Simple Landscape Research Articles

Exploring Protein Energy Landscapes with Time-Dependent Principal Component Analysis

Protein function crucially depends on protein dynamics. Large-scale molecular dynamics simulations of small globular proteins show an anomalous diffusion behavior for the principal motions of proteins over multiple time scales. Specifically the variance of the essential principal components increases with a power law σ ∼ T α with trajectory length T. This behavior suggests a hierarchical structure of the energy landscape as first proposed by Frauenfelder.To quantify how the anomalous diffusion exponents found in the molecular dynamics simulations give insight into the hierarchical structure of the underlying energy landscape, we compared our results to the simple discrete energy landscape shown in the figure. In this model, a hierarchy of energy barriers separating adjecent states is assumed. This hierarchy is characterized by its “ruggedness” ΔF as shown in the figure. We show that ΔF can be derived from the power law exponent α measured in the simulations via ΔF=log(2)(2/α-1). Typical values of 5-7 kT are obtained.View Large Image | View Hi-Res Image | Download PowerPoint Slide

Predictability of evolution depends nonmonotonically on population size

To gauge the relative importance of contingency and determinism in evolution is a fundamental problem that continues to motivate much theoretical and empirical research. In recent evolution experiments with microbes, this question has been explored by monitoring the repeatability of adaptive changes in replicate populations. Here, we present the results of an extensive computational study of evolutionary predictability based on an experimentally measured eight-locus fitness landscape for the filamentous fungus Aspergillus niger. To quantify predictability, we define entropy measures on observed mutational trajectories and endpoints. In contrast to the common expectation of increasingly deterministic evolution in large populations, we find that these entropies display an initial decrease and a subsequent increase with population size N, governed, respectively, by the scales Nμ and Nμ(2), corresponding to the supply rates of single and double mutations, where μ denotes the mutation rate. The amplitude of this pattern is determined by μ. We show that these observations are generic by comparing our findings for the experimental fitness landscape to simulations on simple model landscapes.

Habitat selection and coexistence in wintering passerine steppe birds

This study evaluates the relative contributions of landscape features and biotic (conspecific and heterospecific) relationships to habitat selection of three sympatric passerine species, Skylark (Alauda arvensis), Corn Bunting (Emberiza calandra) and Calandra Lark (Melanocorypha calandra) during winter. Between December 2007 and January 2008, winter populations of the three species were censused in three Central Spanish locations by means of linear transects (n = 60). An explanatory model-averaging approach was used to determine the weight and effect of different landscape and biotic variables in each species’ habitat selection patterns using their respective abundance as the dependent variable. A deviance partitioning approach was used to determine the relative contributions of these two sets of predictors. Only the Calandra Lark showed a significant influence of landscape variables, preferring relatively simplified landscapes with a low density of field margins. The three species showed preferences for proximity of con- and heterospecifics. This can be explained in relation to their gregarious behaviour during this season, which results in the formation of big multispecific flocks that confer some individual advantages (such as a better feeding efficiency or anti-predator benefits). This is also supported by the results of the deviance partitioning analysis, which showed the much higher importance of biotic interaction factors in relation to the contribution of landscape (which is negligible) for Skylark and Corn Bunting. However, for Calandra Lark, although biotic interactions are also the most important factors, both landscape and the combined effect of landscape and biotic interactions are slightly larger. Finally, we also found an effect of flock size on habitat selection, so that, for bigger flocks, habitat and biotic interaction factors will have a weaker effect on abundance and selection patterns.

Search for the optimality signature of river network development

Whether the evolution of natural river networks pursues a certain optimal state has been a most intriguing and fundamental question. There have been many optimality hypotheses proposed but it has yet to be proved which of these best serves as a quantitative signature of river network development. Here, this fundamental question is investigated for the five hypotheses of "minimum total energy expenditure," "minimum total energy dissipation rate," "minimum total stream power," "minimum global energy expenditure rate," and "minimum topological energy." Using simple example landscapes, I examined whether any of these hypotheses pursues both the treelike river network formation and the concave stream longitudinal profile, the two characteristic patterns of natural landscapes. It is found that none of these hypotheses captures both patterns under the steady-state condition where the balance between tectonic uplift and sediment loss is satisfied. These findings are further verified through simulations of landscapes that satisfy given optimality criteria using an optimization method.

A importância cultural das águas no Amazonas

Amid the old “region of Manaus” (and in the vicinity thereof ), the article discusses the value of the complex water for amazonidas beyond a simple landscape environment. In light of some memories of our interviewees, we encourage the river water of the place as a territory of more plural cohabitation, living and working environment, a source of peculiar stories not only make known the ideas and imagination of local residents, as an intrinsic part their cultural identity

Pest control experiments show benefits of complexity at landscape and local scales

Farms benefit from pest control services provided by nature, but management of these services requires an understanding of how habitat complexity within and around the farm impacts the relationship between agricultural pests and their enemies. Using cage experiments, this study measures the effect of habitat complexity across scales on pest suppression of the cabbage aphid Brevicoryne brassicae in broccoli. Our results reveal that proportional reduction of pest density increases with complexity both at the landscape scale (measured by natural habitat cover in the 1 km around the farm) and at the local scale (plant diversity). While high local complexity can compensate for low complexity at landscape scales and vice versa, a delay in natural enemy arrival to locally complex sites in simple landscapes may compromise the enemies' ability to provide adequate control. Local complexity in simplified landscapes may only provide adequate top-down pest control in cooler microclimates with relatively low aphid colonization rates. Even so, strong natural enemy function can be overwhelmed by high rates of pest reproduction or colonization from nearby source habitat.

ANTIBIOTIC RESISTANCE AND STRESS IN THE LIGHT OF FISHER'S MODEL

The role of mutations in evolution depends upon the distribution of their effects on fitness. This distribution is likely to depend on the environment. Indeed genotype-by-environment interactions are key for the process of local adaptation and ecological specialization. An important trait in bacterial evolution is antibiotic resistance, which presents a clear case of change in the direction of selection between environments with and without antibiotics. Here, we study the distribution of fitness effects of mutations, conferring antibiotic resistance to Escherichia coli, in benign and stressful environments without drugs. We interpret the distributions in the light of a fitness landscape model that assumes a single fitness peak. We find that mutation effects (s) are well described by a shifted gamma distribution, with a shift parameter that reflects the distance to the fitness peak and varies across environments. Consistent with the theoretical predictions of Fisher's geometrical model, with a Gaussian relationship between phenotype and fitness, we find that the main effect of stress is to increase the variance in s. Our findings are in agreement with the results of a recent meta-analysis, which suggest that a simple fitness landscape model may capture the variation of mutation effects across species and environments.

Response of ground-nesting farmland birds to agricultural intensification across Europe: Landscape and field level management factors

European farmland bird populations have decreased dramatically in recent decades and agricultural intensification has been identified as the main cause contributing to these declines. Identifying which specific intensification pressures are driving those population trends seems vital for bird conservation in European farmland.We investigated the response of ground-nesting farmland birds to the multivariate process of agricultural intensification in six European countries covering a bio-geographical and intensification gradient. Supported by PCA analysis, two groups of factors, related to field management and landscape modification, were considered, seeking to discriminate the relative importance of the effects of these main intensification components.Variance partition analysis showed that landscape factors accounted for most of the variation of ground-nesting farmland bird individual and breeding pair densities, as well as Skylark (i.e. our single model species) individual densities. In the case of Skylark breeders, field factors were found to be more important to explain their density. Our results suggest that in general farmland bird densities as well as Skylark densities are higher in simple landscapes dominated by agriculture, but with smaller fields and more different crops on the farms. In addition, high yields were negatively related to bird densities.We conclude that while management actions aimed at farmland bird conservation taken at landscape level may exert a strong positive effect on overall bird densities, those taken at field level are also relevant, particularly for breeders and, therefore, may potentially influence the persistence of these species’ populations.

THE DISTRIBUTION OF MUTATIONAL FITNESS EFFECTS OF PHAGE φX174 ON DIFFERENT HOSTS

Adaptation depends greatly on the distribution of mutation fitness effects (DMFE), but the phenotypic expression of mutations is often environment dependent. The environments faced by multihost pathogens are mostly governed by their hosts and therefore measuring the DMFE on multiple hosts can inform on the likelihood of short-term establishment and longer term adaptation of emerging pathogens. We explored this by measuring the growth rate of 36 mutants of the lytic bacteriophage φX174 on two host backgrounds, Escherichia coli (EcC) and Salmonella typhimurium (StGal). The DMFE showed higher mean and variance on EcC than on StGal. Most mutations were either deleterious or neutral on both hosts, but a greater proportion of mutations were deleterious on StGal. We identified two mutations with beneficial fitness effects on EcC that were neutral on StGal. Host-specific differences in fitness were associated with particular functional classes of genes involved in the initial stages of infection in accordance with previous studies of host specificity. Overall, there was a positive correlation between the effects of mutations on each host, suggesting that most new mutations will have general, rather than host-specific fitness effects. We consider these results in light of simple fitness landscape models of adaptation and discuss the relevance of context-dependent DMFE for multihost pathogens.

Agricultural intensification and cereal aphid–parasitoid–hyperparasitoid food webs: network complexity, temporal variability and parasitism rates

Agricultural intensification (AI) is currently a major driver of biodiversity loss and related ecosystem functioning decline. However, spatio-temporal changes in community structure induced by AI, and their relation to ecosystem functioning, remain largely unexplored. Here, we analysed 16 quantitative cereal aphid–parasitoid and parasitoid–hyperparasitoid food webs, replicated four times during the season, under contrasting AI regimes (organic farming in complex landscapes vs. conventional farming in simple landscapes). High AI increased food web complexity but also temporal variability in aphid–parasitoid food webs and in the dominant parasitoid species identity. Enhanced complexity and variability appeared to be controlled bottom-up by changes in aphid dominance structure and evenness. Contrary to the common expectations of positive biodiversity–ecosystem functioning relationships, community complexity (food-web complexity, species richness and evenness) was negatively related to primary parasitism rates. However, this relationship was positive for secondary parasitoids. Despite differences in community structures among different trophic levels, ecosystem services (parasitism rates) and disservices (aphid abundances and hyperparasitism rates) were always higher in fields with low AI. Hence, community structure and ecosystem functioning appear to be differently influenced by AI, and change differently over time and among trophic levels. In conclusion, intensified agriculture can support diverse albeit highly variable parasitoid–host communities, but ecosystem functioning might not be easy to predict from observed changes in community structure and composition.Electronic supplementary materialThe online version of this article (doi:10.1007/s00442-012-2366-0) contains supplementary material, which is available to authorized users.

Aphids and their natural enemies are differently affected by habitat features at local and landscape scales

Biological control, an essential ecosystem service to agriculture, can be affected by ecological processes operating at landscape scales. Here we assessed the effect of landscape complexity, measured as proportion of arable land (PAL), on the abundance of aphids, parasitoids, and specialist and generalist predators. In addition we set up cage experiments to test the ability of these groups of enemies to suppress aphid densities. Landscape context did not significantly explain differences in aphid or parasitoid densities between fields. However, aphid densities were significantly higher in field interior compared to the margin. Coccinellid (specialist predator) abundance showed a similar pattern, with higher density in the field interior, indicating an aggregative response to aphid prey. In addition, Coccinellid abundance increased with PAL, but only in field interiors and not at the field margins. The abundance of carabids (generalist predators) increased with PAL, suggesting that they benefit from landscape simplification. The cage experiment revealed that specialist as well as generalist predators were able to reduce the number of aphids on barley tillers and that a combination of both guilds did not provide a greater reduction of aphids.Our results suggest higher densities of generalist predators with increasing PAL. Nonetheless, the greater abundance of coccinellids and carabid beetles in cereal fields embedded in simple landscapes does not necessarily imply better pest control since natural enemies may compete, thereby limiting their ability to control pests.

Agricultural intensification drives landscape‐context effects on host–parasitoid interactions in agroecosystems

Summary1. Agricultural land use threatens ecosystem services such as biological control by natural enemies because of simplification of habitat structure and intensification of disturbance and agrochemical inputs. Low parasitism rates of agricultural pests have typically been attributed to a lack of resources for parasitoids in highly simplified landscapes, but this could be confounded by the nearly ubiquitous correlation between landscape complexity and the cover of intensively farmed agricultural crops.2. Here, we disentangle the mechanisms driving landscape‐scale effects on host–parasitoid interactions by taking advantage of a landscape modification gradient in which the diversity of habitat types and annual crop cover in the landscape were uncorrelated. We quantified herbivore densities and parasitism and hyperparasitism rates on two important crop pests (aphids and Plutella xylostella) across 30 landscapes. We used structural equation modelling (SEM) to test whether land‐use intensity (insecticide application and habitat disturbance) or resource availability for parasitoids (floral resources and alternative host plants) was mediating the effects of habitat diversity and annual crop cover on the landscape.3. Rates of primary‐ and hyperparasitism of aphids and primary parasitism of P. xylostella decreased with increasing annual crop cover, whereas decreasing habitat diversity in the landscape had little effect on parasitism rates. These effects were mediated almost entirely by greater habitat disturbance and greater frequency of insecticide application, rather than by changes in resource availability.4. Parasitoids were more sensitive to intensive farming practices than were their herbivore hosts, and in turn hyperparasitoids were more sensitive than were primary parasitoids. This supports the theoretical prediction that higher trophic levels should be increasingly sensitive to the disturbances associated with land‐use change.5. Synthesis and applications. Our work suggests that increased land‐use intensity (e.g. higher insecticide inputs and greater levels of disturbance associated with increasing area of annual crops) has been underestimated as a driver of landscape effects on host–parasitoid interactions. These findings have important implications for the maintenance of ecosystem services such as biological control. The promotion of low‐intensity farming practices that limit the extent and frequency of agrochemical inputs and habitat disturbances will be essential for the maintenance of effective biological control by parasitoids in agroecosystems.

Effects of local landscape richness on in-field weed metrics across the Great Britain scale

Weeds sit at the crux of issues of arable biodiversity and productivity. We test whether the effects of a simple local landscape richness score are apparent on in-field data for the predominant weeds, in the seedbank and as standing weeds, across the Great Britain (GB) scale. We test two hypotheses: (H1) that in-field weed species richness is positively related to local landscape richness around arable fields; and (H2) that in-field weed abundance is positively related to local landscape richness. We maintain H1, but find little evidence of a consistent effect of local landscape on the species richness of in-field weeds. Convincing evidence for local landscape richness affecting weed abundance lead us to accept H2 as a working hypothesis for in-field weed abundance. However, we have no mechanism to explain why in-field weed abundance should be linked to off-field landscape features, as expectations for farmer management intensity and local bee abundance affecting weed abundance were not significant.The effects of landscape on weed abundance were consistent across the GB scale dataset despite systematic sources of error due to cropping and regional differences. These results suggest that local landscape might be managed to achieve goals of changing in-field weed abundance at policy-relevant scales.

Landscape structure and habitat management differentially influence insect natural enemies in an agricultural landscape

Increasing evidence suggests that landscape composition is an important driver of beneficial insect populations and resulting ecosystem services. Additionally, local-scale manipulations such as planting floral strips are used at the field-level to provide resources for beneficial insects to increase their services. It has been proposed that the benefits of local manipulations will depend on the landscape context, with greater benefits in simplified landscapes and smaller benefits in landscapes with an abundance of non-crop resources. To test this, we used soybean aphid, Aphis glycines, and its coccinellid predators as a model system to elucidate the effects of habitat management and landscape on biocontrol services in soybean. We selected pairs of soybean fields in landscapes of varying composition and planted buckwheat, Fagopyrum esculentum, strips adjacent to one field in each pair. We measured coccinellid abundance and biocontrol in each field. Coccinellid abundance was higher in buckwheat than in control field margins in all landscapes, and coccinellid abundance in soybean was positively related to amount of semi-natural vegetation in the landscape. We found no evidence of an interaction between landscape and local variables, and biocontrol services were high in all contexts. For soybean aphid suppression, landscape factors are the key drivers of predator abundance.

Characteristic time in quasispecies evolution

The time a phenotype takes to achieve a stationary state from an initial condition depends on multiple factors. In particular, it is a function of both its fitness and its mutation rate. We evaluate the average time, referred to as the characteristic time, Tc, that the system takes to reach a final steady state of simple models of populations formed by self-replicative sequences. The dependence of Tc on the mutation rate and on the fitness landscape is also studied. For simple fitness landscapes, e.g. single peak, the characteristic time can be analytically obtained as a function of the system parameters. In this case, Tc for obtaining the quasispecies distribution presents a maximum at a Q-value that depends on the initial conditions and decreases monotonously as the mutation rate tends to zero. For most of the complex landscapes handled in this paper, the characteristic time to achieve the quasispecies distribution picked around the fittest phenotype attains a local minimum for a given mutation rate between 0 and the Q-value at which Tc reaches its local maximum. Thus, in these cases, an optimum value for the mutation rate exists that corresponds to the lowest value of the characteristic time for quasispecies evolution.

Synanthropy of wild mammals as a determinant of emerging infectious diseases in the Asian-Australasian region.

Humans create ecologically simplified landscapes that favour some wildlife species, but not others. Here, we explore the possibility that those species that tolerate or do well in human-modified environments, or ‘synanthropic’ species, are predominantly the hosts of zoonotic emerging and re-emerging infectious diseases (EIDs). We do this using global wildlife conservation data and wildlife host information extracted from systematically reviewed emerging infectious disease literature. The evidence for this relationship is examined with special emphasis on the Australasian, South East Asian and East Asian regions. We find that synanthropic wildlife hosts are approximately 15 times more likely than other wildlife in this region to be the source of emerging infectious diseases, and this association is essentially independent of the taxonomy of the species. A significant positive association with EIDs is also evident for those wildlife species of low conservation risk. Since the increase and spread of native and introduced species able to adapt to human-induced landscape change is at the expense of those species most vulnerable to habitat loss, our findings suggest a mechanism linking land conversion, global decline in biodiversity and a rise in EIDs of wildlife origin.

An exact tunneling solution in a simple realistic landscape

We present an analytical solution for the tunneling process in a piecewise linear and quadratic potential which does not make use of the thin-wall approximation. A quadratic potential allows for the smooth attachment of various slopes exiting into the final minimum of a realistic potential. Our tunneling solution thus serves as a realistic approximation to situations such as populating a landscape of slow-roll inflationary regions by tunneling, and it is valid for all regimes of the barrier parameters. We comment briefly on the inclusion of gravity.

Insect pollination enhances seed yield, quality, and market value in oilseed rape

The relationships between landscape intensification, the abundance and diversity of pollinating insects, and their contributions to crop yield, quality, and market value are poorly studied, despite observed declines in wild and domesticated pollinators. Abundance and species richness of pollinating insects were estimated in ten fields of spring oilseed rape, Brassica napus var. SW Stratos™, located along a gradient of landscape compositions ranging from simple landscapes dominated by arable land to heterogeneous landscapes with extensive cover of semi-natural habitats. In each field, we assessed the contribution of wind and insect pollination to seed yield, seed quality (individual seed weight and oil and chlorophyll contents), and market value in a block experiment with four replicates and two treatments: (1) all flowers were accessible to insects, self and wind pollination, and (2) flowers enclosed in tulle net bags (mesh: 1 × 1 mm) were accessible only to wind and self pollination. Complex landscapes enhanced the overall abundance of wild insects as well as the abundance and species richness of hoverflies. This did not translate to a higher yield, probably due to consistent pollination by honey bees across all fields. However, the pollination experiment showed that insects increased seed weight per plant by 18% and market value by 20%. Seed quality was enhanced by insect pollination, rendering heavier seeds as well as higher oil and lower chlorophyll contents, clearly showing that insect pollination is required to reach high seed yield and quality in oilseed rape. Our study demonstrates considerable and previously underestimated contributions from pollinating insects to both the yield and the market value of oilseed rape.

Analysis of landscape-scale insect pest dynamics and pesticide use: an empirical and modeling study

Diverse agricultural landscapes help support many ecosystem services, including insect pest suppression. Yet questions remain about how landscape diversification affects insects with differing life histories, and how interactions between pest management and land use alter insect population dynamics. Here we introduce empirical data illustrating how population dynamics and pest management of two economically important insect pests in maize (Zea mays), the European corn borer (ECB; Ostrinia nubilalis) and the western corn rootworm (WCR; Diabrotica virgifera), may vary with land use. We then explore the role of landscape in agricultural pest suppression with a spatially explicit computational model of herbivore population dynamics that includes pest management measures and insect life-history parameters (diet breadth, dispersal distance, and reproductive rate). While field results showed that WCR densities were lower in diverse than in simple agricultural landscapes, ECB damage to maize appeared unrelated to land use. Indeed, our stable carbon isotope analysis shows that one critical difference in the life histories of the two insects is host utilization: WCR utilized non-maize hosts (0%) at a lower rate than ECB (11%). However, management for both pests was consistently related to land use: less transgenic Bt maize and less insecticide is used per maize hectare in U.S. states with less maize. Consistent with field observations, our model predicts that landscape diversification results in reduced insecticide use and suggests that specialist pests are more affected by land-use changes than generalists. The model further predicts that insects with high reproductive rates are less sensitive to land-use change than insects with low reproductive rates and that dispersal distance is not an important factor regulating densities of highly dispersive insect pests in agricultural landscapes. While our study suggests that landscape diversification may not suppress all pests, it also suggests that diverse agricultural landscapes are correlated with consistently lower pesticide usage.

Effects of landscape, conspecifics and heterospecifics on habitat selection by breeding farmland birds: the case of the Calandra Lark (Melanocorypha calandra) and Corn Bunting (Emberiza calandra)

The aim of habitat selection studies is to understand the effect of the different factors affecting the spatial distribution of individuals. Within this framework, the aim of this study was to evaluate the relative contributions of landscape features and conspecific and heterospecific interactions to habitat selection by two sympatric species, the Calandra Lark Melanocorypha calandra and the Corn Bunting Emberiza calandra, during the breeding season. During the 2008 breeding season, the population of both species was censused in three Central Spanish locations by means of transects (N = 58). A model-averaging approach was used to determine the weight and effect of landscape and interaction variables in each species’ habitat selection using abundance as the dependent variable. Deviance partitioning was used to determine the unique and shared contributions of these two sets of variables to the variation explained by the models. Calandra Lark was positively associated with mean field size, which reflects its preference for relatively simplified landscapes with a low density of field margins and, consequently, small land-use diversity. Corn Bunting selected areas with high land-use diversity, namely, a highly heterogeneous landscape with a high density of field margins. Attraction between conspecifics was found in both cases. Calandra Lark seems to negatively respond to the proximity of Corn Buntings, which indicates a partitioning of space and food resources. However, Corn Bunting responded positively to the proximity of Calandra Larks, which reflects a higher tolerance of Corn Buntings to the presence of other species nearby. Deviance partitioning showed that interactions were more important for Calandra Lark, while Corn Bunting was equally affected by both components. An appropriate management should combine the requirements of both species to achieve effective conservation at the bird assemblage level.