Coarse-grained Landscape Research Articles

Range expansion can promote the evolution of plastic generalism in coarse-grained landscapes.

Phenotypic plasticity is one way for organisms to deal with variable environments through generalism. However, plasticity is not found universally and its evolution may be constrained by costs and other limitations such as complexity: the need for multiple mutational steps before the adaptation is realized. Theory predicts that greater experienced heterogeneity, such as organisms may encounter when spatial heterogeneity is fine-grained relative to dispersal, should favor the evolution of a broader niche. Here we tested this prediction via simulation. We found that, contrary to classical predictions, coarse-grained landscapes can be the most favorable for the evolution of plasticity, but only when populations encounter those landscapes through range expansion. During these range expansions, coarse-grained landscapes select for each step in the complex mutational pathway to plastic generalism by blocking the dispersal of specialists. These circumstances provide ecological opportunities for innovative mutations that change the niche. Our results indicate a new mechanism by which range expansion and spatially structured landscapes interact to shape evolution and reveal that the environments in which a complex adaptation has the highest fitness may not be the most favorable for its evolution.

Large scale Malware analysis

Malware overview reports are valuable information to understand threats behavior and develop proper countermeasures. Currently, most of these studies are focused on either fine-grained, individual sample analysis or coarse-grained landscapes. On the one hand, only the first allows professionals to handle specific security breaches. On the other hand, only the second allows understanding threat scenario as a whole. We claim that a complete security treatment is only possible when combining both approaches. Therefore, this work presents an analysis of a large malware dataset, showing the distinctions between coarse-grained and fine-grained analysis results. It presents both a general threat scenario based on coarse-grained results as well as it details fine-grained results to identify particular malicious constructions to anticipate incident response of future threats.

Multi-scale habitat associations of the black-footed rock-wallaby in north-western South Australia

Context Research on species’ habitat associations is strengthened if it combines coarse-grained landscape data with finer-scale parameters. However, due to the effort required to measure fine-scale parameters, studies on threatened species that unite these two scales remain relatively rare. Aim This study aimed to undertake a multi-scale analysis of the habitat association of the threatened Petrogale lateralis (MacDonnell Ranges race) in the Anangu Pitjantjatjara Yankunytjatjara (APY) Lands, South Australia. Method Analyses were conducted at four spatial scales: (1) across the Central Ranges IBRA Region (regional scale); (2) on hills in the APY Lands at which P. lateralis is extant and extinct (site scale); (3) at ‘core’ and ‘non-core’ areas within those hills (hillside scale); and (4) at rocky refuges. The maximum entropy approach through the software MaxEnt was used for the analysis at the regional scale. At the remaining scales, fieldwork was used to collect, and regression modelling to analyse, data. Key results At the regional scale, presence was associated with slope and geology. At the site scale, aspect, rock abundance and habitat type are likely to have facilitated animal persistence at extant sites. At the hillside scale, the aspect, vegetation type and rock complexity of core areas are likely to have contributed to their higher use. Size, exposure and accessibility were significant predictors of the use of rocky refuges. Conclusions All four spatial scales yielded novel information on the habitat associations of P. lateralis, supporting previous researchers’ suggestions that habitat modelling should be conducted at multiple spatial scales. Implications The study exemplifies the utility of combining MaxEnt modelling with fieldwork-derived data. The results may have conservation implications for this threatened race, and may also provide a model for other studies of faunal habitat associations.

Distributions of experimental protein structures on coarse-grained free energy landscapes.

Predicting conformational changes of proteins is needed in order to fully comprehend functional mechanisms. With the large number of available structures in sets of related proteins, it is now possible to directly visualize the clusters of conformations and their conformational transitions through the use of principal component analysis. The most striking observation about the distributions of the structures along the principal components is their highly non-uniform distributions. In this work, we use principal component analysis of experimental structures of 50 diverse proteins to extract the most important directions of their motions, sample structures along these directions, and estimate their free energy landscapes by combining knowledge-based potentials and entropy computed from elastic network models. When these resulting motions are visualized upon their coarse-grained free energy landscapes, the basis for conformational pathways becomes readily apparent. Using three well-studied proteins, T4 lysozyme, serum albumin, and sarco-endoplasmic reticular Ca(2+) adenosine triphosphatase (SERCA), as examples, we show that such free energy landscapes of conformational changes provide meaningful insights into the functional dynamics and suggest transition pathways between different conformational states. As a further example, we also show that Monte Carlo simulations on the coarse-grained landscape of HIV-1 protease can directly yield pathways for force-driven conformational changes.

Structural complexity of arthropod guilds is affected by the agricultural landscape heterogeneity generated by fencerows

Intensive farming imposes harsh conditions impeding the persistence of most arthropod species within crop fields. Hence, arthropods surviving the unfavourable conditions prevailing within crop fields may disperse towards nearby uncropped margins, such as fencerows. Here, we evaluate the influence of landscape heterogeneity on the abundance of different guilds, particularly herbivores and their natural enemies. Said heterogeneity mostly derives from fencerow network density. Hence, we developed an approach based on fitting linear-mixed models to elucidate the effects of landscape heterogeneity and field position (fencerows and crop interiors) on arthropod diversity. Mixed models were fitted to arthropod data obtained by pitfall trap samplings in 36 crop fields. Arthropod communities were structurally and functionally more complex along fencerows than within nearby crop interiors. Arthropods abundance was modulated by landscape heterogeneity, increasing the abundance of natural enemies as the landscape heterogeneity increased. On the contrary, herbivores abundance decreased as landscape heterogeneity increased. Consequently, the ratio between herbivores and natural enemies also decreased as landscapes became more heterogeneous. Natural enemies with larger body sizes, mostly carabid beetles, were more sensitive to landscape homogenisation. Our study reveals that, despite the coarse-grained landscapes in the Rolling Pampa, fencerow density appears as a key factor for structuring complex arthropod guilds in intensively farmed agricultural mosaics. In landscapes with higher density of fencerows, arthropods tend to concentrate along them, thus increasing the community structural complexity as well as the predation pressure over herbivores. This structural complexity of upper trophic levels enhances the ‘top-down’ regulation of herbivore populations, consequently decreasing the probability of pest outbreaks within crop fields.

Assessing the Quality of Cotranscriptional Folding Simulations.

Structural changes in RNAs are an important contributor to controlling gene expression not only at the posttranscriptional stage but also during transcription. A subclass of riboswitches and RNA thermometers located in the 5' region of the primary transcript regulates the downstream functional unit - usually an ORF - through premature termination of transcription. Not only such elements occur naturally, but they are also attractive devices in synthetic biology. The possibility to design such riboswitches or RNA thermometers is thus of considerable practical interest. Since these functional RNA elements act already during transcription, it is important to model and understand the dynamics of folding and, in particular, the formation of intermediate structures concurrently with transcription. Cotranscriptional folding simulations are therefore an important step to verify the functionality of design constructs before conducting expensive and labor-intensive wet lab experiments. For RNAs, full-fledged molecular dynamics simulations are far beyond practical reach because of both the size of the molecules and the timescales of interest. Even at the simplified level of secondary structures, further approximations are necessary. The BarMap approach is based on representing the secondary structure landscape for each individual transcription step by a coarse-grained representation that only retains a small set of low-energy local minima and the energy barriers between them. The folding dynamics between two transcriptional elongation steps is modeled as a Markov process on this representation. Maps between pairs of consecutive coarse-grained landscapes make it possible to follow the folding process as it changes in response to transcription elongation. In its original implementation, the BarMap software provides a general framework to investigate RNA folding dynamics on temporally changing landscapes. It is, however, difficult to use in particular for specific scenarios such as cotranscriptional folding. To overcome this limitation, we developed the user-friendly BarMap-QA pipeline described in detail in this contribution. It is illustrated here by an elaborate example that emphasizes the careful monitoring of several quality measures. Using an iterative workflow, a reliable and complete kinetics simulation of a synthetic, transcription-regulating riboswitch is obtained using minimal computational resources. All programs and scripts used in this contribution are free software and available for download as a source distribution for Linux® or as a platform-independent Docker® image including support for Apple macOS® and Microsoft Windows®.

Movement behavior in response to landscape structure: the role of functional grain

Landscape structure can influence the fine-scale movement behavior of dispersing animals, which ultimately may influence ecological patterns and processes at broader scales. Functional grain refers to the finest scale at which an organism responds to spatial heterogeneity among patches and extends to the limits of its perceptual range. To determine the functional grain of a model insect, red flour beetle (Tribolium castaneum), we examined its movement behavior in response to experimental flour landscapes. Landscape structure was varied by manipulating habitat abundance (0%, 10%, 30%, and 100%) and grain size of patches (fine-2 × 2 cm, intermediate-5 × 5 cm, and coarse-10 × 10 cm) in 50 × 50 cm landscapes. Pathway metrics indicated that beetles used a similar proportion of all landscape types. Several pathway metrics indicated a graded response from the fine to the coarse grain landscape. Lacunarity analysis of beetle pathways indicated a non-linear change in space use between the fine and intermediate landscapes and the coarse-grained landscape. Beetles moved more slowly and tortuously (with many turns), and remained longer in both the overall landscape and individual patches, in fine-grained compared to coarse-grained landscapes. Our research demonstrates how detailed examination of movement pathways and measures of lacunarity can be useful in determining functional grain. Spatially explicit, organism-centered studies focusing on behavioral responses to different habitat configurations can serve as an important first step to identify behavioral rules of movement that may ultimately lead to more accurate predictions of space use in landscapes.

Effects of fragmentation on cattle in African savannas under variable precipitation

Cattle move to access patches that vary in forage quantity and quality. Fragmentation can prevent animals from reaching patches. I used an integrative ecosystem model applied to three African landscapes to explore the sensitivity of cattle populations to fragmentation (here, changes in populations as parcel areas decreased) under different precipitation patterns. I hypothesized that low and high precipitation would yield populations relatively insensitive to fragmentation, intermediate precipitation would yield more sensitive populations, and more variable inter-annual precipitation would reduce sensitivity to fragmentation. Precipitation data were altered to yield averages of 100–1,000 mm year−1 and inter-annual coefficients of variation of 0–60%. A 1,000 km2 landscape in each area was divided into progressively smaller parcels and simulations conducted for each parcel. Rainfall at 100 mm year−1 supported low populations that were insensitive to fragmentation. Populations peaked at rainfall levels similar to those observed, and declined under higher precipitation, due in-part to shrub expansion. Fragmenting landscapes caused up to a 62% decline in cattle. High inter-annual variation in precipitation reduced sensitivity to fragmentation when precipitation was above that observed. The pattern was opposite when precipitation was below what was observed. Cattle on the landscape with fine-scale heterogeneity were relatively insensitive to fragmentation, and those on the heterogeneous but coarse-grained landscape were extremely sensitive. Fragmentation in landscapes where populations are sensitive will require more intensive inputs to offset losses, and changes in the frequency of extreme weather associated with climate change will alter the sensitivity of some populations to fragmentation.

THE CO-DISTRIBUTION OF SPECIES IN RELATION TO THE NEUTRAL THEORY OF COMMUNITY ECOLOGY

Patterns of species co-distribution have often been used to infer the operation of processes such as competition and selection among species. Ecological specialization should create unexpectedly strong species associations, reflected by high positive or negative correlations between species that are adapted to similar or different kinds of site. Two systematic surveys of plant communities do indeed show stronger associations than are expected in randomly assembled communities. Neutral community models, however, also predict nonrandom patterns of co-distribution. Local selection in heterogeneous landscapes, where species are sorted into the sites to which they are best adapted, will produce even stronger associations, provided that different kinds of site are correlated in space, forming repeated combinations or “habitats.” In practice, however, this effect is readily detectable only for intense selection in coarse-grained landscapes. In contrast, classification of species or sites into prior categories co...

Building and evaluating predictive occupancy models for the Siberian flying squirrel using forest planning data

We analyzed the applicability of forest planning data in predicting the occurrence of the Siberian flying squirrel ( Pteromys volans) in managed northern boreal forests, in northeast Finland. Forest planning data is a source of information about forest characteristics for forest managers that may be used in estimating the availability of certain habitats for species conservation. Flying squirrel populations have declined in Finland, most probably due to habitat change and loss and maintenance of suitable habitats can be seen as a fundamental task in species conservation. First, we surveyed 715 ha of older spruce-dominated forest consisting of 91 stands, of which 35 were found occupied by flying squirrel. Flying squirrels inhabited larger stands, which had a higher volume of spruce and birch. Occupied stands also had more good quality forests surrounding them than the unoccupied stands. We based the model building on already existing knowledge of the habitat preferences of the species and built four alternative predictive models with logistic regression. Forest planning data seemed useful in estimating the forest quality and the suitability of habitats for the flying squirrel, with a model fit of ca. 72% with the original data. Second, we built the predictive models similarly with data from another study area ( n = 98) situating ca. 150 km south from the first area. Third, we evaluated the first models using data of the second study area and also using new independent data from three municipalities situating almost in between the two study areas. Moreover, we reciprocally evaluated one model of the second study area using data of the first study area and of the three municipalities. The prediction success of our models indicated some applicability to other areas. The results also showed that the structure of the surrounding landscape is more important in a coarse-grained landscape than in a fine-grained landscape. However, because of some inaccuracies, predictive occupancy models built for the flying squirrel cannot replace field surveys and their generalizations to other areas must be made with caution.

Assessing Sexual Segregation in Deer

Sexual segregation in temperate and arctic ruminants is defined as the differential use of space by the sexes outside the mating season. This phenomenon is widespread among taxa, and is especially prevalent among sexually dimorphic deer (Cervidae). Understanding how different genders are distributed across the landscape and how to assess these spatial patterns is of theoretical and applied importance. We developed a simple model to evaluate effects of landscape grain (i.e., patch characteristics), sampling scale, and population density of deer on detection of sexual segregation. We created landscape maps of 2 areas in which landscape grain was changed while other landscape metrics (e.g., area, shape, and diversity) were held relatively constant. We created a high-density population of deer to emulate conditions near ecological carrying capacity (K), and a low-density population at <K/2. Sexes of deer were assigned to 4 habitats based on differences in habitat selection derived from an ideal-free distribution, which created spatial separation of the sexes similar to observations in empirical studies. We sampled this pattern of sexual segregation for both areas at large and small scales of measurement using quadrats arranged systematically. We also compared the degree of sexual segregation for the coarse-grained landscape, where the sexes used habitats differently, with a null model in which habitat preferences were identical for each gender of deer. The null model emulated conditions during rut when the sexes were aggregated. Sexual segregation was significantly greater where habitat use differed between sexes, indicating that our model was correct and that the degree of spatial segregation was not an artifact of patch configuration, sampling scale, or population density. Logistic regression revealed that population density and the size of the sample unit significantly affected our ability to assess differences in the spatial distributions of male and female deer where differential use of habitats occurred. Variation in landscape grain, however, did not influence the detection of sexual segregation. Results from our model emphasize the importance of evaluating effects of population density and especially sampling scale on assessing spatial separation of the sexes. Failure to do so may result in not recognizing patterns of sexual segregation on the landscape, or in misinterpreting that phenomenon, which clearly holds consequences for those managing large herbivores or their habitats.

Small wetlands lost: a biological conservation hazard in Mediterranean landscapes

In Spain, it is estimated that 60% of wetlands have disappeared in the last 50 years. The present study aimed to describe the relationships between loss of wetlands and land-use change in Azuaga County, Central-western Iberian Peninsula where during the period 1896-1996, 94% of the original wetlands disappeared. Forest, scrub, holm oak dehesas and olive groves have become fragmented or disappeared completely, having been substituted by eucalyptus plantations in areas of low productivity and by dry cultivation of herbaceous crops, mainly cereals, in more productive areas. These substitutions have resulted in a homogeneous, coarse-grained landscape with low diversity and high dominance. The type of land-use has depended on the evolution of demographic processes, with high human immigration rates toward the end of the nineteenth century and beginning of the twentieth century, and high emigration rates during the 1960s and 1970s. The mechanization of agriculture and transition from closed to market economy in the second half of the twentieth century also played an essential role in the landscape changes described.

Status and population changes of farmland birds in southern Sweden

Since 1950 there have been considerable changes in the use of Swedish farmland which have led to a more large-scale, homogeneous and intensively managed agricultural landscape. These changes in Swedish farmland have affected the populations of many farmland birds. We give the densities of 29 selected farmland birds and 15 selected species of forest birds at eight large study sites (farmland landscapes of 14.5–21.5 km2 size; total of 140 km2) in southern Sweden and review the population changes of 48 species of farmland birds in southern Sweden. The number of breeding farmland bird species at the different sites was positively correlated with total farmland area, area of scrub and trivial deciduous forest, as well as with the fragmentation of the forest landscape; there were more farmland species in fine-grained than in coarse-grained landscapes. Species found in forest edges and dry pastures were the most widespread ones (found at most sites), and included several species with high densities. Most of these species have not decreased as dramatically as other species. Several species of arable land were also widespread, but most of them have declined in numbers since 1950, possibly as a consequence of changes in farming practices. Meadow is the farmland habitat that has declined most, and this is reflected in the low densities and scattered distribution of many species found on cut or grazed meadows. Several of these species are now largely confined to marginal habitats and areas where farmland still has a traditional structure. However, on abandoned meadows overgrown with bushes and trees a few successful colonists are increasing in numbers. Of the 48 farmland birds breeding in Sweden the populations of only 10 have remained relatively stable since 1950; seventeen have increased (8 markedly) while 21 have decreased (12 markedly). Of the 21 species that primarily breed on farmland, 9 (43%) have declined markedly compared with only 3 (11%) of the 27 secondary farmland birds, which have a large proportion of the population in other habitats. Similarly, only 5% of the primary species have increased markedly compared with 26% of the secondary species. More primary than secondary farmland species are also extinct, or categorized as endangered, vulnerable or requiring consideration on Swedish Red Data lists. Large parts of the Swedish farmland are now being taken out of production, which probably will have negative effects on several farmland bird populations.