized nutrition. PMID:25768022

Mutational Effects and Population Dynamics During Viral Adaptation Challenge Current Models

PubMed Central

Miller, Craig R.; Joyce, Paul; Wichman, Holly A.

2011-01-01

Adaptation in haploid organisms has been extensively modeled but little tested. Using a microvirid bacteriophage (ID11), we conducted serial passage adaptations at two bottleneck sizes (104 and 106), followed by fitness assays and whole-genome sequencing of 631 individual isolates. Extensive genetic variation was observed including 22 beneficial, several nearly neutral, and several deleterious mutations. In the three large bottleneck lines, up to eight different haplotypes were observed in samples of 23 genomes from the final time point. The small bottleneck lines were less diverse. The small bottleneck lines appeared to operate near the transition between isolated selective sweeps and conditions of complex dynamics (e.g., clonal interference). The large bottleneck lines exhibited extensive interference and less stochasticity, with multiple beneficial mutations establishing on a variety of backgrounds. Several leapfrog events occurred. The distribution of first-step adaptive mutations differed significantly from the distribution of second-steps, and a surprisingly large number of second-step beneficial mutations were observed on a highly fit first-step background. Furthermore, few first-step mutations appeared as second-steps and second-steps had substantially smaller selection coefficients. Collectively, the results indicate that the fitness landscape falls between the extremes of smooth and fully uncorrelated, violating the assumptions of many current mutational landscape models. PMID:21041559

Weathering and landscape evolution

NASA Astrophysics Data System (ADS)

Turkington, Alice V.; Phillips, Jonathan D.; Campbell, Sean W.

2005-04-01

In recognition of the fundamental control exerted by weathering on landscape evolution and topographic development, the 35th Binghamton Geomorphology Symposium was convened under the theme of Weathering and Landscape Evolution. The papers and posters presented at the conference imparted the state-of-the-art in weathering geomorphology, tackled the issue of scale linkage in geomorphic studies and offered a vehicle for interdisciplinary communication on research into weathering and landscape evolution. The papers included in this special issue are encapsulated here under the general themes of weathering mantles, weathering and relative dating, weathering and denudation, weathering processes and controls and the 'big picture'.

The promise of genomics in the study of plant-pollinator interactions

PubMed Central

2013-01-01

Flowers exist in exceedingly complex fitness landscapes, in which subtle variation in each trait can affect the pollinators, herbivores and pleiotropically linked traits in other plant tissues. A whole-genome approach to flower evolution will help our understanding of plant-pollinator interactions. PMID:23796166

Living on the Future Edge: Windows on Tomorrow

ERIC Educational Resources Information Center

Jukes, Ian; McCain, Ted; Crockett, Lee

2010-01-01

"Living on the Future Edge" challenges school leaders to rethink longstanding paradigms and transform pedagogy for tomorrow's learners. Apple Computer, Inc. co-founder Steve Wozniak's foreword underscores the overwhelming need to adjust traditional instruction to fit today's high-tech world. The book explores this new landscape and…

Scale-dependent erosional patterns in steady-state and transient-state landscapes

PubMed Central

Tejedor, Alejandro; Singh, Arvind; Zaliapin, Ilya; Densmore, Alexander L.; Foufoula-Georgiou, Efi

2017-01-01

Landscape topography is the expression of the dynamic equilibrium between external forcings (for example, climate and tectonics) and the underlying lithology. The magnitude and spatial arrangement of erosional and depositional fluxes dictate the evolution of landforms during both statistical steady state (SS) and transient state (TS) of major landscape reorganization. For SS landscapes, the common expectation is that any point of the landscape has an equal chance to erode below or above the landscape median erosion rate. We show that this is not the case. Afforded by a unique experimental landscape that provided a detailed space-time recording of erosional fluxes and by defining the so-called E50-area curve, we reveal for the first time that there exists a hierarchical pattern of erosion. Specifically, hillslopes and fluvial channels erode more rapidly than the landscape median erosion rate, whereas intervening parts of the landscape in terms of upstream contributing areas (colluvial regime) erode more slowly. We explain this apparent paradox by documenting the dynamic nature of SS landscapes—landscape locations may transition from being a hillslope to being a valley and then to being a fluvial channel due to ridge migration, channel piracy, and small-scale landscape dynamics through time. Under TS conditions caused by increased precipitation, we show that the E50-area curve drastically changes shape during landscape reorganization. Scale-dependent erosional patterns, as observed in this study, suggest benchmarks in evaluating numerical models and interpreting the variability of sampled erosional rates in field landscapes. PMID:28959728

Using ancient protein kinases to unravel a modern cancer drug's mechanism

DOE PAGES

Wilson, C.; Agafonov, R. V.; Hoemberger, M.; ...

2015-02-19

Macromolecular function is rooted in energy landscapes, where sequence determines not a single structure but an ensemble of conformations. Hence, evolution modifies a protein’s function by altering its energy landscape. Consequently, we recreate the evolutionary pathway between two modern human oncogenes, Src and Abl, by reconstructing their common ancestors. Our evolutionary reconstruction combined with x-ray structures of the common ancestor and pre–steady-state kinetics reveals a detailed atomistic mechanism for selectivity of the successful cancer drug Gleevec. Gleevec affinity is gained during the evolutionary trajectory toward Abl and lost toward Src, primarily by shifting an induced-fit equilibrium that is also disruptedmore » in the clinical T315I resistance mutation. Lastly, this work reveals the mechanism of Gleevec specificity while offering insights into how energy landscapes evolve.« less

Farmers' contribution to landscape services in the Netherlands under different rural development scenarios.

PubMed

Pfeifer, Catherine; Sonneveld, Marthijn P W; Stoorvogel, Jetse J

2012-11-30

Landscape services represent the benefits human populations derive, directly or indirectly, from (agro-)ecosystem functions at the landscape scale. Many of these services are the result of farmers' decision making to allocate resources to other activities than food production and therefore are the result of farm the adoption of on-farm rural activities. With changing agricultural and rural policies, the future provision of landscape services to fulfill societal demands is not guaranteed. This study aims at mapping the spatial distribution of the adoption of on-farm rural activities under different explorative scenarios. For a Dutch landscape, storylines at the landscape scale were developed by combining global storylines, resulting from the Global Environmental Outlook, with local storylines resulting from key informant interviews. Subsequently these storylines were translated into quantitative scenarios that were implemented into a simulation procedure based on spatially explicit econometric models of farmer's decision making. Results show that further market liberalization leads to a decrease of landscape services in the study area. In our study, only increased cooperation between government, farmers and citizens appears to result in a general increase of all landscape services across the entire landscape. Copyright © 2012 Elsevier Ltd. All rights reserved.

Improving the Fitness of High-Dimensional Biomechanical Models via Data-Driven Stochastic Exploration

PubMed Central

Bustamante, Carlos D.; Valero-Cuevas, Francisco J.

2010-01-01

The field of complex biomechanical modeling has begun to rely on Monte Carlo techniques to investigate the effects of parameter variability and measurement uncertainty on model outputs, search for optimal parameter combinations, and define model limitations. However, advanced stochastic methods to perform data-driven explorations, such as Markov chain Monte Carlo (MCMC), become necessary as the number of model parameters increases. Here, we demonstrate the feasibility and, what to our knowledge is, the first use of an MCMC approach to improve the fitness of realistically large biomechanical models. We used a Metropolis–Hastings algorithm to search increasingly complex parameter landscapes (3, 8, 24, and 36 dimensions) to uncover underlying distributions of anatomical parameters of a “truth model” of the human thumb on the basis of simulated kinematic data (thumbnail location, orientation, and linear and angular velocities) polluted by zero-mean, uncorrelated multivariate Gaussian “measurement noise.” Driven by these data, ten Markov chains searched each model parameter space for the subspace that best fit the data (posterior distribution). As expected, the convergence time increased, more local minima were found, and marginal distributions broadened as the parameter space complexity increased. In the 36-D scenario, some chains found local minima but the majority of chains converged to the true posterior distribution (confirmed using a cross-validation dataset), thus demonstrating the feasibility and utility of these methods for realistically large biomechanical problems. PMID:19272906

Present Day Biology seen in the Looking Glass of Physics of Complexity

NASA Astrophysics Data System (ADS)

Schuster, P.

Darwin's theory of variation and selection in its simplest form is directly applicable to RNA evolution in vitro as well as to virus evolution, and it allows for quantitative predictions. Understanding evolution at the molecular level is ultimately related to the central paradigm of structural biology: sequence⇒ structure ⇒ function. We elaborate on the state of the art in modeling and understanding evolution of RNA driven by reproduction and mutation. The focus will be laid on the landscape concept—originally introduced by Sewall Wright—and its application to problems in biology. The relation between genotypes and phenotypes is the result of two consecutive mappings from a space of genotypes called sequence space onto a space of phenotypes or structures, and fitness is the result of a mapping from phenotype space into non-negative real numbers. Realistic landscapes as derived from folding of RNA sequences into structures are characterized by two properties: (i) they are rugged in the sense that sequences lying nearby in sequence space may have very different fitness values and (ii) they are characterized by an appreciable degree of neutrality implying that a certain fraction of genotypes and/or phenotypes cannot be distinguished in the selection process. Evolutionary dynamics on realistic landscapes will be studied as a function of the mutation rate, and the role of neutrality in the selection process will be discussed.

Prediction of fish and sediment mercury in streams using landscape variables and historical mining.

PubMed

Alpers, Charles N; Yee, Julie L; Ackerman, Joshua T; Orlando, James L; Slotton, Darrel G; Marvin-DiPasquale, Mark C

2016-11-15

Widespread mercury (Hg) contamination of aquatic systems in the Sierra Nevada of California, U.S., is associated with historical use to enhance gold (Au) recovery by amalgamation. In areas affected by historical Au mining operations, including the western slope of the Sierra Nevada and downstream areas in northern California, such as San Francisco Bay and the Sacramento River-San Joaquin River Delta, microbial conversion of Hg to methylmercury (MeHg) leads to bioaccumulation of MeHg in food webs, and increased risks to humans and wildlife. This study focused on developing a predictive model for THg in stream fish tissue based on geospatial data, including land use/land cover data, and the distribution of legacy Au mines. Data on total mercury (THg) and MeHg concentrations in fish tissue and streambed sediment collected during 1980-2012 from stream sites in the Sierra Nevada, California were combined with geospatial data to estimate fish THg concentrations across the landscape. THg concentrations of five fish species (Brown Trout, Rainbow Trout, Sacramento Pikeminnow, Sacramento Sucker, and Smallmouth Bass) within stream sections were predicted using multi-model inference based on Akaike Information Criteria, using geospatial data for mining history and landscape characteristics as well as fish species and length (r(2)=0.61, p<0.001). Including THg concentrations in streambed sediment did not improve the model's fit, however including MeHg concentrations in streambed sediment, organic content (loss on ignition), and sediment grain size resulted in an improved fit (r(2)=0.63, p<0.001). These models can be used to estimate THg concentrations in stream fish based on landscape variables in the Sierra Nevada in areas where direct measurements of THg concentration in fish are unavailable. Published by Elsevier B.V.

Prediction of fish and sediment mercury in streams using landscape variables and historical mining

USGS Publications Warehouse

Alpers, Charles N.; Yee, Julie L.; Ackerman, Joshua T.; Orlando, James L.; Slotton, Darrell G.; Marvin-DiPasquale, Mark C.

2016-01-01

Widespread mercury (Hg) contamination of aquatic systems in the Sierra Nevada of California, U.S., is associated with historical use to enhance gold (Au) recovery by amalgamation. In areas affected by historical Au mining operations, including the western slope of the Sierra Nevada and downstream areas in northern California, such as San Francisco Bay and the Sacramento River–San Joaquin River Delta, microbial conversion of Hg to methylmercury (MeHg) leads to bioaccumulation of MeHg in food webs, and increased risks to humans and wildlife. This study focused on developing a predictive model for THg in stream fish tissue based on geospatial data, including land use/land cover data, and the distribution of legacy Au mines. Data on total mercury (THg) and MeHg concentrations in fish tissue and streambed sediment collected during 1980–2012 from stream sites in the Sierra Nevada, California were combined with geospatial data to estimate fish THg concentrations across the landscape. THg concentrations of five fish species (Brown Trout, Rainbow Trout, Sacramento Pikeminnow, Sacramento Sucker, and Smallmouth Bass) within stream sections were predicted using multi-model inference based on Akaike Information Criteria, using geospatial data for mining history and landscape characteristics as well as fish species and length (r2 = 0.61, p < 0.001). Including THg concentrations in streambed sediment did not improve the model's fit, however including MeHg concentrations in streambed sediment, organic content (loss on ignition), and sediment grain size resulted in an improved fit (r2 = 0.63, p < 0.001). These models can be used to estimate THg concentrations in stream fish based on landscape variables in the Sierra Nevada in areas where direct measurements of THg concentration in fish are unavailable.

A consistent positive association between landscape simplification and insecticide use across the Midwestern US from 1997 through 2012

DOE PAGES

Meehan, Timothy D.; Gratton, Claudio

2015-10-27

During 2007, counties across the Midwestern US with relatively high levels of landscape simplification (i.e., widespread replacement of seminatural habitats with cultivated crops) had relatively high crop-pest abundances which, in turn, were associated with relatively high insecticide application. These results suggested a positive relationship between landscape simplification and insecticide use, mediated by landscape effects on crop pests or their natural enemies. A follow-up study, in the same region but using different statistical methods, explored the relationship between landscape simplification and insecticide use between 1987 and 2007, and concluded that the relationship varied substantially in sign and strength across years. Here,more » we explore this relationship from 1997 through 2012, using a single dataset and two different analytical approaches. We demonstrate that, when using ordinary least squares (OLS) regression, the relationship between landscape simplification and insecticide use is, indeed, quite variable over time. However, the residuals from OLS models show strong spatial autocorrelation, indicating spatial structure in the data not accounted for by explanatory variables, and violating a standard assumption of OLS. When modeled using spatial regression techniques, relationships between landscape simplification and insecticide use were consistently positive between 1997 and 2012, and model fits were dramatically improved. We argue that spatial regression methods are more appropriate for these data, and conclude that there remains compelling correlative support for a link between landscape simplification and insecticide use in the Midwestern US. We discuss the limitations of inference from this and related studies, and suggest improved data collection campaigns for better understanding links between landscape structure, crop-pest pressure, and pest-management practices.« less

A consistent positive association between landscape simplification and insecticide use across the Midwestern US from 1997 through 2012

DOE Office of Scientific and Technical Information (OSTI.GOV)

Meehan, Timothy D.; Gratton, Claudio

During 2007, counties across the Midwestern US with relatively high levels of landscape simplification (i.e., widespread replacement of seminatural habitats with cultivated crops) had relatively high crop-pest abundances which, in turn, were associated with relatively high insecticide application. These results suggested a positive relationship between landscape simplification and insecticide use, mediated by landscape effects on crop pests or their natural enemies. A follow-up study, in the same region but using different statistical methods, explored the relationship between landscape simplification and insecticide use between 1987 and 2007, and concluded that the relationship varied substantially in sign and strength across years. Here,more » we explore this relationship from 1997 through 2012, using a single dataset and two different analytical approaches. We demonstrate that, when using ordinary least squares (OLS) regression, the relationship between landscape simplification and insecticide use is, indeed, quite variable over time. However, the residuals from OLS models show strong spatial autocorrelation, indicating spatial structure in the data not accounted for by explanatory variables, and violating a standard assumption of OLS. When modeled using spatial regression techniques, relationships between landscape simplification and insecticide use were consistently positive between 1997 and 2012, and model fits were dramatically improved. We argue that spatial regression methods are more appropriate for these data, and conclude that there remains compelling correlative support for a link between landscape simplification and insecticide use in the Midwestern US. We discuss the limitations of inference from this and related studies, and suggest improved data collection campaigns for better understanding links between landscape structure, crop-pest pressure, and pest-management practices.« less

Anthropogenic Habitats Facilitate Dispersal of an Early Successional Obligate: Implications for Restoration of an Endangered Ecosystem.

PubMed

Amaral, Katrina E; Palace, Michael; O'Brien, Kathleen M; Fenderson, Lindsey E; Kovach, Adrienne I

2016-01-01

Landscape modification and habitat fragmentation disrupt the connectivity of natural landscapes, with major consequences for biodiversity. Species that require patchily distributed habitats, such as those that specialize on early successional ecosystems, must disperse through a landscape matrix with unsuitable habitat types. We evaluated landscape effects on dispersal of an early successional obligate, the New England cottontail (Sylvilagus transitionalis). Using a landscape genetics approach, we identified barriers and facilitators of gene flow and connectivity corridors for a population of cottontails in the northeastern United States. We modeled dispersal in relation to landscape structure and composition and tested hypotheses about the influence of habitat fragmentation on gene flow. Anthropogenic and natural shrubland habitats facilitated gene flow, while the remainder of the matrix, particularly development and forest, impeded gene flow. The relative influence of matrix habitats differed between study areas in relation to a fragmentation gradient. Barrier features had higher explanatory power in the more fragmented site, while facilitating features were important in the less fragmented site. Landscape models that included a simultaneous barrier and facilitating effect of roads had higher explanatory power than models that considered either effect separately, supporting the hypothesis that roads act as both barriers and facilitators at all spatial scales. The inclusion of LiDAR-identified shrubland habitat improved the fit of our facilitator models. Corridor analyses using circuit and least cost path approaches revealed the importance of anthropogenic, linear features for restoring connectivity between the study areas. In fragmented landscapes, human-modified habitats may enhance functional connectivity by providing suitable dispersal conduits for early successional specialists.

Anthropogenic Habitats Facilitate Dispersal of an Early Successional Obligate: Implications for Restoration of an Endangered Ecosystem

PubMed Central

Amaral, Katrina E.; Palace, Michael; O’Brien, Kathleen M.; Fenderson, Lindsey E.; Kovach, Adrienne I.

2016-01-01

Landscape modification and habitat fragmentation disrupt the connectivity of natural landscapes, with major consequences for biodiversity. Species that require patchily distributed habitats, such as those that specialize on early successional ecosystems, must disperse through a landscape matrix with unsuitable habitat types. We evaluated landscape effects on dispersal of an early successional obligate, the New England cottontail (Sylvilagus transitionalis). Using a landscape genetics approach, we identified barriers and facilitators of gene flow and connectivity corridors for a population of cottontails in the northeastern United States. We modeled dispersal in relation to landscape structure and composition and tested hypotheses about the influence of habitat fragmentation on gene flow. Anthropogenic and natural shrubland habitats facilitated gene flow, while the remainder of the matrix, particularly development and forest, impeded gene flow. The relative influence of matrix habitats differed between study areas in relation to a fragmentation gradient. Barrier features had higher explanatory power in the more fragmented site, while facilitating features were important in the less fragmented site. Landscape models that included a simultaneous barrier and facilitating effect of roads had higher explanatory power than models that considered either effect separately, supporting the hypothesis that roads act as both barriers and facilitators at all spatial scales. The inclusion of LiDAR-identified shrubland habitat improved the fit of our facilitator models. Corridor analyses using circuit and least cost path approaches revealed the importance of anthropogenic, linear features for restoring connectivity between the study areas. In fragmented landscapes, human-modified habitats may enhance functional connectivity by providing suitable dispersal conduits for early successional specialists. PMID:26954014

History of the incipient Icelandic plume: Observations from ancient buried landscapes

NASA Astrophysics Data System (ADS)

Stucky de Quay, Gaia; Roberts, Gareth G.; Watson, Jonathan S.; Jackson, Christopher A.-L.

2017-04-01

Ancient buried terrestrial landscapes contain records of vertical motions which can be used to probe histories of geodynamical processes. In the North Atlantic Ocean, sedimentary basins contain excellent evidence that the continental shelf experienced staged subaerial exposure. For example, now buried landscapes were uplifted, rapidly eroded, and drowned close to the Paleocene-Eocene boundary. We use commercial wells and three-dimensional seismic data to reconstruct a 57-55 Ma landscape now buried 1.5 km beneath the seabed in the Bressay area of the northern North Sea. Geochemical analyses of organic matter from core samples intersecting the erosional landscape indicate the presence of angiosperm (flowering plant) debris. Combined with the presence of coarse clastic material, mapped beach ridges, and dendritic drainage patterns, these observations indicate that this landscape was of terrestrial origin. Longitudinal profiles of ancient rivers were extracted and inverted for an uplift rate history. The best-fitting uplift rate history has three phases and total cumulative uplift of 350 m. Biostratigraphic data from surrounding marine stratigraphy indicate that this landscape formed within 1-1.5 Ma. This uplift history is similar to that of a slightly older buried landscape in the Faeroe-Shetland basin 400 km to the west. These records of vertical motion can explained by pulses of anomalously hot asthenosphere spreading out from the incipient Icelandic plume. Using simple isostatic calculations we estimate that the maximum thermal anomaly beneath Bressay was 50˚. Our observations suggest that a thermal anomaly departed the Icelandic plume as early as 58.5 Ma and had highest average temperatures at 55.6 Ma.

Seed transfer zones for a native grass Festuca roemeri: genecological evidence

Treesearch

Barbara L. Wilson; Dale C. Darris; Rob Fiegener; Matthew E. Horning; Keli Kuykendall

2008-01-01

A common-garden study of Festuca roemeri (Pavlick) E. B. Alexeev (Poaceae) revealed substantial genetic variation within and among 47 populations from throughout its range in the Pacific Northwest, USA, for growth, fitness, phenological, and morphological traits. Using climatic and physiographic variables, genetic patterns over the landscape were...

Investigation of denitrifying microbe communities within an agricultural drainage system fitted with low-grade weirs

USDA-ARS?s Scientific Manuscript database

Enhancing wetland characteristics in agricultural drainage ditches with the use of low-grade weirs, has been identified as a potential best management practice (BMP) to mitigate nutrient runoff from agriculture landscapes. This study examined microbe community abundance and diversity involved in den...

"Thrash Yourself Thursday": The Production of the "Healthy" Child through a Fitness-Based PE Practice

ERIC Educational Resources Information Center

McDermott, Lisa

2012-01-01

Saturating the Canadian landscape are media and health industry discourses representing childhood physical "(in)activity" and "obesity" as being at "epidemic" proportion. Increasingly identified as a focus of concern within such representations is the school setting, simultaneously positioned both as a cause of…

Projecting land-use and land cover change in a subtropical urban watershed

Treesearch

John J. Lagrosa IV; Wayne C. Zipperer; Michael G. Andreu

2018-01-01

Urban landscapes are heterogeneous mosaics that develop via significant land-use and land cover (LULC) change. Current LULC models project future landscape patterns, but generally avoid urban landscapes due to heterogeneity. To project LULC change for an urban landscape, we parameterize an established LULC model (Dyna-CLUE) under baseline conditions (continued current...

Influence of forest planning alternatives on landscape pattern and ecosystem processes in northern Wisconsin, USA

Treesearch

Patrick A. Zollner; L. Jay Roberts; Eric J. Gustafson; Hong S. He; Volker Radeloff

2008-01-01

Incorporating an ecosystem management perspective into forest planning requires consideration of the impacts of timber management on a suite of landscape characteristics at broad spatial and long temporal scales. We used the LANDIS forest landscape simulation model to predict forest composition and landscape pattern under seven alternative forest management plans...

A Simple General Model of Evolutionary Dynamics

NASA Astrophysics Data System (ADS)

Thurner, Stefan

Evolution is a process in which some variations that emerge within a population (of, e.g., biological species or industrial goods) get selected, survive, and proliferate, whereas others vanish. Survival probability, proliferation, or production rates are associated with the "fitness" of a particular variation. We argue that the notion of fitness is an a posteriori concept in the sense that one can assign higher fitness to species or goods that survive but one can generally not derive or predict fitness per se. Whereas proliferation rates can be measured, fitness landscapes, that is, the inter-dependence of proliferation rates, cannot. For this reason we think that in a physical theory of evolution such notions should be avoided. Here we review a recent quantitative formulation of evolutionary dynamics that provides a framework for the co-evolution of species and their fitness landscapes (Thurner et al., 2010, Physica A 389, 747; Thurner et al., 2010, New J. Phys. 12, 075029; Klimek et al., 2009, Phys. Rev. E 82, 011901 (2010). The corresponding model leads to a generic evolutionary dynamics characterized by phases of relative stability in terms of diversity, followed by phases of massive restructuring. These dynamical modes can be interpreted as punctuated equilibria in biology, or Schumpeterian business cycles (Schumpeter, 1939, Business Cycles, McGraw-Hill, London) in economics. We show that phase transitions that separate phases of high and low diversity can be approximated surprisingly well by mean-field methods. We demonstrate that the mathematical framework is suited to understand systemic properties of evolutionary systems, such as their proneness to collapse, or their potential for diversification. The framework suggests that evolutionary processes are naturally linked to self-organized criticality and to properties of production matrices, such as their eigenvalue spectra. Even though the model is phrased in general terms it is also practical in the sense that it's predictions can be used to understand a series of experimental data ranging from the fossil record to macroeconomic indices.

Quantifying the underlying landscape and paths of cancer

PubMed Central

Li, Chunhe; Wang, Jin

2014-01-01

Cancer is a disease regulated by the underlying gene networks. The emergence of normal and cancer states as well as the transformation between them can be thought of as a result of the gene network interactions and associated changes. We developed a global potential landscape and path framework to quantify cancer and associated processes. We constructed a cancer gene regulatory network based on the experimental evidences and uncovered the underlying landscape. The resulting tristable landscape characterizes important biological states: normal, cancer and apoptosis. The landscape topography in terms of barrier heights between stable state attractors quantifies the global stability of the cancer network system. We propose two mechanisms of cancerization: one is by the changes of landscape topography through the changes in regulation strengths of the gene networks. The other is by the fluctuations that help the system to go over the critical barrier at fixed landscape topography. The kinetic paths from least action principle quantify the transition processes among normal state, cancer state and apoptosis state. The kinetic rates provide the quantification of transition speeds among normal, cancer and apoptosis attractors. By the global sensitivity analysis of the gene network parameters on the landscape topography, we uncovered some key gene regulations determining the transitions between cancer and normal states. This can be used to guide the design of new anti-cancer tactics, through cocktail strategy of targeting multiple key regulation links simultaneously, for preventing cancer occurrence or transforming the early cancer state back to normal state. PMID:25232051

On the evolution of dispersal via heterogeneity in spatial connectivity

PubMed Central

Henriques-Silva, Renato; Boivin, Frédéric; Calcagno, Vincent; Urban, Mark C.; Peres-Neto, Pedro R.

2015-01-01

Dispersal has long been recognized as a mechanism that shapes many observed ecological and evolutionary processes. Thus, understanding the factors that promote its evolution remains a major goal in evolutionary ecology. Landscape connectivity may mediate the trade-off between the forces in favour of dispersal propensity (e.g. kin-competition, local extinction probability) and those against it (e.g. energetic or survival costs of dispersal). It remains, however, an open question how differing degrees of landscape connectivity may select for different dispersal strategies. We implemented an individual-based model to study the evolution of dispersal on landscapes that differed in the variance of connectivity across patches ranging from networks with all patches equally connected to highly heterogeneous networks. The parthenogenetic individuals dispersed based on a flexible logistic function of local abundance. Our results suggest, all else being equal, that landscapes differing in their connectivity patterns will select for different dispersal strategies and that these strategies confer a long-term fitness advantage to individuals at the regional scale. The strength of the selection will, however, vary across network types, being stronger on heterogeneous landscapes compared with the ones where all patches have equal connectivity. Our findings highlight how landscape connectivity can determine the evolution of dispersal strategies, which in turn affects how we think about important ecological dynamics such as metapopulation persistence and range expansion. PMID:25673685

Using landscape epidemiological models to understand the distribution of chronic wasting disease in the Midwestern USA

USGS Publications Warehouse

Robinson, Stacie J.; Samuel, Michael D.; Rolley, Robert E.; Shelton, Paul

2013-01-01

Animal movement across the landscape plays a critical role in the ecology of infectious wildlife diseases. Dispersing animals can spread pathogens between infected areas and naïve populations. While tracking free-ranging animals over the geographic scales relevant to landscape-level disease management is challenging, landscape features that influence gene flow among wildlife populations may also influence the contact rates and disease spread between populations. We used spatial diffusion and barriers to white-tailed deer gene flow, identified through landscape genetics, to model the distribution of chronic wasting disease (CWD) in the infected region of southern Wisconsin and northern Illinois, USA. Our generalized linear model showed that risk of CWD infection declined exponentially with distance from current outbreaks, and inclusion of gene flow barriers dramatically improved fit and predictive power of the model. Our results indicate that CWD is spreading across the Midwestern landscape from these two endemic foci, but spread is strongly influenced by highways and rivers that also reduce deer gene flow. We used our model to plot a risk map, providing important information for CWD management by identifying likely routes of disease spread and providing a tool for prioritizing disease monitoring and containment efforts. The current analysis may serve as a framework for modeling future disease risk drawing on genetic information to investigate barriers to spread and extending management and monitoring beyond currently affected regions.

Preservation of a Preglacial Landscape Under the Center of the Greenland Ice Sheet

NASA Technical Reports Server (NTRS)

Bierman, Paul R.; Corbett, Lee B.; Graly, Joseph A.; Neumann, Thomas Allen; Lini, Andrea; Crosby, Benjamin T.; Rood, Dylan H.

2014-01-01

Continental ice sheets typically sculpt landscapes via erosion; under certain conditions, ancient landscapes can be preserved beneath ice and can survive extensive and repeated glaciation. We used concentrations of atmospherically produced cosmogenic beryllium-10, carbon, and nitrogen to show that ancient soil has been preserved in basal ice for millions of years at the center of the ice sheet at Summit, Greenland. This finding suggests ice sheet stability through the Pleistocene (i.e., the past 2.7 million years). The preservation of this soil implies that the ice has been non-erosive and frozen to the bed for much of that time, that there was no substantial exposure of central Greenland once the ice sheet became fully established, and that preglacial landscapes can remain preserved for long periods under continental ice sheets

Demographic source-sink dynamics restrict local adaptation in Elliott's blueberry (Vaccinium elliottii).

PubMed

Anderson, Jill T; Geber, Monica A

2010-02-01

In heterogeneous landscapes, divergent selection can favor the evolution of locally adapted ecotypes, especially when interhabitat gene flow is minimal. However, if habitats differ in size or quality, source-sink dynamics can shape evolutionary trajectories. Upland and bottomland forests of the southeastern USA differ in water table depth, light availability, edaphic conditions, and plant community. We conducted a multiyear reciprocal transplant experiment to test whether Elliott's blueberry (Vaccinium elliottii) is locally adapted to these contrasting environments. Additionally, we exposed seedlings and cuttings to prolonged drought and flooding in the greenhouse to assess fitness responses to abiotic stress. Contrary to predictions of local adaptation, V. elliottii families exhibited significantly higher survivorship and growth in upland than in bottomland forests and under drought than flooded conditions, regardless of habitat of origin. Neutral population differentiation was minimal, suggesting widespread interhabitat migration. Population density, reproductive output, and genetic diversity were all significantly greater in uplands than in bottomlands. These disparities likely result in asymmetric gene flow from uplands to bottomlands. Thus, adaptation to a marginal habitat can be constrained by small populations, limited fitness, and immigration from a benign habitat. Our study highlights the importance of demography and genetic diversity in the evolution of local (mal)adaptation.

Landscape dynamics analysis of the Yongding River watershed (Mentougou section) by multi-temporal Landsat imagery

NASA Astrophysics Data System (ADS)

Zhang, Yuhu; Yu, Changqing; Qi, Jiaguo; Zhang, Zili; Shi, Qinshan

2007-11-01

The problem of efficient use of multi-temporal remotely sensed data for land-cover and landscape pattern dynamics has already considerable attention in landscape ecology and some other disciplines. This research develops and tests a methodological approach to monitor and analysis landscape dynamics change of Yongding river watershed (Mentougou section) as study area from 1988 to 2005, The result shows that the OIF is the best method of optimal bands selection in Landsat TM remote sensing data, TM3, 4, 5 bands is optimal band combination ;the Mentougou Reach of Yongding river watershed landscape changed significantly in terms of its composition over the period 1988-2005, The total landscape patches of study area in 2005 are more those in 1988,2001, Mean patch size(MPS)decreased sharply, Number of patches(NP) increased sharply, The landscape pattern takes on the fragmentation trends under the effect on the human activity. The forest (woodland and shrubland)are the main landscape matrix. with a significant decrease in croplands and a increase in built-up (residential, urban land) and industrial minerals mining land(coal, open-pit)over the 17 years, And the underlying socio-economic and other drivers of landscape change in study area are discussed.

Energy landscapes for a machine-learning prediction of patient discharge

NASA Astrophysics Data System (ADS)

Das, Ritankar; Wales, David J.

2016-06-01

The energy landscapes framework is applied to a configuration space generated by training the parameters of a neural network. In this study the input data consists of time series for a collection of vital signs monitored for hospital patients, and the outcomes are patient discharge or continued hospitalisation. Using machine learning as a predictive diagnostic tool to identify patterns in large quantities of electronic health record data in real time is a very attractive approach for supporting clinical decisions, which have the potential to improve patient outcomes and reduce waiting times for discharge. Here we report some preliminary analysis to show how machine learning might be applied. In particular, we visualize the fitting landscape in terms of locally optimal neural networks and the connections between them in parameter space. We anticipate that these results, and analogues of thermodynamic properties for molecular systems, may help in the future design of improved predictive tools.

Crystallization of hard spheres revisited. I. Extracting kinetics and free energy landscape from forward flux sampling.

PubMed

Richard, David; Speck, Thomas

2018-03-28

We investigate the kinetics and the free energy landscape of the crystallization of hard spheres from a supersaturated metastable liquid though direct simulations and forward flux sampling. In this first paper, we describe and test two different ways to reconstruct the free energy barriers from the sampled steady state probability distribution of cluster sizes without sampling the equilibrium distribution. The first method is based on mean first passage times, and the second method is based on splitting probabilities. We verify both methods for a single particle moving in a double-well potential. For the nucleation of hard spheres, these methods allow us to probe a wide range of supersaturations and to reconstruct the kinetics and the free energy landscape from the same simulation. Results are consistent with the scaling predicted by classical nucleation theory although a quantitative fit requires a rather large effective interfacial tension.

Crystallization of hard spheres revisited. I. Extracting kinetics and free energy landscape from forward flux sampling

NASA Astrophysics Data System (ADS)

Richard, David; Speck, Thomas

2018-03-01

We investigate the kinetics and the free energy landscape of the crystallization of hard spheres from a supersaturated metastable liquid though direct simulations and forward flux sampling. In this first paper, we describe and test two different ways to reconstruct the free energy barriers from the sampled steady state probability distribution of cluster sizes without sampling the equilibrium distribution. The first method is based on mean first passage times, and the second method is based on splitting probabilities. We verify both methods for a single particle moving in a double-well potential. For the nucleation of hard spheres, these methods allow us to probe a wide range of supersaturations and to reconstruct the kinetics and the free energy landscape from the same simulation. Results are consistent with the scaling predicted by classical nucleation theory although a quantitative fit requires a rather large effective interfacial tension.

Interactions of landscape disturbances and climate change dictate ecological pattern and process: spatial modeling of wildfire, insect, and disease dynamics under future climates

USGS Publications Warehouse

Loehman, Rachel A.; Keane, Robert E.; Holsinger, Lisa M.; Wu, Zhiwei

2016-01-01

ContextInteractions among disturbances, climate, and vegetation influence landscape patterns and ecosystem processes. Climate changes, exotic invasions, beetle outbreaks, altered fire regimes, and human activities may interact to produce landscapes that appear and function beyond historical analogs.ObjectivesWe used the mechanistic ecosystem-fire process model FireBGCv2 to model interactions of wildland fire, mountain pine beetle (Dendroctonus ponderosae), and white pine blister rust (Cronartium ribicola) under current and future climates, across three diverse study areas.MethodsWe assessed changes in tree basal area as a measure of landscape response over a 300-year simulation period for the Crown of the Continent in north-central Montana, East Fork of the Bitterroot River in western Montana, and Yellowstone Central Plateau in western Wyoming, USA.ResultsInteracting disturbances reduced overall basal area via increased tree mortality of host species. Wildfire decreased basal area more than beetles or rust, and disturbance interactions modeled under future climate significantly altered landscape basal area as compared with no-disturbance and current climate scenarios. Responses varied among landscapes depending on species composition, sensitivity to fire, and pathogen and beetle suitability and susceptibility.ConclusionsUnderstanding disturbance interactions is critical for managing landscapes because forest responses to wildfires, pathogens, and beetle attacks may offset or exacerbate climate influences, with consequences for wildlife, carbon, and biodiversity.

Ornamental and Vegetable Production in the Gulf South

USDA-ARS?s Scientific Manuscript database

Sun coleus (Solenostenum scutellarioides) are commonly used in the southern landscape. However, with the introduction of new cultivars, producers and consumers may be unaware of the selection and landscape performance of sun coleus. Sun coleus cultivars were trialed under landscape conditions at t...

Consumer Survery of Garden Chrysanthemums in Mississippi

USDA-ARS?s Scientific Manuscript database

Sun coleus (Solenostenum scutellarioides) are commonly used in the southern landscape. However, with the introduction of new cultivars, producers and consumers may be unaware of the selection and landscape performance of sun coleus. Sun coleus cultivars were trialed under landscape conditions at t...

What can we learn from fitness landscapes?

PubMed

Hartl, Daniel L

2014-10-01

A combinatorially complete data set consists of studies of all possible combinations of a set of mutant sites in a gene or mutant alleles in a genome. Among the most robust conclusions from these studies is that epistasis between beneficial mutations often shows a pattern of diminishing returns, in which favorable mutations are less fit when combined than would be expected. Another robust inference is that the number of adaptive evolutionary paths is often limited to a relatively small fraction of the theoretical possibilities, owing largely to sign epistasis requiring evolutionary steps that would entail a decrease in fitness. Here we summarize these and other results while also examining issues that remain unresolved and future directions that seem promising. Copyright © 2014 Elsevier Ltd. All rights reserved.

Biological evolution and statistical physics

NASA Astrophysics Data System (ADS)

Drossel, Barbara

2001-03-01

This review is an introduction to theoretical models and mathematical calculations for biological evolution, aimed at physicists. The methods in the field are naturally very similar to those used in statistical physics, although the majority of publications have appeared in biology journals. The review has three parts, which can be read independently. The first part deals with evolution in fitness landscapes and includes Fisher's theorem, adaptive walks, quasispecies models, effects of finite population sizes, and neutral evolution. The second part studies models of coevolution, including evolutionary game theory, kin selection, group selection, sexual selection, speciation, and coevolution of hosts and parasites. The third part discusses models for networks of interacting species and their extinction avalanches. Throughout the review, attention is paid to giving the necessary biological information, and to pointing out the assumptions underlying the models, and their limits of validity.

Measuring internal friction of an ultrafast-folding protein.

PubMed

Cellmer, Troy; Henry, Eric R; Hofrichter, James; Eaton, William A

2008-11-25

Nanosecond laser T-jump was used to measure the viscosity dependence of the folding kinetics of the villin subdomain under conditions where the viscogen has no effect on its equilibrium properties. The dependence of the unfolding/refolding relaxation time on solvent viscosity indicates a major contribution to the dynamics from internal friction. The internal friction increases with increasing temperature, suggesting a shift in the transition state along the reaction coordinate toward the native state with more compact structures, and therefore, a smaller diffusion coefficient due to increased landscape roughness. Fitting the data with an Ising-like model yields a relatively small position dependence for the diffusion coefficient. This finding is consistent with the excellent correlation found between experimental and calculated folding rates based on free energy barrier heights using the same diffusion coefficient for every protein.

Feedbacks Between Channel Adjustment, Sediment Calibre and Landscape Dynamics in Tectonically Perturbed Landscapes (Invited)

NASA Astrophysics Data System (ADS)

Attal, M.; Cowie, P. A.; Whittaker, A. C.; Tucker, G. E.; Mudd, S. M.; Hurst, M. D.

2010-12-01

Knowledge of the coupling between channel geometry and sediment input to rivers is central to understanding the mechanisms and timescales over which landscapes respond to a tectonic perturbation. Here, we document changes to channel geometry and sediment calibre in catchments experiencing a well-constrained increase in relative uplift rate in the Central Apennines (Italy) and the Sierra Nevada (California). In both landscapes, channels and hillslopes steepen and knickpoints propagate upstream through the catchments, leading to the formation of a break in both hillslope and channel gradient that separates the steepened landscape from lower relief topography which has not yet responded to the change in uplift rate. Downstream of this break in slope, channels narrow markedly as river gradient increases. In addition, they are supplied with coarser sediment from the steepened hillslopes, in particular when sediment is supplied via landslides and debris fans. In Italy, channel narrowing can be explained using the equation proposed by Finnegan et al. [2005]: W = kQ3/8S-3/16, where W is channel width, k is a constant, Q is river discharge and S is channel slope. However, to model our field data, the prefactor k must be strongly dependent on uplift rate: the higher the uplift rate, the smaller the prefactor k. Using the Channel-Hillslope Integrated Landscape Development (CHILD) model, we show that the location of the main break in slope along the river profiles in Italy (in terms of height and along stream distance) can be fitted using a detachment-limited model with dynamic channel adjustment (equation above), k dependent on uplift rate and a threshold for erosion. A threshold corresponding to the shear stress required to entrain the median grain size of the sediment along the steepened reaches of the channels best fits the data. Our modelling results show that the response time of the landscape in this setting is strongly dependent on relative uplift rate, since knickpoint retreat rate in the detachment-limited model is a function of channel width and that the higher the relative uplift rate, the narrower the river. In a catchment uplifted at 1.5 mm/yr, knickpoint retreat rate can be up to 3 times higher than in a catchment uplifted at 0.25 mm/yr. This result is in agreement with measurements of knickpoint retreat rates using field data in the Apennines [Whittaker et al., 2008]. Steepened hillslopes along the rapidly incising Feather River, Sierra Nevada, California

The Changing HIV/AIDS Landscape: Where Do Biologics Fit In?

PubMed Central

BUTCHER, LOLA

2007-01-01

The number of therapies available to improve and extend the lives of HIV/AIDS patients is increasing. So is the cost of providing them. Biotechs and others are working on HIV blockers, vaccines, and gene therapies that may one day benefit patients and keep the cost of staying healthy down. PMID:23372512

Is brood parasitism related to host nestling diet and nutrition?

Treesearch

Zachary S. Ladin; Vincent D' Amico; Deb P. Jaisi; W. Gregory Shriver

2015-01-01

Food and nutrient limitation can have negative effects on survival, fecundity, and lifetime fitness of individuals, which can ultimately limit populations. Changes in trophic dynamics and diet patterns, affected by anthropogenic environmental and landscape change, are poorly understood yet may play an important role in population regulation. We determined diets of Wood...

The Landscape of Elementary School Physical Education

ERIC Educational Resources Information Center

Graber, Kim C.; Locke, Lawrence F.; Lambdin, Dolly; Solmon, Melinda A.

2008-01-01

Elementary school physical education has repeatedly been shaped by the forces of history. Presently, concerns about the obesity epidemic and the low levels of physical activity in children are exerting a major influence on curriculum. Whereas building physical fitness has been a dominant influence during wartime, the focus today is on (a)…

sGD software for estimating spatially explicit indices of genetic diversity

Treesearch

A. J. Shirk; Samuel Cushman

2011-01-01

Anthropogenic landscape changes have greatly reduced the population size, range and migration rates of many terrestrial species. The small local effective population size of remnant populations favours loss of genetic diversity leading to reduced fitness and adaptive potential, and thus ultimately greater extinction risk. Accurately quantifying genetic diversity is...

Location Isn’t Everything: Timing of Spawning Aggregations Optimizes Larval Replenishment

PubMed Central

Donahue, Megan J.; Karnauskas, Mandy; Toews, Carl; Paris, Claire B.

2015-01-01

Many species of reef fishes form large spawning aggregations that are highly predictable in space and time. Prior research has suggested that aggregating fish derive fitness benefits not just from mating at high density but, also, from oceanographic features of the spatial locations where aggregations occur. Using a probabilistic biophysical model of larval dispersal coupled to a fine resolution hydrodynamic model of the Florida Straits, we develop a stochastic landscape of larval fitness. Tracking virtual larvae from release to settlement and incorporating changes in larval behavior through ontogeny, we found that larval success was sensitive to the timing of spawning. Indeed, propagules released during the observed spawning period had higher larval success rates than those released outside the observed spawning period. In contrast, larval success rates were relatively insensitive to the spatial position of the release site. In addition, minimum (rather than mean) larval survival was maximized during the observed spawning period, indicating a reproductive strategy that minimizes the probability of recruitment failure. Given this landscape of larval fitness, we take an inverse optimization approach to define a biological objective function that reflects a tradeoff between the mean and variance of larval success in a temporally variable environment. Using this objective function, we suggest that the length of the spawning period can provide insight into the tradeoff between reproductive risk and reward. PMID:26103162

Evolution of flowering strategies in Oenothera glazioviana: an integral projection model approach.

PubMed Central

Rees, Mark; Rose, Karen E

2002-01-01

The timing of reproduction is a key determinant of fitness. Here, we develop parameterized integral projection models of size-related flowering for the monocarpic perennial Oenothera glazioviana and use these to predict the evolutionarily stable strategy (ESS) for flowering. For the most part there is excellent agreement between the model predictions and the results of quantitative field studies. However, the model predicts a much steeper relationship between plant size and the probability of flowering than observed in the field, indicating selection for a 'threshold size' flowering function. Elasticity and sensitivity analysis of population growth rate lambda and net reproductive rate R(0) are used to identify the critical traits that determine fitness and control the ESS for flowering. Using the fitted model we calculate the fitness landscape for invading genotypes and show that this is characterized by a ridge of approximately equal fitness. The implications of these results for the maintenance of genetic variation are discussed. PMID:12137582

Evolution of flowering strategies in Oenothera glazioviana: an integral projection model approach.

PubMed

Rees, Mark; Rose, Karen E

2002-07-22

The timing of reproduction is a key determinant of fitness. Here, we develop parameterized integral projection models of size-related flowering for the monocarpic perennial Oenothera glazioviana and use these to predict the evolutionarily stable strategy (ESS) for flowering. For the most part there is excellent agreement between the model predictions and the results of quantitative field studies. However, the model predicts a much steeper relationship between plant size and the probability of flowering than observed in the field, indicating selection for a 'threshold size' flowering function. Elasticity and sensitivity analysis of population growth rate lambda and net reproductive rate R(0) are used to identify the critical traits that determine fitness and control the ESS for flowering. Using the fitted model we calculate the fitness landscape for invading genotypes and show that this is characterized by a ridge of approximately equal fitness. The implications of these results for the maintenance of genetic variation are discussed.

Geomorphology applied to landscape analysis for planning and management of natural spaces. Case study: Las Batuecas-S. de Francia and Quilamas natural parks, (Salamanca, Spain).

PubMed

Martínez-Graña, A M; Silva, P G; Goy, J L; Elez, J; Valdés, V; Zazo, C

2017-04-15

Geomorphology is fundamental to landscape analysis, as it represents the main parameter that determines the land spatial configuration and facilitates reliefs classification. The goal of this article is the elaboration of thematic maps that enable the determination of different landscape units and elaboration of quality and vulnerability synthetic maps for landscape fragility assessment prior to planning human activities. For two natural spaces, the final synthetic maps were created with direct (visual-perceptual features) and indirect (cartographic models and 3D simulations) methods from thematic maps with GIS technique. This enabled the creation of intrinsic and extrinsic landscape quality maps showing sectors needing most preservation, as well as intrinsic and extrinsic landscape fragility maps (environment response capacity or vulnerability towards human actions). The resulting map shows absorption capacity for areas of maximum and/or minimum human intervention. Sectors of high absorption capacity (minimum need for preservation) are found where the incidence of human intervention is minimum: escarpment bottoms, fitted rivers, sinuous high lands with thick vegetation coverage and valley interiors, or those areas with high landscape quality, low fragility and high absorption capacity, whose average values are found across lower hillsides of some valleys, and sectors with low absorption capacity (areas needing most preservation) found mainly in the inner parts of natural spaces: peaks and upper hillsides, synclines flanks and scattered areas. For the integral analysis of landscape, a mapping methodology has been set. It comprises a valid criterion for rational and sustainable planning, management and protection of natural spaces. Copyright © 2017 Elsevier B.V. All rights reserved.

Spatial heterogeneity regulates plant-pollinator networks across multiple landscape scales.

PubMed

Moreira, Eduardo Freitas; Boscolo, Danilo; Viana, Blandina Felipe

2015-01-01

Mutualistic plant-pollinator interactions play a key role in biodiversity conservation and ecosystem functioning. In a community, the combination of these interactions can generate emergent properties, e.g., robustness and resilience to disturbances such as fluctuations in populations and extinctions. Given that these systems are hierarchical and complex, environmental changes must have multiple levels of influence. In addition, changes in habitat quality and in the landscape structure are important threats to plants, pollinators and their interactions. However, despite the importance of these phenomena for the understanding of biological systems, as well as for conservation and management strategies, few studies have empirically evaluated these effects at the network level. Therefore, the objective of this study was to investigate the influence of local conditions and landscape structure at multiple scales on the characteristics of plant-pollinator networks. This study was conducted in agri-natural lands in Chapada Diamantina, Bahia, Brazil. Pollinators were collected in 27 sampling units distributed orthogonally along a gradient of proportion of agriculture and landscape diversity. The Akaike information criterion was used to select models that best fit the metrics for network characteristics, comparing four hypotheses represented by a set of a priori candidate models with specific combinations of the proportion of agriculture, the average shape of the landscape elements, the diversity of the landscape and the structure of local vegetation. The results indicate that a reduction of habitat quality and landscape heterogeneity can cause species loss and decrease of networks nestedness. These structural changes can reduce robustness and resilience of plant-pollinator networks what compromises the reproductive success of plants, the maintenance of biodiversity and the pollination service stability. We also discuss the possible explanations for these relationships and the implications for landscape planning in agricultural areas.

Spatial Heterogeneity Regulates Plant-Pollinator Networks across Multiple Landscape Scales

PubMed Central

Moreira, Eduardo Freitas; Boscolo, Danilo; Viana, Blandina Felipe

2015-01-01

Mutualistic plant-pollinator interactions play a key role in biodiversity conservation and ecosystem functioning. In a community, the combination of these interactions can generate emergent properties, e.g., robustness and resilience to disturbances such as fluctuations in populations and extinctions. Given that these systems are hierarchical and complex, environmental changes must have multiple levels of influence. In addition, changes in habitat quality and in the landscape structure are important threats to plants, pollinators and their interactions. However, despite the importance of these phenomena for the understanding of biological systems, as well as for conservation and management strategies, few studies have empirically evaluated these effects at the network level. Therefore, the objective of this study was to investigate the influence of local conditions and landscape structure at multiple scales on the characteristics of plant-pollinator networks. This study was conducted in agri-natural lands in Chapada Diamantina, Bahia, Brazil. Pollinators were collected in 27 sampling units distributed orthogonally along a gradient of proportion of agriculture and landscape diversity. The Akaike information criterion was used to select models that best fit the metrics for network characteristics, comparing four hypotheses represented by a set of a priori candidate models with specific combinations of the proportion of agriculture, the average shape of the landscape elements, the diversity of the landscape and the structure of local vegetation. The results indicate that a reduction of habitat quality and landscape heterogeneity can cause species loss and decrease of networks nestedness. These structural changes can reduce robustness and resilience of plant-pollinator networks what compromises the reproductive success of plants, the maintenance of biodiversity and the pollination service stability. We also discuss the possible explanations for these relationships and the implications for landscape planning in agricultural areas. PMID:25856293

The Sensitivity of Genetic Connectivity Measures to Unsampled and Under-Sampled Sites

PubMed Central

Koen, Erin L.; Bowman, Jeff; Garroway, Colin J.; Wilson, Paul J.

2013-01-01

Landscape genetic analyses assess the influence of landscape structure on genetic differentiation. It is rarely possible to collect genetic samples from all individuals on the landscape and thus it is important to assess the sensitivity of landscape genetic analyses to the effects of unsampled and under-sampled sites. Network-based measures of genetic distance, such as conditional genetic distance (cGD), might be particularly sensitive to sampling intensity because pairwise estimates are relative to the entire network. We addressed this question by subsampling microsatellite data from two empirical datasets. We found that pairwise estimates of cGD were sensitive to both unsampled and under-sampled sites, and FST, Dest, and deucl were more sensitive to under-sampled than unsampled sites. We found that the rank order of cGD was also sensitive to unsampled and under-sampled sites, but not enough to affect the outcome of Mantel tests for isolation by distance. We simulated isolation by resistance and found that although cGD estimates were sensitive to unsampled sites, by increasing the number of sites sampled the accuracy of conclusions drawn from landscape genetic analyses increased, a feature that is not possible with pairwise estimates of genetic differentiation such as FST, Dest, and deucl. We suggest that users of cGD assess the sensitivity of this measure by subsampling within their own network and use caution when making extrapolations beyond their sampled network. PMID:23409155

Spatial resilience of forested landscapes under climate change and management

Treesearch

Melissa S. Lucash; Robert M. Scheller; Eric J. Gustafson; Brian R. Sturtevant

2017-01-01

Context Resilience, the ability to recover from disturbance, has risen to the forefront of scientific policy, but is difficult to quantify, particularly in large, forested landscapes subject to disturbances, management, and climate change. Objectives Our objective was to determine which spatial drivers will control landscape...

Thinking big: linking rivers to landscapes

Treesearch

Joan O’Callaghan; Ashley E. Steel; Kelly M. Burnett

2012-01-01

Exploring relationships between landscape characteristics and rivers is an emerging field, enabled by the proliferation of satellite date, advances in statistical analysis, and increased emphasis on large-scale monitoring. Landscapes features such as road networks, underlying geology, and human developments, determine the characteristics of the rivers flowing through...

[Landscape structure and ecological coupling analysis of ecotone on the west Sonnen Plain].

PubMed

Song, Changchun; Deng, Wei; Song, Xinshan

2003-09-01

Ecotone is a special zone in the landscape, which is very susceptive to the changes in environmental conditions, and hence, is prone to the disturbance by unfavorable conditions. Human activity has a series of positive and negative effects on it, and greatly changes the geo-chemical process in the ecosystem. In the ecosystem, especially in the ecotone, different systems and regimes are interconnected and inter-determined. For the sustainable development of ecosystem and the protection and rational utilization of resources, it is of great importance to study this internal relationship and to seek rational regulation and control measures. With the ecotone in the west Songnen Plain as an example, and based on the studies of the topography, physiognomy, soil, vegetation, and their geographic distribution in the ecotone., this paper explained the structure of the ecological landscape, and quantitatively analyzed the ecological geo-chemical processes under different landscape conditions. In addition, this paper also tried to make coupling analyses to the ecologic succession and the landscape geo-chemical environment. Under current conditions, the succession of plant communities and the shift of soil landscape geo-chemical conditions in the west Songnen Plain are almost co-instantaneous, and these two factors can inter-determined under certain conditions.

Fitness Probability Distribution of Bit-Flip Mutation.

PubMed

Chicano, Francisco; Sutton, Andrew M; Whitley, L Darrell; Alba, Enrique

2015-01-01

Bit-flip mutation is a common mutation operator for evolutionary algorithms applied to optimize functions over binary strings. In this paper, we develop results from the theory of landscapes and Krawtchouk polynomials to exactly compute the probability distribution of fitness values of a binary string undergoing uniform bit-flip mutation. We prove that this probability distribution can be expressed as a polynomial in p, the probability of flipping each bit. We analyze these polynomials and provide closed-form expressions for an easy linear problem (Onemax), and an NP-hard problem, MAX-SAT. We also discuss a connection of the results with runtime analysis.

How biochemical constraints of cellular growth shape evolutionary adaptations in metabolism.

PubMed

Berkhout, Jan; Bosdriesz, Evert; Nikerel, Emrah; Molenaar, Douwe; de Ridder, Dick; Teusink, Bas; Bruggeman, Frank J

2013-06-01

Evolutionary adaptations in metabolic networks are fundamental to evolution of microbial growth. Studies on unneeded-protein synthesis indicate reductions in fitness upon nonfunctional protein synthesis, showing that cell growth is limited by constraints acting on cellular protein content. Here, we present a theory for optimal metabolic enzyme activity when cells are selected for maximal growth rate given such growth-limiting biochemical constraints. We show how optimal enzyme levels can be understood to result from an enzyme benefit minus cost optimization. The constraints we consider originate from different biochemical aspects of microbial growth, such as competition for limiting amounts of ribosomes or RNA polymerases, or limitations in available energy. Enzyme benefit is related to its kinetics and its importance for fitness, while enzyme cost expresses to what extent resource consumption reduces fitness through constraint-induced reductions of other enzyme levels. A metabolic fitness landscape is introduced to define the fitness potential of an enzyme. This concept is related to the selection coefficient of the enzyme and can be expressed in terms of its fitness benefit and cost.

Scaling laws and universality for the strength of genetic interactions in yeast

NASA Astrophysics Data System (ADS)

Velenich, Andrea; Dai, Mingjie; Gore, Jeff

2012-02-01

Genetic interactions provide a window to the organization of the thousands of biochemical reactions in living cells. If two mutations affect unrelated cellular functions, the fitness effects of their combination can be easily predicted from the two separate fitness effects. However, because of interactions, for some pairs of mutations their combined fitness effect deviates from the naive prediction. We study genetic interactions in yeast cells by analyzing a publicly available database containing experimental growth rates of 5 million double mutants. We show that the characteristic strength of genetic interactions has a simple power law dependence on the fitness effects of the two interacting mutations and that the probability distribution of genetic interactions is a universal function. We further argue that the strength of genetic interactions depends only on the fitness effects of the interacting mutations and not on their biological origin in terms of single point mutations, entire gene knockouts or even more complicated physiological perturbations. Finally, we discuss the implications of the power law scaling of genetic interactions on the ruggedness of fitness landscapes and the consequent evolutionary dynamics.

Linking occurrence and fitness to persistence: Habitat-based approach for endangered Greater Sage-Grouse

USGS Publications Warehouse

Aldridge, Cameron L.; Boyce, Mark S.

2007-01-01

Detailed empirical models predicting both species occurrence and fitness across a landscape are necessary to understand processes related to population persistence. Failure to consider both occurrence and fitness may result in incorrect assessments of habitat importance leading to inappropriate management strategies. We took a two-stage approach to identifying critical nesting and brood-rearing habitat for the endangered Greater Sage-Grouse (Centrocercus urophasianus) in Alberta at a landscape scale. First, we used logistic regression to develop spatial models predicting the relative probability of use (occurrence) for Sage-Grouse nests and broods. Secondly, we used Cox proportional hazards survival models to identify the most risky habitats across the landscape. We combined these two approaches to identify Sage-Grouse habitats that pose minimal risk of failure (source habitats) and attractive sink habitats that pose increased risk (ecological traps). Our models showed that Sage-Grouse select for heterogeneous patches of moderate sagebrush cover (quadratic relationship) and avoid anthropogenic edge habitat for nesting. Nests were more successful in heterogeneous habitats, but nest success was independent of anthropogenic features. Similarly, broods selected heterogeneous high-productivity habitats with sagebrush while avoiding human developments, cultivated cropland, and high densities of oil wells. Chick mortalities tended to occur in proximity to oil and gas developments and along riparian habitats. For nests and broods, respectively, approximately 10% and 5% of the study area was considered source habitat, whereas 19% and 15% of habitat was attractive sink habitat. Limited source habitats appear to be the main reason for poor nest success (39%) and low chick survival (12%). Our habitat models identify areas of protection priority and areas that require immediate management attention to enhance recruitment to secure the viability of this population. This novel approach to habitat-based population viability modeling has merit for many species of concern. ?? 2007 by the Ecological Society of America.

[Responses of boreal forest landscape in northern Great Xing'an Mountains of Northeast China to climate change].

PubMed

Li, Xiao-Na; He, Hong-Shi; Wu, Zhi-Wei; Liang, Yu

2012-12-01

With the combination of forest landscape model (LANDIS) and forest gap model (LINKAGES), this paper simulated the effects of climate change on the boreal forest landscape in the Great Xing'an Mountains, and compared the direct effects of climate change and the effects of climate warming-induced fires on the forest landscape. The results showed that under the current climate conditions and fire disturbances, the forest landscape in the study area could maintain its dynamic balance, and Larix gmelinii was still the dominant tree species. Under the future climate and fire disturbances scenario, the distribution area of L. gmelinii and Pinus pumila would be decreased, while that of Betula platyphylla, Populus davidiana, Populus suaveolens, Chosenia arbutifolia, and Pinus sylvestris var. mongolica would be increased, and the forest fragmentation and forest diversity would have an increase. The changes of the forest landscape lagged behind climate change. Climate warming would increase the growth of most tree species except L. gmelinii, while the increased fires would increase the distribution area of P. davidiana, P. suaveolens, and C. arbutifolia and decrease the distribution area of L. gmelinii, P. sylvestris var. mongolica, and P. pumila. The effects of climate warming-induced fires on the forest landscape were almost equal to the direct effects of climate change, and aggravated the direct effects of climate change on forest composition, forest landscape fragmentation, and forest landscape diversity.

Honeybees can learn the relationship between the solar ephemeris and a newly experienced landscape: a confirmation.

PubMed

Kemfort, Jordan R; Towne, William F

2013-10-15

Honeybees learn the spatial relationship between the sun's pattern of movement and the landscape immediately surrounding their nest, which allows bees to locate the sun under overcast skies by reference to the landscape alone. Surprisingly, when bees have been transplanted from their natal landscape to a rotated twin landscape - such as from one treeline to a similar but differently oriented treeline - they fail to learn the relationship between the sun and the second landscape. This raises the question of whether bees can ever learn the relationship between the sun's pattern of movement and a landscape other than their natal one. Here we confirm, with new and necessary controls, that bees can indeed learn the relationship between the sun's pattern of movement and a second (that is, non-natal) landscape, if the second landscape is panoramically different from the bees' natal site. We transplanted bees from their natal site to a panoramically different second site and, 3 days later, tested the bees' knowledge of the relationship between the sun and the second landscape. The test involved observing the bees' communicative dances under overcast skies at a third site that was a rotated twin of the second. These bees oriented their dances using a memory of the sun's course in relation to the second landscape, indicating that they had learned this relationship. Meanwhile, control bees transplanted directly from the natal site to the third site, skipping the second, danced differently, confirming the importance of the experimental bees' experience at the second site.

The nature and ecology of aesthetic experiences in the landscape

Treesearch

Richard E. Chenoweth; Paul H. Gobster

1990-01-01

The assumption that aesthetically pleasing environments provide valued experiences that can improve people's quality of life underlies many government landscape policies and their resultant assessment procedures. Although the aesthetic experience has been discussed by philosophers and some psychologists, the aesthetic experience of landscapes has not been studied...

75 FR 39969 - National Mall and Memorial Parks, Washington, DC; Final Environmental Impact Statement and...

Federal Register 2010, 2011, 2012, 2013, 2014

2010-07-13

... experience for the visitors to this symbolic and historic cultural landscape. During the preparation of the... landscape reports and inventories. No-Action Alternative Under the No-Action Alternative, current management... landscape, with the large amount of deferred maintenance and aging infrastructure, pedestrian and bicycle...

Mapping the Dynamics Landscape of Conformational Transitions in Enzyme: The Adenylate Kinase Case

PubMed Central

Li, Dechang; Liu, Ming S.; Ji, Baohua

2015-01-01

Conformational transition describes the essential dynamics and mechanism of enzymes in pursuing their various functions. The fundamental and practical challenge to researchers is to quantitatively describe the roles of large-scale dynamic transitions for regulating the catalytic processes. In this study, we tackled this challenge by exploring the pathways and free energy landscape of conformational changes in adenylate kinase (AdK), a key ubiquitous enzyme for cellular energy homeostasis. Using explicit long-timescale (up to microseconds) molecular dynamics and bias-exchange metadynamics simulations, we determined at the atomistic level the intermediate conformational states and mapped the transition pathways of AdK in the presence and absence of ligands. There is clearly chronological operation of the functional domains of AdK. Specifically in the ligand-free AdK, there is no significant energy barrier in the free energy landscape separating the open and closed states. Instead there are multiple intermediate conformational states, which facilitate the rapid transitions of AdK. In the ligand-bound AdK, the closed conformation is energetically most favored with a large energy barrier to open it up, and the conformational population prefers to shift to the closed form coupled with transitions. The results suggest a perspective for a hybrid of conformational selection and induced fit operations of ligand binding to AdK. These observations, depicted in the most comprehensive and quantitative way to date, to our knowledge, emphasize the underlying intrinsic dynamics of AdK and reveal the sophisticated conformational transitions of AdK in fulfilling its enzymatic functions. The developed methodology can also apply to other proteins and biomolecular systems. PMID:26244746

Scientific uncertainty in media content: Introduction to this special issue.

PubMed

Peters, Hans Peter; Dunwoody, Sharon

2016-11-01

This introduction sets the stage for the special issue on the public communication of scientific uncertainty that follows by sketching the wider landscape of issues related to the communication of uncertainty and showing how the individual contributions fit into that landscape. The first part of the introduction discusses the creation of media content as a process involving journalists, scientific sources, stakeholders, and the responsive audience. The second part then provides an overview of the perception of scientific uncertainty presented by the media and the consequences for the recipients' own assessments of uncertainty. Finally, we briefly describe the six research articles included in this special issue. © The Author(s) 2016.

Non-equilibrium physics of neural networks for leaning, memory and decision making: landscape and flux perspectives

NASA Astrophysics Data System (ADS)

Wang, Jin

Cognitive behaviors are determined by underlying neural networks. Many brain functions, such as learning and memory, can be described by attractor dynamics. We developed a theoretical framework for global dynamics by quantifying the landscape associated with the steady state probability distributions and steady state curl flux, measuring the degree of non-equilibrium through detailed balance breaking. We found the dynamics and oscillations in human brains responsible for cognitive processes and physiological rhythm regulations are determined not only by the landscape gradient but also by the flux. We found that the flux is closely related to the degrees of the asymmetric connections in neural networks and is the origin of the neural oscillations. The neural oscillation landscape shows a closed-ring attractor topology. The landscape gradient attracts the network down to the ring. The flux is responsible for coherent oscillations on the ring. We suggest the flux may provide the driving force for associations among memories. Both landscape and flux determine the kinetic paths and speed of decision making. The kinetics and global stability of decision making are explored by quantifying the landscape topography through the barrier heights and the mean first passage time. The theoretical predictions are in agreement with experimental observations: more errors occur under time pressure. We quantitatively explored two mechanisms of the speed-accuracy tradeoff with speed emphasis and further uncovered the tradeoffs among speed, accuracy, and energy cost. Our results show an optimal balance among speed, accuracy, and the energy cost in decision making. We uncovered possible mechanisms of changes of mind and how mind changes improve performance in decision processes. Our landscape approach can help facilitate an understanding of the underlying physical mechanisms of cognitive processes and identify the key elements in neural networks.

[Application of 3S techniques in ecological landscape planning of Harbin suburb].

PubMed

Fan, Wenyi; Gong, Wenfeng; Liu, Dandan; Zhou, Hongze; Zhu, Ning

2005-12-01

With the image data (SPOT), soil utilization map (1:50000) and other related materials of Harbin, and under the support of GIS, RS and GPS techniques, this paper obtained the landscape pattern of Harbin suburb and the Digital Elevation Model (DEM) of Harbin. Indices including mean patch area, landscape dominance, mean slope, mean altitude, and fragmentation degree were selected and synthetically analyzed, with the ecological landscape planning made by DEM model. The results showed that 3S techniques could help to decide typical landscape types. The landscape type database was established, and the landscape type thematic map was generated, with land use status and landscape distribution, physiognomy, and land use types combined. The ecological landscape planning was described in large scale with the image data and DEM combined, and the landscape structure of Harbin suburb was reflected directly with the ecological landscape planning and DEM combined, which improved the ecological function in this region, and provided scientific bases to the healthy development in urban-rural integration area.

Visual land-use compatibility and scenic-resource quality

Treesearch

William G. Hendrix

1977-01-01

The effect that land-use relationships have upon perceived quality of the visual landscape is discussed, and a case is made for expansion of fit-misfit theory into what has been called visual land-use compatibility. An assessment methodology that was designed to test people's perceptions of land-use relationships is presented and the results are discussed.

Movements of four native Hawaiian birds across a naturally fragmented landscape

Treesearch

Jessie L. Knowlton; David J. Flaspohler; Eben H. Paxton; Tadashi Fukami; Christian P. Giardina; Daniel S. Gruner; Erin E. Wilson Rankin

2017-01-01

Animals often increase their fitness by moving across space in response to temporal variation in habitat quality and resource availability, and as a result of intra and inter-specific interactions. The long-term persistence of populations and even whole species depends on the collective patterns of individual movements, yet animal movements have been poorly studied at...

Outdoor Recreation in Exergames: A New Step in the Detachment from Nature?

ERIC Educational Resources Information Center

Öhman, Johan; Öhman, Marie; Sandell, Klas

2016-01-01

A new teaching aid--exergames--is increasing in popularity in schools and is regarded as an interesting, varied and effective way of improving students' fitness. These exercise television games often contain references to physical activities carried out in different outdoor landscapes. The purpose of this article is to examine the views of…

An Absent Body in a Present Landscape

ERIC Educational Resources Information Center

Marcussen, Jens

2012-01-01

The wilderness expedition experience will always be a confluence of emotional, cognitive and bodily processes. The author wants to show that the body is an important but often forgotten part of the wilderness expedition experience. In society, the focus on the body is often polarised. Sometimes, there is an extreme focus on the thin and fit body…

School Bullying and Fitting into the Peer Landscape: A Grounded Theory Field Study

ERIC Educational Resources Information Center

Thornberg, Robert

2018-01-01

Research on school bullying has its roots in the field of developmental and educational psychology, and appeals to the need for a theoretical and methodological widening in order to grasp its ambiguity and complexity. The article draws on ethnographic fieldwork in which 144 pupils and seven teachers participated from seven school classes in three…

Protein functional landscapes, dynamics, allostery: a tortuous path towards a universal theoretical framework.

PubMed

Zhuravlev, Pavel I; Papoian, Garegin A

2010-08-01

Energy landscape theories have provided a common ground for understanding the protein folding problem, which once seemed to be overwhelmingly complicated. At the same time, the native state was found to be an ensemble of interconverting states with frustration playing a more important role compared to the folding problem. The landscape of the folded protein - the native landscape - is glassier than the folding landscape; hence, a general description analogous to the folding theories is difficult to achieve. On the other hand, the native basin phase volume is much smaller, allowing a protein to fully sample its native energy landscape on the biological timescales. Current computational resources may also be used to perform this sampling for smaller proteins, to build a 'topographical map' of the native landscape that can be used for subsequent analysis. Several major approaches to representing this topographical map are highlighted in this review, including the construction of kinetic networks, hierarchical trees and free energy surfaces with subsequent structural and kinetic analyses. In this review, we extensively discuss the important question of choosing proper collective coordinates characterizing functional motions. In many cases, the substates on the native energy landscape, which represent different functional states, can be used to obtain variables that are well suited for building free energy surfaces and analyzing the protein's functional dynamics. Normal mode analysis can provide such variables in cases where functional motions are dictated by the molecule's architecture. Principal component analysis is a more expensive way of inferring the essential variables from the protein's motions, one that requires a long molecular dynamics simulation. Finally, the two popular models for the allosteric switching mechanism, 'preexisting equilibrium' and 'induced fit', are interpreted within the energy landscape paradigm as extreme points of a continuum of transition mechanisms. Some experimental evidence illustrating each of these two models, as well as intermediate mechanisms, is presented and discussed.

Spatially explicit modeling of mixed-severity fire regimes and landscape dynamics

Treesearch

Michael C. Wimberly; Rebecca S.H. Kennedy

2008-01-01

Simulation models of disturbance and succession are being increasingly applied to characterize landscape composition and dynamics under natural fire regimes, and to evaluate alternative management strategies for ecological restoration and fire hazard reduction. However, we have a limited understanding of how landscapes respond to changes in fire frequency, and about...

Landscape Hazards in Yukon Communities: Geological Mapping for Climate Change Adaptation Planning

NASA Astrophysics Data System (ADS)

Kennedy, K.; Kinnear, L.

2010-12-01

Climate change is considered to be a significant challenge for northern communities where the effects of increased temperature and climate variability are beginning to affect infrastructure and livelihoods (Arctic Climate Impact Assessment, 2004). Planning for and adapting to ongoing and future changes in climate will require the identification and characterization of social, economic, cultural, political and biophysical vulnerabilities. This pilot project addresses physical landscape vulnerabilities in two communities in the Yukon Territory through community-scale landscape hazard mapping and focused investigations of community permafrost conditions. Landscape hazards are identified by combining pre-existing data from public utilities and private-sector consultants with new geophysical techniques (ground penetrating radar and electrical resistivity), shallow drilling, surficial geological mapping, and permafrost characterization. Existing landscape vulnerabilities are evaluated based on their potential for hazard (low, medium or high) under current climate conditions, as well as under future climate scenarios. Detailed hazard maps and landscape characterizations for both communities will contribute to overall adaptation plans and allow for informed development, planning and mitigation of potentially threatening hazards in and around the communities.

Resampling method for applying density-dependent habitat selection theory to wildlife surveys.

PubMed

Tardy, Olivia; Massé, Ariane; Pelletier, Fanie; Fortin, Daniel

2015-01-01

Isodar theory can be used to evaluate fitness consequences of density-dependent habitat selection by animals. A typical habitat isodar is a regression curve plotting competitor densities in two adjacent habitats when individual fitness is equal. Despite the increasing use of habitat isodars, their application remains largely limited to areas composed of pairs of adjacent habitats that are defined a priori. We developed a resampling method that uses data from wildlife surveys to build isodars in heterogeneous landscapes without having to predefine habitat types. The method consists in randomly placing blocks over the survey area and dividing those blocks in two adjacent sub-blocks of the same size. Animal abundance is then estimated within the two sub-blocks. This process is done 100 times. Different functional forms of isodars can be investigated by relating animal abundance and differences in habitat features between sub-blocks. We applied this method to abundance data of raccoons and striped skunks, two of the main hosts of rabies virus in North America. Habitat selection by raccoons and striped skunks depended on both conspecific abundance and the difference in landscape composition and structure between sub-blocks. When conspecific abundance was low, raccoons and striped skunks favored areas with relatively high proportions of forests and anthropogenic features, respectively. Under high conspecific abundance, however, both species preferred areas with rather large corn-forest edge densities and corn field proportions. Based on random sampling techniques, we provide a robust method that is applicable to a broad range of species, including medium- to large-sized mammals with high mobility. The method is sufficiently flexible to incorporate multiple environmental covariates that can reflect key requirements of the focal species. We thus illustrate how isodar theory can be used with wildlife surveys to assess density-dependent habitat selection over large geographic extents.

Comparing the energy landscapes for native folding and aggregation of PrP

PubMed Central

Dee, Derek R.; Woodside, Michael T.

2016-01-01

ABSTRACT Protein sequences are evolved to encode generally one folded structure, out of a nearly infinite array of possible folds. Underlying this code is a funneled free energy landscape that guides folding to the native conformation. Protein misfolding and aggregation are also a manifestation of free-energy landscapes. The detailed mechanisms of these processes are poorly understood, but often involve rare, transient species and a variety of different pathways. The inherent complexity of misfolding has hampered efforts to measure aggregation pathways and the underlying energy landscape, especially using traditional methods where ensemble averaging obscures important rare and transient events. We recently studied the misfolding and aggregation of prion protein by examining 2 monomers tethered in close proximity as a dimer, showing how the steps leading to the formation of a stable aggregated state can be resolved in the single-molecule limit and the underlying energy landscape thereby reconstructed. This approach allows a more quantitative comparison of native folding versus misfolding, including fundamental differences in the dynamics for misfolding. By identifying key steps and interactions leading to misfolding, it should help to identify potential drug targets. Here we describe the importance of characterizing free-energy landscapes for aggregation and the challenges involved in doing so, and we discuss how single-molecule studies can help test proposed structural models for PrP aggregates. PMID:27191683

Genomic investigations of evolutionary dynamics and epistasis in microbial evolution experiments.

PubMed

Jerison, Elizabeth R; Desai, Michael M

2015-12-01

Microbial evolution experiments enable us to watch adaptation in real time, and to quantify the repeatability and predictability of evolution by comparing identical replicate populations. Further, we can resurrect ancestral types to examine changes over evolutionary time. Until recently, experimental evolution has been limited to measuring phenotypic changes, or to tracking a few genetic markers over time. However, recent advances in sequencing technology now make it possible to extensively sequence clones or whole-population samples from microbial evolution experiments. Here, we review recent work exploiting these techniques to understand the genomic basis of evolutionary change in experimental systems. We first focus on studies that analyze the dynamics of genome evolution in microbial systems. We then survey work that uses observations of sequence evolution to infer aspects of the underlying fitness landscape, concentrating on the epistatic interactions between mutations and the constraints these interactions impose on adaptation. Copyright © 2015 Elsevier Ltd. All rights reserved.

Neutrality and Robustness in Evo-Devo: Emergence of Lateral Inhibition

PubMed Central

Munteanu, Andreea; Solé, Ricard V.

2008-01-01

Embryonic development is defined by the hierarchical dynamical process that translates genetic information (genotype) into a spatial gene expression pattern (phenotype) providing the positional information for the correct unfolding of the organism. The nature and evolutionary implications of genotype–phenotype mapping still remain key topics in evolutionary developmental biology (evo-devo). We have explored here issues of neutrality, robustness, and diversity in evo-devo by means of a simple model of gene regulatory networks. The small size of the system allowed an exhaustive analysis of the entire fitness landscape and the extent of its neutrality. This analysis shows that evolution leads to a class of robust genetic networks with an expression pattern characteristic of lateral inhibition. This class is a repertoire of distinct implementations of this key developmental process, the diversity of which provides valuable clues about its underlying causal principles. PMID:19023404

Applications of graph theory to landscape genetics

PubMed Central

Garroway, Colin J; Bowman, Jeff; Carr, Denis; Wilson, Paul J

2008-01-01

We investigated the relationships among landscape quality, gene flow, and population genetic structure of fishers (Martes pennanti) in ON, Canada. We used graph theory as an analytical framework considering each landscape as a network node. The 34 nodes were connected by 93 edges. Network structure was characterized by a higher level of clustering than expected by chance, a short mean path length connecting all pairs of nodes, and a resiliency to the loss of highly connected nodes. This suggests that alleles can be efficiently spread through the system and that extirpations and conservative harvest are not likely to affect their spread. Two measures of node centrality were negatively related to both the proportion of immigrants in a node and node snow depth. This suggests that central nodes are producers of emigrants, contain high-quality habitat (i.e., deep snow can make locomotion energetically costly) and that fishers were migrating from high to low quality habitat. A method of community detection on networks delineated five genetic clusters of nodes suggesting cryptic population structure. Our analyses showed that network models can provide system-level insight into the process of gene flow with implications for understanding how landscape alterations might affect population fitness and evolutionary potential. PMID:25567802

Using Landscape metrics to analyze the landscape evolution under land abandonment

NASA Astrophysics Data System (ADS)

Pelorosso, Raffaele; Della Chiesa, Stefano; Gobattoni, Federica; Leone, Antonio

2010-05-01

The human actions and the human-linked land use changes are the main responsible of the present landscapes and vegetation patterns (Antrop, 2005; Pelorosso et al., 2009). Hence, revised concept of potential natural vegetation has been developed in landscape ecology. In fact, it cannot more be considered as the optimum for a certain landscape, but only as a general indication never widely reached. In particular Ingegnoli and Pignatti (2007) introduced the concept of fittest vegetation as "the most suitable or suited vegetation for the specific climate and geomorphic conditions, in a limited period of time and in a certain defined place with a particular range of incorporable disturbances (including man's) under natural or not natural conditions". Anthropic exploitation of land and its resources to obtain goods and services (Willemen et al, 2008) can be considered therefore the main cause of landscape change as an integrant part of nature, not external. The abandon of the land by farmers or other users it is one of the more felt problems for the marginal territories of Mediterranean basin. It is therefore caused by socio-economic changes of last decades and cause several impact on biodiversity (Geri et al. 2010) and hydro-geological assessment. A mountain landscape has however the capacity to provide goods like timber and services like aesthetic pleasure or regulation of water system. The necessity of a conservation strategy and the development of sustainable socio-economic management plan play a very important role in governing land and quality of life for people and ecosystems also for marginal territory. After a land abandonment, soil conditions and several climatic and orographic characteristic plus human disturbance affect the length of time required by secondary succession, throwing the establishment of vegetation with different association, structure and composition until a (stable or meta-stable) equilibrium is reached (Ingegnoli and Pignatti, 2007). In this view, therefore, not all the abandoned land will be covered by woods also after a reasonable time (e.g 20-30 years); open areas patches can resist over time as a consequence of different (more o less natural) disturbances, pointing out a landscape mosaic and vegetation pattern almost never completely homogeneous. This spatial and temporal differentiation of landscape pattern, therefore, require both the individuation of disturbances and their effect on land abandonment process to be analyzed for each different landscape. Many types of analysis and models were developed and used to understand the reason of abandonment, its evolution, likelihood future landscape scenarios and the leading consequences on environment and population in order to establish right land-uses to obtain suitable and sustainable goods and services from landscape itself. One of these analysis recurs to landscape metrics. Landscape metrics have been widely applied in ecology and landscape ecology (Rainis, 2003; Romero-Calcerrada and Perry, 2004 ; Narumalani et al., 2004; Rocchini et al., 2006) because they allow an objective description of the temporal pattern of landscape change and a comparison with other landscapes (Turner et al., 2001). Furthermore, a description of the shape, size and spatial arrangement of patches of vegetation can be used to link the observed pattern with the ecological processes that may have generated it (Rocchini et al., 2006). So these metrics can be used to see how an abandoned landscape can evolve under the effects of different constrictions that, also if not completely knew, have been affecting the present assessment. Through historical and recent aerial photos (1954-1985-1999) and several landscape metrics, the evolution of marginal municipality of central Apennine under abandonment is presented here. Temporal evolution of landscape metrics was discussed to underline the importance of such descriptors of vegetation pattern dynamics and the key role played by these useful tools for the evaluation of reachable future vegetation pattern equilibriums.

Yield-trait performance landscapes: from theory to application in breeding maize for drought tolerance.

PubMed

Messina, Carlos D; Podlich, Dean; Dong, Zhanshan; Samples, Mitch; Cooper, Mark

2011-01-01

The effectiveness of breeding strategies to increase drought resistance in crops could be increased further if some of the complexities in gene-to-phenotype (G → P) relations associated with epistasis, pleiotropy, and genotype-by-environment interactions could be captured in realistic G → P models, and represented in a quantitative manner useful for selection. This paper outlines a promising methodology. First, the concept of landscapes was extended from the study of fitness landscapes used in evolutionary genetics to the characterization of yield-trait-performance landscapes for agricultural environments and applications in plant breeding. Second, the E(NK) model of trait genetic architecture was extended to incorporate biophysical, physiological, and statistical components. Third, a graphical representation is proposed to visualize the yield-trait performance landscape concept for use in selection decisions. The methodology was demonstrated at a particular stage of a maize breeding programme with the objective of improving the drought tolerance of maize hybrids for the US Western Corn-Belt. The application of the framework to the genetic improvement of drought tolerance in maize supported selection of Doubled Haploid (DH) lines with improved levels of drought tolerance based on physiological genetic knowledge, prediction of test-cross yield within the target population of environments, and their predicted potential to sustain further genetic progress with additional cycles of selection. The existence of rugged yield-performance landscapes with multiple peaks and intervening valleys of lower performance, as shown in this study, supports the proposition that phenotyping strategies, and the directions emphasized in genomic selection can be improved by creating knowledge of the topology of yield-trait performance landscapes.

Integrating ecophysiology and forest landscape models to improve projections of drought effects under climate change

Treesearch

Eric J. Gustafson; Arjan M.G. De Bruijn; Robert E. Pangle; Jean-Marc Limousin; Nate G. McDowell; William T. Pockman; Brian R. Sturtevant; Jordan D. Muss; Mark E. Kubiske

2015-01-01

Fundamental drivers of ecosystem processes such as temperature and precipitation are rapidly changing and creating novel environmental conditions. Forest landscape models (FLM) are used by managers and policy-makers to make projections of future ecosystem dynamics under alternative management or policy options, but the links between the fundamental drivers and...

Restricted cross-scale habitat selection by American beavers.

PubMed

Francis, Robert A; Taylor, Jimmy D; Dibble, Eric; Strickland, Bronson; Petro, Vanessa M; Easterwood, Christine; Wang, Guiming

2017-12-01

Animal habitat selection, among other ecological phenomena, is spatially scale dependent. Habitat selection by American beavers Castor canadensis (hereafter, beaver) has been studied at singular spatial scales, but to date no research addresses multi-scale selection. Our objectives were to determine if beaver habitat selection was specialized to semiaquatic habitats and if variables explaining habitat selection are consistent between landscape and fine spatial scales. We built maximum entropy (MaxEnt) models to relate landscape-scale presence-only data to landscape variables, and used generalized linear mixed models to evaluate fine spatial scale habitat selection using global positioning system (GPS) relocation data. Explanatory variables between the landscape and fine spatial scale were compared for consistency. Our findings suggested that beaver habitat selection at coarse (study area) and fine (within home range) scales was congruent, and was influenced by increasing amounts of woody wetland edge density and shrub edge density, and decreasing amounts of open water edge density. Habitat suitability at the landscape scale also increased with decreasing amounts of grass frequency. As territorial, central-place foragers, beavers likely trade-off open water edge density (i.e., smaller non-forested wetlands or lodges closer to banks) for defense and shorter distances to forage and obtain construction material. Woody plants along edges and expanses of open water for predator avoidance may limit beaver fitness and subsequently determine beaver habitat selection.

Restricted cross-scale habitat selection by American beavers

PubMed Central

Taylor, Jimmy D; Dibble, Eric; Strickland, Bronson; Petro, Vanessa M; Easterwood, Christine; Wang, Guiming

2017-01-01

Abstract Animal habitat selection, among other ecological phenomena, is spatially scale dependent. Habitat selection by American beavers Castor canadensis (hereafter, beaver) has been studied at singular spatial scales, but to date no research addresses multi-scale selection. Our objectives were to determine if beaver habitat selection was specialized to semiaquatic habitats and if variables explaining habitat selection are consistent between landscape and fine spatial scales. We built maximum entropy (MaxEnt) models to relate landscape-scale presence-only data to landscape variables, and used generalized linear mixed models to evaluate fine spatial scale habitat selection using global positioning system (GPS) relocation data. Explanatory variables between the landscape and fine spatial scale were compared for consistency. Our findings suggested that beaver habitat selection at coarse (study area) and fine (within home range) scales was congruent, and was influenced by increasing amounts of woody wetland edge density and shrub edge density, and decreasing amounts of open water edge density. Habitat suitability at the landscape scale also increased with decreasing amounts of grass frequency. As territorial, central-place foragers, beavers likely trade-off open water edge density (i.e., smaller non-forested wetlands or lodges closer to banks) for defense and shorter distances to forage and obtain construction material. Woody plants along edges and expanses of open water for predator avoidance may limit beaver fitness and subsequently determine beaver habitat selection. PMID:29492032

A Local to National Scale Catchment Model Simulation Framework for Hydrological Predictions and Impact Assessments Under Uncertainty

NASA Astrophysics Data System (ADS)

Freer, Jim; Coxon, Gemma; Quinn, Niall; Dunne, Toby; Lane, Rosie; Bates, Paul; Wagener, Thorsten; Woods, Ross; Neal, Jeff; Howden, Nicholas; Musuuza, Jude

2017-04-01

There is a huge challenge in developing hydrological model structures that can be used for hypothesis testing, prediction, impact assessment and risk analyses over a wide range of spatial scales. There are many reasons why this is the case, from computational demands, to how we define and characterize different features and pathway connectivities in the landscape, that differ depending on the objectives of the study. However there is certainly a need more than ever to explore the trade-offs between the complexity of modelling applied (i.e. spatial discretization, levels of process representation, complexity of landscape representation) compared to the benefits realized in terms of predictive capability and robustness of these predictions during hydrological extremes and during change. Furthermore, there is a further balance, particularly associated with prediction uncertainties, in that it is not desirable to have modelling systems that are too complex compared to the observed data that would ever be available to apply them. This is particularly the case when models are applied to quantify national impact assessments, especially if these are based on validation assessments from smaller more detailed case studies. Therefore the hydrological community needs modelling tools and approaches that enable these trade-offs to be explored and to understand the level of representation needed in models to be 'fit-for-purpose' for a given application. This paper presents a catchment scale national modelling framework based on Dynamic-TOPMODEL specifically setup to fulfil these aims. A key component of the modelling framework is it's structural flexibility, as is the ability to assess model outputs using Monte Carlo simulation techniques. The model build has been automated to work at any spatial scale to the national scale, and within that to control the level of spatial discretisation and connectivity of locally accounted landscape elements in the form of hydrological response units (HRU's). This allows for the explicit consideration of spatial rainfall fields, landscape, soils and geological attributes and the spatial connectivity of hydrological flow pathways to explore what level of modelling complexity we need for different prediction problems. We shall present this framework and show how it can be used in flood and drought risk analyses as well as include attributes and features within the landscape to explore societal and climate impacts effectively within an uncertainty analyses framework.

Quantitative relations between soil heavy metal contamination and landscape pattern in Wuxi, China

NASA Astrophysics Data System (ADS)

Zhu, Ming; Pu, Lijie; Xu, Yan

2017-04-01

Land use practices changed landscape pattern and meanwhile, brought forth numerous environmental problems including heavy metal contamination in soil. In this study, we investigated the quantitative relations between soil heavy metal contamination and its surrounding landscape pattern based on topsoil samples and land use map of Wuxi in 2009. The results of vector fitting with Redundancy analysis in R package vegan showed that Percent Coverage of build-up area (PCB) within 2500 m, Perimeter-Area Fractal Dimension (PAFD) within 2500 m, Edge Density (ED) within 2500 m, Patch Density (PD) within 200 m, Percent Coverage of wetland (PCW) within 2000 m and Patch Cohesion (PC) within 200 m significantly affected the contents of heavy metal elements. The results of Stepwise regression suggested that increase of build-up area and fragmentation would increase Cu and Zn, while increase of wetland would decrease the contents of As and Cu. PAFD was negative with Cd, Hg, Pb and Zn.

Planning Routes Across Economic Terrains: Maximizing Utility, Following Heuristics

PubMed Central

Zhang, Hang; Maddula, Soumya V.; Maloney, Laurence T.

2010-01-01

We designed an economic task to investigate human planning of routes in landscapes where travel in different kinds of terrain incurs different costs. Participants moved their finger across a touch screen from a starting point to a destination. The screen was divided into distinct kinds of terrain and travel within each kind of terrain imposed a cost proportional to distance traveled. We varied costs and spatial configurations of terrains and participants received fixed bonuses minus the total cost of the routes they chose. We first compared performance to a model maximizing gain. All but one of 12 participants failed to adopt least-cost routes and their failure to do so reduced their winnings by about 30% (median value). We tested in detail whether participants’ choices of routes satisfied three necessary conditions (heuristics) for a route to maximize gain. We report failures of one heuristic for 7 out of 12 participants. Last of all, we modeled human performance with the assumption that participants assign subjective utilities to costs and maximize utility. For 7 out 12 participants, the fitted utility function was an accelerating power function of actual cost and for the remaining 5, a decelerating power function. We discuss connections between utility aggregation in route planning and decision under risk. Our task could be adapted to investigate human strategy and optimality of route planning in full-scale landscapes. PMID:21833269

Untangling human development and natural gradients: implications of underlying correlation structure for linking landscapes and riverine ecosystems

Treesearch

Yasmin Lucero; E. Ashley Steel; Kelly M. Burnett; Kelly Christiansen

2011-01-01

Increasingly, ecologists seek to identify and quantify relationships between landscape gradients and aquatic ecosystems. Considerable statistical challenges emerge in this effort, some of which are attributable to multicollinearity between human development and landscape gradients. In this paper, we measure the covariation between human development—such as agriculture...

Model forest landscape change in the Missouri Ozarks under alternative management practices

Treesearch

Stephen R. Shifley; Frank R. Thompson; David R. Larsen; William D. Dijak

2000-01-01

We used a spatially explicit landscape model, LANDIS, to simulate the effects of five management alternatives on a 3216 ha forest landscape in southeast Missouri, USA. We compared management alternatives among two intensities of even-aged management with clearcutting, uneven-aged management with group selection harvest, a mixture of even- and uneven-aged management,...

Interactions of landscape disturbances and climate change dictate ecological pattern and process: spatial modeling of wildfire, insect, and disease dynamics under future climates

Treesearch

Rachel A. Loehman; Robert E. Keane; Lisa M. Holsinger; Zhiwei Wu

2017-01-01

Context: Interactions among disturbances, climate, and vegetation influence landscape patterns and ecosystem processes. Climate changes, exotic invasions, beetle outbreaks, altered fire regimes, and human activities may interact to produce landscapes that appear and function beyond historical analogs. Objectives We used the mechanistic...

Combining aesthetic with ecological values for landscape sustainability.

PubMed

Yang, Dewei; Luo, Tao; Lin, Tao; Qiu, Quanyi; Luo, Yunjian

2014-01-01

Humans receive multiple benefits from various landscapes that foster ecological services and aesthetic attractiveness. In this study, a hybrid framework was proposed to evaluate ecological and aesthetic values of five landscape types in Houguanhu Region of central China. Data from the public aesthetic survey and professional ecological assessment were converted into a two-dimensional coordinate system and distribution maps of landscape values. Results showed that natural landscapes (i.e. water body and forest) contributed positively more to both aesthetic and ecological values than semi-natural and human-dominated landscapes (i.e. farmland and non-ecological land). The distribution maps of landscape values indicated that the aesthetic, ecological and integrated landscape values were significantly associated with landscape attributes and human activity intensity. To combine aesthetic preferences with ecological services, the methods (i.e. field survey, landscape value coefficients, normalized method, a two-dimensional coordinate system, and landscape value distribution maps) were employed in landscape assessment. Our results could facilitate to identify the underlying structure-function-value chain, and also improve the understanding of multiple functions in landscape planning. The situation context could also be emphasized to bring ecological and aesthetic goals into better alignment.

Combining Aesthetic with Ecological Values for Landscape Sustainability

PubMed Central

Yang, Dewei; Luo, Tao; Lin, Tao; Qiu, Quanyi; Luo, Yunjian

2014-01-01

Humans receive multiple benefits from various landscapes that foster ecological services and aesthetic attractiveness. In this study, a hybrid framework was proposed to evaluate ecological and aesthetic values of five landscape types in Houguanhu Region of central China. Data from the public aesthetic survey and professional ecological assessment were converted into a two-dimensional coordinate system and distribution maps of landscape values. Results showed that natural landscapes (i.e. water body and forest) contributed positively more to both aesthetic and ecological values than semi-natural and human-dominated landscapes (i.e. farmland and non-ecological land). The distribution maps of landscape values indicated that the aesthetic, ecological and integrated landscape values were significantly associated with landscape attributes and human activity intensity. To combine aesthetic preferences with ecological services, the methods (i.e. field survey, landscape value coefficients, normalized method, a two-dimensional coordinate system, and landscape value distribution maps) were employed in landscape assessment. Our results could facilitate to identify the underlying structure-function-value chain, and also improve the understanding of multiple functions in landscape planning. The situation context could also be emphasized to bring ecological and aesthetic goals into better alignment. PMID:25050886

Development, survival, and phenotypic plasticity in anthropogenic landscapes: trade-offs between offspring quantity and quality in the nettle-feeding peacock butterfly.

PubMed

Serruys, Mélanie; Van Dyck, Hans

2014-10-01

Habitats selected for development may have important fitness consequences. This is relevant within the framework of niche shifts in human-dominated landscapes. Currently, the peacock butterfly (Aglais io) occurs ubiquitously, covering many habitat types, whereas its distribution used to be much more restricted. Indeed, its host plant (stinging nettle Urtica dioica) was limited to natural forest gaps on relatively nitrogen-rich soil, but due to land use changes and eutrophication, host plants are now quasi-omnipresent in Western Europe. In order to assess the impact of specific anthropogenic habitat types on host plant quality and environmental conditions for phenotypic trait values, an experiment was conducted in woodlands, field margins, and urban gardens. Larval development was studied in field enclosures, and adult traits were analyzed to test predicted effects of warmer and more nitrogen-rich conditions in field margins compared to woodlands and urban gardens. Survival to the adult stage was highest in woodlands and lowest in field margins, and whilst development time did not differ amongst habitat types, butterflies that developed in field margins were larger and had higher lipid content and wing loadings than conspecifics from woodlands and urban gardens. Nettles in field margins provided warmer microclimates. However, and contrary to predictions, the nitrogen level within host plant leaves was highest in woodlands. Hence, anthropogenic landscapes may pose a conflict for choosing what is ultimately the best breeding habitat, as survival was highest in woodlands (followed by urban gardens), but adults with highest fitness predictions were produced in field margins (and secondarily urban gardens).

Division of labour and the evolution of multicellularity

PubMed Central

Ispolatov, Iaroslav; Ackermann, Martin; Doebeli, Michael

2012-01-01

Understanding the emergence and evolution of multicellularity and cellular differentiation is a core problem in biology. We develop a quantitative model that shows that a multicellular form emerges from genetically identical unicellular ancestors when the compartmentalization of poorly compatible physiological processes into component cells of an aggregate produces a fitness advantage. This division of labour between the cells in the aggregate occurs spontaneously at the regulatory level owing to mechanisms present in unicellular ancestors and does not require any genetic predisposition for a particular role in the aggregate or any orchestrated cooperative behaviour of aggregate cells. Mathematically, aggregation implies an increase in the dimensionality of phenotype space that generates a fitness landscape with new fitness maxima, in which the unicellular states of optimized metabolism become fitness saddle points. Evolution of multicellularity is modelled as evolution of a hereditary parameter: the propensity of cells to stick together, which determines the fraction of time a cell spends in the aggregate form. Stickiness can increase evolutionarily owing to the fitness advantage generated by the division of labour between cells in an aggregate. PMID:22158952

Type of fitness cost influences the rate of evolution of resistance to transgenic Bt crops.

PubMed

Hackett, Sean C; Bonsall, Michael B

2016-10-01

The evolution of resistance to pesticides by insect pests is a significant challenge for sustainable agriculture. For transgenic crops expressing Bacillus thuringiensis (Bt), crystalline (Cry) toxins resistance evolution may be delayed by the high-dose/refuge strategy in which a non-toxic refuge is planted to promote the survival of susceptible insects. The high-dose/refuge strategy may interact with fitness costs associated with resistance alleles to further delay resistance. However, while a diverse range of fitness costs are reported in the field, they are typically represented as a fixed reduction in survival or viability which is insensitive to ecological conditions such as competition. Furthermore, the potential dynamic consequences of restricting susceptible insects to a refuge which represents only a fraction of the available space have rarely been considered.We present a generalized discrete time model which utilizes dynamic programming methods to derive the optimal management decisions for the control of a theoretical insect pest population exposed to Bt crops. We consider three genotypes (susceptible homozygotes, resistant homozygotes and heterozygotes) and implement fitness costs of resistance to Bt toxins as either a decrease in the relative competitive ability of resistant insects or as a penalty on fecundity. Model analysis is repeated and contrasted for two types of density dependence: uniform density dependence which operates equally across the landscape and heterogeneous density dependence where the intensity of competition scales inversely with patch size and is determined separately for the refuge and Bt crop.When the planting of Bt is decided optimally, fitness costs to fecundity allow for the planting of larger areas of Bt crops than equivalent fitness costs that reduce the competitive ability of resistant insects.Heterogeneous competition only influenced model predictions when the proportional area of Bt planted in each season was decided optimally and resistance was not recessive. Synthesis and applications . The high-dose/refuge strategy alone is insufficient to preserve susceptibility to transgenic Bacillus thuringiensis (Bt) crops in the long term when constraints upon the evolution of resistance are not insurmountable. Fitness costs may enhance the delaying effect of the refuge, but the extent to which they do so depends upon how the cost is realized biologically. Fitness costs which apply independently of other variables may be more beneficial to resistance management than costs which are only visible to selection under a limited range of ecological conditions.

Bird-landscape relations in the Chihuahuan Desert: Coping with uncertainties about predictive models

USGS Publications Warehouse

Gutzwiller, K.J.; Barrow, W.C.

2001-01-01

During the springs of 1995-1997, we studied birds and landscapes in the Chihuahuan Desert along part of the Texas-Mexico border. Our objectives were to assess bird-landscape relations and their interannual consistency and to identify ways to cope with associated uncertainties that undermine confidence in using such relations in conservation decision processes. Bird distributions were often significantly associated with landscape features, and many bird-landscape models were valid and useful for predictive purposes. Differences in early spring rainfall appeared to influence bird abundance, but there was no evidence that annual differences in bird abundance affected model consistency. Model consistency for richness (42%) was higher than mean model consistency for 26 focal species (mean 30%, range 0-67%), suggesting that relations involving individual species are, on average, more subject to factors that cause variation than are richness-landscape relations. Consistency of bird-landscape relations may be influenced by such factors as plant succession, exotic species invasion, bird species' tolerances for environmental variation, habitat occupancy patterns, and variation in food density or weather. The low model consistency that we observed for most species indicates the high variation in bird-landscape relations that managers and other decision makers may encounter. The uncertainty of interannual variation in bird-landscape relations can be reduced by using projections of bird distributions from different annual models to determine the likely range of temporal and spatial variation in a species' distribution. Stochastic simulation models can be used to incorporate the uncertainty of random environmental variation into predictions of bird distributions based on bird-landscape relations and to provide probabilistic projections with which managers can weigh the costs and benefits of various decisions, Uncertainty about the true structure of bird-landscape relations (structural uncertainty) can be reduced by ensuring that models meet important statistical assumptions, designing studies with sufficient statistical power, validating the predictive ability of models, and improving model accuracy through continued field sampling and model fitting. Un certainty associated with sampling variation (partial observability) can be reduced by ensuring that sample sizes are large enough to provide precise estimates of both bird and landscape parameters. By decreasing the uncertainty due to partial observability, managers will improve their ability to reduce structural uncertainty.

The Circle of Trust[R] Approach and a Counselor Training Program: A Hand in Glove Fit

ERIC Educational Resources Information Center

Goodell, Judith A.

2012-01-01

The Circle of Trust[R] approach (www.couragerenewal.org) is dedicated to principles and practices that support exploration of the inner landscape of one's life. Participants share time in a trustworthy environment, connect with inner wisdom, and seek harmony in their personal and professional selves. In this chapter, the author describes her…

Understanding and Assessing the Charter School Movement. Critical Issues in Educational Leadership Series.

ERIC Educational Resources Information Center

Murphy, Joseph; Shiffman, Catherine Dunn

This volume presents a "big picture" perspective on the charter-school movement. It provides a definition of charter schools, what they are, and where they fit on the landscape of school reform; an explanation of why charters enjoy widespread bipartisan support; a look at how charters are situated in the larger school-reform movement of the last…

Predicting local adaptation in fragmented plant populations: implications for restoration genetics

PubMed Central

Pickup, Melinda; Field, David L; Rowell, David M; Young, Andrew G

2012-01-01

Understanding patterns and correlates of local adaptation in heterogeneous landscapes can provide important information in the selection of appropriate seed sources for restoration. We assessed the extent of local adaptation of fitness components in 12 population pairs of the perennial herb Rutidosis leptorrhynchoides (Asteraceae) and examined whether spatial scale (0.7–600 km), environmental distance, quantitative (QST) and neutral (FST) genetic differentiation, and size of the local and foreign populations could predict patterns of adaptive differentiation. Local adaptation varied among populations and fitness components. Including all population pairs, local adaptation was observed for seedling survival, but not for biomass, while foreign genotype advantage was observed for reproduction (number of inflorescences). Among population pairs, local adaptation increased with QST and local population size for biomass. QST was associated with environmental distance, suggesting ecological selection for phenotypic divergence. However, low FST and variation in population structure in small populations demonstrates the interaction of gene flow and drift in constraining local adaptation in R. leptorrhynchoides. Our study indicates that for species in heterogeneous landscapes, collecting seed from large populations from similar environments to candidate sites is likely to provide the most appropriate seed sources for restoration. PMID:23346235

Reconstructing Folding Energy Landscapes by Single-Molecule Force Spectroscopy

PubMed Central

Woodside, Michael T.; Block, Steven M.

2015-01-01

Folding may be described conceptually in terms of trajectories over a landscape of free energies corresponding to different molecular configurations. In practice, energy landscapes can be difficult to measure. Single-molecule force spectroscopy (SMFS), whereby structural changes are monitored in molecules subjected to controlled forces, has emerged as a powerful tool for probing energy landscapes. We summarize methods for reconstructing landscapes from force spectroscopy measurements under both equilibrium and nonequilibrium conditions. Other complementary, but technically less demanding, methods provide a model-dependent characterization of key features of the landscape. Once reconstructed, energy landscapes can be used to study critical folding parameters, such as the characteristic transition times required for structural changes and the effective diffusion coefficient setting the timescale for motions over the landscape. We also discuss issues that complicate measurement and interpretation, including the possibility of multiple states or pathways and the effects of projecting multiple dimensions onto a single coordinate. PMID:24895850

Gut microbiomes of mobile predators vary with landscape context and species identity.

PubMed

Tiede, Julia; Scherber, Christoph; Mutschler, James; McMahon, Katherine D; Gratton, Claudio

2017-10-01

Landscape context affects predator-prey interactions and predator diet composition, yet little is known about landscape effects on insect gut microbiomes, a determinant of physiology and condition. Here, we combine laboratory and field experiments to examine the effects of landscape context on the gut bacterial community and body condition of predatory insects. Under laboratory conditions, we found that prey diversity increased bacterial richness in insect guts. In the field, we studied the performance and gut microbiota of six predatory insect species along a landscape complexity gradient in two local habitat types (soybean fields vs. prairie). Insects from soy fields had richer gut bacteria and lower fat content than those from prairies, suggesting better feeding conditions in prairies. Species origin mediated landscape context effects, suggesting differences in foraging of exotic and native predators on a landscape scale. Overall, our study highlights complex interactions among gut microbiota, predator identity, and landscape context.

Semiconservative quasispecies equations for polysomic genomes: The general case

NASA Astrophysics Data System (ADS)

Itan, Eran; Tannenbaum, Emmanuel

2010-06-01

This paper develops a formulation of the quasispecies equations appropriate for polysomic, semiconservatively replicating genomes. This paper is an extension of previous work on the subject, which considered the case of haploid genomes. Here, we develop a more general formulation of the quasispecies equations that is applicable to diploid and even polyploid genomes. Interestingly, with an appropriate classification of population fractions, we obtain a system of equations that is formally identical to the haploid case. As with the work for haploid genomes, we consider both random and immortal DNA strand chromosome segregation mechanisms. However, in contrast to the haploid case, we have found that an analytical solution for the mean fitness is considerably more difficult to obtain for the polyploid case. Accordingly, whereas for the haploid case we obtained expressions for the mean fitness for the case of an analog of the single-fitness-peak landscape for arbitrary lesion repair probabilities (thereby allowing for noncomplementary genomes), here we solve for the mean fitness for the restricted case of perfect lesion repair.

From Understanding the Development Landscape of the Canonical Fate-Switch Pair to Constructing a Dynamic Landscape for Two-Step Neural Differentiation

PubMed Central

2012-01-01

Abstract Recent progress in stem cell biology, notably cell fate conversion, calls for novel theoretical understanding for cell differentiation. The existing qualitative concept of Waddington’s “epigenetic landscape” has attracted particular attention because it captures subsequent fate decision points, thus manifesting the hierarchical (“tree-like”) nature of cell fate diversification. Here, we generalized a recent work and explored such a developmental landscape for a two-gene fate decision circuit by integrating the underlying probability landscapes with different parameters (corresponding to distinct developmental stages). The change of entropy production rate along the parameter changes indicates which parameter changes can represent a normal developmental process while other parameters’ change can not. The transdifferentiation paths over the landscape under certain conditions reveal the possibility of a direct and reversible phenotypic conversion. As the intensity of noise increases, we found that the landscape becomes flatter and the dominant paths more straight, implying the importance of biological noise processing mechanism in development and reprogramming. We further extended the landscape of the one-step fate decision to that for two-step decisions in central nervous system (CNS) differentiation. A minimal network and dynamic model for CNS differentiation was firstly constructed where two three-gene motifs are coupled. We then implemented the SDEs (Stochastic Differentiation Equations) simulation for the validity of the network and model. By integrating the two landscapes for the two switch gene pairs, we constructed the two-step development landscape for CNS differentiation. Our work provides new insights into cellular differentiation and important clues for better reprogramming strategies. PMID:23300518

Predicting the spread of sudden oak death in California (2010-2030): epidemic outcomes under no control

Treesearch

Ross K. Meentemeyer; Nik Cunniffe; Alex Cook; David M. Rizzo; Chris A. Gilligan

2010-01-01

Landscape- to regional-scale models of plant epidemics are direly needed to predict largescale impacts of disease and assess practicable options for control. While landscape heterogeneity is recognized as a major driver of disease dynamics, epidemiological models are rarely applied to realistic landscape conditions due to computational and data limitations. Here we...

Exploring the role of fire, succession, climate, and weather on landscape dynamics using comparative modeling

Treesearch

Robert E. Keane; Geoffrey J. Cary; Mike D. Flannigan; Russell A. Parsons; Ian D. Davies; Karen J. King; Chao Li; Ross A. Bradstock; Malcolm Gill

2013-01-01

An assessment of the relative importance of vegetation change and disturbance as agents of landscape change under current and future climates would (1) provide insight into the controls of landscape dynamics, (2) help inform the design and development of coarse scale spatially explicit ecosystem models such as Dynamic Global Vegetation Models (DGVMs), and (3) guide...

Dynamics of a temperate deciduous forest under landscape-scale management: Implications for adaptability to climate change

Treesearch

Matthew G. Olson; Benjamin O. Knapp; John M. Kabrick

2017-01-01

Landscape forest management is an approach to meeting diverse objectives that collectively span multiple spatial scales. It is critical that we understand the long-term effects of landscape management on the structure and composition of forest tree communities to ensure that these practices are sustainable. Furthermore, it is increasingly important to also consider...

Forecasting landscape effects of Mississippi River diversions on elevation and accretion in Louisiana deltaic wetlands under future environmental uncertainty scenarios

USGS Publications Warehouse

Wang, Hongqing; Steyer, Gregory D.; Couvillion, Brady R.; John M. Rybczyk,; Beck, Holly J.; William J. Sleavin,; Ehab A. Meselhe,; Mead A. Allison,; Ronald G. Boustany,; Craig J. Fischenich,; Victor H. Rivera-Monroy,

2014-01-01

Large sediment diversions are proposed and expected to build new wetlands to alleviate the extensive wetland loss (5,000 km2) affecting coastal Louisiana during the last 78 years. Current assessment and prediction of the impacts of sediment diversions have focused on the capture and dispersal of both water and sediment on the adjacent river side and the immediate outfall marsh area. However, little is known about the effects of sediment diversions on existing wetland surface elevation and vertical accretion dynamics in the receiving basin at the landscape scale. In this study, we used a spatial wetland surface elevation model developed in support of Louisiana's 2012 Coastal Master Plan to examine such landscape-scale effects of sediment diversions. Multiple sediment diversion projects were incorporated in the model to simulate surface elevation and vertical accretion for the next 50 years (2010-2060) under two environmental (moderate and less optimistic) scenarios. Specifically, we examined landscape-scale surface elevation and vertical accretion trends under diversions with different geographical locations, diverted discharge rates, and geomorphic characteristics of the receiving basin. Model results indicate that small diversions (< 283 m3 s-1) tend to have limited effects of reducing landscape-scale elevation loss (< 3%) compared to a future without action (FWOA) condition. Large sediment diversions (> 1,500 m3 s-1) are required to achieve landscape-level benefits to promote surface elevation via vertical accretion to keep pace with rising sea level.

Specificity and Affinity Quantification of Flexible Recognition from Underlying Energy Landscape Topography

PubMed Central

Chu, Xiakun; Wang, Jin

2014-01-01

Flexibility in biomolecular recognition is essential and critical for many cellular activities. Flexible recognition often leads to moderate affinity but high specificity, in contradiction with the conventional wisdom that high affinity and high specificity are coupled. Furthermore, quantitative understanding of the role of flexibility in biomolecular recognition is still challenging. Here, we meet the challenge by quantifying the intrinsic biomolecular recognition energy landscapes with and without flexibility through the underlying density of states. We quantified the thermodynamic intrinsic specificity by the topography of the intrinsic binding energy landscape and the kinetic specificity by association rate. We found that the thermodynamic and kinetic specificity are strongly correlated. Furthermore, we found that flexibility decreases binding affinity on one hand, but increases binding specificity on the other hand, and the decreasing or increasing proportion of affinity and specificity are strongly correlated with the degree of flexibility. This shows more (less) flexibility leads to weaker (stronger) coupling between affinity and specificity. Our work provides a theoretical foundation and quantitative explanation of the previous qualitative studies on the relationship among flexibility, affinity and specificity. In addition, we found that the folding energy landscapes are more funneled with binding, indicating that binding helps folding during the recognition. Finally, we demonstrated that the whole binding-folding energy landscapes can be integrated by the rigid binding and isolated folding energy landscapes under weak flexibility. Our results provide a novel way to quantify the affinity and specificity in flexible biomolecular recognition. PMID:25144525

Specificity and affinity quantification of flexible recognition from underlying energy landscape topography.

PubMed

Chu, Xiakun; Wang, Jin

2014-08-01

Flexibility in biomolecular recognition is essential and critical for many cellular activities. Flexible recognition often leads to moderate affinity but high specificity, in contradiction with the conventional wisdom that high affinity and high specificity are coupled. Furthermore, quantitative understanding of the role of flexibility in biomolecular recognition is still challenging. Here, we meet the challenge by quantifying the intrinsic biomolecular recognition energy landscapes with and without flexibility through the underlying density of states. We quantified the thermodynamic intrinsic specificity by the topography of the intrinsic binding energy landscape and the kinetic specificity by association rate. We found that the thermodynamic and kinetic specificity are strongly correlated. Furthermore, we found that flexibility decreases binding affinity on one hand, but increases binding specificity on the other hand, and the decreasing or increasing proportion of affinity and specificity are strongly correlated with the degree of flexibility. This shows more (less) flexibility leads to weaker (stronger) coupling between affinity and specificity. Our work provides a theoretical foundation and quantitative explanation of the previous qualitative studies on the relationship among flexibility, affinity and specificity. In addition, we found that the folding energy landscapes are more funneled with binding, indicating that binding helps folding during the recognition. Finally, we demonstrated that the whole binding-folding energy landscapes can be integrated by the rigid binding and isolated folding energy landscapes under weak flexibility. Our results provide a novel way to quantify the affinity and specificity in flexible biomolecular recognition.

Canada lynx Lynx canadensis habitat and forest succession in northern Maine, USA

USGS Publications Warehouse

Hoving, C.L.; Harrison, D.J.; Krohn, W.B.; Jakubas, W.J.; McCollough, M.A.

2004-01-01

The contiguous United States population of Canada lynx Lynx canadensis was listed as threatened in 2000. The long-term viability of lynx populations at the southern edge of their geographic range has been hypothesized to be dependent on old growth forests; however, lynx are a specialist predator on snowshoe hare Lepus americanus, a species associated with early-successional forests. To quantify the effects of succession and forest management on landscape-scale (100 km2) patterns of habitat occupancy by lynx, we compared landscape attributes in northern Maine, USA, where lynx had been detected on snow track surveys to landscape attributes where surveys had been conducted, but lynx tracks had not been detected. Models were constructed a priori and compared using logistic regression and Akaike's Information Criterion (AIC), which quantitatively balances data fit and parsimony. In the models with the lowest (i.e. best) AIC, lynx were more likely to occur in landscapes with much regenerating forest, and less likely to occur in landscapes with much recent clearcut, partial harvest and forested wetland. Lynx were not associated positively or negatively with mature coniferous forest. A probabilistic map of the model indicated a patchy distribution of lynx habitat in northern Maine. According to an additional survey of the study area for lynx tracks during the winter of 2003, the model correctly classified 63.5% of the lynx occurrences and absences. Lynx were more closely associated with young forests than mature forests; however, old-growth forests were functionally absent from the landscape. Lynx habitat could be reduced in northern Maine, given recent trends in forest management practices. Harvest strategies have shifted from clearcutting to partial harvesting. If this trend continues, future landscapes will shift away from extensive regenerating forests and toward landscapes dominated by pole-sized and larger stands. Because Maine presently supports the only verified populations of this federally threatened species in the eastern United States, changes in forest management practices could affect recovery efforts throughout that region.

Evidence and opportunities for integrating landscape ecology into natural resource planning across multiple-use landscapes

USGS Publications Warehouse

Trammel, E. Jamie; Carter, Sarah; Haby, Travis S.; Taylor, Jason J.

2018-01-01

Enhancing natural resource management has been a focus of landscape ecology since its inception, but numerous authors argue that landscape ecology has not yet been effective in achieving the underlying goal of planning and designing sustainable landscapes. We developed nine questions reflecting the application of fundamental research topics in landscape ecology to the landscape planning process and reviewed two recent landscape-scale plans in western North America for evidence of these concepts in plan decisions. Both plans considered multiple resources, uses, and values, including energy development, recreation, conservation, and protection of cultural and historic resources. We found that land use change and multiscale perspectives of resource uses and values were very often apparent in planning decisions. Pattern-process relationships, connectivity and fragmentation, ecosystem services, landscape history, and climate change were reflected less frequently. Landscape sustainability was considered only once in the 295 decisions reviewed, and outputs of landscape models were not referenced. We suggest six actionable opportunities for further integrating landscape ecology concepts into landscape planning efforts: 1) use landscape sustainability as an overarching goal, 2) adopt a broad ecosystem services framework, 3) explore the role of landscape history more comprehensively, 4) regularly consider and accommodate potential effects of climate change, 5) use landscape models to support plan decisions, and 6) promote a greater presence of landscape ecologists within agencies that manage large land bases and encourage active involvement in agency planning efforts. Together these actions may improve the defensibility, durability, and sustainability of landscape plan decisions.

Uncovering the mechanisms of Caenorhabditis elegans ageing from global quantification of the underlying landscape.

PubMed

Zhao, Lei; Wang, Jin

2016-11-01

Recent studies on Caenorhabditis elegans reveal that gene manipulations can extend its lifespan several fold. However, how the genes work together to determine longevity is still an open question. Here we construct a gene regulatory network for worm ageing and quantify its underlying potential and flux landscape. We found ageing and rejuvenation states can emerge as basins of attraction at certain gene expression levels. The system state can switch from one attractor to another driven by the intrinsic or external perturbations through genetics or the environment. Furthermore, we simulated gene silencing experiments and found that the silencing of longevity-promoting or lifespan-limiting genes leads to ageing or rejuvenation domination, respectively. This indicates that the difference in depths between ageing and the rejuvenation attractor is highly correlated with worm longevity. We further uncovered some key genes and regulations which have a strong influence on landscape basin stability. A dynamic landscape model is proposed to describe the whole process of ageing: the ageing attractor dominates when senescence progresses. We also uncovered the oscillation dynamics, and a similar behaviour was observed in the long-lived creature Turritopsis dohrnii Our landscape theory provides a global and physical approach to explore the underlying mechanisms of ageing. © 2016 The Author(s).

Physical mechanism of mind changes and tradeoffs among speed, accuracy, and energy cost in brain decision making: Landscape, flux, and path perspectives

NASA Astrophysics Data System (ADS)

Han, Yan; Kun, Zhang; Jin, Wang

2016-07-01

Cognitive behaviors are determined by underlying neural networks. Many brain functions, such as learning and memory, have been successfully described by attractor dynamics. For decision making in the brain, a quantitative description of global attractor landscapes has not yet been completely given. Here, we developed a theoretical framework to quantify the landscape associated with the steady state probability distributions and associated steady state curl flux, measuring the degree of non-equilibrium through the degree of detailed balance breaking for decision making. We quantified the decision-making processes with optimal paths from the undecided attractor states to the decided attractor states, which are identified as basins of attractions, on the landscape. Both landscape and flux determine the kinetic paths and speed. The kinetics and global stability of decision making are explored by quantifying the landscape topography through the barrier heights and the mean first passage time. Our theoretical predictions are in agreement with experimental observations: more errors occur under time pressure. We quantitatively explored two mechanisms of the speed-accuracy tradeoff with speed emphasis and further uncovered the tradeoffs among speed, accuracy, and energy cost. Our results imply that there is an optimal balance among speed, accuracy, and the energy cost in decision making. We uncovered the possible mechanisms of changes of mind and how mind changes improve performance in decision processes. Our landscape approach can help facilitate an understanding of the underlying physical mechanisms of cognitive processes and identify the key factors in the corresponding neural networks. Project supported by the National Natural Science Foundation of China (Grant Nos. 21190040, 91430217, and 11305176).

Exploring the Mechanisms of Differentiation, Dedifferentiation, Reprogramming and Transdifferentiation

PubMed Central

Xu, Li; Zhang, Kun; Wang, Jin

2014-01-01

We explored the underlying mechanisms of differentiation, dedifferentiation, reprogramming and transdifferentiation (cell type switchings) from landscape and flux perspectives. Lineage reprogramming is a new regenerative method to convert a matured cell into another cell including direct transdifferentiation without undergoing a pluripotent cell state and indirect transdifferentiation with an initial dedifferentiation-reversion (reprogramming) to a pluripotent cell state. Each cell type is quantified by a distinct valley on the potential landscape with higher probability. We investigated three driving forces for cell fate decision making: stochastic fluctuations, gene regulation and induction, which can lead to cell type switchings. We showed that under the driving forces the direct transdifferentiation process proceeds from a differentiated cell valley to another differentiated cell valley through either a distinct stable intermediate state or a certain series of unstable indeterminate states. The dedifferentiation process proceeds through a pluripotent cell state. Barrier height and the corresponding escape time from the valley on the landscape can be used to quantify the stability and efficiency of cell type switchings. We also uncovered the mechanisms of the underlying processes by quantifying the dominant biological paths of cell type switchings on the potential landscape. The dynamics of cell type switchings are determined by both landscape gradient and flux. The flux can lead to the deviations of the dominant biological paths for cell type switchings from the naively expected landscape gradient path. As a result, the corresponding dominant paths of cell type switchings are irreversible. We also classified the mechanisms of cell fate development from our landscape theory: super-critical pitchfork bifurcation, sub-critical pitchfork bifurcation, sub-critical pitchfork with two saddle-node bifurcation, and saddle-node bifurcation. Our model showed good agreements with the experiments. It provides a general framework to explore the mechanisms of differentiation, dedifferentiation, reprogramming and transdifferentiation. PMID:25133589

Habitat and landscape characteristics underlying anuran community structure along an urban-rural gradient.

PubMed

Pillsbury, Finn C; Miller, James R

2008-07-01

Urbanization has been cited as an important factor in worldwide amphibian declines, and although recent work has illustrated the important influence of broad-scale ecological patterns and processes on amphibian populations, little is known about the factors structuring amphibian communities in urban landscapes. We therefore examined amphibian community responses to wetland habitat availability and landscape characteristics along an urban-rural gradient in central Iowa, USA, a region experiencing rapid suburban growth. We conducted call surveys at 61 wetlands to estimate anuran calling activity, and quantified wetland habitat structure and landscape context. We used canonical correspondence analysis (CCA) to examine patterns in anuran community structure and identify the most important variables associated with those patterns. Urban density at the landscape scale had a significant negative influence on overall anuran abundance and diversity. While every species exhibited a decrease in abundance with increasing urban density, this pattern was especially pronounced for species requiring post-breeding upland habitats. Anurans most affected by urbanization were those associated with short hydroperiods, early breeding activity, and substantial upland habitat use. We suggest that broad-scale landscape fragmentation is an important factor underlying anuran community structure in this region, possibly due to limitations on the accessibility of otherwise suitable habitat in fragmented urban landscapes. This study underscores the importance of a regional approach to amphibian conservation in urban and urbanizing areas; in fragmented landscapes, a network of interconnected wetland and upland habitats may be more likely to support a successful, diverse anuran community than will isolated sites.

[Landscape pattern change and its driving forces in Xixi National Wetland Park since 1993].

PubMed

Cheng, Qian; Wu, Xiuju

2006-09-01

Under the support of GIS technology and the TM images of Xixi National Wetland Park, this paper studied the past ten years' landscape pattern change and its driving forces of Xixi Wetland. The results showed that the landscape diversity index increased from 1.7854 in 1993 to 1.8438 in 2001 and 2.2096 in 2003, and the landscape fragmentation index increased from 0.0036 in 1993 to 0.0042 in 2001, and 0.0047 in 2003, suggesting that the landscape fragmentation was increased with time. Human activity was the main driving force, while the exploitation of real estate was the main internal factor of the landscape pattern change of Xixi wetland. In addition, social and economic development level had a strong effect on the overall diversity of the landscape.

Landscape-scale modelling of soil carbon dynamics under land use and climate change

NASA Astrophysics Data System (ADS)

Lacoste, Marine; Viaud, Valérie; Michot, Didier; Christian, Walter

2013-04-01

Soil organic carbon (SOC) sequestration is highly linked to soil use and farming practices, but also to soil redistributions, soil properties, and climate. In a global change context, landscape, farming practice and climate changes are expected; and they will most probably impact SOC dynamics. To assess their respective impacts, we modelled the SOC contents and stocks evolution at the scale of an agricultural landscape, by taking into account the soil redistribution by tillage and water processes. The simulations were conducted from 2010 to 2100 under different scenarios of landscape and climate. These scenarios combined different land uses associated to specific farming practices (mixed dairy with rotations of crops and grasslands, intensive cropping with only crops rotations or permanent grasslands), landscape managements (hedges planting or removal), and climates (business-as-usual climate and climate change, with temperature and precipitations increase). We used a spatially SOC dynamic model (adapted from RothC), coupled to a soil redistribution model (LandSoil). SOC dynamics were spatially modelled with a lateral resolution of 2-m and for soil organic layers up to 105 cm. Initial SOC stocks were described with a 2-m resolution map based on field data and produced with digital soil mapping methods. The major factor of change in SOC stocks was land use change, the second factor of importance was climate change, and finally landscape management: for the total SOC stocks (0-to-105 cm soil layer) the change of land use, climate and landscape management induced a respective mean absolute variation of 10 to 20 tC ha-1, 9 tC ha-1 and 0.4 tC ha-1. When considering the 0-to-105 cm soil layer, the different modelled landscapes showed the same sensitivity to climate change, with induced a mean decrease of 10 tC ha-1. However, the impact of climate change was found different according to the different modelled landscape when considering the 0-to-7.5 and 0-to-30 cm soil layers: the more sensitive landscapes were those of intensive cropping. This shows the importance of considering not only the plough layer, but also the vertical distribution of SOC stocks to assess the variation in SOC dynamics under land use, landscape management or climate change. Finally, rural hedgerow landscapes were proved to be quite well adapted for soil protection in a context of climate change, focusing on both carbon storage and soil erosion.

Stability and Response of Polygenic Traits to Stabilizing Selection and Mutation

PubMed Central

de Vladar, Harold P.; Barton, Nick

2014-01-01

When polygenic traits are under stabilizing selection, many different combinations of alleles allow close adaptation to the optimum. If alleles have equal effects, all combinations that result in the same deviation from the optimum are equivalent. Furthermore, the genetic variance that is maintained by mutation–selection balance is 2μ/S per locus, where μ is the mutation rate and S the strength of stabilizing selection. In reality, alleles vary in their effects, making the fitness landscape asymmetric and complicating analysis of the equilibria. We show that that the resulting genetic variance depends on the fraction of alleles near fixation, which contribute by 2μ/S, and on the total mutational effects of alleles that are at intermediate frequency. The interplay between stabilizing selection and mutation leads to a sharp transition: alleles with effects smaller than a threshold value of 2μ/S remain polymorphic, whereas those with larger effects are fixed. The genetic load in equilibrium is less than for traits of equal effects, and the fitness equilibria are more similar. We find that if the optimum is displaced, alleles with effects close to the threshold value sweep first, and their rate of increase is bounded by μS. Long-term response leads in general to well-adapted traits, unlike the case of equal effects that often end up at a suboptimal fitness peak. However, the particular peaks to which the populations converge are extremely sensitive to the initial states and to the speed of the shift of the optimum trait value. PMID:24709633

Ecomorphological convergence in planktivorous surgeonfishes.

PubMed

Friedman, S T; Price, S A; Hoey, A S; Wainwright, P C

2016-05-01

Morphological convergence plays a central role in the study of evolution. Often induced by shared ecological specialization, homoplasy hints at underlying selective pressures and adaptive constraints that deterministically shape the diversification of life. Although midwater zooplanktivory has arisen in adult surgeonfishes (family Acanthuridae) at least four independent times, it represents a clearly specialized state, requiring the capacity to swiftly swim in midwater locating and sucking small prey items. Whereas this diet has commonly been associated with specific functional adaptations in fishes, acanthurids present an interesting case study as all nonplanktivorous species feed by grazing on benthic algae and detritus, requiring a vastly different functional morphology that emphasizes biting behaviours. We examined the feeding morphology in 30 acanthurid species and, combined with a pre-existing phylogenetic tree, compared the fit of evolutionary models across two diet regimes: zooplanktivores and nonzooplanktivorous grazers. Accounting for phylogenetic relationships, the best-fitting model indicates that zooplanktivorous species are converging on a separate adaptive peak from their grazing relatives. Driving this bimodal landscape, zooplanktivorous acanthurids tend to develop a slender body, reduced facial features, smaller teeth and weakened jaw adductor muscles. However, despite these phenotypic changes, model fitting suggests that lineages have not yet reached the adaptive peak associated with plankton feeding even though some transitions appear to be over 10 million years old. These findings demonstrate that the selective demands of pelagic feeding promote repeated - albeit very gradual - ecomorphological convergence within surgeonfishes, while allowing local divergences between closely related species, contributing to the overall diversity of the clade. © 2016 European Society For Evolutionary Biology. Journal of Evolutionary Biology © 2016 European Society For Evolutionary Biology.

Simulating fire and forest dynamics for a coordinated landscape fuel treatment project in the Sierra Nevada

Treesearch

Brandon M. Collins; Scott L. Stephens; Gary B. Roller; John Battles

2011-01-01

We evaluate an actual landscape fuel treatment project that was designed by local U. S. Forest Service managers in the northern Sierra Nevada. We model the effects of this project at reducing landscape-level fire behavior at multiple time steps, up to nearly 30 yr beyond treatment implementation. Additionally, we modeled planned treatments under multiple diameter-...

Landscape-and regional-scale shifts in forest composition under climate change in the Central Hardwood Region of the United States

Treesearch

Wen J. Wang; Hong S. He; Frank R. Thompson; Jacob S. Fraser; William D. Dijak

2016-01-01

Tree species distribution and abundance are affected by forces operating at multiple scales. Niche and biophysical process models have been commonly used to predict climate change effects at regional scales, however, these models have limited capability to include site-scale population dynamics and landscape- scale disturbance and dispersal. We applied a landscape...

Simulated cavity tree dynamics under alternative timber harvest regimes

Treesearch

Zhaofei Fan; Stephen R Shifley; Frank R Thompson; David R Larsen

2004-01-01

We modeled cavity tree abundance on a landscape as a function of forest stand age classes and as a function of aggregate stand size classes.We explored the impact of five timber harvest regimes on cavity tree abundance on a 3261 ha landscape in southeast Missouri, USA, by linking the stand level cavity tree distribution model to the landscape age structure simulated by...

A Case Study of Introducing Innovation Through Design

DTIC Science & Technology

2014-03-01

contacts, freeing more of their mental energy to assist the CO in developing and tackling the overall complexities of the mission. With more energy ...organizations experiencing change while design thinking is devoted to finding solutions to difficult problems by harnessing the creative energy inherent...change. “Rather than focusing on one major opportunity, [embedded actors] pepper the landscape with many cultivated opportunities.”53 (2) Fitting the

Home Range Use and Movement Patterns of Non-Native Feral Goats in a Tropical Island Montane Dry Landscape

PubMed Central

Chynoweth, Mark W.; Lepczyk, Christopher A.; Litton, Creighton M.; Hess, Steven C.; Kellner, James R.; Cordell, Susan

2015-01-01

Advances in wildlife telemetry and remote sensing technology facilitate studies of broad-scale movements of ungulates in relation to phenological shifts in vegetation. In tropical island dry landscapes, home range use and movements of non-native feral goats (Capra hircus) are largely unknown, yet this information is important to help guide the conservation and restoration of some of the world’s most critically endangered ecosystems. We hypothesized that feral goats would respond to resource pulses in vegetation by traveling to areas of recent green-up. To address this hypothesis, we fitted six male and seven female feral goats with Global Positioning System (GPS) collars equipped with an Argos satellite upload link to examine goat movements in relation to the plant phenology using the Normalized Difference Vegetation Index (NDVI). Movement patterns of 50% of males and 40% of females suggested conditional movement between non-overlapping home ranges throughout the year. A shift in NDVI values corresponded with movement between primary and secondary ranges of goats that exhibited long-distance movement, suggesting that vegetation phenology as captured by NDVI is a good indicator of the habitat and movement patterns of feral goats in tropical island dry landscapes. In the context of conservation and restoration of tropical island landscapes, the results of our study identify how non-native feral goats use resources across a broad landscape to sustain their populations and facilitate invasion of native plant communities. PMID:25807275

Scale-dependent mechanisms of habitat selection for a migratory passerine: an experimental approach

USGS Publications Warehouse

Donovan, Therese M.; Cornell, Kerri L.

2010-01-01

Habitat selection theory predicts that individuals choose breeding habitats that maximize fitness returns on the basis of indirect environmental cues at multiple spatial scales. We performed a 3-year field experiment to evaluate five alternative hypotheses regarding whether individuals choose breeding territories in heterogeneous landscapes on the basis of (1) shrub cover within a site, (2) forest land-cover pattern surrounding a site, (3) conspecific song cues during prebreeding settlement periods, (4) a combination of these factors, and (5) interactions among these factors. We tested hypotheses with playbacks of conspecific song across a gradient of landscape pattern and shrub density and evaluated changes in territory occupancy patterns in a forest-nesting passerine, the Black-throated Blue Warbler (Dendroica caerulescens). Our results support the hypothesis that vegetation structure plays a primary role during presettlement periods in determining occupancy patterns in this species. Further, both occupancy rates and territory turnover were affected by an interaction between local shrub density and amount of forest in the surrounding landscape, but not by interactions between habitat cues and social cues. Although previous studies of this species in unfragmented landscapes found that social postbreeding song cues played a key role in determining territory settlement, our prebreeding playbacks were not associated with territory occupancy or turnover. Our results suggest that in heterogeneous landscapes during spring settlement, vegetation structure may be a more reliable signal of reproductive performance than the physical location of other individuals.

Annual dynamics of wild bee densities: attractiveness and productivity effects of oilseed rape.

PubMed

Riedinger, Verena; Mitesser, Oliver; Hovestadt, Thomas; Steffan-Dewenter, Ingolf; Holzschuh, Andrea

2015-05-01

Mass-flowering crops may affect long-term population dynamics, but effects on pollinators have never been studied across several years. We monitored wild bees in oilseed rape fields in 16 landscapes in Germany in two consecutive years. Effects on bee densities of landscape oilseed rape cover in the years of monitoring and in the previous years were evaluated with landscape data from three consecutive years. We fit empirical data to a mechanistic model to provide estimates for oilseed rape attractiveness and its effect on bee productivity in comparison to the rest of the landscape, and we evaluated consequences for pollinator densities in consecutive years. Our results show that high oilseed rape cover in the previous year enhances current densities of wild bees (except for bumble bees). Moreover, we show a strong attractiveness of and dilution on (i.e., decreasing bee densities with increasing landscape oilseed rape cover) oilseed rape for bees during flowering in the current year, modifying the effect of the previous year's oilseed rape cover in the case of wild bees (excluding Bombus). As long as other factors such as nesting sites or natural enemies do not limit bee reproduction, our findings suggest long-term positive effects of mass-flowering crops on bee populations, at least for non-Bombus generalists, which possibly help to maintain crop pollination services even when crop area increases. Similar effects are conceivable for other organisms providing ecosystem services in annual crops and should be considered in future studies.

Home range use and movement patterns of non-native feral goats in a tropical island montane dry landscape.

PubMed

Chynoweth, Mark W; Lepczyk, Christopher A; Litton, Creighton M; Hess, Steven C; Kellner, James R; Cordell, Susan

2015-01-01

Advances in wildlife telemetry and remote sensing technology facilitate studies of broad-scale movements of ungulates in relation to phenological shifts in vegetation. In tropical island dry landscapes, home range use and movements of non-native feral goats (Capra hircus) are largely unknown, yet this information is important to help guide the conservation and restoration of some of the world's most critically endangered ecosystems. We hypothesized that feral goats would respond to resource pulses in vegetation by traveling to areas of recent green-up. To address this hypothesis, we fitted six male and seven female feral goats with Global Positioning System (GPS) collars equipped with an Argos satellite upload link to examine goat movements in relation to the plant phenology using the Normalized Difference Vegetation Index (NDVI). Movement patterns of 50% of males and 40% of females suggested conditional movement between non-overlapping home ranges throughout the year. A shift in NDVI values corresponded with movement between primary and secondary ranges of goats that exhibited long-distance movement, suggesting that vegetation phenology as captured by NDVI is a good indicator of the habitat and movement patterns of feral goats in tropical island dry landscapes. In the context of conservation and restoration of tropical island landscapes, the results of our study identify how non-native feral goats use resources across a broad landscape to sustain their populations and facilitate invasion of native plant communities.

Scale-dependent factors affecting North American river otter distribution in the midwest

USGS Publications Warehouse

Jeffress, Mackenzie R.; Paukert, C.P.; Whittier, Joanna B.; Sandercock, B.K.; Gipson, P.S.

2011-01-01

The North American river otter (Lontra canadensis) is recovering from near extirpation throughout much of its range. Although reintroductions, trapping regulations and habitat improvements have led to the reestablishment of river otters in the Midwest, little is known about how their distribution is influenced by local- and landscape-scale habitat. We conducted river otter sign surveys from Jan. to Apr. in 2008 and 2009 in eastern Kansas to assess how local- and landscape-scale habitat factors affect river otter occupancy. We surveyed three to nine 400-m stretches of stream and reservoir shorelines for 110 sites and measured local-scale variables (e.g., stream order, land cover types) within a 100 m buffer of the survey site and landscape-scale variables (e.g., road density, land cover types) for Hydrological Unit Code 14 watersheds. We then used occupancy models that account for the probability of detection to estimate occupancy as a function of these covariates using Program PRESENCE. The best-fitting model indicated river otter occupancy increased with the proportion of woodland cover and decreased with the proportion of cropland and grassland cover at the local scale. Occupancy also increased with decreased shoreline diversity, waterbody density and stream density at the landscape scale. Occupancy was not affected by land cover or human disturbance at the landscape scale. Understanding the factors and scale important to river otter occurrence will be useful in identifying areas for management and continued restoration. ?? 2011, American Midland Naturalist.

Tropical Forest Fragmentation Limits Movements, but Not Occurrence of a Generalist Pollinator Species

PubMed Central

Volpe, Noelia L.; Robinson, W. Douglas; Frey, Sarah J. K.; Hadley, Adam S.; Betts, Matthew G.

2016-01-01

Habitat loss and fragmentation influence species distributions and therefore ecological processes that depend upon them. Pollination may be particularly susceptible to fragmentation, as it depends on frequent pollinator movement. Unfortunately, most pollinators are too small to track efficiently which has precluded testing the hypothesis that habitat fragmentation reduces or eliminates pollen flow by disrupting pollinator movement. We used radio-telemetry to examine space use of the green hermit hummingbird (Phaethornis guy), an important ‘hub’ pollinator of understory flowering plants across substantial portions of the neotropics and the primary pollinator of a keystone plant which shows reduced pollination success in fragmented landscapes. We found that green hermits strongly avoided crossing large stretches of non-forested matrix and preferred to move along stream corridors. Forest gaps as small as 50 m diminished the odds of movement by 50%. Green hermits occurred almost exclusively inside the forest, with the odds of occurrence being 8 times higher at points with >95% canopy cover compared with points having <5% canopy cover. Nevertheless, surprisingly. the species occurred in fragmented landscapes with low amounts of forest (~30% within a 2 km radius). Our results indicate that although green hermits are present even in landscapes with low amounts of tropical forest, movement within these landscapes ends up strongly constrained by forest gaps. Restricted movement of pollinators may be an underappreciated mechanism for widespread declines in pollination and plant fitness in fragmented landscapes, even when in the presence of appropriate pollinators. PMID:27941984

Home range use and movement patterns of non-native feral goats in a tropical island montane dry landscape

USGS Publications Warehouse

Chynoweth, Mark W.; Lepczyk, Christopher A.; Litton, Creighton M.; Hess, Steve; Kellner, James; Cordell, Susan

2015-01-01

Advances in wildlife telemetry and remote sensing technology facilitate studies of broad-scale movements of ungulates in relation to phenological shifts in vegetation. In tropical island dry landscapes, home range use and movements of non-native feral goats (Capra hircus) are largely unknown, yet this information is important to help guide the conservation and restoration of some of the world’s most critically endangered ecosystems. We hypothesized that feral goats would respond to resource pulses in vegetation by traveling to areas of recent green-up. To address this hypothesis, we fitted six male and seven female feral goats with Global Positioning System (GPS) collars equipped with an Argos satellite upload link to examine goat movements in relation to the plant phenology using the Normalized Difference Vegetation Index (NDVI). Movement patterns of 50% of males and 40% of females suggested conditional movement between non-overlapping home ranges throughout the year. A shift in NDVI values corresponded with movement between primary and secondary ranges of goats that exhibited long-distance movement, suggesting that vegetation phenology as captured by NDVI is a good indicator of the habitat and movement patterns of feral goats in tropical island dry landscapes. In the context of conservation and restoration of tropical island landscapes, the results of our study identify how non-native feral goats use resources across a broad landscape to sustain their populations and facilitate invasion of native plant communities.

The landscape of W± and Z bosons produced in pp collisions up to LHC energies

NASA Astrophysics Data System (ADS)

Basso, Eduardo; Bourrely, Claude; Pasechnik, Roman; Soffer, Jacques

2017-10-01

We consider a selection of recent experimental results on electroweak W± , Z gauge boson production in pp collisions at BNL RHIC and CERN LHC energies in comparison to prediction of perturbative QCD calculations based on different sets of NLO parton distribution functions including the statistical PDF model known from fits to the DIS data. We show that the current statistical PDF parametrization (fitted to the DIS data only) underestimates the LHC data on W± , Z gauge boson production cross sections at the NLO by about 20%. This suggests that there is a need to refit the parameters of the statistical PDF including the latest LHC data.

Emergence and dynamics of self-producing information niches as a step towards pre-evolutionary organization

PubMed Central

Carter, Richard J.; Wiesner, Karoline

2018-01-01

As a step towards understanding pre-evolutionary organization in non-genetic systems, we develop a model to investigate the emergence and dynamics of proto-autopoietic networks in an interacting population of simple information processing entities (automata). Our simulations indicate that dynamically stable strongly connected networks of mutually producing communication channels emerge under specific environmental conditions. We refer to these distinct organizational steady states as information niches. In each case, we measure the information content by the Shannon entropy, and determine the fitness landscape, robustness and transition pathways for information niches subjected to intermittent environmental perturbations under non-evolutionary conditions. By determining the information required to generate each niche, we show that niche transitions are only allowed if accompanied by an equal or increased level of information production that arises internally or via environmental perturbations that serve as an exogenous source of population diversification. Overall, our simulations show how proto-autopoietic networks of basic information processors form and compete, and under what conditions they persist over time or go extinct. These findings may be relevant to understanding how inanimate systems such as chemically communicating protocells can initiate the transition to living matter prior to the onset of contemporary evolutionary and genetic mechanisms. PMID:29343630

Appendix E: Research papers. Use of remote sensing in landscape stratification for environmental impact assessment

NASA Technical Reports Server (NTRS)

Stanturf, J. A.; Heimbuch, D. G.

1980-01-01

A refinement to the matrix approach to environmental impact assessment is to use landscape units in place of separate environmental elements in the analysis. Landscape units can be delineated by integrating remotely sensed data and available single-factor data. A remote sensing approach to landscape stratification is described and the conditions under which it is superior to other approaches that require single-factor maps are indicated. Flowcharts show the steps necessary to develop classification criteria, delineate units and a map legend, and use the landscape units in impact assessment. Application of the approach to assessing impacts of a transmission line in Montana is presented to illustrate the method.

Vulnerability of landscape carbon fluxes to future climate and fire in the Greater Yellowstone Ecosystem

Treesearch

Erica A. H. Smithwick; Anthony L. Westerling; Monica G. Turner; William H. Romme; Michael G. Ryan

2011-01-01

More frequent fires under climate warming are likely to alter terrestrial carbon (C) stocks by reducing the amount of C stored in biomass and soil. However, the thresholds of fire frequency that could shift landscapes from C sinks to C sources under future climates are not known. We used the Greater Yellowstone Ecosystem (GYE) as a case study to explore the conditions...

Negative vacuum energy densities and the causal diamond measure

DOE Office of Scientific and Technical Information (OSTI.GOV)

Salem, Michael P.

2009-07-15

Arguably a major success of the landscape picture is the prediction of a small, nonzero vacuum energy density. The details of this prediction depend in part on how the diverging spacetime volume of the multiverse is regulated, a question that remains unresolved. One proposal, the causal diamond measure, has demonstrated many phenomenological successes, including predicting a distribution of positive vacuum energy densities in good agreement with observation. In the string landscape, however, the vacuum energy density is expected to take positive and negative values. We find the causal diamond measure gives a poor fit to observation in such a landscapemore » - in particular, 99.6% of observers in galaxies seemingly just like ours measure a vacuum energy density smaller than we do, most of them measuring it to be negative.« less

Habitat management utilizing native wildflowers to foster pollinator abundance

USDA-ARS?s Scientific Manuscript database

Pollinators provide essential ecosystem services to agricultural crops, however their population has come under threat globally as a result of intensive agricultural practices and landscape simplification. Designing diverse heterogeneous agricultural landscapes to provide optimal resources serves as...

Free-Energy Landscape of Reverse tRNA Translocation through the Ribosome Analyzed by Electron Microscopy Density Maps and Molecular Dynamics Simulations

PubMed Central

Ishida, Hisashi; Matsumoto, Atsushi

2014-01-01

To understand the mechanism of reverse tRNA translocation in the ribosome, all-atom molecular dynamics simulations of the ribosome-tRNAs-mRNA-EFG complex were performed. The complex at the post-translocational state was directed towards the translocational and pre-translocational states by fitting the complex into cryo-EM density maps. Between a series of the fitting simulations, umbrella sampling simulations were performed to obtain the free-energy landscape. Multistep structural changes, such as a ratchet-like motion and rotation of the head of the small subunit were observed. The free-energy landscape showed that there were two main free-energy barriers: one between the post-translocational and intermediate states, and the other between the pre-translocational and intermediate states. The former corresponded to a clockwise rotation, which was coupled to the movement of P-tRNA over the P/E-gate made of G1338, A1339 and A790 in the small subunit. The latter corresponded to an anticlockwise rotation of the head, which was coupled to the location of the two tRNAs in the hybrid state. This indicates that the coupled motion of the head rotation and tRNA translocation plays an important role in opening and closing of the P/E-gate during the ratchet-like movement in the ribosome. Conformational change of EF-G was interpreted to be the result of the combination of the external motion by L12 around an axis passing near the sarcin-ricin loop, and internal hinge-bending motion. These motions contributed to the movement of domain IV of EF-G to maintain its interaction with A/P-tRNA. PMID:24999999

Free-energy landscape of reverse tRNA translocation through the ribosome analyzed by electron microscopy density maps and molecular dynamics simulations.

PubMed

Ishida, Hisashi; Matsumoto, Atsushi

2014-01-01

To understand the mechanism of reverse tRNA translocation in the ribosome, all-atom molecular dynamics simulations of the ribosome-tRNAs-mRNA-EFG complex were performed. The complex at the post-translocational state was directed towards the translocational and pre-translocational states by fitting the complex into cryo-EM density maps. Between a series of the fitting simulations, umbrella sampling simulations were performed to obtain the free-energy landscape. Multistep structural changes, such as a ratchet-like motion and rotation of the head of the small subunit were observed. The free-energy landscape showed that there were two main free-energy barriers: one between the post-translocational and intermediate states, and the other between the pre-translocational and intermediate states. The former corresponded to a clockwise rotation, which was coupled to the movement of P-tRNA over the P/E-gate made of G1338, A1339 and A790 in the small subunit. The latter corresponded to an anticlockwise rotation of the head, which was coupled to the location of the two tRNAs in the hybrid state. This indicates that the coupled motion of the head rotation and tRNA translocation plays an important role in opening and closing of the P/E-gate during the ratchet-like movement in the ribosome. Conformational change of EF-G was interpreted to be the result of the combination of the external motion by L12 around an axis passing near the sarcin-ricin loop, and internal hinge-bending motion. These motions contributed to the movement of domain IV of EF-G to maintain its interaction with A/P-tRNA.

Modeling bark beetles and fuels on landscapes: A demonstration of ArcFuels and a discussion of possible model enhancements

Treesearch

Andrew J. McMahan; Alan A. Ager; Helen Maffei; Jane L. Hayes; Eric L. Smith

2008-01-01

The Westwide Pine Beetle Model and the Fire and Fuels Extension were used to simulate a mountain pine beetle outbreak under different fuel treatment scenarios on a 173,000 acre landscape on the Deschutes National Forest. The goal was to use these models within ArcFuels to analyze the interacting impacts of bark beetles and management activities on landscape fuel...

[Application of spatially explicit landscape model in soil loss study in Huzhong area].

PubMed

Xu, Chonggang; Hu, Yuanman; Chang, Yu; Li, Xiuzhen; Bu, Renchang; He, Hongshi; Leng, Wenfang

2004-10-01

Universal Soil Loss Equation (USLE) has been widely used to estimate the average annual soil loss. In most of the previous work on soil loss evaluation on forestland, cover management factor was calculated from the static forest landscape. The advent of spatially explicit forest landscape model in the last decade, which explicitly simulates the forest succession dynamics under natural and anthropogenic disturbances (fire, wind, harvest and so on) on heterogeneous landscape, makes it possible to take into consideration the change of forest cover, and to dynamically simulate the soil loss in different year (e.g. 10 years and 20 years after current year). In this study, we linked a spatially explicit landscape model (LANDIS) with USLE to simulate the soil loss dynamics under two scenarios: fire and no harvest, fire and harvest. We also simulated the soil loss with no fire and no harvest as a control. The results showed that soil loss varied periodically with simulation year, and the amplitude of change was the lowest under the control scenario and the highest under the fire and no harvest scenario. The effect of harvest on soil loss could not be easily identified on the map; however, the cumulative effect of harvest on soil loss was larger than that of fire. Decreasing the harvest area and the percent of bare soil increased by harvest could significantly reduce soil loss, but had no significant effects on the dynamic of soil loss. Although harvest increased the annual soil loss, it tended to decrease the variability of soil loss between different simulation years.

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

PubMed

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.

Landscape Structure Shapes Habitat Finding Ability in a Butterfly

PubMed Central

Öckinger, Erik; Van Dyck, Hans

2012-01-01

Land-use intensification and habitat fragmentation is predicted to impact on the search strategies animals use to find habitat. We compared the habitat finding ability between populations of the speckled wood butterfly (Pararge aegeria L.) from landscapes that differ in degree of habitat fragmentation. Naïve butterflies reared under standardized laboratory conditions but originating from either fragmented agricultural landscapes or more continuous forested landscapes were released in the field, at fixed distances from a target habitat patch, and their flight paths were recorded. Butterflies originating from fragmented agricultural landscapes were better able to find a woodlot habitat from a distance compared to conspecifics from continuous forested landscapes. To manipulate the access to olfactory information, a subset of individuals from both landscape types were included in an antennae removal experiment. This confirmed the longer perceptual range for butterflies from agricultural landscapes and indicated the significance of both visual and olfactory information for orientation towards habitat. Our results are consistent with selection for increased perceptual range in fragmented landscapes to reduce dispersal costs. An increased perceptual range will alter the functional connectivity and thereby the chances for population persistence for the same level of structural connectivity in a fragmented landscape. PMID:22870227

Scientific discovery as a combinatorial optimisation problem: how best to navigate the landscape of possible experiments?

PubMed

Kell, Douglas B

2012-03-01

A considerable number of areas of bioscience, including gene and drug discovery, metabolic engineering for the biotechnological improvement of organisms, and the processes of natural and directed evolution, are best viewed in terms of a 'landscape' representing a large search space of possible solutions or experiments populated by a considerably smaller number of actual solutions that then emerge. This is what makes these problems 'hard', but as such these are to be seen as combinatorial optimisation problems that are best attacked by heuristic methods known from that field. Such landscapes, which may also represent or include multiple objectives, are effectively modelled in silico, with modern active learning algorithms such as those based on Darwinian evolution providing guidance, using existing knowledge, as to what is the 'best' experiment to do next. An awareness, and the application, of these methods can thereby enhance the scientific discovery process considerably. This analysis fits comfortably with an emerging epistemology that sees scientific reasoning, the search for solutions, and scientific discovery as Bayesian processes. Copyright © 2012 WILEY Periodicals, Inc.

Vegetation-modulated landscape evolution: Effects of vegetation on landscape processes, drainage density, and topography

NASA Astrophysics Data System (ADS)

Istanbulluoglu, Erkan; Bras, Rafael L.

2005-06-01

Topography acts as a template for numerous landscape processes that include hydrologic, ecologic, and biologic phenomena. These processes not only interact with each other but also contribute to shaping the landscape as they influence geomorphic processes. We have investigated the effects of vegetation on thresholds for channel initiation and landform evolution using both analytical and numerical approaches. Vegetation is assumed to form a uniform ground cover. Runoff erosion is modeled based on a power function of excess shear stress, in which shear stress efficiency is inversely proportional to vegetation cover. This approach is validated using data. Plant effect on slope stability is represented by additional cohesion provided by plant roots. Vegetation cover is assumed to reduce sediment transport rates due to physical creep processes (rainsplash, dry ravel, and expansion and contraction of sediments) according to a negative exponential relationship. Vegetation grows as a function of both available cover and unoccupied space by plants and is killed by geomorphic disturbances (runoff erosion and landsliding) and wildfires. Analytical results suggest that in an equilibrium basin with a fixed vegetation cover, plants may cause a transition in the dominant erosion process at the channel head. A runoff erosion-dominated landscape, under none or poor vegetation cover, may become landslide dominated under a denser vegetation cover. The sign of the predicted relationship between drainage density and vegetation cover depends on the relative influence of vegetation on different erosion phenomena. With model parameter values representative of the Oregon Coast Range (OCR), numerical experiments conducted using the Channel Hillslope Integrated Landscape Development (CHILD) model confirm the findings based on the analytical theory. A highly dissected fluvial landscape emerges when surface is assumed bare. When vegetation cover is modeled, landscape relief increases, resulting in hollow erosion dominated by landsliding. Interestingly, our simulations underscore the importance of vegetation disturbances by geomorphic events and wildfires on the landscape structure. Simulated landscapes resemble real-world catchments in the OCR when such disturbances are considered.

Landscape contexts and commonalities: building the LTAR network

USDA-ARS?s Scientific Manuscript database

The United States Department of Agriculture has established a Long-Term Agroecosystem Research Network to provide a coordinated framework to, “Enable understanding and forecasting of regional landscape capacities to provide agricultural commodities and ecosystem services under changing conditions.” ...

Ecological enrichment in agroecosystems: Utilizing wildflowers to promote beneficial arthropod communities

USDA-ARS?s Scientific Manuscript database

Beneficial arthropods which provide important ecosystems services have come under threat as a result of intensive agricultural practices and landscape simplification. Engineering diverse heterogeneous agricultural landscapes to provide optimal resources for beneficial arthropods may recover and enha...

Rapid evolution accelerates plant population spread in fragmented experimental landscapes.

PubMed

Williams, Jennifer L; Kendall, Bruce E; Levine, Jonathan M

2016-07-29

Predicting the speed of biological invasions and native species migrations requires an understanding of the ecological and evolutionary dynamics of spreading populations. Theory predicts that evolution can accelerate species' spread velocity, but how landscape patchiness--an important control over traits under selection--influences this process is unknown. We manipulated the response to selection in populations of a model plant species spreading through replicated experimental landscapes of varying patchiness. After six generations of change, evolving populations spread 11% farther than nonevolving populations in continuously favorable landscapes and 200% farther in the most fragmented landscapes. The greater effect of evolution on spread in patchier landscapes was consistent with the evolution of dispersal and competitive ability. Accounting for evolutionary change may be critical when predicting the velocity of range expansions. Copyright © 2016, American Association for the Advancement of Science.

Landscape moderation of biodiversity patterns and processes - eight hypotheses.

PubMed

Tscharntke, Teja; Tylianakis, Jason M; Rand, Tatyana A; Didham, Raphael K; Fahrig, Lenore; Batáry, Péter; Bengtsson, Janne; Clough, Yann; Crist, Thomas O; Dormann, Carsten F; Ewers, Robert M; Fründ, Jochen; Holt, Robert D; Holzschuh, Andrea; Klein, Alexandra M; Kleijn, David; Kremen, Claire; Landis, Doug A; Laurance, William; Lindenmayer, David; Scherber, Christoph; Sodhi, Navjot; Steffan-Dewenter, Ingolf; Thies, Carsten; van der Putten, Wim H; Westphal, Catrin

2012-08-01

Understanding how landscape characteristics affect biodiversity patterns and ecological processes at local and landscape scales is critical for mitigating effects of global environmental change. In this review, we use knowledge gained from human-modified landscapes to suggest eight hypotheses, which we hope will encourage more systematic research on the role of landscape composition and configuration in determining the structure of ecological communities, ecosystem functioning and services. We organize the eight hypotheses under four overarching themes. Section A: 'landscape moderation of biodiversity patterns' includes (1) the landscape species pool hypothesis-the size of the landscape-wide species pool moderates local (alpha) biodiversity, and (2) the dominance of beta diversity hypothesis-landscape-moderated dissimilarity of local communities determines landscape-wide biodiversity and overrides negative local effects of habitat fragmentation on biodiversity. Section B: 'landscape moderation of population dynamics' includes (3) the cross-habitat spillover hypothesis-landscape-moderated spillover of energy, resources and organisms across habitats, including between managed and natural ecosystems, influences landscape-wide community structure and associated processes and (4) the landscape-moderated concentration and dilution hypothesis-spatial and temporal changes in landscape composition can cause transient concentration or dilution of populations with functional consequences. Section C: 'landscape moderation of functional trait selection' includes (5) the landscape-moderated functional trait selection hypothesis-landscape moderation of species trait selection shapes the functional role and trajectory of community assembly, and (6) the landscape-moderated insurance hypothesis-landscape complexity provides spatial and temporal insurance, i.e. high resilience and stability of ecological processes in changing environments. Section D: 'landscape constraints on conservation management' includes (7) the intermediate landscape-complexity hypothesis-landscape-moderated effectiveness of local conservation management is highest in structurally simple, rather than in cleared (i.e. extremely simplified) or in complex landscapes, and (8) the landscape-moderated biodiversity versus ecosystem service management hypothesis-landscape-moderated biodiversity conservation to optimize functional diversity and related ecosystem services will not protect endangered species. Shifting our research focus from local to landscape-moderated effects on biodiversity will be critical to developing solutions for future biodiversity and ecosystem service management. © 2012 The Authors. Biological Reviews © 2012 Cambridge Philosophical Society.

A Biologically Based Approach to the Mutation of Code

DTIC Science & Technology

1999-09-01

SECOND POSITION U c A G u phenyl- alanine serine tyro sine cysteine U C leucine stop stop A stop tryptophan G o c leucine proline histidine...individuals, is a means to explore the fitness landscape and find more solutions. B. INTRODUCTION TO EVOLUTIONARY COMPUTATION There are several...respiration and are responsible for making adenosine triphosphate (ATP), which is the cellular energy source. G. The Lysosomes These organelles are

Using interviews and biological sign surveys to infer seasonal use of forested and agricultural portions of a human-dominated landscape by Asian elephants in Nepal

USGS Publications Warehouse

Lamichhane, Babu Ram; Subedi, Naresh; Pokheral, Chiranjibi Prasad; Dhakal, Maheshwar; Acharya, Krishna Prasad; Pradhan, Narendra Man Babu; Smith, James L. David; Malla, Sabita; Thakuri, Bishnu Singh; Yackulic, Charles B.

2018-01-01

Understanding how wide-ranging animals use landscapes in which human use is highly heterogeneous is important for determining patterns of human–wildlife conflict and designing mitigation strategies. Here, we show how biological sign surveys in forested components of a human-dominated landscape can be combined with human interviews in agricultural portions of a landscape to provide a full picture of seasonal use of different landscape components by wide-ranging animals and resulting human–wildlife conflict. We selected Asian elephants (Elephas maximus) in Nepal to illustrate this approach. Asian elephants are threatened throughout their geographic range, and there are large gaps in our understanding of their landscape-scale habitat use. We identified all potential elephant habitat in Nepal and divided the potential habitat into sampling units based on a 10 km by 10 km grid. Forested areas within grids were surveyed for signs of elephant use, and local villagers were interviewed regarding elephant use of agricultural areas and instances of conflict. Data were analyzed using single-season and multi-season (dynamic) occupancy models. A single-season occupancy model applied to data from 139 partially or wholly forested grid cells estimated that 0.57 of grid cells were used by elephants. Dynamic occupancy models fit to data from interviews across 158 grid cells estimated that monthly use of non-forested, human-dominated areas over the preceding year varied between 0.43 and 0.82 with a minimum in February and maximum in October. Seasonal patterns of crop raiding by elephants coincided with monthly elephant use of human-dominated areas, and serious instances of human–wildlife conflict were common. Efforts to mitigate human–elephant conflict in Nepal are likely to be most effective if they are concentrated during August through December when elephant use of human-dominated landscapes and human–elephant conflict are most common.

Principal component analysis of molecular dynamics: On the use of Cartesian vs. internal coordinates

NASA Astrophysics Data System (ADS)

Sittel, Florian; Jain, Abhinav; Stock, Gerhard

2014-07-01

Principal component analysis of molecular dynamics simulations is a popular method to account for the essential dynamics of the system on a low-dimensional free energy landscape. Using Cartesian coordinates, first the translation and overall rotation need to be removed from the trajectory. Since the rotation depends via the moment of inertia on the molecule's structure, this separation is only straightforward for relatively rigid systems. Adopting millisecond molecular dynamics simulations of the folding of villin headpiece and the functional dynamics of BPTI provided by D. E. Shaw Research, it is demonstrated via a comparison of local and global rotational fitting that the structural dynamics of flexible molecules necessarily results in a mixing of overall and internal motion. Even for the small-amplitude functional motion of BPTI, the conformational distribution obtained from a Cartesian principal component analysis therefore reflects to some extend the dominant overall motion rather than the much smaller internal motion of the protein. Internal coordinates such as backbone dihedral angles, on the other hand, are found to yield correct and well-resolved energy landscapes for both examples. The virtues and shortcomings of the choice of various fitting schemes and coordinate sets as well as the generality of these results are discussed in some detail.

Principal component analysis of molecular dynamics: on the use of Cartesian vs. internal coordinates.

PubMed

Sittel, Florian; Jain, Abhinav; Stock, Gerhard

2014-07-07

Principal component analysis of molecular dynamics simulations is a popular method to account for the essential dynamics of the system on a low-dimensional free energy landscape. Using Cartesian coordinates, first the translation and overall rotation need to be removed from the trajectory. Since the rotation depends via the moment of inertia on the molecule's structure, this separation is only straightforward for relatively rigid systems. Adopting millisecond molecular dynamics simulations of the folding of villin headpiece and the functional dynamics of BPTI provided by D. E. Shaw Research, it is demonstrated via a comparison of local and global rotational fitting that the structural dynamics of flexible molecules necessarily results in a mixing of overall and internal motion. Even for the small-amplitude functional motion of BPTI, the conformational distribution obtained from a Cartesian principal component analysis therefore reflects to some extend the dominant overall motion rather than the much smaller internal motion of the protein. Internal coordinates such as backbone dihedral angles, on the other hand, are found to yield correct and well-resolved energy landscapes for both examples. The virtues and shortcomings of the choice of various fitting schemes and coordinate sets as well as the generality of these results are discussed in some detail.

Tropical amphibians in shifting thermal landscapes under land-use and climate change.

PubMed

Nowakowski, A Justin; Watling, James I; Whitfield, Steven M; Todd, Brian D; Kurz, David J; Donnelly, Maureen A

2017-02-01

Land-cover and climate change are both expected to alter species distributions and contribute to future biodiversity loss. However, the combined effects of land-cover and climate change on assemblages, especially at the landscape scale, remain understudied. Lowland tropical amphibians may be particularly susceptible to changes in land cover and climate warming because many species have narrow thermal safety margins resulting from air and body temperatures that are close to their critical thermal maxima (CT max ). We examined how changing thermal landscapes may alter the area of thermally suitable habitat (TSH) for tropical amphibians. We measured microclimates in 6 land-cover types and CT max of 16 frog species in lowland northeastern Costa Rica. We used a biophysical model to estimate core body temperatures of frogs exposed to habitat-specific microclimates while accounting for evaporative cooling and behavior. Thermally suitable habitat area was estimated as the portion of the landscape where species CT max exceeded their habitat-specific maximum body temperatures. We projected changes in TSH area 80 years into the future as a function of land-cover change only, climate change only, and combinations of land-cover and climate-change scenarios representing low and moderate rates of change. Projected decreases in TSH area ranged from 16% under low emissions and reduced forest loss to 30% under moderate emissions and business-as-usual land-cover change. Under a moderate emissions scenario (A1B), climate change alone contributed to 1.7- to 4.5-fold greater losses in TSH area than land-cover change only, suggesting that future decreases in TSH from climate change may outpace structural habitat loss. Forest-restricted species had lower mean CT max than species that occurred in altered habitats, indicating that thermal tolerances will likely shape assemblages in changing thermal landscapes. In the face of ongoing land-cover and climate change, it will be critical to consider changing thermal landscapes in strategies to conserve ectotherm species. © 2016 Society for Conservation Biology.

Error-based Extraction of States and Energy Landscapes from Experimental Single-Molecule Time-Series

NASA Astrophysics Data System (ADS)

Taylor, J. Nicholas; Li, Chun-Biu; Cooper, David R.; Landes, Christy F.; Komatsuzaki, Tamiki

2015-03-01

Characterization of states, the essential components of the underlying energy landscapes, is one of the most intriguing subjects in single-molecule (SM) experiments due to the existence of noise inherent to the measurements. Here we present a method to extract the underlying state sequences from experimental SM time-series. Taking into account empirical error and the finite sampling of the time-series, the method extracts a steady-state network which provides an approximation of the underlying effective free energy landscape. The core of the method is the application of rate-distortion theory from information theory, allowing the individual data points to be assigned to multiple states simultaneously. We demonstrate the method's proficiency in its application to simulated trajectories as well as to experimental SM fluorescence resonance energy transfer (FRET) trajectories obtained from isolated agonist binding domains of the AMPA receptor, an ionotropic glutamate receptor that is prevalent in the central nervous system.

Theory Can Help Structure Regression Models for Projecting Stream Conditions Under Alternative Land Use Scenarios

NASA Astrophysics Data System (ADS)

van Sickle, J.; Baker, J.; Herlihy, A.

2005-05-01

We built multiple regression models for Emphemeroptera/ Plecoptera/ Tricoptera (EPT) taxon richness and other indicators of biological condition in streams of the Willamette River Basin, Oregon, USA. The models were used to project the changes in condition that would be expected in all 2-4th order streams of the 30000 sq km basin under alternative scenarios of future land use. In formulating the models, we invoked the theory of limiting factors to express the interactive effects of stream power and watershed land use on EPT richness. The resulting models were parsimonious, and they fit the data in our wedge-shaped scatterplots slightly better than did a naive additive-effects model. Just as theory helped formulate our regression models, the models in turn helped us identify a new research need for the Basin's streams. Our future scenarios project that conversions of agricultural to urban uses may dominate landscape dynamics in the basin over the next 50 years. But our models could not detect any difference between the effects of agricultural and urban development in watersheds on stream biota. This result points to an increased need for understanding how agricultural and urban land uses in the Basin differentially influence stream ecosystems.

The potential energy landscape contribution to the dynamic heat capacity

NASA Astrophysics Data System (ADS)

Brown, Jonathan R.; McCoy, John D.

2011-05-01

The dynamic heat capacity of a simple polymeric, model glassformer was computed using molecular dynamics simulations by sinusoidally driving the temperature and recording the resultant energy. The underlying potential energy landscape of the system was probed by taking a time series of particle positions and quenching them. The resulting dynamic heat capacity demonstrates that the long time relaxation is the direct result of dynamics resulting from the potential energy landscape. Moreover, the equilibrium (low frequency) portion of the potential energy landscape contribution to the heat capacity is found to increase rapidly at low temperatures and at high packing fractions. This increase in the heat capacity is explained by a statistical mechanical model based on the distribution of minima in the potential energy landscape.

Simple landscape modifications for pollinator and arthropod natural enemy enhancement

USDA-ARS?s Scientific Manuscript database

Beneficial arthropods which play an important role in providing ecosystem services (pollination and pest control) have come under threat as a result of intensive agricultural practices and simplification of habitats. Ecological intensification in agricultural landscapes by diversifying the habitat r...

Enzymes with lid-gated active sites must operate by an induced fit mechanism instead of conformational selection

DOE Office of Scientific and Technical Information (OSTI.GOV)

Sullivan, Sarah M.; Holyoak, Todd

2008-09-17

The induced fit and conformational selection/population shift models are two extreme cases of a continuum aimed at understanding the mechanism by which the final key-lock or active enzyme conformation is achieved upon formation of the correctly ligated enzyme. Structures of complexes representing the Michaelis and enolate intermediate complexes of the reaction catalyzed by phosphoenolpyruvate carboxykinase provide direct structural evidence for the encounter complex that is intrinsic to the induced fit model and not required by the conformational selection model. In addition, the structural data demonstrate that the conformational selection model is not sufficient to explain the correlation between dynamics andmore » catalysis in phosphoenolpyruvate carboxykinase and other enzymes in which the transition between the uninduced and the induced conformations occludes the active site from the solvent. The structural data are consistent with a model in that the energy input from substrate association results in changes in the free energy landscape for the protein, allowing for structural transitions along an induced fit pathway.« less

Enzymes With Lid-Gated Active Sites Must Operate By An Induced Fit Mechanism Instead of Conformational Selection

DOE Office of Scientific and Technical Information (OSTI.GOV)

Sullivan, S.M.; Holyoak, T.

2009-05-26

The induced fit and conformational selection/population shift models are two extreme cases of a continuum aimed at understanding the mechanism by which the final key-lock or active enzyme conformation is achieved upon formation of the correctly ligated enzyme. Structures of complexes representing the Michaelis and enolate intermediate complexes of the reaction catalyzed by phosphoenolpyruvate carboxykinase provide direct structural evidence for the encounter complex that is intrinsic to the induced fit model and not required by the conformational selection model. In addition, the structural data demonstrate that the conformational selection model is not sufficient to explain the correlation between dynamics andmore » catalysis in phosphoenolpyruvate carboxykinase and other enzymes in which the transition between the uninduced and the induced conformations occludes the active site from the solvent. The structural data are consistent with a model in that the energy input from substrate association results in changes in the free energy landscape for the protein, allowing for structural transitions along an induced fit pathway.« less

Tree cover at fine and coarse spatial grains interacts with shade tolerance to shape plant species distributions across the Alps

PubMed Central

Nieto-Lugilde, Diego; Lenoir, Jonathan; Abdulhak, Sylvain; Aeschimann, David; Dullinger, Stefan; Gégout, Jean-Claude; Guisan, Antoine; Pauli, Harald; Renaud, Julien; Theurillat, Jean-Paul; Thuiller, Wilfried; Van Es, Jérémie; Vittoz, Pascal; Willner, Wolfgang; Wohlgemuth, Thomas; Zimmermann, Niklaus E.; Svenning, Jens-Christian

2015-01-01

The role of competition for light among plants has long been recognised at local scales, but its importance for plant species distributions at larger spatial scales has generally been ignored. Tree cover modifies the local abiotic conditions below the canopy, notably by reducing light availability, and thus, also the performance of species that are not adapted to low-light conditions. However, this local effect may propagate to coarser spatial grains, by affecting colonisation probabilities and local extinction risks of herbs and shrubs. To assess the effect of tree cover at both the plot- and landscape-grain sizes (approximately 10-m and 1-km), we fit Generalised Linear Models (GLMs) for the plot-level distributions of 960 species of herbs and shrubs using 6,935 vegetation plots across the European Alps. We ran four models with different combinations of variables (climate, soil and tree cover) at both spatial grains for each species. We used partial regressions to evaluate the independent effects of plot- and landscape-grain tree cover on plot-level plant communities. Finally, the effects on species-specific elevational range limits were assessed by simulating a removal experiment comparing the species distributions under high and low tree cover. Accounting for tree cover improved the model performance, with the probability of the presence of shade-tolerant species increasing with increasing tree cover, whereas shade-intolerant species showed the opposite pattern. The tree cover effect occurred consistently at both the plot and landscape spatial grains, albeit most strongly at the former. Importantly, tree cover at the two grain sizes had partially independent effects on plot-level plant communities. With high tree cover, shade-intolerant species exhibited narrower elevational ranges than with low tree cover whereas shade-tolerant species showed wider elevational ranges at both limits. These findings suggest that forecasts of climate-related range shifts for herb and shrub species may be modified by tree cover dynamics. PMID:26290621

[Dynamic evolution of landscape spatial pattern in Taihu Lake basin, China].

PubMed

Wang, Fang; Xie, Xiao Ping; Chen, Zhi Cong

2017-11-01

Based on the land-use satellite image datasets of 2000, 2010 and 2015, the landscape index, dynamic change model, landscape transfer matrix and CLUE-S model were integrated to analyze the dynamic evolution of the landscape spatial pattern of Taihu Lake basin. The results showed that the landscape type of the basin was dominated by cultivated land and construction land, and the degree of landscape fragmentation was strengthened from 2000 to 2015, and the distribution showed a uniform trend. From the point of transfer dynamic change, the cultivated land and construction land changed significantly, which was reduced by 6761 km 2 (2.1%) and increased by 6615.33 km 2 (8.4%), respectively. From the landscape transfer, it could be seen that the main change direction of the cultivated land reduction was the construction land, and the cultivated land with 7866.30 km 2 was converted into construction land, accounting for 91.6% of the cultivated land change, and the contribution to the construction land was 96.5%. The trend of dynamic changes of cultivated and construction land in the counties and cities was the same as that of the whole Taihu Lake basin. For Shanghai Central Urban, as well as Pudong District, Lin'an City, Baoshan District, Minhang District, Jiading District and Changzhou City, the area of the cultivated land and construction land changed more prominently. However, compared with the CLUE-S model for the landscape pattern change in 2030, the change of cultivated and construction lands would be the largest in the natural development scenario. Under the ecological protection scenario, the area of grassland would increase and the dynamic degree would reach 54.5%. Under the situation of cultivated land protection, the conversion of cultivated land to construction land would be decreased.

Hydrological resiliency in the Western Boreal Plains: classification of hydrological responses using wavelet analysis to assess landscape resilience

NASA Astrophysics Data System (ADS)

Probert, Samantha; Kettridge, Nicholas; Devito, Kevin; Hannah, David; Parkin, Geoff

2017-04-01

The Boreal represents a system of substantial resilience to climate change, with minimal ecological change over the past 6000 years. However, unprecedented climatic warming, coupled with catchment disturbances could exceed thresholds of hydrological function in the Western Boreal Plains. Knowledge of ecohydrological and climatic feedbacks that shape the resilience of boreal forests has advanced significantly in recent years, but this knowledge is yet to be applied and understood at landscape scales. Hydrological modelling at the landscape scale is challenging in the WBP due to diverse, non-topographically driven hydrology across the mosaic of terrestrial and aquatic ecosystems. This study functionally divides the geologic and ecological components of the landscape into Hydrologic Response Areas (HRAs) and wetland, forestland, interface and pond Hydrologic Units (HUs) to accurately characterise water storage and infer transmission at multiple spatial and temporal scales. Wavelet analysis is applied to pond and groundwater levels to describe the patterns of water storage in response to climate signals; to isolate dominant controls on hydrological responses and to assess the relative importance of physical controls between wet and dry climates. This identifies which components of the landscape exhibit greater magnitude and frequency of variability to wetting and drying trends, further to testing the hierarchical framework for hydrological storage controls of: climate, bedrock geology, surficial geology, soil, vegetation, and topography. Classifying HRA and HU hydrological function is essential to understand and predict water storage and redistribution through drought cycles and wet periods. This work recognises which landscape components are most sensitive under climate change and disturbance and also creates scope for hydrological resiliency research in Boreal systems by recognising critical landscape components and their role in landscape collapse or catastrophic shift in ecosystem function under future climatic scenarios.

Engineering of a synthetic quadrastable gene network to approach Waddington landscape and cell fate determination.

PubMed

Wu, Fuqing; Su, Ri-Qi; Lai, Ying-Cheng; Wang, Xiao

2017-04-11

The process of cell fate determination has been depicted intuitively as cells travelling and resting on a rugged landscape, which has been probed by various theoretical studies. However, few studies have experimentally demonstrated how underlying gene regulatory networks shape the landscape and hence orchestrate cellular decision-making in the presence of both signal and noise. Here we tested different topologies and verified a synthetic gene circuit with mutual inhibition and auto-activations to be quadrastable, which enables direct study of quadruple cell fate determination on an engineered landscape. We show that cells indeed gravitate towards local minima and signal inductions dictate cell fates through modulating the shape of the multistable landscape. Experiments, guided by model predictions, reveal that sequential inductions generate distinct cell fates by changing landscape in sequence and hence navigating cells to different final states. This work provides a synthetic biology framework to approach cell fate determination and suggests a landscape-based explanation of fixed induction sequences for targeted differentiation.

Quantifying the Energy Landscape Statistics in Proteins - a Relaxation Mode Analysis

NASA Astrophysics Data System (ADS)

Cai, Zhikun; Zhang, Yang

Energy landscape, the hypersurface in the configurational space, has been a useful concept in describing complex processes that occur over a very long time scale, such as the multistep slow relaxations of supercooled liquids and folding of polypeptide chains into structured proteins. Despite extensive simulation studies, its experimental characterization still remains a challenge. To address this challenge, we developed a relaxation mode analysis (RMA) for liquids under a framework analogous to the normal mode analysis for solids. Using RMA, important statistics of the activation barriers of the energy landscape becomes accessible from experimentally measurable two-point correlation functions, e.g. using quasi-elastic and inelastic scattering experiments. We observed a prominent coarsening effect of the energy landscape. The results were further confirmed by direct sampling of the energy landscape using a metadynamics-like adaptive autonomous basin climbing computation. We first demonstrate RMA in a supercooled liquid when dynamical cooperativity emerges in the landscape-influenced regime. Then we show this framework reveals encouraging energy landscape statistics when applied to proteins.

A methodology to find the elementary landscape decomposition of combinatorial optimization problems.

PubMed

Chicano, Francisco; Whitley, L Darrell; Alba, Enrique

2011-01-01

A small number of combinatorial optimization problems have search spaces that correspond to elementary landscapes, where the objective function f is an eigenfunction of the Laplacian that describes the neighborhood structure of the search space. Many problems are not elementary; however, the objective function of a combinatorial optimization problem can always be expressed as a superposition of multiple elementary landscapes if the underlying neighborhood used is symmetric. This paper presents theoretical results that provide the foundation for algebraic methods that can be used to decompose the objective function of an arbitrary combinatorial optimization problem into a sum of subfunctions, where each subfunction is an elementary landscape. Many steps of this process can be automated, and indeed a software tool could be developed that assists the researcher in finding a landscape decomposition. This methodology is then used to show that the subset sum problem is a superposition of two elementary landscapes, and to show that the quadratic assignment problem is a superposition of three elementary landscapes.

Circuit theory and model-based inference for landscape connectivity

USGS Publications Warehouse

Hanks, Ephraim M.; Hooten, Mevin B.

2013-01-01

Circuit theory has seen extensive recent use in the field of ecology, where it is often applied to study functional connectivity. The landscape is typically represented by a network of nodes and resistors, with the resistance between nodes a function of landscape characteristics. The effective distance between two locations on a landscape is represented by the resistance distance between the nodes in the network. Circuit theory has been applied to many other scientific fields for exploratory analyses, but parametric models for circuits are not common in the scientific literature. To model circuits explicitly, we demonstrate a link between Gaussian Markov random fields and contemporary circuit theory using a covariance structure that induces the necessary resistance distance. This provides a parametric model for second-order observations from such a system. In the landscape ecology setting, the proposed model provides a simple framework where inference can be obtained for effects that landscape features have on functional connectivity. We illustrate the approach through a landscape genetics study linking gene flow in alpine chamois (Rupicapra rupicapra) to the underlying landscape.

Navigating the patent landscapes for nanotechnology: English gardens or tangled grounds?

PubMed

Sylvester, Douglas J; Bowman, Diana M

2011-01-01

The patent landscape, like a garden, can tell you much about its designers and users: their motivations, biases, and general interests. While both patent landscapes and gardens may appear to the casual observer as refined and ordered, an in-depth exploration of the terrain is likely to reveal unforeseen challenges including, for example, alien species, thickets, and trolls. As this chapter illustrates, patent landscapes are dynamic and have been forced to continually evolve in response to technological innovation. While emerging technologies such as biotechnology and information communication technology have challenged the traditional patent landscape, the overarching framework and design have largely remained intact. But will this always be the case? The aim of this chapter is to highlight how nanotechnology is challenging the existing structures and underlying foundation of the patent landscape and the implications thereof for the technology, industry, and public more generally. The chapter concludes by asking the question whether the current patent landscape will be able to withstand the ubiquitous nature of the technology, or whether nanotechnology will be a catalyst for governments and policy makers for overhauling the current landscape design.

Farmers' Preferences for Future Agricultural Land Use Under the Consideration of Climate Change

NASA Astrophysics Data System (ADS)

Pröbstl-Haider, Ulrike; Mostegl, Nina M.; Kelemen-Finan, Julia; Haider, Wolfgang; Formayer, Herbert; Kantelhardt, Jochen; Moser, Tobias; Kapfer, Martin; Trenholm, Ryan

2016-09-01

Cultural landscapes in Austria are multifunctional through their simultaneous support of productive, habitat, regulatory, social, and economic functions. This study investigates, if changing climatic conditions in Austria will lead to landscape change. Based on the assumption that farmers are the crucial decision makers when it comes to the implementation of agricultural climate change policies, this study analyzes farmers' decision-making under the consideration of potential future climate change scenarios and risk, varying economic conditions, and different policy regimes through a discrete choice experiment. Results show that if a warming climate will offer new opportunities to increase income, either through expansion of cash crop cultivation or new land use options such as short-term rotation forestry, these opportunities will almost always be seized. Even if high environmental premiums were offered to maintain current cultural landscapes, only 43 % of farmers would prefer the existing grassland cultivation. Therefore, the continuity of characteristic Austrian landscape patterns seems unlikely. In conclusion, despite governmental regulations of and incentives for agriculture, climate change will have significant effects on traditional landscapes. Any opportunities for crop intensification will be embraced, which will ultimately impact ecosystem services, tourism opportunities, and biodiversity.

Farmers' Preferences for Future Agricultural Land Use Under the Consideration of Climate Change.

PubMed

Pröbstl-Haider, Ulrike; Mostegl, Nina M; Kelemen-Finan, Julia; Haider, Wolfgang; Formayer, Herbert; Kantelhardt, Jochen; Moser, Tobias; Kapfer, Martin; Trenholm, Ryan

2016-09-01

Cultural landscapes in Austria are multifunctional through their simultaneous support of productive, habitat, regulatory, social, and economic functions. This study investigates, if changing climatic conditions in Austria will lead to landscape change. Based on the assumption that farmers are the crucial decision makers when it comes to the implementation of agricultural climate change policies, this study analyzes farmers' decision-making under the consideration of potential future climate change scenarios and risk, varying economic conditions, and different policy regimes through a discrete choice experiment. Results show that if a warming climate will offer new opportunities to increase income, either through expansion of cash crop cultivation or new land use options such as short-term rotation forestry, these opportunities will almost always be seized. Even if high environmental premiums were offered to maintain current cultural landscapes, only 43 % of farmers would prefer the existing grassland cultivation. Therefore, the continuity of characteristic Austrian landscape patterns seems unlikely. In conclusion, despite governmental regulations of and incentives for agriculture, climate change will have significant effects on traditional landscapes. Any opportunities for crop intensification will be embraced, which will ultimately impact ecosystem services, tourism opportunities, and biodiversity.

Checkpoint Inhibition in Hodgkin Lymphoma - a Review.

PubMed

Bröckelmann, Paul J; Engert, Andreas

2017-01-01

Physiological immune checkpoint pathways are important to regulate self-tolerance, limit immune reactions, and moderate autoimmunity. Various cancers are commonly exploiting these mechanisms to evade the host immune system by restraining a durable, efficient anti-tumor immune response. Immune checkpoints include, but are not limited to, the programmed death 1 (PD1) and the cytotoxic T-lymphocyte-associated protein-4 (CTLA4) axis, which are both druggable by monoclonal antibodies referred to as checkpoint inhibitors (CIs). To date, the anti-PD1 antibodies nivolumab and pembrolizumab are approved for relapsed or refractory classical Hodgkin lymphoma (cHL) due to high response rates with a favorable yet distinct safety profile, and other agents are under investigation. This review summarizes the available preclinical and clinical data including the toxicity and efficacy of different CIs in cHL. It also provides future perspectives based on ongoing clinical trials, potentially synergistic combinatory approaches, and their fit in the therapeutic landscape in cHL. © 2017 S. Karger GmbH, Freiburg.

Species- and sex-specific connectivity effects of habitat fragmentation in a suite of woodland birds.

PubMed

Amos, Nevil; Harrisson, Katherine A; Radford, James Q; White, Matt; Newell, Graeme; Mac Nally, Ralph; Sunnucks, Paul; Pavlova, Alexandra

2014-06-01

Loss of functional connectivity following habitat loss and fragmentation could drive species declines. A comprehensive understanding of fragmentation effects on functional connectivity of an ecological assemblage requires investigation of multiple species with different mobilities, at different spatial scales, for each sex, and in different landscapes. Based on published data on mobility and ecological responses to fragmentation of 10 woodland-dependent birds, and using simulation studies, we predicted that (1) fragmentation would impede dispersal and gene flow of eight "decliners" (species that disappear from suitable patches when landscape-level tree cover falls below species-specific thresholds), but not of two "tolerant" species (whose occurrence in suitable habitat patches is independent of landscape tree cover); and that fragmentation effects would be stronger (2) in the least mobile species, (3) in the more philopatric sex, and (4) in the more fragmented region. We tested these predictions by evaluating spatially explicit isolation-by-landscape-resistance models of gene flow in fragmented landscapes across a 50 x 170 km study area in central Victoria, Australia, using individual and population genetic distances. To account for sex-biased dispersal and potential scale- and configuration-specific effects, we fitted models specific to sex and geographic zones. As predicted, four of the least mobile decliners showed evidence of reduced genetic connectivity. The responses were strongly sex specific, but in opposite directions in the two most sedentary species. Both tolerant species and (unexpectedly) four of the more mobile decliners showed no reduction in gene flow. This is unlikely to be due to time lags because more mobile species develop genetic signatures of fragmentation faster than do less mobile ones. Weaker genetic effects were observed in the geographic zone with more aggregated vegetation, consistent with gene flow being unimpeded by landscape structure. Our results indicate that for all but the most sedentary species in our system, the movement of the more dispersive sex (females in most cases) maintains overall genetic connectivity across fragmented landscapes in the study area, despite some small-scale effects on the more philopatric sex for some species. Nevertheless, to improve population viability for the less mobile bird species, structural landscape connectivity must be increased.

Catchment-Scale Sampling Reveals the Consistent Function of the Sediment-Water Interface to Remove Landscape Scale Dissolved Organic Carbon Properties

NASA Astrophysics Data System (ADS)

Lee-Cullin, J. A.; Zarnetske, J. P.; Wiewiora, E.; Ruhala, S.; Hampton, T. B.

2016-12-01

Dissolved organic carbon (DOC) is a critical component to biogeochemical cycling and water quality in surface waters. As DOC moves through stream networks, from headwaters to higher order streams, the sediment-water interface (SWI), where streams and groundwater readily interact, exerts a strong influence on DOC concentrations and compositional characteristics (i.e., molecular properties). Few studies examine SWI patterns at larger spatial scales, instead focusing primarily on site-level studies because sampling in the SWI is methodologically time and labor intensive. It is presently unknown how land use and landcover influence the fate of DOC in the SWI and therefore the function of the SWI on catchment-scale DOC conditions. Here, we performed a catchment-scale, high spatial-resolution SWI sampling campaign to test how landscape pattern DOC signatures are propagated into the stream and groundwater, and to assess the fate of these signatures when DOC travels through the SWI. We sampled across 39 sites composed of first-, second-, and third-order locations in a lowland, third-order catchment composed of diverse landscape units and properties, including wetland, upland forest, and agriculture. At each of these locations, surface water, groundwater, and SWI water were collected, including six discrete depths across the SWI. The major land use and landcover properties were also determined for each of these locations. We developed two simple generalized linear models to identify the landscape properties with greatest explanatory power for DOC conditions - one for stream water and one for groundwater. The correlation between landscape properties and surface water DOC characteristics was stronger than between landscape properties and groundwater DOC characteristics. To test if the DOC properties from surface and groundwater were preserved or removed by the SWI, the resulting best-fit models for each water source were used to predict the DOC conditions across the SWI. The models were unable to predict SWI DOC conditions, indicating that the landscape signature present in both the surface water and groundwater is removed by processes occurring in the SWI. Overall, this suggests that the SWI functions as and effective zone for processing the landscape-derived DOC signatures.

Catchment-Scale Sampling Reveals the Consistent Function of the Sediment-Water Interface to Remove Landscape Scale Dissolved Organic Carbon Properties

NASA Astrophysics Data System (ADS)

Lee-Cullin, J. A.; Zarnetske, J. P.; Wiewiora, E.; Ruhala, S.; Hampton, T. B.

2017-12-01

Dissolved organic carbon (DOC) is a critical component to biogeochemical cycling and water quality in surface waters. As DOC moves through stream networks, from headwaters to higher order streams, the sediment-water interface (SWI), where streams and groundwater readily interact, exerts a strong influence on DOC concentrations and compositional characteristics (i.e., molecular properties). Few studies examine SWI patterns at larger spatial scales, instead focusing primarily on site-level studies because sampling in the SWI is methodologically time and labor intensive. It is presently unknown how land use and landcover influence the fate of DOC in the SWI and therefore the function of the SWI on catchment-scale DOC conditions. Here, we performed a catchment-scale, high spatial-resolution SWI sampling campaign to test how landscape pattern DOC signatures are propagated into the stream and groundwater, and to assess the fate of these signatures when DOC travels through the SWI. We sampled across 39 sites composed of first-, second-, and third-order locations in a lowland, third-order catchment composed of diverse landscape units and properties, including wetland, upland forest, and agriculture. At each of these locations, surface water, groundwater, and SWI water were collected, including six discrete depths across the SWI. The major land use and landcover properties were also determined for each of these locations. We developed two simple generalized linear models to identify the landscape properties with greatest explanatory power for DOC conditions - one for stream water and one for groundwater. The correlation between landscape properties and surface water DOC characteristics was stronger than between landscape properties and groundwater DOC characteristics. To test if the DOC properties from surface and groundwater were preserved or removed by the SWI, the resulting best-fit models for each water source were used to predict the DOC conditions across the SWI. The models were unable to predict SWI DOC conditions, indicating that the landscape signature present in both the surface water and groundwater is removed by processes occurring in the SWI. Overall, this suggests that the SWI functions as and effective zone for processing the landscape-derived DOC signatures.

Topography of funneled landscapes determines the thermodynamics and kinetics of protein folding

PubMed Central

Wang, Jin; Oliveira, Ronaldo J.; Chu, Xiakun; Whitford, Paul C.; Chahine, Jorge; Han, Wei; Wang, Erkang; Onuchic, José N.; Leite, Vitor B.P.

2012-01-01

The energy landscape approach has played a fundamental role in advancing our understanding of protein folding. Here, we quantify protein folding energy landscapes by exploring the underlying density of states. We identify three quantities essential for characterizing landscape topography: the stabilizing energy gap between the native and nonnative ensembles δE, the energetic roughness ΔE, and the scale of landscape measured by the entropy S. We show that the dimensionless ratio between the gap, roughness, and entropy of the system accurately predicts the thermodynamics, as well as the kinetics of folding. Large Λ implies that the energy gap (or landscape slope towards the native state) is dominant, leading to more funneled landscapes. We investigate the role of topological and energetic roughness for proteins of different sizes and for proteins of the same size, but with different structural topologies. The landscape topography ratio Λ is shown to be monotonically correlated with the thermodynamic stability against trapping, as characterized by the ratio of folding temperature versus trapping temperature. Furthermore, Λ also monotonically correlates with the folding kinetic rates. These results provide the quantitative bridge between the landscape topography and experimental folding measurements. PMID:23019359

Estimating HIV-1 Fitness Characteristics from Cross-Sectional Genotype Data

PubMed Central

Gopalakrishnan, Sathej; Montazeri, Hesam; Menz, Stephan; Beerenwinkel, Niko; Huisinga, Wilhelm

2014-01-01

Despite the success of highly active antiretroviral therapy (HAART) in the management of human immunodeficiency virus (HIV)-1 infection, virological failure due to drug resistance development remains a major challenge. Resistant mutants display reduced drug susceptibilities, but in the absence of drug, they generally have a lower fitness than the wild type, owing to a mutation-incurred cost. The interaction between these fitness costs and drug resistance dictates the appearance of mutants and influences viral suppression and therapeutic success. Assessing in vivo viral fitness is a challenging task and yet one that has significant clinical relevance. Here, we present a new computational modelling approach for estimating viral fitness that relies on common sparse cross-sectional clinical data by combining statistical approaches to learn drug-specific mutational pathways and resistance factors with viral dynamics models to represent the host-virus interaction and actions of drug mechanistically. We estimate in vivo fitness characteristics of mutant genotypes for two antiretroviral drugs, the reverse transcriptase inhibitor zidovudine (ZDV) and the protease inhibitor indinavir (IDV). Well-known features of HIV-1 fitness landscapes are recovered, both in the absence and presence of drugs. We quantify the complex interplay between fitness costs and resistance by computing selective advantages for different mutants. Our approach extends naturally to multiple drugs and we illustrate this by simulating a dual therapy with ZDV and IDV to assess therapy failure. The combined statistical and dynamical modelling approach may help in dissecting the effects of fitness costs and resistance with the ultimate aim of assisting the choice of salvage therapies after treatment failure. PMID:25375675

Spatial discontinuity in the distribution of soil properties: underlying landscape properties or management

USDA-ARS?s Scientific Manuscript database

Landscape responses to applied treatments have traditionally been accounted for in statistical analyses with blocking criteria (slope position, etc.), to compartmentalize variance and allow more accurate definition of treatment effects. However, within-unit distributions of soil properties can conta...

LANDSCAPE-LEVEL INDICATORS IN SMALL GEORGIA WATERSHEDS

EPA Science Inventory

Landscape level indicators in small watersheds can be used as a screening tool to guide in-situ monitoring to confirm stream condition problems, aid listing of impaired waters under Section 303(d) of the Clean Water Act and total maximum daily load (TMDL) development, and provide...

ACHP | News

Science.gov Websites

Landscapes Plan ACHP Fall Business Meeting, November 10, 2011 The Native American Traditional Cultural Landscapes Action Plan emphasizes consultation early in project planning and identification of areas of now begin to implement specific actions under the plan. If you have any comments or questions, please

Accounting for the influence of vegetation and landscape improves model transferability in a tropical savannah region

NASA Astrophysics Data System (ADS)

Gao, Hongkai; Hrachowitz, Markus; Sriwongsitanon, Nutchanart; Fenicia, Fabrizio; Gharari, Shervan; Savenije, Hubert H. G.

2016-10-01

Understanding which catchment characteristics dominate hydrologic response and how to take them into account remains a challenge in hydrological modeling, particularly in ungauged basins. This is even more so in nontemperate and nonhumid catchments, where—due to the combination of seasonality and the occurrence of dry spells—threshold processes are more prominent in rainfall runoff behavior. An example is the tropical savannah, the second largest climatic zone, characterized by pronounced dry and wet seasons and high evaporative demand. In this study, we investigated the importance of landscape variability on the spatial variability of stream flow in tropical savannah basins. We applied a stepwise modeling approach to 23 subcatchments of the Upper Ping River in Thailand, where gradually more information on landscape was incorporated. The benchmark is represented by a classical lumped model (FLEXL), which does not account for spatial variability. We then tested the effect of accounting for vegetation information within the lumped model (FLEXLM), and subsequently two semidistributed models: one accounting for the spatial variability of topography-based landscape features alone (FLEXT), and another accounting for both topographic features and vegetation (FLEXTM). In cross validation, each model was calibrated on one catchment, and then transferred with its fitted parameters to the remaining catchments. We found that when transferring model parameters in space, the semidistributed models accounting for vegetation and topographic heterogeneity clearly outperformed the lumped model. This suggests that landscape controls a considerable part of the hydrological function and explicit consideration of its heterogeneity can be highly beneficial for prediction in ungauged basins in tropical savannah.

The landscape configuration of zoonotic transmission of Ebola virus disease in West and Central Africa: interaction between population density and vegetation cover.

PubMed

Walsh, Michael G; Haseeb, Ma

2015-01-01

Ebola virus disease (EVD) is an emerging infectious disease of zoonotic origin that has been responsible for high mortality and significant social disruption in West and Central Africa. Zoonotic transmission of EVD requires contact between susceptible human hosts and the reservoir species for Ebolaviruses, which are believed to be fruit bats. Nevertheless, features of the landscape that may facilitate such points of contact have not yet been adequately identified. Nor have spatial dependencies between zoonotic EVD transmission and landscape structures been delineated. This investigation sought to describe the spatial relationship between zoonotic EVD transmission events, or spillovers, and population density and vegetation cover. An inhomogeneous Poisson process model was fitted to all precisely geolocated zoonotic transmissions of EVD in West and Central Africa. Population density was strongly associated with spillover; however, there was significant interaction between population density and green vegetation cover. In areas of very low population density, increasing vegetation cover was associated with a decrease in risk of zoonotic transmission, but as population density increased in a given area, increasing vegetation cover was associated with increased risk of zoonotic transmission. This study showed that the spatial dependencies of Ebolavirus spillover were associated with the distribution of population density and vegetation cover in the landscape, even after controlling for climate and altitude. While this is an observational study, and thus precludes direct causal inference, the findings do highlight areas that may be at risk for zoonotic EVD transmission based on the spatial configuration of important features of the landscape.

Variational and PDE-Based Methods for Big Data Analysis, Classification and Image Processing Using Graphs

DTIC Science & Technology

2015-01-01

explain the accuracy and speed increase. Exploring the underlying connections of the energy evolution of these methods and the energy landscape for the...unwanted trivial global minimizers from the energy landscape . Note that the second eigenvector of the Laplacian already provides a solution to a cut...von Brecht. Convergence and energy landscape for Cheeger cut clustering. Advances in Neural Information Processing Systems, 25:1394– 1402, 2012. [13] X

Deformation of Attractor Landscape via Cholinergic Presynaptic Modulations: A Computational Study Using a Phase Neuron Model

PubMed Central

Kanamaru, Takashi; Fujii, Hiroshi; Aihara, Kazuyuki

2013-01-01

Corticopetal acetylcholine (ACh) is released transiently from the nucleus basalis of Meynert (NBM) into the cortical layers and is associated with top-down attention. Recent experimental data suggest that this release of ACh disinhibits layer 2/3 pyramidal neurons (PYRs) via muscarinic presynaptic effects on inhibitory synapses. Together with other possible presynaptic cholinergic effects on excitatory synapses, this may result in dynamic and temporal modifications of synapses associated with top-down attention. However, the system-level consequences and cognitive relevance of such disinhibitions are poorly understood. Herein, we propose a theoretical possibility that such transient modifications of connectivity associated with ACh release, in addition to top-down glutamatergic input, may provide a neural mechanism for the temporal reactivation of attractors as neural correlates of memories. With baseline levels of ACh, the brain returns to quasi-attractor states, exhibiting transitive dynamics between several intrinsic internal states. This suggests that top-down attention may cause the attention-induced deformations between two types of attractor landscapes: the quasi-attractor landscape (Q-landscape, present under low-ACh, non-attentional conditions) and the attractor landscape (A-landscape, present under high-ACh, top-down attentional conditions). We present a conceptual computational model based on experimental knowledge of the structure of PYRs and interneurons (INs) in cortical layers 1 and 2/3 and discuss the possible physiological implications of our results. PMID:23326520

The DYNAFLUX / DYNACOLD (Dynamics, Fluxes, Stability, Succession and Landscape Formation in Cold Environments) Network (2004-2017)

NASA Astrophysics Data System (ADS)

Beylich, Achim A.

2017-04-01

There is a wide range of high-latitude and high-altitude cold climate landscapes within Europe, covering a significant proportion of the total land surface area. This spectrum of defined cold-climate landscapes represents a variety of stages of deglaciation history and landscape formation. We can find landscapes at different levels of postglacial stabilization which is providing the unique opportunity to study the interactions between geo-, bio-, social and socio-economic systems at the land surface. The DYNAFLUX / DYNACOLD Network (2004-2017) bridges across the geo-, bio-, social and socio-economic sciences in order to analyze the complex dynamics of adjustment, stabilization, succession and landscape formation during and after ice retreat and under ongoing anthropogenic influences. The network provides a multidisciplinary forum where researchers come together and discuss. In addition, this network is linking a number of other scientific networks, working groups and programs and creates an umbrella network and a forum for sharing knowledge and experience. The scientific focus of DYNAFLUX / DYNACOLD is also relevant for a number of end users, including risk and vulnerability assessment, sustainable land use, land management and conservation. In addition, present key questions related to environmental change like, e.g., hazards, permafrost degradation and loss of biodiversity are addressed and discussed. Further information is found under http://www.ngu.no/sediflux.

Protein dynamics and motions in relation to their functions: several case studies and the underlying mechanisms

PubMed Central

Yang, Li-Quan; Sang, Peng; Tao, Yan; Fu, Yun-Xin; Zhang, Ke-Qin; Xie, Yue-Hui; Liu, Shu-Qun

2013-01-01

Proteins are dynamic entities in cellular solution with functions governed essentially by their dynamic personalities. We review several dynamics studies on serine protease proteinase K and HIV-1 gp120 envelope glycoprotein to demonstrate the importance of investigating the dynamic behaviors and molecular motions for a complete understanding of their structure–function relationships. Using computer simulations and essential dynamic (ED) analysis approaches, the dynamics data obtained revealed that: (i) proteinase K has highly flexible substrate-binding site, thus supporting the induced-fit or conformational selection mechanism of substrate binding; (ii) Ca2+ removal from proteinase K increases the global conformational flexibility, decreases the local flexibility of substrate-binding region, and does not influence the thermal motion of catalytic triad, thus explaining the experimentally determined decreased thermal stability, reduced substrate affinity, and almost unchanged catalytic activity upon Ca2+ removal; (iii) substrate binding affects the large concerted motions of proteinase K, and the resulting dynamic pocket can be connected to substrate binding, orientation, and product release; (iv) amino acid mutations 375 S/W and 423 I/P of HIV-1 gp120 have distinct effects on molecular motions of gp120, facilitating 375 S/W mutant to assume the CD4-bound conformation, while 423 I/P mutant to prefer for CD4-unliganded state. The mechanisms underlying protein dynamics and protein–ligand binding, including the concept of the free energy landscape (FEL) of the protein–solvent system, how the ruggedness and variability of FEL determine protein's dynamics, and how the three ligand-binding models, the lock-and-key, induced-fit, and conformational selection are rationalized based on the FEL theory are discussed in depth. PMID:23527883

Protein dynamics and motions in relation to their functions: several case studies and the underlying mechanisms.

PubMed

Yang, Li-Quan; Sang, Peng; Tao, Yan; Fu, Yun-Xin; Zhang, Ke-Qin; Xie, Yue-Hui; Liu, Shu-Qun

2014-01-01

Proteins are dynamic entities in cellular solution with functions governed essentially by their dynamic personalities. We review several dynamics studies on serine protease proteinase K and HIV-1 gp120 envelope glycoprotein to demonstrate the importance of investigating the dynamic behaviors and molecular motions for a complete understanding of their structure-function relationships. Using computer simulations and essential dynamic (ED) analysis approaches, the dynamics data obtained revealed that: (i) proteinase K has highly flexible substrate-binding site, thus supporting the induced-fit or conformational selection mechanism of substrate binding; (ii) Ca(2+) removal from proteinase K increases the global conformational flexibility, decreases the local flexibility of substrate-binding region, and does not influence the thermal motion of catalytic triad, thus explaining the experimentally determined decreased thermal stability, reduced substrate affinity, and almost unchanged catalytic activity upon Ca(2+) removal; (iii) substrate binding affects the large concerted motions of proteinase K, and the resulting dynamic pocket can be connected to substrate binding, orientation, and product release; (iv) amino acid mutations 375 S/W and 423 I/P of HIV-1 gp120 have distinct effects on molecular motions of gp120, facilitating 375 S/W mutant to assume the CD4-bound conformation, while 423 I/P mutant to prefer for CD4-unliganded state. The mechanisms underlying protein dynamics and protein-ligand binding, including the concept of the free energy landscape (FEL) of the protein-solvent system, how the ruggedness and variability of FEL determine protein's dynamics, and how the three ligand-binding models, the lock-and-key, induced-fit, and conformational selection are rationalized based on the FEL theory are discussed in depth.

Modeling the spatio-temporal variability in subsurface thermal regimes across a low-relief polygonal tundra landscape: Modeling Archive

DOE Data Explorer

Kumar, Jitendra; Collier, Nathan; Bisht, Gautam; Mills, Richard T.; Thornton, Peter E.; Iversen, Colleen M.; Romanovsky, Vladimir

2016-01-27

This Modeling Archive is in support of an NGEE Arctic discussion paper under review and available at http://www.the-cryosphere-discuss.net/tc-2016-29/. Vast carbon stocks stored in permafrost soils of Arctic tundra are under risk of release to atmosphere under warming climate. Ice--wedge polygons in the low-gradient polygonal tundra create a complex mosaic of microtopographic features. The microtopography plays a critical role in regulating the fine scale variability in thermal and hydrological regimes in the polygonal tundra landscape underlain by continuous permafrost. Modeling of thermal regimes of this sensitive ecosystem is essential for understanding the landscape behaviour under current as well as changing climate. We present here an end-to-end effort for high resolution numerical modeling of thermal hydrology at real-world field sites, utilizing the best available data to characterize and parameterize the models. We develop approaches to model the thermal hydrology of polygonal tundra and apply them at four study sites at Barrow, Alaska spanning across low to transitional to high-centered polygon and representative of broad polygonal tundra landscape. A multi--phase subsurface thermal hydrology model (PFLOTRAN) was developed and applied to study the thermal regimes at four sites. Using high resolution LiDAR DEM, microtopographic features of the landscape were characterized and represented in the high resolution model mesh. Best available soil data from field observations and literature was utilized to represent the complex hetogeneous subsurface in the numerical model. This data collection provides the complete set of input files, forcing data sets and computational meshes for simulations using PFLOTRAN for four sites at Barrow Environmental Observatory. It also document the complete computational workflow for this modeling study to allow verification, reproducibility and follow up studies.

Mutation Supply and Relative Fitness Shape the Genotypes of Ciprofloxacin-Resistant Escherichia coli.

PubMed

Huseby, Douglas L; Pietsch, Franziska; Brandis, Gerrit; Garoff, Linnéa; Tegehall, Angelica; Hughes, Diarmaid

2017-05-01

Ciprofloxacin is an important antibacterial drug targeting Type II topoisomerases, highly active against Gram-negatives including Escherichia coli. The evolution of resistance to ciprofloxacin in E. coli always requires multiple genetic changes, usually including mutations affecting two different drug target genes, gyrA and parC. Resistant mutants selected in vitro or in vivo can have many different mutations in target genes and efflux regulator genes that contribute to resistance. Among resistant clinical isolates the genotype, gyrA S83L D87N, parC S80I is significantly overrepresented suggesting that it has a selective advantage. However, the evolutionary or functional significance of this high frequency resistance genotype is not fully understood. By combining experimental data and mathematical modeling, we addressed the reasons for the predominance of this specific genotype. The experimental data were used to model trajectories of mutational resistance evolution under different conditions of drug exposure and population bottlenecks. We identified the order in which specific mutations are selected in the clinical genotype, showed that the high frequency genotype could be selected over a range of drug selective pressures, and was strongly influenced by the relative fitness of alternative mutations and factors affecting mutation supply. Our data map for the first time the fitness landscape that constrains the evolutionary trajectories taken during the development of clinical resistance to ciprofloxacin and explain the predominance of the most frequently selected genotype. This study provides strong support for the use of in vitro competition assays as a tool to trace evolutionary trajectories, not only in the antibiotic resistance field. © The Author 2017. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

Green‐wave surfing increases fat gain in a migratory ungulate

USGS Publications Warehouse

Middleton, Arthur D.; Merkle, Jerod A.; McWhirter, Douglas E.; Cook, John G.; Cook, Rachel C.; White, P.J.; Kauffman, Matthew J.

2018-01-01

Each spring, migratory herbivores around the world track or ‘surf’ green waves of newly emergent vegetation to distant summer or wet‐season ranges. This foraging tactic may help explain the great abundance of migratory herbivores on many seasonal landscapes. However, the underlying fitness benefits of this life‐history strategy remain poorly understood. A fundamental prediction of the green‐wave hypothesis is that migratory herbivores obtain fitness benefits from surfing waves of newly emergent vegetation more closely than their resident counterparts. Here we evaluate whether this behavior increases body‐fat levels – a critically important correlate of reproduction and survival for most ungulates – in elk Cervus elaphus of the Greater Yellowstone Ecosystem. Using satellite imagery and GPS tracking data, we found evidence that migrants (n = 23) indeed surfed the green wave, occupying sites 12.7 days closer to peak green‐up than residents (n = 16). Importantly, individual variation in surfing may help account for up to 6 kg of variation in autumn body‐fat levels. Our findings point to a pathway for anthropogenic changes to the green wave (e.g. climate change) or migrants’ ability to surf it (e.g. development) to impact migratory populations. To explore this possibility, we evaluated potential population‐level consequences of constrained surfing with a heuristic model. If green‐wave surfing deteriorates by 5–15 days from observed, our model predicts up to a 20% decrease in pregnancy rates, a 2.5% decrease in population growth, and a 30% decrease in abundance over 50 years. By linking green‐wave surfing to fitness and illustrating potential effects on population growth, our study provides new insights into the evolution of migratory behavior and the prospects for the persistence of migratory ungulate populations in a changing world.

Conformational flexibility and packing plausibility of repaglinide polymorphs

NASA Astrophysics Data System (ADS)

Rani, Dimpy; Goyal, Parnika; Chadha, Renu

2018-04-01

The present manuscript highlights the structural insight into the repaglinide polymorphs. The experimental screening for the possible crystal forms were carried out using various solvents, which generated three forms. The crystal structure of Form II and III was determined using PXRD pattern whereas structural analysis of Form I has already been reported. Form I, II and II was found to exist in P212121, PNA21 and P21/c space groups respectively. Conformational analysis was performed to account the conformational flexibility of RPG. The obtained conformers were further utilized to obtain the information about the crystal packing pattern of RPG polymorphs by polymorph prediction module. The lattice energy landscape, depicting the relationship between lattice energy and density of the polymorphs has been obtained for various possible polymorphs. The experimentally isolated polymorphs were successfully fitted into lattice energy landscape.

Bluetongue virus spread in Europe is a consequence of climatic, landscape and vertebrate host factors as revealed by phylogeographic inference

PubMed Central

Palmarini, Massimo; Mertens, Peter

2017-01-01

Spatio-temporal patterns of the spread of infectious diseases are commonly driven by environmental and ecological factors. This is particularly true for vector-borne diseases because vector populations can be strongly affected by host distribution as well as by climatic and landscape variables. Here, we aim to identify environmental drivers for bluetongue virus (BTV), the causative agent of a major vector-borne disease of ruminants that has emerged multiple times in Europe in recent decades. In order to determine the importance of climatic, landscape and host-related factors affecting BTV diffusion across Europe, we fitted different phylogeographic models to a dataset of 113 time-stamped and geo-referenced BTV genomes, representing multiple strains and serotypes. Diffusion models using continuous space revealed that terrestrial habitat below 300 m altitude, wind direction and higher livestock densities were associated with faster BTV movement. Results of discrete phylogeographic analysis involving generalized linear models broadly supported these findings, but varied considerably with the level of spatial partitioning. Contrary to common perception, we found no evidence for average temperature having a positive effect on BTV diffusion, though both methodological and biological reasons could be responsible for this result. Our study provides important insights into the drivers of BTV transmission at the landscape scale that could inform predictive models of viral spread and have implications for designing control strategies. PMID:29021180

Factors limiting mallard brood survival in prairie pothole landscapes

USGS Publications Warehouse

Krapu, Gary L.; Pietz, Pamela J.; Brandt, David A.; Cox, Robert R.

2000-01-01

In order to estimate mallard (Anas platyrhynchos) production from managed and unmanaged lands, waterfowl biologists need measurable predictors of brood survival. We evaluated effects of percent of seasonal basins holding water (WETSEAS), percent of upland landscape in perennial cover (PERNCOVER), rainfall (RAIN), daily minimum ambient temperature (TMIN), hatch date (HATCHDATE), brood age (BA; 0-7 or 8-30 days), age of brood females, and brood size on mallard brood survival in prairie pothole landscapes, and developed a predictive model using factors found to have significant effects. Sixteen of 56 radiomarked broods experienced total loss during 1,250 exposure days. Our final fitted model of brood survival contained only main effects of WETSEAS, HATCHDATE, and RAIN. Total brood loss during the first 30 days of exposure was 11.2 times more likely for broods hatched on areas with 59% WETSEAS. Total brood loss was 5.2 times more likely during rainy conditions than during dry periods, and the hazard of total brood loss increased by 5% for each 1-day delay in hatching between 17 May and 12 August. High survival of mallard broods in landscapes where most seasonal basins contain water underscores the importance of maintaining seasonal wetlands as a major component of wetland complexes managed for mallard production. Because early hatched broods have higher survival, we also suggest that waterfowl managers focus their efforts on enhancing nest success of early laid clutches, especially in wet years.

The interaction between the spatial distribution of resource patches and population density: consequences for intraspecific growth and morphology.

PubMed

Jacobson, Bailey; Grant, James W A; Peres-Neto, Pedro R

2015-07-01

How individuals within a population distribute themselves across resource patches of varying quality has been an important focus of ecological theory. The ideal free distribution predicts equal fitness amongst individuals in a 1 : 1 ratio with resources, whereas resource defence theory predicts different degrees of monopolization (fitness variance) as a function of temporal and spatial resource clumping and population density. One overlooked landscape characteristic is the spatial distribution of resource patches, altering the equitability of resource accessibility and thereby the effective number of competitors. While much work has investigated the influence of morphology on competitive ability for different resource types, less is known regarding the phenotypic characteristics conferring relative ability for a single resource type, particularly when exploitative competition predominates. Here we used young-of-the-year rainbow trout (Oncorhynchus mykiss) to test whether and how the spatial distribution of resource patches and population density interact to influence the level and variance of individual growth, as well as if functional morphology relates to competitive ability. Feeding trials were conducted within stream channels under three spatial distributions of nine resource patches (distributed, semi-clumped and clumped) at two density levels (9 and 27 individuals). Average trial growth was greater in high-density treatments with no effect of resource distribution. Within-trial growth variance had opposite patterns across resource distributions. Here, variance decreased at low-population, but increased at high-population densities as patches became increasingly clumped as the result of changes in the levels of interference vs. exploitative competition. Within-trial growth was related to both pre- and post-trial morphology where competitive individuals were those with traits associated with swimming capacity and efficiency: larger heads/bodies/caudal fins and less angled pectoral fins. The different degrees of within-population growth variance at the same density level found here, as a function of spatial resource distribution, provide an explanation for the inconsistencies in within-site growth variance and population regulation often noted with regard to density dependence in natural landscapes. © 2015 The Authors. Journal of Animal Ecology © 2015 British Ecological Society.

Processes on the emergent landscapes of biochemical reaction networks and heterogeneous cell population dynamics: differentiation in living matters

PubMed Central

Li, Fangting

2017-01-01

The notion of an attractor has been widely employed in thinking about the nonlinear dynamics of organisms and biological phenomena as systems and as processes. The notion of a landscape with valleys and mountains encoding multiple attractors, however, has a rigorous foundation only for closed, thermodynamically non-driven, chemical systems, such as a protein. Recent advances in the theory of nonlinear stochastic dynamical systems and its applications to mesoscopic reaction networks, one reaction at a time, have provided a new basis for a landscape of open, driven biochemical reaction systems under sustained chemostat. The theory is equally applicable not only to intracellular dynamics of biochemical regulatory networks within an individual cell but also to tissue dynamics of heterogeneous interacting cell populations. The landscape for an individual cell, applicable to a population of isogenic non-interacting cells under the same environmental conditions, is defined on the counting space of intracellular chemical compositions x = (x1,x2, … ,xN) in a cell, where xℓ is the concentration of the ℓth biochemical species. Equivalently, for heterogeneous cell population dynamics xℓ is the number density of cells of the ℓth cell type. One of the insights derived from the landscape perspective is that the life history of an individual organism, which occurs on the hillsides of a landscape, is nearly deterministic and ‘programmed’, while population-wise an asynchronous non-equilibrium steady state resides mostly in the lowlands of the landscape. We argue that a dynamic ‘blue-sky’ bifurcation, as a representation of Waddington's landscape, is a more robust mechanism for a cell fate decision and subsequent differentiation than the widely pictured pitch-fork bifurcation. We revisit, in terms of the chemostatic driving forces upon active, living matter, the notions of near-equilibrium thermodynamic branches versus far-from-equilibrium states. The emergent landscape perspective permits a quantitative discussion of a wide range of biological phenomena as nonlinear, stochastic dynamics. PMID:28490602

Patterns in Calabi-Yau Distributions

NASA Astrophysics Data System (ADS)

He, Yang-Hui; Jejjala, Vishnu; Pontiggia, Luca

2017-09-01

We explore the distribution of topological numbers in Calabi-Yau manifolds, using the Kreuzer-Skarke dataset of hypersurfaces in toric varieties as a testing ground. While the Hodge numbers are well-known to exhibit mirror symmetry, patterns in frequencies of combination thereof exhibit striking new patterns. We find pseudo-Voigt and Planckian distributions with high confidence and exact fit for many substructures. The patterns indicate typicality within the landscape of Calabi-Yau manifolds of various dimension.

Development of Adaptive Management Tools to Guide Habitat Allocations for At-Risk Species

DTIC Science & Technology

2014-01-01

Results indicated that the mating system assumptions can have a large impact on the ability of the model to approximate data collected in the field...indicated that strength of habitat preferences during dispersal for juvenile and subadult male dispersal also significantly impacted model fit. Certainly...the influence of habitat loss, as these structural (or geometric) changes are often confounded in real landscapes, the impact of fragmentation is

Little Blue Prehistory: Archaeological Investigations at Blue Springs and Longview Lakes, Jackson County, Missouri. Volume 1

DTIC Science & Technology

1989-01-01

processing is indicated by sandstone pestles and grinding stones. 17 It is uncertain exactly how these three rockshelter sites fit into a Dalton... Atlantic time (ca. 5000 B.P.) on, climatic change was minor. Major vegetation zones present on the pre-settlement landscape would thus represent basic...areas included sumac and poison ivy, persimmon (Diospyros virginiana), red cedar (Juniperus virgin - iana), knotweed (Polygonum aviculare), lambs

Quantifying the topography of the intrinsic energy landscape of flexible biomolecular recognition

PubMed Central

Chu, Xiakun; Gan, Linfeng; Wang, Erkang; Wang, Jin

2013-01-01

Biomolecular functions are determined by their interactions with other molecules. Biomolecular recognition is often flexible and associated with large conformational changes involving both binding and folding. However, the global and physical understanding for the process is still challenging. Here, we quantified the intrinsic energy landscapes of flexible biomolecular recognition in terms of binding–folding dynamics for 15 homodimers by exploring the underlying density of states, using a structure-based model both with and without considering energetic roughness. By quantifying three individual effective intrinsic energy landscapes (one for interfacial binding, two for monomeric folding), the association mechanisms for flexible recognition of 15 homodimers can be classified into two-state cooperative “coupled binding–folding” and three-state noncooperative “folding prior to binding” scenarios. We found that the association mechanism of flexible biomolecular recognition relies on the interplay between the underlying effective intrinsic binding and folding energy landscapes. By quantifying the whole global intrinsic binding–folding energy landscapes, we found strong correlations between the landscape topography measure Λ (dimensionless ratio of energy gap versus roughness modulated by the configurational entropy) and the ratio of the thermodynamic stable temperature versus trapping temperature, as well as between Λ and binding kinetics. Therefore, the global energy landscape topography determines the binding–folding thermodynamics and kinetics, crucial for the feasibility and efficiency of realizing biomolecular function. We also found “U-shape” temperature-dependent kinetic behavior and a dynamical cross-over temperature for dividing exponential and nonexponential kinetics for two-state homodimers. Our study provides a unique way to bridge the gap between theory and experiments. PMID:23754431

Effects of scale and logging on landscape structure in a forest mosaic.

PubMed

Leimgruber, P; McShea, W J; Schnell, G D

2002-03-01

Landscape structure in a forest mosaic changes with spatial scale (i.e. spatial extent) and thresholds may occur where structure changes markedly. Forest management alters landscape structure and may affect the intensity and location of thresholds. Our purpose was to examine landscape structure at different scales to determine thresholds where landscape structure changes markedly in managed forest mosaics of the Appalachian Mountains in the eastern United States. We also investigated how logging influences landscape structure and whether these management activities change threshold values. Using threshold and autocorrelation analyses, we found that thresholds in landscape indices exist at 400, 500, and 800 m intervals from the outer edge of management units in our study region. For landscape indices that consider all landcover categories, such as dominance and contagion, landscape structure and thresholds did not change after logging occurred. Measurements for these overall landscape indices were strongly influenced by midsuccessional deciduous forest, the most common landcover category in the landscape. When restricting analyses for mean patch size and percent cover to individual forest types, thresholds for early-successional forests changed after logging. However, logging changed the landscape structure at small spatial scale, but did not alter the structure of the entire forest mosaic. Previous forest management may already have increased the heterogeneity of the landscape beyond the point where additional small cuts alter the overall structure of the forest. Because measurements for landscape indices yield very different results at different spatial scales, it is important first to identify thresholds in order to determine the appropriate scales for landscape ecological studies. We found that threshold and autocorrelation analyses were simple but powerful tools for the detection of appropriate scales in the managed forest mosaic under study.

The genetic architecture of novel trophic specialists: larger effect sizes are associated with exceptional oral jaw diversification in a pupfish adaptive radiation.

PubMed

Martin, Christopher H; Erickson, Priscilla A; Miller, Craig T

2017-01-01

The genetic architecture of adaptation is fundamental to understanding the mechanisms and constraints governing diversification. However, most case studies focus on loss of complex traits or parallel speciation in similar environments. It is still unclear how the genetic architecture of these local adaptive processes compares to the architecture of evolutionary transitions contributing to morphological and ecological novelty. Here, we identify quantitative trait loci (QTL) between two trophic specialists in an excellent case study for examining the origins of ecological novelty: a sympatric radiation of pupfishes endemic to San Salvador Island, Bahamas, containing a large-jawed scale-eater and a short-jawed molluscivore with a skeletal nasal protrusion. These specialized niches and trophic traits are unique among over 2000 related species. Measurements of the fitness landscape on San Salvador demonstrate multiple fitness peaks and a larger fitness valley isolating the scale-eater from the putative ancestral intermediate phenotype of the generalist, suggesting that more large-effect QTL should contribute to its unique phenotype. We evaluated this prediction using an F2 intercross between these specialists. We present the first linkage map for pupfishes and detect significant QTL for sex and eight skeletal traits. Large-effect QTL contributed more to enlarged scale-eater jaws than the molluscivore nasal protrusion, consistent with predictions from the adaptive landscape. The microevolutionary genetic architecture of large-effect QTL for oral jaws parallels the exceptional diversification rates of oral jaws within the San Salvador radiation observed over macroevolutionary timescales and may have facilitated exceptional trophic novelty in this system. © 2016 John Wiley & Sons Ltd.

Combining landscape variables and species traits can improve the utility of climate change vulnerability assessments

USGS Publications Warehouse

Nadeau, Christopher P.; Fuller, Angela K.

2016-01-01

Conservation organizations worldwide are investing in climate change vulnerability assessments. Most vulnerability assessment methods focus on either landscape features or species traits that can affect a species vulnerability to climate change. However, landscape features and species traits likely interact to affect vulnerability. We compare a landscape-based assessment, a trait-based assessment, and an assessment that combines landscape variables and species traits for 113 species of birds, herpetofauna, and mammals in the northeastern United States. Our aim is to better understand which species traits and landscape variables have the largest influence on assessment results and which types of vulnerability assessments are most useful for different objectives. Species traits were most important for determining which species will be most vulnerable to climate change. The sensitivity of species to dispersal barriers and the species average natal dispersal distance were the most important traits. Landscape features were most important for determining where species will be most vulnerable because species were most vulnerable in areas where multiple landscape features combined to increase vulnerability, regardless of species traits. The interaction between landscape variables and species traits was important when determining how to reduce climate change vulnerability. For example, an assessment that combines information on landscape connectivity, climate change velocity, and natal dispersal distance suggests that increasing landscape connectivity may not reduce the vulnerability of many species. Assessments that include landscape features and species traits will likely be most useful in guiding conservation under climate change.

[Landscape pattern change of ethnic townships under the background of urbanization: Case of Aerla Town in Molidawa Daur Autonomous Banner, Inner Mongolia, China.

PubMed

Yang, Jin Yao; Huang, Lu; Yan, Li Jiao; Huo, Si Gao

2016-08-01

With the stable development of new countryside construction and new-type urbanization, the changing of the landscape pattern in countryside attracts more attention, especially in the ethnic townships which are hardly accessible. To explore the development of these areas, it is crucial to understand the spatial and temporal variation of the landscape pattern. In this paper, the landscape pattern change was analyzed at both patch type level and landscape level based on the landscape ecology theory. The land use data (format: vector) got from Aerla Town (a typical Daur ethnic township in Inner Mongolia) for the duration from 2008 to 2013 was studied by ArcGIS platform and Fragstats. For the type level, the grassland, farmland, and forest turned into building land gra-dually. Regarding the landscape level, the landscape diversity index and landscape connectivity index were relatively low, the heterogeneity index and the landscape fragmentation were relatively high. With considering the correlation analysis and grey correlation of the above indexes as well as the social and economic development in Aerla Town, the results indicated that population change and GDP growth were the main driving forces of landscape pattern change. Finally, the driving forces which resulted in the variation of landscape pattern with the incorporation of the economic, cultural, policy, and natural effects were discussed. The research could provide basic information and theoretical foundation for the development of minority areas in Northeast China.

Solid-State Solvation and Enhanced Exciton Diffusion in Doped Organic Thin Films under Mechanical Pressure.

PubMed

Chang, Wendi; Akselrod, Gleb M; Bulović, Vladimir

2015-04-28

Direct modification of exciton energy has been previously used to optimize the operation of organic optoelectronic devices. One demonstrated method for exciton energy modification is through the use of the solvent dielectric effects in doped molecular films. To gain a deeper appreciation of the underlying physical mechanisms, in this work we test the solid-state solvation effect in molecular thin films under applied external pressure. We observe that external mechanical pressure increases dipole-dipole interactions, leading to shifts in the Frenkel exciton energy and enhancement of the time-resolved spectral red shift associated with the energy-transfer-mediated exciton diffusion. Measurements are performed on host:dopant molecular thin films, which show bathochromic shifts in photoluminescence (PL) under increasing pressure. This is in agreement with a simple solvation theory model of exciton energetics with a fitting parameter based on the mechanical properties of the host matrix material. We measure no significant change in exciton lifetime with increasing pressure, consistent with unchanged aggregation in molecular films under compression. However, we do observe an increase in exciton spectral thermalization rate for compressed molecular films, indicating enhanced exciton diffusion for increased dipole-dipole interactions under pressure. The results highlight the contrast between molecular energy landscapes obtained when dipole-dipole interactions are increased by the pressure technique versus the conventional dopant concentration variation methods, which can lead to extraneous effects such as aggregation at higher doping concentrations. The present work demonstrates the use of pressure-probing techniques in studying energy disorder and exciton dynamics in amorphous molecular thin films.

Solid-State Solvation and Enhanced Exciton Diffusion in Doped Organic Thin Films under Mechanical Pressure

DOE Office of Scientific and Technical Information (OSTI.GOV)

Chang, Wendi; Akselrod, Gleb M.; Bulović, Vladimir

2015-04-28

Direct modification of exciton energy has been previously used to optimize the operation of organic optoelectronic devices. One demonstrated method for exciton energy modification is through the use of the solvent dielectric effects in doped molecular films. To gain a deeper appreciation of the underlying physical mechanisms, in this work we test the solid-state solvation effect in molecular thin films under applied external pressure. We observe that external mechanical pressure increases dipole–dipole interactions, leading to shifts in the Frenkel exciton energy and enhancement of the time-resolved spectral red shift associated with the energy-transfer-mediated exciton diffusion. Measurements are performed on host:dopantmore » molecular thin films, which show bathochromic shifts in photoluminescence (PL) under increasing pressure. This is in agreement with a simple solvation theory model of exciton energetics with a fitting parameter based on the mechanical properties of the host matrix material. We measure no significant change in exciton lifetime with increasing pressure, consistent with unchanged aggregation in molecular films under compression. However, we do observe an increase in exciton spectral thermalization rate for compressed molecular films, indicating enhanced exciton diffusion for increased dipole–dipole interactions under pressure. The results highlight the contrast between molecular energy landscapes obtained when dipole–dipole interactions are increased by the pressure technique versus the conventional dopant concentration variation methods, which can lead to extraneous effects such as aggregation at higher doping concentrations. The present work demonstrates the use of pressure-probing techniques in studying energy disorder and exciton dynamics in amorphous molecular thin films.« less

Setting technical standards for visual assessment procedures

Treesearch

Kenneth H. Craik; Nickolaus R. Feimer

1979-01-01

Under the impetus of recent legislative and administrative mandates concerning analysis and management of the landscape, governmental agencies are being called upon to adopt or develop visual resource and impact assessment (VRIA) systems. A variety of techniques that combine methods of psychological assessment and landscape analysis to serve these purposes is being...

Importance of ecotone type to landscape dynamics at biome transition zones

USDA-ARS?s Scientific Manuscript database

Landscapes in biome transition zones consist of a mosaic of patches dominated or codominated by species from adjacent biomes. Shifts in the vegetation composition and dynamics of a biome transition zone depend upon the underlying patch dynamics of the ecotones between these dominant species. Landsc...

Comparing Nitrous Oxide Emissions from Three Residential Landscapes under Different Management Schemes Following Natural Rainfall Events

EPA Science Inventory

Cultural lawn management practices that produce aesthetically appealing landscapes may also create environmental conditions that stimulate soil nitrous oxide (N2O) emissions. The purpose of this study is to investigate the effects of lawn management practices on N2O fluxes from ...

Carbon benefits from fuel treatments

Treesearch

Jim Cathcart; Alan A. Ager; Andrew McMahan; Mark Finney; Brian Watt

2010-01-01

Landscape simulation modeling is used to examine whether fuel treatments result in a carbon offset from avoided wildfire emissions. The study landscape was a 169,200-acre watershed located in south-central Oregon. Burn probability modeling was employed under extreme weather and fuel moisture conditions. Expected carbon stocks post-treatment, post-wildfire were...

Applying a framework for landscape planning under climate change for the conservation of biodiversity in the Finnish boreal forest.

PubMed

Mazziotta, Adriano; Triviño, Maria; Tikkanen, Olli-Pekka; Kouki, Jari; Strandman, Harri; Mönkkönen, Mikko

2015-02-01

Conservation strategies are often established without consideration of the impact of climate change. However, this impact is expected to threaten species and ecosystem persistence and to have dramatic effects towards the end of the 21st century. Landscape suitability for species under climate change is determined by several interacting factors including dispersal and human land use. Designing effective conservation strategies at regional scales to improve landscape suitability requires measuring the vulnerabilities of specific regions to climate change and determining their conservation capacities. Although methods for defining vulnerability categories are available, methods for doing this in a systematic, cost-effective way have not been identified. Here, we use an ecosystem model to define the potential resilience of the Finnish forest landscape by relating its current conservation capacity to its vulnerability to climate change. In applying this framework, we take into account the responses to climate change of a broad range of red-listed species with different niche requirements. This framework allowed us to identify four categories in which representation in the landscape varies among three IPCC emission scenarios (B1, low; A1B, intermediate; A2, high emissions): (i) susceptible (B1 = 24.7%, A1B = 26.4%, A2 = 26.2%), the most intact forest landscapes vulnerable to climate change, requiring management for heterogeneity and resilience; (ii) resilient (B1 = 2.2%, A1B = 0.5%, A2 = 0.6%), intact areas with low vulnerability that represent potential climate refugia and require conservation capacity maintenance; (iii) resistant (B1 = 6.7%, A1B = 0.8%, A2 = 1.1%), landscapes with low current conservation capacity and low vulnerability that are suitable for restoration projects; (iv) sensitive (B1 = 66.4%, A1B = 72.3%, A2 = 72.0%), low conservation capacity landscapes that are vulnerable and for which alternative conservation measures are required depending on the intensity of climate change. Our results indicate that the Finnish landscape is likely to be dominated by a very high proportion of sensitive and susceptible forest patches, thereby increasing uncertainty for landscape managers in the choice of conservation strategies. © 2014 John Wiley & Sons Ltd.

Frugivorous birds influence the spatial organization of tropical forests through the generation of seedling recruitment foci under zoochoric trees

NASA Astrophysics Data System (ADS)

Trolliet, Franck; Forget, Pierre-Michel; Doucet, Jean-Louis; Gillet, Jean-François; Hambuckers, Alain

2017-11-01

Animal-mediated seed dispersal is recognized to influence the spatial organization of plant communities but little is known about how frugivores cause such patterns. Here, we explored the role of hornbills and primates in generating recruitment foci under two zoochoric trees, namely Staudtia kamerunensis (Myristicaceae) and Dialium spp. (Fabaceae - Caesalpiniodea) in a forest-savanna mosaic landscape in D.R. Congo. We also examined the influence of the availability of fruits in the neighborhood and the amount of forest cover in the landscape on such clumping patterns. The density and species richness of hornbill-dispersed and the density of primate-dispersed seedlings were significantly higher under Staudtia kamerunensis trees than at control locations. However, we did not find such patterns under Dialium spp. trees compared to control locations except for the density of hornbill-dispersed seedlings which was lower at control locations. Also, we found that an increasing amount of forest cover in the landscape was associated with an increase in the density of hornbill-dispersed seedlings, although the tendency was weak (R2 = 0.065). We concluded that S. kamerunensis acts as a recruitment foci and plays a structuring role in Afrotropical forests. Hornbills were probably the main frugivore taxon responsible for the clumping under that tree and appear as a key ecological component in fragmented and disturbed landscapes where the diversity of large frugivores such as primates is reduced. Our findings improve our understanding of the causal mechanisms responsible for the spatial organization of tropical forests.

Unraveling Landscape Complexity: Land Use/Land Cover Changes and Landscape Pattern Dynamics (1954-2008) in Contrasting Peri-Urban and Agro-Forest Regions of Northern Italy.

PubMed

Smiraglia, D; Ceccarelli, T; Bajocco, S; Perini, L; Salvati, L

2015-10-01

This study implements an exploratory data analysis of landscape metrics and a change detection analysis of land use and population density to assess landscape dynamics (1954-2008) in two physiographic zones (plain and hilly-mountain area) of Emilia Romagna, northern Italy. The two areas are characterized by different landscape types: a mixed urban-rural landscape dominated by arable land and peri-urban settlements in the plain and a traditional agro-forest landscape in the hilly-mountain area with deciduous and conifer forests, scrublands, meadows, and crop mosaic. Urbanization and, to a lesser extent, agricultural intensification were identified as the processes underlying landscape change in the plain. Land abandonment determining natural forestation and re-forestation driven by man was identified as the process of change most representative of the hilly-mountain area. Trends in landscape metrics indicate a shift toward more fragmented and convoluted patterns in both areas. Number of patches, the interspersion and juxtaposition index, and the large patch index are the metrics discriminating the two areas in terms of landscape patterns in 1954. In 2008, mean patch size, edge density, interspersion and juxtaposition index, and mean Euclidean nearest neighbor distance were the metrics with the most different spatial patterns in the two areas. The exploratory data analysis of landscape metrics contributed to link changes over time in both landscape composition and configuration providing a comprehensive picture of landscape transformations in a wealthy European region. Evidence from this study are hoped to inform sustainable land management designed for homogeneous landscape units in similar socioeconomic contexts.

Domestication and fitness in the wild: A multivariate view.

PubMed

Tufto, Jarle

2017-09-01

Domesticated species continually escaping and interbreeding with wild relatives impose a migration load on wild populations. As domesticated stocks become increasingly different as a result of artificial and natural selection in captivity, fitness of escapees in the wild is expected to decline, reducing the effective rate of migration into wild populations. Recent theory suggest that this may alleviate and eventually eliminate the resulting migration load. I develop a multivariate model of trait and wild fitness evolution resulting from the joint effects of artificial and natural selection in the captive environment. Initially, the evolutionary trajectory is dominated by the effects of artificial selection causing a fast initial decline in fitness of escapees in the wild. In later phases, through the counteracting effects of correlational multivariate natural selection in captivity, the mean phenotype is pushed in directions of weak stabilizing selection, allowing a sustained response in the trait subject to artificial selection. Provided that there is some alignment between the adaptive landscapes in the wild and in captivity, these phases are associated with slower rates of decline in wild fitness of the domesticated stock, suggesting that detrimental effects on wild populations are likely to remain a concern in the foreseeable future. © 2017 The Author(s). Evolution © 2017 The Society for the Study of Evolution.

Research and Application of Remote Sensing Monitoring Method for Desertification Land Under Time and Space Constraints

NASA Astrophysics Data System (ADS)

Zhang, Nannnan; Wang, Rongbao; Zhang, Feng

2018-04-01

Serious land desertification and sandified threaten the urban ecological security and the sustainable economic and social development. In recent years, a large number of mobile sand dunes in Horqin sandy land flow into the northwest of Liaoning Province under the monsoon, make local agriculture suffer serious harm. According to the characteristics of desertification land in northwestern Liaoning, based on the First National Geographical Survey data, the Second National Land Survey data and the 1984-2014 Landsat satellite long time sequence data and other multi-source data, we constructed a remote sensing monitoring index system of desertification land in Northwest Liaoning. Through the analysis of space-time-spectral characteristics of desertification land, a method for multi-spectral remote sensing image recognition of desertification land under time-space constraints is proposed. This method was used to identify and extract the distribution and classification of desertification land of Chaoyang City (a typical citie of desertification in northwestern Liaoning) in 2008 and 2014, and monitored the changes and transfers of desertification land from 2008 to 2014. Sandification information was added to the analysis of traditional landscape changes, improved the analysis model of desertification land landscape index, and the characteristics and laws of landscape dynamics and landscape pattern change of desertification land from 2008 to 2014 were analyzed and revealed.

Dynamics of Tumor Heterogeneity Derived from Clonal Karyotypic Evolution.

PubMed

Laughney, Ashley M; Elizalde, Sergi; Genovese, Giulio; Bakhoum, Samuel F

2015-08-04

Numerical chromosomal instability is a ubiquitous feature of human neoplasms. Due to experimental limitations, fundamental characteristics of karyotypic changes in cancer are poorly understood. Using an experimentally inspired stochastic model, based on the potency and chromosomal distribution of oncogenes and tumor suppressor genes, we show that cancer cells have evolved to exist within a narrow range of chromosome missegregation rates that optimizes phenotypic heterogeneity and clonal survival. Departure from this range reduces clonal fitness and limits subclonal diversity. Mapping of the aneuploid fitness landscape reveals a highly favorable, commonly observed, near-triploid state onto which evolving diploid- and tetraploid-derived populations spontaneously converge, albeit at a much lower fitness cost for the latter. Finally, by analyzing 1,368 chromosomal translocation events in five human cancers, we find that karyotypic evolution also shapes chromosomal translocation patterns by selecting for more oncogenic derivative chromosomes. Thus, chromosomal instability can generate the heterogeneity required for Darwinian tumor evolution. Copyright © 2015 The Authors. Published by Elsevier Inc. All rights reserved.

Sustainability of terraced paddy fields in traditional satoyama landscapes of Japan.

PubMed

Fukamachi, Katsue

2017-11-01

Terraced paddy fields are essential components of the traditional cultural landscape of Japan, the satoyama landscape. They have been sustainably cultivated in a variety of ecological and social environments through time, and are highly valued as local resources with multiple functions. This paper reviews the recent nationwide movement for conservation of satoyama landscapes and shows that over the last decades, the government has increasingly created policies based on national regulation or international frameworks that concern the culture and environment in rural areas. Recent measures for the sustainability of terraced paddy fields do not only focus on rice terraces, but are directed at each satoyama landscape as a whole under careful consideration of how landscape elements are connected while taking into account the unique features of each area. Nevertheless, it has become difficult to ensure the continued use and maintenance of terraced rice paddies both in depopulated and suburban satoyama landscapes. The motivation for conserving satoyama landscapes, including those with terraced rice paddies, can be found in the awareness and appreciation of the unique characteristics of each locality that offer opportunities that can only be experienced in that particular area. A satoyama landscape that offers such opportunities allows continuity of traditional practices while integrating necessary changes. Copyright © 2016 Elsevier Ltd. All rights reserved.

The concept of landscape education at school level with respect to the directions of the science of landscape

NASA Astrophysics Data System (ADS)

Szczęsna, Joanna

2010-01-01

School education is both a starting point for the development of various scientific disciplines (school educates future researchers) and the result of science. The landscape research is conducted within many scientific disciplines and has a long tradition. Lanscape education, which is the result of a scientific dimension, is implemented in primary school under the nature subject. Primary school education is the only level at which the geographical contents are carried out on landscape. The landscape is of interest to many disciplines: geography, architecture, social sciences and the arts. In recent years, there were many studies which contained an overview of the main strands of the science of landscape, presented the differences in the meaning of the concept and objectives of individual research disciplines. These studies have become the ground for the characterization of the concept of landscape education implemented in Polish school and its evaluation in terms of scientific achievements. A review of educational purposes, the basic content of education and achievements of students, demonstrate the influence of multiple scientific disciplines in school landscape education. The most significant share of the course content are achievements of geography disciplines, particularly: physical geography, environmental protection and landscape ecology. Other scientific fields: literature, art, psychology, sociology, and architecture do not have any impact on the school landscape education or their impact remains marginal.

Engineering of a synthetic quadrastable gene network to approach Waddington landscape and cell fate determination

PubMed Central

Wu, Fuqing; Su, Ri-Qi; Lai, Ying-Cheng; Wang, Xiao

2017-01-01

The process of cell fate determination has been depicted intuitively as cells travelling and resting on a rugged landscape, which has been probed by various theoretical studies. However, few studies have experimentally demonstrated how underlying gene regulatory networks shape the landscape and hence orchestrate cellular decision-making in the presence of both signal and noise. Here we tested different topologies and verified a synthetic gene circuit with mutual inhibition and auto-activations to be quadrastable, which enables direct study of quadruple cell fate determination on an engineered landscape. We show that cells indeed gravitate towards local minima and signal inductions dictate cell fates through modulating the shape of the multistable landscape. Experiments, guided by model predictions, reveal that sequential inductions generate distinct cell fates by changing landscape in sequence and hence navigating cells to different final states. This work provides a synthetic biology framework to approach cell fate determination and suggests a landscape-based explanation of fixed induction sequences for targeted differentiation. DOI: http://dx.doi.org/10.7554/eLife.23702.001 PMID:28397688

[Regional ecological construction and mission of landscape ecology].

PubMed

Xiao, Duning; Xie, Fuju; Wei, Jianbing

2004-10-01

The eco-construction on regional and landscape scale is the one which can be used to specific landscape and intercrossing ecosystem in specific region including performing scientific administration of ecosystem and optimizing environmental function. Recently, the government has taken a series of significant projects into action, such as national forest protection item, partly forest restoration, and adjustment of water, etc. Enforcing regional eco-construction and maintaining the ecology security of the nation have become the strategic requisition. In various regions, different eco-construction should be applied, for example, performing ecological safeguard measure in ecological sensitive zone, accommodating the ecological load in ecological fragile zone, etc., which can control the activities of human being, so that, sustainable development can be reached. Facing opportunity and challenge in the development of landscape ecology, we have some key topics: landscape pattern of ecological security, land use and ecological process, landscape changes under human activity stress, quantitative evaluation of the influence on human being activities, evaluation of zonal ecological security and advance warning of ecological risk, and planning and optimizing of model in landscape eco-construction.

Patterns of spatial distribution of golden eagles across North America: How do they fit into existing landscape-scale mapping systems?

USGS Publications Warehouse

Brown, Jessi L.; Bedrosian, Bryan; Bell, Douglas A.; Braham, Melissa A.; Cooper, Jeff; Crandall, Ross H.; DiDonato, Joe; Domenech, Robert; Duerr, Adam E.; Katzner, Todd; Lanzone, Michael J.; LaPlante, David W.; McIntyre, Carol L.; Miller, Tricia A.; Murphy, Robert K.; Shreading, Adam; Slater, Steven J.; Smith, Jeff P.; Smith, Brian W.; Watson, James W.; Woodbridge, Brian

2017-01-01

Conserving wide-ranging animals requires knowledge about their year-round movements and resource use. Golden Eagles (Aquila chrysaetos) exhibit a wide range of movement patterns across North America. We combined tracking data from 571 Golden Eagles from multiple independent satellite-telemetry projects from North America to provide a comprehensive look at the magnitude and extent of these movements on a continental scale. We compared patterns of use relative to four alternative administrative and ecological mapping systems, namely Bird Conservation Regions (BCRs), U.S. administrative migratory bird flyways, Migratory Bird Joint Ventures, and Landscape Conservation Cooperatives. Our analyses suggested that eagles initially captured in eastern North America used space differently than those captured in western North America. Other groups of eagles that exhibited distinct patterns in space use included long-distance migrants from northern latitudes, and southwestern and Californian desert residents. There were also several groupings of eagles in the Intermountain West. Using this collaborative approach, we have identified large-scale movement patterns that may not have been possible with individual studies. These results will support landscape-scale conservation measures for Golden Eagles across North America.

The depth of the honeybee's backup sun-compass systems.

PubMed

Dovey, Katelyn M; Kemfort, Jordan R; Towne, William F

2013-06-01

Honeybees have at least three compass mechanisms: a magnetic compass; a celestial or sun compass, based on the daily rotation of the sun and sun-linked skylight patterns; and a backup celestial compass based on a memory of the sun's movements over time in relation to the landscape. The interactions of these compass systems have yet to be fully elucidated, but the celestial compass is primary in most contexts, the magnetic compass is a backup in certain contexts, and the bees' memory of the sun's course in relation to the landscape is a backup system for cloudy days. Here we ask whether bees have any further compass systems, for example a memory of the sun's movements over time in relation to the magnetic field. To test this, we challenged bees to locate the sun when their known celestial compass systems were unavailable, that is, under overcast skies in unfamiliar landscapes. We measured the bees' knowledge of the sun's location by observing their waggle dances, by which foragers indicate the directions toward food sources in relation to the sun's compass bearing. We found that bees have no celestial compass systems beyond those already known: under overcast skies in unfamiliar landscapes, bees attempt to use their landscape-based backup system to locate the sun, matching the landscapes or skylines at the test sites with those at their natal sites as best they can, even if the matches are poor and yield weak or inconsistent orientation.

The Potential and Flux Landscape Theory of Ecology

PubMed Central

Zhang, Kun; Wang, Erkang; Wang, Jin

2014-01-01

The species in ecosystems are mutually interacting and self sustainable stable for a certain period. Stability and dynamics are crucial for understanding the structure and the function of ecosystems. We developed a potential and flux landscape theory of ecosystems to address these issues. We show that the driving force of the ecological dynamics can be decomposed to the gradient of the potential landscape and the curl probability flux measuring the degree of the breaking down of the detailed balance (due to in or out flow of the energy to the ecosystems). We found that the underlying intrinsic potential landscape is a global Lyapunov function monotonically going down in time and the topology of the landscape provides a quantitative measure for the global stability of the ecosystems. We also quantified the intrinsic energy, the entropy, the free energy and constructed the non-equilibrium thermodynamics for the ecosystems. We studied several typical and important ecological systems: the predation, competition, mutualism and a realistic lynx-snowshoe hare model. Single attractor, multiple attractors and limit cycle attractors emerge from these studies. We studied the stability and robustness of the ecosystems against the perturbations in parameters and the environmental fluctuations. We also found that the kinetic paths between the multiple attractors do not follow the gradient paths of the underlying landscape and are irreversible because of the non-zero flux. This theory provides a novel way for exploring the global stability, function and the robustness of ecosystems. PMID:24497975

Design-with-Nature for Multifunctional Landscapes: Environmental Benefits and Social Barriers in Community Development

PubMed Central

Yang, Bo; Li, Ming-Han; Li, Shujuan

2013-01-01

Since the early 1970s, Ian McHarg’s design-with-nature concept has been inspiring landscape architects, community and regional planners, and liked-minded professionals to create designs that take advantage of ecosystem services and promote environmental and public health. This study bridges the gap in the literature that has resulted from a lack of empirical examinations on the multiple performance benefits derived through design-with-nature and the under-investigated social aspect emanated from McHarg’s Ecological Determinism design approach. The Woodlands, TX, USA, an ecologically designed community development under McHarg’s approach, is compared with two adjacent communities that follow the conventional design approach. Using national environmental databases and multiple-year residents’ survey information, this study assesses three landscape performance metrics of McHarg’s approach: stormwater runoff, urban heat island effect, and social acceptance. Geographic Information Systems (GIS) was used to assess the development extent and land surface temperature distribution. Results show that McHarg’s approach demonstrates benefits in reducing runoff and urban heat island effect, whereas it confronts challenges with the general acceptance of manicured landscapes and thus results in a low safety perception level when residents interact with naturally designed landscapes. The authors argue that design-with-nature warrants multifunctionality because of its intrinsic interdisciplinary approach. Moreover, education and dissemination of successful examples can achieve a greater level of awareness among the public and further promote multifunctional design for landscape sustainability. PMID:24169408

Design-with-nature for multifunctional landscapes: environmental benefits and social barriers in community development.

PubMed

Yang, Bo; Li, Ming-Han; Li, Shujuan

2013-10-28

Since the early 1970s, Ian McHarg's design-with-nature concept has been inspiring landscape architects, community and regional planners, and liked-minded professionals to create designs that take advantage of ecosystem services and promote environmental and public health. This study bridges the gap in the literature that has resulted from a lack of empirical examinations on the multiple performance benefits derived through design-with-nature and the under-investigated social aspect emanated from McHarg's Ecological Determinism design approach. The Woodlands, TX, USA, an ecologically designed community development under McHarg's approach, is compared with two adjacent communities that follow the conventional design approach. Using national environmental databases and multiple-year residents' survey information, this study assesses three landscape performance metrics of McHarg's approach: stormwater runoff, urban heat island effect, and social acceptance. Geographic Information Systems (GIS) was used to assess the development extent and land surface temperature distribution. Results show that McHarg's approach demonstrates benefits in reducing runoff and urban heat island effect, whereas it confronts challenges with the general acceptance of manicured landscapes and thus results in a low safety perception level when residents interact with naturally designed landscapes. The authors argue that design-with-nature warrants multifunctionality because of its intrinsic interdisciplinary approach. Moreover, education and dissemination of successful examples can achieve a greater level of awareness among the public and further promote multifunctional design for landscape sustainability.

Vegetation modulated landscape evolution: Effects of vegetation on landscape processes, drainage density and topography

NASA Astrophysics Data System (ADS)

Bras, R. L.; Istanbulluoglu, E.

2004-12-01

Topography acts as a template for numerous landscape processes that includes hydrologic, ecologic and biologic phenomena. These processes not only interact with each other but also contribute to shaping the landscape as they influence geomorphic processes. We have investigated the effects of vegetation on known geomorphic relations, thresholds for channel initiation and landform evolution, using both analytical and numerical approaches. Vegetation is assumed to form a uniform ground cover. Runoff erosion is modeled based on power function of excess shear stress, in which shear stress efficiency is inversely proportional to vegetation cover. Plant effect on slope stability is represented by additional cohesion provided by plant roots. Vegetation cover is assumed to reduce sediment transport rates due to physical creep processes (rainsplash, dry ravel, and expansion and contraction of sediments) according to a negative exponential relationship. Vegetation grows as a function of both available cover and unoccupied space by plants, and is killed by geomorphic disturbances (runoff erosion and landsliding), and wildfires. Analytical results suggest that, in an equilibrium basin with a fixed vegetation cover, plants may cause a transition in the dominant erosion process at the channel head. A runoff erosion dominated landscape, under none or loose vegetation cover, may become landslide dominated under a denser vegetation cover. The sign of the predicted relationship between drainage density and vegetation cover depends on the relative influence of vegetation on different erosion phenomena. With model parameter values representative of the Oregon Coast Range (OCR), numerical experiments conducted using the CHILD model. Numerical experiments reveal the importance of vegetation disturbances on the landscape structure. Simulated landscapes resemble real-world catchments in the OCR when vegetation disturbances are considered.

Conservation of Pollinators in Traditional Agricultural Landscapes – New Challenges in Transylvania (Romania) Posed by EU Accession and Recommendations for Future Research

PubMed Central

Kovács-Hostyánszki, Anikó; Földesi, Rita; Mózes, Edina; Szirák, Ádám; Fischer, Joern; Hanspach, Jan; Báldi, András

2016-01-01

Farmland biodiversity is strongly declining in most of Western Europe, but still survives in traditional low intensity agricultural landscapes in Central and Eastern Europe. Accession to the EU however intensifies agriculture, which leads to the vanishing of traditional farming. Our aim was to describe the pollinator assemblages of the last remnants of these landscapes, thus set the baseline of sustainable farming for pollination, and to highlight potential measures of conservation. In these traditional farmlands in the Transylvanian Basin, Romania (EU accession in 2007), we studied the major pollinator groups—wild bees, hoverflies and butterflies. Landscape scale effects of semi-natural habitats, land cover diversity, the effects of heterogeneity and woody vegetation cover and on-site flower resources were tested on pollinator communities in traditionally managed arable fields and grasslands. Our results showed: (i) semi-natural habitats at the landscape scale have a positive effect on most pollinators, especially in the case of low heterogeneity of the direct vicinity of the studied sites; (ii) both arable fields and grasslands hold abundant flower resources, thus both land use types are important in sustaining pollinator communities; (iii) thus, pollinator conservation can rely even on arable fields under traditional management regime. This has an indirect message that the tiny flower margins around large intensive fields in west Europe can be insufficient conservation measures to restore pollinator communities at the landscape scale, as this is still far the baseline of necessary flower resources. This hypothesis needs further study, which includes more traditional landscapes providing baseline, and exploration of other factors behind the lower than baseline level biodiversity values of fields under agri-environmental schemes (AES). PMID:27285118

Conservation of Pollinators in Traditional Agricultural Landscapes - New Challenges in Transylvania (Romania) Posed by EU Accession and Recommendations for Future Research.

PubMed

Kovács-Hostyánszki, Anikó; Földesi, Rita; Mózes, Edina; Szirák, Ádám; Fischer, Joern; Hanspach, Jan; Báldi, András

2016-01-01

Farmland biodiversity is strongly declining in most of Western Europe, but still survives in traditional low intensity agricultural landscapes in Central and Eastern Europe. Accession to the EU however intensifies agriculture, which leads to the vanishing of traditional farming. Our aim was to describe the pollinator assemblages of the last remnants of these landscapes, thus set the baseline of sustainable farming for pollination, and to highlight potential measures of conservation. In these traditional farmlands in the Transylvanian Basin, Romania (EU accession in 2007), we studied the major pollinator groups-wild bees, hoverflies and butterflies. Landscape scale effects of semi-natural habitats, land cover diversity, the effects of heterogeneity and woody vegetation cover and on-site flower resources were tested on pollinator communities in traditionally managed arable fields and grasslands. Our results showed: (i) semi-natural habitats at the landscape scale have a positive effect on most pollinators, especially in the case of low heterogeneity of the direct vicinity of the studied sites; (ii) both arable fields and grasslands hold abundant flower resources, thus both land use types are important in sustaining pollinator communities; (iii) thus, pollinator conservation can rely even on arable fields under traditional management regime. This has an indirect message that the tiny flower margins around large intensive fields in west Europe can be insufficient conservation measures to restore pollinator communities at the landscape scale, as this is still far the baseline of necessary flower resources. This hypothesis needs further study, which includes more traditional landscapes providing baseline, and exploration of other factors behind the lower than baseline level biodiversity values of fields under agri-environmental schemes (AES).

Desert Pavement Process and Form: Modes and Scales of Landscape Stability and Instability in Arid Regions

NASA Astrophysics Data System (ADS)

Wells, Stephen G.; McFadden, Leslie D.; McDonald, Eric V.; Eppes, Martha C.; Young, Michael H.; Wood, Yvonne A.

2014-05-01

Desert pavements are recognized in arid landscapes around the world, developing via diminution of constructional/depositional landform relief and creating a 1-2 stone thick armor over a "stone free" layer. Surface exposure dating demonstrates that clasts forming the desert pavements are maintained at the land surface over hundreds of thousands of years, as aeolian fines are deposited on the land surface, transported into the underlying parent material and incorporated into accretionary soil horizons (e.g., the stone free or vesicular [Av] horizon). This surface armor provides long-term stability over extensive regions of the landscape. Over shorter time periods and at the landform-element scale, dynamic surficial processes (i.e., weathering, runoff) continue to modify the pavement form. Clast size reduction in comparison to underlying parent material, along with armoring and packing of clasts in pavements contribute to their persistence, and studies of crack orientations in pavement clasts indicate physical weathering and diminution of particle size are driven by diurnal solar insolation. Over geologic time, cracks form and propagate from tensile stresses related to temporal and spatial gradients in temperature that evolve and rotate in alignment with the sun's rays. Observed multimodal nature of crack orientations appear related to seasonally varying, latitude-dependent temperature fields resulting from solar angle and weather conditions. Surface properties and their underlying soil profiles vary across pavement surfaces, forming a landscape mosaic and controlling surface hydrology, ecosystem function and the ultimate life-cycle of arid landscapes. In areas of well-developed pavements, surface infiltration and soluble salt concentrations indicate that saturated hydraulic conductivity of Av horizons decline on progressively older alluvial fan surfaces. Field observations and measurements from well-developed desert pavement surfaces landforms also yield significantly lower infiltration rates, enhanced rates of overland flow characterized by high water:sediment ratios and reduced production of desert ecosystems. Consequently, regionally extensive pavement and significantly decreased infiltration over geologic time have resulted in widespread overland flow, elaborate drainage networks on alluvial and eolian-mantled bedrock landscapes, and channel incision and regional dissection of the pavement-mantled landforms. However, these once stable landscapes become progressively unstable with time, serving as sediment source areas for younger alluvial deposits (i.e., geologic life-cycle). Thus, regional dissection (instability) of these desert landscapes can be influenced by the intrinsic properties of pavement-mantled landscapes and not necessarily to external forces of climate change and tectonics.

Habitat and forage associations of a naturally colonising insect pollinator, the tree bumblebee Bombus hypnorum.

PubMed

Crowther, Liam P; Hein, Pierre-Louis; Bourke, Andrew F G

2014-01-01

Bumblebees (Bombus species) are major pollinators of commercial crops and wildflowers but factors affecting their abundance, including causes of recent population declines, remain unclear. Investigating the ecology of species with expanding ranges provides a potentially powerful means of elucidating these factors. Such species may also bring novel pollination services to their new ranges. We therefore investigated landscape-scale habitat use and foraging preferences of the Tree Bumblebee, B. hypnorum, a recent natural colonist that has rapidly expanded its range in the UK over the past decade. Counts of B. hypnorum and six other Bombus species were made in March-June 2012 within a mixed landscape in south-eastern Norfolk, UK. The extent of different landscape elements around each transect was quantified at three scales (250 m, 500 m and 1500 m). We then identified the landscape elements that best predicted the density of B. hypnorum and other Bombus species. At the best fitting scale (250 m), B. hypnorum density was significantly positively associated with extent of both urban and woodland cover and significantly negatively associated with extent of oilseed rape cover. This combination of landscape predictors was unique to B. hypnorum. Urban and woodland cover were associated with B. hypnorum density at three and two, respectively, of the three scales studied. Relative to other Bombus species, B. hypnorum exhibited a significantly higher foraging preference for two flowering trees, Crataegus monogyna and Prunus spinosa, and significantly lower preferences for Brassica napus, Glechoma hederacea and Lamium album. Our study provides novel, quantitative support for an association of B. hypnorum with urban and woodland landscape elements. Range expansion in B. hypnorum appears to depend, on exploitation of widespread habitats underutilised by native Bombus species, suggesting B. hypnorum will readily co-exist with these species. These findings suggest that management could target bumblebee species with distinctive habitat requirements to help maintain pollination services.

Evaluation of spatial models to predict vulnerability of forest birds to brood parasitism by cowbirds

USGS Publications Warehouse

Gustafson, E.J.; Knutson, M.G.; Niemi, G.J.; Friberg, M.

2002-01-01

We constructed alternative spatial models at two scales to predict Brown-headed Cowbird (Molothrus ater) parasitism rates from land cover maps. The local-scale models tested competing hypotheses about the relationship between cowbird parasitism and distance of host nests from a forest edge (forest-nonforest boundary). The landscape models tested competing hypotheses about how landscape features (e.g., forests, agricultural fields) interact to determine rates of cowbird parasitism. The models incorporate spatial neighborhoods with a radius of 2.5 km in their formulation, reflecting the scale of the majority of cowbird commuting activity. Field data on parasitism by cowbirds (parasitism rate and number of cowbird eggs per nest) were collected at 28 sites in the Driftless Area Ecoregion of Wisconsin, Minnesota, and Iowa and were compared to the predictions of the alternative models. At the local scale, there was a significant positive relationship between cowbird parasitism and mean distance of nest sites from the forest edge. At the landscape scale, the best fitting models were the forest-dependent and forest-fragmentation-dependent models, in which more heavily forested and less fragmented landscapes had higher parasitism rates. However, much of the explanatory power of these models results from the inclusion of the local-scale relationship in these models. We found lower rates of cowbird parasitism than did most Midwestern studies, and we identified landscape patterns of cowbird parasitism that are opposite to those reported in several other studies of Midwestern songbirds. We caution that cowbird parasitism patterns can be unpredictable, depending upon ecoregional location and the spatial extent, and that our models should be tested in other ecoregions before they are applied there. Our study confirms that cowbird biology has a strong spatial component, and that improved spatial models applied at multiple spatial scales will be required to predict the effects of landscape and forest management on cowbird parasitism of forest birds.

Multiple coupled landscapes and non-adiabatic dynamics with applications to self-activating genes.

PubMed

Chen, Cong; Zhang, Kun; Feng, Haidong; Sasai, Masaki; Wang, Jin

2015-11-21

Many physical, chemical and biochemical systems (e.g. electronic dynamics and gene regulatory networks) are governed by continuous stochastic processes (e.g. electron dynamics on a particular electronic energy surface and protein (gene product) synthesis) coupled with discrete processes (e.g. hopping among different electronic energy surfaces and on and off switching of genes). One can also think of the underlying dynamics as the continuous motion on a particular landscape and discrete hoppings among different landscapes. The main difference of such systems from the intra-landscape dynamics alone is the emergence of the timescale involved in transitions among different landscapes in addition to the timescale involved in a particular landscape. The adiabatic limit when inter-landscape hoppings are fast compared to continuous intra-landscape dynamics has been studied both analytically and numerically, but the analytical treatment of the non-adiabatic regime where the inter-landscape hoppings are slow or comparable to continuous intra-landscape dynamics remains challenging. In this study, we show that there exists mathematical mapping of the dynamics on 2(N) discretely coupled N continuous dimensional landscapes onto one single landscape in 2N dimensional extended continuous space. On this 2N dimensional landscape, eddy current emerges as a sign of non-equilibrium non-adiabatic dynamics and plays an important role in system evolution. Many interesting physical effects such as the enhancement of fluctuations, irreversibility, dissipation and optimal kinetics emerge due to non-adiabaticity manifested by the eddy current illustrated for an N = 1 self-activator. We further generalize our theory to the N-gene network with multiple binding sites and multiple synthesis rates for discretely coupled non-equilibrium stochastic physical and biological systems.

Dispersal ability and habitat requirements determine landscape-level genetic patterns in desert aquatic insects.

PubMed

Phillipsen, Ivan C; Kirk, Emily H; Bogan, Michael T; Mims, Meryl C; Olden, Julian D; Lytle, David A

2015-01-01

Species occupying the same geographic range can exhibit remarkably different population structures across the landscape, ranging from highly diversified to panmictic. Given limitations on collecting population-level data for large numbers of species, ecologists seek to identify proximate organismal traits-such as dispersal ability, habitat preference and life history-that are strong predictors of realized population structure. We examined how dispersal ability and habitat structure affect the regional balance of gene flow and genetic drift within three aquatic insects that represent the range of dispersal abilities and habitat requirements observed in desert stream insect communities. For each species, we tested for linear relationships between genetic distances and geographic distances using Euclidean and landscape-based metrics of resistance. We found that the moderate-disperser Mesocapnia arizonensis (Plecoptera: Capniidae) has a strong isolation-by-distance pattern, suggesting migration-drift equilibrium. By contrast, population structure in the flightless Abedus herberti (Hemiptera: Belostomatidae) is influenced by genetic drift, while gene flow is the dominant force in the strong-flying Boreonectes aequinoctialis (Coleoptera: Dytiscidae). The best-fitting landscape model for M. arizonensis was based on Euclidean distance. Analyses also identified a strong spatial scale-dependence, where landscape genetic methods only performed well for species that were intermediate in dispersal ability. Our results highlight the fact that when either gene flow or genetic drift dominates in shaping population structure, no detectable relationship between genetic and geographic distances is expected at certain spatial scales. This study provides insight into how gene flow and drift interact at the regional scale for these insects as well as the organisms that share similar habitats and dispersal abilities. © 2014 John Wiley & Sons Ltd.

Effect of landscape tree cover, sex and season on the bioaccumulation of persistent organochlorine pesticides in fruit bats of riparian corridors in eastern Mexico.

PubMed

Valdespino, Carolina; Sosa, Vinicio J

2017-05-01

Riparian forests are recognized as important ecosystems for biodiversity conservation in transformed landscapes. Many animal species that use this type of vegetation facilitate its recovery through pollination and seed dispersal. In landscapes dominated by agrosystems and cattle ranching, persistent organochlorine pesticides (OCPs) in the riparian system may have an effect on the physiology and fitness of animals. In this study, we measured bioaccumulation of OCPs in the most abundant frugivorous bat, Sturnira hondurensis, from the upper part of La Antigua basin, Veracruz, Mexico and, from these data, estimated accumulation by the frugivorous bat community of riparian forests in contrasting, transformed (TL) and forested (FL) landscapes. Concentration of ΣDDT, Σdrines, Σclordano, ΣHCH, Σheptachlor and Σendosulfan was measured by gas-chromatography in 23 female and 33 male adult Sturnira captured during the dry and rainy seasons. Using censored data statistics, we found that the sex of the individual was significant for ΣHCH, and that interactions of landscape type (TL vs. FL) and season (dry vs. wet), and sex and season were significant for Σendosulfan and Σdrines, respectively. Mean ΣDDT (6.86 μg/g) and ΣHCH (28.22 μg/g) concentrations were lower than those reported for frugivorous bats in India but concentrations of Σdrines (13.86 μg/g) were higher than those reported in insectivorous bats. In our study sites, frugivorous bats are bioaccumulating higher amounts of OCPs in TL than in FL. We discuss the potential of this species as a bio-indicator of OCPs contamination in river basins. Copyright © 2017. Published by Elsevier Ltd.

Landscape-scale evaluation of asymmetric interactions between Brown Trout and Brook Trout using two-species occupancy models

USGS Publications Warehouse

Wagner, Tyler; Jefferson T. Deweber,; Jason Detar,; John A. Sweka,

2013-01-01

Predicting the distribution of native stream fishes is fundamental to the management and conservation of many species. Modeling species distributions often consists of quantifying relationships between species occurrence and abundance data at known locations with environmental data at those locations. However, it is well documented that native stream fish distributions can be altered as a result of asymmetric interactions between dominant exotic and subordinate native species. For example, the naturalized exotic Brown Trout Salmo trutta has been identified as a threat to native Brook Trout Salvelinus fontinalis in the eastern United States. To evaluate large-scale patterns of co-occurrence and to quantify the potential effects of Brown Trout presence on Brook Trout occupancy, we used data from 624 stream sites to fit two-species occupancy models. These models assumed that asymmetric interactions occurred between the two species. In addition, we examined natural and anthropogenic landscape characteristics we hypothesized would be important predictors of occurrence of both species. Estimated occupancy for Brook Trout, from a co-occurrence model with no landscape covariates, at sites with Brown Trout present was substantially lower than sites where Brown Trout were absent. We also observed opposing patterns for Brook and Brown Trout occurrence in relation to percentage forest, impervious surface, and agriculture within the network catchment. Our results are consistent with other studies and suggest that alterations to the landscape, and specifically the transition from a forested catchment to one that contains impervious surface or agriculture, reduces the occurrence probability of wild Brook Trout. Our results, however, also suggest that the presence of Brown Trout results in lower occurrence probability of Brook Trout over a range of anthropogenic landscape characteristics, compared with streams where Brown Trout were absent.

Testing Lithospheric versus Deep-Mantle Dynamics on Post-100 Ma Evolution of Western U.S. using Landscape Evolution Modeling

NASA Astrophysics Data System (ADS)

Chang, C.; Liu, L.

2017-12-01

Driving mechanisms of the topographic evolution of central-western North America from the Cretaceous Western Interior Seaway (WIS) to its present-day high elevation remain ellusive. Quantifying the effects of lithospheric deformation versus deep-mantle induced topography on the landscape evolution of the region is a key to better constraining the history of North American tectonics and mantle dynamics. One way to tackle this problem is through running landscape evolution simulation coupled with uplift histories characteristic to these tectonic processes. We then use available surface observations, e.g., sedimentation records, land erosion, and drainage evolution, to infer the likely lithospheric and mantle processes that formed the WIS, the subsequent Laramide orogeny, and the present-day high topography of central-western North America. In practice, we use BadLands to simulate the evolution of surface process. To validate a given uplift history, we quantitatively compare model predictions with onshore and offshore stratigraphy data from the literature. Furthermore, critical forcings of landscape evolution, such as climate, lithology and sea level, will also be examined to better attest the effects of different uplift scenarios. Preliminary results demonstrate that only with geographically migratory subsidence, as predicted by an inverse mantle convection model, can we re-produce large scale tilted strata and shifting sediment deposition observed in the WIS basins. Ongoing work will also look into styles of Cenozoic uplift events that ended the WIS and produced the landscape features today. Eventually, we hope to place new constraints on the evolution and properties of lithospheric and deep-mantle dynamics of North American and to locate the best-fit scenario of its coresponding surface evolution since 100 Ma.

Adaptive Landscapes of Resistance Genes Change as Antibiotic Concentrations Change.

PubMed

Mira, Portia M; Meza, Juan C; Nandipati, Anna; Barlow, Miriam

2015-10-01

Most studies on the evolution of antibiotic resistance are focused on selection for resistance at lethal antibiotic concentrations, which has allowed the detection of mutant strains that show strong phenotypic traits. However, solely focusing on lethal concentrations of antibiotics narrowly limits our perspective of antibiotic resistance evolution. New high-resolution competition assays have shown that resistant bacteria are selected at relatively low concentrations of antibiotics. This finding is important because sublethal concentrations of antibiotics are found widely in patients undergoing antibiotic therapies, and in nonmedical conditions such as wastewater treatment plants, and food and water used in agriculture and farming. To understand the impacts of sublethal concentrations on selection, we measured 30 adaptive landscapes for a set of TEM β-lactamases containing all combinations of the four amino acid substitutions that exist in TEM-50 for 15 β-lactam antibiotics at multiple concentrations. We found that there are many evolutionary pathways within this collection of landscapes that lead to nearly every TEM-genotype that we studied. While it is known that the pathways change depending on the type of β-lactam, this study demonstrates that the landscapes including fitness optima also change dramatically as the concentrations of antibiotics change. Based on these results we conclude that the presence of multiple concentrations of β-lactams in an environment result in many different adaptive landscapes through which pathways to nearly every genotype are available. Ultimately this may increase the diversity of genotypes in microbial populations. © 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.

Approximate scaling properties of RNA free energy landscapes

NASA Technical Reports Server (NTRS)

Baskaran, S.; Stadler, P. F.; Schuster, P.

1996-01-01

RNA free energy landscapes are analysed by means of "time-series" that are obtained from random walks restricted to excursion sets. The power spectra, the scaling of the jump size distribution, and the scaling of the curve length measured with different yard stick lengths are used to describe the structure of these "time series". Although they are stationary by construction, we find that their local behavior is consistent with both AR(1) and self-affine processes. Random walks confined to excursion sets (i.e., with the restriction that the fitness value exceeds a certain threshold at each step) exhibit essentially the same statistics as free random walks. We find that an AR(1) time series is in general approximately self-affine on timescales up to approximately the correlation length. We present an empirical relation between the correlation parameter rho of the AR(1) model and the exponents characterizing self-affinity.

The Changing UK Careers Landscape: Tidal Waves, Turbulence and Transformation

ERIC Educational Resources Information Center

Hughes, Deirdre

2013-01-01

This article explores how the UK careers landscape in each of the four home nations is changing in response to neo-liberal policies. In this context, careers services are increasingly under pressure to demonstrate their added value, impact and returns on investment. As fiscal arrangements tighten and governments state their preferences and…

The effect of heterogeneous landscape dynamics on ecotone types at two convergent semi-arid biomes

USDA-ARS?s Scientific Manuscript database

Landscapes in biome transition zones consist of a mosaic of patches dominated or codominated by species from adjacent biomes. Shifts in the vegetation composition and dynamics of a biome transition zone depend upon the underlying patch dynamics of the ecotones between these dominant species. Landsca...

Policy capturing as a method of quantifying the determinants of landscape preference

Treesearch

Dennis B. Propst

1979-01-01

Policy Capturing, a potential methodology for evaluating landscape preference, was described and tested. This methodology results in a mathematical model that theoretically represents the human decision-making process. Under experimental conditions, judges were asked to express their preferences for scenes of the Blue Ridge Parkway. An equation which "captures,...

Disturbance regimes and the historical range and variation in terrestrial ecosystems

Treesearch

Robert Keane

2017-01-01

Disturbances are major drivers of ecological dynamics and it is the cumulative effects of disturbances across space and time that define a disturbance regime and dictate biodiversity by influencing the ranges of vegetation structures, compositions, and processes on landscapes. This range and variation of landscape characteristics under historical disturbance regimes...

Why sampling scheme matters: the effect of sampling scheme on landscape genetic results

Treesearch

Michael K. Schwartz; Kevin S. McKelvey

2008-01-01

There has been a recent trend in genetic studies of wild populations where researchers have changed their sampling schemes from sampling pre-defined populations to sampling individuals uniformly across landscapes. This reflects the fact that many species under study are continuously distributed rather than clumped into obvious "populations". Once individual...

Effects of forest roads on habitat quality for Ovenbirds in a forested landscape

Treesearch

Yvette K. Ortega; David E. Capen

1999-01-01

Numerous studies have reported lower densities of breeding Ovenbirds (Seiurus aurocapillus) adjacent to forest edges. However, none of these studies has considered habitat use and reproductive success to address mechanisms underlying the observed pattern, and most were conducted in fragmented landscapes and ignored juxtapositions of forest with...

Inventory-based landscape-scale simulation of management effectiveness and economic feasibility with BioSum

Treesearch

Jeremy S. Fried; Larry D. Potts; Sara M. Loreno; Glenn A. Christensen; R. Jamie Barbour

2017-01-01

The Forest Inventory and Analysis (FIA)-based BioSum (Bioregional Inventory Originated Simulation Under Management) is a free policy analysis framework and workflow management software solution. It addresses complex management questions concerning forest health and vulnerability for large, multimillion acre, multiowner landscapes using FIA plot data as the initial...

Landscape Based Modeling of Nonpoint Source Nitrogen Loading in the Neuse River Basin, North Carolina

DOE Office of Scientific and Technical Information (OSTI.GOV)

Garten, C.T.

2001-01-11

The objective of this research was to arrive at a quantitative and qualitative assessment of nonpoint sources of potential excess N under different land use/land cover (LULC) categories in the Neuse River Basin on a seasonal time scale. This assessment is being supplied to EPA's Landscape Characterization Branch, National Exposure Research Laboratory, in Research Triangle Park, NC, for inclusion in a hydrologic model to predict seasonal fluxes of N from the terrestrial landscape to surface receiving waters and groundwater in the Neuse River Basin. The analysis was performed in the following five steps: (1) development of a conceptual model tomore » predict potential excess N on land, (2) a literature review to parameterize N fluxes under LULC categories found in the Neuse River Basin, (3) acquisition of high resolution (15-m pixel) LULC data from EPA's Landscape Characterization Branch, National Exposure Research Laboratory, in Research Triangle Park, NC, (4) acquisition of a soil N inventory map for the Neuse River Basin, (5) calculations of potential excess N on a seasonal basis for the entire Neuse River Basin.« less

Multi-scale analysis of a household level agent-based model of landcover change.

PubMed

Evans, Tom P; Kelley, Hugh

2004-08-01

Scale issues have significant implications for the analysis of social and biophysical processes in complex systems. These same scale implications are likewise considerations for the design and application of models of landcover change. Scale issues have wide-ranging effects from the representativeness of data used to validate models to aggregation errors introduced in the model structure. This paper presents an analysis of how scale issues affect an agent-based model (ABM) of landcover change developed for a research area in the Midwest, USA. The research presented here explores how scale factors affect the design and application of agent-based landcover change models. The ABM is composed of a series of heterogeneous agents who make landuse decisions on a portfolio of cells in a raster-based programming environment. The model is calibrated using measures of fit derived from both spatial composition and spatial pattern metrics from multi-temporal landcover data interpreted from historical aerial photography. A model calibration process is used to find a best-fit set of parameter weights assigned to agents' preferences for different landuses (agriculture, pasture, timber production, and non-harvested forest). Previous research using this model has shown how a heterogeneous set of agents with differing preferences for a portfolio of landuses produces the best fit to landcover changes observed in the study area. The scale dependence of the model is explored by varying the resolution of the input data used to calibrate the model (observed landcover), ancillary datasets that affect land suitability (topography), and the resolution of the model landscape on which agents make decisions. To explore the impact of these scale relationships the model is run with input datasets constructed at the following spatial resolutions: 60, 90, 120, 150, 240, 300 and 480 m. The results show that the distribution of landuse-preference weights differs as a function of scale. In addition, with the gradient descent model fitting method used in this analysis the model was not able to converge to an acceptable fit at the 300 and 480 m spatial resolutions. This is a product of the ratio of the input cell resolution to the average parcel size in the landscape. This paper uses these findings to identify scale considerations in the design, development, validation and application of ABMs of landcover change.

Foraging optimally for home ranges

USGS Publications Warehouse

Mitchell, Michael S.; Powell, Roger A.

2012-01-01

Economic models predict behavior of animals based on the presumption that natural selection has shaped behaviors important to an animal's fitness to maximize benefits over costs. Economic analyses have shown that territories of animals are structured by trade-offs between benefits gained from resources and costs of defending them. Intuitively, home ranges should be similarly structured, but trade-offs are difficult to assess because there are no costs of defense, thus economic models of home-range behavior are rare. We present economic models that predict how home ranges can be efficient with respect to spatially distributed resources, discounted for travel costs, under 2 strategies of optimization, resource maximization and area minimization. We show how constraints such as competitors can influence structure of homes ranges through resource depression, ultimately structuring density of animals within a population and their distribution on a landscape. We present simulations based on these models to show how they can be generally predictive of home-range behavior and the mechanisms that structure the spatial distribution of animals. We also show how contiguous home ranges estimated statistically from location data can be misleading for animals that optimize home ranges on landscapes with patchily distributed resources. We conclude with a summary of how we applied our models to nonterritorial black bears (Ursus americanus) living in the mountains of North Carolina, where we found their home ranges were best predicted by an area-minimization strategy constrained by intraspecific competition within a social hierarchy. Economic models can provide strong inference about home-range behavior and the resources that structure home ranges by offering falsifiable, a priori hypotheses that can be tested with field observations.

BEESCOUT: A model of bee scouting behaviour and a software tool for characterizing nectar/pollen landscapes for BEEHAVE.

PubMed

Becher, M A; Grimm, V; Knapp, J; Horn, J; Twiston-Davies, G; Osborne, J L

2016-11-24

Social bees are central place foragers collecting floral resources from the surrounding landscape, but little is known about the probability of a scouting bee finding a particular flower patch. We therefore developed a software tool, BEESCOUT, to theoretically examine how bees might explore a landscape and distribute their scouting activities over time and space. An image file can be imported, which is interpreted by the model as a "forage map" with certain colours representing certain crops or habitat types as specified by the user. BEESCOUT calculates the size and location of these potential food sources in that landscape relative to a bee colony. An individual-based model then determines the detection probabilities of the food patches by bees, based on parameter values gathered from the flight patterns of radar-tracked honeybees and bumblebees. Various "search modes" describe hypothetical search strategies for the long-range exploration of scouting bees. The resulting detection probabilities of forage patches can be used as input for the recently developed honeybee model BEEHAVE, to explore realistic scenarios of colony growth and death in response to different stressors. In example simulations, we find that detection probabilities for food sources close to the colony fit empirical data reasonably well. However, for food sources further away no empirical data are available to validate model output. The simulated detection probabilities depend largely on the bees' search mode, and whether they exchange information about food source locations. Nevertheless, we show that landscape structure and connectivity of food sources can have a strong impact on the results. We believe that BEESCOUT is a valuable tool to better understand how landscape configurations and searching behaviour of bees affect detection probabilities of food sources. It can also guide the collection of relevant data and the design of experiments to close knowledge gaps, and provides a useful extension to the BEEHAVE honeybee model, enabling future users to explore how landscape structure and food availability affect the foraging decisions and patch visitation rates of the bees and, in consequence, to predict colony development and survival.

Regional Assessment of the Relationship Between Landscape Attributes and Water Quality in Five National Parks of the Rocky Mountains

NASA Astrophysics Data System (ADS)

Nanus, L.; Williams, M. W.; Campbell, D. H.

2005-12-01

Atmospheric deposition of pollutants threatens pristine environments around the world. However, scientifically-based decisions regarding management of these environments has been confounded by spatial variability of atmospheric deposition, particularly across regional scales at which resource management is typically considered. A statistically based methodology coupled within GIS is presented that builds on small alpine lake and sub-alpine catchments scale to identify deposition-sensitive lakes across larger watershed and regional scales. The sensitivity of 874 alpine and subalpine lakes to acidification from atmospheric deposition of nitrogen and sulfur was estimated using statistical models relating water quality and landscape attributes in Glacier National Park, Yellowstone National Park, Grand Teton National Park, Rocky Mountain National Park and Great Sand Dunes National Park and Preserve. Water-quality data measured during synoptic lake surveys were used to calibrate statistical models of lake sensitivity. In the case of nitrogen deposition, water quality data were supplemented with dual isotopic measurements of d15N and d18O of nitrate. Landscape attributes for the lake basins were derived from GIS including the following explanatory variables; topography (basin slope, basin aspect, basin elevation), bedrock type, vegetation type, and soil type. Using multivariate logistic regression analysis, probability estimates were developed for acid-neutralizing capacity, nitrate, sulfate and DOC concentrations, and lakes with a high probability of being sensitive to atmospheric deposition were identified. Water-quality data collected at 60 lakes during fall 2004 were used to validate statistical models. Relationships between landscape attributes and water quality vary by constituent, due to spatial variability in landscape attributes and spatial variation in the atmospheric deposition of pollutants within and among the five National Parks. Predictive ability, model fit and sensitivity were first assessed for each of the five National Parks individually, to evaluate the utility of this methodology for prediction of alpine and sub-alpine lake sensitivity across the catchment scale. A similar assessment was then performed, treating the five parks as a group. Validation results showed that 85 percent of lakes sampled were accurately identified by the model as having a greater than 60 percent probability of acid-neutralizing capacity concentrations less than 200 microequivalents per liter. Preliminary findings indicate good predictive ability and reasonable model fit and sensitivity, suggesting that logistic regression modeling coupled within a GIS framework is an appropriate approach for remote identification of deposition-sensitive lakes across the Rocky Mountain region. To assist resource management decisions regarding alpine and sub-alpine lakes across this region, screening procedures were developed based on terrain and landscape attribute information available to all participating parks. Since the screening procedure is based on publicly available data, our methodology and similar screening procedures may be applicable to other National Parks with deposition-sensitive surface waters.

Quantifying selection in evolving populations using time-resolved genetic data

NASA Astrophysics Data System (ADS)

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.

Evolution of Fitness in Experimental Populations of Vesicular Stomatitis Virus

PubMed Central

Elena, S. F.; Gonzalez-Candelas, F.; Novella, I. S.; Duarte, E. A.; Clarke, D. K.; Domingo, E.; Holland, J. J.; Moya, A.

1996-01-01

The evolution of fitness in experimental clonal populations of vesicular stomatitis virus (VSV) has been compared under different genetic (fitness of initial clone) and demographic (population dynamics) regimes. In spite of the high genetic heterogeneity among replicates within experiments, there is a clear effect of population dynamics on the evolution of fitness. Those populations that went through strong periodic bottlenecks showed a decreased fitness in competition experiments with wild type. Conversely, mutant populations that were transferred under the dynamics of continuous population expansions increased their fitness when compared with the same wild type. The magnitude of the observed effect depended on the fitness of the original viral clone. Thus, high fitness clones showed a larger reduction in fitness than low fitness clones under dynamics with included periodic bottleneck. In contrast, the gain in fitness was larger the lower the initial fitness of the viral clone. The quantitative genetic analysis of the trait ``fitness'' in the resulting populations shows that genetic variation for the trait is positively correlated with the magnitude of the change in the same trait. The results are interpreted in terms of the operation of MULLER's ratchet and genetic drift as opposed to the appearance of beneficial mutations. PMID:8849878

Probing the Gaps: A Synthesis of Well-known and Lesser-known Hydrological Feedbacks Influencing Vegetation Patterning and Long-term Geomorphic Change in Low-gradient Fluvial Landscapes

NASA Astrophysics Data System (ADS)

Larsen, L.; Christensen, A.; Harvey, J. W.; Ma, H.; Newman, S.; Saunders, C.; Twilley, R.

2017-12-01

Emergence of vegetation patterning in fluvial landscapes is a classic example of how autogenic processes can drive long term fluvial and geomorphic adjustments in aquatic ecosystems. Studies elucidating the physics of flow through vegetation patches have produced understanding of how patterning in topography and vegetation commonly emerges and what effect it has on long term geomorphic change. However, with regard to mechanisms underlying pattern existence and resilience, several knowledge gaps remain, including the role of landscape-scale flow-vegetation feedbacks, feedbacks that invoke additional biogeochemical or biological agents, and determination of the relative importance of autogenic processes relative to external drivers. Here we provide a synthesis of the processes over a range of scales known to drive vegetation patterning and sedimentation in low gradient fluvial landscapes, emphasizing recent field and modeling studies in the Everglades, FL and Wax Lake Delta, LA that address these gaps. In the Everglades, while flow routing and sediment redistribution at the patch scale is known to be a primary driver of vegetation pattern emergence, landscape-scale routing of flow, as driven by the landscape's connectivity, can set up positive feedbacks that influence the rate of pattern degradation. Recent flow release experiments reveal that an additional feedback, involving phosphorus concentrations, flow, and floating vegetation communities that are abundant under low phosphorus, low flow conditions further stabilizes the alternative landscape states established through local scale sediment redistribution. Biogeochemistry-vegetation-sediment feedbacks may also be important for geomorphic development of newly emerging landscapes such as the Wax Lake Delta. There, fine sediment deposition shapes hydrogeomorphic zones with vegetation patterns that stimulate the growth of biofilm, while biofilm characteristics override the physical characteristics of vegetation canopies in determining fine sediment deposition rates and influence nitrogen and carbon biogeochemistry. Emerging tools and data streams, such as information flow analysis of lidar-derived vegetation biovolume and topography, can help identify the relative roles of autogenic vs. external forcing in these landscapes.

[Impacts of dominated landscape types on hydrogen and oxygen isotope effects of spring water in the Hani Rice Terraces].

PubMed

Jiao, Yuan Mei; Liu, Cheng Jing; Liu, Xin; Liu, Zhi Lin; Ding, Yin Ping

2017-07-18

Analysis of hydrogen and oxygen stable isotopes is an effective method to track the water cycle in watershed. Impact of landscape pattern on the isotope effects of spring water is a new interdisciplinary topic between landscape ecology and isotope hydrology. Taking the Quanfuzhuang River basin located in the core area of UNESCO World Cultural Heritage of Honghe Hani Rice Terrace as the object, collecting the monthly samples of 78 points of spring water and 39 precipitation at altitude of 1500 m (terraces), 1700 m (terraces) and 1900 m (forest) from March 2015 to March 2016, we analyzed the hydrogen and oxygen stable isotopes of water samples under the different landscape types. The results indicated that the dominated landscape types were forests and rice terraces, being 66.6% and 22.1% of the whole landscape area respectively, and they had a spatial vertical pattern of forest located at the mountain top and rice terraces at the down-slope. The correlation analysis showed that the spring water not only came from the precipitation, but also from other water sources which had a more positive δ 18 O and δD values, the spring water in up-slope forests mainly came from precipitation, while that in down-slope rice terraces came from precipitation, ri-ver water, rice terrace water and under ground water. Therefore, the mixing effects of spring water δ 18 O and δD were more significant in rice terraces. The overall altitude effect of the hydrogen and oxygen stable isotopes in spring water was obvious. The linear decreasing rates of δ 18 O and δD values were -0.125‰·(100 m) -1 and -0.688‰·(100 m) -1 , respectively. The deuterium surplus value increased with the altitude because of the impacts of landscape pattern and the local cycle of water isotopes. In summary, the dominant landscape types had a significant impact on the hydrogen and oxygen isotopes of spring water, which could be used as response indicator to reveal the impacts of landscape pattern on hydrological process.

When perception reflects reality: Non-native grass invasion alters small mammal risk landscapes and survival

USGS Publications Warehouse

Ceradnini, Joseph P.; Chalfoun, Anna D.

2017-01-01

Modification of habitat structure due to invasive plants can alter the risk landscape for wildlife by, for example, changing the quality or availability of refuge habitat. Whether perceived risk corresponds with actual fitness outcomes, however, remains an important open question. We simultaneously measured how habitat changes due to a common invasive grass (cheatgrass, Bromus tectorum) affected the perceived risk, habitat selection, and apparent survival of a small mammal, enabling us to assess how well perceived risk influenced important behaviors and reflected actual risk. We measured perceived risk by nocturnal rodents using a giving-up density foraging experiment with paired shrub (safe) and open (risky) foraging trays in cheatgrass and native habitats. We also evaluated microhabitat selection across a cheatgrass gradient as an additional assay of perceived risk and behavioral responses for deer mice (Peromyscus maniculatus) at two spatial scales of habitat availability. Finally, we used mark-recapture analysis to quantify deer mouse apparent survival across a cheatgrass gradient while accounting for detection probability and other habitat features. In the foraging experiment, shrubs were more important as protective cover in cheatgrass-dominated habitats, suggesting that cheatgrass increased perceived predation risk. Additionally, deer mice avoided cheatgrass and selected shrubs, and marginally avoided native grass, at two spatial scales. Deer mouse apparent survival varied with a cheatgrass–shrub interaction, corresponding with our foraging experiment results, and providing a rare example of a native plant mediating the effects of an invasive plant on wildlife. By synthesizing the results of three individual lines of evidence (foraging behavior, habitat selection, and apparent survival), we provide a rare example of linkage between behavioral responses of animals indicative of perceived predation risk and actual fitness outcomes. Moreover, our results suggest that exotic grass invasions can influence wildlife populations by altering risk landscapes and survival.

Seasonal Habitat Use by Greater Sage-Grouse (Centrocercus urophasianus) on a Landscape with Low Density Oil and Gas Development.

PubMed

Rice, Mindy B; Rossi, Liza G; Apa, Anthony D

2016-01-01

Fragmentation of the sagebrush (Artemisia spp.) ecosystem has led to concern about a variety of sagebrush obligates including the greater sage-grouse (Centrocercus urophasianus). Given the increase of energy development within greater sage-grouse habitats, mapping seasonal habitats in pre-development populations is critical. The North Park population in Colorado is one of the largest and most stable in the state and provides a unique case study for investigating resource selection at a relatively low level of energy development compared to other populations both within and outside the state. We used locations from 117 radio-marked female greater sage-grouse in North Park, Colorado to develop seasonal resource selection models. We then added energy development variables to the base models at both a landscape and local scale to determine if energy variables improved the fit of the seasonal models. The base models for breeding and winter resource selection predicted greater use in large expanses of sagebrush whereas the base summer model predicted greater use along the edge of riparian areas. Energy development variables did not improve the winter or the summer models at either scale of analysis, but distance to oil/gas roads slightly improved model fit at both scales in the breeding season, albeit in opposite ways. At the landscape scale, greater sage-grouse were closer to oil/gas roads whereas they were further from oil/gas roads at the local scale during the breeding season. Although we found limited effects from low level energy development in the breeding season, the scale of analysis can influence the interpretation of effects. The lack of strong effects from energy development may be indicative that energy development at current levels are not impacting greater sage-grouse in North Park. Our baseline seasonal resource selection maps can be used for conservation to help identify ways of minimizing the effects of energy development.

Assessing Potential Future Carbon Dynamics with Climate Change and Fire Management in a Mountainous Landscape on the Olympic Peninsula, Washington, USA

NASA Astrophysics Data System (ADS)

Kennedy, R. S.

2010-12-01

Forests of the mountainous landscapes of the maritime Pacific Northwestern USA may have high carbon sequestration potential via their high productivity and moderate to infrequent fire regimes. With climate change, there may be shifts in incidence and severity of fire, especially in the drier areas of the region, via changes to forest productivity and hydrology, and consequent effects to C sequestration and forest structure. To explore this issue, I assessed potential effects of fire management (little fire suppression/wildland fire management/highly effective fire suppression) under two climate change scenarios on future C sequestration dynamics (amounts and spatial pattern) in Olympic National Park, WA, over a 500-year simulation period. I used the simulation platform FireBGCv2, which contains a mechanistic, individual tree succession model, a spatially explicit climate-based biophysical model that uses daily weather data, and a spatially explicit fire model incorporating ignition, spread, and effects on ecosystem components. C sequestration patterns varied over time and spatial and temporal patterns differed somewhat depending on the climate change scenario applied and the fire management methods employed. Under the more extreme climate change scenario with little fire suppression, fires were most frequent and severe and C sequestration decreased. General trends were similar under the more moderate climate change scenario, as compared to current climate, but spatial patterns differed. Both climate change scenarios under highly effective fire suppression showed about 50% of starting total C after the initial transition phase, whereas with 10% fire suppression both scenarios exhibited about 10% of starting amounts. Areas of the landscape that served as refugia for older forest under increasing frequency of high severity fire were also hotspots for C sequestration in a landscape experiencing increasing frequency of disturbance with climate change.

The connection between landscapes and the solar ephemeris in honeybees.

PubMed

Towne, William F; Moscrip, Heather

2008-12-01

Honeybees connect the sun's daily pattern of azimuthal movement to some aspect of the landscape around their nests. In the present study, we ask what aspect of the landscape is used in this context--the entire landscape panorama or only sectors seen along familiar flight routes. Previous studies of the solar ephemeris memory in bees have generally used bees that had experience flying a specific route, usually along a treeline, to a feeder. When such bees were moved to a differently oriented treeline on overcast days, the bees oriented their communicative dances as if they were still at the first treeline, based on a memory of the sun's course in relation to some aspect of the site, possibly the familiar route along the treeline or possibly the entire landscape or skyline panorama. Our results show that bees lacking specific flight-route training can nonetheless recall the sun's compass bearing relative to novel flight routes in their natal landscape. Specifically, we moved a hive from one landscape to a differently oriented twin landscape, and only after transplantation under overcast skies did we move a feeder away from the hive. These bees nonetheless danced accurately by memory of the sun's course in relation to their natal landscape. The bees' knowledge of the relationship between the sun and landscape, therefore, is not limited to familiar flight routes and so may encompass, at least functionally, the entire panorama. Further evidence suggests that the skyline in particular may be the bees' preferred reference in this context.

System dynamic modelling of industrial growth and landscape ecology in China.

PubMed

Xu, Jian; Kang, Jian; Shao, Long; Zhao, Tianyu

2015-09-15

With the rapid development of large industrial corridors in China, the landscape ecology of the country is currently being affected. Therefore, in this study, a system dynamic model with multi-dimensional nonlinear dynamic prediction function that considers industrial growth and landscape ecology is developed and verified to allow for more sustainable development. Firstly, relationships between industrial development and landscape ecology in China are examined, and five subsystems are then established: industry, population, urban economy, environment and landscape ecology. The main influencing factors are then examined for each subsystem to establish flow charts connecting those factors. Consequently, by connecting the subsystems, an overall industry growth and landscape ecology model is established. Using actual data and landscape index calculated based on GIS of the Ha-Da-Qi industrial corridor, a typical industrial corridor in China, over the period 2005-2009, the model is validated in terms of historical behaviour, logical structure and future prediction, where for 84.8% of the factors, the error rate of the model is less than 5%, the mean error rate of all factors is 2.96% and the error of the simulation test for the landscape ecology subsystem is less than 2%. Moreover, a model application has been made to consider the changes in landscape indices under four industrial development modes, and the optimal industrial growth plan has been examined for landscape ecological protection through the simulation prediction results over 2015-2020. Copyright © 2015 Elsevier Ltd. All rights reserved.

Detectability of landscape effects on recolonization increases with regional population density

PubMed Central

Liman, Anna-Sara; Dalin, Peter; Björkman, Christer

2015-01-01

Variation in population size over time can influence our ability to identify landscape-moderated differences in community assembly. To date, however, most studies at the landscape scale only cover snapshots in time, thereby overlooking the temporal dynamics of populations and communities. In this paper, we present data that illustrate how temporal variation in population density at a regional scale can influence landscape-moderated variation in recolonization and population buildup in disturbed habitat patches. Four common insect species, two omnivores and two herbivores, were monitored over 8 years in 10 willow short-rotation coppice bio-energy stands with a four-year disturbance regime (coppice cycle). The population densities in these regularly disturbed stands were compared to densities in 17 undisturbed natural Salix cinerea (grey willow) stands in the same region. A time series approach was used, utilizing the natural variation between years to statistically model recolonization as a function of landscape composition under two different levels of regional density. Landscape composition, i.e. relative amount of forest vs. open agricultural habitats, largely determined the density of re-colonizing populations following willow coppicing in three of the four species. However, the impact of landscape composition was not detectable in years with low regional density. Our results illustrate that landscape-moderated recolonization can change over time and that considering the temporal dynamics of populations may be crucial when designing and evaluating studies at landscape level. PMID:26257881

Detectability of landscape effects on recolonization increases with regional population density.

PubMed

Liman, Anna-Sara; Dalin, Peter; Björkman, Christer

2015-07-01

Variation in population size over time can influence our ability to identify landscape-moderated differences in community assembly. To date, however, most studies at the landscape scale only cover snapshots in time, thereby overlooking the temporal dynamics of populations and communities. In this paper, we present data that illustrate how temporal variation in population density at a regional scale can influence landscape-moderated variation in recolonization and population buildup in disturbed habitat patches. Four common insect species, two omnivores and two herbivores, were monitored over 8 years in 10 willow short-rotation coppice bio-energy stands with a four-year disturbance regime (coppice cycle). The population densities in these regularly disturbed stands were compared to densities in 17 undisturbed natural Salix cinerea (grey willow) stands in the same region. A time series approach was used, utilizing the natural variation between years to statistically model recolonization as a function of landscape composition under two different levels of regional density. Landscape composition, i.e. relative amount of forest vs. open agricultural habitats, largely determined the density of re-colonizing populations following willow coppicing in three of the four species. However, the impact of landscape composition was not detectable in years with low regional density. Our results illustrate that landscape-moderated recolonization can change over time and that considering the temporal dynamics of populations may be crucial when designing and evaluating studies at landscape level.

Evaluating landscape health: Integrating societal goals and biophysical process

USGS Publications Warehouse

Rapport, D.J.; Gaudet, C.; Karr, J.R.; Baron, Jill S.; Bohlen, C.; Jackson, W.; Jones, Bruce; Naiman, R.J.; Norton, B.; Pollock, M. M.

1998-01-01

Evaluating landscape change requires the integration of the social and natural sciences. The social sciences contribute to articulating societal values that govern landscape change, while the natural sciences contribute to understanding the biophysical processes that are influenced by human activity and result in ecological change. Building upon Aldo Leopold's criteria for landscape health, the roles of societal values and biophysical processes in shaping the landscape are explored. A framework is developed for indicators of landscape health and integrity. Indicators of integrity are useful in measuring biological condition relative to the condition in landscapes largely unaffected by human activity, while indicators of health are useful in evaluating changes in highly modified landscapes. Integrating societal goals and biophysical processes requires identification of ecological services to be sustained within a given landscape. It also requires the proper choice of temporal and spatial scales. Societal values are based upon inter-generational concerns at regional scales (e.g. soil and ground water quality). Assessing the health and integrity of the environment at the landscape scale over a period of decades best integrates societal values with underlying biophysical processes. These principles are illustrated in two contrasting case studies: (1) the South Platte River study demonstrates the role of complex biophysical processes acting at a distance; and (2) the Kissimmee River study illustrates the critical importance of social, cultural and economic concerns in the design of remedial action plans. In both studies, however, interactions between the social and the biophysical governed the landscape outcomes. The legacy of evolution and the legacy of culture requires integration for the purpose of effectively coping with environmental change.

The effect of induced mutations on quantitative traits in Arabidopsis thaliana: Natural versus artificial conditions.

PubMed

Stearns, Frank W; Fenster, Charles B

2016-12-01

Mutations are the ultimate source of all genetic variations. New mutations are expected to affect quantitative traits differently depending on the extent to which traits contribute to fitness and the environment in which they are tested. The dogma is that the preponderance of mutations affecting fitness will be skewed toward deleterious while their effects on nonfitness traits will be bidirectionally distributed. There are mixed views on the role of stress in modulating these effects. We quantify mutation effects by inducing mutations in Arabidopsis thaliana (Columbia accession) using the chemical ethylmethane sulfonate. We measured the effects of new mutations relative to a premutation founder for fitness components under both natural (field) and artificial (growth room) conditions. Additionally, we measured three other quantitative traits, not expected to contribute directly to fitness, under artificial conditions. We found that induced mutations were equally as likely to increase as decrease a trait when that trait was not closely related to fitness (traits that were neither survivorship nor reproduction). We also found that new mutations were more likely to decrease fitness or fitness-related traits under more stressful field conditions than under relatively benign artificial conditions. In the benign condition, the effect of new mutations on fitness components was similar to traits not as closely related to fitness. These results highlight the importance of measuring the effects of new mutations on fitness and other traits under a range of conditions.

Evolution dynamics of a model for gene duplication under adaptive conflict

NASA Astrophysics Data System (ADS)

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.

Weak bedrock allows north-south elongation of channels in semi-arid landscapes

NASA Astrophysics Data System (ADS)

Johnstone, Samuel A.; Finnegan, Noah J.; Hilley, George E.

2017-11-01

Differences in the lengths of pole- and equator-facing slopes are observed in a variety of landscapes. These differences are generally attributed to relative variations in the intensity of mass-transport processes on slopes receiving different magnitudes of solar radiation. By measuring anomalies in the planform characteristics of drainage networks, we demonstrate that in the most asymmetric landscapes this asymmetry primarily arises from the equator-ward alignment of low-order valley networks. Valley network asymmetry is more severe in rocks expected to offer little resistance to erosion than in more resistant rocks when controlling for climate. This suggests that aspect-driven differences in surface processes that drive differences in landscape evolution are also sensitive to underlying rock type.

Constraints on the evolution of tolerance to herbicide in the common morning glory: resistance and tolerance are mutually exclusive.

PubMed

Baucom, Regina S; Mauricio, Rodney

2008-11-01

Evolutionary biologists explain the maintenance of intermediate levels of defense in plant populations as being due to trade-offs, or negative genetic covariances among ecologically important traits. Attempts at detecting trade-offs as constraints on the evolution of defense have not always been successful, leading some to conclude that such trade-offs rarely explain current levels of defense in the population. Using the agricultural pest Ipomoea purpurea, we measured correlations between traits involved in defense to glyphosate, the active ingredient in Roundup, a widely used herbicide. We found significant allocation costs of tolerance, as well as trade-offs between resistance and two measures of tolerance to glyphosate. Selection on resistance and tolerance exhibited differing patterns: tolerance to leaf damage was under negative directional selection, whereas resistance was under positive directional selection. The joint pattern of selection on resistance and tolerance to leaf damage indicated the presence of alternate peaks in the fitness landscape such that a combination of either high tolerance and low resistance, or high resistance and low tolerance was favored. The widespread use of this herbicide suggests that it is likely an important selective agent on weed populations. Understanding the evolutionary dynamics of herbicide defense traits is thus of increasing importance in the context of human-mediated evolution.

Assessing wild bees in perennial bioenergy landscapes: effects of bioenergy crop composition, landscape configuration, and bioenergy crop area

DOE Office of Scientific and Technical Information (OSTI.GOV)

Graham, John B.; Nassauer, Joan I.; Currie, William S.

Wild bee populations are currently under threat, which has led to recent efforts to increase pollinator habitat in North America. Simultaneously, U.S. federal energy policies are beginning to encourage perennial bioenergy cropping (PBC) systems, which have the potential to support native bees. Our objective was to explore the potentially interactive effects of crop composition, total PBC area, and PBC patches in different landscape configurations. Using a spatially-explicit modeling approach, the Lonsdorf model, we simulated the impacts of three perennial bioenergy crops (PBC: willow, switchgrass, and prairie), three scenarios with different total PBC area (11.7%, 23.5% and 28.8% of agricultural landmore » converted to PBC) and two types of landscape configurations (PBC in clustered landscape patterns that represent realistic future configurations or in dispersed neutral landscape models) on a nest abundance index in an Illinois landscape. Our modeling results suggest that crop composition and PBC area are particularly important for bee nest abundance, whereas landscape configuration is associated with bee nest abundance at the local scale but less so at the regional scale. Moreover, strategies to enhance wild bee habitat should therefore emphasize the crop composition and amount of PBC.« less

Assessing wild bees in perennial bioenergy landscapes: effects of bioenergy crop composition, landscape configuration, and bioenergy crop area

DOE PAGES

Graham, John B.; Nassauer, Joan I.; Currie, William S.; ...

2017-03-25

Wild bee populations are currently under threat, which has led to recent efforts to increase pollinator habitat in North America. Simultaneously, U.S. federal energy policies are beginning to encourage perennial bioenergy cropping (PBC) systems, which have the potential to support native bees. Our objective was to explore the potentially interactive effects of crop composition, total PBC area, and PBC patches in different landscape configurations. Using a spatially-explicit modeling approach, the Lonsdorf model, we simulated the impacts of three perennial bioenergy crops (PBC: willow, switchgrass, and prairie), three scenarios with different total PBC area (11.7%, 23.5% and 28.8% of agricultural landmore » converted to PBC) and two types of landscape configurations (PBC in clustered landscape patterns that represent realistic future configurations or in dispersed neutral landscape models) on a nest abundance index in an Illinois landscape. Our modeling results suggest that crop composition and PBC area are particularly important for bee nest abundance, whereas landscape configuration is associated with bee nest abundance at the local scale but less so at the regional scale. Moreover, strategies to enhance wild bee habitat should therefore emphasize the crop composition and amount of PBC.« less