Process-Driven Ecological Modeling for Landscape Change Analysis

NASA Astrophysics Data System (ADS)

Altman, S.; Reif, M. K.; Swannack, T. M.

2013-12-01

Landscape pattern is an important driver in ecosystem dynamics and can control system-level functions such as nutrient cycling, connectivity, biodiversity and carbon sequestration. However, the links between process, pattern and function remain ambiguous. Understanding the quantitative relationship between ecological processes and landscape pattern across temporal and spatial scales is vital for successful management and implementation of ecosystem-level projects. We used remote sensing imagery to develop critical landscape metrics to understand the factors influencing landscape change. Our study area, a coastal area in southwest Florida, is highly dynamic with critically eroding beaches and a range of natural and developed land cover types. Hurricanes in 2004 and 2005 caused a breach along the coast of North Captiva Island that filled in by 2010. We used a time series of light detection and ranging (lidar) elevation data and hyperspectral imagery from 2006 and 2010 to determine land cover changes. Landscape level metrics used included: Largest Patch Index, Class Area, Area-weighted mean area, Clumpiness, Area-weighted Contiguity Index, Number of Patches, Percent of landcover, Area-weighted Shape. Our results showed 1) 27% increase in sand/soil class as the channel repaired itself and shoreline was reestablished, 2) 40% decrease in the mudflat class area due to conversion to sand/soil and water, 3) 30% increase in non-wetland vegetation class as a result of new vegetation around the repaired channel, and 4) the water class only slightly increased though there was a marked increase in the patch size area. Thus, the smaller channels disappeared with the infilling of the channel, leaving much larger, less complex patches behind the breach. Our analysis demonstrated that quantification of landscape pattern is critical to linking patterns to ecological processes and understanding how both affect landscape change. Our proof of concept indicated that ecological processes can correlate to landscape pattern and that ecosystem function changes significantly as pattern changes. However, the number of links between landscape metrics and ecological processes are highly variable. Extensively studied processes such as biodiversity can be linked to numerous landscape metrics. In contrast, correlations between sediment cycling and landscape pattern have only been evaluated for a limited number of metrics. We are incorporating these data into a relational database linking landscape and ecological patterns, processes and metrics. The database will be used to parameterize site-specific landscape evolution models projecting how landscape pattern will change as a result of future ecosystem restoration projects. The model is a spatially-explicit, grid-based model that projects changes in community composition based on changes in soil elevations. To capture scalar differences in landscape change, local and regional landscape metrics are analyzed at each time step and correlated with ecological processes to determine how ecosystem function changes with scale over time.

Integrating landscape system and meta-ecosystem frameworks to advance the understanding of ecosystem function in heterogeneous landscapes: An analysis on the carbon fluxes in the Northern Highlands Lake District (NHLD) of Wisconsin and Michigan.

PubMed

Yang, Haile; Chen, Jiakuan

2018-01-01

The successful integration of ecosystem ecology with landscape ecology would be conducive to understanding how landscapes function. There have been several attempts at this, with two main approaches: (1) an ecosystem-based approach, such as the meta-ecosystem framework and (2) a landscape-based approach, such as the landscape system framework. These two frameworks are currently disconnected. To integrate these two frameworks, we introduce a protocol, and then demonstrate application of the protocol using a case study. The protocol includes four steps: 1) delineating landscape systems; 2) classifying landscape systems; 3) adjusting landscape systems to meta-ecosystems and 4) integrating landscape system and meta-ecosystem frameworks through meta-ecosystems. The case study is the analyzing of the carbon fluxes in the Northern Highlands Lake District (NHLD) of Wisconsin and Michigan using this protocol. The application of this protocol revealed that one could follow this protocol to construct a meta-ecosystem and analyze it using the integrative framework of landscape system and meta-ecosystem frameworks. That is, one could (1) appropriately describe and analyze the spatial heterogeneity of the meta-ecosystem; (2) understand the emergent properties arising from spatial coupling of local ecosystems in the meta-ecosystem. In conclusion, this protocol is a useful approach for integrating the meta-ecosystem framework and the landscape system framework, which advances the describing and analyzing of the spatial heterogeneity and ecosystem function of interconnected ecosystems.

Integrating landscape system and meta-ecosystem frameworks to advance the understanding of ecosystem function in heterogeneous landscapes: An analysis on the carbon fluxes in the Northern Highlands Lake District (NHLD) of Wisconsin and Michigan

PubMed Central

Chen, Jiakuan

2018-01-01

The successful integration of ecosystem ecology with landscape ecology would be conducive to understanding how landscapes function. There have been several attempts at this, with two main approaches: (1) an ecosystem-based approach, such as the meta-ecosystem framework and (2) a landscape-based approach, such as the landscape system framework. These two frameworks are currently disconnected. To integrate these two frameworks, we introduce a protocol, and then demonstrate application of the protocol using a case study. The protocol includes four steps: 1) delineating landscape systems; 2) classifying landscape systems; 3) adjusting landscape systems to meta-ecosystems and 4) integrating landscape system and meta-ecosystem frameworks through meta-ecosystems. The case study is the analyzing of the carbon fluxes in the Northern Highlands Lake District (NHLD) of Wisconsin and Michigan using this protocol. The application of this protocol revealed that one could follow this protocol to construct a meta-ecosystem and analyze it using the integrative framework of landscape system and meta-ecosystem frameworks. That is, one could (1) appropriately describe and analyze the spatial heterogeneity of the meta-ecosystem; (2) understand the emergent properties arising from spatial coupling of local ecosystems in the meta-ecosystem. In conclusion, this protocol is a useful approach for integrating the meta-ecosystem framework and the landscape system framework, which advances the describing and analyzing of the spatial heterogeneity and ecosystem function of interconnected ecosystems. PMID:29415066

The impact of urban planning on land use and land cover in Pudong of Shanghai, China.

PubMed

Zhao, Bin; Nakagoshi, Nobukazu; Chen, Jia-kuan; Kong, Ling-yi

2003-03-01

Functional zones in cities constitute the most conspicuous components of newly developed urban area, and have been a hot spot for domestic and foreign investors in China, which not only show the expanse of urban space accompanied by the shifts both in landscape (from rural to urban) and land use (from less extensive to extensive), but also display the transformation of regional ecological functions. By using the theories and methods of landscape ecology, the structure of landscape and landscape ecological planning can be analyzed and evaluated for studying the urban functional zones' layout. In 1990, the Central Government of China declared to develop and open up Pudong New Area so as to promote economic development in Shanghai. Benefited from the advantages of Shanghai's location and economy, the government of Pudong New Area has successively built up 7 different functional zones over the past decade according to their functions and strategic goals. Based on the multi-spectral satellite imageries taken in 1990, 1997 and 2000, a landscape ecology analysis was carried out for Pudong New Area of Shanghai, supported by GIS technology. Green space (including croplands) and built-up area are the major factors considered in developing urban landscape. This paper was mainly concerned with the different spatial patterns and dynamic of green space, built-up areas and new buildings in different functional zones, influenced by different functional layouts and development strategies. The rapid urbanization in Pudong New Area resulted in a more homogeneous landscape. Agricultural landscape and suburban landscape were gradually replaced by urban landscape as the degree of urbanization increased. As consequence of urbanization in Pudong, not only built-up patches, but also newly-built patches and green patches merged into one large patch, which should be attributed to the construction policy of extensive green space as the urban development process in Pudong New Area. The shape of green area of 7 functional zones became more and more regular because of the horticultural needs in Shanghai urban planning. Some suggestions were finally made for the study of future urban planning and layout.

Multiscale analysis of restoration priorities for marine shoreline planning.

PubMed

Diefenderfer, Heida L; Sobocinski, Kathryn L; Thom, Ronald M; May, Christopher W; Borde, Amy B; Southard, Susan L; Vavrinec, John; Sather, Nichole K

2009-10-01

Planners are being called on to prioritize marine shorelines for conservation status and restoration action. This study documents an approach to determining the management strategy most likely to succeed based on current conditions at local and landscape scales. The conceptual framework based in restoration ecology pairs appropriate restoration strategies with sites based on the likelihood of producing long-term resilience given the condition of ecosystem structures and processes at three scales: the shorezone unit (site), the drift cell reach (nearshore marine landscape), and the watershed (terrestrial landscape). The analysis is structured by a conceptual ecosystem model that identifies anthropogenic impacts on targeted ecosystem functions. A scoring system, weighted by geomorphic class, is applied to available spatial data for indicators of stress and function using geographic information systems. This planning tool augments other approaches to prioritizing restoration, including historical conditions and change analysis and ecosystem valuation.

Impact of Plant Functional Types on Coherence Between Precipitation and Soil Moisture: A Wavelet Analysis

NASA Astrophysics Data System (ADS)

Liu, Qi; Hao, Yonghong; Stebler, Elaine; Tanaka, Nobuaki; Zou, Chris B.

2017-12-01

Mapping the spatiotemporal patterns of soil moisture within heterogeneous landscapes is important for resource management and for the understanding of hydrological processes. A critical challenge in this mapping is comparing remotely sensed or in situ observations from areas with different vegetation cover but subject to the same precipitation regime. We address this challenge by wavelet analysis of multiyear observations of soil moisture profiles from adjacent areas with contrasting plant functional types (grassland, woodland, and encroached) and precipitation. The analysis reveals the differing soil moisture patterns and dynamics between plant functional types. The coherence at high-frequency periodicities between precipitation and soil moisture generally decreases with depth but this is much more pronounced under woodland compared to grassland. Wavelet analysis provides new insights on soil moisture dynamics across plant functional types and is useful for assessing differences and similarities in landscapes with heterogeneous vegetation cover.

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.

CDMetaPOP: An individual-based, eco-evolutionary model for spatially explicit simulation of landscape demogenetics

USGS Publications Warehouse

Landguth, Erin L; Bearlin, Andrew; Day, Casey; Dunham, Jason B.

2016-01-01

1. Combining landscape demographic and genetics models offers powerful methods for addressing questions for eco-evolutionary applications.2. Using two illustrative examples, we present Cost–Distance Meta-POPulation, a program to simulate changes in neutral and/or selection-driven genotypes through time as a function of individual-based movement, complex spatial population dynamics, and multiple and changing landscape drivers.3. Cost–Distance Meta-POPulation provides a novel tool for questions in landscape genetics by incorporating population viability analysis, while linking directly to conservation applications.

Honey bee success predicted by landscape composition in Ohio, USA.

PubMed

Sponsler, D B; Johnson, R M

2015-01-01

Foraging honey bees (Apis mellifera L.) can routinely travel as far as several kilometers from their hive in the process of collecting nectar and pollen from floral patches within the surrounding landscape. Since the availability of floral resources at the landscape scale is a function of landscape composition, apiculturists have long recognized that landscape composition is a critical determinant of honey bee colony success. Nevertheless, very few studies present quantitative data relating colony success metrics to local landscape composition. We employed a beekeeper survey in conjunction with GIS-based landscape analysis to model colony success as a function of landscape composition in the State of Ohio, USA, a region characterized by intensive cropland, urban development, deciduous forest, and grassland. We found that colony food accumulation and wax production were positively related to cropland and negatively related to forest and grassland, a pattern that may be driven by the abundance of dandelion and clovers in agricultural areas compared to forest or mature grassland. Colony food accumulation was also negatively correlated with urban land cover in sites dominated by urban and agricultural land use, which does not support the popular opinion that the urban environment is more favorable to honey bees than cropland.

Analysis of Alaskan burn severity patterns using remotely sensed data

USGS Publications Warehouse

Duffy, P.A.; Epting, J.; Graham, J.M.; Rupp, T.S.; McGuire, A.D.

2007-01-01

Wildland fire is the dominant large-scale disturbance mechanism in the Alaskan boreal forest, and it strongly influences forest structure and function. In this research, patterns of burn severity in the Alaskan boreal forest are characterised using 24 fires. First, the relationship between burn severity and area burned is quantified using a linear regression. Second, the spatial correlation of burn severity as a function of topography is modelled using a variogram analysis. Finally, the relationship between vegetation type and spatial patterns of burn severity is quantified using linear models where variograms account for spatial correlation. These results show that: 1) average burn severity increases with the natural logarithm of the area of the wildfire, 2) burn severity is more variable in topographically complex landscapes than in flat landscapes, and 3) there is a significant relationship between burn severity and vegetation type in flat landscapes but not in topographically complex landscapes. These results strengthen the argument that differential flammability of vegetation exists in some boreal landscapes of Alaska. Additionally, these results suggest that through feedbacks between vegetation and burn severity, the distribution of forest vegetation through time is likely more stable in flat terrain than it is in areas with more complex topography. ?? IAWF 2007.

Connecting the Kinetics and Energy Landscape of tRNA Translocation on the Ribosome

PubMed Central

Whitford, Paul C.; Blanchard, Scott C.; Cate, Jamie H. D.; Sanbonmatsu, Karissa Y.

2013-01-01

Functional rearrangements in biomolecular assemblies result from diffusion across an underlying energy landscape. While bulk kinetic measurements rely on discrete state-like approximations to the energy landscape, single-molecule methods can project the free energy onto specific coordinates. With measures of the diffusion, one may establish a quantitative bridge between state-like kinetic measurements and the continuous energy landscape. We used an all-atom molecular dynamics simulation of the 70S ribosome (2.1 million atoms; 1.3 microseconds) to provide this bridge for specific conformational events associated with the process of tRNA translocation. Starting from a pre-translocation configuration, we identified sets of residues that collectively undergo rotary rearrangements implicated in ribosome function. Estimates of the diffusion coefficients along these collective coordinates for translocation were then used to interconvert between experimental rates and measures of the energy landscape. This analysis, in conjunction with previously reported experimental rates of translocation, provides an upper-bound estimate of the free-energy barriers associated with translocation. While this analysis was performed for a particular kinetic scheme of translocation, the quantitative framework is general and may be applied to energetic and kinetic descriptions that include any number of intermediates and transition states. PMID:23555233

Connecting the kinetics and energy landscape of tRNA translocation on the ribosome.

PubMed

Whitford, Paul C; Blanchard, Scott C; Cate, Jamie H D; Sanbonmatsu, Karissa Y

2013-01-01

Functional rearrangements in biomolecular assemblies result from diffusion across an underlying energy landscape. While bulk kinetic measurements rely on discrete state-like approximations to the energy landscape, single-molecule methods can project the free energy onto specific coordinates. With measures of the diffusion, one may establish a quantitative bridge between state-like kinetic measurements and the continuous energy landscape. We used an all-atom molecular dynamics simulation of the 70S ribosome (2.1 million atoms; 1.3 microseconds) to provide this bridge for specific conformational events associated with the process of tRNA translocation. Starting from a pre-translocation configuration, we identified sets of residues that collectively undergo rotary rearrangements implicated in ribosome function. Estimates of the diffusion coefficients along these collective coordinates for translocation were then used to interconvert between experimental rates and measures of the energy landscape. This analysis, in conjunction with previously reported experimental rates of translocation, provides an upper-bound estimate of the free-energy barriers associated with translocation. While this analysis was performed for a particular kinetic scheme of translocation, the quantitative framework is general and may be applied to energetic and kinetic descriptions that include any number of intermediates and transition states.

Nonequilibrium landscape theory of neural networks.

PubMed

Yan, Han; Zhao, Lei; Hu, Liang; Wang, Xidi; Wang, Erkang; Wang, Jin

2013-11-05

The brain map project aims to map out the neuron connections of the human brain. Even with all of the wirings mapped out, the global and physical understandings of the function and behavior are still challenging. Hopfield quantified the learning and memory process of symmetrically connected neural networks globally through equilibrium energy. The energy basins of attractions represent memories, and the memory retrieval dynamics is determined by the energy gradient. However, the realistic neural networks are asymmetrically connected, and oscillations cannot emerge from symmetric neural networks. Here, we developed a nonequilibrium landscape-flux theory for realistic asymmetrically connected neural networks. We uncovered the underlying potential landscape and the associated Lyapunov function for quantifying the global stability and function. 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. We applied our theory to rapid-eye movement sleep cycle. We identified the key regulation factors for function through global sensitivity analysis of landscape topography against wirings, which are in good agreements with experiments.

[Spatial characteristics analysis of Huizhou-Styled Village based on ideal ecosystem model and 3D landscape indices: A case in Chengkan, China].

PubMed

Yao, Meng Yuan; Yan, Shi Jiang; Wu, Yan Lan

2016-12-01

Huizhou-Styled Village is a typical representative of the traditional Chinese ancient villages. It preserves plentiful information of the regional culture and ecological connotation. The Huizhou-Style is the apotheosis of harmony between the Chinese ancient people and nature. The research and protection of Huizhou-Styled Village plays a very important role in fields of ecology, geography, architecture and esthetics. This paper took Chengkan Village of Anhui Province as an exa-mple, and proposed a new model of ideal ecosystem oriented in theories of Feng-shui and psychological field. The new method of characterizing 3D landscape index was introduced to explore the spatial patterns of Huizhou-Styled Village and the functionality of the composited landscape components in a quantitative way. The results indicated that, Chengkan Village showed a spatially composited pattern of "mountain-forest-village-river-forest". It formed an ideal settlement ring structure with human architecture in the center and natural landscape around in the horizontal and vertical horizons. The traditional method based on the projection distance caused the deviation of the landscape index, such as underestimating the area and distance of landscape patch. The 3D landscape index of average patch area was 6.7% higher than the 2D landscape index. The increasing rate ofarea proportion in 3D index was 1.0% higher than that of 2D index in forest lands. Area proportion of the other landscapes decreased, especially the artificial landscapes like construction and cropland landscapes. The area and perimeter metric were underestimated, whereas the shape metric and the diversity metric were overestimated. This caused the underestimation of the dominance of natural patches was underestimated and the overestimation of the dominance of artificial patches during the analysis of landscape pattern. The 3D landscape index showed that the natural elements and their combination in Chengkan Village ecosystem reflected better ecological function, the key elements and the composited landscape ecosystem preserved higher stability, connectivity and aggregation. The quantitative confirmation showed that the Huizhou-Styled Village represented by Chengkan Village is an ideal ecosystem.

Functional planning units for the management of an endangered Brazilian titi monkey.

PubMed

Gouveia, Sidney F; Souza-Alves, João Pedro; de Souza, Bruno B; Beltrão-Mendes, Raone; Jerusalinsky, Leandro; Ferrari, Stephen F

2017-05-01

Conservation practices in the tropics often rely on the data available for a few, better-known species and the adoption of an appropriate spatial scale. By defining a set of landscape units that account for critical aspects of the focal species, the information available on these conservation targets can support regional conservation policies. Here, we define and classify adjacent landscapes, termed planning units, to orientate management decisions within and among these landscapes, which are occupied by an endangered flagship primate species (Coimbra-Filho's titi monkey, Callicebus coimbrai) from eastern Brazil. We use landscape boundaries (highways and river systems), and a high-resolution map of forest remnants to identify continuous and manageable landscapes. We employed functional landscape metrics based on the species' dispersal ability and home range size to characterize and classify these landscapes. We classified planning units by scoring them according to a suite of selected metrics through a Principal Component Analysis. We propose 31 planning units, containing one to six C. coimbrai populations, most with low values of habitat availability, functional connectivity and carrying capacity, and a high degree of degradation. Due to this poor landscape configuration, basic management practices are recommendable. However, additional aspects of the landscapes and the populations they contain (e.g., matrix type and genetic variability) should improve the scheme, which will require a closer integration of research aims with socio-political strategies. Even so, our scheme should prove useful for the combination of information on conservation targets (i.e., focal species) with management strategies on an administrative scale. © 2017 Wiley Periodicals, Inc.

Adaptive Classification of Landscape Process and Function: An Integration of Geoinformatics and Self-Organizing Maps

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

Coleman, Andre M.

2009-07-17

The advanced geospatial information extraction and analysis capabilities of a Geographic Information System (GISs) and Artificial Neural Networks (ANNs), particularly Self-Organizing Maps (SOMs), provide a topology-preserving means for reducing and understanding complex data relationships in the landscape. The Adaptive Landscape Classification Procedure (ALCP) is presented as an adaptive and evolutionary capability where varying types of data can be assimilated to address different management needs such as hydrologic response, erosion potential, habitat structure, instrumentation placement, and various forecast or what-if scenarios. This paper defines how the evaluation and analysis of spatial and/or temporal patterns in the landscape can provide insight intomore » complex ecological, hydrological, climatic, and other natural and anthropogenic-influenced processes. Establishing relationships among high-dimensional datasets through neurocomputing based pattern recognition methods can help 1) resolve large volumes of data into a structured and meaningful form; 2) provide an approach for inferring landscape processes in areas that have limited data available but exhibit similar landscape characteristics; and 3) discover the value of individual variables or groups of variables that contribute to specific processes in the landscape. Classification of hydrologic patterns in the landscape is demonstrated.« less

Geometry analysis for landscape fragmentation in coastal areas of China

NASA Astrophysics Data System (ADS)

Zhang, Tianhai; Yu, Ning; Mu, Hongdu; Tuo, Tao

2017-08-01

In recent years, the continuous expansion of urban-transport networks in China has aggravated the fragmentation of regional landscapes and led to the degradation of multiple ecological functions. In this study, Geographic Information System (GIS) techniques, patch size of fragmentation geometry were used to identify and monitor spatial distribution patterns of landscape fragmentation due to urban-transport networks in Fujian Province. This network has caused serious damage to regional ecological functions, and risks to the persistence of animal populations and biodiversity. This analysis revealed that the smallest patch class (0-15 km2) occurred with a much greater frequency than all other larger patch sizes. In the coastal cities of Xiamen, Zhangzhou and Quanzhou, the percentage of the number of patches less than 300 km2 was higher than in the western cities of Nanping, Sanming and Longyan, and the percentage of the area of patches less than 300 km2 was also higher. Based on a holistic identification of the structure of the network and its landscape division, we found that: Fujian Province has a spatial pattern of landscape fragmentation, with less fragmentation in western and northern regions, and most fragmentation in southern and eastern regions. Coastal regions and areas close to the main transport routes were more seriously fragmented and contained most of the small patches.

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

PubMed Central

Liu, Jie; Jernigan, Robert L.

2015-01-01

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 Ca2+ 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. PMID:26723638

Thermal Infrared Remote Sensing for Analysis of Landscape Ecological Processes: Methods and Applications

NASA Technical Reports Server (NTRS)

Quattrochi, Dale A.; Luvall, Jeffrey C.

1998-01-01

Thermal Infrared (TIR) remote sensing data can provide important measurements of surface energy fluxes and temperatures, which are integral to understanding landscape processes and responses. One example of this is the successful application of TIR remote sensing data to estimate evapotranspiration and soil moisture, where results from a number of studies suggest that satellite-based measurements from TIR remote sensing data can lead to more accurate regional-scale estimates of daily evapotranspiration. With further refinement in analytical techniques and models, the use of TIR data from airborne and satellite sensors could be very useful for parameterizing surface moisture conditions and developing better simulations of landscape energy exchange over a variety of conditions and space and time scales. Thus, TIR remote sensing data can significantly contribute to the observation, measurement, and analysis of energy balance characteristics (i.e., the fluxes and redistribution of thermal energy within and across the land surface) as an implicit and important aspect of landscape dynamics and landscape functioning. The application of TIR remote sensing data in landscape ecological studies has been limited, however, for several fundamental reasons that relate primarily to the perceived difficulty in use and availability of these data by the landscape ecology community, and from the fragmentation of references on TIR remote sensing throughout the scientific literature. It is our purpose here to provide evidence from work that has employed TIR remote sensing for analysis of landscape characteristics to illustrate how these data can provide important data for the improved measurement of landscape energy response and energy flux relationships. We examine the direct or indirect use of TIR remote sensing data to analyze landscape biophysical characteristics, thereby offering some insight on how these data can be used more robustly to further the understanding and modeling of landscape ecological processes.

Landscape-scale processes influence riparian plant composition along a regulated river

USGS Publications Warehouse

Palmquist, Emily C.; Ralston, Barbara; Merritt, David M.; Shafroth, Patrick B.

2018-01-01

Hierarchical frameworks are useful constructs when exploring landscape- and local-scale factors affecting patterns of vegetation in riparian areas. In drylands, which have steep environmental gradients and high habitat heterogeneity, landscape-scale variables, such as climate, can change rapidly along a river's course, affecting the relative influence of environmental variables at different scales. To assess how landscape-scale factors change the structure of riparian vegetation, we measured riparian vegetation composition along the Colorado River through Grand Canyon, determined which factors best explain observed changes, identified how richness and functional diversity vary, and described the implications of our results for river management. Cluster analysis identified three divergent floristic groups that are distributed longitudinally along the river. These groups were distributed along gradients of elevation, temperature and seasonal precipitation, but were not associated with annual precipitation or local-scale factors. Species richness and functional diversity decreased as a function of distance downstream showing that changing landscape-scale factors result in changes to ecosystem characteristics. Species composition and distribution remain closely linked to seasonal precipitation and temperature. These patterns in floristic composition in a semiarid system inform management and provide insights into potential future changes as a result of shifts in climate and changes in flow management.

Nonequilibrium landscape theory of neural networks

PubMed Central

Yan, Han; Zhao, Lei; Hu, Liang; Wang, Xidi; Wang, Erkang; Wang, Jin

2013-01-01

The brain map project aims to map out the neuron connections of the human brain. Even with all of the wirings mapped out, the global and physical understandings of the function and behavior are still challenging. Hopfield quantified the learning and memory process of symmetrically connected neural networks globally through equilibrium energy. The energy basins of attractions represent memories, and the memory retrieval dynamics is determined by the energy gradient. However, the realistic neural networks are asymmetrically connected, and oscillations cannot emerge from symmetric neural networks. Here, we developed a nonequilibrium landscape–flux theory for realistic asymmetrically connected neural networks. We uncovered the underlying potential landscape and the associated Lyapunov function for quantifying the global stability and function. 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. We applied our theory to rapid-eye movement sleep cycle. We identified the key regulation factors for function through global sensitivity analysis of landscape topography against wirings, which are in good agreements with experiments. PMID:24145451

A landscape character assessment of three terraced areas in Campania region, Italy

NASA Astrophysics Data System (ADS)

Gravagnuolo, Antonia; Ronza, Maria; Di Martino, Ferdinando; De Rosa, Fortuna

2017-04-01

Agricultural terraces represent the territorial structure of many cultural landscapes in the Campania region, Italy. Historic urban/rural settlements and hydraulic-agrarian systems have been developed on mountains and hills, producing diverse cultural landscapes depending on the specific geological, pedological and geomorphological characteristics, which influenced the character and functions of terraces. These unique landscapes are multi-functional and provide many ecosystem services: provisioning (food, water retention, building materials); regulating and maintenance (hydrogeological stability, soil fertility, protection from soil erosion, maintenance of genetic diversity, habitat); cultural services (heritage and traditional knowledge conservation, tourism and recreation, spiritual experience, education, aesthetic quality). Three terraced landscapes in Campania are analysed, which present a rich diversity in the geological structure and formal/functional characteristics: the Roccamonfina vulcanic area, a highly fertile and lapillous soil; the Monte di Bulgheria, a clay-rich area; and finally the well-known UNESCO World Heritage site of the Amalfi Coast, a calcareous, steep rock faced area. A landscape character assessment of the three sites is processed, identifying the biophysical structure of the sites, natural systems and land use, and cultural and anthropic elements. Terraced landscapes in Campania can be regenerated, taking again an active social and economic role for the society, enhancing their multifunctionality as a key source of wellbeing. Ecosystem services are mapped and evaluated to assess benefits and costs in a multidimensional framework. Spatial analysis in GIS environment supports this process, providing a decision-support tool for mapping and assessment of terraced landscapes, to convert their actual and potential value into a resource of economic sustainable development.

Testing Adaptive Hypotheses of Convergence with Functional Landscapes: A Case Study of Bone-Cracking Hypercarnivores

PubMed Central

Tseng, Zhijie Jack

2013-01-01

Morphological convergence is a well documented phenomenon in mammals, and adaptive explanations are commonly employed to infer similar functions for convergent characteristics. I present a study that adopts aspects of theoretical morphology and engineering optimization to test hypotheses about adaptive convergent evolution. Bone-cracking ecomorphologies in Carnivora were used as a case study. Previous research has shown that skull deepening and widening are major evolutionary patterns in convergent bone-cracking canids and hyaenids. A simple two-dimensional design space, with skull width-to-length and depth-to-length ratios as variables, was used to examine optimized shapes for two functional properties: mechanical advantage (MA) and strain energy (SE). Functionality of theoretical skull shapes was studied using finite element analysis (FEA) and visualized as functional landscapes. The distribution of actual skull shapes in the landscape showed a convergent trend of plesiomorphically low-MA and moderate-SE skulls evolving towards higher-MA and moderate-SE skulls; this is corroborated by FEA of 13 actual specimens. Nevertheless, regions exist in the landscape where high-MA and lower-SE shapes are not represented by existing species; their vacancy is observed even at higher taxonomic levels. Results highlight the interaction of biomechanical and non-biomechanical factors in constraining general skull dimensions to localized functional optima through evolution. PMID:23734244

Status analysis and vision on urban landscape planning-take Chengdu city as an example

NASA Astrophysics Data System (ADS)

Liu, Hanyun

2017-10-01

Appropriate urban planning can forge a proper and safe city framework so as to achieve safety, health, convenience and comfort. A personalized urban planning is a name card of city development which can demonstrate the unique culture and function of a city. This essay concludes the concept and principles of urban landscape planning; takes the status of landscape planning in Chengdu City as an object, concludes its merits and demerits and offers solutions to the weak points; looks into the future of urban landscape planning so as to offer theoretical support for the development of an ecologically and environmentally friendly low-carbon city.

Effigy mound sites as cultural landscapes: A geophysical spatial analysis of two Late Woodland sites in southeastern Wisconsin

NASA Astrophysics Data System (ADS)

Kaufmann, Kira E.

This dissertation is a spatial analysis of a class of sacred sites known as Effigy Mounds during the Late Woodland period in southeast Wisconsin, circa A.D. 700--1100. Effigy Mounds are earthworks in the shape of animals, conical, linear, or geometric shapes. The research is focused on the upper Rock River Drainage in southern Wisconsin, a region where Effigy Mounds are very common. Although there are many theories concerning the meanings of Effigy Mounds, there is no cohesive description of Effigy Mounds as landscape elements and their function in the use of space by Late Woodland people. This research connects cultural and cognitive aspects of Native American cosmology with physical manifestations on the landscape. Effigy Mounds are examined from ideological and physical perspectives that are not mutually exclusive. Effigy Mounds are viewed as signifiers with multiple levels of function and meaning including sacred space, territorial markers, and mechanisms of social control and cohesion. Investigation at two Late Woodland Effigy Mound sites, Indian Mounds County Park in Jefferson County and Nitschke Mounds County Park in Dodge County, shows that landscape utilization varied significantly within and among Effigy Mound sites. An alternative model to understand Late Woodland Effigy Mound sites as ritual landscapes explores these features, their distribution across space, and the connection to internal site structures by synthesizing multidisciplinary data from historical ethnographic accounts, previous archaeological surveys, and new geophysical data. This multidisciplinary approach provides an example applicable to other landscape studies.

A comparison of regression methods for model selection in individual-based landscape genetic analysis.

PubMed

Shirk, Andrew J; Landguth, Erin L; Cushman, Samuel A

2018-01-01

Anthropogenic migration barriers fragment many populations and limit the ability of species to respond to climate-induced biome shifts. Conservation actions designed to conserve habitat connectivity and mitigate barriers are needed to unite fragmented populations into larger, more viable metapopulations, and to allow species to track their climate envelope over time. Landscape genetic analysis provides an empirical means to infer landscape factors influencing gene flow and thereby inform such conservation actions. However, there are currently many methods available for model selection in landscape genetics, and considerable uncertainty as to which provide the greatest accuracy in identifying the true landscape model influencing gene flow among competing alternative hypotheses. In this study, we used population genetic simulations to evaluate the performance of seven regression-based model selection methods on a broad array of landscapes that varied by the number and type of variables contributing to resistance, the magnitude and cohesion of resistance, as well as the functional relationship between variables and resistance. We also assessed the effect of transformations designed to linearize the relationship between genetic and landscape distances. We found that linear mixed effects models had the highest accuracy in every way we evaluated model performance; however, other methods also performed well in many circumstances, particularly when landscape resistance was high and the correlation among competing hypotheses was limited. Our results provide guidance for which regression-based model selection methods provide the most accurate inferences in landscape genetic analysis and thereby best inform connectivity conservation actions. Published 2017. This article is a U.S. Government work and is in the public domain in the USA.

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.

Land use-based landscape planning and restoration in mine closure areas.

PubMed

Zhang, Jianjun; Fu, Meichen; Hassani, Ferri P; Zeng, Hui; Geng, Yuhuan; Bai, Zhongke

2011-05-01

Landscape planning and restoration in mine closure areas is not only an inevitable choice to sustain mining areas but also an important path to maximize landscape resources and to improve ecological function in mine closure areas. The analysis of the present mine development shows that many mines are unavoidably facing closures in China. This paper analyzes the periodic impact of mining activities on landscapes and then proposes planning concepts and principles. According to the landscape characteristics in mine closure areas, this paper classifies available landscape resources in mine closure areas into the landscape for restoration, for limited restoration and for protection, and then summarizes directions for their uses. This paper establishes the framework of spatial control planning and design of landscape elements from "macro control, medium allocation and micro optimization" for the purpose of managing and using this kind of special landscape resources. Finally, this paper applies the theories and methods to a case study in Wu'an from two aspects: the construction of a sustainable land-use pattern on a large scale and the optimized allocation of typical mine landscape resources on a small scale.

Landscape biogeochemistry reflected in shifting distributions of chemical traits in the Amazon forest canopy

NASA Astrophysics Data System (ADS)

Asner, Gregory P.; Anderson, Christopher B.; Martin, Roberta E.; Tupayachi, Raul; Knapp, David E.; Sinca, Felipe

2015-07-01

Tropical forest functional diversity, which is a measure of the diversity of organismal interactions with the environment, is poorly understood despite its importance for linking evolutionary biology to ecosystem biogeochemistry. Functional diversity is reflected in functional traits such as the concentrations of different compounds in leaves or the density of leaf mass, which are related to plant activities such as plant defence, nutrient cycling, or growth. In the Amazonian lowlands, river movement and microtopography control nutrient mobility, which may influence functional trait distributions. Here we use airborne laser-guided imaging spectroscopy to develop maps of 16 forest canopy traits, throughout four large landscapes that harbour three common forest community types on the Madre de Dios and Tambopata rivers in southwestern Amazonia. Our maps, which are based on quantitative chemometric analysis of forest canopies with visible-to-near infrared (400-2,500 nm) spectroscopy, reveal substantial variation in canopy traits and their distributions within and among forested landscapes. Forest canopy trait distributions are arranged in a nested pattern, with location along rivers controlling trait variation between different landscapes, and microtopography controlling trait variation within landscapes. We suggest that processes of nutrient deposition and depletion drive increasing phosphorus limitation, and a corresponding increase in plant defence, in an eastward direction from the base of the Andes into the Amazon Basin.

Perception and landscape: conceptions and misconceptions

Treesearch

Stephen Kaplan

1979-01-01

The focus here is on a functional approach to landscape aesthetics. People's reactions are viewed in terms of what sense they are able to make of the scene and what interest they are able to find in it. This analysis applies first to the two-dimensional space of the "picture plane," where the assessment is in terms of coherence and complexity. In...

Land-use change in oil palm dominated tropical landscapes-An agent-based model to explore ecological and socio-economic trade-offs.

PubMed

Dislich, Claudia; Hettig, Elisabeth; Salecker, Jan; Heinonen, Johannes; Lay, Jann; Meyer, Katrin M; Wiegand, Kerstin; Tarigan, Suria

2018-01-01

Land-use changes have dramatically transformed tropical landscapes. We describe an ecological-economic land-use change model as an integrated, exploratory tool used to analyze how tropical land-use change affects ecological and socio-economic functions. The model analysis seeks to determine what kind of landscape mosaic can improve the ensemble of ecosystem functioning, biodiversity, and economic benefit based on the synergies and trade-offs that we have to account for. More specifically, (1) how do specific ecosystem functions, such as carbon storage, and economic functions, such as household consumption, relate to each other? (2) How do external factors, such as the output prices of crops, affect these relationships? (3) How do these relationships change when production inefficiency differs between smallholder farmers and learning is incorporated? We initialize the ecological-economic model with artificially generated land-use maps parameterized to our study region. The economic sub-model simulates smallholder land-use management decisions based on a profit maximization assumption. Each household determines factor inputs for all household fields and decides on land-use change based on available wealth. The ecological sub-model includes a simple account of carbon sequestration in above-ground and below-ground vegetation. We demonstrate model capabilities with results on household consumption and carbon sequestration from different output price and farming efficiency scenarios. The overall results reveal complex interactions between the economic and ecological spheres. For instance, model scenarios with heterogeneous crop-specific household productivity reveal a comparatively high inertia of land-use change. Our model analysis even shows such an increased temporal stability in landscape composition and carbon stocks of the agricultural area under dynamic price trends. These findings underline the utility of ecological-economic models, such as ours, to act as exploratory tools which can advance our understanding of the mechanisms underlying the trade-offs and synergies of ecological and economic functions in tropical landscapes.

Places of Faith: A Reflection on Landscape of Manila Cathedral Plaza de Roma and Istiqlal Mosque Sacred Grounds of Jakarta

NASA Astrophysics Data System (ADS)

Pujalte, MM; Navarra, N.

2017-10-01

Crossing boundaries of faith from Manila to Jakarta, this study is to classify the open spaces in their sacred grounds according to its characteristics, elements, use of space and hierarchy of importance in landscape design approach. The reflection of their religious landscape in preserving the traditional, and exploring the non-traditional aspect of their landscape design in global setting is carried out thru a spatial analysis for Plaza de Roma of Manila Cathedral and the sacred grounds of Istiqlal Mosque. The design framework would tackle: concepts, planning approach, functional symbolic values, and aesthetics used. The data and information are all examined based on observation, historical background, analyses, and literature content in determining spatial functions. Finally, when results are completed, this will give a better understanding on the importance of open areas in Manila and Jakarta’s sacred spaces; paving way for a better sense of comfort in spiritual contemplation. This will also help reveal the commonalities in spiritual practices between Islam and Christianity, and the role of landscape in their religion and faith.

Measures of safeguard and rehabilitation for landscape protection planning: a qualitative approach based on diversity indicators.

PubMed

La Rosa, Daniele; Privitera, Riccardo; Martinico, Francesco; La Greca, Paolo

2013-09-01

Maintaining existing levels of landscape diversity is becoming more and more important for planning considering the increasing pressures on agricultural ecosystems due to soil sealing, sprawl processes and intensive agriculture. Norms for land-use regulation and measures for landscape Safeguard and Rehabilitation have to take into consideration these threats in landscape planning. Evaluating the diversity of agricultural ecosystems is a fundamental step for proposing sound approaches to planning and managing both soil and landscape, as well as maintaining the related ecosystem services. The paper proposes a method aimed at the qualitative evaluation of spatial diversity of agricultural landscapes using a reduced set of ecological indicators based on land-use vector data. Indicators are calculated for defined landscape units characterized by landscape homogeneity. GIS geoprocessing and spatial analysis functions are employed. The study area is the Province of Enna in Sicily (Italy), which is characterized by cultivation mosaics in its southern region, cereal cultivation in the central region and prevailing natural environments in the northern region. Results from the indicator calculations are used to define measures to be included in a Landscape Protection Plan. Safeguard and Rehabilitation measures are introduced, which link indicator scores to planning protection aims. The results highlight the relevance of some agricultural mosaics in proximity to streams and seasonal fluvial environments, where some undamaged natural environments are still present. For these areas, specific landscape safeguard measures are proposed to preserve their diversity features together with their original agricultural functions. The work shows that even with a reduced number of indicators, a differentiated set of measures can be proposed for a Landscape Protection Plan. Copyright © 2013 Elsevier Ltd. All rights reserved.

Landscape approach to the formation of the ecological frame of Moscow

NASA Astrophysics Data System (ADS)

Nizovtsev, Vyacheslav; Natalia, Erman

2015-04-01

The territory of Moscow, in particular in its former borders, is distinct for its strong transformation of the natural properties of virtually all types of landscape complexes. The modern landscape structure is characterized by fragmentation of natural land cover. Natural and quasinatural (natural and anthropogenic) landscape complexes with preserved natural structure are represented by isolated areas and occupy small areas. During recent years landscape diversity in general and biodiversity in particular have been rapidly declining, and many of the natural landscape complexes are under ever-increasing degradation. Ecological balance is broken, and preserved natural landscapes are not able to maintain it. Effective territorial organization of Moscow and the rational use of its territory are impossible without taking into account the natural component of the city as well as the properties and potential of the landscape complexes that integrate all natural features in specific areas. The formation of the ecological framework of the city is particularly important. It should be a single system of interrelated and complementary components that make up a single environmental space: habitat-forming cores (junctions), ecological corridors and elements of environmental infrastructure. Systemic unity of the environmental framework can support the territorial ecological compensation where a break of the ecological functions of one part of the system is compensated by maintaining or restoring them in another part and contribute to the polarization of incompatible types of land use. Habitat-forming cores should include as mandatory parts all the specifically protected natural areas (SPNAs), particularly valuable landscape complexes, as well as preserved adjacent forest areas. Their most important function should be to maintain resources and area reproducing abilities of landscapes, landscape diversity and biodiversity. Ecological corridors which perform environmental and operating transit functions should include unified landscape systems of river valleys, their hollow-beam upstreams and drained lows. The most important elements of environmental infrastructure include the most valuable forest and wetland complexes, springs and other landscape and aquatic complexes, cultural and historical landscape complexes, landscape complexes with high concentration of cultural heritage sites, sites of natural and green areas with great potential of natural and recreational resources, natural and recreational parks, natural monuments. They can serve as centers of landscape and biological diversity and perform partial transit (migration) and buffer functions. The territory of the ecological framework can be used for strictly regulated or limited recreation (tourism, short leisure). The adjacent natural and green spaces and natural parks may play a buffer role for the SPNAs and valuable landscape complexes. The spatial pattern of the landscape complexes of Moscow allows to create a single ecological framework based on the landscape, distinct for its interrelated and complementary components. Its basis may be consisted of uniform landscape complexes of valley outwash plains and river valleys, their hollow-beam upstreams and drained lows which perform system forming, environmental and transit functions. In the plan river valleys and small erosional forms are as if enclosed in the gullies and constitute single paradynamic systems unified by lateral flows. Therefore not only the edges of river valleys, but also the rear seams of the valley outwash plains should become important natural boundaries, limiting urban development of the area. Their most important functional feature is that they serve as local collectors and surface water runoff channels. These landscape complexes are distinct for most dynamic natural processes and thus negative exogenous processes. The authors have drawn indigenous (conditionally restored) and modern landscapes of Moscow on a scale of 1: 50,000 and on their basis an ecological framework map of Moscow. These maps are an important natural basis for the analysis of conditions and identification of limiting factors of the urban development of the big city.

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

[Landscape classification: research progress and development trend].

PubMed

Liang, Fa-Chao; Liu, Li-Ming

2011-06-01

Landscape classification is the basis of the researches on landscape structure, process, and function, and also, the prerequisite for landscape evaluation, planning, protection, and management, directly affecting the precision and practicability of landscape research. This paper reviewed the research progress on the landscape classification system, theory, and methodology, and summarized the key problems and deficiencies of current researches. Some major landscape classification systems, e. g. , LANMAP and MUFIC, were introduced and discussed. It was suggested that a qualitative and quantitative comprehensive classification based on the ideology of functional structure shape and on the integral consideration of landscape classification utility, landscape function, landscape structure, physiogeographical factors, and human disturbance intensity should be the major research directions in the future. The integration of mapping, 3S technology, quantitative mathematics modeling, computer artificial intelligence, and professional knowledge to enhance the precision of landscape classification would be the key issues and the development trend in the researches of landscape classification.

Protection of Landscape Values of Historical Post Military Objects - Complexes in Spatial, Urban and Architectural Planning of Polish Cities

NASA Astrophysics Data System (ADS)

Gawryluk, Dorota; Zagroba, Marek

2017-12-01

Within the borders of modern Poland there are numerous barracks units erected at the turn of the 19th and 20th centuries by the invaders from Russia, Austria and Prussia. Former barracks are a clear element of the history of the place. Historical complexes have a strong influence on the urban landscape and on building their former and contemporary identity. The analysis of functional and landscape absorption of postmodern complexes allows for their adaptation and modern use without limiting the readability of historical values. For this reason, their landscape should be protected comprehensively within the scope of subsequent exposure scales. The aim of the work is to justify the conditions of comprehensive protection of the fortified landscape of the former barracks of the former Russian partition in the landscape of contemporary Polish cities. The article contains a review of the literature on the protection, supplement and access to fortified buildings from the turn of the 19th and 20th centuries in contemporary Poland. A review of current research conducted at various academic centres in Poland, concerning the exposition of fortified buildings in the landscape, is presented. Particular attention was paid to the scales and forms of exposition, proposed for the fortifications and barracks. The paper presents justification for the protection of barracks complexes from the turn of the 19th and 20th centuries in the landscape of Polish cities of the former Russian partition area. Protection of the landscape was proposed in the following scales: superregional, landscape (panorama of the centre), urban (urban structure of the complex in the context of the urban space), architectural and landscape interiors of the complex (WAK) such as alleys, alarm squares, greenery) and detail (view of the building from the outside), interior of the building (characteristic interior spaces, e.g. home chapels, staircases). Taking account of exposures analysis of individual scales should result in appropriate records at all levels of planning documents to protect the fortified landscape of the historic barracks. The article points to the use of greenery as a means to correct barracks exposures and to improve the standard of using historic complexes for new, contemporary functions.

Modeling the Effects of Hydrogeomorphology and Climactic Factors on Nitrogen, Phosphorus, and Greenhouse Gas Dynamics in Riparian Zones.

NASA Astrophysics Data System (ADS)

Hassanzadeh, Y.; Vidon, P.; Gold, A.; Pradhanang, S. M.; Addy, K.

2017-12-01

Vegetated riparian zones are often considered for use as best management practices to mitigate the impacts of agriculture on water quality. However, riparian zones can also be a source of greenhouse gases and their influence on water quality varies depending on landscape hydrogeomorphic characteristics and climate. Methods used to evaluate riparian zone functions include conceptual models, and spatially explicit and process based models (REMM), but very few attempts have been made to connect riparian zone characteristics with function using easily accessible landscape scale data. Here, we present comprehensive statistical models that can be used to assess riparian zone functions with easily obtainable landscape-scale hydrogeomorphic attributes and climate data. Models were developed from a database spanning 88 years and 36 sites. Statistical methods including principal component analysis and stepwise regression were used to reduced data dimensionality and identify significant predictors. Models were validated using additional data collected from scientific literature. The 8 models developed connect landscape characteristics to nitrogen and phosphorus concentration and removal (1-4), greenhouse gas emissions (5-7), and water table depth (8). Results show the range of influence that various climate and landscape characteristics have on riparian zone functions, and the tradeoffs that exist with regards to nitrogen, phosphorous, and greenhouse gases. These models will help reduce the need for extensive field measurements and help scientists and land managers make more informed decisions regarding the use of riparian zones for water quality management.

Exploring Energy Landscapes

NASA Astrophysics Data System (ADS)

Wales, David J.

2018-04-01

Recent advances in the potential energy landscapes approach are highlighted, including both theoretical and computational contributions. Treating the high dimensionality of molecular and condensed matter systems of contemporary interest is important for understanding how emergent properties are encoded in the landscape and for calculating these properties while faithfully representing barriers between different morphologies. The pathways characterized in full dimensionality, which are used to construct kinetic transition networks, may prove useful in guiding such calculations. The energy landscape perspective has also produced new procedures for structure prediction and analysis of thermodynamic properties. Basin-hopping global optimization, with alternative acceptance criteria and generalizations to multiple metric spaces, has been used to treat systems ranging from biomolecules to nanoalloy clusters and condensed matter. This review also illustrates how all this methodology, developed in the context of chemical physics, can be transferred to landscapes defined by cost functions associated with machine learning.

Indicators of hydrological, biogeochemical and ecological integrity for estimating potential loss of ecosystem services from wetlands on domesticated landscapes

NASA Astrophysics Data System (ADS)

Creed, I. F.; Aldred, D.; Spargo, A.; Bayley, S.

2012-12-01

Wetlands are being lost at an alarming rate in the prairie pothole landscape of North America. The full consequence of this loss is not fully understood or recognized due to (1) inadequate or incomplete wetland inventories (with mapping emphasizing permanent and not ephemeral wetlands, and only capturing "easy to observe" wetland area defined by open water and not the true dynamic wetland extent defined by saturated soils), and (2) lack of appropriate theoretical frameworks to assess the functions and benefits of these wetlands. We present a theoretical framework that integrates indicators to estimate functions and benefits of wetland integrity in central Alberta. We establish indicators using the principles that are representative of the dominant processes operating on the landscape, are simple and are scalable. While some of these indicators may be widely recognized, their implementation is often not comprehensive or complete. First, we develop an automated method for fine scale mapping of permanent and ephemeral wetlands from a fusion of high-resolution elevation data and aerial photography. Second, we estimate historic wetland loss over the past 50 years during which intensive domestication of the landscape occurred by modeling the distribution of wetlands in an undisturbed landscape using area-frequency power functions and calculating the difference in the actual wetland inventory. Third, we define relative wetland assessment units using cluster analysis of hydrological and ecological variables, including climate, geology, topography, soils and land use/land covers. Fourth, for each assessment unit we define indicators of functions and benefits of aquatic ecosystem services including water storage (surface and subsurface), phosphorus retention, nitrate removal, sediment retention, ecological health/biodiversity and human use, and then use practical strategies rooted in the fusion of digital terrain analysis and remote sensing techniques to measure and monitor these indicators over the past years. For a time series of wetlands loss we derive these indicators of functions and benefits to estimate changes in the provision of specific aquatic ecosystem services on the landscape. Last, we develop formulae for integrating these indicators to determine whether a specific wetland or wetland complex should be prioritized for conservation, exemplifying potential trade-offs among ecosystem services in setting conservation targets on this wetland dominated landscapes. The proposed theoretical framework evolved from close collaboration between scientists and resource managers, and will inform those engaged in developing wetland policies for a broad range of jurisdictions.

State of the Art of the Landscape Architecture Spatial Data Model from a Geospatial Perspective

NASA Astrophysics Data System (ADS)

Kastuari, A.; Suwardhi, D.; Hanan, H.; Wikantika, K.

2016-10-01

Spatial data and information had been used for some time in planning or landscape design. For a long time, architects were using spatial data in the form of topographic map for their designs. This method is not efficient, and it is also not more accurate than using spatial analysis by utilizing GIS. Architects are sometimes also only accentuating the aesthetical aspect for their design, but not taking landscape process into account which could cause the design could be not suitable for its use and its purpose. Nowadays, GIS role in landscape architecture has been formalized by the emergence of Geodesign terminology that starts in Representation Model and ends in Decision Model. The development of GIS could be seen in several fields of science that now have the urgency to use 3 dimensional GIS, such as in: 3D urban planning, flood modeling, or landscape planning. In this fields, 3 dimensional GIS is able to support the steps in modeling, analysis, management, and integration from related data, that describe the human activities and geophysics phenomena in more realistic way. Also, by applying 3D GIS and geodesign in landscape design, geomorphology information can be better presented and assessed. In some research, it is mentioned that the development of 3D GIS is not established yet, either in its 3D data structure, or in its spatial analysis function. This study literature will able to accommodate those problems by providing information on existing development of 3D GIS for landscape architecture, data modeling, the data accuracy, representation of data that is needed by landscape architecture purpose, specifically in the river area.

Two-dimensional gap analysis: a tool for efficient conservation planning and biodiversity policy implementation.

PubMed

Angelstam, Per; Mikusiński, Grzegorz; Rönnbäck, Britt-Inger; Ostman, Anders; Lazdinis, Marius; Roberge, Jean-Michel; Arnberg, Wolter; Olsson, Jan

2003-12-01

The maintenance of biodiversity by securing representative and well-connected habitat networks in managed landscapes requires a wise combination of protection, management, and restoration of habitats at several scales. We suggest that the integration of natural and social sciences in the form of "Two-dimensional gap analysis" is an efficient tool for the implementation of biodiversity policies. The tool links biologically relevant "horizontal" ecological issues with "vertical" issues related to institutions and other societal issues. Using forest biodiversity as an example, we illustrate how one can combine ecological and institutional aspects of biodiversity conservation, thus facilitating environmentally sustainable regional development. In particular, we use regional gap analysis for identification of focal forest types, habitat modelling for ascertaining the functional connectivity of "green infrastructures", as tools for the horizontal gap analysis. For the vertical dimension we suggest how the social sciences can be used for assessing the success in the implementation of biodiversity policies in real landscapes by identifying institutional obstacles while implementing policies. We argue that this interdisciplinary approach could be applied in a whole range of other environments including other terrestrial biota and aquatic ecosystems where functional habitat connectivity, nonlinear response to habitat loss and a multitude of economic and social interests co-occur in the same landscape.

Management intensity at field and landscape levels affects the structure of generalist predator communities.

PubMed

Rusch, Adrien; Birkhofer, Klaus; Bommarco, Riccardo; Smith, Henrik G; Ekbom, Barbara

2014-07-01

Agricultural intensification is recognised as a major driver of biodiversity loss in human-modified landscapes. Several agro-environmental measures at different spatial scales have been suggested to mitigate the negative impact of intensification on biodiversity and ecosystem services. The effect of these measures on the functional structure of service-providing communities remains, however, largely unexplored. Using two distinct landscape designs, we examined how the management options of organic farming at the field scale and crop diversification at the landscape level affect the taxonomic and functional structure of generalist predator communities and how these effects vary along a landscape complexity gradient. Organic farming as well as landscapes with longer and more diversified crop rotations enhanced the activity-density of spiders and rove beetles, but not the species richness or evenness. Our results indicate that the two management options affected the functional composition of communities, as they primarily enhanced the activity-density of functionally similar species. The two management options increased the functional similarity between spider species in regards to hunting mode and habitat preference. Organic farming enhanced the functional similarity of rove beetles. Management options at field and landscape levels were generally more important predictors of community structure when compared to landscape complexity. Our study highlights the importance of considering the functional composition of generalist predators in order to understand how agro-environmental measures at various scales shape community assemblages and ecosystem functioning in agricultural landscapes.

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

An Integrative Platform for Three-dimensional Quantitative Analysis of Spatially Heterogeneous Metastasis Landscapes

NASA Astrophysics Data System (ADS)

Guldner, Ian H.; Yang, Lin; Cowdrick, Kyle R.; Wang, Qingfei; Alvarez Barrios, Wendy V.; Zellmer, Victoria R.; Zhang, Yizhe; Host, Misha; Liu, Fang; Chen, Danny Z.; Zhang, Siyuan

2016-04-01

Metastatic microenvironments are spatially and compositionally heterogeneous. This seemingly stochastic heterogeneity provides researchers great challenges in elucidating factors that determine metastatic outgrowth. Herein, we develop and implement an integrative platform that will enable researchers to obtain novel insights from intricate metastatic landscapes. Our two-segment platform begins with whole tissue clearing, staining, and imaging to globally delineate metastatic landscape heterogeneity with spatial and molecular resolution. The second segment of our platform applies our custom-developed SMART 3D (Spatial filtering-based background removal and Multi-chAnnel forest classifiers-based 3D ReconsTruction), a multi-faceted image analysis pipeline, permitting quantitative interrogation of functional implications of heterogeneous metastatic landscape constituents, from subcellular features to multicellular structures, within our large three-dimensional (3D) image datasets. Coupling whole tissue imaging of brain metastasis animal models with SMART 3D, we demonstrate the capability of our integrative pipeline to reveal and quantify volumetric and spatial aspects of brain metastasis landscapes, including diverse tumor morphology, heterogeneous proliferative indices, metastasis-associated astrogliosis, and vasculature spatial distribution. Collectively, our study demonstrates the utility of our novel integrative platform to reveal and quantify the global spatial and volumetric characteristics of the 3D metastatic landscape with unparalleled accuracy, opening new opportunities for unbiased investigation of novel biological phenomena in situ.

Associations between forest characteristics and socio-economic development: a case study from Portugal.

PubMed

Ribeiro, Sónia Carvalho; Lovett, Andrew

2009-07-01

The integration of socio-economic and environmental objectives is a major challenge in developing strategies for sustainable landscapes. We investigated associations between socio-economic variables, landscape metrics and measures of forest condition in the context of Portugal. The main goals of the study were to 1) investigate relationships between forest conditions and measures of socio-economic development at national and regional scales, 2) test the hypothesis that a systematic variation in forest landscape metrics occurs according to the stage of socio-economic development and, 3) assess the extent to which landscape metrics can inform strategies to enhance forest sustainability. A ranking approach and statistical techniques such as Principal Component Analysis were used to achieve these objectives. Relationships between socio-economic characteristics, landscape metrics and measures of forest condition were only significant in the regional analysis of municipalities in Northern Portugal. Landscape metrics for different tree species displayed significant variations across socio-economic groups of municipalities and these differences were consistent with changes in characteristics suggested by the forest transition model. The use of metrics also helped inform place-specific strategies to improve forest management, though it was also apparent that further work was required to better incorporate differences in forest functions into sustainability planning.

Systems biology: A tool for charting the antiviral landscape.

PubMed

Bowen, James R; Ferris, Martin T; Suthar, Mehul S

2016-06-15

The host antiviral programs that are initiated following viral infection form a dynamic and complex web of responses that we have collectively termed as "the antiviral landscape". Conventional approaches to studying antiviral responses have primarily used reductionist systems to assess the function of a single or a limited subset of molecules. Systems biology is a holistic approach that considers the entire system as a whole, rather than individual components or molecules. Systems biology based approaches facilitate an unbiased and comprehensive analysis of the antiviral landscape, while allowing for the discovery of emergent properties that are missed by conventional approaches. The antiviral landscape can be viewed as a hierarchy of complexity, beginning at the whole organism level and progressing downward to isolated tissues, populations of cells, and single cells. In this review, we will discuss how systems biology has been applied to better understand the antiviral landscape at each of these layers. At the organismal level, the Collaborative Cross is an invaluable genetic resource for assessing how genetic diversity influences the antiviral response. Whole tissue and isolated bulk cell transcriptomics serves as a critical tool for the comprehensive analysis of antiviral responses at both the tissue and cellular levels of complexity. Finally, new techniques in single cell analysis are emerging tools that will revolutionize our understanding of how individual cells within a bulk infected cell population contribute to the overall antiviral landscape. Copyright © 2016 Elsevier B.V. All rights reserved.

Functional decay in tree community within tropical fragmented landscapes: Effects of landscape-scale forest cover.

PubMed

Rocha-Santos, Larissa; Benchimol, Maíra; Mayfield, Margaret M; Faria, Deborah; Pessoa, Michaele S; Talora, Daniela C; Mariano-Neto, Eduardo; Cazetta, Eliana

2017-01-01

As tropical rainforests are cleared, forest remnants are increasingly isolated within agricultural landscapes. Understanding how forest loss impacts on species diversity can, therefore, contribute to identifying the minimum amount of habitat required for biodiversity maintenance in human-modified landscapes. Here, we evaluate how the amount of forest cover, at the landscape scale, affects patterns of species richness, abundance, key functional traits and common taxonomic families of adult trees in twenty Brazilian Atlantic rainforest landscapes. We found that as forest cover decreases, both tree community richness and abundance decline, without exhibiting a threshold. At the family-level, species richness and abundance of the Myrtaceae and Sapotaceae were also negatively impacted by the percent forest remaining at the landscape scale. For functional traits, we found a reduction in shade-tolerant, animal-dispersed and small-seeded species following a decrease in the amount of forest retained in landscapes. These results suggest that the amount of forest in a landscape is driving non-random losses in phylogenetic and functional tree diversity in Brazil's remaining Atlantic rainforests. Our study highlights potential restraints on the conservation value of Atlantic rainforest remnants in deforested landscapes in the future.

Functional decay in tree community within tropical fragmented landscapes: Effects of landscape-scale forest cover

PubMed Central

Benchimol, Maíra; Mayfield, Margaret M.; Faria, Deborah; Pessoa, Michaele S.; Talora, Daniela C.; Mariano-Neto, Eduardo; Cazetta, Eliana

2017-01-01

As tropical rainforests are cleared, forest remnants are increasingly isolated within agricultural landscapes. Understanding how forest loss impacts on species diversity can, therefore, contribute to identifying the minimum amount of habitat required for biodiversity maintenance in human-modified landscapes. Here, we evaluate how the amount of forest cover, at the landscape scale, affects patterns of species richness, abundance, key functional traits and common taxonomic families of adult trees in twenty Brazilian Atlantic rainforest landscapes. We found that as forest cover decreases, both tree community richness and abundance decline, without exhibiting a threshold. At the family-level, species richness and abundance of the Myrtaceae and Sapotaceae were also negatively impacted by the percent forest remaining at the landscape scale. For functional traits, we found a reduction in shade-tolerant, animal-dispersed and small-seeded species following a decrease in the amount of forest retained in landscapes. These results suggest that the amount of forest in a landscape is driving non-random losses in phylogenetic and functional tree diversity in Brazil’s remaining Atlantic rainforests. Our study highlights potential restraints on the conservation value of Atlantic rainforest remnants in deforested landscapes in the future. PMID:28403166

Land use/ land cover and ecosystem functions change in the grassland restoration program areas in China from 2000 to 2010

NASA Astrophysics Data System (ADS)

Zhang, H.; Fan, J.

2015-12-01

The grassland restoration areas in China, most of which was located in arid and semi-arid areas, are affected by climate change and anthropogenic activities. Using the 3S (RS, GIS, GPS) technologies, quantitative analysis method of landscape patterns and ecological simulation, this study examines the spatiotemporal characteristics of land use/ land cover and ecosystem functions change in the grassland restoration areas in China from 2000 to 2010. We apply two parameters land use transfer matrix and land use dynamic degree to explore the speed and regional differentiation of land use change. We propose vegetation coverage, net primary production (NPP), soil and water conservation capacity to assess the ecosystem functions. This study analyzes the characteristics of landscape patterns at the class and landscape levels and explores the ecological effect of land use pattern and regional ecological processes. The results show that: (1) Grassland and others were the main landscape types in the study area in the past decade. The ecosystem structure was stable. About 0.37% of the total grassland area in 2000 experienced change in land use / land cover types. The area of woodlands, wetlands, farmlands, and built-up areas expanded. The area of others has declined. (2) The dynamic degree of regional land use was less than one percent in the recent ten years. The speed of land use and land cover change was low, and regional differentiation of change between the provinces was small. (3) The matrix of the landscape did not change in the study area. Landscape fragmentation index values decreased progressively; landscape diversity rose continuously; landscape aggregation and continuity decreased slightly; the landscape maintained relative integrity. (4) Ecosystem functions has increased as a whole. The vegetation coverages with significant increase (with a 1.99% yr-1 slope of regression) in the total study area; NPP has a fluctuating and increasing tendency, ranging from 218.23 gC·m-2yr-1 in 2000, to 226.30 gC·m-2yr-1 in 2010, with a 3.70% increase; Soil and water conservation capacity has showed an obvious increment. (5) The grassland restoration program implementation evidently improved the structure and stability of the land use/ land cover. The climatic variations (temperature and precipitation) promoted vegetation growth.

Bacterial structures and ecosystem functions in glaciated floodplains: contemporary states and potential future shifts

PubMed Central

Freimann, Remo; Bürgmann, Helmut; Findlay, Stuart EG; Robinson, Christopher T

2013-01-01

Glaciated alpine floodplains are responding quickly to climate change through shrinking ice masses. Given the expected future changes in their physicochemical environment, we anticipated variable shifts in structure and ecosystem functioning of hyporheic microbial communities in proglacial alpine streams, depending on present community characteristics and landscape structures. We examined microbial structure and functioning during different hydrologic periods in glacial (kryal) streams and, as contrasting systems, groundwater-fed (krenal) streams. Three catchments were chosen to cover an array of landscape features, including interconnected lakes, differences in local geology and degree of deglaciation. Community structure was assessed by automated ribosomal intergenic spacer analysis and microbial function by potential enzyme activities. We found each catchment to contain a distinct bacterial community structure and different degrees of separation in structure and functioning that were linked to the physicochemical properties of the waters within each catchment. Bacterial communities showed high functional plasticity, although achieved by different strategies in each system. Typical kryal communities showed a strong linkage of structure and function that indicated a major prevalence of specialists, whereas krenal sediments were dominated by generalists. With the rapid retreat of glaciers and therefore altered ecohydrological characteristics, lotic microbial structure and functioning are likely to change substantially in proglacial floodplains in the future. The trajectory of these changes will vary depending on contemporary bacterial community characteristics and landscape structures that ultimately determine the sustainability of ecosystem functioning. PMID:23842653

Bacterial structures and ecosystem functions in glaciated floodplains: contemporary states and potential future shifts.

PubMed

Freimann, Remo; Bürgmann, Helmut; Findlay, Stuart E G; Robinson, Christopher T

2013-12-01

Glaciated alpine floodplains are responding quickly to climate change through shrinking ice masses. Given the expected future changes in their physicochemical environment, we anticipated variable shifts in structure and ecosystem functioning of hyporheic microbial communities in proglacial alpine streams, depending on present community characteristics and landscape structures. We examined microbial structure and functioning during different hydrologic periods in glacial (kryal) streams and, as contrasting systems, groundwater-fed (krenal) streams. Three catchments were chosen to cover an array of landscape features, including interconnected lakes, differences in local geology and degree of deglaciation. Community structure was assessed by automated ribosomal intergenic spacer analysis and microbial function by potential enzyme activities. We found each catchment to contain a distinct bacterial community structure and different degrees of separation in structure and functioning that were linked to the physicochemical properties of the waters within each catchment. Bacterial communities showed high functional plasticity, although achieved by different strategies in each system. Typical kryal communities showed a strong linkage of structure and function that indicated a major prevalence of specialists, whereas krenal sediments were dominated by generalists. With the rapid retreat of glaciers and therefore altered ecohydrological characteristics, lotic microbial structure and functioning are likely to change substantially in proglacial floodplains in the future. The trajectory of these changes will vary depending on contemporary bacterial community characteristics and landscape structures that ultimately determine the sustainability of ecosystem functioning.

Potential corridors and barriers for plague spread in Central Asia.

PubMed

Wilschut, Liesbeth I; Addink, Elisabeth A; Heesterbeek, Hans; Heier, Lise; Laudisoit, Anne; Begon, Mike; Davis, Stephen; Dubyanskiy, Vladimir M; Burdelov, Leonid A; de Jong, Steven M

2013-10-31

Plague (Yersinia pestis infection) is a vector-borne disease which caused millions of human deaths in the Middle Ages. The hosts of plague are mostly rodents, and the disease is spread by the fleas that feed on them. Currently, the disease still circulates amongst sylvatic rodent populations all over the world, including great gerbil (Rhombomys opimus) populations in Central Asia. Great gerbils are social desert rodents that live in family groups in burrows, which are visible on satellite images. In great gerbil populations an abundance threshold exists, above which plague can spread causing epizootics. The spatial distribution of the host species is thought to influence the plague dynamics, such as the direction of plague spread, however no detailed analysis exists on the possible functional or structural corridors and barriers that are present in this population and landscape. This study aims to fill that gap. Three 20 by 20 km areas with known great gerbil burrow distributions were used to analyse the spatial distribution of the burrows. Object-based image analysis was used to map the landscape at several scales, and was linked to the burrow maps. A novel object-based method was developed - the mean neighbour absolute burrow density difference (MNABDD) - to identify the optimal scale and evaluate the efficacy of using landscape objects as opposed to square cells. Multiple regression using raster maps was used to identify the landscape-ecological variables that explain burrow density best. Functional corridors and barriers were mapped using burrow density thresholds. Cumulative resistance of the burrow distribution to potential disease spread was evaluated using cost distance analysis. A 46-year plague surveillance dataset was used to evaluate whether plague spread was radially symmetric. The burrow distribution was found to be non-random and negatively correlated with Greenness, especially in the floodplain areas. Corridors and barriers showed a mostly NWSE alignment, suggesting easier spreading along this axis. This was confirmed by the analysis of the plague data. Plague spread had a predominantly NWSE direction, which is likely due to the NWSE alignment of corridors and barriers in the burrow distribution and the landscape. This finding may improve predictions of plague in the future and emphasizes the importance of including landscape analysis in wildlife disease studies.

Potential corridors and barriers for plague spread in central Asia

PubMed Central

2013-01-01

Background Plague (Yersinia pestis infection) is a vector-borne disease which caused millions of human deaths in the Middle Ages. The hosts of plague are mostly rodents, and the disease is spread by the fleas that feed on them. Currently, the disease still circulates amongst sylvatic rodent populations all over the world, including great gerbil (Rhombomys opimus) populations in Central Asia. Great gerbils are social desert rodents that live in family groups in burrows, which are visible on satellite images. In great gerbil populations an abundance threshold exists, above which plague can spread causing epizootics. The spatial distribution of the host species is thought to influence the plague dynamics, such as the direction of plague spread, however no detailed analysis exists on the possible functional or structural corridors and barriers that are present in this population and landscape. This study aims to fill that gap. Methods Three 20 by 20 km areas with known great gerbil burrow distributions were used to analyse the spatial distribution of the burrows. Object-based image analysis was used to map the landscape at several scales, and was linked to the burrow maps. A novel object-based method was developed – the mean neighbour absolute burrow density difference (MNABDD) – to identify the optimal scale and evaluate the efficacy of using landscape objects as opposed to square cells. Multiple regression using raster maps was used to identify the landscape-ecological variables that explain burrow density best. Functional corridors and barriers were mapped using burrow density thresholds. Cumulative resistance of the burrow distribution to potential disease spread was evaluated using cost distance analysis. A 46-year plague surveillance dataset was used to evaluate whether plague spread was radially symmetric. Results The burrow distribution was found to be non-random and negatively correlated with Greenness, especially in the floodplain areas. Corridors and barriers showed a mostly NWSE alignment, suggesting easier spreading along this axis. This was confirmed by the analysis of the plague data. Conclusions Plague spread had a predominantly NWSE direction, which is likely due to the NWSE alignment of corridors and barriers in the burrow distribution and the landscape. This finding may improve predictions of plague in the future and emphasizes the importance of including landscape analysis in wildlife disease studies. PMID:24171709

The non-small cell lung cancer immune landscape: emerging complexity, prognostic relevance and prospective significance in the context of immunotherapy.

PubMed

Anichini, Andrea; Tassi, Elena; Grazia, Giulia; Mortarini, Roberta

2018-06-01

Immunotherapy of non-small cell lung cancer (NSCLC), by immune checkpoint inhibitors, has profoundly improved the clinical management of advanced disease. However, only a fraction of patients respond and no effective predictive factors have been defined. Here, we discuss the prospects for identification of such predictors of response to immunotherapy, by fostering an in-depth analysis of the immune landscape of NSCLC. The emerging picture, from several recent studies, is that the immune contexture of NSCLC lesions is a complex and heterogeneous feature, as documented by analysis for frequency, phenotype and spatial distribution of innate and adaptive immune cells, and by characterization of functional status of inhibitory receptor + T cells. The complexity of the immune landscape of NSCLC stems from the interaction of several factors, including tumor histology, molecular subtype, main oncogenic drivers, nonsynonymous mutational load, tumor aneuploidy, clonal heterogeneity and tumor evolution, as well as the process of epithelial-mesenchymal transition. All these factors contribute to shape NSCLC immune profiles that have clear prognostic significance. An integrated analysis of the immune and molecular profile of the neoplastic lesions may allow to define the potential predictive role of the immune landscape for response to immunotherapy.

An Analysis Framework Using Satellite Remote Sensing to Understand Landscape Patterns of High Severity Burns from Wildfires in Coastal Woodlands of California and Italy

NASA Astrophysics Data System (ADS)

Potter, C. S.

2016-12-01

The central California coastal landscape has a history of frequent large wildfires that have threatened or destroyed many residential structures at the wildland interface. This study starts with the largest wildfires on the Central Coast over the past 30 years and analyzes the fraction and landscape patterns of high severity burned (HBS) areas from the Landsat-based Monitoring Trends in Burn Severity (MTBS) data base as a function of weather conditions and topographic variations. Results indicate that maximum temperatures at the time of fire and the previous 12 months of rainfall explained a significant portion of the variation in total area burned and the fraction of HBS area. Average patch size and aggregation metrics of HBS areas were included in the analysis framework. Within each burned area, the Landsat (30-meter resolution) differenced Normalized Burn Ratio (dNBR), a continuous index of vegetation burn severity, was correlated against slope, aspect, and elevation to better understand landscape level-controls over HBS patches. The Landsat dNBR analysis framework is being extended next to the island of Sardinia, Italy for a comparison of Mediterranean climates and wildfire patterns since the mid-1980s.

Riparian landscape management in the midstream of Ciliwung River as supporting Water Sensitive Cities program with priority of productive landscape

NASA Astrophysics Data System (ADS)

Noviandi, T. U. Z.; Kaswanto, R. L.; Arifin, H. S.

2017-10-01

Nowadays, Ciliwung River is facing problem of the settlement occupation in its riparian zones. This phenomenon caused ecological damage in riparian, so it can aggravate the disaster of annual flooding in Jakarta. As an effort to control this catastrophe, riparian landscape management of Ciliwung River is needed. Based on its topography, Ciliwung River is divided into three segments, there are the upstream, the midstream, and the downstream. Data shows that riparian in the midstream is the largest area, it covers more than 60% of the total riparian area. This segment is very important to be managed in order to reduce runoff towards the downstream. The method used was comparing many standards to get the ideal riparian width in the midstream, which is 50 m for urban areas and 100 m for outside the urban areas. Next method was analyzing spatially to get riparian landscape characteristic of Ciliwung River. The result showed that 37.11% of riparian zones in the midstream had occupied by settlement. Analysis of riparian function and utilization had held by using Analytical Hierarchy Process. Priority of riparian function in the midstream of Ciliwung River is production. This can be realized with the plan of community garden or inland fisheries. Riparian landscape management in the midstream aims to support the food consumption diversification, and maximize the function of water catchment and water retention in order to support the program of Water Sensitive Cities.

A simple approach for a spatial terrestrial exposure assessment of the insecticide fenoxycarb, based on a high-resolution landscape analysis.

PubMed

Thomas, Kai; Resseler, Herbert; Spatz, Robert; Hendley, Paul; Sweeney, Paul; Urban, Martin; Kubiak, Roland

2016-11-01

The objective was to refine the standard regulatory exposure scenario used in plant protection product authorisations by developing a more realistic landscape-related GIS-based exposure assessment for terrestrial non-target arthropods. We quantified the proportion of adjacent off-target area in agricultural landscapes potentially exposed to insecticide drift from applications of the active substance fenoxycarb. High-resolution imagery, landscape classification and subsequent stepwise analysis of a whole landscape using drift and interception functions were applied to selected areas in representative fruit-producing regions in Germany. Even under worst-case assumptions regarding treated area, use rate and drift, less than 12% of the non-agricultural habitat area would potentially be exposed to fenoxycarb drift above regulatory acceptable concentrations. Additionally, if the filtering effect of tall vegetation were taken into account, this number would decrease to 6.6%. Further refinements to landscape elements and application conditions indicate that less than 5% of the habitat area might be exposed above regulatory acceptable concentrations, meaning that 95% of the non-agricultural habitat area will be unimpacted (i.e. no unacceptable effects) and can serve as refuge for recolonisation. Approaches and tools are proposed for standardisable and transparent refinements in regulatory risk assessments on the landscape level. © 2016 The Authors. Pest Management Science published by John Wiley & Sons Ltd on behalf of Society of Chemical Industry. © 2016 The Authors. Pest Management Science published by John Wiley & Sons Ltd on behalf of Society of Chemical Industry.

Influence of landscape structure and human modifications on insect biomass and bat foraging activity in an urban landscape.

PubMed

Threlfall, Caragh G; Law, Bradley; Banks, Peter B

2012-01-01

Urban landscapes are often located in biologically diverse, productive regions. As such, urbanization may have dramatic consequences for this diversity, largely due to changes in the structure and function of urban communities. We examined the influence of landscape productivity (indexed by geology), housing density and vegetation clearing on the spatial distribution of nocturnal insect biomass and the foraging activity of insectivorous bats in the urban landscape of Sydney, Australia. Nocturnal insect biomass (g) and bat foraging activity were sampled from 113 sites representing backyard, open space, bushland and riparian landscape elements, across urban, suburban and vegetated landscapes within 60 km of Sydney's Central Business District. We found that insect biomass was at least an order of magnitude greater within suburban landscapes in bushland and backyard elements located on the most fertile shale influenced geologies (both p<0.001) compared to nutrient poor sandstone landscapes. Similarly, the feeding activity of bats was greatest in bushland, and riparian elements within suburbs on fertile geologies (p = 0.039). Regression tree analysis indicated that the same three variables explained the major proportion of the variation in insect biomass and bat foraging activity. These were ambient temperature (positive), housing density (negative) and the percent of fertile shale geologies (positive) in the landscape; however variation in insect biomass did not directly explain bat foraging activity. We suggest that prey may be unavailable to bats in highly urbanized areas if these areas are avoided by many species, suggesting that reduced feeding activity may reflect under-use of urban habitats by bats. Restoration activities to improve ecological function and maintain the activity of a diversity of bat species should focus on maintaining and restoring bushland and riparian habitat, particularly in areas with fertile geology as these were key bat foraging habitats.

Influence of Landscape Structure and Human Modifications on Insect Biomass and Bat Foraging Activity in an Urban Landscape

PubMed Central

Threlfall, Caragh G.; Law, Bradley; Banks, Peter B.

2012-01-01

Urban landscapes are often located in biologically diverse, productive regions. As such, urbanization may have dramatic consequences for this diversity, largely due to changes in the structure and function of urban communities. We examined the influence of landscape productivity (indexed by geology), housing density and vegetation clearing on the spatial distribution of nocturnal insect biomass and the foraging activity of insectivorous bats in the urban landscape of Sydney, Australia. Nocturnal insect biomass (g) and bat foraging activity were sampled from 113 sites representing backyard, open space, bushland and riparian landscape elements, across urban, suburban and vegetated landscapes within 60 km of Sydney's Central Business District. We found that insect biomass was at least an order of magnitude greater within suburban landscapes in bushland and backyard elements located on the most fertile shale influenced geologies (both p<0.001) compared to nutrient poor sandstone landscapes. Similarly, the feeding activity of bats was greatest in bushland, and riparian elements within suburbs on fertile geologies (p = 0.039). Regression tree analysis indicated that the same three variables explained the major proportion of the variation in insect biomass and bat foraging activity. These were ambient temperature (positive), housing density (negative) and the percent of fertile shale geologies (positive) in the landscape; however variation in insect biomass did not directly explain bat foraging activity. We suggest that prey may be unavailable to bats in highly urbanized areas if these areas are avoided by many species, suggesting that reduced feeding activity may reflect under-use of urban habitats by bats. Restoration activities to improve ecological function and maintain the activity of a diversity of bat species should focus on maintaining and restoring bushland and riparian habitat, particularly in areas with fertile geology as these were key bat foraging habitats. PMID:22685608

Quantifying the linear and nonlinear relations between the urban form fragmentation and the carbon emission distribution

NASA Astrophysics Data System (ADS)

Zuo, S.; Dai, S.; Ren, Y.; Yu, Z.

2017-12-01

Scientifically revealing the spatial heterogeneity and the relationship between the fragmentation of urban landscape and the direct carbon emissions are of great significance to land management and urban planning. In fact, the linear and nonlinear effects among the various factors resulted in the carbon emission spatial map. However, there is lack of the studies on the direct and indirect relations between the carbon emission and the city functional spatial form changes, which could not be reflected by the land use change. The linear strength and direction of the single factor could be calculated through the correlation and Geographically Weighted Regression (GWR) analysis, the nonlinear power of one factor and the interaction power of each two factors could be quantified by the Geodetector analysis. Therefore, we compared the landscape fragmentation metrics of the urban land cover and functional district patches to characterize the landscape form and then revealed the relations between the landscape fragmentation level and the direct the carbon emissions based on the three methods. The results showed that fragmentation decreased and the fragmented patches clustered at the coarser resolution. The direct CO2 emission density and the population density increased when the fragmentation level aggregated. The correlation analysis indicated the weak linear relation between them. The spatial variation of GWR output indicated the fragmentation indicator (MESH) had the positive influence on the carbon emission located in the relatively high emission region, and the negative effects regions accounted for the small part of the area. The Geodetector which explores the nonlinear relation identified the DIVISION and MESH as the most powerful direct factor for the land cover patches, NP and PD for the functional district patches, and the interactions between fragmentation indicator (MESH) and urban sprawl metrics (PUA and DIS) had the greatly increased explanation powers on the urban carbon emission. Overall, this study provides a framework to understand the relation between the urban landscape fragmentation and the carbon emission for the low carbon city construction planning in the other cities.

Ecosystem engineering affects ecosystem functioning in high-Andean landscapes.

PubMed

Badano, Ernesto I; Marquet, Pablo A

2008-04-01

Ecosystem engineers are organisms that change the distribution of materials and energy in the abiotic environment, usually creating and maintaining new habitat patches in the landscape. Such changes in habitat conditions have been widely documented to affect the distributions and performances of other species but up to now no studies have addressed how such effects can impact the biotically driven physicochemical processes associated with these landscapes, or ecosystem functions. Based on the widely accepted positive relationship between species diversity and ecosystem functions, we propose that the effects of ecosystem engineers on other species could have an impact on ecosystem functions via two mutually inclusive mechanisms: (1) by adding new species into landscapes, hence increasing species diversity; and (2) by improving the performances of species already present in the landscape. To test these hypotheses, we focused on the effects of a high-Andean ecosystem engineer, the cushion plant Azorella monantha, by comparing the accumulation of plant biomass and nitrogen fixed in plant tissues as species richness increases in landscapes with and without the engineer species. Our results show that both ecosystem functions increased with species richness in both landscape types, but landscapes including A. monantha cushions reached higher outcomes of plant biomass and nitrogen fixed in plant tissues than landscapes without cushions. Moreover, our results indicate that such positive effects on ecosystem functions could be mediated by the two mechanisms proposed above. Then, given the conspicuousness of ecosystem engineering in nature and its strong influence on species diversity, and given the well-known relationship between species diversity and ecosystem function, we suggest that the application of the conceptual framework proposed herein to other ecosystems would help to advance our understanding of the forces driving ecosystem functioning.

Land-use change in oil palm dominated tropical landscapes—An agent-based model to explore ecological and socio-economic trade-offs

PubMed Central

Dislich, Claudia; Hettig, Elisabeth; Heinonen, Johannes; Lay, Jann; Meyer, Katrin M.; Wiegand, Kerstin; Tarigan, Suria

2018-01-01

Land-use changes have dramatically transformed tropical landscapes. We describe an ecological-economic land-use change model as an integrated, exploratory tool used to analyze how tropical land-use change affects ecological and socio-economic functions. The model analysis seeks to determine what kind of landscape mosaic can improve the ensemble of ecosystem functioning, biodiversity, and economic benefit based on the synergies and trade-offs that we have to account for. More specifically, (1) how do specific ecosystem functions, such as carbon storage, and economic functions, such as household consumption, relate to each other? (2) How do external factors, such as the output prices of crops, affect these relationships? (3) How do these relationships change when production inefficiency differs between smallholder farmers and learning is incorporated? We initialize the ecological-economic model with artificially generated land-use maps parameterized to our study region. The economic sub-model simulates smallholder land-use management decisions based on a profit maximization assumption. Each household determines factor inputs for all household fields and decides on land-use change based on available wealth. The ecological sub-model includes a simple account of carbon sequestration in above-ground and below-ground vegetation. We demonstrate model capabilities with results on household consumption and carbon sequestration from different output price and farming efficiency scenarios. The overall results reveal complex interactions between the economic and ecological spheres. For instance, model scenarios with heterogeneous crop-specific household productivity reveal a comparatively high inertia of land-use change. Our model analysis even shows such an increased temporal stability in landscape composition and carbon stocks of the agricultural area under dynamic price trends. These findings underline the utility of ecological-economic models, such as ours, to act as exploratory tools which can advance our understanding of the mechanisms underlying the trade-offs and synergies of ecological and economic functions in tropical landscapes. PMID:29351290

Spatial exposure-hazard and landscape models for assessing the impact of GM crops on non-target organisms.

PubMed

Leclerc, Melen; Walker, Emily; Messéan, Antoine; Soubeyrand, Samuel

2018-05-15

The cultivation of Genetically Modified (GM) crops may have substantial impacts on populations of non-target organisms (NTOs) in agroecosystems. These impacts should be assessed at larger spatial scales than the cultivated field, and, as landscape-scale experiments are difficult, if not impossible, modelling approaches are needed to address landscape risk management. We present an original stochastic and spatially explicit modelling framework for assessing the risk at the landscape level. We use techniques from spatial statistics for simulating simplified landscapes made up of (aggregated or non-aggregated) GM fields, neutral fields and NTO's habitat areas. The dispersal of toxic pollen grains is obtained by convolving the emission of GM plants and validated dispersal kernel functions while the locations of exposed individuals are drawn from a point process. By taking into account the adherence of the ambient pollen on plants, the loss of pollen due to climatic events, and, an experimentally-validated mortality-dose function we predict risk maps and provide a distribution giving how the risk varies within exposed individuals in the landscape. Then, we consider the impact of the Bt maize on Inachis io in worst-case scenarii where exposed individuals are located in the vicinity of GM fields and pollen shedding overlaps with larval emergence. We perform a Global Sensitivity Analysis (GSA) to explore numerically how our input parameters influence the risk. Our results confirm the important effects of pollen emission and loss. Most interestingly they highlight that the optimal spatial distribution of GM fields that mitigates the risk depends on our knowledge of the habitats of NTOs, and finally, moderate the influence of the dispersal kernel function. Copyright © 2017 Elsevier B.V. All rights reserved.

Protein Science by DNA Sequencing: How Advances in Molecular Biology Are Accelerating Biochemistry.

PubMed

Higgins, Sean A; Savage, David F

2018-01-09

A fundamental goal of protein biochemistry is to determine the sequence-function relationship, but the vastness of sequence space makes comprehensive evaluation of this landscape difficult. However, advances in DNA synthesis and sequencing now allow researchers to assess the functional impact of every single mutation in many proteins, but challenges remain in library construction and the development of general assays applicable to a diverse range of protein functions. This Perspective briefly outlines the technical innovations in DNA manipulation that allow massively parallel protein biochemistry and then summarizes the methods currently available for library construction and the functional assays of protein variants. Areas in need of future innovation are highlighted with a particular focus on assay development and the use of computational analysis with machine learning to effectively traverse the sequence-function landscape. Finally, applications in the fundamentals of protein biochemistry, disease prediction, and protein engineering are presented.

PolyUbiquitin Chain Linkage Topology Selects the Functions from the Underlying Binding Landscape

PubMed Central

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

2014-01-01

Ubiquitin (Ub) can generate versatile molecular signals and lead to different celluar fates. The functional poly-valence of Ub is believed to be resulted from its ability to form distinct polymerized chains with eight linkage types. To provide a full picture of ubiquitin code, we explore the binding landscape of two free Ub monomers and also the functional landscapes of of all eight linkage types by theoretical modeling. Remarkably, we found that most of the compact structures of covalently connected dimeric Ub chains (diUbs) pre-exist on the binding landscape. These compact functional states were subsequently validated by corresponding linkage models. This leads to the proposal that the folding architecture of Ub monomer has encoded all functional states into its binding landscape, which is further selected by different topologies of polymeric Ub chains. Moreover, our results revealed that covalent linkage leads to symmetry breaking of interfacial interactions. We further propose that topological constraint not only limits the conformational space for effective switching between functional states, but also selects the local interactions for realizing the corresponding biological function. Therefore, the topological constraint provides a way for breaking the binding symmetry and reaching the functional specificity. The simulation results also provide several predictions that qualitatively and quantitatively consistent with experiments. Importantly, the K48 linkage model successfully predicted intermediate states. The resulting multi-state energy landscape was further employed to reconcile the seemingly contradictory experimental data on the conformational equilibrium of K48-diUb. Our results further suggest that hydrophobic interactions are dominant in the functional landscapes of K6-, K11-, K33- and K48 diUbs, while electrostatic interactions play a more important role in the functional landscapes of K27, K29, K63 and linear linkages. PMID:24992446

PolyUbiquitin chain linkage topology selects the functions from the underlying binding landscape.

PubMed

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

2014-07-01

Ubiquitin (Ub) can generate versatile molecular signals and lead to different celluar fates. The functional poly-valence of Ub is believed to be resulted from its ability to form distinct polymerized chains with eight linkage types. To provide a full picture of ubiquitin code, we explore the binding landscape of two free Ub monomers and also the functional landscapes of of all eight linkage types by theoretical modeling. Remarkably, we found that most of the compact structures of covalently connected dimeric Ub chains (diUbs) pre-exist on the binding landscape. These compact functional states were subsequently validated by corresponding linkage models. This leads to the proposal that the folding architecture of Ub monomer has encoded all functional states into its binding landscape, which is further selected by different topologies of polymeric Ub chains. Moreover, our results revealed that covalent linkage leads to symmetry breaking of interfacial interactions. We further propose that topological constraint not only limits the conformational space for effective switching between functional states, but also selects the local interactions for realizing the corresponding biological function. Therefore, the topological constraint provides a way for breaking the binding symmetry and reaching the functional specificity. The simulation results also provide several predictions that qualitatively and quantitatively consistent with experiments. Importantly, the K48 linkage model successfully predicted intermediate states. The resulting multi-state energy landscape was further employed to reconcile the seemingly contradictory experimental data on the conformational equilibrium of K48-diUb. Our results further suggest that hydrophobic interactions are dominant in the functional landscapes of K6-, K11-, K33- and K48 diUbs, while electrostatic interactions play a more important role in the functional landscapes of K27, K29, K63 and linear linkages.

Using THz Spectroscopy, Evolutionary Network Analysis Methods, and MD Simulation to Map the Evolution of Allosteric Communication Pathways in c-Type Lysozymes.

PubMed

Woods, Kristina N; Pfeffer, Juergen

2016-01-01

It is now widely accepted that protein function is intimately tied with the navigation of energy landscapes. In this framework, a protein sequence is not described by a distinct structure but rather by an ensemble of conformations. And it is through this ensemble that evolution is able to modify a protein's function by altering its landscape. Hence, the evolution of protein functions involves selective pressures that adjust the sampling of the conformational states. In this work, we focus on elucidating the evolutionary pathway that shaped the function of individual proteins that make-up the mammalian c-type lysozyme subfamily. Using both experimental and computational methods, we map out specific intermolecular interactions that direct the sampling of conformational states and accordingly, also underlie shifts in the landscape that are directly connected with the formation of novel protein functions. By contrasting three representative proteins in the family we identify molecular mechanisms that are associated with the selectivity of enhanced antimicrobial properties and consequently, divergent protein function. Namely, we link the extent of localized fluctuations involving the loop separating helices A and B with shifts in the equilibrium of the ensemble of conformational states that mediate interdomain coupling and concurrently moderate substrate binding affinity. This work reveals unique insights into the molecular level mechanisms that promote the progression of interactions that connect the immune response to infection with the nutritional properties of lactation, while also providing a deeper understanding about how evolving energy landscapes may define present-day protein function. © The Author 2015. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

Continental-scale quantification of landscape values using social media data.

PubMed

van Zanten, Boris T; Van Berkel, Derek B; Meentemeyer, Ross K; Smith, Jordan W; Tieskens, Koen F; Verburg, Peter H

2016-11-15

Individuals, communities, and societies ascribe a diverse array of values to landscapes. These values are shaped by the aesthetic, cultural, and recreational benefits and services provided by those landscapes. However, across the globe, processes such as urbanization, agricultural intensification, and abandonment are threatening landscape integrity, altering the personally meaningful connections people have toward specific places. Existing methods used to study landscape values, such as social surveys, are poorly suited to capture dynamic landscape-scale processes across large geographic extents. Social media data, by comparison, can be used to indirectly measure and identify valuable features of landscapes at a regional, continental, and perhaps even worldwide scale. We evaluate the usefulness of different social media platforms-Panoramio, Flickr, and Instagram-and quantify landscape values at a continental scale. We find Panoramio, Flickr, and Instagram data can be used to quantify landscape values, with features of Instagram being especially suitable due to its relatively large population of users and its functional ability of allowing users to attach personally meaningful comments and hashtags to their uploaded images. Although Panoramio, Flickr, and Instagram have different user profiles, our analysis revealed similar patterns of landscape values across Europe across the three platforms. We also found variables describing accessibility, population density, income, mountainous terrain, or proximity to water explained a significant portion of observed variation across data from the different platforms. Social media data can be used to extend our understanding of how and where individuals ascribe value to landscapes across diverse social, political, and ecological boundaries.

Continental-scale quantification of landscape values using social media data

PubMed Central

van Zanten, Boris T.; Van Berkel, Derek B.; Meentemeyer, Ross K.; Smith, Jordan W.; Tieskens, Koen F.

2016-01-01

Individuals, communities, and societies ascribe a diverse array of values to landscapes. These values are shaped by the aesthetic, cultural, and recreational benefits and services provided by those landscapes. However, across the globe, processes such as urbanization, agricultural intensification, and abandonment are threatening landscape integrity, altering the personally meaningful connections people have toward specific places. Existing methods used to study landscape values, such as social surveys, are poorly suited to capture dynamic landscape-scale processes across large geographic extents. Social media data, by comparison, can be used to indirectly measure and identify valuable features of landscapes at a regional, continental, and perhaps even worldwide scale. We evaluate the usefulness of different social media platforms—Panoramio, Flickr, and Instagram—and quantify landscape values at a continental scale. We find Panoramio, Flickr, and Instagram data can be used to quantify landscape values, with features of Instagram being especially suitable due to its relatively large population of users and its functional ability of allowing users to attach personally meaningful comments and hashtags to their uploaded images. Although Panoramio, Flickr, and Instagram have different user profiles, our analysis revealed similar patterns of landscape values across Europe across the three platforms. We also found variables describing accessibility, population density, income, mountainous terrain, or proximity to water explained a significant portion of observed variation across data from the different platforms. Social media data can be used to extend our understanding of how and where individuals ascribe value to landscapes across diverse social, political, and ecological boundaries. PMID:27799537

News from the protein mutability landscape.

PubMed

Hecht, Maximilian; Bromberg, Yana; Rost, Burkhard

2013-11-01

Some mutations of protein residues matter more than others, and these are often conserved evolutionarily. The explosion of deep sequencing and genotyping increasingly requires the distinction between effect and neutral variants. The simplest approach predicts all mutations of conserved residues to have an effect; however, this works poorly, at best. Many computational tools that are optimized to predict the impact of point mutations provide more detail. Here, we expand the perspective from the view of single variants to the level of sketching the entire mutability landscape. This landscape is defined by the impact of substituting every residue at each position in a protein by each of the 19 non-native amino acids. We review some of the powerful conclusions about protein function, stability and their robustness to mutation that can be drawn from such an analysis. Large-scale experimental and computational mutagenesis experiments are increasingly furthering our understanding of protein function and of the genotype-phenotype associations. We also discuss how these can be used to improve predictions of protein function and pathogenicity of missense variants. Copyright © 2013 The Authors. Published by Elsevier Ltd.. All rights reserved.

Designing future landscapes from principles of form and function

Treesearch

Larry D. Harris; Patrick Kangas

1979-01-01

Future landscapes will consist of a gradient of types ranging from wilderness areas to totally "humanized" environments. The man-dominated landscapes will be required to fulfill multiple functions only one of which is aesthetic enjoyment. It is suggested that basic principles of form and function may contribute to design criteria. Applications to the...

Improving Urban Water Environment in Eastern China by Blending Traditional with Modern Landscape Planning.

PubMed

Cao, Jiajie; Yu, Junjun; Tian, Yuan; Zhao, Cai; Wang, Hao

2017-01-01

As a fundamental part of greenspace, urban water landscape contributes greatly to the ecological system and at the same time supplies a leisure area for residents. The paper did an analysis on the number of aquatic plant communities, the form of water spaces, and water quality condition by investigating 135 quadrats (90 at amphibious boundary and the land, 45 in the water) in 45 transects of 15 urban and suburban parks. We found that water spaces had monotonous forms with low biodiversity and poor water quality. In addition, urban water landscapes hardly provided ecological functions given excessive construction. Accordingly, a proposition to connect tradition with modernism in the improvement and innovation of urban water landscape planning was put forward, and further, the way to achieve it was explored. By taking Qinhu Wetland Park as a case, the principles and specific planning methods on macro- and microperspectives were discussed to guide the development of urban landscape in eastern China.

Improving Urban Water Environment in Eastern China by Blending Traditional with Modern Landscape Planning

PubMed Central

Cao, Jiajie; Yu, Junjun; Tian, Yuan; Zhao, Cai

2017-01-01

As a fundamental part of greenspace, urban water landscape contributes greatly to the ecological system and at the same time supplies a leisure area for residents. The paper did an analysis on the number of aquatic plant communities, the form of water spaces, and water quality condition by investigating 135 quadrats (90 at amphibious boundary and the land, 45 in the water) in 45 transects of 15 urban and suburban parks. We found that water spaces had monotonous forms with low biodiversity and poor water quality. In addition, urban water landscapes hardly provided ecological functions given excessive construction. Accordingly, a proposition to connect tradition with modernism in the improvement and innovation of urban water landscape planning was put forward, and further, the way to achieve it was explored. By taking Qinhu Wetland Park as a case, the principles and specific planning methods on macro- and microperspectives were discussed to guide the development of urban landscape in eastern China. PMID:28386514

Landscape simplification filters species traits and drives biotic homogenization

PubMed Central

Gámez-Virués, Sagrario; Perović, David J.; Gossner, Martin M.; Börschig, Carmen; Blüthgen, Nico; de Jong, Heike; Simons, Nadja K.; Klein, Alexandra-Maria; Krauss, Jochen; Maier, Gwen; Scherber, Christoph; Steckel, Juliane; Rothenwöhrer, Christoph; Steffan-Dewenter, Ingolf; Weiner, Christiane N.; Weisser, Wolfgang; Werner, Michael; Tscharntke, Teja; Westphal, Catrin

2015-01-01

Biodiversity loss can affect the viability of ecosystems by decreasing the ability of communities to respond to environmental change and disturbances. Agricultural intensification is a major driver of biodiversity loss and has multiple components operating at different spatial scales: from in-field management intensity to landscape-scale simplification. Here we show that landscape-level effects dominate functional community composition and can even buffer the effects of in-field management intensification on functional homogenization, and that animal communities in real-world managed landscapes show a unified response (across orders and guilds) to both landscape-scale simplification and in-field intensification. Adults and larvae with specialized feeding habits, species with shorter activity periods and relatively small body sizes are selected against in simplified landscapes with intense in-field management. Our results demonstrate that the diversity of land cover types at the landscape scale is critical for maintaining communities, which are functionally diverse, even in landscapes where in-field management intensity is high. PMID:26485325

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...

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...

Landscape of an exact energy functional

NASA Astrophysics Data System (ADS)

Cohen, Aron J.; Mori-Sánchez, Paula

2016-04-01

One of the great challenges of electronic structure theory is the quest for the exact functional of density functional theory. Its existence is proven, but it is a complicated multivariable functional that is almost impossible to conceptualize. In this paper the asymmetric two-site Hubbard model is studied, which has a two-dimensional universe of density matrices. The exact functional becomes a simple function of two variables whose three-dimensional energy landscape can be visualized and explored. A walk on this unique landscape, tilted to an angle defined by the one-electron Hamiltonian, gives a valley whose minimum is the exact total energy. This is contrasted with the landscape of some approximate functionals, explaining their failure for electron transfer in the strongly correlated limit. We show concrete examples of pure-state density matrices that are not v representable due to the underlying nonconvex nature of the energy landscape. The exact functional is calculated for all numbers of electrons, including fractional, allowing the derivative discontinuity to be visualized and understood. The fundamental gap for all possible systems is obtained solely from the derivatives of the exact functional.

Control landscapes are almost always trap free: a geometric assessment

NASA Astrophysics Data System (ADS)

Russell, Benjamin; Rabitz, Herschel; Wu, Re-Bing

2017-05-01

A proof is presented that almost all closed, finite dimensional quantum systems have trap free (i.e. free from local optima) landscapes for a large and physically general class of circumstances, which includes qubit evolutions in quantum computing. This result offers an explanation for why gradient-based methods succeed so frequently in quantum control. The role of singular controls is analyzed using geometric tools in the case of the control of the propagator, and thus in the case of observables as well. Singular controls have been implicated as a source of landscape traps. The conditions under which singular controls can introduce traps, and thus interrupt the progress of a control optimization, are discussed and a geometrical characterization of the issue is presented. It is shown that a control being singular is not sufficient to cause control optimization progress to halt, and sufficient conditions for a trap free landscape are presented. It is further shown that the local surjectivity (full rank) assumption of landscape analysis can be refined to the condition that the end-point map is transverse to each of the level sets of the fidelity function. This mild condition is shown to be sufficient for a quantum system’s landscape to be trap free. The control landscape is shown to be trap free for all but a null set of Hamiltonians using a geometric technique based on the parametric transversality theorem. Numerical evidence confirming this analysis is also presented. This new result is the analogue of the work of Altifini, wherein it was shown that controllability holds for all but a null set of quantum systems in the dipole approximation. These collective results indicate that the availability of adequate control resources remains the most physically relevant issue for achieving high fidelity control performance while also avoiding landscape traps.

The VALS: A new tool to measure people's general valued attributes of landscapes.

PubMed

Kendal, Dave; Ford, Rebecca M; Anderson, Nerida M; Farrar, Alison

2015-11-01

Research on values for natural areas has largely focussed on theoretical concerns such as distinguishing different kinds of values held by people. However practice, policymaking, planning and management is typically focused on more tangible valued attributes of the landscape such as biodiversity and recreation infrastructure that can be manipulated by management actions. There is a need for valid psychometric measures of such values that are suited to informing land management policies. A Valued Attributes of Landscape Scale (VALS) was developed, derived from a document analysis of values expressed in public land policy documents. The validity of the VALS was tested in an online survey comparing values across one of three randomly presented landscape contexts in Victoria, Australia: all publicly managed natural land, coastal areas, and large urban parks. A purposive snowball sample was used to recruit participants with a range of views and professional experience with land management, including members of the urban public. Factor analysis of responses (n = 646) separated concepts relating to natural attributes, social functions, the experience of being in natural areas, cultural attributes and productive uses. Relative importance of valued attribute factors was similar across all landscape contexts, although there were small but significant differences in the way people valued social functions (higher in urban parks) and productive uses (lower in urban parks). We conclude that the concept of valued attributes is useful for linking theoretical understandings of people's environmental values to the way values are considered by land managers, and that these attributes can be measured using the VALS instrument to produce data that should be useful for the policy and planning of natural resources. Copyright © 2015 Elsevier Ltd. All rights reserved.

2D and 3D similarity landscape analysis identifies PARP as a novel off-target for the drug Vatalanib.

PubMed

Gohlke, Bjoern-Oliver; Overkamp, Tim; Richter, Anja; Richter, Antje; Daniel, Peter T; Gillissen, Bernd; Preissner, Robert

2015-09-24

Searching for two-dimensional (2D) structural similarities is a useful tool to identify new active compounds in drug-discovery programs. However, as 2D similarity measures neglect important structural and functional features, similarity by 2D might be underestimated. In the present study, we used combined 2D and three-dimensional (3D) similarity comparisons to reveal possible new functions and/or side-effects of known bioactive compounds. We utilised more than 10,000 compounds from the SuperTarget database with known inhibition values for twelve different anti-cancer targets. We performed all-against-all comparisons resulting in 2D similarity landscapes. Among the regions with low 2D similarity scores are inhibitors of vascular endothelial growth factor receptor (VEGFR) and inhibitors of poly ADP-ribose polymerase (PARP). To demonstrate that 3D landscape comparison can identify similarities, which are untraceable in 2D similarity comparisons, we analysed this region in more detail. This 3D analysis showed the unexpected structural similarity between inhibitors of VEGFR and inhibitors of PARP. Among the VEGFR inhibitors that show similarities to PARP inhibitors was Vatalanib, an oral "multi-targeted" small molecule protein kinase inhibitor being studied in phase-III clinical trials in cancer therapy. An in silico docking simulation and an in vitro HT universal colorimetric PARP assay confirmed that the VEGFR inhibitor Vatalanib exhibits off-target activity as a PARP inhibitor, broadening its mode of action. In contrast to the 2D-similarity search, the 3D-similarity landscape comparison identifies new functions and side effects of the known VEGFR inhibitor Vatalanib.

Hydrologic Connectivity: a Framework to Understand Threshold Behaviour in Semi-Arid Landscapes.

NASA Astrophysics Data System (ADS)

Saco, Patricia; Rodriguez, Jose; Keesstra, Saskia; Moreno-de las Heras, Mariano; Sandi, Steven; Baartman, Jantiene; Cerdà, Artemi

2017-04-01

Anthropogenic activities and climate change are imposing an unprecedented pressure on arid and semi-arid ecosystems, where shortage of water can trigger shifts in landscapes' structures and function leading to degradation and desertification. Hydrological connectivity is a useful framework for understanding water redistribution and scaling issues associated to runoff and sediment production, since human and/or natural disturbances alter the surface water availability and pathways increasing/decreasing connectivity. In this presentation, we illustrate the use of the connectivity framework for several examples of dryland systems that are analysed at a variety of spatial and temporal scales. In doing so, we draw particular attention to the analysis of co-evolution of system structures and function, and how they drive threshold behaviour leading to desertification and degradation. We first analyse the case of semi-arid rangelands, where feedbacks between decline in vegetation density and landscape erosion reinforces degradation processes driven by changes in connectivity until a threshold is crossed above which the return to a functional system is unlikely. We then focus on semi-arid wetlands, where decreases in water volumes promotes dryland vegetation encroachment that changes drainage conditions and connectivity potentially reinforcing redistribution of flow paths to other wetland areas. The examples presented highlight the need to incorporate a co-evolutionary framework for the analysis of changing connectivity patterns and the emergence of thresholds in arid and semi-arid systems.

Structural habitat predicts functional dispersal habitat of a large carnivore: how leopards change spots.

PubMed

Fattebert, Julien; Robinson, Hugh S; Balme, Guy; Slotow, Rob; Hunter, Luke

2015-10-01

Natal dispersal promotes inter-population linkage, and is key to spatial distribution of populations. Degradation of suitable landscape structures beyond the specific threshold of an individual's ability to disperse can therefore lead to disruption of functional landscape connectivity and impact metapopulation function. Because it ignores behavioral responses of individuals, structural connectivity is easier to assess than functional connectivity and is often used as a surrogate for landscape connectivity modeling. However using structural resource selection models as surrogate for modeling functional connectivity through dispersal could be erroneous. We tested how well a second-order resource selection function (RSF) models (structural connectivity), based on GPS telemetry data from resident adult leopard (Panthera pardus L.), could predict subadult habitat use during dispersal (functional connectivity). We created eight non-exclusive subsets of the subadult data based on differing definitions of dispersal to assess the predictive ability of our adult-based RSF model extrapolated over a broader landscape. Dispersing leopards used habitats in accordance with adult selection patterns, regardless of the definition of dispersal considered. We demonstrate that, for a wide-ranging apex carnivore, functional connectivity through natal dispersal corresponds to structural connectivity as modeled by a second-order RSF. Mapping of the adult-based habitat classes provides direct visualization of the potential linkages between populations, without the need to model paths between a priori starting and destination points. The use of such landscape scale RSFs may provide insight into predicting suitable dispersal habitat peninsulas in human-dominated landscapes where mitigation of human-wildlife conflict should be focused. We recommend the use of second-order RSFs for landscape conservation planning and propose a similar approach to the conservation of other wide-ranging large carnivore species where landscape-scale resource selection data already exist.

Defining the human deubiquitinating enzyme interaction landscape.

PubMed

Sowa, Mathew E; Bennett, Eric J; Gygi, Steven P; Harper, J Wade

2009-07-23

Deubiquitinating enzymes (Dubs) function to remove covalently attached ubiquitin from proteins, thereby controlling substrate activity and/or abundance. For most Dubs, their functions, targets, and regulation are poorly understood. To systematically investigate Dub function, we initiated a global proteomic analysis of Dubs and their associated protein complexes. This was accomplished through the development of a software platform called CompPASS, which uses unbiased metrics to assign confidence measurements to interactions from parallel nonreciprocal proteomic data sets. We identified 774 candidate interacting proteins associated with 75 Dubs. Using Gene Ontology, interactome topology classification, subcellular localization, and functional studies, we link Dubs to diverse processes, including protein turnover, transcription, RNA processing, DNA damage, and endoplasmic reticulum-associated degradation. This work provides the first glimpse into the Dub interaction landscape, places previously unstudied Dubs within putative biological pathways, and identifies previously unknown interactions and protein complexes involved in this increasingly important arm of the ubiquitin-proteasome pathway.

Defining the Human Deubiquitinating Enzyme Interaction Landscape

PubMed Central

Sowa, Mathew E.; Bennett, Eric J.; Gygi, Steven P.; Harper, J. Wade

2009-01-01

Summary Deubiquitinating enzymes (Dubs) function to remove covalently attached ubiquitin from proteins, thereby controlling substrate activity and/or abundance. For most Dubs, their functions, targets, and regulation are poorly understood. To systematically investigate Dub function, we initiated a global proteomic analysis of Dubs and their associated protein complexes. This was accomplished through the development of a software platform, called CompPASS, which uses unbiased metrics to assign confidence measurements to interactions from parallel non-reciprocal proteomic datasets. We identified 774 candidate interacting proteins associated with 75 Dubs. Using Gene Ontology, interactome topology classification, sub-cellular localization and functional studies, we link Dubs to diverse processes, including protein turnover, transcription, RNA processing, DNA damage, and endoplasmic reticulum-associated degradation. This work provides the first glimpse into the Dub interaction landscape, places previously unstudied Dubs within putative biological pathways, and identifies previously unknown interactions and protein complexes involved in this increasingly important arm of the ubiquitin-proteasome pathway. PMID:19615732

Dynamic Energy Landscapes of Riboswitches Help Interpret Conformational Rearrangements and Function

PubMed Central

Quarta, Giulio; Sin, Ken; Schlick, Tamar

2012-01-01

Riboswitches are RNAs that modulate gene expression by ligand-induced conformational changes. However, the way in which sequence dictates alternative folding pathways of gene regulation remains unclear. In this study, we compute energy landscapes, which describe the accessible secondary structures for a range of sequence lengths, to analyze the transcriptional process as a given sequence elongates to full length. In line with experimental evidence, we find that most riboswitch landscapes can be characterized by three broad classes as a function of sequence length in terms of the distribution and barrier type of the conformational clusters: low-barrier landscape with an ensemble of different conformations in equilibrium before encountering a substrate; barrier-free landscape in which a direct, dominant “downhill” pathway to the minimum free energy structure is apparent; and a barrier-dominated landscape with two isolated conformational states, each associated with a different biological function. Sharing concepts with the “new view” of protein folding energy landscapes, we term the three sequence ranges above as the sensing, downhill folding, and functional windows, respectively. We find that these energy landscape patterns are conserved in various riboswitch classes, though the order of the windows may vary. In fact, the order of the three windows suggests either kinetic or thermodynamic control of ligand binding. These findings help understand riboswitch structure/function relationships and open new avenues to riboswitch design. PMID:22359488

Ecological functions of riparian zones in Oregon hydrological landscapes

EPA Science Inventory

The ecological functions of streams and associated riparian zones are strongly influenced by the hydrological attributes of watersheds and landscapes in which they occur. Oregon hydrologic landscape regions (HLRs) have been defined based on four types of GIS data: 1) climate, 2) ...

Understanding human uses and values in watershed analysis.

Treesearch

Roger D. Fight; Linda E. Kruger; Christopher Hansen-Murray; Arnold Holden; Dale Bays

2000-01-01

Watershed analysis is used as a tool to understand the functioning of aquatic and terrestrial ecosystem processes at the landscape scale and to assess opportunities to restore or improve those processes and associated watershed conditions. Assessing those opportunities correctly requires an understanding of how humans have interacted with the watershed in the past and...

Replicated landscape genetic and network analyses reveal wide variation in functional connectivity for American pikas.

PubMed

Castillo, Jessica A; Epps, Clinton W; Jeffress, Mackenzie R; Ray, Chris; Rodhouse, Thomas J; Schwalm, Donelle

2016-09-01

Landscape connectivity is essential for maintaining viable populations, particularly for species restricted to fragmented habitats or naturally arrayed in metapopulations and facing rapid climate change. The importance of assessing both structural connectivity (physical distribution of favorable habitat patches) and functional connectivity (how species move among habitat patches) for managing such species is well understood. However, the degree to which functional connectivity for a species varies among landscapes, and the resulting implications for conservation, have rarely been assessed. We used a landscape genetics approach to evaluate resistance to gene flow and, thus, to determine how landscape and climate-related variables influence gene flow for American pikas (Ochotona princeps) in eight federally managed sites in the western United States. We used empirically derived, individual-based landscape resistance models in conjunction with predictive occupancy models to generate patch-based network models describing functional landscape connectivity. Metareplication across landscapes enabled identification of limiting factors for dispersal that would not otherwise have been apparent. Despite the cool microclimates characteristic of pika habitat, south-facing aspects consistently represented higher resistance to movement, supporting the previous hypothesis that exposure to relatively high temperatures may limit dispersal in American pikas. We found that other barriers to dispersal included areas with a high degree of topographic relief, such as cliffs and ravines, as well as streams and distances greater than 1-4 km depending on the site. Using the empirically derived network models of habitat patch connectivity, we identified habitat patches that were likely disproportionately important for maintaining functional connectivity, areas in which habitat appeared fragmented, and locations that could be targeted for management actions to improve functional connectivity. We concluded that climate change, besides influencing patch occupancy as predicted by other studies, may alter landscape resistance for pikas, thereby influencing functional connectivity through multiple pathways simultaneously. Spatial autocorrelation among genotypes varied across study sites and was largest where habitat was most dispersed, suggesting that dispersal distances increased with habitat fragmentation, up to a point. This study demonstrates how landscape features linked to climate can affect functional connectivity for species with naturally fragmented distributions, and reinforces the importance of replicating studies across landscapes. © 2016 by the Ecological Society of America.

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.

Differential network analysis reveals the genome-wide landscape of estrogen receptor modulation in hormonal cancers

PubMed Central

Hsiao, Tzu-Hung; Chiu, Yu-Chiao; Hsu, Pei-Yin; Lu, Tzu-Pin; Lai, Liang-Chuan; Tsai, Mong-Hsun; Huang, Tim H.-M.; Chuang, Eric Y.; Chen, Yidong

2016-01-01

Several mutual information (MI)-based algorithms have been developed to identify dynamic gene-gene and function-function interactions governed by key modulators (genes, proteins, etc.). Due to intensive computation, however, these methods rely heavily on prior knowledge and are limited in genome-wide analysis. We present the modulated gene/gene set interaction (MAGIC) analysis to systematically identify genome-wide modulation of interaction networks. Based on a novel statistical test employing conjugate Fisher transformations of correlation coefficients, MAGIC features fast computation and adaption to variations of clinical cohorts. In simulated datasets MAGIC achieved greatly improved computation efficiency and overall superior performance than the MI-based method. We applied MAGIC to construct the estrogen receptor (ER) modulated gene and gene set (representing biological function) interaction networks in breast cancer. Several novel interaction hubs and functional interactions were discovered. ER+ dependent interaction between TGFβ and NFκB was further shown to be associated with patient survival. The findings were verified in independent datasets. Using MAGIC, we also assessed the essential roles of ER modulation in another hormonal cancer, ovarian cancer. Overall, MAGIC is a systematic framework for comprehensively identifying and constructing the modulated interaction networks in a whole-genome landscape. MATLAB implementation of MAGIC is available for academic uses at https://github.com/chiuyc/MAGIC. PMID:26972162

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.

Breaking Functional Connectivity into Components: A Novel Approach Using an Individual-Based Model, and First Outcomes

PubMed Central

Pe'er, Guy; Henle, Klaus; Dislich, Claudia; Frank, Karin

2011-01-01

Landscape connectivity is a key factor determining the viability of populations in fragmented landscapes. Predicting ‘functional connectivity’, namely whether a patch or a landscape functions as connected from the perspective of a focal species, poses various challenges. First, empirical data on the movement behaviour of species is often scarce. Second, animal-landscape interactions are bound to yield complex patterns. Lastly, functional connectivity involves various components that are rarely assessed separately. We introduce the spatially explicit, individual-based model FunCon as means to distinguish between components of functional connectivity and to assess how each of them affects the sensitivity of species and communities to landscape structures. We then present the results of exploratory simulations over six landscapes of different fragmentation levels and across a range of hypothetical bird species that differ in their response to habitat edges. i) Our results demonstrate that estimations of functional connectivity depend not only on the response of species to edges (avoidance versus penetration into the matrix), the movement mode investigated (home range movements versus dispersal), and the way in which the matrix is being crossed (random walk versus gap crossing), but also on the choice of connectivity measure (in this case, the model output examined). ii) We further show a strong effect of the mortality scenario applied, indicating that movement decisions that do not fully match the mortality risks are likely to reduce connectivity and enhance sensitivity to fragmentation. iii) Despite these complexities, some consistent patterns emerged. For instance, the ranking order of landscapes in terms of functional connectivity was mostly consistent across the entire range of hypothetical species, indicating that simple landscape indices can potentially serve as valuable surrogates for functional connectivity. Yet such simplifications must be carefully evaluated in terms of the components of functional connectivity they actually predict. PMID:21829617

Sensitivity of landscape metrics to changing scale of remote sensing data in spatial pattern analysis: effect, criticality and scaling.

NASA Astrophysics Data System (ADS)

Xu, C.; Zhao, S.; Zhao, B.

2017-12-01

Spatial heterogeneity is scale-dependent, that is, the quantification and representation of spatial pattern vary with the resolution and extent. Overwhelming practices focused on scale effect of landscape metrics, and predicable scaling relationships found among some of them are thought to be the most effective and precise way to quantify multi-scale characteristics. However, previous studies tended to consider a narrow range of scales, and few focused on the critical threshold of scaling function. Here we examine the scalograms of 38 widely-used landscape-level metrics in a more integral spectrum of grain size among 96 landscapes with various extent (i.e. from 25km2 up towards to 221 km2), which sampled randomly from NLCD product. Our goal is to explore the existence of scaling domain and whether the response of metrics to changing resolution would be influenced by spatial extent. Results clearly show the existence of scaling domain for 13 of them (Type II), while the behaviors of other 13 (Type I) exhibit simple scaling functions and the rest (Type III) demonstrate various forms like no obvious change or fluctuation across the integral spectrum of grain size. In addition, an invariant power law scaling relationship was found between critical resolution and spatial extent for metrics falling into Type II, as the critical resolution is proportional to Eρ (ρ is a constant, and E is the extent). All the scaling exponents (ρ) are positive, suggesting that the critical resolutions for these characteristics of landscape structure can be relaxed as the spatial extent expands. This agrees well with empirical perception that coarser grain size might be allowed for spatial data with larger extent. Furthermore, the parameters of scaling functions for metrics falling into Type I and Type II vary with spatial extent, and power law or logarithmic relationships could be identified between them for some metrics. Our finding support the existence of self-organized criticality for a hierarchically-structured landscape. Although the underlying mechanism driving the scaling relationship remains unclear, it could provide guidance toward general principles in spatial pattern analysis and on selecting the proper resolution to avoid the misrepresentation of spatial pattern and profound biases in further ecological progress research.

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

Characterizing the Connectivity and Cumulative Effects of Wetlands on Downstream Hydrology: A Modeling Analysis

EPA Science Inventory

Geographically isolated wetlands (GIWs) are depressional landscape features entirely surrounded by uplands. While “GIW” may imply functional isolation from other surface waters, these systems exhibit a gradient of hydrologic, biological, and/or chemical connectivity. ...

Anthropogenic Matrices Favor Homogenization of Tree Reproductive Functions in a Highly Fragmented Landscape.

PubMed

Carneiro, Magda Silva; Campos, Caroline Cambraia Furtado; Beijo, Luiz Alberto; Ramos, Flavio Nunes

2016-01-01

Species homogenization or floristic differentiation are two possible consequences of the fragmentation process in plant communities. Despite the few studies, it seems clear that fragments with low forest cover inserted in anthropogenic matrices are more likely to experience floristic homogenization. However, the homogenization process has two other components, genetic and functional, which have not been investigated. The purpose of this study was to verify whether there was homogenization of tree reproductive functions in a fragmented landscape and, if found, to determine how the process was influenced by landscape composition. The study was conducted in eight fragments in southwest Brazil. The study was conducted in eight fragments in southwestern Brazil. In each fragment, all individual trees were sampled that had a diameter at breast height ≥3 cm, in ten plots (0.2 ha) and, classified within 26 reproductive functional types (RFTs). The process of functional homogenization was evaluated using additive partitioning of diversity. Additionally, the effect of landscape composition on functional diversity and on the number of individuals within each RFT was evaluated using a generalized linear mixed model. appeared to be in a process of functional homogenization (dominance of RFTs, alpha diversity lower than expected by chance and and low beta diversity). More than 50% of the RFTs and the functional diversity were affected by the landscape parameters. In general, the percentage of forest cover has a positive effect on RFTs while the percentage of coffee matrix has a negative one. The process of functional homogenization has serious consequences for biodiversity conservation because some functions may disappear that, in the long term, would threaten the fragments. This study contributes to a better understanding of how landscape changes affect the functional diversity, abundance of individuals in RFTs and the process of functional homogenization, as well as how to manage fragmented landscapes.

Anthropogenic Matrices Favor Homogenization of Tree Reproductive Functions in a Highly Fragmented Landscape

PubMed Central

2016-01-01

Species homogenization or floristic differentiation are two possible consequences of the fragmentation process in plant communities. Despite the few studies, it seems clear that fragments with low forest cover inserted in anthropogenic matrices are more likely to experience floristic homogenization. However, the homogenization process has two other components, genetic and functional, which have not been investigated. The purpose of this study was to verify whether there was homogenization of tree reproductive functions in a fragmented landscape and, if found, to determine how the process was influenced by landscape composition. The study was conducted in eight fragments in southwest Brazil. The study was conducted in eight fragments in southwestern Brazil. In each fragment, all individual trees were sampled that had a diameter at breast height ≥3 cm, in ten plots (0.2 ha) and, classified within 26 reproductive functional types (RFTs). The process of functional homogenization was evaluated using additive partitioning of diversity. Additionally, the effect of landscape composition on functional diversity and on the number of individuals within each RFT was evaluated using a generalized linear mixed model. appeared to be in a process of functional homogenization (dominance of RFTs, alpha diversity lower than expected by chance and and low beta diversity). More than 50% of the RFTs and the functional diversity were affected by the landscape parameters. In general, the percentage of forest cover has a positive effect on RFTs while the percentage of coffee matrix has a negative one. The process of functional homogenization has serious consequences for biodiversity conservation because some functions may disappear that, in the long term, would threaten the fragments. This study contributes to a better understanding of how landscape changes affect the functional diversity, abundance of individuals in RFTs and the process of functional homogenization, as well as how to manage fragmented landscapes. PMID:27760218

Hydrochemical buffer assessment in agricultural landscapes: from local to catchment scale.

PubMed

Viaud, Valérie; Merot, Philippe; Baudry, Jacques

2004-10-01

Non-point-source pollution of surface and groundwater is a prominent environmental issue in rural catchments, with major consequences on water supply and aquatic ecosystem quality. Among surface-water protection measures, environmental or landscape management policies support the implementation and the management of buffer zones. Although a great number of studies have focused on buffer zones, quantification of the buffer effect is still a recurring question. The purpose of this article is a critical review of the assessment of buffer-zone functioning. Our objective is to provide land planners and managers with a set of variables to assess the limits and possibilities for quantifying buffer impact at the catchment scale. We first consider the scale of the local landscape feature. The most commonly used empirical method for assessing buffers is to calculate water/nutrient budgets from inflow-outflow monitoring at the level of landscape structures. We show that several other parameters apart from mean depletion of flux can be used to describe buffer functions. Such parameters include variability, with major implication for water management. We develop a theoretical framework to clarify the assessment of the buffer effect and propose a systematic analysis taking account of temporal variability. Second, we review the current assessment of buffer effects at the catchment scale according to the theoretical framework established at the local scale. Finally, we stress the limits of direct empirical assessment at the catchment scale and, in particular, we emphasize the hierarchy in hydrological processes involved at the catchment scale: The landscape feature function is constrained by other factors (climate and geology) that are of importance at a broader spatial and temporal scale.

Analysis of landscape character for visual resource management

Treesearch

Paul F. Anderson

1979-01-01

Description, classification and delineation of visual landscape character are initial steps in developing visual resource management plans. Landscape characteristics identified as key factors in visual landscape analysis include land cover/land use and landform. Landscape types, which are combinations of landform and surface features, were delineated for management...

Targeting Neuronal-like Metabolism of Metastatic Tumor Cells as a Novel Therapy for Breast Cancer Brain Metastasis

DTIC Science & Technology

2017-03-01

Contribution to Project: Ian primarily focuses on developing tissue imaging pipeline and perform imaging data analysis . Funding Support: Partially...3D ReconsTruction), a multi-faceted image analysis pipeline , permitting quantitative interrogation of functional implications of heterogeneous... analysis pipeline , to observe and quantify phenotypic metastatic landscape heterogeneity in situ with spatial and molecular resolution. Our implementation

Comparing production function models for wildfire risk analysis in the wildland-urban interface

Treesearch

D. Evan Mercer; Jeffrey P. Prestemon

2005-01-01

Wildfires create damages in the wildland-urban interface (WUI) that total hundreds of millions of dollars annually in the United States. Understanding how fires are produced in built-up areas near and within fire prone landscapes requires evaluating and quantifling the roles that humans play in fire regimes. We outline a typology of wildfire production functions (WPFs...

Simulating forest management and its effect on landscape pattern

Treesearch

Eric J. Gustafson

2017-01-01

Landscapes are characterized by their structure (the spatial arrangement of landscape elements), their ecological function (how ecological processes operate within that structure), and the dynamics of change (disturbance and recovery). Thus, understanding the dynamic nature of landscapes and predicting their future dynamics are of particular emphasis. Landscape change...

Functional diversity response to hardwood forest management varies across taxa and spatial scales.

PubMed

Murray, Bryan D; Holland, Jeffrey D; Summerville, Keith S; Dunning, John B; Saunders, Michael R; Jenkins, Michael A

2017-06-01

Contemporary forest management offers a trade-off between the potential positive effects of habitat heterogeneity on biodiversity, and the potential harm to mature forest communities caused by habitat loss and perforation of the forest canopy. While the response of taxonomic diversity to forest management has received a great deal of scrutiny, the response of functional diversity is largely unexplored. However, functional diversity may represent a more direct link between biodiversity and ecosystem function. To examine how forest management affects diversity at multiple spatial scales, we analyzed a long-term data set that captured changes in taxonomic and functional diversity of moths (Lepidoptera), longhorned beetles (Coleoptera: Cerambycidae), and breeding birds in response to contemporary silvicultural systems in oak-hickory hardwood forests. We used these data sets to address the following questions: how do even- and uneven-aged silvicultural systems affect taxonomic and functional diversity at the scale of managed landscapes compared to the individual harvested and unharvested forest patches that comprise the landscapes, and how do these silvicultural systems affect the functional similarity of assemblages at the scale of managed landscapes and patches? Due to increased heterogeneity within landscapes, we expected even-aged silviculture to increase and uneven-aged silviculture to decrease functional diversity at the landscape level regardless of impacts at the patch level. Functional diversity responses were taxon-specific with respect to the direction of change and time since harvest. Responses were also consistent across patch and landscape levels within each taxon. Moth assemblage species richness, functional richness, and functional divergence were negatively affected by harvesting, with stronger effects resulting from uneven-aged than even-aged management. Longhorned beetle assemblages exhibited a peak in species richness two years after harvesting, while functional diversity metrics did not differ between harvested and unharvested patches and managed landscapes. The species and functional richness of breeding bird assemblages increased in response to harvesting with more persistent effects in uneven- than in even-aged managed landscapes. For moth and bird assemblages, species turnover was driven by species with more extreme trait combinations. Our study highlights the variability of multi-taxon functional diversity in response to forest management across multiple spatial scales. © 2017 by the Ecological Society of America.

Mapping the Conformation Space of Wildtype and Mutant H-Ras with a Memetic, Cellular, and Multiscale Evolutionary Algorithm

PubMed Central

Clausen, Rudy; Ma, Buyong; Nussinov, Ruth; Shehu, Amarda

2015-01-01

An important goal in molecular biology is to understand functional changes upon single-point mutations in proteins. Doing so through a detailed characterization of structure spaces and underlying energy landscapes is desirable but continues to challenge methods based on Molecular Dynamics. In this paper we propose a novel algorithm, SIfTER, which is based instead on stochastic optimization to circumvent the computational challenge of exploring the breadth of a protein’s structure space. SIfTER is a data-driven evolutionary algorithm, leveraging experimentally-available structures of wildtype and variant sequences of a protein to define a reduced search space from where to efficiently draw samples corresponding to novel structures not directly observed in the wet laboratory. The main advantage of SIfTER is its ability to rapidly generate conformational ensembles, thus allowing mapping and juxtaposing landscapes of variant sequences and relating observed differences to functional changes. We apply SIfTER to variant sequences of the H-Ras catalytic domain, due to the prominent role of the Ras protein in signaling pathways that control cell proliferation, its well-studied conformational switching, and abundance of documented mutations in several human tumors. Many Ras mutations are oncogenic, but detailed energy landscapes have not been reported until now. Analysis of SIfTER-computed energy landscapes for the wildtype and two oncogenic variants, G12V and Q61L, suggests that these mutations cause constitutive activation through two different mechanisms. G12V directly affects binding specificity while leaving the energy landscape largely unchanged, whereas Q61L has pronounced, starker effects on the landscape. An implementation of SIfTER is made available at http://www.cs.gmu.edu/~ashehu/?q=OurTools. We believe SIfTER is useful to the community to answer the question of how sequence mutations affect the function of a protein, when there is an abundance of experimental structures that can be exploited to reconstruct an energy landscape that would be computationally impractical to do via Molecular Dynamics. PMID:26325505

Validation of elk resource selection models with spatially independent data

Treesearch

Priscilla K. Coe; Bruce K. Johnson; Michael J. Wisdom; John G. Cook; Marty Vavra; Ryan M. Nielson

2011-01-01

Knowledge of how landscape features affect wildlife resource use is essential for informed management. Resource selection functions often are used to make and validate predictions about landscape use; however, resource selection functions are rarely validated with data from landscapes independent of those from which the models were built. This problem has severely...

Anticipating Forest and Range Land Development in Central Oregon (USA) for Landscape Analysis, with an Example Application Involving Mule Deer

NASA Astrophysics Data System (ADS)

Kline, Jeffrey D.; Moses, Alissa; Burcsu, Theresa

2010-05-01

Forest policymakers, public lands managers, and scientists in the Pacific Northwest (USA) seek ways to evaluate the landscape-level effects of policies and management through the multidisciplinary development and application of spatially explicit methods and models. The Interagency Mapping and Analysis Project (IMAP) is an ongoing effort to generate landscape-wide vegetation data and models to evaluate the integrated effects of disturbances and management activities on natural resource conditions in Oregon and Washington (USA). In this initial analysis, we characterized the spatial distribution of forest and range land development in a four-county pilot study region in central Oregon. The empirical model describes the spatial distribution of buildings and new building construction as a function of population growth, existing development, topography, land-use zoning, and other factors. We used the model to create geographic information system maps of likely future development based on human population projections to inform complementary landscape analyses underway involving vegetation, habitat, and wildfire interactions. In an example application, we use the model and resulting maps to show the potential impacts of future forest and range land development on mule deer ( Odocoileus hemionus) winter range. Results indicate significant development encroachment and habitat loss already in 2000 with development located along key migration routes and increasing through the projection period to 2040. The example application illustrates a simple way for policymakers and public lands managers to combine existing data and preliminary model outputs to begin to consider the potential effects of development on future landscape conditions.

Topological data analysis of financial time series: Landscapes of crashes

NASA Astrophysics Data System (ADS)

Gidea, Marian; Katz, Yuri

2018-02-01

We explore the evolution of daily returns of four major US stock market indices during the technology crash of 2000, and the financial crisis of 2007-2009. Our methodology is based on topological data analysis (TDA). We use persistence homology to detect and quantify topological patterns that appear in multidimensional time series. Using a sliding window, we extract time-dependent point cloud data sets, to which we associate a topological space. We detect transient loops that appear in this space, and we measure their persistence. This is encoded in real-valued functions referred to as a 'persistence landscapes'. We quantify the temporal changes in persistence landscapes via their Lp-norms. We test this procedure on multidimensional time series generated by various non-linear and non-equilibrium models. We find that, in the vicinity of financial meltdowns, the Lp-norms exhibit strong growth prior to the primary peak, which ascends during a crash. Remarkably, the average spectral density at low frequencies of the time series of Lp-norms of the persistence landscapes demonstrates a strong rising trend for 250 trading days prior to either dotcom crash on 03/10/2000, or to the Lehman bankruptcy on 09/15/2008. Our study suggests that TDA provides a new type of econometric analysis, which complements the standard statistical measures. The method can be used to detect early warning signals of imminent market crashes. We believe that this approach can be used beyond the analysis of financial time series presented here.

Landscape genomics in Atlantic salmon (Salmo salar): searching for gene-environment interactions driving local adaptation.

PubMed

Vincent, Bourret; Dionne, Mélanie; Kent, Matthew P; Lien, Sigbjørn; Bernatchez, Louis

2013-12-01

A growing number of studies are examining the factors driving historical and contemporary evolution in wild populations. By combining surveys of genomic variation with a comprehensive assessment of environmental parameters, such studies can increase our understanding of the genomic and geographical extent of local adaptation in wild populations. We used a large-scale landscape genomics approach to examine adaptive and neutral differentiation across 54 North American populations of Atlantic salmon representing seven previously defined genetically distinct regional groups. Over 5500 genome-wide single nucleotide polymorphisms were genotyped in 641 individuals and 28 bulk assays of 25 pooled individuals each. Genome scans, linkage map, and 49 environmental variables were combined to conduct an innovative landscape genomic analysis. Our results provide valuable insight into the links between environmental variation and both neutral and potentially adaptive genetic divergence. In particular, we identified markers potentially under divergent selection, as well as associated selective environmental factors and biological functions with the observed adaptive divergence. Multivariate landscape genetic analysis revealed strong associations of both genetic and environmental structures. We found an enrichment of growth-related functions among outlier markers. Climate (temperature-precipitation) and geological characteristics were significantly associated with both potentially adaptive and neutral genetic divergence and should be considered as candidate loci involved in adaptation at the regional scale in Atlantic salmon. Hence, this study significantly contributes to the improvement of tools used in modern conservation and management schemes of Atlantic salmon wild populations. © 2013 The Author(s). Evolution © 2013 The Society for the Study of Evolution.

[Recognition of landscape characteristic scale based on two-dimension wavelet analysis].

PubMed

Gao, Yan-Ni; Chen, Wei; He, Xing-Yuan; Li, Xiao-Yu

2010-06-01

Three wavelet bases, i. e., Haar, Daubechies, and Symlet, were chosen to analyze the validity of two-dimension wavelet analysis in recognizing the characteristic scales of the urban, peri-urban, and rural landscapes of Shenyang. Owing to the transform scale of two-dimension wavelet must be the integer power of 2, some characteristic scales cannot be accurately recognized. Therefore, the pixel resolution of images was resampled to 3, 3.5, 4, and 4.5 m to densify the scale in analysis. It was shown that two-dimension wavelet analysis worked effectively in checking characteristic scale. Haar, Daubechies, and Symle were the optimal wavelet bases to the peri-urban landscape, urban landscape, and rural landscape, respectively. Both Haar basis and Symlet basis played good roles in recognizing the fine characteristic scale of rural landscape and in detecting the boundary of peri-urban landscape. Daubechies basis and Symlet basis could be also used to detect the boundary of urban landscape and rural landscape, respectively.

Dynamics and function of distal regulatory elements during neurogenesis and neuroplasticity

PubMed Central

Thakurela, Sudhir; Sahu, Sanjeeb Kumar; Garding, Angela; Tiwari, Vijay K.

2015-01-01

Gene regulation in mammals involves a complex interplay between promoters and distal regulatory elements that function in concert to drive precise spatiotemporal gene expression programs. However, the dynamics of the distal gene regulatory landscape and its function in the transcriptional reprogramming that underlies neurogenesis and neuronal activity remain largely unknown. Here, we performed a combinatorial analysis of genome-wide data sets for chromatin accessibility (FAIRE-seq) and the enhancer mark H3K27ac, revealing the highly dynamic nature of distal gene regulation during neurogenesis, which gets progressively restricted to distinct genomic regions as neurons acquire a post-mitotic, terminally differentiated state. We further find that the distal accessible and active regions serve as target sites for distinct transcription factors that function in a stage-specific manner to contribute to the transcriptional program underlying neuronal commitment and maturation. Mature neurons respond to a sustained activity of NMDA receptors by epigenetic reprogramming at a large number of distal regulatory regions as well as dramatic reorganization of super-enhancers. Such massive remodeling of the distal regulatory landscape in turn results in a transcriptome that confers a transient loss of neuronal identity and gain of cellular plasticity. Furthermore, NMDA receptor activity also induces many novel prosurvival genes that function in neuroprotective pathways. Taken together, these findings reveal the dynamics of the distal regulatory landscape during neurogenesis and uncover novel regulatory elements that function in concert with epigenetic mechanisms and transcription factors to generate the transcriptome underlying neuronal development and activity. PMID:26170447

Conceptual ecological models to guide integrated landscape monitoring of the Great Basin

USGS Publications Warehouse

Miller, D.M.; Finn, S.P.; Woodward, Andrea; Torregrosa, Alicia; Miller, M.E.; Bedford, D.R.; Brasher, A.M.

2010-01-01

The Great Basin Integrated Landscape Monitoring Pilot Project was developed in response to the need for a monitoring and predictive capability that addresses changes in broad landscapes and waterscapes. Human communities and needs are nested within landscapes formed by interactions among the hydrosphere, geosphere, and biosphere. Understanding the complex processes that shape landscapes and deriving ways to manage them sustainably while meeting human needs require sophisticated modeling and monitoring. This document summarizes current understanding of ecosystem structure and function for many of the ecosystems within the Great Basin using conceptual models. The conceptual ecosystem models identify key ecological components and processes, identify external drivers, develop a hierarchical set of models that address both site and landscape attributes, inform regional monitoring strategy, and identify critical gaps in our knowledge of ecosystem function. The report also illustrates an approach for temporal and spatial scaling from site-specific models to landscape models and for understanding cumulative effects. Eventually, conceptual models can provide a structure for designing monitoring programs, interpreting monitoring and other data, and assessing the accuracy of our understanding of ecosystem functions and processes.

Landscape genetics of high mountain frog metapopulations

USGS Publications Warehouse

Murphy, M.A.; Dezzani, R.; Pilliod, D.S.; Storfer, A.

2010-01-01

Explaining functional connectivity among occupied habitats is crucial for understanding metapopulation dynamics and species ecology. Landscape genetics has primarily focused on elucidating how ecological features between observations influence gene flow. Functional connectivity, however, may be the result of both these between-site (landscape resistance) landscape characteristics and at-site (patch quality) landscape processes that can be captured using network based models. We test hypotheses of functional connectivity that include both between-site and at-site landscape processes in metapopulations of Columbia spotted frogs (Rana luteiventris) by employing a novel justification of gravity models for landscape genetics (eight microsatellite loci, 37 sites, n = 441). Primarily used in transportation and economic geography, gravity models are a unique approach as flow (e.g. gene flow) is explained as a function of three basic components: distance between sites, production/attraction (e.g. at-site landscape process) and resistance (e.g. between-site landscape process). The study system contains a network of nutrient poor high mountain lakes where we hypothesized a short growing season and complex topography between sites limit R. luteiventris gene flow. In addition, we hypothesized production of offspring is limited by breeding site characteristics such as the introduction of predatory fish and inherent site productivity. We found that R. luteiventris connectivity was negatively correlated with distance between sites, presence of predatory fish (at-site) and topographic complexity (between-site). Conversely, site productivity (as measured by heat load index, at-site) and growing season (as measured by frost-free period between-sites) were positively correlated with gene flow. The negative effect of predation and positive effect of site productivity, in concert with bottleneck tests, support the presence of source-sink dynamics. In conclusion, gravity models provide a powerful new modelling approach for examining a wide range of both basic and applied questions in landscape genetics.

Framework and tools for agricultural landscape assessment relating to water quality protection.

PubMed

Gascuel-Odoux, Chantal; Massa, Florence; Durand, Patrick; Merot, Philippe; Troccaz, Olivier; Baudry, Jacques; Thenail, Claudine

2009-05-01

While many scientific studies show the influence of agricultural landscape patterns on water cycle and water quality, only a few of these have proposed scientifically based and operational methods to improve water management. Territ'eau is a framework developed to adapt agricultural landscapes to water quality protection, using components such as farmers' fields, seminatural areas, and human infrastructures, which can act as sources, sinks, or buffers on water quality. This framework allows us to delimit active areas contributing to water quality, defined by the following three characteristics: (i) the dominant hydrological processes and their flow pathways, (ii) the characteristics of each considered pollutant, and (iii) the main landscape features. These areas are delineated by analyzing the flow connectivity from the stream to the croplands, by assessing the buffer functions of seminatural areas according to their flow pathways. Hence, this framework allows us to identify functional seminatural areas in terms of water quality and assess their limits and functions; it helps in proposing different approaches for changing agricultural landscape, acting on agricultural practices or systems, and/or conserving or rebuilding seminatural areas in controversial landscapes. Finally, it allows us to objectivize the functions of the landscape components, for adapting these components to new environmental constraints.

Fitness Landscapes of Functional RNAs.

PubMed

Kun, Ádám; Szathmáry, Eörs

2015-08-21

The notion of fitness landscapes, a map between genotype and fitness, was proposed more than 80 years ago. For most of this time data was only available for a few alleles, and thus we had only a restricted view of the whole fitness landscape. Recently, advances in genetics and molecular biology allow a more detailed view of them. Here we review experimental and theoretical studies of fitness landscapes of functional RNAs, especially aptamers and ribozymes. We find that RNA structures can be divided into critical structures, connecting structures, neutral structures and forbidden structures. Such characterisation, coupled with theoretical sequence-to-structure predictions, allows us to construct the whole fitness landscape. Fitness landscapes then can be used to study evolution, and in our case the development of the RNA world.

The patch mosaic and ecological decomposition across spatial scales in a managed landscape of northern Wisconsin, USA

Treesearch

Sari C. ​Saunders; Jiquan Chen; Thomas D. Drummer; Thomas R. Crow; Kimberley D. Brosofske; Eric J. Gustafson

2002-01-01

Understanding landscape organization across scales is vital for determining the impacts of management and retaining structurally and functionally diverse ecosystems. We studied the relationships of a functional variable, decomposition, to microclimatic, vegetative and structural features at multiple scales in two distinct landscapes of northern Wisconsin, USA. We hoped...

Influence of Interspecific Competition and Landscape Structure on Spatial Homogenization of Avian Assemblages

PubMed Central

Robertson, Oliver J.; McAlpine, Clive; House, Alan; Maron, Martine

2013-01-01

Human-induced biotic homogenization resulting from landscape change and increased competition from widespread generalists or ‘winners’, is widely recognized as a global threat to biodiversity. However, it remains unclear what aspects of landscape structure influence homogenization. This paper tests the importance of interspecific competition and landscape structure, for the spatial homogeneity of avian assemblages within a fragmented agricultural landscape of eastern Australia. We used field observations of the density of 128 diurnal bird species to calculate taxonomic and functional similarity among assemblages. We then examined whether taxonomic and functional similarity varied with patch type, the extent of woodland habitat, land-use intensity, habitat subdivision, and the presence of Manorina colonies (a competitive genus of honeyeaters). We found the presence of a Manorina colony was the most significant factor positively influencing both taxonomic and functional similarity of bird assemblages. Competition from members of this widespread genus of native honeyeater, rather than landscape structure, was the main cause of both taxonomic and functional homogenization. These species have not recently expanded their range, but rather have increased in density in response to agricultural landscape change. The negative impacts of Manorina honeyeaters on assemblage similarity were most pronounced in landscapes of moderate land-use intensity. We conclude that in these human-modified landscapes, increased competition from dominant native species, or ‘winners’, can result in homogeneous avian assemblages and the loss of specialist species. These interacting processes make biotic homogenization resulting from land-use change a global threat to biodiversity in modified agro-ecosystems. PMID:23724136

Environmental condition assessment of US military installations using GIS based spatial multi-criteria decision analysis.

PubMed

Singer, Steve; Wang, Guangxing; Howard, Heidi; Anderson, Alan

2012-08-01

Environment functions in various aspects including soil and water conservation, biodiversity and habitats, and landscape aesthetics. Comprehensive assessment of environmental condition is thus a great challenge. The issues include how to assess individual environmental components such as landscape aesthetics and integrate them into an indicator that can comprehensively quantify environmental condition. In this study, a geographic information systems based spatial multi-criteria decision analysis was used to integrate environmental variables and create the indicator. This approach was applied to Fort Riley Military installation in which land condition and its dynamics due to military training activities were assessed. The indicator was derived by integrating soil erosion, water quality, landscape fragmentation, landscape aesthetics, and noise based on the weights from the experts by assessing and ranking the environmental variables in terms of their importance. The results showed that landscape level indicator well quantified the overall environmental condition and its dynamics, while the indicator at level of patch that is defined as a homogeneous area that is different from its surroundings detailed the spatiotemporal variability of environmental condition. The environmental condition was mostly determined by soil erosion, then landscape fragmentation, water quality, landscape aesthetics, and noise. Overall, environmental condition at both landscape and patch levels greatly varied depending on the degree of ground and canopy disturbance and their spatial patterns due to military training activities and being related to slope. It was also determined the environment itself could be recovered quickly once military training was halt or reduced. Thus, this study provided an effective tool for the army land managers to monitor environmental dynamics and plan military training activities. Its limitation lies at that the obtained values of the indicator vary and are subjective to the experts' knowledge and experience. Thus, further advancing this approach is needed by developing a scientific method to derive the weights of environmental variables.

Exploring constrained quantum control landscapes

NASA Astrophysics Data System (ADS)

Moore, Katharine W.; Rabitz, Herschel

2012-10-01

The broad success of optimally controlling quantum systems with external fields has been attributed to the favorable topology of the underlying control landscape, where the landscape is the physical observable as a function of the controls. The control landscape can be shown to contain no suboptimal trapping extrema upon satisfaction of reasonable physical assumptions, but this topological analysis does not hold when significant constraints are placed on the control resources. This work employs simulations to explore the topology and features of the control landscape for pure-state population transfer with a constrained class of control fields. The fields are parameterized in terms of a set of uniformly spaced spectral frequencies, with the associated phases acting as the controls. This restricted family of fields provides a simple illustration for assessing the impact of constraints upon seeking optimal control. Optimization results reveal that the minimum number of phase controls necessary to assure a high yield in the target state has a special dependence on the number of accessible energy levels in the quantum system, revealed from an analysis of the first- and second-order variation of the yield with respect to the controls. When an insufficient number of controls and/or a weak control fluence are employed, trapping extrema and saddle points are observed on the landscape. When the control resources are sufficiently flexible, solutions producing the globally maximal yield are found to form connected "level sets" of continuously variable control fields that preserve the yield. These optimal yield level sets are found to shrink to isolated points on the top of the landscape as the control field fluence is decreased, and further reduction of the fluence turns these points into suboptimal trapping extrema on the landscape. Although constrained control fields can come in many forms beyond the cases explored here, the behavior found in this paper is illustrative of the impacts that constraints can introduce.

Simulation of the Vortex Dynamics in a Real Pinning Landscape of YBa 2 Cu 3 O 7 - δ Coated Conductors

DOE PAGES

Sadovskyy, I. A.; Koshelev, A. E.; Glatz, A.; ...

2016-01-01

The ability of high-temperature superconductors (HTSs) to carry very large currents with almost no dissipation makes them irreplaceable for high-power applications. The development and further improvement of HTS-based cables require an in-depth understanding of the superconducting vortex dynamics in the presence of complex pinning landscapes. We present a critical current analysis of a real HTS sample in a magnetic field by combining state-of-the-art large-scale Ginzburg-Landau simulations with reconstructive three-dimensional scanning-transmission-electron-microscopy tomography of the pinning landscape in Dy-doped YBa 2Cu 3O 7-δ. This methodology provides a unique look at the vortex dynamics in the presence of a complex pinning landscape responsiblemore » for the high-current-carrying-capacity characteristic of commercial HTS wires. Finally, our method demonstrates very good functional and quantitative agreement of the critical current between simulation and experiment, providing a new predictive tool for HTS wire designs.« less

Simulation of the Vortex Dynamics in a Real Pinning Landscape of YBa 2 Cu 3 O 7 - δ Coated Conductors

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

Sadovskyy, I. A.; Koshelev, A. E.; Glatz, A.

The ability of high-temperature superconductors (HTSs) to carry very large currents with almost no dissipation makes them irreplaceable for high-power applications. The development and further improvement of HTS-based cables require an in-depth understanding of the superconducting vortex dynamics in the presence of complex pinning landscapes. We present a critical current analysis of a real HTS sample in a magnetic field by combining state-of-the-art large-scale Ginzburg-Landau simulations with reconstructive three-dimensional scanning-transmission-electron-microscopy tomography of the pinning landscape in Dy-doped YBa 2Cu 3O 7-δ. This methodology provides a unique look at the vortex dynamics in the presence of a complex pinning landscape responsiblemore » for the high-current-carrying-capacity characteristic of commercial HTS wires. Finally, our method demonstrates very good functional and quantitative agreement of the critical current between simulation and experiment, providing a new predictive tool for HTS wire designs.« less

Simulation of the Vortex Dynamics in a Real Pinning Landscape of YBa 2 Cu 3 O 7 - δ Coated Conductors

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

Sadovskyy, I. A.; Koshelev, A. E.; Glatz, A.

Tmore » he ability of high-temperature superconductors (HSs) to carry very large currents with almost no dissipation makes them irreplaceable for high-power applications. he development and further improvement of HS-based cables require an in-depth understanding of the superconducting vortex dynamics in the presence of complex pinning landscapes. Here, we present a critical current analysis of a real HS sample in a magnetic field by combining state-of-the-art large-scale Ginzburg-Landau simulations with reconstructive three-dimensional scanning-transmission-electron-microscopy tomography of the pinning landscape in Dy-doped YBa 2 Cu 3 O 7 - δ . his methodology provides a unique look at the vortex dynamics in the presence of a complex pinning landscape responsible for the high-current-carrying-capacity characteristic of commercial HS wires. Our method demonstrates very good functional and quantitative agreement of the critical current between simulation and experiment, providing a new predictive tool for HS wire designs.« less

The Landscape Evolution Observatory: a large-scale controllable infrastructure to study coupled Earth-surface processes

USGS Publications Warehouse

Pangle, Luke A.; DeLong, Stephen B.; Abramson, Nate; Adams, John; Barron-Gafford, Greg A.; Breshears, David D.; Brooks, Paul D.; Chorover, Jon; Dietrich, William E.; Dontsova, Katerina; Durcik, Matej; Espeleta, Javier; Ferré, T.P.A.; Ferriere, Regis; Henderson, Whitney; Hunt, Edward A.; Huxman, Travis E.; Millar, David; Murphy, Brendan; Niu, Guo-Yue; Pavao-Zuckerman, Mitch; Pelletier, Jon D.; Rasmussen, Craig; Ruiz, Joaquin; Saleska, Scott; Schaap, Marcel; Sibayan, Michael; Troch, Peter A.; Tuller, Markus; van Haren, Joost; Zeng, Xubin

2015-01-01

Zero-order drainage basins, and their constituent hillslopes, are the fundamental geomorphic unit comprising much of Earth's uplands. The convergent topography of these landscapes generates spatially variable substrate and moisture content, facilitating biological diversity and influencing how the landscape filters precipitation and sequesters atmospheric carbon dioxide. In light of these significant ecosystem services, refining our understanding of how these functions are affected by landscape evolution, weather variability, and long-term climate change is imperative. In this paper we introduce the Landscape Evolution Observatory (LEO): a large-scale controllable infrastructure consisting of three replicated artificial landscapes (each 330 m2 surface area) within the climate-controlled Biosphere 2 facility in Arizona, USA. At LEO, experimental manipulation of rainfall, air temperature, relative humidity, and wind speed are possible at unprecedented scale. The Landscape Evolution Observatory was designed as a community resource to advance understanding of how topography, physical and chemical properties of soil, and biological communities coevolve, and how this coevolution affects water, carbon, and energy cycles at multiple spatial scales. With well-defined boundary conditions and an extensive network of sensors and samplers, LEO enables an iterative scientific approach that includes numerical model development and virtual experimentation, physical experimentation, data analysis, and model refinement. We plan to engage the broader scientific community through public dissemination of data from LEO, collaborative experimental design, and community-based model development.

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.

The importance of biodiversity and dominance for multiple ecosystem functions in a human-modified tropical landscape.

PubMed

Lohbeck, Madelon; Bongers, Frans; Martinez-Ramos, Miguel; Poorter, Lourens

2016-10-01

Many studies suggest that biodiversity may be particularly important for ecosystem multifunctionality, because different species with different traits can contribute to different functions. Support, however, comes mostly from experimental studies conducted at small spatial scales in low-diversity systems. Here, we test whether different species contribute to different ecosystem functions that are important for carbon cycling in a high-diversity human-modified tropical forest landscape in Southern Mexico. We quantified aboveground standing biomass, primary productivity, litter production, and wood decomposition at the landscape level, and evaluated the extent to which tree species contribute to these ecosystem functions. We used simulations to tease apart the effects of species richness, species dominance and species functional traits on ecosystem functions. We found that dominance was more important than species traits in determining a species' contribution to ecosystem functions. As a consequence of the high dominance in human-modified landscapes, the same small subset of species mattered across different functions. In human-modified landscapes in the tropics, biodiversity may play a limited role for ecosystem multifunctionality due to the potentially large effect of species dominance on biogeochemical functions. However, given the spatial and temporal turnover in species dominance, biodiversity may be critically important for the maintenance and resilience of ecosystem functions. © 2016 The Authors. Ecology, published by Wiley Periodicals, Inc., on behalf of the Ecological Society of America.

Inferring genome-wide interplay landscape between DNA methylation and transcriptional regulation.

PubMed

Tang, Binhua; Wang, Xin

2015-01-01

DNA methylation and transcriptional regulation play important roles in cancer cell development and differentiation processes. Based on the currently available cell line profiling information from the ENCODE Consortium, we propose a Bayesian inference model to infer and construct genome-wide interaction landscape between DNA methylation and transcriptional regulation, which sheds light on the underlying complex functional mechanisms important within the human cancer and disease context. For the first time, we select all the currently available cell lines (>=20) and transcription factors (>=80) profiling information from the ENCODE Consortium portal. Through the integration of those genome-wide profiling sources, our genome-wide analysis detects multiple functional loci of interest, and indicates that DNA methylation is cell- and region-specific, due to the interplay mechanisms with transcription regulatory activities. We validate our analysis results with the corresponding RNA-sequencing technique for those detected genomic loci. Our results provide novel and meaningful insights for the interplay mechanisms of transcriptional regulation and gene expression for the human cancer and disease studies.

The evolutionary landscape of intergenic trans-splicing events in insects

PubMed Central

Kong, Yimeng; Zhou, Hongxia; Yu, Yao; Chen, Longxian; Hao, Pei; Li, Xuan

2015-01-01

To explore the landscape of intergenic trans-splicing events and characterize their functions and evolutionary dynamics, we conduct a mega-data study of a phylogeny containing eight species across five orders of class Insecta, a model system spanning 400 million years of evolution. A total of 1,627 trans-splicing events involving 2,199 genes are identified, accounting for 1.58% of the total genes. Homology analysis reveals that mod(mdg4)-like trans-splicing is the only conserved event that is consistently observed in multiple species across two orders, which represents a unique case of functional diversification involving trans-splicing. Thus, evolutionarily its potential for generating proteins with novel function is not broadly utilized by insects. Furthermore, 146 non-mod trans-spliced transcripts are found to resemble canonical genes from different species. Trans-splicing preserving the function of ‘breakup' genes may serve as a general mechanism for relaxing the constraints on gene structure, with profound implications for the evolution of genes and genomes. PMID:26521696

How vegetation and sediment transport feedbacks drive landscape change in the Everglades and wetlands worldwide

USGS Publications Warehouse

Larsen, Laurel G.; Harvey, Judson W.

2010-01-01

Mechanisms reported to promote landscape self‐organization cannot explain vegetation patterning oriented parallel to flow. Recent catastrophic shifts in Everglades landscape pattern and ecological function highlight the need to understand the feedbacks governing these ecosystems. We modeled feedback between vegetation, hydrology, and sediment transport on the basis of a decade of experimentation. Results from more than 100 simulations showed that flows just sufficient to redistribute sediment from sparsely vegetated sloughs to dense ridges were needed for an equilibrium patterned landscape oriented parallel to flow. Surprisingly, although vegetation heterogeneity typically conveys resilience, in wetlands governed by flow/sediment feedbacks it indicates metastability, whereby the landscape is prone to catastrophic shifts. Substantial increases or decreases in flow relative to the equilibrium condition caused an expansion of emergent vegetation and loss of open‐water areas that was unlikely to revert upon restoration of the equilibrium hydrology. Understanding these feedbacks is critical in forecasting wetland responses to changing conditions and designing management strategies that optimize ecosystem services, such as carbon sequestration or habitat provision. Our model and new sensitivity analysis techniques address these issues and make it newly apparent that simply returning flow to predrainage conditions in the Everglades may not be sufficient to restore historic landscape patterns and processes.

State of the science and challenges of breeding landscape plants with ecological function

PubMed Central

Wilde, H Dayton; Gandhi, Kamal J K; Colson, Gregory

2015-01-01

Exotic plants dominate esthetically-managed landscapes, which cover 30–40 million hectares in the United States alone. Recent ecological studies have found that landscaping with exotic plant species can reduce biodiversity on multiple trophic levels. To support biodiversity in urbanized areas, the increased use of native landscaping plants has been advocated by conservation groups and US federal and state agencies. A major challenge to scaling up the use of native species in landscaping is providing ornamental plants that are both ecologically functional and economically viable. Depending on ecological and economic constraints, accelerated breeding approaches could be applied to ornamental trait development in native plants. This review examines the impact of landscaping choices on biodiversity, the current status of breeding and selection of native ornamental plants, and the interdisciplinary research needed to scale up landscaping plants that can support native biodiversity. PMID:26504560

[Identification of ecological corridors and its importance by integrating circuit theory].

PubMed

Song, Li Li; Qin, Ming Zhou

2016-10-01

Landscape connectivity is considered as an extraordinarily important factor affecting various ecological processes. The least cost path (LCP) on the basis of minimum cumulative resis-tance model (MCRM) may provide a more efficient approach to identify functional connectivity in heterogeneous landscapes, and is already adopted by the research of landscape functional connecti-vity assessment and ecological corridor simulation. Connectivity model on circuit theory (CMCT) replaced the edges in the graph theory with resistors, cost distance with resistance distance to measure the functional connectivity in heterogeneous landscapes. By means of Linkage Mapper tool and Circuitscape software, the simulated landscape generated from SIMMAP 2.0 software was viewed as the study object in this article, aimed at exploring how to integrate MCRM with CMCT to identify ecological corridors and relative importance of landscape factors. The results showed that two models had their individual advantages and mutual complement. MCRM could effectively identify least cost corridors among habitats. CMCT could effectively identify important landscape factor and pinch point, which had important influence on landscape connectivity. We also found that the position of pinch point was not affected by corridor width, which had obvious advantage in the research of identifying the importance of corridors. The integrated method could provide certain scientific basis for regional ecological protection planning and ecological corridor design.

Spatial organization of agricultural landscape, farming activities and hydrological risk assessment

NASA Astrophysics Data System (ADS)

Viaud, V.; Merot, P.

2003-04-01

Agriculture intensification is considered as a major cause of water pollution since it has gone both with an increasing use of fertilisers and significant changes in land-use patterns. Among the prescriptions for pollution control, the management of buffer zones at the landscape scale is supported by the environmental policies, but often without consideration of the systems of human activities they are aimed at. Agricultural landscapes, with fields potentially source of pollution and buffer zones, are spatially organized and managed by farming activities. In a perspective of sustainable management, an integrating approach of environmental issues and farming activities is thus required. This approach was applied to bocage landscapes (landscapes with cultivated fields surrounded by hedgerow systems) in Brittany (Western France). Bocage landscapes are frequently encountered, especially in Europe, and many studies put forward their hydrological and hydrochemical buffer functions. Those results provide informations on the link between spatial organization of hedgerow systems and their environmental effectiveness. They enable to design models of functional bocage landscapes. The objective of this work was to pick out, among those theoretical models, the models compatible with the farming activities. The results will be presented and the additional constraints for the farming systems created by a functional landscape, from a hydrological and hydrochemical perspective, will be discussed.

Land use changing and land use optimization of Lake Baikal basin on the example of two key areas

NASA Astrophysics Data System (ADS)

Solodyankina, S.

2012-04-01

Lake Baikal contains roughly 20% of the world's unfrozen surface fresh water. It was declared a UNESCO World Heritage Site in 1996. Today levels of urbanization and economic stress on environmental resources is increasing on the shorts of the lake Baikal. The potential of economic development (industry, local tourism, and mining) of the Severobaykalsky and Sludyansky districts is rather high although they are characterized not only by beneficial features for local economy but also by considerable disadvantages for nature of this world valuable territory. This investigation show human-caused landscape changes during economic development of the two key areas in Baikal water catchment basin during 10 years (point of reference is 2000 year). Key areas are 1) the Baikalo-Patomskoe highland in the north of the Baikal catchment basin (Severobaykalsky district, Republic of Buryatia); 2) Khamar-Daban mountain system in the south of the Baikal catchment basin (Sludyansky districy, Irkutsk region). Since 2000 year land use of the territory has changed. Areas of agriculture were reduced but recreation activity on the bank of the lake was increased. Methods of GIS analysis and local statistic analysis of landscape characteristic were used. Nature, rural and urban areas ratio are estimated. Vegetation and soil condition assessment were made. The essence of this research is in helping to make decisions linked to upcoming problems: situation identification, evaluation and forecasting of the potential landscape condition, optimization of land use, mitigation of impact and mapping of territories and nature resources which have a high ecological value or endangered by industrial impact. For this purpose landscape maps of the territories on the base of the remote sensing information and field investigations were created. They used to calculate potential landscape functions of the territory without taking into account present impact of anthropogenic actions. Land use maps for years 2000 and 2010 were created to show: 1) how many landscape functions (ecosystem services) have been missed in time period of 2000-2010 years; 2) trends of land use changing. The nature-anthropogenic landscapes classification is developed, where natural and anthropogenic factors are taken into account in one system. It used to considerate of cumulative impacts of anthropogenic actions for each relevant resource, and to analyse of all past, present, and reasonably foreseeable future condition of whole landscape and its components (parent rock, surface and ground water, soil, flora and fauna, air).

Modelling the Constraints of Spatial Environment in Fauna Movement Simulations: Comparison of a Boundaries Accurate Function and a Cost Function

NASA Astrophysics Data System (ADS)

Jolivet, L.; Cohen, M.; Ruas, A.

2015-08-01

Landscape influences fauna movement at different levels, from habitat selection to choices of movements' direction. Our goal is to provide a development frame in order to test simulation functions for animal's movement. We describe our approach for such simulations and we compare two types of functions to calculate trajectories. To do so, we first modelled the role of landscape elements to differentiate between elements that facilitate movements and the ones being hindrances. Different influences are identified depending on landscape elements and on animal species. Knowledge were gathered from ecologists, literature and observation datasets. Second, we analysed the description of animal movement recorded with GPS at fine scale, corresponding to high temporal frequency and good location accuracy. Analysing this type of data provides information on the relation between landscape features and movements. We implemented an agent-based simulation approach to calculate potential trajectories constrained by the spatial environment and individual's behaviour. We tested two functions that consider space differently: one function takes into account the geometry and the types of landscape elements and one cost function sums up the spatial surroundings of an individual. Results highlight the fact that the cost function exaggerates the distances travelled by an individual and simplifies movement patterns. The geometry accurate function represents a good bottom-up approach for discovering interesting areas or obstacles for movements.

Mapping specificity landscapes of RNA-protein interactions by high throughput sequencing.

PubMed

Jankowsky, Eckhard; Harris, Michael E

2017-04-15

To function in a biological setting, RNA binding proteins (RBPs) have to discriminate between alternative binding sites in RNAs. This discrimination can occur in the ground state of an RNA-protein binding reaction, in its transition state, or in both. The extent by which RBPs discriminate at these reaction states defines RBP specificity landscapes. Here, we describe the HiTS-Kin and HiTS-EQ techniques, which combine kinetic and equilibrium binding experiments with high throughput sequencing to quantitatively assess substrate discrimination for large numbers of substrate variants at ground and transition states of RNA-protein binding reactions. We discuss experimental design, practical considerations and data analysis and outline how a combination of HiTS-Kin and HiTS-EQ allows the mapping of RBP specificity landscapes. Copyright © 2017 Elsevier Inc. All rights reserved.

A methodology for creating greenways through multidisciplinary sustainable landscape planning.

PubMed

Pena, Selma Beatriz; Abreu, Maria Manuela; Teles, Rui; Espírito-Santo, Maria Dalila

2010-01-01

This research proposes a methodology for defining greenways via sustainable planning. This approach includes the analysis and discussion of culture and natural processes that occur in the landscape. The proposed methodology is structured in three phases: eco-cultural analysis; synthesis and diagnosis; and proposal. An interdisciplinary approach provides an assessment of the relationships between landscape structure and landscape dynamics, which are essential to any landscape management or land use. The landscape eco-cultural analysis provides a biophysical, dynamic (geomorphologic rate), vegetation (habitats from directive 92/43/EEC) and cultural characterisation. The knowledge obtained by this analysis then supports the definition of priority actions to stabilise the landscape and the management measures for the habitats. After the analysis and diagnosis phases, a proposal for the development of sustainable greenways can be achieved. This methodology was applied to a study area of the Azambuja Municipality in the Lisbon Metropolitan Area (Portugal). The application of the proposed methodology to the study area shows that landscape stability is crucial for greenway users in order to appreciate the landscape and its natural and cultural elements in a sustainable and healthy way, both by cycling or by foot. A balanced landscape will increase the value of greenways and in return, they can develop socio-economic activities with benefits for rural communities. Copyright 2009 Elsevier Ltd. All rights reserved.

Ecological Functions of Landscapes

NASA Astrophysics Data System (ADS)

Kiryushin, V. I.

2018-01-01

Ecological functions of landscapes are considered a system of processes ensuring the development, preservation, and evolution of ecosystems and the biosphere as a whole. The concept of biogeocenosis can be considered a model that integrates biotic and environmental functions. The most general biogeocenotic functions specify the biodiversity, biotic links, self-organization, and evolution of ecosystems. Close interaction between biocenosis and the biotope (ecotope) is ensured by the continuous exchange of matter, energy, and information. Ecotope determines the biocenosis. The group of ecotopic functions includes atmospheric (gas exchange, heat exchange, hydroatmospheric, climate-forming), lithospheric (geodynamic, geophysical, and geochemical), hydrologic and hydrogeologic functions of landscape and ecotopic functions of soils. Bioecological functions emerge as a result of the biotope and ecotope interaction; these are the bioproductive, destructive, organoaccumulative, biochemical (gas, concentration, redox, biochemical, biopedological), pedogenetic, and energy functions

Discussions on the Design of the Pool Landscape in the Rain Garden Construction

NASA Astrophysics Data System (ADS)

Zou, Shuzhen; Zhu, Yirong; Wei, Chaojun; Tao, Biaohong

2018-03-01

With rapid urbanization, the environmental problems are becoming increasingly prominent and diversified ecological landscape designs consequently appear with the rain garden landscape design as a typical. Based on the introduction to rain garden ecological functions and in combination with domestic and international rain garden landscape design cases, this paper discussed the rain garden pool landscape design.

Complexity of free energy landscapes of peptides revealed by nonlinear principal component analysis.

PubMed

Nguyen, Phuong H

2006-12-01

Employing the recently developed hierarchical nonlinear principal component analysis (NLPCA) method of Saegusa et al. (Neurocomputing 2004;61:57-70 and IEICE Trans Inf Syst 2005;E88-D:2242-2248), the complexities of the free energy landscapes of several peptides, including triglycine, hexaalanine, and the C-terminal beta-hairpin of protein G, were studied. First, the performance of this NLPCA method was compared with the standard linear principal component analysis (PCA). In particular, we compared two methods according to (1) the ability of the dimensionality reduction and (2) the efficient representation of peptide conformations in low-dimensional spaces spanned by the first few principal components. The study revealed that NLPCA reduces the dimensionality of the considered systems much better, than did PCA. For example, in order to get the similar error, which is due to representation of the original data of beta-hairpin in low dimensional space, one needs 4 and 21 principal components of NLPCA and PCA, respectively. Second, by representing the free energy landscapes of the considered systems as a function of the first two principal components obtained from PCA, we obtained the relatively well-structured free energy landscapes. In contrast, the free energy landscapes of NLPCA are much more complicated, exhibiting many states which are hidden in the PCA maps, especially in the unfolded regions. Furthermore, the study also showed that many states in the PCA maps are mixed up by several peptide conformations, while those of the NLPCA maps are more pure. This finding suggests that the NLPCA should be used to capture the essential features of the systems. (c) 2006 Wiley-Liss, Inc.

Resource diversity and provenance underpin spatial patterns in functional diversity across native and exotic species.

PubMed

Méndez, Verónica; Wood, Jamie R; Butler, Simon J

2018-05-01

Functional diversity metrics are increasingly used to augment or replace taxonomic diversity metrics to deliver more mechanistic insights into community structure and function. Metrics used to describe landscape structure and characteristics share many of the same limitations as taxonomy-based metrics, particularly their reliance on anthropogenically defined typologies with little consideration of structure, management, or function. However, the development of alternative metrics to describe landscape characteristics has been limited. Here, we extend the functional diversity framework to characterize landscapes based on the diversity of resources available across habitats present. We then examine the influence of resource diversity and provenance on the functional diversities of native and exotic avian communities in New Zealand. Invasive species are increasingly prevalent and considered a global threat to ecosystem function, but the characteristics of and interactions between sympatric native and exotic communities remain unresolved. Understanding their comparative responses to environmental change and the mechanisms underpinning them is of growing importance in predicting community dynamics and changing ecosystem function. We use (i) matrices of resource use (species) and resource availability (habitats) and (ii) occurrence data for 62 native and 25 exotic species and 19 native and 13 exotic habitats in 2015 10 × 10 km quadrats to examine the relationship between native and exotic avian and landscape functional diversity. The numbers of species in, and functional diversities of, native and exotic communities were positively related. Each community displayed evidence of environmental filtering, but it was significantly stronger for exotic species. Less environmental filtering occurred in landscapes providing a more diverse combination of resources, with resource provenance also an influential factor. Landscape functional diversity explained a greater proportion of variance in native and exotic community characteristics than the number of habitat types present. Resource diversity and provenance should be explicitly accounted for when characterizing landscape structure and change as they offer additional mechanistic understanding of the links between environmental filtering and community structure. Manipulating resource diversity through the design and implementation of management actions could prove a powerful tool for the delivery of conservation objectives, be they to protect native species, control exotic species, or maintain ecosystem service provision.

Environmental and spatial drivers of taxonomic, functional, and phylogenetic characteristics of bat communities in human-modified landscapes.

PubMed

Cisneros, Laura M; Fagan, Matthew E; Willig, Michael R

2016-01-01

Assembly of species into communities following human disturbance (e.g., deforestation, fragmentation) may be governed by spatial (e.g., dispersal) or environmental (e.g., niche partitioning) mechanisms. Variation partitioning has been used to broadly disentangle spatial and environmental mechanisms, and approaches utilizing functional and phylogenetic characteristics of communities have been implemented to determine the relative importance of particular environmental (or niche-based) mechanisms. Nonetheless, few studies have integrated these quantitative approaches to comprehensively assess the relative importance of particular structuring processes. We employed a novel variation partitioning approach to evaluate the relative importance of particular spatial and environmental drivers of taxonomic, functional, and phylogenetic aspects of bat communities in a human-modified landscape in Costa Rica. Specifically, we estimated the amount of variation in species composition (taxonomic structure) and in two aspects of functional and phylogenetic structure (i.e., composition and dispersion) along a forest loss and fragmentation gradient that are uniquely explained by landscape characteristics (i.e., environment) or space to assess the importance of competing mechanisms. The unique effects of space on taxonomic, functional and phylogenetic structure were consistently small. In contrast, landscape characteristics (i.e., environment) played an appreciable role in structuring bat communities. Spatially-structured landscape characteristics explained 84% of the variation in functional or phylogenetic dispersion, and the unique effects of landscape characteristics significantly explained 14% of the variation in species composition. Furthermore, variation in bat community structure was primarily due to differences in dispersion of species within functional or phylogenetic space along the gradient, rather than due to differences in functional or phylogenetic composition. Variation among bat communities was related to environmental mechanisms, especially niche-based (i.e., environmental) processes, rather than spatial mechanisms. High variation in functional or phylogenetic dispersion, as opposed to functional or phylogenetic composition, suggests that loss or gain of niche space is driving the progressive loss or gain of species with particular traits from communities along the human-modified gradient. Thus, environmental characteristics associated with landscape structure influence functional or phylogenetic aspects of bat communities by effectively altering the ways in which species partition niche space.

Environmental and spatial drivers of taxonomic, functional, and phylogenetic characteristics of bat communities in human-modified landscapes

PubMed Central

Fagan, Matthew E.; Willig, Michael R.

2016-01-01

Background Assembly of species into communities following human disturbance (e.g., deforestation, fragmentation) may be governed by spatial (e.g., dispersal) or environmental (e.g., niche partitioning) mechanisms. Variation partitioning has been used to broadly disentangle spatial and environmental mechanisms, and approaches utilizing functional and phylogenetic characteristics of communities have been implemented to determine the relative importance of particular environmental (or niche-based) mechanisms. Nonetheless, few studies have integrated these quantitative approaches to comprehensively assess the relative importance of particular structuring processes. Methods We employed a novel variation partitioning approach to evaluate the relative importance of particular spatial and environmental drivers of taxonomic, functional, and phylogenetic aspects of bat communities in a human-modified landscape in Costa Rica. Specifically, we estimated the amount of variation in species composition (taxonomic structure) and in two aspects of functional and phylogenetic structure (i.e., composition and dispersion) along a forest loss and fragmentation gradient that are uniquely explained by landscape characteristics (i.e., environment) or space to assess the importance of competing mechanisms. Results The unique effects of space on taxonomic, functional and phylogenetic structure were consistently small. In contrast, landscape characteristics (i.e., environment) played an appreciable role in structuring bat communities. Spatially-structured landscape characteristics explained 84% of the variation in functional or phylogenetic dispersion, and the unique effects of landscape characteristics significantly explained 14% of the variation in species composition. Furthermore, variation in bat community structure was primarily due to differences in dispersion of species within functional or phylogenetic space along the gradient, rather than due to differences in functional or phylogenetic composition. Discussion Variation among bat communities was related to environmental mechanisms, especially niche-based (i.e., environmental) processes, rather than spatial mechanisms. High variation in functional or phylogenetic dispersion, as opposed to functional or phylogenetic composition, suggests that loss or gain of niche space is driving the progressive loss or gain of species with particular traits from communities along the human-modified gradient. Thus, environmental characteristics associated with landscape structure influence functional or phylogenetic aspects of bat communities by effectively altering the ways in which species partition niche space. PMID:27761338

Thermal Remote Sensing: A Powerful Tool in the Characterization of Landscapes on a Functional Basis

NASA Technical Reports Server (NTRS)

Jeffrey, Luvall C.; Kay, James; Fraser, Roydon

1999-01-01

Thermal remote sensing instruments can function as environmental measuring tools, with capabilities leading toward new directions in functional landscape ecology. Theoretical deduction and phenomenological observation leads us to believe that the second law of thermodynamics requires that all dynamically systems develop in a manner which dissipates gradients as rapidly as possible within the constraints of the system at hand. The ramification of this requirement is that dynamical systems will evolve dissipative structures which grow and complexify over time. This perspective has allowed us to develop a framework for discussing ecosystem development and integrity. In the context of this framework we have developed measures of development and integrity for ecosystems. One set of these measures is based on destruction of the exergy content of incoming solar energy. More developed ecosystems will be more effective at dissipating the solar gradient (destroying its exergy content). This can be measured by the effective surface temperature of the ecosystem on a landscape scale. These surface temperatures are measured using airborne thermal scanners such as the Thermal Infrared Multispectral Scanner (TIMS) and the Airborne Thermal/Visible Land Application Sensor(ATLAS) sensors. An analysis of agriculture and forest ecosystems will be used to illustrate the concept of ecological thermodynamics and the development of ecosystems.

Avian Species and Functional Diversity in Agricultural Landscapes: Does Landscape Heterogeneity Matter?

PubMed Central

2017-01-01

While the positive relationship between avian diversity and habitat heterogeneity is widely accepted, it is primarily based on observed species richness without accounting for imperfect detection. Other facets of diversity such as functional diversity are also rarely explored. We investigated the avian diversity-landscape heterogeneity relationship in agricultural landscapes by considering two aspects of diversity: taxonomic diversity (species richness) estimated from a multi-species dynamic occupancy model, and functional diversity (functional evenness [FEve] and divergence [FDiv]) based on traits of occurring species. We also assessed how agricultural lands enrolled in a conservation program managed on behalf of declining early successional bird species (hereafter CP38 fields, an agri-environment scheme) influenced avian diversity. We analyzed breeding bird data collected at CP38 fields in Mississippi, USA, during 2010–2012, and two principal components of environmental variables: a gradient of heterogeneity (Shannon’s landscape diversity index) and of the amount of CP38 fields (percent cover of CP38 fields; CP38). FEve did not show significant responses to environmental variables, whereas FDiv responded positively to heterogeneity and negatively to CP38. However, most FDiv values did not significantly differ from random expectations along an environmental gradient. When there was a significant difference, FDiv was lower than that expected. Unlike functional diversity, species richness showed a clear pattern. Species richness increased with increasing landscape heterogeneity but decreased with increasing amounts of CP38 fields. Only one species responded negatively to heterogeneity and positively to CP38. Our results suggest that the relationships between avian diversity and landscape heterogeneity may vary depending on the aspect of diversity considered: strong positive effects of heterogeneity on taxonomic diversity, but weakly positive or non-significant effects on functional diversity. Our results also indicate that effectiveness of CP38 in conserving avian diversity, particularly, taxonomic diversity, could be limited without the consideration of landscape heterogeneity. PMID:28125653

Avian Species and Functional Diversity in Agricultural Landscapes: Does Landscape Heterogeneity Matter?

PubMed

Lee, Myung-Bok; Martin, James A

2017-01-01

While the positive relationship between avian diversity and habitat heterogeneity is widely accepted, it is primarily based on observed species richness without accounting for imperfect detection. Other facets of diversity such as functional diversity are also rarely explored. We investigated the avian diversity-landscape heterogeneity relationship in agricultural landscapes by considering two aspects of diversity: taxonomic diversity (species richness) estimated from a multi-species dynamic occupancy model, and functional diversity (functional evenness [FEve] and divergence [FDiv]) based on traits of occurring species. We also assessed how agricultural lands enrolled in a conservation program managed on behalf of declining early successional bird species (hereafter CP38 fields, an agri-environment scheme) influenced avian diversity. We analyzed breeding bird data collected at CP38 fields in Mississippi, USA, during 2010-2012, and two principal components of environmental variables: a gradient of heterogeneity (Shannon's landscape diversity index) and of the amount of CP38 fields (percent cover of CP38 fields; CP38). FEve did not show significant responses to environmental variables, whereas FDiv responded positively to heterogeneity and negatively to CP38. However, most FDiv values did not significantly differ from random expectations along an environmental gradient. When there was a significant difference, FDiv was lower than that expected. Unlike functional diversity, species richness showed a clear pattern. Species richness increased with increasing landscape heterogeneity but decreased with increasing amounts of CP38 fields. Only one species responded negatively to heterogeneity and positively to CP38. Our results suggest that the relationships between avian diversity and landscape heterogeneity may vary depending on the aspect of diversity considered: strong positive effects of heterogeneity on taxonomic diversity, but weakly positive or non-significant effects on functional diversity. Our results also indicate that effectiveness of CP38 in conserving avian diversity, particularly, taxonomic diversity, could be limited without the consideration of landscape heterogeneity.

An Analysis of the Landscaping Occupation.

ERIC Educational Resources Information Center

Stemple, Lynn L.; Dilley, John E.

The general purpose of the occupational analysis is to provide workable, basic information dealing with the many and varied duties performed in the landscape services occupation. Depending on the preparation and abilities of the individual student, he may enter the landscape area as (1) nursery worker, (2) landscape planter, (3) 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...

Quantitative study on spatio-temporal change of urban landscape pattern based on RS/GIS: a case of Xi'an metropolitan area in China

NASA Astrophysics Data System (ADS)

Chen, Meiwu; Zong, Yueguang; Ma, Qiang; Li, Jian

2007-06-01

The study on landscape pattern is an important field of urban land use and ecological change. Since 1990s, the widely accepted Patch-Corridor-Matrix model is generally used in qualitative description of landscape pattern. In recent years, quantitative evaluation on urban landscape dynamics is becoming hot in research. By making a critical review on existing research methods of landscape pattern, a new approach based on RS/GIS is put forward in this paper, comprising three steps, "General pattern characteristics - Gradient differentiation feature- Directional signature of the landscape", and we call it GGD. This method is applied to the case study of Xi'an metropolitan area in China. The result shows that the method is effective on quantitative study of urban landscape. The preparation of the method GGD is setting up research platform based on RS and GIS. By using the software of Geographical Information System (Arcgis9.0 & Erdas), the authors got the interpretation of remote sensing images of different years, and carried on the division of the landscape type of the research region. By calculating various index of landscape level with software Fragstats3.3 as an assistant tool and adopting three steps of GGD combined with landscape index, this paper can assesses the landscape spatial pattern of urban area: 1) General pattern characteristics analysis is to get transition probability of various landscape through Markov chain and to predict the landscape transformation by introducing CA model. The analysis emphasizes on total landscape structure and its change over time; 2) Gradient characteristic analysis, which makes gradient zone by taking city as a center outwardly with certain distance and contrastively analyzes the landscape index of each subarea, stresses the spatial character of landscape pattern, verifies urban morphology theories and provides the quantitative warranty for establishment of urban modality. Therefore, the analysis is useful for supervising urban expanding speed; 3)Direction characteristic analysis, which is setting up radiate strip on west-east, south-north, southwest-northeast and northwest-southeast and form certain width on each direction, can precisely and quantitatively indicate different characteristic of urban landscape at each development direction, and by combined with gradient analysis it is highly advantageous to the examination and planning of urban expanding direction. In the case study on Xi'an metropolitan area, remote sensing images of 1988 and 2005 Landsat-TM were handled, and the division of the landscape type of the region was also carried on. According to the above approach, the result was got and some valuable information was showed as follows: 1) The diversity of overall landscape of Xi'an metropolitan area tends to increase and the degree of fragmentation tends to deepen. With the increase of urbanization level, the visual component of landscape is more and more diversified, the shapes of landscape is more and more complicated and ecologically more and more fragmented. In the region where urbanization level is low, natural landscape is the main component of the landscape, the diversity of the landscape is low. And because landscape is seriously disturbed by human activities with urbanization, fragmentation of the landscape emerges periodically. 2) In the process of transect gradient analysis, the landscape pattern index can explore the urbanization gradient, and its trend to reduce gradually towards the suburban. The landscape of area with a high urbanization level is mainly man-created, and its patches show large number, small area, simple shape and higher landscape heterogeneity. The transect gradient analysis on different time series indicates the relationship between urbanization level and landscape pattern. The landscape of urban area suffers intensely from human being, and its pattern component and spatial collocation depends on the interference intensity to a large degree. In the area with a high urbanization level, its pattern component is more man-created and less natural landscape. The landscape collocation characteristic of its patches takes on a large number, little average area, simple shape and low polymerization degree. 3) Analysis of direction and gradient of Xi'an metropolitan area can quantitatively reflect influence of urbanization and characteristics of urban landscape in the main development axes of north-south and east. Result shows that the degree of internal integration between Xi'an city and Xianyang city is gradually enhanced with the quickly urbanization course in China.

A multi-resolution analysis of lidar-DTMs to identify geomorphic processes from characteristic topographic length scales

NASA Astrophysics Data System (ADS)

Sangireddy, H.; Passalacqua, P.; Stark, C. P.

2013-12-01

Characteristic length scales are often present in topography, and they reflect the driving geomorphic processes. The wide availability of high resolution lidar Digital Terrain Models (DTMs) allows us to measure such characteristic scales, but new methods of topographic analysis are needed in order to do so. Here, we explore how transitions in probability distributions (pdfs) of topographic variables such as (log(area/slope)), defined as topoindex by Beven and Kirkby[1979], can be measured by Multi-Resolution Analysis (MRA) of lidar DTMs [Stark and Stark, 2001; Sangireddy et al.,2012] and used to infer dominant geomorphic processes such as non-linear diffusion and critical shear. We show this correlation between dominant geomorphic processes to characteristic length scales by comparing results from a landscape evolution model to natural landscapes. The landscape evolution model MARSSIM Howard[1994] includes components for modeling rock weathering, mass wasting by non-linear creep, detachment-limited channel erosion, and bedload sediment transport. We use MARSSIM to simulate steady state landscapes for a range of hillslope diffusivity and critical shear stresses. Using the MRA approach, we estimate modal values and inter-quartile ranges of slope, curvature, and topoindex as a function of resolution. We also construct pdfs at each resolution and identify and extract characteristic scale breaks. Following the approach of Tucker et al.,[2001], we measure the average length to channel from ridges, within the GeoNet framework developed by Passalacqua et al.,[2010] and compute pdfs for hillslope lengths at each scale defined in the MRA. We compare the hillslope diffusivity used in MARSSIM against inter-quartile ranges of topoindex and hillslope length scales, and observe power law relationships between the compared variables for simulated landscapes at steady state. We plot similar measures for natural landscapes and are able to qualitatively infer the dominant geomorphic processes. Also, we explore the variability in hillslope length scales as a function of hillslope diffusivity coefficients and critical shear stress in natural landscapes and show that we can infer signatures of dominant geomorphic processes by analyzing characteristic topographic length scales present in topography. References: Beven, K. and Kirkby, M. J.: A physically based variable contributing area model of basin hydrology, Hydrol. Sci. Bull., 24, 43-69, 1979 Howard, A. D. (1994). A detachment-limited model of drainage basin evolution.Water resources research, 30(7), 2261-2285. Passalacqua, P., Do Trung, T., Foufoula Georgiou, E., Sapiro, G., & Dietrich, W. E. (2010). A geometric framework for channel network extraction from lidar: Nonlinear diffusion and geodesic paths. Journal of Geophysical. Research: Earth Surface (2003-2012), 115(F1). Sangireddy, H., Passalacqua, P., Stark, C.P.(2012). Multi-resolution estimation of lidar-DTM surface flow metrics to identify characteristic topographic length scales, EP13C-0859: AGU Fall meeting 2012. Stark, C. P., & Stark, G. J. (2001). A channelization model of landscape evolution. American Journal of Science, 301(4-5), 486-512. Tucker, G. E., Catani, F., Rinaldo, A., & Bras, R. L. (2001). Statistical analysis of drainage density from digital terrain data. Geomorphology, 36(3), 187-202.

A Flexible Approach for Assessing Functional Landscape Connectivity, with Application to Greater Sage-Grouse (Centrocercus urophasianus)

PubMed Central

Harju, Seth M.; Olson, Chad V.; Dzialak, Matthew R.; Mudd, James P.; Winstead, Jeff B.

2013-01-01

Connectivity of animal populations is an increasingly prominent concern in fragmented landscapes, yet existing methodological and conceptual approaches implicitly assume the presence of, or need for, discrete corridors. We tested this assumption by developing a flexible conceptual approach that does not assume, but allows for, the presence of discrete movement corridors. We quantified functional connectivity habitat for greater sage-grouse (Centrocercus urophasianus) across a large landscape in central western North America. We assigned sample locations to a movement state (encamped, traveling and relocating), and used Global Positioning System (GPS) location data and conditional logistic regression to estimate state-specific resource selection functions. Patterns of resource selection during different movement states reflected selection for sagebrush and general avoidance of rough topography and anthropogenic features. Distinct connectivity corridors were not common in the 5,625 km2 study area. Rather, broad areas functioned as generally high or low quality connectivity habitat. A comprehensive map predicting the quality of connectivity habitat across the study area validated well based on a set of GPS locations from independent greater sage-grouse. The functional relationship between greater sage-grouse and the landscape did not always conform to the idea of a discrete corridor. A more flexible consideration of landscape connectivity may improve the efficacy of management actions by aligning those actions with the spatial patterns by which animals interact with the landscape. PMID:24349241

A flexible approach for assessing functional landscape connectivity, with application to greater sage-grouse (Centrocercus urophasianus).

PubMed

Harju, Seth M; Olson, Chad V; Dzialak, Matthew R; Mudd, James P; Winstead, Jeff B

2013-01-01

Connectivity of animal populations is an increasingly prominent concern in fragmented landscapes, yet existing methodological and conceptual approaches implicitly assume the presence of, or need for, discrete corridors. We tested this assumption by developing a flexible conceptual approach that does not assume, but allows for, the presence of discrete movement corridors. We quantified functional connectivity habitat for greater sage-grouse (Centrocercus urophasianus) across a large landscape in central western North America. We assigned sample locations to a movement state (encamped, traveling and relocating), and used Global Positioning System (GPS) location data and conditional logistic regression to estimate state-specific resource selection functions. Patterns of resource selection during different movement states reflected selection for sagebrush and general avoidance of rough topography and anthropogenic features. Distinct connectivity corridors were not common in the 5,625 km(2) study area. Rather, broad areas functioned as generally high or low quality connectivity habitat. A comprehensive map predicting the quality of connectivity habitat across the study area validated well based on a set of GPS locations from independent greater sage-grouse. The functional relationship between greater sage-grouse and the landscape did not always conform to the idea of a discrete corridor. A more flexible consideration of landscape connectivity may improve the efficacy of management actions by aligning those actions with the spatial patterns by which animals interact with the landscape.

Large-scale geomorphology: Classical concepts reconciled and integrated with contemporary ideas via a surface processes model

NASA Astrophysics Data System (ADS)

Kooi, Henk; Beaumont, Christopher

1996-02-01

Linear systems analysis is used to investigate the response of a surface processes model (SPM) to tectonic forcing. The SPM calculates subcontinental scale denudational landscape evolution on geological timescales (1 to hundreds of million years) as the result of simultaneous hillslope transport, modeled by diffusion, and fluvial transport, modeled by advection and reaction. The tectonically forced SPM accommodates the large-scale behavior envisaged in classical and contemporary conceptual geomorphic models and provides a framework for their integration and unification. The following three model scales are considered: micro-, meso-, and macroscale. The concepts of dynamic equilibrium and grade are quantified at the microscale for segments of uniform gradient subject to tectonic uplift. At the larger meso- and macroscales (which represent individual interfluves and landscapes including a number of drainage basins, respectively) the system response to tectonic forcing is linear for uplift geometries that are symmetric with respect to baselevel and which impose a fully integrated drainage to baselevel. For these linear models the response time and the transfer function as a function of scale characterize the model behavior. Numerical experiments show that the styles of landscape evolution depend critically on the timescales of the tectonic processes in relation to the response time of the landscape. When tectonic timescales are much longer than the landscape response time, the resulting dynamic equilibrium landscapes correspond to those envisaged by Hack (1960). When tectonic timescales are of the same order as the landscape response time and when tectonic variations take the form of pulses (much shorter than the response time), evolving landscapes conform to the Penck type (1972) and to the Davis (1889, 1899) and King (1953, 1962) type frameworks, respectively. The behavior of the SPM highlights the importance of phase shifts or delays of the landform response and sediment yield in relation to the tectonic forcing. Finally, nonlinear behavior resulting from more general uplift geometries is discussed. A number of model experiments illustrate the importance of "fundamental form," which is an expression of the conformity of antecedent topography with the current tectonic regime. Lack of conformity leads to models that exhibit internal thresholds and a complex response.

Clarifying the landscape approach: A Letter to the Editor on "Integrated landscape approaches to managing social and environmental issues in the tropics".

PubMed

Erbaugh, James; Agrawal, Arun

2017-11-01

Objectives, assumptions, and methods for landscape restoration and the landscape approach. World leaders have pledged 350 Mha for restoration using a landscape approach. The landscape approach is thus poised to become one of the most influential methods for multi-functional land management. Reed et al (2016) meaningfully advance scholarship on the landscape approach, but they incorrectly define the approach as it exists within their text. This Letter to the Editor clarifies the landscape approach as an ethic for land management, demonstrates how it relates to landscape restoration, and motivates continued theoretical development and empirical assessment of the landscape approach. © 2017 John Wiley & Sons Ltd.

THE USE OF SCENARIO ANALYSIS TO ASSESS LANDSCAPE CHANGE ON WATERSHED CONDITION IN THE PACKIFIC NORTHWEST (USA)

EPA Science Inventory

The ability to assess, report, and forecast the life support functions of ecosystems is absolutely critical to our capacity to make informed decisions which will maintain the sustainable nature of our environmental services and secure these resources into the future. Scenario ana...

The genomic landscape of rapid, repeated evolutionary rescue from toxic pollution in wild fish

USDA-ARS?s Scientific Manuscript database

Here we describe evolutionary rescue from intense pollution via multiple modes of selection in killifish populations from 4 urban estuaries of the US eastern seaboard. Comparative transcriptomics and analysis of 384 whole genome sequences show that the functioning of a receptor-based signaling pathw...

Spring distributions and relationships with land cover and hydrogeologic strata in a karst landscape in Winona County, Minnesota, USA

USGS Publications Warehouse

Williams, M.A.; Vondracek, B.

2010-01-01

Karst aquifers are important groundwater resources, but are vulnerable to contamination due to relatively rapid subsurface transport. Springs, points where the landscape and water table intersect and cold groundwater discharges, link aquifer systems with land surfaces and water bodies. As such, in many regions, they are critical to the viability of lakes, streams and cold-water fish communities. An understanding of where springs are located is important to watershed, fishery and environmental management efforts in karst regions. To better understand spatial distribution of springs and as a potential method for identifying variables that characterize locations of springs for improved land and watershed management, a nearest-neighbor analysis and a discriminant function analysis (DFA) of springs were conducted in Winona County, Minnesota USA, a karst landscape. Nearestneighbor analysis examined the spatial spring distribution. Twenty-two variables describing the locations of springs were analyzed to ascertain their ability to discriminate correct aquifer unit or bedrock unit classification for each spring. Springs were clumped with the highest densities in the lowest elevations. Springs were correctly assigned to aquifer units and bedrock units with eight and 11 landscape variables, respectively. Forest land cover was the only land cover type contributing to spring discrimination. Consideration of upland human activities, particularly in forested areas, on spring discharge along with a better understanding of characteristics describing spring locations could lead to better management activities that locate and protect springs and their important contributions to regional ecohydrology. ?? 2010 Springer-Verlag.

Spring distribution in Winona County, Minnesota, USA and the relationship with geologic strata in a karst landscape

USGS Publications Warehouse

Vondracek, Bruce C.; Williams, Mary A.

2010-01-01

Karst aquifers are important groundwater resources, but are vulnerable to contamination due to relatively rapid subsurface transport. Springs, points where the landscape and water table intersect and cold groundwater discharges, link aquifer systems with land surfaces and water bodies. As such, in many regions, they are critical to the viability of lakes, streams and cold-water fish communities. An understanding of where springs are located is important to watershed, fishery and environmental management efforts in karst regions. To better understand spatial distribution of springs and as a potential method for identifying variables that characterize locations of springs for improved land and watershed management, a nearest-neighbor analysis and a discriminant function analysis (DFA) of springs were conducted in Winona County, Minnesota, USA, a karst landscape. Nearest-neighbor analysis examined the spatial spring distribution. Twenty-two variables describing the locations of springs were analyzed to ascertain their ability to discriminate correct aquifer unit or bedrock unit classification for each spring. Springs were clumped with the highest densities in the lowest elevations. Springs were correctly assigned to aquifer units and bedrock units with eight and 11 landscape variables, respectively. Forest land cover was the only land cover type contributing to spring discrimination. Consideration of upland human activities, particularly in forested areas, on spring discharge along with a better understanding of characteristics describing spring locations could lead to better management activities that locate and protect springs and their important contributions to regional ecohydrology.

Diversity and potential activity of methanotrophs in high methane-emitting permafrost thaw ponds

PubMed Central

Vincent, Warwick F.; Comte, Jérôme; Matveev, Alex; Lovejoy, Connie

2017-01-01

Lakes and ponds derived from thawing permafrost are strong emitters of carbon dioxide and methane to the atmosphere, but little is known about the methane oxidation processes in these waters. Here we investigated the distribution and potential activity of aerobic methanotrophic bacteria in thaw ponds in two types of eroding permafrost landscapes in subarctic Québec: peatlands and mineral soils. We hypothesized that methanotrophic community composition and potential activity differ regionally as a function of the landscape type and permafrost degradation stage, and locally as a function of depth-dependent oxygen conditions. Our analysis of pmoA transcripts by Illumina amplicon sequencing and quantitative PCR showed that the communities were composed of diverse and potentially active lineages. Type I methanotrophs, particularly Methylobacter, dominated all communities, however there was a clear taxonomic separation between the two landscape types, consistent with environmental control of community structure. In contrast, methanotrophic potential activity, measured by pmoA transcript concentrations, did not vary with landscape type, but correlated with conductivity, phosphorus and total suspended solids. Methanotrophic potential activity was also detected in low-oxygen bottom waters, where it was inversely correlated with methane concentrations, suggesting methane depletion by methanotrophs. Methanotrophs were present and potentially active throughout the water column regardless of oxygen concentration, and may therefore be resilient to future mixing and oxygenation regimes in the warming subarctic. PMID:29182670

Diversity and potential activity of methanotrophs in high methane-emitting permafrost thaw ponds.

PubMed

Crevecoeur, Sophie; Vincent, Warwick F; Comte, Jérôme; Matveev, Alex; Lovejoy, Connie

2017-01-01

Lakes and ponds derived from thawing permafrost are strong emitters of carbon dioxide and methane to the atmosphere, but little is known about the methane oxidation processes in these waters. Here we investigated the distribution and potential activity of aerobic methanotrophic bacteria in thaw ponds in two types of eroding permafrost landscapes in subarctic Québec: peatlands and mineral soils. We hypothesized that methanotrophic community composition and potential activity differ regionally as a function of the landscape type and permafrost degradation stage, and locally as a function of depth-dependent oxygen conditions. Our analysis of pmoA transcripts by Illumina amplicon sequencing and quantitative PCR showed that the communities were composed of diverse and potentially active lineages. Type I methanotrophs, particularly Methylobacter, dominated all communities, however there was a clear taxonomic separation between the two landscape types, consistent with environmental control of community structure. In contrast, methanotrophic potential activity, measured by pmoA transcript concentrations, did not vary with landscape type, but correlated with conductivity, phosphorus and total suspended solids. Methanotrophic potential activity was also detected in low-oxygen bottom waters, where it was inversely correlated with methane concentrations, suggesting methane depletion by methanotrophs. Methanotrophs were present and potentially active throughout the water column regardless of oxygen concentration, and may therefore be resilient to future mixing and oxygenation regimes in the warming subarctic.

Study on the oasis corridor landscape in the arid regions based on RS and GIS methods--application of Jinta Oasis, China.

PubMed

Ma, Ming-guo; Wang, Xue-mei; Cheng, Guo-dong

2003-03-01

The study on the oasis corridor landsape is a new hotspot in the ecological environment research in the arid regions. In oasis, main corridor landscape types include river, ditch, shelterbelt and road. This paper introduces the basic ecological effects of the corridor landscape on the transporting mass and energy and obstructing desert landscape expansion and incursion. Using Geographic Information System (GIS), we have researched the corridor distribution and its spatial relationship with other landscape types in the Jinta Oasis. Based on the dynamically monitoring on the landscape pattern change of the Jinta Oasis during the latter 10 years by using Remote Sensing (RS) and GIS, the driving functions of the corridors on this change have been analyzed in detail. The analysis results showed that all kinds of corridors' characteristics can be quantified by the indexes such as length and width, ratio of perimeter and area, density and non-heterogeneity. The total corridor length of Jinta Oasis is 1838.5 km and its density is 2.1 km/km2. The corridor density of the irrigation land, forest and resident area is maximal, which shows that affection degree of the oasis corridors on them is the most. The improvement of the corridors quality is one of the important driving factors on the irrigation land and so on. The organic combination of the RS and GIS technologies and landscape research methods would be an effective means for the corridor landscape research on arid region oasis.

Determining the size of a complete disturbance landscape: multi-scale, continental analysis of forest change.

PubMed

Buma, Brian; Costanza, Jennifer K; Riitters, Kurt

2017-11-21

The scale of investigation for disturbance-influenced processes plays a critical role in theoretical assumptions about stability, variance, and equilibrium, as well as conservation reserve and long-term monitoring program design. Critical consideration of scale is required for robust planning designs, especially when anticipating future disturbances whose exact locations are unknown. This research quantified disturbance proportion and pattern (as contagion) at multiple scales across North America. This pattern of scale-associated variability can guide selection of study and management extents, for example, to minimize variance (measured as standard deviation) between any landscapes within an ecoregion. We identified the proportion and pattern of forest disturbance (30 m grain size) across multiple landscape extents up to 180 km 2 . We explored the variance in proportion of disturbed area and the pattern of that disturbance between landscapes (within an ecoregion) as a function of the landscape extent. In many ecoregions, variance between landscapes within an ecoregion was minimal at broad landscape extents (low standard deviation). Gap-dominated regions showed the least variance, while fire-dominated showed the largest. Intensively managed ecoregions displayed unique patterns. A majority of the ecoregions showed low variance between landscapes at some scale, indicating an appropriate extent for incorporating natural regimes and unknown future disturbances was identified. The quantification of the scales of disturbance at the ecoregion level provides guidance for individuals interested in anticipating future disturbances which will occur in unknown spatial locations. Information on the extents required to incorporate disturbance patterns into planning is crucial for that process.

Remote Sensing as a Landscape Epidemiologic Tool to Identify Villages at High Risk for Malaria Transmission

NASA Technical Reports Server (NTRS)

Beck, Louisa R.; Rodriquez, Mario H.; Dister, Sheri W.; Rodriquez, Americo D.; Rejmankova, Eliska; Ulloa, Armando; Meza, Rosa A.; Roberts, Donald R.; Paris, Jack F.; Spanner, Michael A.;

Roosting habitat use and selection by northern spotted owls during natal dispersal

USGS Publications Warehouse

Sovern, Stan G.; Forsman, Eric D.; Dugger, Catherine M.; Taylor, Margaret

2015-01-01

We studied habitat selection by northern spotted owls (Strix occidentalis caurina) during natal dispersal in Washington State, USA, at both the roost site and landscape scales. We used logistic regression to obtain parameters for an exponential resource selection function based on vegetation attributes in roost and random plots in 76 forest stands that were used for roosting. We used a similar analysis to evaluate selection of landscape habitat attributes based on 301 radio-telemetry relocations and random points within our study area. We found no evidence of within-stand selection for any of the variables examined, but 78% of roosts were in stands with at least some large (>50 cm dbh) trees. At the landscape scale, owls selected for stands with high canopy cover (>70%). Dispersing owls selected vegetation types that were more similar to habitat selected by adult owls than habitat that would result from following guidelines previously proposed to maintain dispersal habitat. Our analysis indicates that juvenile owls select stands for roosting that have greater canopy cover than is recommended in current agency guidelines.

RS- and GIS-based study on landscape pattern change in the Poyang Lake wetland area, China

NASA Astrophysics Data System (ADS)

Chen, Xiaoling; Li, Hui; Bao, Shuming; Wu, Zhongyi; Fu, Weijuan; Cai, Xiaobin; Zhao, Hongmei; Guo, Peng

2006-10-01

As wetland has been recognized as an important component of ecosystem, it is received ever-increasing attention worldwide. Poyang Lake wetlands, the international wetlands and the largest bird habitat in Asia, play an important role in biodiversity and ecologic protection. However, with the rapid economic growth and urbanization, landscape patterns in the wetlands have dramatically changed in the past three decades. To better understand the wetland landscape dynamics, remote sensing, geographic information system technologies, and the FRAGSTATS landscape analysis program were used to measure landscape patterns. Statistical approach was employed to illustrate the driving forces. In this study, Landsat images (TM and ETM+) from 1989 and 2000 were acquired for the wetland area. The landscapes in the wetland area were classified as agricultural land, urban, wetland, forest, grassland, unused land, and water body using a combination of supervised and unsupervised classification techniques integrated with Digital Elevation Model (DEM). Landscape indices, which are popular for the quantitative analysis of landscape pattern, were then employed to analyze the landscape pattern changes between the two dates in a GIS. From this analysis an understanding of the spatial-temporal patterns of landscape evolution was generated. The results show that wetland area was reduced while fragmentation was increased over the study period. Further investigation was made to examine the relationship between landscape metrics and some other parameters such as urbanization to address the driving forces for those changes. The urban was chosen as center to conduct buffer analysis in a GIS to study the impact of human-induced activities on landscape pattern dynamics. It was found that the selected parameters were significantly correlated with the landscape metrics, which may well indicate the impact of human-induced activities on the wetland landscape pattern dynamics and account for the driving forces.

Visual unit analysis: a descriptive approach to landscape assessment

Treesearch

R. J. Tetlow; S. R. J. Sheppard

1979-01-01

Analysis of the visible attributes of landscapes is an important component of the planning process. When landscapes are at regional scale, economical and effective methodologies are critical. The Visual Unit concept appears to offer a logical and useful framework for description and evaluation. The concept subdivides landscape into coherent, spatially-defined units....

Methods for integrated modeling of landscape change: Interior Northwest Landscape Analysis System.

Treesearch

Jane L. Hayes; Alan. A. Ager; R. James Barbour

2004-01-01

The Interior Northwest Landscape Analysis System (INLAS) links a number of resource, disturbance, and landscape simulations models to examine the interactions of vegetative succession, management, and disturbance with policy goals. The effects of natural disturbance like wildfire, herbivory, forest insects and diseases, as well as specific management actions are...

Are Protected Areas Required to Maintain Functional Diversity in Human-Modified Landscapes?

PubMed Central

Cottee-Jones, H. Eden W.; Matthews, Thomas J.; Bregman, Tom P.; Barua, Maan; Tamuly, Jatin; Whittaker, Robert J.

2015-01-01

The conversion of forest to agriculture across the world’s tropics, and the limited space for protected areas, has increased the need to identify effective conservation strategies in human-modified landscapes. Isolated trees are believed to conserve elements of ecological structure, providing micro-sites for conservation in matrix landscapes, and facilitating seed dispersal and forest restoration. Here we investigate the role of isolated Ficus trees, which are of critical importance to tropical forest ecosystems, in conserving frugivore composition and function in a human-modified landscape in Assam, India. We surveyed the frugivorous birds feeding at 122 isolated Ficus trees, 33 fruit trees, and 31 other large trees across a range of 32 km from the nearest intact forest. We found that Ficus trees attracted richer and more abundant assemblages of frugivores than the other tree categories. However, incidence function estimates revealed that forest specialist species decreased dramatically within the first kilometre of the forest edge. Despite this, species richness and functional diversity remained consistent across the human-modified landscape, as habitat generalists replaced forest-dependent frugivores, and accounted for most of the ecological function found in Ficus trees near the forest edge. We recommend that isolated Ficus trees are awarded greater conservation status, and suggest that their conservation can support ecologically functional networks of frugivorous bird communities. PMID:25946032

Functionality limit of classical simulated annealing

NASA Astrophysics Data System (ADS)

Hasegawa, M.

2015-09-01

By analyzing the system dynamics in the landscape paradigm, optimization function of classical simulated annealing is reviewed on the random traveling salesman problems. The properly functioning region of the algorithm is experimentally determined in the size-time plane and the influence of its boundary on the scalability test is examined in the standard framework of this method. From both results, an empirical choice of temperature length is plausibly explained as a minimum requirement that the algorithm maintains its scalability within its functionality limit. The study exemplifies the applicability of computational physics analysis to the optimization algorithm research.

Exotic species patterns and function in urban landscapes

Treesearch

Wayne C. Zipperer

2003-01-01

Mack et al. (2000) state "Biotic invaders are species that establish a new range in which they proliferate, spread, and persist to the detriment of the environment." This statement is true for many natural landscapes. In urban landscapes, however, exotic species are critical components of the landscape and enhance its livability. Exotic species provide...

Identification of Potential Wild Herbal as parts of Landscape Elements

NASA Astrophysics Data System (ADS)

Sulistyantara, Bambang; Mentari, Nio

2017-10-01

Many landscape plants can grow on their own without cultivated by humans. They are type of plants that can be found anywhere, so they can be categorized as wild plants. The economic value of wild plants are easy to obtain and their maintenance costs are low. Because wild plants not widely known even a just a few of people that aware of their existence, it is necessary to do a study to learn the potential of the wild plants to be used as an element of landscape. This research aims to identify the species that have potential to be used in landscape design, to describe the benefits of the their implementation as a landscape element, and to recommend the wild plants that have functional value and visual. This research used a scoring method based on the functional and visual criteria, and questionnaires were conducted to 50 students of Landscape Architecture IPB who have completed Landscape Plants courses. Based on the research, there are 150 species of wild plants that found in the study site, and 60 of them are recommended as landscape elements. Then all of the species were arranged as a recommendations book so they can be used as alternative landscape plants.

Do Geographically Isolated Wetlands Influence Landscape Functions?

EPA Science Inventory

Landscape functions such as flow generation, nutrient and sediment retention, and biodiversity support depend on the exchange of solutes, particles, energy, and organisms between elements in hydrological and habitat networks. Wetlands are important network elements, providing hyd...

[Scale effect of Nanjing urban green infrastructure network pattern and connectivity analysis.

PubMed

Yu, Ya Ping; Yin, Hai Wei; Kong, Fan Hua; Wang, Jing Jing; Xu, Wen Bin

2016-07-01

Based on ArcGIS, Erdas, GuidosToolbox, Conefor and other software platforms, using morphological spatial pattern analysis (MSPA) and landscape connectivity analysis methods, this paper quantitatively analysed the scale effect, edge effect and distance effect of the Nanjing urban green infrastructure network pattern in 2013 by setting different pixel sizes (P) and edge widths in MSPA analysis, and setting different dispersal distance thresholds in landscape connectivity analysis. The results showed that the type of landscape acquired based on the MSPA had a clear scale effect and edge effect, and scale effects only slightly affected landscape types, whereas edge effects were more obvious. Different dispersal distances had a great impact on the landscape connectivity, 2 km or 2.5 km dispersal distance was a critical threshold for Nanjing. When selecting the pixel size 30 m of the input data and the edge wide 30 m used in the morphological model, we could get more detailed landscape information of Nanjing UGI network. Based on MSPA and landscape connectivity, analysis of the scale effect, edge effect, and distance effect on the landscape types of the urban green infrastructure (UGI) network was helpful for selecting the appropriate size, edge width, and dispersal distance when developing these networks, and for better understanding the spatial pattern of UGI networks and the effects of scale and distance on the ecology of a UGI network. This would facilitate a more scientifically valid set of design parameters for UGI network spatiotemporal pattern analysis. The results of this study provided an important reference for Nanjing UGI networks and a basis for the analysis of the spatial and temporal patterns of medium-scale UGI landscape networks in other regions.

Local Knowledge About The Structure, Function And Conversion Of Landscape In The Karangwangi Village, Cianjur, West Java, Indonesia

NASA Astrophysics Data System (ADS)

Ulfa Dwi Amelia, Fatiya; Iskandar, Johan

2017-10-01

Karangwangi people is one of indigenous people in West Java who has local knowledge about their nature thoroughly. They have local tradition about landscape ecosystem arrangement that based on sakral (sacred) norm. With this rule, local people will always try to preserve the sustainability of their natural environment. However, modernization, increasing population, decreasing forest, and increasing market economic penetration, causing this rule and structure of landscape in Karangwangi village has changed. Land conversion in Karangwangi was occur because of settlement and land investment by people outside the village. These behavior changes in tradition and landscape (structure, function and conversion) in Karangwangi may impact on their daily activities, and so do the changes in daily activities can change their behavior in tradition and landscape. This research was undertaken in the Village of Karangwangi, Sub-district of Cidaun, District of Cianjur, Province of West Java, Indonesia. This paper aims to identify how indigenous people in Karangwangi understand kinds of landscape and another conversion that was happen as a result of management. The method used in this paper is qualitative with ethno ecological approach. The resulted of the study show that local people in Karangwangi Village understand how chronological of landscape structure, function and conversion.

Landscape Management of Public Open Space in Bogor Heritage City

NASA Astrophysics Data System (ADS)

Pusparini, F. D.; Nurhayati; Arifin, H. S.

2017-10-01

Public open space landscape plays important role in Bogor Heritage City. Although these spaces can carry various kind of public activities and enhance environment quality, they are fragile to disturbance and changing due to city development. Therefore, as an effort to maintain public open space landscape in 8 zones within Heritage City of Bogor, management of public open space landscape is necessary. Syntesys of public open space landscape management had held by using Analytical Hierarchy Process (AHP). The AHP result showed public open space landscape in Palace and Botanical Garden of Bogor zone (20%) is in high priority to be maintained. The other zone are Situ Gede (16,9%), Plan Karsten (12,3%), European Settlement (12%), Suryakencana (11,2%), Batu Tulis (10,2%), Empang (9.2%) and West Development (8,2%). Ecological function (34,8%) becomes the most important function to be maintained (34.8%) then social culture (31.2%), economic (17%), and aesthetics (17%).

Simulating streamflow in ungauged basins under a changing climate: The importance of landscape characteristics

NASA Astrophysics Data System (ADS)

Teutschbein, Claudia; Grabs, Thomas; Laudon, Hjalmar; Karlsen, Reinert H.; Bishop, Kevin

2018-06-01

In this paper we explored how landscape characteristics such as topography, geology, soils and land cover influence the way catchments respond to changing climate conditions. Based on an ensemble of 15 regional climate models bias-corrected with a distribution-mapping approach, present and future streamflow in 14 neighboring and rather similar catchments in Northern Sweden was simulated with the HBV model. We established functional relationships between a range of landscape characteristics and projected changes in streamflow signatures. These were then used to analyze hydrological consequences of physical perturbations in a hypothetically ungauged basin in a climate change context. Our analysis showed a strong connection between the forest cover extent and the sensitivity of different components of a catchment's hydrological regime to changing climate conditions. This emphasizes the need to redefine forestry goals and practices in advance of climate change-related risks and uncertainties.

Frustration Sculpts the Early Stages of Protein Folding.

PubMed

Di Silvio, Eva; Brunori, Maurizio; Gianni, Stefano

2015-09-07

The funneled energy landscape theory implies that protein structures are minimally frustrated. Yet, because of the divergent demands between folding and function, regions of frustrated patterns are present at the active site of proteins. To understand the effects of such local frustration in dictating the energy landscape of proteins, here we compare the folding mechanisms of the two alternative spliced forms of a PDZ domain (PDZ2 and PDZ2as) that share a nearly identical sequence and structure, while displaying different frustration patterns. The analysis, based on the kinetic characterization of a large number of site-directed mutants, reveals that although the late stages for folding are very robust and biased by native topology, the early stages are more malleable and dominated by local frustration. The results are briefly discussed in the context of the energy-landscape theory. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Scale dependent drivers of wild bee diversity in tropical heterogeneous agricultural landscapes.

PubMed

Basu, Parthiba; Parui, Arpan Kumar; Chatterjee, Soumik; Dutta, Aditi; Chakraborty, Pushan; Roberts, Stuart; Smith, Barbara

2016-10-01

Factors associated with agricultural intensification, for example, loss of seminatural vegetation and pesticide use has been shown to adversely affect the bee community. These factors may impact the bee community differently at different landscape scales. The scale dependency is expected to be more pronounced in heterogeneous landscapes. However, the scale-dependent response of the bee community to drivers of its decline is relatively understudied, especially in the tropics where the agricultural landscape is often heterogeneous. This study looked at effects of agricultural intensification on bee diversity at patch and landscape scales in a tropical agricultural landscape. Wild bees were sampled using 12 permanent pan trap stations. Patch and landscape characteristics were measured within a 100 m (patch scale) and a 500 m (landscape scale) radius of pan trap stations. Information on pesticide input was obtained from farmer surveys. Data on vegetation cover, productivity, and percentage of agricultural and fallow land (FL) were collected using satellite imagery. Intensive areas in a bee-site network were less specialized in terms of resources to attract rare bee species while the less intensive areas, which supported more rare species, were more vulnerable to disturbance. A combination of patch quality and diversity as well as pesticide use regulates species diversity at the landscape scale (500 m), whereas pesticide quantity drove diversity at the patch scale (100 m). At the landscape scale, specialization of each site in terms of resources for bees increased with increasing patch diversity and FL while at the patch scale specialization declined with increased pesticide use. Bee functional groups responded differentially to landscape characteristics as well as pesticide use. Wood nesting bees were negatively affected by the number of pesticides used but other bee functional groups were not sensitive to pesticides. Synthesis and Applications : Different factors affect wild bee diversity at the scale of landscape and patch in heterogeneous tropical agricultural systems. The differential response of bee functional groups to agricultural intensification underpins the need for guild-specific management strategies for wild bee conservation. Less intensively farmed areas support more rare species and are vulnerable to disturbance; consequently, these areas should be prioritized for conservation to maintain heterogeneity in the landscape. It is important to conserve and restore seminatural habitats to maintain complexity in the landscapes through participatory processes and to regulate synthetic chemical pesticides in farm operations to conserve the species and functional diversity of wild bees.

[Applications of 2D and 3D landscape pattern indices in landscape pattern analysis of mountainous area at county level].

PubMed

Lu, Chao; Qi, Wei; Li, Le; Sun, Yao; Qin, Tian-Tian; Wang, Na-Na

2012-05-01

Landscape pattern indices are the commonly used tools for the quantitative analysis of landscape pattern. However, the traditional 2D landscape pattern indices neglect the effects of terrain on landscape, existing definite limitations in quantitatively describing the landscape patterns in mountains areas. Taking the Qixia City, a typical mountainous and hilly region in Shandong Province of East China, as a case, this paper compared the differences between 2D and 3D landscape pattern indices in quantitatively describing the landscape patterns and their dynamic changes in mountainous areas. On the basis of terrain structure analysis, a set of landscape pattern indices were selected, including area and density (class area and mean patch size), edge and shape (edge density, landscape shape index, and fractal dimension of mean patch), diversity (Shannon's diversity index and evenness index) , and gathering and spread (contagion index). There existed obvious differences between the 3D class area, mean patch area, and edge density and the corresponding 2D indices, but no significant differences between the 3D landscape shape index, fractal dimension of mean patch, and Shannon' s diversity index and evenness index and the corresponding 2D indices. The 3D contagion index and 2D contagion index had no difference. Because the 3D landscape pattern indices were calculated by using patch surface area and surface perimeter whereas the 2D landscape pattern indices were calculated by adopting patch projective area and projective perimeter, the 3D landscape pattern indices could be relative accurate and efficient in describing the landscape area, density and borderline, in mountainous areas. However, there were no distinct differences in describing landscape shape, diversity, and gathering and spread between the 3D and 2D landscape pattern indices. Generally, by introducing 3D landscape pattern indices to topographic pattern, the description of landscape pattern and its dynamic change would be relatively accurate.

Functional ecomorphology: Feedbacks between form and function in fluvial landscape ecosystems

NASA Astrophysics Data System (ADS)

Fisher, Stuart G.; Heffernan, James B.; Sponseller, Ryan A.; Welter, Jill R.

2007-09-01

The relationship between form and function has been a central organizing principle in biology throughout its history as a formal science. This concept has been relevant from molecules to organisms but loses meaning at population and community levels where study targets are abstract collectives and assemblages. Ecosystems include organisms and abiotic factors but ecosystem ecology too has developed until recently without a strong spatially explicit reference. Landscape ecology provides an opportunity to once again anneal form and function and to consider reciprocal causation between them. This ecomorphologic view can be applied at a variety of ecologically relevant scales and consists of an investigation of how geomorphology provides a structural template that shapes, and is shaped by ecological processes. Running water ecosystems illustrate several principles governing the interaction of landscape form and ecological function subsumed by the concept of "Functional Ecomorphology". Particularly lucrative are ecosystem-level interactions between geologic form and biogeochemical processes integrated by hydrologic flowpaths. While the utility of a flowpath-based approach is most apparent in streams, spatially explicit biogeochemical processing pervades all landscapes and may be of general ecological application.

Modelling non-Euclidean movement and landscape connectivity in highly structured ecological networks

USGS Publications Warehouse

Sutherland, Christopher; Fuller, Angela K.; Royle, J. Andrew

2015-01-01

The ecological distance SCR model uses spatially indexed capture-recapture data to estimate how activity patterns are influenced by landscape structure. As well as reducing bias in estimates of abundance, this approach provides biologically realistic representations of home range geometry, and direct information about species-landscape interactions. The incorporation of both structural (landscape) and functional (movement) components of connectivity provides a direct measure of species-specific landscape connectivity.

Textural analysis of historical aerial photography to characterize woody plant encroachment in South African savanna

Treesearch

Andrew T. Hudak; Carol A. Wessman

1998-01-01

Transitions from grassland to shrubland through woody plant encroachment result in potentially significant shifts in savanna ecosystem function. Given high resolution imagery, a textural index could prove useful for mapping woody plant densities and monitoring woody plant encroachment across savanna landscapes. Spatial heterogeneity introduced through mixtures of...

Community Landscapes: An Integrative Approach to Determine Overlapping Network Module Hierarchy, Identify Key Nodes and Predict Network Dynamics

PubMed Central

Kovács, István A.; Palotai, Robin; Szalay, Máté S.; Csermely, Peter

2010-01-01

Background Network communities help the functional organization and evolution of complex networks. However, the development of a method, which is both fast and accurate, provides modular overlaps and partitions of a heterogeneous network, has proven to be rather difficult. Methodology/Principal Findings Here we introduce the novel concept of ModuLand, an integrative method family determining overlapping network modules as hills of an influence function-based, centrality-type community landscape, and including several widely used modularization methods as special cases. As various adaptations of the method family, we developed several algorithms, which provide an efficient analysis of weighted and directed networks, and (1) determine pervasively overlapping modules with high resolution; (2) uncover a detailed hierarchical network structure allowing an efficient, zoom-in analysis of large networks; (3) allow the determination of key network nodes and (4) help to predict network dynamics. Conclusions/Significance The concept opens a wide range of possibilities to develop new approaches and applications including network routing, classification, comparison and prediction. PMID:20824084

To what extent does urbanisation affect fragmented grassland functioning?

PubMed

van der Walt, L; Cilliers, S S; Kellner, K; Du Toit, M J; Tongway, D

2015-03-15

Urbanisation creates altered environments characterised by increased human habitation, impermeable surfaces, artificial structures, landscape fragmentation, habitat loss, resulting in different resource loss pathways. The vulnerable Rand Highveld Grassland vegetation unit in the Tlokwe Municipal area, South Africa, has been extensively affected and transformed by urbanisation, agriculture, and mining. Grassland fragments in urban areas are often considered to be less species rich and less functional than in the more untransformed or "natural" exurban environments, and are therefore seldom a priority for conservation. Furthermore, urban grassland fragments are often being more intensely managed than exurban areas, such as consistent mowing in open urban areas. Four urbanisation measures acting as indicators for patterns and processes associated with urban areas were calculated for matrix areas surrounding each selected grassland fragment to quantify the position of each grassland remnant along an urbanisation gradient. The grassland fragments were objectively classified into two classes of urbanisation, namely "exurban" and "urban" based on the urbanisation measure values. Grazing was recorded in some exurban grasslands and mowing in some urban grassland fragments. Unmanaged grassland fragments were present in both urban and exurban areas. Fine-scale biophysical landscape function was determined by executing the Landscape Function Analysis (LFA) method. LFA assesses fine-scale landscape patchiness (entailing resource conserving potential and erosion resistance) and 11 soil surface indicators to produce three main LFA parameters (stability, infiltration, and nutrient cycling), which indicates how well a system is functioning in terms of fine-scale biophysical soil processes and characteristics. The aim of this study was to determine the effects of urbanisation and associated management practices on fine-scale biophysical landscape function of urban and exurban grassland fragments, as well as to determine the potential for the use of LFA in decision-making involving the conservation of grassland fragments. The results indicated that the occurrence, size and characteristics of vegetated patches, and especially the presence of litter abundances, were the main factors determining differences in the LFA indices. Furthermore, mowing resulted in the overall fine-scale biophysical indices being higher for some of the urban grassland fragments. This implied that it is not necessarily the influence of urbanisation entailing high or low resource conserving patchiness and patch quality, but rather the management practices associated with urban and exurban areas. Therefore, from a conservation point of view, the grassland fragments in the City of Potchefstroom are just as conservable (on a biophysical function level involving soil processes) than the more "natural" exurban grassland fragments. Copyright © 2014 Elsevier Ltd. All rights reserved.

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.

Two-generation analysis of pollen flow across a landscape. I. Male gamete heterogeneity among females.

PubMed

Smouse, P E; Dyer, R J; Westfall, R D; Sork, V L

2001-02-01

Gene flow is a key factor in the spatial genetic structure in spatially distributed species. Evolutionary biologists interested in microevolutionary processess and conservation biologists interested in the impact of landscape change require a method that measures the real time process of gene movement. We present a novel two-generation (parent-offspring) approach to the study of genetic structure (TwoGener) that allows us to quantify heterogeneity among the male gamete pools sampled by maternal trees scattered across the landscape and to estimate mean pollination distance and effective neighborhood size. First, we describe the model's elements: genetic distance matrices to estimate intergametic distances, molecular analysis of variance to determine whether pollen profiles differ among mothers, and optimal sampling considerations. Second, we evaluate the model's effectiveness by simulating spatially distributed populations. Spatial heterogeneity in male gametes can be estimated by phiFT, a male gametic analogue of Wright's F(ST) and an inverse function of mean pollination distance. We illustrate TwoGener in cases where the male gamete can be categorically or ambiguously determined. This approach does not require the high level of genetic resolution needed by parentage analysis, but the ambiguous case is vulnerable to bias in the absence of adequate genetic resolution. Finally, we apply TwoGener to an empirical study of Quercus alba in Missouri Ozark forests. We find that phiFT = 0.06, translating into about eight effective pollen donors per female and an effective pollination neighborhood as a circle of radius about 17 m. Effective pollen movement in Q. alba is more restricted than previously realized, even though pollen is capable of moving large distances. This case study illustrates that, with a modest investment in field survey and laboratory analysis, the TwoGener approach permits inferences about landscape-level gene movements.

Evaluating the impact of abrupt changes in forest policy and management practices on landscape dynamics: analysis of a Landsat image time series in the Atlantic Northern Forest.

PubMed

Legaard, Kasey R; Sader, Steven A; Simons-Legaard, Erin M

2015-01-01

Sustainable forest management is based on functional relationships between management actions, landscape conditions, and forest values. Changes in management practices make it fundamentally more difficult to study these relationships because the impacts of current practices are difficult to disentangle from the persistent influences of past practices. Within the Atlantic Northern Forest of Maine, U.S.A., forest policy and management practices changed abruptly in the early 1990s. During the 1970s-1980s, a severe insect outbreak stimulated salvage clearcutting of large contiguous tracts of spruce-fir forest. Following clearcut regulation in 1991, management practices shifted abruptly to near complete dependence on partial harvesting. Using a time series of Landsat satellite imagery (1973-2010) we assessed cumulative landscape change caused by these very different management regimes. We modeled predominant temporal patterns of harvesting and segmented a large study area into groups of landscape units with similar harvest histories. Time series of landscape composition and configuration metrics averaged within groups revealed differences in landscape dynamics caused by differences in management history. In some groups (24% of landscape units), salvage caused rapid loss and subdivision of intact mature forest. Persistent landscape change was created by large salvage clearcuts (often averaging > 100 ha) and conversion of spruce-fir to deciduous and mixed forest. In groups that were little affected by salvage (56% of landscape units), contemporary partial harvesting caused loss and subdivision of intact mature forest at even greater rates. Patch shape complexity and edge density reached high levels even where cumulative harvest area was relatively low. Contemporary practices introduced more numerous and much smaller patches of stand-replacing disturbance (typically averaging <15 ha) and a correspondingly large amount of edge. Management regimes impacted different areas to different degrees, producing different trajectories of landscape change that should be recognized when studying the impact of policy and management practices on forest ecology.

Evaluating the Impact of Abrupt Changes in Forest Policy and Management Practices on Landscape Dynamics: Analysis of a Landsat Image Time Series in the Atlantic Northern Forest

PubMed Central

Legaard, Kasey R.; Sader, Steven A.; Simons-Legaard, Erin M.

2015-01-01

Sustainable forest management is based on functional relationships between management actions, landscape conditions, and forest values. Changes in management practices make it fundamentally more difficult to study these relationships because the impacts of current practices are difficult to disentangle from the persistent influences of past practices. Within the Atlantic Northern Forest of Maine, U.S.A., forest policy and management practices changed abruptly in the early 1990s. During the 1970s-1980s, a severe insect outbreak stimulated salvage clearcutting of large contiguous tracts of spruce-fir forest. Following clearcut regulation in 1991, management practices shifted abruptly to near complete dependence on partial harvesting. Using a time series of Landsat satellite imagery (1973-2010) we assessed cumulative landscape change caused by these very different management regimes. We modeled predominant temporal patterns of harvesting and segmented a large study area into groups of landscape units with similar harvest histories. Time series of landscape composition and configuration metrics averaged within groups revealed differences in landscape dynamics caused by differences in management history. In some groups (24% of landscape units), salvage caused rapid loss and subdivision of intact mature forest. Persistent landscape change was created by large salvage clearcuts (often averaging > 100 ha) and conversion of spruce-fir to deciduous and mixed forest. In groups that were little affected by salvage (56% of landscape units), contemporary partial harvesting caused loss and subdivision of intact mature forest at even greater rates. Patch shape complexity and edge density reached high levels even where cumulative harvest area was relatively low. Contemporary practices introduced more numerous and much smaller patches of stand-replacing disturbance (typically averaging <15 ha) and a correspondingly large amount of edge. Management regimes impacted different areas to different degrees, producing different trajectories of landscape change that should be recognized when studying the impact of policy and management practices on forest ecology. PMID:26106893

Oregon Hydrologic Landscapes: A Classification Framework

EPA Science Inventory

There is a growing need for hydrologic classification systems that can provide a basis for broad-scale assessments of the hydrologic functions of landscapes and watersheds and their responses to stressors such as climate change. We developed a hydrologic landscape (HL) classifica...

Conversion of woodlands changes soil related ecosystem services in Subsaharan Africa

NASA Astrophysics Data System (ADS)

Groengroeft, Alexander; Landschreiber, Lars; Luther-Mosebach, Jona; Masamba, Wellington; Zimmermann, Ibo; Eschenbach, Annette

2015-04-01

In remote areas of Subsaharan Africa, growing population, changes in consumption patterns and increasing global influences are leading to a strong pressure on the land resources. Smallholders convert woodlands by fire, grazing and clearing in different intensities thus changing soil properties and their ecosystem functioning. As the extraction of ecosystem services forms the basis of local wellbeing for many communities, the role of soils in providing ecosystem services is of high importance. Since 2010, "The Future Okavango" project investigates the quantification of ecosystem functions and services at four core research sites along the Okavango river basin (Angola, Namibia, Botswana, see http://www.future-okavango.org/). These research sites have an extent of 100 km2 each. Within our subproject the soil functions underlying ecosystem services are studied: The amount and spatial variation of soil nutrient reserves in woodland and their changes by land use activities, the water storage function as a basis for plant growth, and their effect on groundwater recharge and the carbon storage function. The scientific framework consists of four major parts including soil survey and mapping, lab analysis, field measurements and modeling approaches on different scales. A detailed soil survey leads to a measure of the spatial distribution, extent and heterogeneity of soil types for each research site. For generalization purposes, geomorphological and pedological characteristics are merged to derive landscape units. These landscape units have been overlaid by recent land use types to stratify the research site for subsequent soil sampling. On the basis of field and laboratory analysis, spatial distribution of soil properties as well as boundaries between neighboring landscape units are derived. The parameters analysed describe properties according to grain size distribution, organic carbon content, saturated and unsaturated hydraulic conductivity as well as pore space distribution. At nine selected sites, soil water contents and pressure heads are logged throughout the year with a 12 hour resolution in depth of 10 to 160 cm. This monitoring gives information about soil water dynamics at point scale and the database is used to evaluate model outputs of soil water balances later on. To derive point scale soil water balances for each landscape unit the one dimensional and physically based model SWAP 3.2 is applied. The presentation will demonstrate the conceptual framework, exemplary results and will discuss, if the ecosystem service approach can help to avoid future land degradation. Key word: Okavango catchment, soil functions, conceptual approach

RCHILD - an R-package for flexible use of the landscape evolution model CHILD

NASA Astrophysics Data System (ADS)

Dietze, Michael

2014-05-01

Landscape evolution models provide powerful approaches to numerically assess earth surface processes, to quantify rates of landscape change, infer sediment transfer rates, estimate sediment budgets, investigate the consequences of changes in external drivers on a geomorphic system, to provide spatio-temporal interpolations between known landscape states or to test conceptual hypotheses. CHILD (Channel-Hillslope Integrated Landscape Development Model) is one of the most-used models of landscape change in the context of at least tectonic and geomorphologic process interactions. Running CHILD from command line and working with the model output can be a rather awkward task (static model control via text input file, only numeric output in text files). The package RCHILD is a collection of functions for the free statistical software R that help using CHILD in a flexible, dynamic and user-friendly way. The comprised functions allow creating maps, real-time scenes, animations and further thematic plots from model output. The model input files can be modified dynamically and, hence, (feedback-related) changes in external factors can be implemented iteratively. Output files can be written to common formats that can be readily imported to standard GIS software. This contribution presents the basic functionality of the model CHILD as visualised and modified by the package. A rough overview of the available functions is given. Application examples help to illustrate the great potential of numeric modelling of geomorphologic processes.

Benefits and Challenges of Linking Green Infrastructure and Highway Planning in the United States

NASA Astrophysics Data System (ADS)

Marcucci, Daniel J.; Jordan, Lauren M.

2013-01-01

Landscape-level green infrastructure creates a network of natural and semi-natural areas that protects and enhances ecosystem services, regenerative capacities, and ecological dynamism over long timeframes. It can also enhance quality of life and certain economic activity. Highways create a network for moving goods and services efficiently, enabling commerce, and improving mobility. A fundamentally profound conflict exists between transportation planning and green infrastructure planning because they both seek to create connected, functioning networks across the same landscapes and regions, but transportation networks, especially in the form of highways, fragment and disconnect green infrastructure networks. A key opportunity has emerged in the United States during the last ten years with the promotion of measures to link transportation and environmental concerns. In this article we examined the potential benefits and challenges of linking landscape-level green infrastructure planning and implementation with integrated transportation planning and highway project development in the United States policy context. This was done by establishing a conceptual model that identified logical flow lines from planning to implementation as well as the potential interconnectors between green infrastructure and highway infrastructure. We analyzed the relationship of these activities through literature review, policy analysis, and a case study of a suburban Maryland, USA landscape. We found that regionally developed and adopted green infrastructure plans can be instrumental in creating more responsive regional transportation plans and streamlining the project environmental review process while enabling better outcomes by enabling more targeted mitigation. In order for benefits to occur, however, landscape-scale green infrastructure assessments and plans must be in place before integrated transportation planning and highway project development occurs. It is in the transportation community's interests to actively facilitate green infrastructure planning because it creates a more predictable environmental review context. On the other hand, for landscape-level green infrastructure, transportation planning and development is much more established and better funded and can provide a means of supporting green infrastructure planning and implementation, thereby enhancing conservation of ecological function.

Benefits and challenges of linking green infrastructure and highway planning in the United States.

PubMed

Marcucci, Daniel J; Jordan, Lauren M

2013-01-01

Landscape-level green infrastructure creates a network of natural and semi-natural areas that protects and enhances ecosystem services, regenerative capacities, and ecological dynamism over long timeframes. It can also enhance quality of life and certain economic activity. Highways create a network for moving goods and services efficiently, enabling commerce, and improving mobility. A fundamentally profound conflict exists between transportation planning and green infrastructure planning because they both seek to create connected, functioning networks across the same landscapes and regions, but transportation networks, especially in the form of highways, fragment and disconnect green infrastructure networks. A key opportunity has emerged in the United States during the last ten years with the promotion of measures to link transportation and environmental concerns. In this article we examined the potential benefits and challenges of linking landscape-level green infrastructure planning and implementation with integrated transportation planning and highway project development in the United States policy context. This was done by establishing a conceptual model that identified logical flow lines from planning to implementation as well as the potential interconnectors between green infrastructure and highway infrastructure. We analyzed the relationship of these activities through literature review, policy analysis, and a case study of a suburban Maryland, USA landscape. We found that regionally developed and adopted green infrastructure plans can be instrumental in creating more responsive regional transportation plans and streamlining the project environmental review process while enabling better outcomes by enabling more targeted mitigation. In order for benefits to occur, however, landscape-scale green infrastructure assessments and plans must be in place before integrated transportation planning and highway project development occurs. It is in the transportation community's interests to actively facilitate green infrastructure planning because it creates a more predictable environmental review context. On the other hand, for landscape-level green infrastructure, transportation planning and development is much more established and better funded and can provide a means of supporting green infrastructure planning and implementation, thereby enhancing conservation of ecological function.

[Landscape connectivity of waterbody network in the new reclamation region of Lianyungang based on effective distance model].

PubMed

Qiao, Fu-Zhen; Zheng, Zhong-Ming; Li, Jia-Lin; Zheng, Wen-Bing

2014-08-01

Landscape connectivity is an important indicator to measure effectiveness of landscape ecological services. Waterbody connectivity in Lianyun New City, the new reclamation region of Lianyungang, was investigated based on GIS technology and effective distance model. The results showed that the total connectivity of waterbodies was poor in Lanyun New City. Connectivity of patches was related to characteristics of ecological process, ecological services value and spatial arrangement. The higher the ecosystem services value of patches was, the greater its contribution to the overall water landscape connectivity was. Some patches with long strip structure played a key role to improve the landscape connectivity. By classifying the importance of connectivity and functional groups of waterbody patches, planning of waterbodies in Lianyun New City conformed to the theory of non-substitutable pattern developed by Forman. Waterbody patches with corresponding functions should be considered with priority when planning and building a new city. The present study demonstrated that connectivity of patches should be an important factor to be considered in ecological landscape planning. Construction of ecological corridors should not only take the number of ecological landscapes into consideration, but also pay attention to spatial arrangement of landscapes in order to improve the overall landscape connectivity.

Relation between the Dynamics of Glassy Clusters and Characteristic Features of their Energy Landscape

NASA Astrophysics Data System (ADS)

De, Sandip; Schaefer, Bastian; Sadeghi, Ali; Sicher, Michael; Kanhere, D. G.; Goedecker, Stefan

2014-02-01

Based on a recently introduced metric for measuring distances between configurations, we introduce distance-energy (DE) plots to characterize the potential energy surface of clusters. Producing such plots is computationally feasible on the density functional level since it requires only a few hundred stable low energy configurations including the global minimum. By using standard criteria based on disconnectivity graphs and the dynamics of Lennard-Jones clusters, we show that the DE plots convey the necessary information about the character of the potential energy surface and allow us to distinguish between glassy and nonglassy systems. We then apply this analysis to real clusters at the density functional theory level and show that both glassy and nonglassy clusters can be found in simulations. It turns out that among our investigated clusters only those can be synthesized experimentally which exhibit a nonglassy landscape.

From Forest Landscape to Agricultural Landscape in the Developing Tropical Country of Malaysia: Pattern, Process, and Their Significance on Policy

NASA Astrophysics Data System (ADS)

Abdullah, Saiful Arif; Hezri, Adnan A.

2008-11-01

Agricultural expansion and deforestation are spatial processes of land transformation that impact on landscape pattern. In peninsular Malaysia, the conversion of forested areas into two major cash crops—rubber and oil palm plantations—has been identified as driving significant environmental change. To date, there has been insufficient literature studying the link between changes in landscape patterns and land-related development policies. Therefore, this paper examines: (i) the links between development policies and changes in land use/land cover and landscape pattern and (ii) the significance and implications of these links for future development policies. The objective is to generate insights on the changing process of land use/land cover and landscape pattern as a functional response to development policies and their consequences for environmental conditions. Over the last century, the development of cash crops has changed the country from one dominated by natural landscapes to one dominated by agricultural landscapes. But the last decade of the century saw urbanization beginning to impact significantly. This process aligned with the establishment of various development policies, from land development for agriculture between the mid 1950s and the 1970s to an emphasis on manufacturing from the 1980s onward. Based on a case study in Selangor, peninsular Malaysia, a model of landscape pattern change is presented. It contains three stages according to the relative importance of rubber (first stage: 1900-1950s), oil palm (second stage: 1960s-1970s), and urban (third stage: 1980s-1990s) development that influenced landscape fragmentation and heterogeneity. The environmental consequences of this change have been depicted through loss of biodiversity, geohazard incidences, and the spread of vector-borne diseases. The spatial ecological information can be useful to development policy formulation, allowing diagnosis of the country’s “health” and sustainability. The final section outlines the usefulness of landscape analysis in the policy-making process to prevent further fragmentation of the landscape and forest loss in Malaysia in the face of rapid economic development.

From forest landscape to agricultural landscape in the developing tropical country of Malaysia: pattern, process, and their significance on policy.

PubMed

Abdullah, Saiful Arif; Hezri, Adnan A

2008-11-01

Agricultural expansion and deforestation are spatial processes of land transformation that impact on landscape pattern. In peninsular Malaysia, the conversion of forested areas into two major cash crops--rubber and oil palm plantations--has been identified as driving significant environmental change. To date, there has been insufficient literature studying the link between changes in landscape patterns and land-related development policies. Therefore, this paper examines: (i) the links between development policies and changes in land use/land cover and landscape pattern and (ii) the significance and implications of these links for future development policies. The objective is to generate insights on the changing process of land use/land cover and landscape pattern as a functional response to development policies and their consequences for environmental conditions. Over the last century, the development of cash crops has changed the country from one dominated by natural landscapes to one dominated by agricultural landscapes. But the last decade of the century saw urbanization beginning to impact significantly. This process aligned with the establishment of various development policies, from land development for agriculture between the mid 1950s and the 1970s to an emphasis on manufacturing from the 1980s onward. Based on a case study in Selangor, peninsular Malaysia, a model of landscape pattern change is presented. It contains three stages according to the relative importance of rubber (first stage: 1900--1950s), oil palm (second stage: 1960s--1970s), and urban (third stage: 1980s--1990s) development that influenced landscape fragmentation and heterogeneity. The environmental consequences of this change have been depicted through loss of biodiversity, geohazard incidences, and the spread of vector-borne diseases. The spatial ecological information can be useful to development policy formulation, allowing diagnosis of the country's "health" and sustainability. The final section outlines the usefulness of landscape analysis in the policy-making process to prevent further fragmentation of the landscape and forest loss in Malaysia in the face of rapid economic development.

Coevolutionary modeling of protein sequences: Predicting structure, function, and mutational landscapes

NASA Astrophysics Data System (ADS)

Weigt, Martin

Over the last years, biological research has been revolutionized by experimental high-throughput techniques, in particular by next-generation sequencing technology. Unprecedented amounts of data are accumulating, and there is a growing request for computational methods unveiling the information hidden in raw data, thereby increasing our understanding of complex biological systems. Statistical-physics models based on the maximum-entropy principle have, in the last few years, played an important role in this context. To give a specific example, proteins and many non-coding RNA show a remarkable degree of structural and functional conservation in the course of evolution, despite a large variability in amino acid sequences. We have developed a statistical-mechanics inspired inference approach - called Direct-Coupling Analysis - to link this sequence variability (easy to observe in sequence alignments, which are available in public sequence databases) to bio-molecular structure and function. In my presentation I will show, how this methodology can be used (i) to infer contacts between residues and thus to guide tertiary and quaternary protein structure prediction and RNA structure prediction, (ii) to discriminate interacting from non-interacting protein families, and thus to infer conserved protein-protein interaction networks, and (iii) to reconstruct mutational landscapes and thus to predict the phenotypic effect of mutations. References [1] M. Figliuzzi, H. Jacquier, A. Schug, O. Tenaillon and M. Weigt ''Coevolutionary landscape inference and the context-dependence of mutations in beta-lactamase TEM-1'', Mol. Biol. Evol. (2015), doi: 10.1093/molbev/msv211 [2] E. De Leonardis, B. Lutz, S. Ratz, S. Cocco, R. Monasson, A. Schug, M. Weigt ''Direct-Coupling Analysis of nucleotide coevolution facilitates RNA secondary and tertiary structure prediction'', Nucleic Acids Research (2015), doi: 10.1093/nar/gkv932 [3] F. Morcos, A. Pagnani, B. Lunt, A. Bertolino, D. Marks, C. Sander, R. Zecchina, J.N. Onuchic, T. Hwa, M. Weigt, ''Direct-coupling analysis of residue co-evolution captures native contacts across many protein families'', Proc. Natl. Acad. Sci. 108, E1293-E1301 (2011).

Contemporary and restorable wetland water storage: A landscape perspective

USDA-ARS?s Scientific Manuscript database

Surface water storage in wetlands drives ecosystem function from local to landscape scales. In many regions, hydrologic modifications have significantly reduced wetland storage capacity and subsequently diminished wetland functions. While the loss of wetland area has been well documented across many...

Restoration of landscape function: Reserves or active management?

Treesearch

A.B. Carey

2003-01-01

A 20-year program of research suggests that old-growth forests are ecologically unique and highly valued by people, that naturally young forests with legacies from old forests sustain many, if not all, the higher organisms associated with old growth, but that many managed forests are impoverished in species. Thus, restoring landscape function entails restoring function...

The derivation of scenic utility functions and surfaces and their role in landscape management

Treesearch

John W. Hamilton; Gregory J. Buhyoff; J. Douglas Wellman

1979-01-01

This paper outlines a methodological approach for determining relevant physical landscape features which people use in formulating judgments about scenic utility. This information, coupled with either empirically derived or rationally stipulated regression techniques, may be used to produce scenic utility functions and surfaces. These functions can provide a means for...

GeoPAT: A toolbox for pattern-based information retrieval from large geospatial databases

NASA Astrophysics Data System (ADS)

Jasiewicz, Jarosław; Netzel, Paweł; Stepinski, Tomasz

2015-07-01

Geospatial Pattern Analysis Toolbox (GeoPAT) is a collection of GRASS GIS modules for carrying out pattern-based geospatial analysis of images and other spatial datasets. The need for pattern-based analysis arises when images/rasters contain rich spatial information either because of their very high resolution or their very large spatial extent. Elementary units of pattern-based analysis are scenes - patches of surface consisting of a complex arrangement of individual pixels (patterns). GeoPAT modules implement popular GIS algorithms, such as query, overlay, and segmentation, to operate on the grid of scenes. To achieve these capabilities GeoPAT includes a library of scene signatures - compact numerical descriptors of patterns, and a library of distance functions - providing numerical means of assessing dissimilarity between scenes. Ancillary GeoPAT modules use these functions to construct a grid of scenes or to assign signatures to individual scenes having regular or irregular geometries. Thus GeoPAT combines knowledge retrieval from patterns with mapping tasks within a single integrated GIS environment. GeoPAT is designed to identify and analyze complex, highly generalized classes in spatial datasets. Examples include distinguishing between different styles of urban settlements using VHR images, delineating different landscape types in land cover maps, and mapping physiographic units from DEM. The concept of pattern-based spatial analysis is explained and the roles of all modules and functions are described. A case study example pertaining to delineation of landscape types in a subregion of NLCD is given. Performance evaluation is included to highlight GeoPAT's applicability to very large datasets. The GeoPAT toolbox is available for download from

The impact of land use change and hydroclimatic variability on landscape connectivity dynamics across surface water networks at subcontinental scale

NASA Astrophysics Data System (ADS)

Tulbure, M. G.; Bishop-Taylor, R.; Broich, M.

2017-12-01

Land use (LU) change and hydroclimatic variability affect spatiotemporal landscape connectivity dynamics, important for species movement and dispersal. Despite the fact that LU change can strongly influence dispersal potential over time, prior research has only focused on the impacts of dynamic changes in the distribution of potential habitats. We used 8 time-steps of historical LU together with a Landsat-derived time-series of surface water habitat dynamics (1986-2011) over the Murray-Darling Basin (MDB), a region with extreme hydroclimatic variability, impacted by LU changes. To assess how changing LU and hydroclimatic variability affect landscape connectivity across time, we compared 4 scenarios, namely one where both climate and LU are dynamic over time, one where climate is kept steady (i.e. a median surface water extent layer), and two scenarios where LU is kept steady (i.e. resistance values associated with the most recent or the first LU layer). We used circuit theory to assign landscape features with `resistance' costs and graph theory network analysis, with surface water habitats as `nodes' connected by dispersal paths or `edges' Findings comparing a dry and an average season show high differences in number of nodes (14581 vs 21544) and resistance distances. The combined effect of LU change and landscape wetness was lower than expected, likely a function of the large, MDB-wide, aggregation scale. Spatially explicit analyses are expected to identify areas where the synergistic effect of LU change and landscape wetness greatly reduce or increase landscape connectivity, as well as areas where the two effects cancel each other out.

Soil cover patterns influence on the land environmental functions, agroecological quality, land-use and monitoring efficiency in the Central Russia

NASA Astrophysics Data System (ADS)

Vasenev, Ivan; Yashin, Ivan; Lukin, Sergey; Valentini, Riccardo

2015-04-01

First decades of XXI century actualized for soil researches the principal methodical problem of most modern geosciences: what spatial and temporal scale would be optimal for land quality evaluation and land-use practice optimizing? It is becoming obvious that this question cannot have one solution and have to be solved with especial attention on the features of concrete region and landscape, land-use history and practical issues, land current state and environmental functions, soil cover patterns and variability, governmental requirements and local society needs, best available technologies and their potential profitability. Central Russia is one of the most dynamical economic regions with naturally high and man-made complicated landscape and soil cover variability, long-term land-use history and self-contradictory issues, high potential of profitable farming and increased risks of land degradation. Global climate and technological changes essentially complicate the originally high and sharply increased in XX century farming land heterogeneity in the Central Russia that actualizes system analysis of its zonal, intra-zonal and azonal soil cover patterns according to their influence on land environmental functions, agroecological quality, and land-use and monitoring efficiency variability. Developed by the Laboratory of agroecological monitoring, ecosystem modeling & prediction (LAMP / RTSAU with support of RF Governmental projects #11.G34.31.0079 and #14.120.14.4266) regional systems of greenhouse gases environmental monitoring RusFluxNet (6 fixed & 1 mobile eddy covariance stations with zonal functional sets of key plots with chamber investigations in 5 Russian regions) and of agroecological monitoring (in representative key plots with different farming practice in 9 RF regions) allow to do this analysis in frame of enough representative regional multi-factorial matrix of soil cover patterns, bioclimatic conditions, landscape features, and land-use history and current practice versions. Well-elaborated monitoring collaboration with the principal natural reserves in south-taiga and forest-steppe zones provides process-based interaction with long-term data on zonal climatic, landscape and soil features necessary to test the process, functional and evaluation models in the specific conditions of each bioclimatic zone. The dominated erosion and dehumification trends have been essentially activated for last 3-4 decades due to hu¬mus negative balance around 0.6-0.7 t ha-1year-1 and connected disaggregation with annual rate between 1 and 25 g/kg for aggregates 10-0.25 mm. "Standard" monitoring objects and regionally generalized data showed characteristic for Chernozems 2-2.5 % humus drop during this period and active processes of CO2 emission and humus eluvial-illuvial profile redistribution too. Forest-steppe Chernozems are usually characterized by higher stability than steppe ones. The ratio between erosive and biological losses in humus stock can be ten¬tatively estimated as fifty-fifty with essential variability within slope landscape. Both these processes have essential impacts on different sets of soil environmental and agroecological functions (including atmospheric air, surface and ground water quality, biodiversity and profitability) that we need to understand and predict. A drop of humus content below threshold values (for different soils between 1.5 and 6%) considerably reduces not only soil environmental regulation functions but also effectiveness of used fertilizers, crop yield quality and possibility of sustainable agricultural land-use. The carried out long-term researches of representative natural, rural and urban landscapes in Tver, Yaroslavl, Vladimir, Moscow, Kaluga, Kursk, Belgorod, Tambov, Voronezh and Saratov regions give us validation and ranging of the limiting factors of the elementary soil cover patterns current features and transformation processes, environmental functions and agroecological quality, monitoring results functional interpretation, spatial and temporal interpolation and extrapolation. These data allow essentially improve our understanding and quantitative assessments of the regional and within-field variability of land agroecological and environmental functions that is crucial for agroecosystem services evaluation, current and planned land-use environmental impacts, and DSS development for land-use agroecological optimizing taking into attention the regional and local landscapes features and most realistic scenarios of climate change and agro-technology transfer. Developed and verified within the project regionally adapted DSS (ACORD-R - RF #2012612944) gives effective informational and methodological support for land-use agroecological optimization.

Spatially Explicit Landscape-Level Ecological Risks Induced by Land Use and Land Cover Change in a National Ecologically Representative Region in China.

PubMed

Gong, Jian; Yang, Jianxin; Tang, Wenwu

2015-11-09

Land use and land cover change is driven by multiple influential factors from environmental and social dimensions in a land system. Land use practices of human decision-makers modify the landscape of the land system, possibly leading to landscape fragmentation, biodiversity loss, or environmental pollution-severe environmental or ecological impacts. While landscape-level ecological risk assessment supports the evaluation of these impacts, investigations on how these ecological risks induced by land use practices change over space and time in response to alternative policy intervention remain inadequate. In this article, we conducted spatially explicit landscape ecological risk analysis in Ezhou City, China. Our study area is a national ecologically representative region experiencing drastic land use and land cover change, and is regulated by multiple policies represented by farmland protection, ecological conservation, and urban development. We employed landscape metrics to consider the influence of potential landscape-level disturbance for the evaluation of landscape ecological risks. Using spatiotemporal simulation, we designed scenarios to examine spatiotemporal patterns in landscape ecological risks in response to policy intervention. Our study demonstrated that spatially explicit landscape ecological risk analysis combined with simulation-driven scenario analysis is of particular importance for guiding the sustainable development of ecologically vulnerable land systems.

Spatially Explicit Landscape-Level Ecological Risks Induced by Land Use and Land Cover Change in a National Ecologically Representative Region in China

PubMed Central

Gong, Jian; Yang, Jianxin; Tang, Wenwu

2015-01-01

Land use and land cover change is driven by multiple influential factors from environmental and social dimensions in a land system. Land use practices of human decision-makers modify the landscape of the land system, possibly leading to landscape fragmentation, biodiversity loss, or environmental pollution—severe environmental or ecological impacts. While landscape-level ecological risk assessment supports the evaluation of these impacts, investigations on how these ecological risks induced by land use practices change over space and time in response to alternative policy intervention remain inadequate. In this article, we conducted spatially explicit landscape ecological risk analysis in Ezhou City, China. Our study area is a national ecologically representative region experiencing drastic land use and land cover change, and is regulated by multiple policies represented by farmland protection, ecological conservation, and urban development. We employed landscape metrics to consider the influence of potential landscape-level disturbance for the evaluation of landscape ecological risks. Using spatiotemporal simulation, we designed scenarios to examine spatiotemporal patterns in landscape ecological risks in response to policy intervention. Our study demonstrated that spatially explicit landscape ecological risk analysis combined with simulation-driven scenario analysis is of particular importance for guiding the sustainable development of ecologically vulnerable land systems. PMID:26569270

Prospects for hydrologic classification of landscapes and watersheds

EPA Science Inventory

The ecological functions of streams and associated riparian zones are strongly influenced by the hydrological attributes of watersheds and landscapes in which they occur. Oregon hydrologic landscape regions (HLRs) have been defined based on four types of GIS data: 1) climate, 2) ...

Evaluating management risks using landscape trajectory analysis: a case study of California fisher

Treesearch

Craig M. Thompson; William J. Zielinski; Kathryn L. Purcell

2011-01-01

Ecosystem management requires an understanding of how landscapes vary in space and time, how this variation can be affected by management decisions or stochastic events, and the potential consequences for species. Landscape trajectory analysis, coupled with a basic knowledge of species habitat selection, offers a straightforward approach to ecological risk analysis and...

Landscape-level movement patterns by lions in western Serengeti: comparing the influence of inter-specific competitors, habitat attributes and prey availability.

PubMed

Kittle, Andrew M; Bukombe, John K; Sinclair, Anthony R E; Mduma, Simon A R; Fryxell, John M

2016-01-01

Where apex predators move on the landscape influences ecosystem structure and function and is therefore key to effective landscape-level management and species-specific conservation. However the factors underlying predator distribution patterns within functional ecosystems are poorly understood. Predator movement should be sensitive to the spatial patterns of inter-specific competitors, spatial variation in prey density, and landscape attributes that increase individual prey vulnerability. We investigated the relative role of these fundamental factors on seasonal resource utilization by a globally endangered apex carnivore, the African lion (Panthera leo) in Tanzania's Serengeti National Park. Lion space use was represented by novel landscape-level, modified utilization distributions (termed "localized density distributions") created from telemetry relocations of individual lions from multiple neighbouring prides. Spatial patterns of inter-specific competitors were similarly determined from telemetry re-locations of spotted hyenas (Crocuta crocuta), this system's primary competitor for lions; prey distribution was derived from 18 months of detailed census data; and remote sensing data was used to represent relevant habitat attributes. Lion space use was consistently influenced by landscape attributes that increase individual prey vulnerability to predation. Wet season activity, when available prey were scarce, was concentrated near embankments, which provide ambush opportunities, and dry season activity, when available prey were abundant, near remaining water sources where prey occurrence is predictable. Lion space use patterns were positively associated with areas of high prey biomass, but only in the prey abundant dry season. Finally, at the broad scale of this analysis, lion and hyena space use was positively correlated in the comparatively prey-rich dry season and unrelated in the wet season, suggesting lion movement was unconstrained by the spatial patterns of their main inter-specific competitors. The availability of potential prey and vulnerability of that prey to predation both motivate lion movement decisions, with their relative importance apparently mediated by overall prey abundance. With practical and theoretical implications, these results suggest that while top carnivores are consistently cognizant of how landscape features influence individual prey vulnerability, they also adopt a flexible approach to range use by adjusting spatial behaviour according to fluctuations in local prey abundance.

Selecting landscape metrics as indicators of spatial heterogeneity-A comparison among Greek landscapes

NASA Astrophysics Data System (ADS)

Plexida, Sofia G.; Sfougaris, Athanassios I.; Ispikoudis, Ioannis P.; Papanastasis, Vasilios P.

2014-02-01

This paper investigates the spatial heterogeneity of three landscapes along an altitudinal gradient and different human land use. The main aim was the identification of appropriate landscape indicators using different extents. ASTER image was used to create a land cover map consisting of three landscapes which differed in altitude and land use. A number of landscape metrics quantifying patch complexity, configuration, diversity and connectivity were derived from the thematic map at the landscape level. There were significant differences among the three landscapes regarding these four aspects of landscape heterogeneity. The analysis revealed a specific pattern of land use where lowlands are being increasingly utilized by humans (percentage of agricultural land = 65.84%) characterized by physical connectedness (high values of Patch Cohesion Index) and relatively simple geometries (low values of fractal dimension index). The landscape pattern of uplands was found to be highly diverse based upon the Shannon Diversity index. After selecting the scale (600 ha) where metrics values stabilized, it was shown that metrics were more correlated at the small scale of 60 ha. From the original 24 metrics, 14 individual metrics with high Spearman correlation coefficient and Variance Inflation Factor criterion were eliminated, leaving 10 representative metrics for subsequent analysis. Data reduction analysis showed that Patch Density, Area-Weighted Mean Fractal Dimension Index and Patch Cohesion Index are suitable to describe landscape patterns irrespective of the scale. A systematic screening of these metrics could enhance a deeper understanding of the results obtained by them and contribute to a sustainable landscape management of Mediterranean landscapes.

Transfer Relations Between Landscape Functions - The Hydrological Point of View

NASA Astrophysics Data System (ADS)

Fohrer, N.; Lenhart, T.; Eckhardt, K.; Frede, H.-G.

EC market policies and regional subsidy programs have an enormous impact on local land use. This has far reaching consequences on various landscape functions. In the joint research project SFB299 at the Giessen University the effect of land use options on economic, ecological and hydrological landscape functions are under investigation. The continuous time step model SWAT-G (Eckhardt et al., 2000; Arnold et al., 1998) is employed to characterize the influence of land use patterns on hydrological processes. The model was calibrated and validated employing a split sample approach. For two mesoscale watersheds (Aar, 60 km2; Dietzhölze, 81 km2) located in the Lahn-Dill- Bergland, Germany, different land use scenarios were analyzed with regard to their hydrological impact. Additionally the effect of land use change was analyzed with an ecological and an agro-economic model. The impact of the stepwise changing land use was expressed as trade off relations between different landscape functions.

Three-dimensional habitat structure and landscape genetics: a step forward in estimating functional connectivity.

PubMed

Milanesi, P; Holderegger, R; Bollmann, K; Gugerli, F; Zellweger, F

2017-02-01

Estimating connectivity among fragmented habitat patches is crucial for evaluating the functionality of ecological networks. However, current estimates of landscape resistance to animal movement and dispersal lack landscape-level data on local habitat structure. Here, we used a landscape genetics approach to show that high-fidelity habitat structure maps derived from Light Detection and Ranging (LiDAR) data critically improve functional connectivity estimates compared to conventional land cover data. We related pairwise genetic distances of 128 Capercaillie (Tetrao urogallus) genotypes to least-cost path distances at multiple scales derived from land cover data. Resulting β values of linear mixed effects models ranged from 0.372 to 0.495, while those derived from LiDAR ranged from 0.558 to 0.758. The identification and conservation of functional ecological networks suffering from habitat fragmentation and homogenization will thus benefit from the growing availability of detailed and contiguous data on three-dimensional habitat structure and associated habitat quality. © 2016 by the Ecological Society of America.

Predicting primate local extinctions within "real-world" forest fragments: a pan-neotropical analysis.

PubMed

Benchimol, Maíra; Peres, Carlos A

2014-03-01

Understanding the main drivers of species extinction in human-modified landscapes has gained paramount importance in proposing sound conservation strategies. Primates play a crucial role in maintaining the integrity of forest ecosystem functions and represent the best studied order of tropical terrestrial vertebrates, yet primate species diverge widely in their responses to forest habitat disturbance and fragmentation. Here, we present a robust quantitative review on the synergistic effects of habitat fragmentation on Neotropical forest primates to pinpoint the drivers of species extinction across a wide range of forest patches from Mexico to Argentina. Presence-absence data on 19 primate functional groups were compiled from 705 forest patches and 55 adjacent continuous forest sites, which were nested within 61 landscapes investigated by 96 studies. Forest patches were defined in terms of their size, surrounding matrix and level of hunting pressure on primates, and each functional group was classified according to seven life-history traits. Generalized linear mixed models showed that patch size, forest cover, level of hunting pressure, home range size and trophic status were the main predictors of species persistence within forest isolates for all functional groups pooled together. However, patterns of local extinction varied greatly across taxa, with Alouatta and Callicebus moloch showing the highest occupancy rates even within tiny forest patches, whereas Brachyteles and Leontopithecus occupied fewer than 50% of sites, even in relatively large forest tracts. Our results uncover the main predictors of platyrrhine primate species extinction, highlighting the importance of considering the history of anthropogenic disturbances, the structure of landscapes, and species life-history attributes in predicting primate persistence in Neotropical forest patches. We suggest that large-scale conservation planning of fragmented forest landscapes should prioritize and set-aside large, well-connected and strictly protected forest reserves to maximize species persistence across the entire spectrum of primate life-history. © 2013 Wiley Periodicals, Inc.

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.

Hydrologic landscape classification evaluates streamflow vulnerability to climate change in Oregon, USA

EPA Science Inventory

Classification can allow assessments of the hydrologic functions of landscapes and their responses to stressors. Here we demonstrate the use of a hydrologic landscape (HL) approach to assess vulnerability to potential future climate change at statewide and basin scales. The HL ...

MULTI-TEMPORAL REMOTE SENSING ANALYTICAL APPROACHES FOR CHARACTERIZING LANDSCAPE CHANGE

EPA Science Inventory

Changes in landscape composition and function result from both acute land-cover conversions and chronic landscape changes. Land-cover conversions are typically mediated by human land-use activities (e.g. conversion from forest to agriculture), while more subtle chronic l...

Ditch network sustains functional connectivity and influences patterns of gene flow in an intensive agricultural landscape

PubMed Central

Favre-Bac, L; Mony, C; Ernoult, A; Burel, F; Arnaud, J-F

2016-01-01

In intensive agricultural landscapes, plant species previously relying on semi-natural habitats may persist as metapopulations within landscape linear elements. Maintenance of populations' connectivity through pollen and seed dispersal is a key factor in species persistence in the face of substantial habitat loss. The goals of this study were to investigate the potential corridor role of ditches and to identify the landscape components that significantly impact patterns of gene flow among remnant populations. Using microsatellite loci, we explored the spatial genetic structure of two hydrochorous wetland plants exhibiting contrasting local abundance and different habitat requirements: the rare and regionally protected Oenanthe aquatica and the more commonly distributed Lycopus europaeus, in an 83 km2 agricultural lowland located in northern France. Both species exhibited a significant spatial genetic structure, along with substantial levels of genetic differentiation, especially for L. europaeus, which also expressed high levels of inbreeding. Isolation-by-distance analysis revealed enhanced gene flow along ditches, indicating their key role in effective seed and pollen dispersal. Our data also suggested that the configuration of the ditch network and the landscape elements significantly affected population genetic structure, with (i) species-specific scale effects on the genetic neighborhood and (ii) detrimental impact of human ditch management on genetic diversity, especially for O. aquatica. Altogether, these findings highlighted the key role of ditches in the maintenance of plant biodiversity in intensive agricultural landscapes with few remnant wetland habitats. PMID:26486611

Landscape Builder: software for the creation of initial landscapes for LANDIS from FIA data

Treesearch

William Dijak

2013-01-01

I developed Landscape Builder to create spatially explicit landscapes as starting conditions for LANDIS Pro 7.0 and LANDIS II landscape forest simulation models from classified satellite imagery and Forest Inventory and Analysis (FIA) data collected over multiple years. LANDIS Pro and LANDIS II models project future landscapes by simulating tree growth, tree species...

Transcriptional atlas of cardiogenesis maps congenital heart disease interactome.

PubMed

Li, Xing; Martinez-Fernandez, Almudena; Hartjes, Katherine A; Kocher, Jean-Pierre A; Olson, Timothy M; Terzic, Andre; Nelson, Timothy J

2014-07-01

Mammalian heart development is built on highly conserved molecular mechanisms with polygenetic perturbations resulting in a spectrum of congenital heart diseases (CHD). However, knowledge of cardiogenic ontogeny that regulates proper cardiogenesis remains largely based on candidate-gene approaches. Mapping the dynamic transcriptional landscape of cardiogenesis from a genomic perspective is essential to integrate the knowledge of heart development into translational applications that accelerate disease discovery efforts toward mechanistic-based treatment strategies. Herein, we designed a time-course transcriptome analysis to investigate the genome-wide dynamic expression landscape of innate murine cardiogenesis ranging from embryonic stem cells to adult cardiac structures. This comprehensive analysis generated temporal and spatial expression profiles, revealed stage-specific gene functions, and mapped the dynamic transcriptome of cardiogenesis to curated pathways. Reconciling known genetic underpinnings of CHD, we deconstructed a disease-centric dynamic interactome encoded within this cardiogenic atlas to identify stage-specific developmental disturbances clustered on regulation of epithelial-to-mesenchymal transition (EMT), BMP signaling, NF-AT signaling, TGFb-dependent EMT, and Notch signaling. Collectively, this cardiogenic transcriptional landscape defines the time-dependent expression of cardiac ontogeny and prioritizes regulatory networks at the interface between health and disease. Copyright © 2014 the American Physiological Society.

Free-energy landscape, principal component analysis, and structural clustering to identify representative conformations from molecular dynamics simulations: the myoglobin case.

PubMed

Papaleo, Elena; Mereghetti, Paolo; Fantucci, Piercarlo; Grandori, Rita; De Gioia, Luca

2009-01-01

Several molecular dynamics (MD) simulations were used to sample conformations in the neighborhood of the native structure of holo-myoglobin (holo-Mb), collecting trajectories spanning 0.22 micros at 300 K. Principal component (PCA) and free-energy landscape (FEL) analyses, integrated by cluster analysis, which was performed considering the position and structures of the individual helices of the globin fold, were carried out. The coherence between the different structural clusters and the basins of the FEL, together with the convergence of parameters derived by PCA indicates that an accurate description of the Mb conformational space around the native state was achieved by multiple MD trajectories spanning at least 0.14 micros. The integration of FEL, PCA, and structural clustering was shown to be a very useful approach to gain an overall view of the conformational landscape accessible to a protein and to identify representative protein substates. This method could be also used to investigate the conformational and dynamical properties of Mb apo-, mutant, or delete versions, in which greater conformational variability is expected and, therefore identification of representative substates from the simulations is relevant to disclose structure-function relationship.

Informational landscapes in art, science, and evolution.

PubMed

Cohen, Irun R

2006-07-01

An informational landscape refers to an array of information related to a particular theme or function. The Internet is an example of an informational landscape designed by humans for purposes of communication. Once it exists, however, any informational landscape may be exploited to serve a new purpose. Listening Post is the name of a dynamic multimedia work of art that exploits the informational landscape of the Internet to produce a visual and auditory environment. Here, I use Listening Post as a prototypic example for considering the creative role of informational landscapes in the processes that beget evolution and science.

Gentlest ascent dynamics for calculating first excited state and exploring energy landscape of Kohn-Sham density functionals.

PubMed

Li, Chen; Lu, Jianfeng; Yang, Weitao

2015-12-14

We develop the gentlest ascent dynamics for Kohn-Sham density functional theory to search for the index-1 saddle points on the energy landscape of the Kohn-Sham density functionals. These stationary solutions correspond to excited states in the ground state functionals. As shown by various examples, the first excited states of many chemical systems are given by these index-1 saddle points. Our novel approach provides an alternative, more robust way to obtain these excited states, compared with the widely used ΔSCF approach. The method can be easily generalized to target higher index saddle points. Our results also reveal the physical interest and relevance of studying the Kohn-Sham energy landscape.

Validation of the OpCost logging cost model using contractor surveys

Treesearch

Conor K. Bell; Robert F. Keefe; Jeremy S. Fried

2017-01-01

OpCost is a harvest and fuel treatment operations cost model developed to function as both a standalone tool and an integrated component of the Bioregional Inventory Originated Simulation Under Management (BioSum) analytical framework for landscape-level analysis of forest management alternatives. OpCost is an updated implementation of the Fuel Reduction Cost Simulator...

Biotic homogenization can decrease landscape-scale forest multifunctionality.

PubMed

van der Plas, Fons; Manning, Pete; Soliveres, Santiago; Allan, Eric; Scherer-Lorenzen, Michael; Verheyen, Kris; Wirth, Christian; Zavala, Miguel A; Ampoorter, Evy; Baeten, Lander; Barbaro, Luc; Bauhus, Jürgen; Benavides, Raquel; Benneter, Adam; Bonal, Damien; Bouriaud, Olivier; Bruelheide, Helge; Bussotti, Filippo; Carnol, Monique; Castagneyrol, Bastien; Charbonnier, Yohan; Coomes, David Anthony; Coppi, Andrea; Bastias, Cristina C; Dawud, Seid Muhie; De Wandeler, Hans; Domisch, Timo; Finér, Leena; Gessler, Arthur; Granier, André; Grossiord, Charlotte; Guyot, Virginie; Hättenschwiler, Stephan; Jactel, Hervé; Jaroszewicz, Bogdan; Joly, François-Xavier; Jucker, Tommaso; Koricheva, Julia; Milligan, Harriet; Mueller, Sandra; Muys, Bart; Nguyen, Diem; Pollastrini, Martina; Ratcliffe, Sophia; Raulund-Rasmussen, Karsten; Selvi, Federico; Stenlid, Jan; Valladares, Fernando; Vesterdal, Lars; Zielínski, Dawid; Fischer, Markus

2016-03-29

Many experiments have shown that local biodiversity loss impairs the ability of ecosystems to maintain multiple ecosystem functions at high levels (multifunctionality). In contrast, the role of biodiversity in driving ecosystem multifunctionality at landscape scales remains unresolved. We used a comprehensive pan-European dataset, including 16 ecosystem functions measured in 209 forest plots across six European countries, and performed simulations to investigate how local plot-scale richness of tree species (α-diversity) and their turnover between plots (β-diversity) are related to landscape-scale multifunctionality. After accounting for variation in environmental conditions, we found that relationships between α-diversity and landscape-scale multifunctionality varied from positive to negative depending on the multifunctionality metric used. In contrast, when significant, relationships between β-diversity and landscape-scale multifunctionality were always positive, because a high spatial turnover in species composition was closely related to a high spatial turnover in functions that were supported at high levels. Our findings have major implications for forest management and indicate that biotic homogenization can have previously unrecognized and negative consequences for large-scale ecosystem multifunctionality.

Biotic homogenization can decrease landscape-scale forest multifunctionality

PubMed Central

van der Plas, Fons; Manning, Pete; Soliveres, Santiago; Allan, Eric; Scherer-Lorenzen, Michael; Verheyen, Kris; Wirth, Christian; Zavala, Miguel A.; Ampoorter, Evy; Baeten, Lander; Barbaro, Luc; Bauhus, Jürgen; Benavides, Raquel; Benneter, Adam; Bonal, Damien; Bouriaud, Olivier; Bruelheide, Helge; Bussotti, Filippo; Carnol, Monique; Castagneyrol, Bastien; Charbonnier, Yohan; Coppi, Andrea; Bastias, Cristina C.; Dawud, Seid Muhie; De Wandeler, Hans; Domisch, Timo; Finér, Leena; Granier, André; Grossiord, Charlotte; Guyot, Virginie; Hättenschwiler, Stephan; Jactel, Hervé; Jaroszewicz, Bogdan; Joly, François-xavier; Jucker, Tommaso; Koricheva, Julia; Milligan, Harriet; Mueller, Sandra; Muys, Bart; Nguyen, Diem; Pollastrini, Martina; Ratcliffe, Sophia; Raulund-Rasmussen, Karsten; Selvi, Federico; Stenlid, Jan; Valladares, Fernando; Vesterdal, Lars; Zielínski, Dawid; Fischer, Markus

2016-01-01

Many experiments have shown that local biodiversity loss impairs the ability of ecosystems to maintain multiple ecosystem functions at high levels (multifunctionality). In contrast, the role of biodiversity in driving ecosystem multifunctionality at landscape scales remains unresolved. We used a comprehensive pan-European dataset, including 16 ecosystem functions measured in 209 forest plots across six European countries, and performed simulations to investigate how local plot-scale richness of tree species (α-diversity) and their turnover between plots (β-diversity) are related to landscape-scale multifunctionality. After accounting for variation in environmental conditions, we found that relationships between α-diversity and landscape-scale multifunctionality varied from positive to negative depending on the multifunctionality metric used. In contrast, when significant, relationships between β-diversity and landscape-scale multifunctionality were always positive, because a high spatial turnover in species composition was closely related to a high spatial turnover in functions that were supported at high levels. Our findings have major implications for forest management and indicate that biotic homogenization can have previously unrecognized and negative consequences for large-scale ecosystem multifunctionality. PMID:26979952

Hydrological landscape analysis based on digital elevation data

NASA Astrophysics Data System (ADS)

Seibert, J.; McGlynn, B.; Grabs, T.; Jensco, K.

2008-12-01

Topography is a major factor controlling both hydrological and soil processes at the landscape scale. While this is well-accepted qualitatively, quantifying relationships between topography and spatial variations of hydrologically relevant variables at the landscape scale still remains a challenging research topic. In this presentation, we describe hydrological landscape analysis HLA) as a way to derive relevant topographic indicies to describe the spatial variations of hydrological variables at the landscape scale. We demonstrate our HLA approach with four high-resolution digital elevation models (DEMs) from Sweden, Switzerland and Montana (USA). To investigate scale effects HLA metrics, we compared DEMs of different resolutions. These LiDAR-derived DEMs of 3m, 10m, and 30m, resolution represent catchments of ~ 5 km2 ranging from low to high relief. A central feature of HLA is the flowpath-based analysis of topography and the separation of hillslopes, riparian areas, and the stream network. We included the following metrics: riparian area delineation, riparian buffer potential, separation of stream inflows into right and left bank components, travel time proxies based on flowpath distances and gradients to the channel, and as a hydrologic similarity to the hypsometric curve we suggest the distribution of elevations above the stream network (computed based on the location where a certain flow pathway enters the stream). Several of these indices depended clearly on DEM resolution, whereas this effect was minor for others. While the hypsometric curves all were S-shaped the 'hillslope-hypsometric curves' had the shape of a power function with exponents less than 1. In a similar way we separated flow pathway lengths and gradients between hillslopes and streams and compared a topographic travel time proxy, which was based on the integration of gradients along the flow pathways. Besides the comparison of HLA-metrics for different catchments and DEM resolutions we present examples from experimental catchments to illustrate how these metrics can be used to describe catchment scale hydrological processes and provide context for plot scale observations.

Dynamically incorporating late-successional forest in sustainable landscapes

Treesearch

Ann E. Camp; Paul F. Hessburg; Richard L. Everett

1996-01-01

Ecosystems and landscapes change over time as a function of vegetation characteristics and disturbance regimes, including fire. Interactions between disturbance events and forest development (succession) create patterns of vegetation across landscapes. These patterns result from, and change with respect to, species compositions and structures that arise from...

Land-use choices follow profitability at the expense of ecological functions in Indonesian smallholder landscapes

NASA Astrophysics Data System (ADS)

Clough, Yann; Krishna, Vijesh V.; Corre, Marife D.; Darras, Kevin; Denmead, Lisa H.; Meijide, Ana; Moser, Stefan; Musshoff, Oliver; Steinebach, Stefanie; Veldkamp, Edzo; Allen, Kara; Barnes, Andrew D.; Breidenbach, Natalie; Brose, Ulrich; Buchori, Damayanti; Daniel, Rolf; Finkeldey, Reiner; Harahap, Idham; Hertel, Dietrich; Holtkamp, A. Mareike; Hörandl, Elvira; Irawan, Bambang; Jaya, I. Nengah Surati; Jochum, Malte; Klarner, Bernhard; Knohl, Alexander; Kotowska, Martyna M.; Krashevska, Valentyna; Kreft, Holger; Kurniawan, Syahrul; Leuschner, Christoph; Maraun, Mark; Melati, Dian Nuraini; Opfermann, Nicole; Pérez-Cruzado, César; Prabowo, Walesa Edho; Rembold, Katja; Rizali, Akhmad; Rubiana, Ratna; Schneider, Dominik; Tjitrosoedirdjo, Sri Sudarmiyati; Tjoa, Aiyen; Tscharntke, Teja; Scheu, Stefan

2016-10-01

Smallholder-dominated agricultural mosaic landscapes are highlighted as model production systems that deliver both economic and ecological goods in tropical agricultural landscapes, but trade-offs underlying current land-use dynamics are poorly known. Here, using the most comprehensive quantification of land-use change and associated bundles of ecosystem functions, services and economic benefits to date, we show that Indonesian smallholders predominantly choose farm portfolios with high economic productivity but low ecological value. The more profitable oil palm and rubber monocultures replace forests and agroforests critical for maintaining above- and below-ground ecological functions and the diversity of most taxa. Between the monocultures, the higher economic performance of oil palm over rubber comes with the reliance on fertilizer inputs and with increased nutrient leaching losses. Strategies to achieve an ecological-economic balance and a sustainable management of tropical smallholder landscapes must be prioritized to avoid further environmental degradation.

Land-use choices follow profitability at the expense of ecological functions in Indonesian smallholder landscapes

PubMed Central

Clough, Yann; Krishna, Vijesh V.; Corre, Marife D.; Darras, Kevin; Denmead, Lisa H.; Meijide, Ana; Moser, Stefan; Musshoff, Oliver; Steinebach, Stefanie; Veldkamp, Edzo; Allen, Kara; Barnes, Andrew D.; Breidenbach, Natalie; Brose, Ulrich; Buchori, Damayanti; Daniel, Rolf; Finkeldey, Reiner; Harahap, Idham; Hertel, Dietrich; Holtkamp, A. Mareike; Hörandl, Elvira; Irawan, Bambang; Jaya, I. Nengah Surati; Jochum, Malte; Klarner, Bernhard; Knohl, Alexander; Kotowska, Martyna M.; Krashevska, Valentyna; Kreft, Holger; Kurniawan, Syahrul; Leuschner, Christoph; Maraun, Mark; Melati, Dian Nuraini; Opfermann, Nicole; Pérez-Cruzado, César; Prabowo, Walesa Edho; Rembold, Katja; Rizali, Akhmad; Rubiana, Ratna; Schneider, Dominik; Tjitrosoedirdjo, Sri Sudarmiyati; Tjoa, Aiyen; Tscharntke, Teja; Scheu, Stefan

2016-01-01

Smallholder-dominated agricultural mosaic landscapes are highlighted as model production systems that deliver both economic and ecological goods in tropical agricultural landscapes, but trade-offs underlying current land-use dynamics are poorly known. Here, using the most comprehensive quantification of land-use change and associated bundles of ecosystem functions, services and economic benefits to date, we show that Indonesian smallholders predominantly choose farm portfolios with high economic productivity but low ecological value. The more profitable oil palm and rubber monocultures replace forests and agroforests critical for maintaining above- and below-ground ecological functions and the diversity of most taxa. Between the monocultures, the higher economic performance of oil palm over rubber comes with the reliance on fertilizer inputs and with increased nutrient leaching losses. Strategies to achieve an ecological-economic balance and a sustainable management of tropical smallholder landscapes must be prioritized to avoid further environmental degradation. PMID:27725673

Land-use choices follow profitability at the expense of ecological functions in Indonesian smallholder landscapes.

PubMed

Clough, Yann; Krishna, Vijesh V; Corre, Marife D; Darras, Kevin; Denmead, Lisa H; Meijide, Ana; Moser, Stefan; Musshoff, Oliver; Steinebach, Stefanie; Veldkamp, Edzo; Allen, Kara; Barnes, Andrew D; Breidenbach, Natalie; Brose, Ulrich; Buchori, Damayanti; Daniel, Rolf; Finkeldey, Reiner; Harahap, Idham; Hertel, Dietrich; Holtkamp, A Mareike; Hörandl, Elvira; Irawan, Bambang; Jaya, I Nengah Surati; Jochum, Malte; Klarner, Bernhard; Knohl, Alexander; Kotowska, Martyna M; Krashevska, Valentyna; Kreft, Holger; Kurniawan, Syahrul; Leuschner, Christoph; Maraun, Mark; Melati, Dian Nuraini; Opfermann, Nicole; Pérez-Cruzado, César; Prabowo, Walesa Edho; Rembold, Katja; Rizali, Akhmad; Rubiana, Ratna; Schneider, Dominik; Tjitrosoedirdjo, Sri Sudarmiyati; Tjoa, Aiyen; Tscharntke, Teja; Scheu, Stefan

2016-10-11

Smallholder-dominated agricultural mosaic landscapes are highlighted as model production systems that deliver both economic and ecological goods in tropical agricultural landscapes, but trade-offs underlying current land-use dynamics are poorly known. Here, using the most comprehensive quantification of land-use change and associated bundles of ecosystem functions, services and economic benefits to date, we show that Indonesian smallholders predominantly choose farm portfolios with high economic productivity but low ecological value. The more profitable oil palm and rubber monocultures replace forests and agroforests critical for maintaining above- and below-ground ecological functions and the diversity of most taxa. Between the monocultures, the higher economic performance of oil palm over rubber comes with the reliance on fertilizer inputs and with increased nutrient leaching losses. Strategies to achieve an ecological-economic balance and a sustainable management of tropical smallholder landscapes must be prioritized to avoid further environmental degradation.

The contribution of reserves and anthropogenic habitat for functional connectivity and resilience of ephemeral wetland networks

NASA Astrophysics Data System (ADS)

Allen, C. R.; Uden, D.; Angeler, D.; Hellman, M.

2015-12-01

Functional connectivity of reserves and other suitable habitat patches is crucial for persistence of spatially structured populations, and therefore for resilience. To maintain or increase connectivity at spatial scales larger than individual patches, conservation actions may focus on creating and maintaining reserves or influencing management actions taken on non-reserves. We assess functional connectivity of isolated wetlands within an intensively managed agricultural matrix. Using a graph-theoretic approach, we assessed the functional connectivity and spatial distribution of wetlands in the Rainwater Basins, Nebraska, U.S.A. at four assumed anuran dispersal distances. We compare the contemporary wetlands landscape to the historical landscape and putative future landscapes and evaluate the importance of individual and aggregated reserve and non-reserve wetlands for maintaining connectivity. Connectivity was greatest in the historical landscape, where wetlands were also the most densely distributed. The construction of irrigation reuse pits for water storage has substantially increased connectivity in the current landscape, but because their distribution is more uniform than historical wetlands, larger and longer-dispersing species may be favored over smaller, shorter-dispersing species. Because of their relatively low number, wetland reserves did not affect connectivity as greatly as non-reserve wetlands or irrigation reuse pits; however, they provide the highest-quality anuran habitat. Future levels of connectivity in the region will be directly impacted by the planned removal of irrigation reuse pits, and on non-reserve wetlands. Multi-scale spatial and temporal assessments of the effects of landuse change and conservation actions on landscape connectivity may be used to direct and prioritize conservation actions, and should also be useful for reserve network and landscape resilience assessments.

Ensemble-based characterization of unbound and bound states on protein energy landscape

PubMed Central

Ruvinsky, Anatoly M; Kirys, Tatsiana; Tuzikov, Alexander V; Vakser, Ilya A

2013-01-01

Physicochemical description of numerous cell processes is fundamentally based on the energy landscapes of protein molecules involved. Although the whole energy landscape is difficult to reconstruct, increased attention to particular targets has provided enough structures for mapping functionally important subspaces associated with the unbound and bound protein structures. The subspace mapping produces a discrete representation of the landscape, further called energy spectrum. We compiled and characterized ensembles of bound and unbound conformations of six small proteins and explored their spectra in implicit solvent. First, the analysis of the unbound-to-bound changes points to conformational selection as the binding mechanism for four proteins. Second, results show that bound and unbound spectra often significantly overlap. Moreover, the larger the overlap the smaller the root mean square deviation (RMSD) between the bound and unbound conformational ensembles. Third, the center of the unbound spectrum has a higher energy than the center of the corresponding bound spectrum of the dimeric and multimeric states for most of the proteins. This suggests that the unbound states often have larger entropy than the bound states. Fourth, the exhaustively long minimization, making small intrarotamer adjustments (all-atom RMSD ≤ 0.7 Å), dramatically reduces the distance between the centers of the bound and unbound spectra as well as the spectra extent. It condenses unbound and bound energy levels into a thin layer at the bottom of the energy landscape with the energy spacing that varies between 0.8–4.6 and 3.5–10.5 kcal/mol for the unbound and bound states correspondingly. Finally, the analysis of protein energy fluctuations showed that protein vibrations itself can excite the interstate transitions, including the unbound-to-bound ones. PMID:23526684

Use and misuse of landscape indices

Treesearch

Harbin Li; Jianguo Wu

2004-01-01

Landscape ecology has generated much excitement in the past two decades. One reason was that it brought spatial analysis and modeling to the forefront of ecological research. However, high expectations for landscape analysis to improve our understanding and prediction of ecological processes have largely been unfulfilled. We identified three kinds of critical issues:...

The genomic landscape of chronic lymphocytic leukaemia: biological and clinical implications.

PubMed

Strefford, Jonathan C

2015-04-01

Chronic lymphocytic leukaemia (CLL) remains at the forefront of the genetic analysis of human tumours, principally due its prevalence, protracted natural history and accessibility to suitable material for analysis. With the application of high-throughput genetic technologies, we have an unbridled view of the architecture of the CLL genome, including a comprehensive description of the copy number and mutational landscape of the disease, a detailed picture of clonal evolution during pathogenesis, and the molecular mechanisms that drive genomic instability and therapeutic resistance. This work has nuanced the prognostic importance of established copy number alterations, and identified novel prognostically relevant gene mutations that function within biological pathways that are attractive treatment targets. Herein, an overview of recent genomic discoveries will be reviewed, with associated biological and clinical implications, and a view into how clinical implementation may be facilitated. © 2014 John Wiley & Sons Ltd.

METAGUI 3: A graphical user interface for choosing the collective variables in molecular dynamics simulations

NASA Astrophysics Data System (ADS)

Giorgino, Toni; Laio, Alessandro; Rodriguez, Alex

2017-08-01

Molecular dynamics (MD) simulations allow the exploration of the phase space of biopolymers through the integration of equations of motion of their constituent atoms. The analysis of MD trajectories often relies on the choice of collective variables (CVs) along which the dynamics of the system is projected. We developed a graphical user interface (GUI) for facilitating the interactive choice of the appropriate CVs. The GUI allows: defining interactively new CVs; partitioning the configurations into microstates characterized by similar values of the CVs; calculating the free energies of the microstates for both unbiased and biased (metadynamics) simulations; clustering the microstates in kinetic basins; visualizing the free energy landscape as a function of a subset of the CVs used for the analysis. A simple mouse click allows one to quickly inspect structures corresponding to specific points in the landscape.

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'.

Geomorpho-Landscapes

NASA Astrophysics Data System (ADS)

Farabollini, Piero; Lugeri, Francesca; Amadio, Vittorio

2014-05-01

Landscape is the object of human perceptions, being the image of spatial organization of elements and structures: mankind lives the first approach with the environment, viewing and feeling the landscape. Many definitions of landscape have been given over time: in this case we refer to the Landscape defined as the result of interaction among physical, biotic and anthropic phenomena acting in a different spatial-temporal scale (Foreman & Godron) Following an Aristotelic approach in studying nature, we can assert that " Shape is synthesis": so it is possible to read the land features as the expression of the endogenous and exogenous processes that mould earth surfaces; moreover, Landscape is the result of the interaction of natural and cultural components, and conditions the spatial-temporal development of a region. The study of the Landscape offers results useful in order to promote sustainable development, ecotourism, enhancement of natural and cultural heritage, popularization of the scientific knowledge. In Italy, a very important GIS-based tool to represent the territory is the "Carta della Natura" ("Map of Nature", presently coordinated by the ISPRA) that aims at assessing the state of the whole Italian territory, analyzing Landscape. The methodology follows a holistic approach, taking into consideration all the components of a landscape and then integrating the information. Each individual landscape, studied at different scales, shows distinctive elements: structural, which depend on physical form and specific spatial organization; functional, which depend on relationships created between biotic and abiotic elements, and dynamic, which depend on the successive evolution of the structure. The identification of the landscape units, recognized at different scales of analysis, allows an evaluation of the state of the land, referring to the dual risk/resource which characterizes the Italian country. An interesting opportunity is to discover those areas of unusual value -referring to biodiversity, geodiversity, culture- which can be considered as a special heritage. Starting from the concept of Geomorphosite, a geomorphologic landform with a scientific, cultural and socio-economical value (Panizza 2001), we propose a further definition, useful in the preliminary steps of the landscape analysis: "geomorpho-landscape" as a spatial object or component of a geological landscape, whose geo-morphological evolution, linked to the geological setting, are elements of aesthetical, semiological as well as historical and cultural value. The structure of the landscape is represented by the physical shape and spatial organization, in dynamic way: it is necessary to provide a readout of the landscape components that supplements the geo-morphological, lithological, geodiversity data (Lugeri et alii, 2012). The concept of "geomorpho-landscape" is conceived to address the need to describe by a synthetic approach the geological processes emerging at the landscape scale, allowing to link spatial patterns to geological processes Each geo-form has in itself geological, geo-morphological, landmark, historical and cultural features, of such special relevance, that they can be defined in terms of scientific quality, rarity, aesthetic appeal and educational and cultural value. Reference List AMADIO V. (2003). Analisi di sistemi e progetti di paesaggio. Franco Angeli, Milano, pp 236 AMADIO V, AMADEI M, BAGNAIA R, DI BUCCI D, LAURETI L, LISI A, LUGERI FR, LUGERI N. (2002). The role of Geomorphology in Landscape Ecology: The Landscape Unit Map of Italy', Scale 1: 250,000 ("Carta della Natura" Project). In: Allison RJ (ed) Applied Geomorphology: theory and practice. John Wiley & Sons, London, pp 265-282 APAT (2003). Carta della natura alla scala 1:250,000: metodologie di realizzazione. APAT, Manuali e linee guida 17/2003, Roma, pp 103 LUGERI F.R., FARABOLLINI P., GRAVIANO G. & AMADIO V. (2012). Geoheritage: Nature and culture in a landscape approach. European Geologist, 34, 23-28. (ISSN 1028-267X) FORMAN R.T.T. & GODRON M. (1986). Landscape ecology. John Wiley and Sons, NewYork, pp 620 PANIZZA M. (2001). Geomorphosites: concepts, methods and example of geomorphological survey. Chinese Science Bulletin, Suppl. Bd, 4-6, p 46

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.

Numerical modeling of eastern connecticut's visual resources

Treesearch

Daniel L. Civco

1979-01-01

A numerical model capable of accurately predicting the preference for landscape photographs of selected points in eastern Connecticut is presented. A function of the social attitudes expressed toward thirty-two salient visual landscape features serves as the independent variable in predicting preferences. A technique for objectively assigning adjectives to landscape...

Ecohydrology and tipping points in semiarid australian rangelands

NASA Astrophysics Data System (ADS)

Saco, P. M.; Azadi, S.; Moreno de las Heras, M.; Willgoose, G. R.

2017-12-01

Semiarid landscapes are often characterised by a spatially heterogeneous vegetation cover forming mosaics of patches with dense vegetation within bare soil. This patchy vegetation cover, which is linked to the healthy function of these ecosystems, is sensitive to human disturbances that can lead to degradation. Previous work suggests that vegetation loss below a critical value can lead to a sudden decrease in landscape functionality following threshold behaviour. The decrease in vegetation cover is linked to erosion and substantial water losses by increasing landscape hydrological connectivity. We study these interactions and the possible existence of tipping points in the Mulga land bioregion, by combining remote sensing observations and results from an eco-geomorphologic model to investigate changes in ecosystem connectivity and the existence of threshold behaviour. More than 30 sites were selected along a precipitation gradient spanning a range from approximately 250 to 500 mm annual rainfall. The analysis of vegetation patterns is derived from high resolution remote sensing images (IKONOS, QuickBird, Pleiades) and MODIS NDVI, which combined with local precipitation data is used to compute rainfall use efficiency to assess the ecosystem function. A critical tipping point associated to loss of vegetation cover appears in the sites with lower annual precipitation. We found that this tipping point behaviour decreases for sites with higher rainfall. We use the model to investigate the relation between structural and functional connectivity and the emergence of threshold behaviour for selected plots along this precipitation gradient. Both observations and modelling results suggest that sites with higher rainfall are more resilient to changes in surface connectivity. The implications for ecosystem resilience and land management are discussed

Hydrological Dynamics In High Mountain Catchment Areas of Central Norway

NASA Astrophysics Data System (ADS)

Löffler, J.; Rössler, O.

Large-scaled landscape structure is regarded as a mosaic of ecotopes where pro- cess dynamics of water and energy fluxes are analysed due to its effects on ecosys- tem functioning. The investigations have been carried out in the continental most Vågå/Oppland high mountains in central Norway since 1994 (LÖFFLER WUN- DRAM 1999, 2000, 2001). Additionally, comparable investigations started in 2000 dealing with the oceanic high mountain landscapes on same latitudes (LÖFFLER et al. 2001). The theoretical and methodological framework of the project is given by the Landscape-Ecological Complex Analysis (MOSIMANN 1984, 1985) and its variations due to technical and principle methodical challenges in this high moun- tain landscape (KÖHLER et al. 1994, LÖFFLER 1998). The aim of the project is to characterize high mountain ecosystem structure, functioning and dynamics within small catchment areas, that are chosen in two different altitudinal belts each in the eastern continental and the western oceanic region of central Norway. In the frame of this research project hydrological and meteorological measurements on ground water, percolation and soil moisture dynamics as well as on evaporation, air humidity and air-, surface- and soil-temperatures have been conducted. On the basis of large-scaled landscape-ecological mappings (LÖFFLER 1997) one basic meteorological station and several major data logger run stations have been installed in representative sites of each two catchment areas in the low and mid alpine belts of the investigation re- gions (JUNG et al. 1997, LÖFFLER WUNDRAM 1997). Moreover, spatial differ- entiations of groundwater level, soil moisture and temperature profiles have been in- vestigated by means of hand held measurements at different times of the day, during different climatic situations and different seasons. Daily and annual air-, surface- and soil-temperature dynamics are demonstrated by means of thermoisopleth-diagrams for different types of ecotopes of the different altitudinal belts. The local differences of temperature dynamics are illustrated in a map as an example of the low alpine al- titudinal belt showing a 4-dimensional characterization (in space and time) of high mountain ecosystem functioning. Hydrological aspects derived from those results are presented showing the large-scaled hydrological dynamics of high mountain catch- ment basins in central Norway. The results of the process analysis of hydrological dynamics in the central Norwegian high mountains are discussed within the frame of 1 investigations on altitudinal changes of mountain ecosystem structure and function- ing (LÖFFLER WUNDRAM [in print]). The poster illustrates the theoretical and methodological conception, methods and techniques, examples from complex data material as well as general outcomes of the project (RÖSSLER [in prep.]. 2

Analysis of Feature Intervisibility and Cumulative Visibility Using GIS, Bayesian and Spatial Statistics: A Study from the Mandara Mountains, Northern Cameroon

PubMed Central

Wright, David K.; MacEachern, Scott; Lee, Jaeyong

2014-01-01

The locations of diy-geδ-bay (DGB) sites in the Mandara Mountains, northern Cameroon are hypothesized to occur as a function of their ability to see and be seen from points on the surrounding landscape. A series of geostatistical, two-way and Bayesian logistic regression analyses were performed to test two hypotheses related to the intervisibility of the sites to one another and their visual prominence on the landscape. We determine that the intervisibility of the sites to one another is highly statistically significant when compared to 10 stratified-random permutations of DGB sites. Bayesian logistic regression additionally demonstrates that the visibility of the sites to points on the surrounding landscape is statistically significant. The location of sites appears to have also been selected on the basis of lower slope than random permutations of sites. Using statistical measures, many of which are not commonly employed in archaeological research, to evaluate aspects of visibility on the landscape, we conclude that the placement of DGB sites improved their conspicuousness for enhanced ritual, social cooperation and/or competition purposes. PMID:25383883

Landscape trajectory of natural boreal forest loss as an impediment to green infrastructure.

PubMed

Svensson, Johan; Andersson, Jon; Sandström, Per; Mikusiński, Grzegorz; Jonsson, Bengt-Gunnar

2018-06-08

Loss of natural forests has been identified as a critical conservation challenge worldwide. This loss impede the establishment of a functional green infrastructure as a spatiotemporally connected landscape-scale network of habitats enhancing biodiversity, favorable conservation status and ecosystem services. In many regions this loss is caused by forest clearcutting. Through retrospective satellite images analysis we assessed a 50-60 year spatiotemporal clearcutting impact trajectory on natural and near-natural boreal forests across a sizable and representative region from the Gulf of Bothnia to the Scandinavian Mountain Range in northern Fennoscandia. Our analysis broadly covers the whole forest clearcutting period and thus our study approach and results can be applied for comprehensive impact assessment of industrial forest management. Our results demonstrate profound disturbance on natural forest landscape configuration. The whole forest landscape is in a late phase in a transition from a natural or near-natural to a land-use modified state. Our results provide evidence of natural forest loss and spatial polarization at the regional scale, with a pre-dominant share of valuable habitats left in the mountain area, whereas the inland area has been more severely impacted. We highlight the importance of interior forest areas as most valuable biodiversity hotspots and the central axis of green infrastructure. Superimposing the effects of edge disturbance on forest fragmentation, the loss of interior forest entities further aggravate the conservation premises. Our results also show a loss of large contiguous forest patches and indicate patch size homogenization. The current forest protection share is low in the region and with geographical imbalance as the absolute majority is located in remote and low productive sites in the mountain area. Our approach provides possibilities to identify forest areas for directed conservation actions in the form of new protection, restoration and nature conservation oriented forest management, for implementing a functional green infrastructure. This article is protected by copyright. All rights reserved. This article is protected by copyright. All rights reserved.

Measuring the effect of fuel treatments on forest carbon using landscape risk analysis

NASA Astrophysics Data System (ADS)

Ager, A. A.; Finney, M. A.; McMahan, A.; Cathcart, J.

2010-12-01

Wildfire simulation modelling was used to examine whether fuel reduction treatments can potentially reduce future wildfire emissions and provide carbon benefits. In contrast to previous reports, the current study modelled landscape scale effects of fuel treatments on fire spread and intensity, and used a probabilistic framework to quantify wildfire effects on carbon pools to account for stochastic wildfire occurrence. The study area was a 68 474 ha watershed located on the Fremont-Winema National Forest in southeastern Oregon, USA. Fuel reduction treatments were simulated on 10% of the watershed (19% of federal forestland). We simulated 30 000 wildfires with random ignition locations under both treated and untreated landscapes to estimate the change in burn probability by flame length class resulting from the treatments. Carbon loss functions were then calculated with the Forest Vegetation Simulator for each stand in the study area to quantify change in carbon as a function of flame length. We then calculated the expected change in carbon from a random ignition and wildfire as the sum of the product of the carbon loss and the burn probabilities by flame length class. The expected carbon difference between the non-treatment and treatment scenarios was then calculated to quantify the effect of fuel treatments. Overall, the results show that the carbon loss from implementing fuel reduction treatments exceeded the expected carbon benefit associated with lowered burn probabilities and reduced fire severity on the treated landscape. Thus, fuel management activities resulted in an expected net loss of carbon immediately after treatment. However, the findings represent a point in time estimate (wildfire immediately after treatments), and a temporal analysis with a probabilistic framework used here is needed to model carbon dynamics over the life cycle of the fuel treatments. Of particular importance is the long-term balance between emissions from the decay of dead trees killed by fire and carbon sequestration by forest regeneration following wildfire.

A landscape genetic analysis of important agricultural pest species in Tunisia: The whitefly Bemisia tabaci

PubMed Central

Fakhfakh, Hatem; Belkadhi, Mohamed Sadok

2017-01-01

Combining landscape ecology and genetics provides an excellent framework to appreciate pest population dynamics and dispersal. The genetic architectures of many species are always shaped by environmental constraints. Because little is known about the ecological and genetic traits of Tunisian whitefly populations, the main objective of this work is to highlight patterns of biodiversity, genetic structure and migration routes of this pest. We used nuclear microsatellite loci to analyze B. tabaci populations collected from various agricultural areas across the country and we determine their biotype status. Molecular data were subsequently interpreted in an ecological context supplied from a species distribution model to infer habitat suitability and hereafter the potential connection paths between sampling localities. An analysis of landscape resistance to B. tabaci genetic flow was thus applied to take into account habitat suitability, genetic relatedness and functional connectivity of habitats within a varied landscape matrix. We shed light on the occurrence of three geographically delineated genetic groups with high levels of genetic differentiation within each of them. Potential migration corridors of this pest were then established providing significant advances toward the understanding of genetic features and the dynamic dispersal of this pest. This study supports the hypothesis of a long-distance dispersal of B. tabaci followed by infrequent long-term isolations. The Inference of population sources and colonization routes is critical for the design and implementation of accurate management strategies against this pest. PMID:28972992

A landscape genetic analysis of important agricultural pest species in Tunisia: The whitefly Bemisia tabaci.

PubMed

Ben Abdelkrim, Ahmed; Hattab, Tarek; Fakhfakh, Hatem; Belkadhi, Mohamed Sadok; Gorsane, Faten

2017-01-01

Combining landscape ecology and genetics provides an excellent framework to appreciate pest population dynamics and dispersal. The genetic architectures of many species are always shaped by environmental constraints. Because little is known about the ecological and genetic traits of Tunisian whitefly populations, the main objective of this work is to highlight patterns of biodiversity, genetic structure and migration routes of this pest. We used nuclear microsatellite loci to analyze B. tabaci populations collected from various agricultural areas across the country and we determine their biotype status. Molecular data were subsequently interpreted in an ecological context supplied from a species distribution model to infer habitat suitability and hereafter the potential connection paths between sampling localities. An analysis of landscape resistance to B. tabaci genetic flow was thus applied to take into account habitat suitability, genetic relatedness and functional connectivity of habitats within a varied landscape matrix. We shed light on the occurrence of three geographically delineated genetic groups with high levels of genetic differentiation within each of them. Potential migration corridors of this pest were then established providing significant advances toward the understanding of genetic features and the dynamic dispersal of this pest. This study supports the hypothesis of a long-distance dispersal of B. tabaci followed by infrequent long-term isolations. The Inference of population sources and colonization routes is critical for the design and implementation of accurate management strategies against this pest.

Solutions for characterising natural landscapes in New Zealand using geographical information systems.

PubMed

Brabyn, Lars

2005-07-01

This paper explores solutions for characterising naturalness in relation to visual landscapes using Geographical Information System (GIS). It is argued that planners need to identify natural landscapes and monitor changes in their extent. Just like the indices that have been developed to describe the state of the economy, indices need to be developed that monitor the state of natural landscapes. The complications in characterising natural landscapes are outlined but it is argued that there is a need to develop definitions of natural landscapes that can be operationalised with a GIS. This will have the advantages of the efficiency of the technology and that the definition will be explicit and the implementation will be independent of the operator. Several GIS solutions are provided and these are an analysis of landcover, a density analysis of roads and utilities, and an analysis of property sizes. The analysis of property sizes is sensitive to many human modifications of the landscape because many developments begin with the subdivision of properties. However, it is argued in this paper that no one definition will suffice and that all three methods provide different, yet important, insights into natural landscape character. An aggregate classification of naturalness based on the majority value of the indices is demonstrated as well as a range of techniques for expressing the uncertainty of the aggregate classification.

Potential and flux field landscape theory. I. Global stability and dynamics of spatially dependent non-equilibrium systems.

PubMed

Wu, Wei; Wang, Jin

2013-09-28

We established a potential and flux field landscape theory to quantify the global stability and dynamics of general spatially dependent non-equilibrium deterministic and stochastic systems. We extended our potential and flux landscape theory for spatially independent non-equilibrium stochastic systems described by Fokker-Planck equations to spatially dependent stochastic systems governed by general functional Fokker-Planck equations as well as functional Kramers-Moyal equations derived from master equations. Our general theory is applied to reaction-diffusion systems. For equilibrium spatially dependent systems with detailed balance, the potential field landscape alone, defined in terms of the steady state probability distribution functional, determines the global stability and dynamics of the system. The global stability of the system is closely related to the topography of the potential field landscape in terms of the basins of attraction and barrier heights in the field configuration state space. The effective driving force of the system is generated by the functional gradient of the potential field alone. For non-equilibrium spatially dependent systems, the curl probability flux field is indispensable in breaking detailed balance and creating non-equilibrium condition for the system. A complete characterization of the non-equilibrium dynamics of the spatially dependent system requires both the potential field and the curl probability flux field. While the non-equilibrium potential field landscape attracts the system down along the functional gradient similar to an electron moving in an electric field, the non-equilibrium flux field drives the system in a curly way similar to an electron moving in a magnetic field. In the small fluctuation limit, the intrinsic potential field as the small fluctuation limit of the potential field for spatially dependent non-equilibrium systems, which is closely related to the steady state probability distribution functional, is found to be a Lyapunov functional of the deterministic spatially dependent system. Therefore, the intrinsic potential landscape can characterize the global stability of the deterministic system. The relative entropy functional of the stochastic spatially dependent non-equilibrium system is found to be the Lyapunov functional of the stochastic dynamics of the system. Therefore, the relative entropy functional quantifies the global stability of the stochastic system with finite fluctuations. Our theory offers an alternative general approach to other field-theoretic techniques, to study the global stability and dynamics of spatially dependent non-equilibrium field systems. It can be applied to many physical, chemical, and biological spatially dependent non-equilibrium systems.

[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.

[Landscape pattern gradient dynamics and desakota features in rapid urbanization area: a case study in Panyu of Guangzhou].

PubMed

Yu, Long-Sheng; Fu, Yi-Fu; Yu, Huai-Yi; Li, Zhi-Qin

2011-01-01

In order to understand the landscape pattern gradient dynamics and desakota features in rapid urbanization area, this paper took the rapidly urbanizing Panyu District of Guangzhou City as a case, and analyzed its land use and land cover data, based on four Landsat TM images from 1990 to 2008. With the combination of gradient analysis and landscape pattern analysis, and by using the landscape indices in both class and landscape scales, the spatial dynamics and desakota feature of this rapidly urbanizing district were quantified. In the study district, there was a significant change in the landscape pattern, and a typical desakota feature presented along buffer gradient zones. Urban landscape increased and expanded annually, accompanied with serious fragmentation of agricultural landscape. The indices patch density, contagion, and landscape diversity, etc., changed regularly in the urbanization gradient, and the peak of landscape indices appeared in the gradient zone of 4-6 km away from the urban center. The landscape patterns at time series also reflected the differences among the dynamics in different gradient zones. The landscape pattern in desakota region was characterized by complex patch shape, high landscape diversity and fragmentation, and remarkable landscape dynamics. The peaks of landscape indices spread from the urban center to border areas, and desakota region was expanding gradually. The general trend of spatiotemporal dynamics in desakota region and its driving forces were discussed, which could be benefit to the regional land use policy-making and sustainable development planning.

Drivers of community assembly in tropical forest restoration sites: role of local environment, landscape, and space.

PubMed

Audino, Lívia D; Murphy, Stephen J; Zambaldi, Ludimila; Louzada, Julio; Comita, Liza S

2017-09-01

There is increasing recognition that community assembly theory can offer valuable insights for ecological restoration. We studied community assembly processes following tropical forest restoration efforts, using dung beetles (Scarabaeinae) as a focal taxon to investigate taxonomic and functional patterns of biodiversity recovery. We evaluated the relative importance of the local environment (i.e., canopy cover, understory cover, tree basal area, and soil texture), landscape context (i.e., habitat patch proximity and availability and percentage of surrounding area classified as natural forest or Eucalyptus spp. plantation), and space (i.e., spatial proximity of the study areas to estimate dispersal limitation or unmeasured spatially structured processes) on dung beetle species and functional trait composition across a gradient of 15 restoration sites in Brazilian Atlantic Forest. We also assessed which factors were the primary determinants in the establishment of individual dung beetle functional groups, classified according to size, food relocation habit, diet, and period of flight activity. Both species and functional trait composition were most strongly influenced by the local environment, indicating that assembly was predominantly driven by niche-based processes. Most of the variation explained by space was co-explained by local environment and landscape context, ruling out a strong influence of dispersal limitation and random colonization on assembly following restoration. In addition, nearly all of the variance explained by landscape context was co-explained by local environment, suggesting that arrival and establishment at a site depends on both local and landscape-scale environmental factors. Despite strong evidence for niche-based assembly, a large amount of variation remained unexplained in all models, suggesting that stochastic processes and/or unmeasured environmental variables also play an important role. The relative importance of local environment, landscape context, and space changed considerably when analyzing the assembly mechanisms of each functional group separately. Therefore, to recover distinct functional traits in restoration sites, it may be necessary to manipulate different components of the local environment and surrounding landscape. Overall, this study shows that assembly rules can help to better understand recovery processes, enabling improvement of future restoration efforts. © 2017 by the Ecological Society of America.

Estimation of Damage Costs Associated with Flood Events

NASA Astrophysics Data System (ADS)

Andrews, T. A.; Wauthier, C.; Zipp, K.

2017-12-01

This study investigates the possibility of creating a mathematical function that enables the estimation of flood-damage costs. We begin by examining the costs associated with past flood events in the United States. The data on these tropical storms and hurricanes are provided by the National Oceanic and Atmospheric Administration. With the location, extent of flooding, and damage reparation costs identified, we analyze variables such as: number of inches rained, land elevation, type of landscape, region development in regards to building density and infrastructure, and population concentration. We seek to identify the leading drivers of high flood-damage costs and understand which variables play a large role in the costliness of these weather events. Upon completion of our mathematical analysis, we turn out attention to the 2017 natural disaster of Texas. We divide the region, as we did above, by land elevation, type of landscape, region development in regards to building density and infrastructure, and population concentration. Then, we overlay the number of inches rained in those regions onto the divided landscape and apply our function. We hope to use these findings to estimate the potential flood-damage costs of Hurricane Harvey. This information is then transformed into a hazard map that could provide citizens and businesses of flood-stricken zones additional resources for their insurance selection process.

Trajectories of the ribosome as a Brownian nanomachine

DOE PAGES

Dashti, Ali; Schwander, Peter; Langlois, Robert; ...

2014-11-24

In a Brownian machine, there is a tiny device buffeted by the random motions of molecules in the environment, is capable of exploiting these thermal motions for many of the conformational changes in its work cycle. Such machines are now thought to be ubiquitous, with the ribosome, a molecular machine responsible for protein synthesis, increasingly regarded as prototypical. We present a new analytical approach capable of determining the free-energy landscape and the continuous trajectories of molecular machines from a large number of snapshots obtained by cryogenic electron microscopy. We demonstrate this approach in the context of experimental cryogenic electron microscopemore » images of a large ensemble of nontranslating ribosomes purified from yeast cells. The free-energy landscape is seen to contain a closed path of low energy, along which the ribosome exhibits conformational changes known to be associated with the elongation cycle. This approach allows model-free quantitative analysis of the degrees of freedom and the energy landscape underlying continuous conformational changes in nanomachines, including those important for biological function.« less

Landscape genetics for the empirical assessment of resistance surfaces: the European pine marten (Martes martes) as a target-species of a regional ecological network.

PubMed

Ruiz-González, Aritz; Gurrutxaga, Mikel; Cushman, Samuel A; Madeira, María José; Randi, Ettore; Gómez-Moliner, Benjamin J

2014-01-01

Coherent ecological networks (EN) composed of core areas linked by ecological corridors are being developed worldwide with the goal of promoting landscape connectivity and biodiversity conservation. However, empirical assessment of the performance of EN designs is critical to evaluate the utility of these networks to mitigate effects of habitat loss and fragmentation. Landscape genetics provides a particularly valuable framework to address the question of functional connectivity by providing a direct means to investigate the effects of landscape structure on gene flow. The goals of this study are (1) to evaluate the landscape features that drive gene flow of an EN target species (European pine marten), and (2) evaluate the optimality of a regional EN design in providing connectivity for this species within the Basque Country (North Spain). Using partial Mantel tests in a reciprocal causal modeling framework we competed 59 alternative models, including isolation by distance and the regional EN. Our analysis indicated that the regional EN was among the most supported resistance models for the pine marten, but was not the best supported model. Gene flow of pine marten in northern Spain is facilitated by natural vegetation, and is resisted by anthropogenic landcover types and roads. Our results suggest that the regional EN design being implemented in the Basque Country will effectively facilitate gene flow of forest dwelling species at regional scale.

Functional evaluations in the monitoring of the river ecosystem processes: the Adige River as a case stu.

PubMed

Braioni, M G; Salmoiraghi, G; Bracco, F; Villani, M; Braioni, A; Girelli, L

2002-03-12

A model of analysis and environmental evaluation was applied to 11 stretches of the Adige River, where an innovative procedure was carried out to interpret ecological results. Within each stretch, the most suitable methods were used to assess the quality and processes of flood plains, banks, water column, bed, and interstitial environment. Indices were applied to evaluate the wild state and ecological quality of the banks (wild state index, buffer strip index) and the landscape quality of wide areas of the fluvial corridor (environmental landscape index). The biotic components (i.e., macrozoobenthos, phytoplankton and zooplankton, interstitial hyporheic fauna, vegetation in the riparian areas) were analysed by both quantitative and functional methods (as productivity, litter--processing and colonisation). The results achieved were then translated into five classes of functional evaluation. These qualitative assessments have thus preserved a high level of precision and sensitivity in quantifying both the quality of the environmental conditions and the integrity of the ecosystem processes. Read together with urban planning data, they indicate what actions are needed to restore and rehabilitate the Adige River corridor.

Analysis of Employment Flow of Landscape Architecture Graduates in Agricultural Universities

ERIC Educational Resources Information Center

Yao, Xia; He, Linchun

2012-01-01

A statistical analysis of employment flow of landscape architecture graduates was conducted on the employment data of graduates major in landscape architecture in 2008 to 2011. The employment flow of graduates was to be admitted to graduate students, industrial direction and regional distribution, etc. Then, the features of talent flow and factors…

The Archeological Record at Bull Shoals Lake and Norfork Lake Arkansas and Missouri

DTIC Science & Technology

1993-06-01

geomorphological analysis of the landscape within the project areas, a review of previously gathered data about the nature and distribution of the...effort. These included a reconnaissance level geomorphological analysis of the landscape within the project areas, a review of previously gathered data...1989) which sought to integrate the description of the archeological record with a geomorphological analysis of the landscape within the areas directly

Descriptive approaches to landscape analysis

Treesearch

R. Burton Litton Jr.

1979-01-01

Descriptive landscape analyses include various procedures used to document visual/scenic resources. Historic and regional examples of landscape description represent desirable insight for contemporary professional inventory work. Routed and areal landscape inventories are discussed as basic tools. From them, qualitative and quantitative evaluations can be developed...

Arctic Tundra Vegetation Functional Types Based on Photosynthetic Physiology and Optical Properties

NASA Technical Reports Server (NTRS)

Huemmrich, Karl Fred; Gamon, John A.; Tweedie, Craig E.; Campbell, Petya K. Entcheva; Landis, David R.; Middleton, Elizabeth M.

2013-01-01

Non-vascular plants (lichens and mosses) are significant components of tundra landscapes and may respond to climate change differently from vascular plants affecting ecosystem carbon balance. Remote sensing provides critical tools for monitoring plant cover types, as optical signals provide a way to scale from plot measurements to regional estimates of biophysical properties, for which spatial-temporal patterns may be analyzed. Gas exchange measurements were collected for pure patches of key vegetation functional types (lichens, mosses, and vascular plants) in sedge tundra at Barrow, AK. These functional types were found to have three significantly different values of light use efficiency (LUE) with values of 0.013 plus or minus 0.0002, 0.0018 plus or minus 0.0002, and 0.0012 plus or minus 0.0001 mol C mol (exp -1) absorbed quanta for vascular plants, mosses and lichens, respectively. Discriminant analysis of the spectra reflectance of these patches identified five spectral bands that separated each of these vegetation functional types as well as nongreen material (bare soil, standing water, and dead leaves). These results were tested along a 100 m transect where midsummer spectral reflectance and vegetation coverage were measured at one meter intervals. Along the transect, area-averaged canopy LUE estimated from coverage fractions of the three functional types varied widely, even over short distances. The patch-level statistical discriminant functions applied to in situ hyperspectral reflectance data collected along the transect successfully unmixed cover fractions of the vegetation functional types. The unmixing functions, developed from the transect data, were applied to 30 m spatial resolution Earth Observing-1 Hyperion imaging spectrometer data to examine variability in distribution of the vegetation functional types for an area near Barrow, AK. Spatial variability of LUE was derived from the observed functional type distributions. Across this landscape, a fivefold variation in tundra LUE was observed. LUE calculated from the functional type cover fractions was also correlated to a spectral vegetation index developed to detect vegetation chlorophyll content. The concurrence of these alternate methods suggest that hyperspectral remote sensing can distinguish functionally distinct vegetation types and can be used to develop regional estimates of photosynthetic LUE in tundra landscapes.

The Long Noncoding RNA Landscape of the Mouse Eye.

PubMed

Chen, Weiwei; Yang, Shuai; Zhou, Zhonglou; Zhao, Xiaoting; Zhong, Jiayun; Reinach, Peter S; Yan, Dongsheng

2017-12-01

Long noncoding RNAs (lncRNAs) are important regulators of diverse biological functions. However, an extensive in-depth analysis of their expression profile and function in mammalian eyes is still lacking. Here we describe comprehensive landscapes of stage-dependent and tissue-specific lncRNA expression in the mouse eye. Affymetrix transcriptome array profiled lncRNA signatures from six different ocular tissue subsets (i.e., cornea, lens, retina, RPE, choroid, and sclera) in newborn and 8-week-old mice. Quantitative RT-PCR analysis validated array findings. Cis analyses and Gene Ontology (GO) annotation of protein-coding genes adjacent to signature lncRNA loci clarified potential lncRNA roles in maintaining tissue identity and regulating eye maturation during the aforementioned phase. In newborn and 8-week-old mice, we identified 47,332 protein-coding and noncoding gene transcripts. LncRNAs comprise 19,313 of these transcripts annotated in public data banks. During this maturation phase of these six different tissue subsets, more than 1000 lncRNAs expression levels underwent ≥2-fold changes. qRT-PCR analysis confirmed part of the gene microarray analysis results. K-means clustering identified 910 lncRNAs in the P0 groups and 686 lncRNAs in the postnatal 8-week-old groups, suggesting distinct tissue-specific lncRNA clusters. GO analysis of protein-coding genes proximal to lncRNA signatures resolved close correlations with their tissue-specific functional maturation between P0 and 8 weeks of age in the 6 tissue subsets. Characterizating maturational changes in lncRNA expression patterns as well as tissue-specific lncRNA signatures in six ocular tissues suggest important contributions made by lncRNA to the control of developmental processes in the mouse eye.

Ecological associations, dispersal ability, and landscape connectivity in the northern Rocky Mountains

Treesearch

Samuel A. Cushman; Erin L. Landguth

2012-01-01

Population connectivity is a function of the dispersal ability of the species, influences of different landscape elements on its movement behavior, density and distribution of the population, and structure of the landscape. Often, researchers have not carefully considered each of these factors when evaluating connectivity and making conservation recommendations. We...

Identification of landscape features influencing gene flow: How useful are habitat selection models?

Treesearch

Gretchen H. Roffler; Michael K. Schwartz; Kristine Pilgrim; Sandra L. Talbot; George K. Sage; Layne G. Adams; Gordon Luikart

2016-01-01

Understanding how dispersal patterns are influenced by landscape heterogeneity is critical for modeling species connectivity. Resource selection function (RSF) models are increasingly used in landscape genetics approaches. However, because the ecological factors that drive habitat selection may be different from those influencing dispersal and gene flow, it is...

INTEGRATING A LANDSCAPE HYDROLOGIC ANALYSIS FOR WATERSHED ASSESSMENT

EPA Science Inventory

Methods to provide linkages between a hydrologic modeling tool (AGW A) and landscape assessment tool (A TtILA) for determining the vulnerability of semi-arid landscapes to natural and human-induced landscape pattern changes have been developed. The objective of this study is to ...

The structural and functional connectivity of the grassland plant Lychnis flos-cuculi

PubMed Central

Aavik, T; Holderegger, R; Bolliger, J

2014-01-01

Understanding the relationship between structural and functional connectivity is essential for successful restoration and conservation management, particularly in intensely managed agricultural landscapes. We evaluated the relationship between structural and functional connectivity of the wetland plant Lychnis flos-cuculi in a fragmented agricultural landscape using landscape genetic and network approaches. First, we studied the effect of structural connectivity, such as geographic distance and various landscape elements (forest, agricultural land, settlements and ditch verges), on gene flow among populations as a measurement of functional connectivity. Second, we examined the effect of structural graph-theoretic connectivity measures on gene flow among populations and on genetic diversity within populations of L. flos-cuculi. Among landscape elements, forests hindered gene flow in L. flos-cuculi, whereas gene flow was independent of geographic distance. Among the structural graph-theoretic connectivity variables, only intrapopulation connectivity, which was based on population size, had a significant positive effect on gene flow, that is, more gene flow took place among larger populations. Unexpectedly, interpopulation connectivity of populations, which takes into account the spatial location and distance among populations, did not influence gene flow in L. flos-cuculi. However, higher observed heterozygosity and lower inbreeding was observed in populations characterised by higher structural interpopulation connectivity. This finding shows that a spatially coherent network of populations is significant for maintaining the genetic diversity of populations. Nevertheless, lack of significant relationships between gene flow and most of the structural connectivity measures suggests that structural connectivity does not necessarily correspond to functional connectivity. PMID:24253937

Integrating landscape analysis and planning: a multi-scale approach for oriented management of tourist recreation.

PubMed

de Aranzabal, Itziar; Schmitz, María F; Pineda, Francisco D

2009-11-01

Tourism and landscape are interdependent concepts. Nature- and culture-based tourism are now quite well developed activities and can constitute an excellent way of exploiting the natural resources of certain areas, and should therefore be considered as key objectives in landscape planning and management in a growing number of countries. All of this calls for careful evaluation of the effects of tourism on the territory. This article focuses on an integrated spatial method for landscape analysis aimed at quantifying the relationship between preferences of visitors and landscape features. The spatial expression of the model relating types of leisure and recreational preferences to the potential capacity of the landscape to meet them involves a set of maps showing degrees of potential visitor satisfaction. The method constitutes a useful tool for the design of tourism planning and management strategies, with landscape conservation as a reference.

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.

An empirical test of a diffusion model: predicting clouded apollo movements in a novel environment.

PubMed

Ovaskainen, Otso; Luoto, Miska; Ikonen, Iiro; Rekola, Hanna; Meyke, Evgeniy; Kuussaari, Mikko

2008-05-01

Functional connectivity is a fundamental concept in conservation biology because it sets the level of migration and gene flow among local populations. However, functional connectivity is difficult to measure, largely because it is hard to acquire and analyze movement data from heterogeneous landscapes. Here we apply a Bayesian state-space framework to parameterize a diffusion-based movement model using capture-recapture data on the endangered clouded apollo butterfly. We test whether the model is able to disentangle the inherent movement behavior of the species from landscape structure and sampling artifacts, which is a necessity if the model is to be used to examine how movements depend on landscape structure. We show that this is the case by demonstrating that the model, parameterized with data from a reference landscape, correctly predicts movements in a structurally different landscape. In particular, the model helps to explain why a movement corridor that was constructed as a management measure failed to increase movement among local populations. We illustrate how the parameterized model can be used to derive biologically relevant measures of functional connectivity, thus linking movement data with models of spatial population dynamics.

Roads in landscape modeling: a case study of a road data layer and use in the interior northwest landscape analysis system.

Treesearch

Marti Aitken; Jane L. Hayes

2006-01-01

Roads are important ecological features of forest landscapes, but their cause-and effect relationships with other ecosystem components are only recently becoming included in integrated landscape analyses. Simulation models can help us to understand how forested landscapes respond over time to disturbance and socioeconomic factors, and potentially to address the...

Landscape preference assessment of Louisiana river landscapes: a methodological study

Treesearch

Michael S. Lee

1979-01-01

The study pertains to the development of an assessment system for the analysis of visual preference attributed to Louisiana river landscapes. The assessment system was utilized in the evaluation of 20 Louisiana river scenes. Individuals were tested for their free choice preference for the same scenes. A statistical analysis was conducted to examine the relationship...

Landscape patterns from mathematical morphology on maps with contagion

Treesearch

Kurt Riitters; Peter Vogt; Pierre Soille; Christine Estreguil

2009-01-01

The perceived realism of simulated maps with contagion (spatial autocorrelation) has led to their use for comparing landscape pattern metrics and as habitat maps for modeling organism movement across landscapes. The objective of this study was to conduct a neutral model analysis of pattern metrics defined by morphological spatial pattern analysis (MSPA) on maps with...

[Wetland landscape pattern change based on GIS and RS: a review].

PubMed

Kong, Fan-Ting; Xi, Min; Li, Yue; Kong, Fan-Long; Chen, Wan

2013-04-01

Wetland is an ecological landscape with most biodiversity in nature, which has unique ecological structure and function, and contains abundant natural resources to provide material guarantee for human's living and development. Wetland landscape pattern is the comprehensive result of various ecological processes, and has become a hot issue in wetland ecological study. At present, the combination of geographic information system (GIS) and remote sensing (RS) technologies is an important way to study the wetland landscape pattern change. This paper reviewed the research progress in the wetland landscape change based on GIS and RS from the aspects of the research methods of wetland landscape pattern, index of wetland landscape pattern, and driving forces of wetland landscape pattern evolution, and discussed the applications of the combination of GIS and RS in monitoring the wetland landscape pattern change, the index selection of wetland landscape pattern, and the driving mechanisms of the combined action of human and nature. Some deficiencies in the current studies were put forward, and the directions of the future-studies were prospected.

Influence of landscape structure on reef fish assemblages

USGS Publications Warehouse

Grober-Dunsmore, R.; Frazer, T.K.; Beets, J.P.; Lindberg, W.J.; Zwick, P.; Funicelli, N.A.

2008-01-01

Management of tropical marine environments calls for interdisciplinary studies and innovative methodologies that consider processes occurring over broad spatial scales. We investigated relationships between landscape structure and reef fish assemblage structure in the US Virgin Islands. Measures of landscape structure were transformed into a reduced set of composite indices using principal component analyses (PCA) to synthesize data on the spatial patterning of the landscape structure of the study reefs. However, composite indices (e.g., habitat diversity) were not particularly informative for predicting reef fish assemblage structure. Rather, relationships were interpreted more easily when functional groups of fishes were related to individual habitat features. In particular, multiple reef fish parameters were strongly associated with reef context. Fishes responded to benthic habitat structure at multiple spatial scales, with various groups of fishes each correlated to a unique suite of variables. Accordingly, future experiments should be designed to test functional relationships based on the ecology of the organisms of interest. Our study demonstrates that landscape-scale habitat features influence reef fish communities, illustrating promise in applying a landscape ecology approach to better understand factors that structure coral reef ecosystems. Furthermore, our findings may prove useful in design of spatially-based conservation approaches such as marine protected areas (MPAs), because landscape-scale metrics may serve as proxies for areas with high species diversity and abundance within the coral reef landscape. ?? 2007 Springer Science+Business Media B.V.

Heritage landscape structure analysis in surrounding environment of the Grand Canal Yangzhou section

NASA Astrophysics Data System (ADS)

Xu, Huan

2018-03-01

The Yangzhou section of the Grand Canal is selected for a case study in this paper. The ZY-3 satellite images of 2016 are adopted as the data source. RS and GIS are used to analyze the landscape classification of the surrounding landscape of the Grand Canal, and the classification results are precisely evaluated. Next, the overall features of the landscape pattern are analyzed. The results showed that the overall accuracy is 82.5% and the Kappa coefficient is 78.17% in the Yangzhou section. The producer’s accuracy of the water landscape is the highest, followed by that of the other landscape, farmland landscape, garden and forest landscape, architectural landscape. The user’s accuracy of different landscape types can be ranked in a descending order, as the water landscape, farmland landscape, road landscape, architectural landscape, other landscape, garden and forest landscape. The farmland landscape and the architectural landscape are the top advantageous landscape types of the heritage site. The research findings can provide basic data for landscape protection, management and sustainable development of the Grand Canal Yangzhou section.

[Quantitative analysis of landscape patterns at the juncture of Shaanxi, Shanxi and Inner Mongolia, based on remote sensing data--taking Yulin sheet TM image as an example].

PubMed

Li, Tuansheng

2004-03-01

Based on the TM image of Yulin sheet and with the help of ERDAS, ARC/INFO and ARC/VIEW software, the landscape of Yulin sheet was classified. Using the spatial pattern analysis software FRAGSTATS of the vector version, a set of landscape indices were calculated at three scale levels of patches, classes and landscape. The results showed that landscape pattern indices could be successfully used in characterizing the spatial pattern of the studied area. However, this study should be further extended to the landscape of the same area in other period to analyze its dynamic change. FRAGSTATS was a good software, but should be improved by adding some indices such as PD2 developed by us.

Longwave infrared observation of urban landscapes

NASA Technical Reports Server (NTRS)

Goward, S. N.

1981-01-01

An investigation is conducted regarding the feasibility to develop improved methods for the identification and analysis of urban landscapes on the basis of a utilization of longwave infrared observations. Attention is given to landscape thermal behavior, urban thermal properties, modeled thermal behavior of pavements and buildings, and observed urban landscape thermal emissions. The differential thermal behavior of buildings, pavements, and natural areas within urban landscapes is found to suggest that integrated multispectral solar radiant reflectance and terrestrial radiant emissions data will significantly increase potentials for analyzing urban landscapes. In particular, daytime satellite observations of the considered type should permit better identification of urban areas and an analysis of the density of buildings and pavements within urban areas. This capability should enhance the utility of satellite remote sensor data in urban applications.

Combining paleo-data and modern exclosure experiments to assess the impact of megafauna extinctions on woody vegetation

PubMed Central

Bakker, Elisabeth S.; Gill, Jacquelyn L.; Johnson, Christopher N.; Vera, Frans W. M.; Sandom, Christopher J.; Asner, Gregory P.; Svenning, Jens-Christian

2016-01-01

Until recently in Earth history, very large herbivores (mammoths, ground sloths, diprotodons, and many others) occurred in most of the World’s terrestrial ecosystems, but the majority have gone extinct as part of the late-Quaternary extinctions. How has this large-scale removal of large herbivores affected landscape structure and ecosystem functioning? In this review, we combine paleo-data with information from modern exclosure experiments to assess the impact of large herbivores (and their disappearance) on woody species, landscape structure, and ecosystem functions. In modern landscapes characterized by intense herbivory, woody plants can persist by defending themselves or by association with defended species, can persist by growing in places that are physically inaccessible to herbivores, or can persist where high predator activity limits foraging by herbivores. At the landscape scale, different herbivore densities and assemblages may result in dynamic gradients in woody cover. The late-Quaternary extinctions were natural experiments in large-herbivore removal; the paleoecological record shows evidence of widespread changes in community composition and ecosystem structure and function, consistent with modern exclosure experiments. We propose a conceptual framework that describes the impact of large herbivores on woody plant abundance mediated by herbivore diversity and density, predicting that herbivore suppression of woody plants is strongest where herbivore diversity is high. We conclude that the decline of large herbivores induces major alterations in landscape structure and ecosystem functions. PMID:26504223

Combining paleo-data and modern exclosure experiments to assess the impact of megafauna extinctions on woody vegetation.

PubMed

Bakker, Elisabeth S; Gill, Jacquelyn L; Johnson, Christopher N; Vera, Frans W M; Sandom, Christopher J; Asner, Gregory P; Svenning, Jens-Christian

2016-01-26

Until recently in Earth history, very large herbivores (mammoths, ground sloths, diprotodons, and many others) occurred in most of the World's terrestrial ecosystems, but the majority have gone extinct as part of the late-Quaternary extinctions. How has this large-scale removal of large herbivores affected landscape structure and ecosystem functioning? In this review, we combine paleo-data with information from modern exclosure experiments to assess the impact of large herbivores (and their disappearance) on woody species, landscape structure, and ecosystem functions. In modern landscapes characterized by intense herbivory, woody plants can persist by defending themselves or by association with defended species, can persist by growing in places that are physically inaccessible to herbivores, or can persist where high predator activity limits foraging by herbivores. At the landscape scale, different herbivore densities and assemblages may result in dynamic gradients in woody cover. The late-Quaternary extinctions were natural experiments in large-herbivore removal; the paleoecological record shows evidence of widespread changes in community composition and ecosystem structure and function, consistent with modern exclosure experiments. We propose a conceptual framework that describes the impact of large herbivores on woody plant abundance mediated by herbivore diversity and density, predicting that herbivore suppression of woody plants is strongest where herbivore diversity is high. We conclude that the decline of large herbivores induces major alterations in landscape structure and ecosystem functions.

Consequences of Landscape Fragmentation on Lyme Disease Risk: A Cellular Automata Approach

PubMed Central

Li, Sen; Hartemink, Nienke; Speybroeck, Niko; Vanwambeke, Sophie O.

2012-01-01

The abundance of infected Ixodid ticks is an important component of human risk of Lyme disease, and various empirical studies have shown that this is associated, at least in part, to landscape fragmentation. In this study, we aimed at exploring how varying woodland fragmentation patterns affect the risk of Lyme disease, through infected tick abundance. A cellular automata model was developed, incorporating a heterogeneous landscape with three interactive components: an age-structured tick population, a classical disease transmission function, and hosts. A set of simplifying assumptions were adopted with respect to the study objective and field data limitations. In the model, the landscape influences both tick survival and host movement. The validation of the model was performed with an empirical study. Scenarios of various landscape configurations (focusing on woodland fragmentation) were simulated and compared. Lyme disease risk indices (density and infection prevalence of nymphs) differed considerably between scenarios: (i) the risk could be higher in highly fragmented woodlands, which is supported by a number of recently published empirical studies, and (ii) grassland could reduce the risk in adjacent woodland, which suggests landscape fragmentation studies of zoonotic diseases should not focus on the patch-level woodland patterns only, but also on landscape-level adjacent land cover patterns. Further analysis of the simulation results indicated strong correlations between Lyme disease risk indices and the density, shape and aggregation level of woodland patches. These findings highlight the strong effect of the spatial patterns of local host population and movement on the spatial dynamics of Lyme disease risks, which can be shaped by woodland fragmentation. In conclusion, using a cellular automata approach is beneficial for modelling complex zoonotic transmission systems as it can be combined with either real world landscapes for exploring direct spatial effects or artificial representations for outlining possible empirical investigations. PMID:22761842

Corridors restore animal-mediated pollination in fragmented tropical forest landscapes

PubMed Central

Kormann, Urs; Scherber, Christoph; Tscharntke, Teja; Klein, Nadja; Larbig, Manuel; Valente, Jonathon J.; Hadley, Adam S.; Betts, Matthew G.

2016-01-01

Tropical biodiversity and associated ecosystem functions have become heavily eroded through habitat loss. Animal-mediated pollination is required in more than 94% of higher tropical plant species and 75% of the world's leading food crops, but it remains unclear if corridors avert deforestation-driven pollination breakdown in fragmented tropical landscapes. Here, we used manipulative resource experiments and field observations to show that corridors functionally connect neotropical forest fragments for forest-associated hummingbirds and increase pollen transfer. Further, corridors boosted forest-associated pollinator availability in fragments by 14.3 times compared with unconnected equivalents, increasing overall pollination success. Plants in patches without corridors showed pollination rates equal to bagged control flowers, indicating pollination failure in isolated fragments. This indicates, for the first time, that corridors benefit tropical forest ecosystems beyond boosting local species richness, by functionally connecting mutualistic network partners. We conclude that small-scale adjustments to landscape configuration safeguard native pollinators and associated pollination services in tropical forest landscapes. PMID:26817765

Language Visibility, Functionality and Meaning across Various Timespace Scales in Brussels' Multilingual Landscapes

ERIC Educational Resources Information Center

Vandenbroucke, Mieke

2015-01-01

This paper addresses the complex multilingual linguistic landscapes (LLs) of three strategically-chosen areas in global city Brussels by examining how language displays on public signage in these areas are used for different purposes, functions or intentions. The focus will be on meaning-construction in the post-Fordist globalised era as shaped by…

Modeling forest harvesting effects on landscape pattern in the Northwest Wisconsin Pine Barrens

Treesearch

Volker C. Radeloff; David J. Mladenoff; Eric J. Gustafson; Robert M. Scheller; Patrick A. Zollner; Hong S. Heilman; H. Resit Akcakaya

2006-01-01

Forest management shapes landscape patterns, and these patterns often differ significantly from those typical for natural disturbance regimes. This may affect wildlife habitat and other aspects of ecosystem function. Our objective was to examine the effects of different forest management decisions on landscape pattern in a fire adapted ecosystem. We used a factorial...

Use of Pictorial Evaluations to Measure Knowledge Gained by Hispanic Landscape Workers Receiving Safety Training

ERIC Educational Resources Information Center

Bauske, Ellen M.; Fuhrman, Nicholas E.; Martinez-Espinoza, Alfredo D.; Orellana, Rolando

2013-01-01

Landscape work is dangerous. In the Southeast, Hispanic workers predominate in landscape industries. The incidence of functional illiteracy in this group of workers is high. A pictorial knowledge-based evaluation instrument was developed to measure the effectiveness of the trainings. No reading skills were required to take the evaluation. The…

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...

A Critique of Patch-Based Landscape Indicators for Detection of Temporal Change in Fragmentation

EPA Science Inventory

Since O’Neill et al. (1988), analysis of landscape indicators based on measurements from land-cover maps has been a core area of research in landscape ecology. Landscape indicator research has focused on development of new measurements, statistical properties, and indictor behav...

Single-molecule FRET reveals the energy landscape of the full-length SAM-I riboswitch.

PubMed

Manz, Christoph; Kobitski, Andrei Yu; Samanta, Ayan; Keller, Bettina G; Jäschke, Andres; Nienhaus, G Ulrich

2017-11-01

S-adenosyl-L-methionine (SAM) ligand binding induces major structural changes in SAM-I riboswitches, through which gene expression is regulated via transcription termination. Little is known about the conformations and motions governing the function of the full-length Bacillus subtilis yitJ SAM-I riboswitch. Therefore, we have explored its conformational energy landscape as a function of Mg 2+ and SAM ligand concentrations using single-molecule Förster resonance energy transfer (smFRET) microscopy and hidden Markov modeling analysis. We resolved four conformational states both in the presence and the absence of SAM and determined their Mg 2+ -dependent fractional populations and conformational dynamics, including state lifetimes, interconversion rate coefficients and equilibration timescales. Riboswitches with terminator and antiterminator folds coexist, and SAM binding only gradually shifts the populations toward terminator states. We observed a pronounced acceleration of conformational transitions upon SAM binding, which may be crucial for off-switching during the brief decision window before expression of the downstream gene.

Thermodynamic properties of solvated peptides from selective integrated tempering sampling with a new weighting factor estimation algorithm

NASA Astrophysics Data System (ADS)

Shen, Lin; Xie, Liangxu; Yang, Mingjun

2017-04-01

Conformational sampling under rugged energy landscape is always a challenge in computer simulations. The recently developed integrated tempering sampling, together with its selective variant (SITS), emerges to be a powerful tool in exploring the free energy landscape or functional motions of various systems. The estimation of weighting factors constitutes a critical step in these methods and requires accurate calculation of partition function ratio between different thermodynamic states. In this work, we propose a new adaptive update algorithm to compute the weighting factors based on the weighted histogram analysis method (WHAM). The adaptive-WHAM algorithm with SITS is then applied to study the thermodynamic properties of several representative peptide systems solvated in an explicit water box. The performance of the new algorithm is validated in simulations of these solvated peptide systems. We anticipate more applications of this coupled optimisation and production algorithm to other complicated systems such as the biochemical reactions in solution.

Neuroethics and fMRI: Mapping a Fledgling Relationship

PubMed Central

Garnett, Alex; Whiteley, Louise; Piwowar, Heather; Rasmussen, Edie; Illes, Judy

2011-01-01

Human functional magnetic resonance imaging (fMRI) informs the understanding of the neural basis of mental function and is a key domain of ethical enquiry. It raises questions about the practice and implications of research, and reflexively informs ethics through the empirical investigation of moral judgments. It is at the centre of debate surrounding the importance of neuroscience findings for concepts such as personhood and free will, and the extent of their practical consequences. Here, we map the landscape of fMRI and neuroethics, using citation analysis to uncover salient topics. We find that this landscape is sparsely populated: despite previous calls for debate, there are few articles that discuss both fMRI and ethical, legal, or social implications (ELSI), and even fewer direct citations between the two literatures. Recognizing that practical barriers exist to integrating ELSI discussion into the research literature, we argue nonetheless that the ethical challenges of fMRI, and controversy over its conceptual and practical implications, make this essential. PMID:21526115

Paws without claws? Ecological effects of large carnivores in anthropogenic landscapes

PubMed Central

Sahlén, E.; Elmhagen, B.; Chamaillé-Jammes, S.; Sand, H.; Lone, K.; Cromsigt, J. P. G. M.

2016-01-01

Large carnivores are frequently presented as saviours of biodiversity and ecosystem functioning through their creation of trophic cascades, an idea largely based on studies coming primarily out of relatively natural landscapes. However, in large parts of the world, particularly in Europe, large carnivores live in and are returning to strongly human-modified ecosystems. At present, we lack a coherent framework to predict the effects of large carnivores in these anthropogenic landscapes. We review how human actions influence the ecological roles of large carnivores by affecting their density or behaviour or those of mesopredators or prey species. We argue that the potential for density-mediated trophic cascades in anthropogenic landscapes is limited to unproductive areas where even low carnivore numbers may impact prey densities or to the limited parts of the landscape where carnivores are allowed to reach ecologically functional densities. The potential for behaviourally mediated trophic cascades may be larger and more widespread, because even low carnivore densities affect prey behaviour. We conclude that predator–prey interactions in anthropogenic landscapes will be highly context-dependent and human actions will often attenuate the ecological effects of large carnivores. We highlight the knowledge gaps and outline a new research avenue to study the role of carnivores in anthropogenic landscapes. PMID:27798302

Interaction of Soil Heavy Metal Pollution with Industrialisation and the Landscape Pattern in Taiyuan City, China

PubMed Central

Liu, Yong; Su, Chao; Zhang, Hong; Li, Xiaoting; Pei, Jingfei

2014-01-01

Many studies indicated that industrialization and urbanization caused serious soil heavy metal pollution from industrialized age. However, fewer previous studies have conducted a combined analysis of the landscape pattern, urbanization, industrialization, and heavy metal pollution. This paper was aimed at exploring the relationships of heavy metals in the soil (Pb, Cu, Ni, As, Cd, Cr, Hg, and Zn) with landscape pattern, industrialisation, urbanisation in Taiyuan city using multivariate analysis. The multivariate analysis included correlation analysis, analysis of variance (ANOVA), independent-sample T test, and principal component analysis (PCA). Geographic information system (GIS) was also applied to determine the spatial distribution of the heavy metals. The spatial distribution maps showed that the heavy metal pollution of the soil was more serious in the centre of the study area. The results of the multivariate analysis indicated that the correlations among heavy metals were significant, and industrialisation could significantly affect the concentrations of some heavy metals. Landscape diversity showed a significant negative correlation with the heavy metal concentrations. The PCA showed that a two-factor model for heavy metal pollution, industrialisation, and the landscape pattern could effectively demonstrate the relationships between these variables. The model explained 86.71% of the total variance of the data. Moreover, the first factor was mainly loaded with the comprehensive pollution index (P), and the second factor was primarily loaded with landscape diversity and dominance (H and D). An ordination of 80 samples could show the pollution pattern of all the samples. The results revealed that local industrialisation caused heavy metal pollution of the soil, but such pollution could respond negatively to the landscape pattern. The results of the study could provide a basis for agricultural, suburban, and urban planning. PMID:25251460

Interaction of soil heavy metal pollution with industrialisation and the landscape pattern in Taiyuan city, China.

PubMed

Liu, Yong; Su, Chao; Zhang, Hong; Li, Xiaoting; Pei, Jingfei

2014-01-01

Many studies indicated that industrialization and urbanization caused serious soil heavy metal pollution from industrialized age. However, fewer previous studies have conducted a combined analysis of the landscape pattern, urbanization, industrialization, and heavy metal pollution. This paper was aimed at exploring the relationships of heavy metals in the soil (Pb, Cu, Ni, As, Cd, Cr, Hg, and Zn) with landscape pattern, industrialisation, urbanisation in Taiyuan city using multivariate analysis. The multivariate analysis included correlation analysis, analysis of variance (ANOVA), independent-sample T test, and principal component analysis (PCA). Geographic information system (GIS) was also applied to determine the spatial distribution of the heavy metals. The spatial distribution maps showed that the heavy metal pollution of the soil was more serious in the centre of the study area. The results of the multivariate analysis indicated that the correlations among heavy metals were significant, and industrialisation could significantly affect the concentrations of some heavy metals. Landscape diversity showed a significant negative correlation with the heavy metal concentrations. The PCA showed that a two-factor model for heavy metal pollution, industrialisation, and the landscape pattern could effectively demonstrate the relationships between these variables. The model explained 86.71% of the total variance of the data. Moreover, the first factor was mainly loaded with the comprehensive pollution index (P), and the second factor was primarily loaded with landscape diversity and dominance (H and D). An ordination of 80 samples could show the pollution pattern of all the samples. The results revealed that local industrialisation caused heavy metal pollution of the soil, but such pollution could respond negatively to the landscape pattern. The results of the study could provide a basis for agricultural, suburban, and urban planning.

Landscape maps as an aid to management of scenic mountain areas

Treesearch

Roland Baumgartner

1979-01-01

Before any question about wise management decisions concerning the visual resource of our environment can be answered, it is necessary to conduct a detailed analysis to determine the integral visual inventory of landscape, as it impresses any involved person. With this method of landscape analysis researchers and planners can specify the potential of any region with an...

A factor analysis of landscape pattern and structure metrics

Treesearch

Kurt H. Riitters; R.V. O' Neill; C.T. Hunsaker; James D. Wickham; D.H. Yankee; S.P. Timmins; K.B. Jones; B.L. Jackson

1995-01-01

Fifty-five metrics of landscape pattern and structure were calculated for 85 maps of land use and land cover. A multivariate factor analysis was used to identify the common axes (or dimensions) of pattern and structure which were measured by a reduced set of 26 metrics. The first six factors explained about 87% of the variation in the 26 landscape metrics. These...

Anticipating forest and range land development in central Oregon (USA) for landscape analysis, with an example application involving mule deer

Treesearch

Jeffrey D. Kline; Alissa Moses; Theresa Burcsu

2010-01-01

Forest policymakers, public lands managers, and scientists in the Pacific Northwest (USA) seek ways to evaluate the landscape-level effects of policies and management through the multidisciplinary development and application of spatially explicit methods and models. The Interagency Mapping and Analysis Project (IMAP) is an ongoing effort to generate landscape-wide...

Multitemporal spatial pattern analysis of Tulum's tropical coastal landscape

NASA Astrophysics Data System (ADS)

Ramírez-Forero, Sandra Carolina; López-Caloca, Alejandra; Silván-Cárdenas, José Luis

2011-11-01

The tropical coastal landscape of Tulum in Quintana Roo, Mexico has a high ecological, economical, social and cultural value, it provides environmental and tourism services at global, national, regional and local levels. The landscape of the area is heterogeneous and presents random fragmentation patterns. In recent years, tourist services of the region has been increased promoting an accelerate expansion of hotels, transportation and recreation infrastructure altering the complex landscape. It is important to understand the environmental dynamics through temporal changes on the spatial patterns and to propose a better management of this ecological area to the authorities. This paper addresses a multi-temporal analysis of land cover changes from 1993 to 2000 in Tulum using Thematic Mapper data acquired by Landsat-5. Two independent methodologies were applied for the analysis of changes in the landscape and for the definition of fragmentation patterns. First, an Iteratively Multivariate Alteration Detection (IR-MAD) algorithm was used to detect and localize land cover change/no-change areas. Second, the post-classification change detection evaluated using the Support Vector Machine (SVM) algorithm. Landscape metrics were calculated from the results of IR-MAD and SVM. The analysis of the metrics indicated, among other things, a higher fragmentation pattern along roadways.

Coastal biodiversity and ecosystem services flows at the landscape scale: The CBESS progamme.

NASA Astrophysics Data System (ADS)

Paterson, David; Bothwell, John; Bradbury, Richard; Burrows, Michael; Burton, Niall; Emmerson, Mark; Garbutt, Angus; Skov, Martin; Solan, Martin; Spencer, Tom; Underwood, Graham

2015-04-01

The health of the European coastline is inextricably linked to the economy and culture of coastal nations but they are sensitive to climate change. As global temperatures increase, sea levels will rise and the forces experienced where land meets sea will become more destructive. Salt marshes, mudflats, beaches will be affected. These landscapes support a wide range of economically valuable animal and plant species, but also act as sites of carbon storage, nutrient recycling, and pollutant capture and amelioration. Their preservation is of utmost importance. Our programme: "A hierarchical approach to the examination of the relationship between biodiversity and ecosystem service flows across coastal margins" (CBESS) is designed to understand the landscape-scale links between the functions that these systems provide (ecosystem service flows) and the organisms that provide these services (biodiversity stocks) and moves beyond most previous studies, conducted at smaller scales. Our consortium of experts ranges from microbial ecologists, through environmental economists, to mathematical modellers, and organisations (RSPB, BTO, CEFAS, EA) with vested interest in the sustainable use of coastal wetlands. CBESS spans the landscape scale, investigating how biodiversity stocks provide ecosystem services (cf. National Ecosystem Assessment: Supporting services; Provisioning services; Regulating services; and Cultural services). CBESS combined a detailed study of two regional landscapes with a broad-scale UK-wide study to allow both specific and general conclusions to be drawn. The regional study compares two areas of great UK national importance: Morecambe Bay on the west coast and the Essex coastline on the east. We carried out biological and physical surveys at more than 600 stations combined with in situ measures of ecosystem funtction to clarify how biodiversity can provide these important ecosystem functions across scales. This information will be shared with those interested in using and managing coastal systems and we will propose practical methods and improved tools for the future analysis, management, and sustainability of coastal wetlands. The progamme and progress over the last 3 years will be described.

Low-Intensity Agricultural Landscapes in Transylvania Support High Butterfly Diversity: Implications for Conservation

PubMed Central

Loos, Jacqueline; Dorresteijn, Ine; Hanspach, Jan; Fust, Pascal; Rakosy, László; Fischer, Joern

2014-01-01

European farmland biodiversity is declining due to land use changes towards agricultural intensification or abandonment. Some Eastern European farming systems have sustained traditional forms of use, resulting in high levels of biodiversity. However, global markets and international policies now imply rapid and major changes to these systems. To effectively protect farmland biodiversity, understanding landscape features which underpin species diversity is crucial. Focusing on butterflies, we addressed this question for a cultural-historic landscape in Southern Transylvania, Romania. Following a natural experiment, we randomly selected 120 survey sites in farmland, 60 each in grassland and arable land. We surveyed butterfly species richness and abundance by walking transects with four repeats in summer 2012. We analysed species composition using Detrended Correspondence Analysis. We modelled species richness, richness of functional groups, and abundance of selected species in response to topography, woody vegetation cover and heterogeneity at three spatial scales, using generalised linear mixed effects models. Species composition widely overlapped in grassland and arable land. Composition changed along gradients of heterogeneity at local and context scales, and of woody vegetation cover at context and landscape scales. The effect of local heterogeneity on species richness was positive in arable land, but negative in grassland. Plant species richness, and structural and topographic conditions at multiple scales explained species richness, richness of functional groups and species abundances. Our study revealed high conservation value of both grassland and arable land in low-intensity Eastern European farmland. Besides grassland, also heterogeneous arable land provides important habitat for butterflies. While butterfly diversity in arable land benefits from heterogeneity by small-scale structures, grasslands should be protected from fragmentation to provide sufficiently large areas for butterflies. These findings have important implications for EU agricultural and conservation policy. Most importantly, conservation management needs to consider entire landscapes, and implement appropriate measures at multiple spatial scales. PMID:25058307

Riparian landscapes: Linking geodiversity with habitat and biodiversity

NASA Astrophysics Data System (ADS)

Chmieleski, Jana; Danzeisen, Laura

2017-04-01

Keywords: Oder valley, biodiversity, geodiversity River landscapes of all scales originally showed a high diversity of structures and habitats at a small spatial entity, such as the stream beds, terrasses, sand and gravel banks. This variety, with a lot of different elements, patches and patterns, represents not only a variety of geoelements or geomorhological features but also a large biodiversity, both of habitats and species. Riparian landscapes are both, a natural as well as a geoheritage, often even a cultural heritage (sustainabe land use practices). Embankments, utilization for agriculture, constructions for navigation, management measures lead to a strong loss of these structures. This impacts the value of the landscape as well ecosystem functions, not only the biodiversity and the geodiversity but also the recreation function or the aesthetic values. A case study from the National Park Lower Oder Valley in the Northeastern part of Germany, wich is also part of a Geopark („Eiszeitland am Oderrand") presents the connections of the diversity of geomorphological features with biodiversity and shows the loss of features (loss of values) due to intensive utilisation by using GIS-analysis and landscape-metrics. The Northern part of the Oder valley (National Park, transnational protection area of Germany and Poland) have been modified by man since centuries but even so remained in near-natural state that allows semi-(natural) stream dynamics. While the Oder's reparian zone is marked by the stream itself, by its bayous, reed beds, periodically flooded wet meadows and by its natural riparian forest the mineral morainic plateaus are marked by semi-natural forests and dry grasslands. Two areas of different degradation states, a) near-natural and wilderness area and b) grassland area will be compared in order to identify: quantity and extent of features, relation of measure and coverage, connectivity with other features, quantity and types of habitats (with evaluation according to Natura2000 habitat types). First results of that survey will be presented.

The role of reserves and anthropogenic elements for functional connectivity and resilience of ephemeral habitats

USGS Publications Warehouse

Uden, Daniel R.; Hellman, Michelle L.; Angeler, David G.; Allen, Craig R.

2014-01-01

Ecological reserves provide important wildlife habitat in many landscapes, and the functional connectivity of reserves and other suitable habitat patches is crucial for the persistence and resilience of spatially structured populations. To maintain or increase connectivity at spatial scales larger than individual patches, conservation actions may focus on creating and maintaining reserves and/or influencing management on non-reserves. Using a graph-theoretic approach, we assessed the functional connectivity and spatial distribution of wetlands in the Rainwater Basin of Nebraska, USA, an intensively cultivated agricultural matrix, at four assumed, but ecologically realistic, anuran dispersal distances. We compared connectivity in the current landscape to the historical landscape and putative future landscapes, and evaluated the importance of individual and aggregated reserve and non-reserve wetlands for maintaining connectivity. Connectivity was greatest in the historical landscape, where wetlands were also the most densely distributed. The construction of irrigation reuse pits for water storage has maintained connectivity in the current landscape by replacing destroyed wetlands, but these pits likely provide suboptimal habitat. Also, because there are fewer total wetlands (i.e., wetlands and irrigation reuse pits) in the current landscape than the historical landscape, and because the distribution of current wetlands is less clustered than that of historical wetlands, larger and longer dispersing, sometimes nonnative species may be favored over smaller, shorter dispersing species of conservation concern. Because of their relatively low number, wetland reserves do not affect connectivity as greatly as non-reserve wetlands or irrigation reuse pits; however, they likely provide the highest quality anuran habitat. To improve future levels of resilience in this wetland habitat network, management could focus on continuing to improve the conservation status of non-reserve wetlands, restoring wetlands at spatial scales that promote movements of shorter dispersing species, and further scrutinizing irrigation reuse pit removal by considering effects on functional connectivity for anurans, an emblematic and threatened group of organisms. However, broader conservation plans will need to give consideration to other wetland-dependent species, incorporate invasive species management, and address additional challenges arising from global change in social-ecological systems like the Rainwater Basin.

FUSE: a profit maximization approach for functional summarization of biological networks.

PubMed

Seah, Boon-Siew; Bhowmick, Sourav S; Dewey, C Forbes; Yu, Hanry

2012-03-21

The availability of large-scale curated protein interaction datasets has given rise to the opportunity to investigate higher level organization and modularity within the protein interaction network (PPI) using graph theoretic analysis. Despite the recent progress, systems level analysis of PPIS remains a daunting task as it is challenging to make sense out of the deluge of high-dimensional interaction data. Specifically, techniques that automatically abstract and summarize PPIS at multiple resolutions to provide high level views of its functional landscape are still lacking. We present a novel data-driven and generic algorithm called FUSE (Functional Summary Generator) that generates functional maps of a PPI at different levels of organization, from broad process-process level interactions to in-depth complex-complex level interactions, through a pro t maximization approach that exploits Minimum Description Length (MDL) principle to maximize information gain of the summary graph while satisfying the level of detail constraint. We evaluate the performance of FUSE on several real-world PPIS. We also compare FUSE to state-of-the-art graph clustering methods with GO term enrichment by constructing the biological process landscape of the PPIS. Using AD network as our case study, we further demonstrate the ability of FUSE to quickly summarize the network and identify many different processes and complexes that regulate it. Finally, we study the higher-order connectivity of the human PPI. By simultaneously evaluating interaction and annotation data, FUSE abstracts higher-order interaction maps by reducing the details of the underlying PPI to form a functional summary graph of interconnected functional clusters. Our results demonstrate its effectiveness and superiority over state-of-the-art graph clustering methods with GO term enrichment.

Analysis to Inform Defense Planning Despite Austerity

DTIC Science & Technology

2014-01-01

available from www.rand.org as a public service of the RAND Corporation. CHILDREN AND FAMILIES EDUCATION AND THE ARTS ENERGY AND ENVIRONMENT HEALTH AND...xvii S.3. Cost-Effectiveness Landscape , by Strategic Perspective . . . . . . xxiii 1.1. Problems Go Far Beyond Fiscal Constraints...objectives for each regional and functional area, as well as such cross-cutting challenges as simul - taneous conflicts. It might also have different

Integrating spatially explicit representations of landscape perceptions into land change research

USGS Publications Warehouse

Dorning, Monica; Van Berkel, Derek B.; Semmens, Darius J.

2017-01-01

Purpose of ReviewHuman perceptions of the landscape can influence land-use and land-management decisions. Recognizing the diversity of landscape perceptions across space and time is essential to understanding land change processes and emergent landscape patterns. We summarize the role of landscape perceptions in the land change process, demonstrate advances in quantifying and mapping landscape perceptions, and describe how these spatially explicit techniques have and may benefit land change research.Recent FindingsMapping landscape perceptions is becoming increasingly common, particularly in research focused on quantifying ecosystem services provision. Spatial representations of landscape perceptions, often measured in terms of landscape values and functions, provide an avenue for matching social and environmental data in land change studies. Integrating these data can provide new insights into land change processes, contribute to landscape planning strategies, and guide the design and implementation of land change models.SummaryChallenges remain in creating spatial representations of human perceptions. Maps must be accompanied by descriptions of whose perceptions are being represented and the validity and uncertainty of those representations across space. With these considerations, rapid advancements in mapping landscape perceptions hold great promise for improving representation of human dimensions in landscape ecology and land change research.

A meta-analysis of crop pest and natural enemy response to landscape complexity.

PubMed

Chaplin-Kramer, Rebecca; O'Rourke, Megan E; Blitzer, Eleanor J; Kremen, Claire

2011-09-01

Many studies in recent years have investigated the relationship between landscape complexity and pests, natural enemies and/or pest control. However, no quantitative synthesis of this literature beyond simple vote-count methods yet exists. We conducted a meta-analysis of 46 landscape-level studies, and found that natural enemies have a strong positive response to landscape complexity. Generalist enemies show consistent positive responses to landscape complexity across all scales measured, while specialist enemies respond more strongly to landscape complexity at smaller scales. Generalist enemy response to natural habitat also tends to occur at larger spatial scales than for specialist enemies, suggesting that land management strategies to enhance natural pest control should differ depending on whether the dominant enemies are generalists or specialists. The positive response of natural enemies does not necessarily translate into pest control, since pest abundances show no significant response to landscape complexity. Very few landscape-scale studies have estimated enemy impact on pest populations, however, limiting our understanding of the effects of landscape on pest control. We suggest focusing future research efforts on measuring population dynamics rather than static counts to better characterise the relationship between landscape complexity and pest control services from natural enemies. © 2011 Blackwell Publishing Ltd/CNRS.

Landscape Character of Pongkor Mining Ecotourism Area

NASA Astrophysics Data System (ADS)

Kusumoarto, A.; Gunawan, A.; Machfud; Hikmat, A.

2017-10-01

Pongkor Mining Ecotourism Area has a diverse landscape character as a potential landscape resources for the development of ecotourism destination. This area is part of the Mount of Botol Resort, Halimun Salak National Park (HSNP). This area also has a fairly high biodiversity. This study aims to identify and analysis the category of landscape character in the Pongkor Mining Ecotourism Area for the development of ecotourism destination. This study used a descriptive approach through field surveys and interviews, was carried out through two steps : 1) identify the landscape character, and 2) analysis of the landscape character. The results showed that in areas set aside for ecotourism destination in Pongkor Mining, landscape character category scattered forests, tailing ponds, river, plain, and the built environment. The Category of landscape character most dominant scattered in the area is forest, here is the river, plain, tailing ponds, the built environment, and plain. The landscape character in a natural environment most preferred for ecotourism activities. The landscape character that spread in the natural environment and the built environment is a potential that must be protected and modified such as elimination of incongruous element, accentuation of natural form, alteration of the natural form, intensification and enhanced visual quality intensively to be developed as a ecotourism destination area.

Dissolved organic carbon fluxes from hydropedologic units in Alaskan coastal temperate rainforest watersheds

Treesearch

David V. D' Amore; Rick T. Edwards; Paul A. Herendeen; Eran Hood; Jason B. Fellman

2015-01-01

Dissolved organic C (DOC) transfer from the landscape to coastal margins is a key component of regional C cycles. Hydropedology provides a conceptual and observational framework for linking soil hydrologic function to landscape C cycling. We used hydropedology to quantify the export of DOC from the terrestrial landscape and understand how soil temperature and water...

Assessing the water needs of riparian and wetland vegetation in the western United States

Treesearch

David J. Cooper; David M. Merritt

2012-01-01

Wetlands and riparian areas are unique landscape elements that perform a disproportionate role in landscape functioning relative to their aerial extent on the landscape. The purpose of this guide is to provide a general foundation for the reader in several interrelated disciplines for the purpose of enabling him/her to characterize and quantify the water needs of...

Children's Liking of Landscape Paintings as a Function of Their Perceptions of Prospect, Refuge, and Hazard

ERIC Educational Resources Information Center

Fischer, Mary Ann; Shrout, Patrick E.

2006-01-01

Prospect-refuge theory was used to study children's aesthetic responses to landscape paintings. Sixty-seven children between the ages of 8 and 15 years reported their liking for 28 landscape paintings and their perceptions of the degree of prospect, refuge, and hazard in those paintings. Consistent with expectations, children were able to express…

[Land use and land cover charnge (LUCC) and landscape service: Evaluation, mapping and modeling].

PubMed

Song, Zhang-jian; Cao, Yu; Tan, Yong-zhong; Chen, Xiao-dong; Chen, Xian-peng

2015-05-01

Studies on ecosystem service from landscape scale aspect have received increasing attention from researchers all over the world. Compared with ecosystem scale, it should be more suitable to explore the influence of human activities on land use and land cover change (LUCC), and to interpret the mechanisms and processes of sustainable landscape dynamics on landscape scale. Based on comprehensive and systematic analysis of researches on landscape service, this paper firstly discussed basic concepts and classification of landscape service. Then, methods of evaluation, mapping and modeling of landscape service were analyzed and concluded. Finally, future trends for the research on landscape service were proposed. It was put forward that, exploring further connotation and classification system of landscape service, improving methods and quantitative indicators for evaluation, mapping and modelling of landscape service, carrying out long-term integrated researches on landscape pattern-process-service-scale relationships and enhancing the applications of theories and methods on landscape economics and landscape ecology are very important fields of the research on landscape service in future.

Verification of hydrologic landscape derived basin-scale classifications in the Pacific Northwest

Treesearch

Keith Sawicz

2016-01-01

The interaction between the physical and climatic attributes of a basin (form) control how water is partitioned, stored, and conveyed through a catchment (function). Hydrologic Landscapes (HLs) were previously...

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

Relationship between tourism development and vegetated landscapes in Luya Mountain Nature Reserve, Shanxi, China.

PubMed

Cheng, Zhan-Hong; Zhang, Jin-Tun

2005-09-01

The relationship between tourism development and vegetated landscapes is analyzed for the Luya Mountain Nature Reserve (LMNR), Shanxi, China, in this study. Indices such as Sensitive Level (SL), Landscape Importance Value (LIV), information index of biodiversity (H'), Shade-tolerant Species Proportion (SSP), and Tourism Influencing Index (TII) are used to characterize vegetated landscapes, the impact of tourism, and their relationship. Their relationship is studied by Two-Way Indicator Species Analysis (TWINSPAN) and Detrended Correspondence Analysis (DCA). TWINSPAN gives correct and rapid partition to the classification, and DCA ordination shows the changing tendency of all vegetation types based on tourism development. These results reflect the ecological relationship between tourism development and vegetated landscapes. In Luya Mountain Nature Reserve, most plant communities are in good or medium condition, which shows that these vegetated landscapes can support more tourism. However, the occurrence of the bad condition shows that there is a severe contradiction between tourism development and vegetated landscapes.

Landscape Genetics for the Empirical Assessment of Resistance Surfaces: The European Pine Marten (Martes martes) as a Target-Species of a Regional Ecological Network

PubMed Central

Ruiz-González, Aritz; Gurrutxaga, Mikel; Cushman, Samuel A.; Madeira, María José; Randi, Ettore; Gómez-Moliner, Benjamin J.

2014-01-01

Coherent ecological networks (EN) composed of core areas linked by ecological corridors are being developed worldwide with the goal of promoting landscape connectivity and biodiversity conservation. However, empirical assessment of the performance of EN designs is critical to evaluate the utility of these networks to mitigate effects of habitat loss and fragmentation. Landscape genetics provides a particularly valuable framework to address the question of functional connectivity by providing a direct means to investigate the effects of landscape structure on gene flow. The goals of this study are (1) to evaluate the landscape features that drive gene flow of an EN target species (European pine marten), and (2) evaluate the optimality of a regional EN design in providing connectivity for this species within the Basque Country (North Spain). Using partial Mantel tests in a reciprocal causal modeling framework we competed 59 alternative models, including isolation by distance and the regional EN. Our analysis indicated that the regional EN was among the most supported resistance models for the pine marten, but was not the best supported model. Gene flow of pine marten in northern Spain is facilitated by natural vegetation, and is resisted by anthropogenic landcover types and roads. Our results suggest that the regional EN design being implemented in the Basque Country will effectively facilitate gene flow of forest dwelling species at regional scale. PMID:25329047

The histone H3 N-terminal tail: a computational analysis of the free energy landscape and kinetics.

PubMed

Zheng, Yuqing; Cui, Qiang

2015-05-28

Histone tails are the short peptide protrusions outside of the nucleosome core particle and they play a critical role in regulating chromatin dynamics and gene activity. A histone H3 N-terminal tail, like other histone tails, can be covalently modified on different residues to activate or repress gene expression. Previous studies have indicated that, despite its intrinsically disordered nature, the histone H3 N-terminal tail has regions of notable secondary structural propensities. To further understand the structure-dynamics-function relationship in this system, we have carried out 75.6 μs long implicit solvent simulations and 29.3 μs long explicit solvent simulations. The extensive samplings allow us to better characterize not only the underlying free energy landscape but also kinetic properties through Markov state models (MSM). Dihedral principal component analysis (dPCA) and locally scaled diffusion map (LSDMap) analysis yield consistent results that indicate an overall flat free energy surface with several shallow basins that correspond to conformations with a high α-helical propensity in two regions of the peptide. Kinetic information extracted from Markov state models reveals rapid transitions between different metastable states with mean first passage times spanning from several hundreds of nanoseconds to hundreds of microseconds. These findings shed light on how the dynamical nature of the histone H3 N-terminal tail is related to its function. The complementary nature of dPCA, LSDMap and MSM for the analysis of biomolecules is also discussed.

Implications of discontinuous elevation gradients on fragmentation and restoration in patterned wetlands

USGS Publications Warehouse

Zweig, Christa L.; Reichert, Brian E.; Kitchens, Wiley M.

2011-01-01

Large wetlands around the world face the possibility of degradation, not only from complete conversion, but also from subtle changes in their structure and function. While fragmentation and isolation of wetlands within heterogeneous landscapes has received much attention, the disruption of spatial patterns/processes within large wetland systems and the resulting fragmentation of community components are less well documented. A greater understanding of pattern/process relationships and landscape gradients, and what occurs when they are altered, could help avoid undesirable consequences of restoration actions. The objective of this study is to determine the amount of fragmentation of sawgrass ridges due to artificial impoundment of water and how that may be differentially affected by spatial position relative to north and south levees. We also introduce groundbreaking evidence of landscape-level discontinuous elevation gradients within WCA3AS by comparing generalized linear and generalized additive models. These relatively abrupt breaks in elevation may have non-linear effects on hydrology and vegetation communities and would be crucial in restoration considerations. Modeling suggests there are abrupt breaks in elevation as a function of northing (Y-coordinate). Fragmentation indices indicate that fragmentation is a function of elevation and easting (X-coordinate), and that fragmentation has increased from 1988-2002. When landscapes change and the changes are compounded by non-linear landscape variables that are described herein, the maintenance processes change with them, creating a degraded feedback loop that alters the system's response to structuring variables and diminishes our ability to predict the effects of restoration projects or climate change. Only when these landscape variables and linkages are clearly defined can we predict the response to potential perturbations and apply the knowledge to other landscape-level wetland systems in need of future restoration.

Reconsideration of dynamic force spectroscopy analysis of streptavidin-biotin interactions.

PubMed

Taninaka, Atsushi; Takeuchi, Osamu; Shigekawa, Hidemi

2010-05-13

To understand and design molecular functions on the basis of molecular recognition processes, the microscopic probing of the energy landscapes of individual interactions in a molecular complex and their dependence on the surrounding conditions is of great importance. Dynamic force spectroscopy (DFS) is a technique that enables us to study the interaction between molecules at the single-molecule level. However, the obtained results differ among previous studies, which is considered to be caused by the differences in the measurement conditions. We have developed an atomic force microscopy technique that enables the precise analysis of molecular interactions on the basis of DFS. After verifying the performance of this technique, we carried out measurements to determine the landscapes of streptavidin-biotin interactions. The obtained results showed good agreement with theoretical predictions. Lifetimes were also well analyzed. Using a combination of cross-linkers and the atomic force microscope that we developed, site-selective measurement was carried out, and the steps involved in bonding due to microscopic interactions are discussed using the results obtained by site-selective analysis.

Pedodiversity and Its Significance in the Context of Modern Soil Geography

NASA Astrophysics Data System (ADS)

Krasilnikov, P. V.; Gerasimova, M. I.; Golovanov, D. L.; Konyushkova, M. V.; Sidorova, V. A.; Sorokin, A. S.

2018-01-01

Methodological basics of the study and quantitative assessment of pedodiversity are discussed. It is shown that the application of various indices and models of pedodiversity can be feasible for solving three major issues in pedology: a comparative geographical analysis of different territories, a comparative historical analysis of soil development in the course of landscape evolution, and the analysis of relationships between biodiversity and pedodiversity. Analogous geographic concepts of geodiversity and landscape diversity are also discussed. Certain limitations in the use of quantitative estimates of pedodiversity related to their linkage to the particular soil classification systems and with the initial soil maps are considered. Problems of the interpretation of the results of pedodiversity assessments are emphasized. It is shown that scientific explanations of biodiversity cannot be adequately applied in soil studies. Promising directions of further studies of pedodiversity are outlined. They include the assessment of the functional diversity of soils on the basis of data on their properties, integration with geostatistical methods of evaluation of soil variability, and assessment of pedodiversity on different scales.

Predicting outcomes of restored Everglades high flow: A model system for scientifically managed floodplains

USGS Publications Warehouse

Choi, Jay; Harvey, Judson

2017-01-01

Restoration of higher flows through the Everglades is intended to reestablish sheetflow to rebuild a well-functioning ridge and slough landscape that supports a productive and diverse ecosystem. Our objective of the study was to use hydrologic simulations and biophysical analysis to predict restoration outcomes for five major subbasins of the Everglades. Five different scenarios of restoration were examined, and for each we predicted an outcome based on metrics describing the present-day condition of the landscape and additional metrics determined by modeling the hydrologic changes accompanying restoration. Restoration scenarios spanned from a baseline case with average annual flows of about 52% of the predrainage flow to the most aggressive scenario that permits 91% of the predrainage flow. Our predictions indicated that all restoration scenarios could benefit the functionality of the ridge-slough ecosystem. However, the difference between any single restoration scenario and the “no restoration” baseline was far greater than was the difference between any two levels of restoration. Interestingly, our analysis suggested that the most extensive (and highest cost) restoration scenarios are not likely to improve ridge and slough function more than less extensive restoration options. However, the value of more aggressive restoration may lie in factors not considered directly in our analysis. For example, an important reason to implement the more aggressive restoration scenarios could be additional flexibility that permitting greater flow allows for adaptively managing the ecosystem while also serving water needs for southeastern Florida in what could be a drier Everglades in the coming decades.

GenomeLandscaper: Landscape analysis of genome-fingerprints maps assessing chromosome architecture.

PubMed

Ai, Hannan; Ai, Yuncan; Meng, Fanmei

2018-01-18

Assessing correctness of an assembled chromosome architecture is a central challenge. We create a geometric analysis method (called GenomeLandscaper) to conduct landscape analysis of genome-fingerprints maps (GFM), trace large-scale repetitive regions, and assess their impacts on the global architectures of assembled chromosomes. We develop an alignment-free method for phylogenetics analysis. The human Y chromosomes (GRCh.chrY, HuRef.chrY and YH.chrY) are analysed as a proof-of-concept study. We construct a galaxy of genome-fingerprints maps (GGFM) for them, and a landscape compatibility among relatives is observed. But a long sharp straight line on the GGFM breaks such a landscape compatibility, distinguishing GRCh38p1.chrY (and throughout GRCh38p7.chrY) from GRCh37p13.chrY, HuRef.chrY and YH.chrY. We delete a 1.30-Mbp target segment to rescue the landscape compatibility, matching the antecedent GRCh37p13.chrY. We re-locate it into the modelled centromeric and pericentromeric region of GRCh38p10.chrY, matching a gap placeholder of GRCh37p13.chrY. We decompose it into sub-constituents (such as BACs, interspersed repeats, and tandem repeats) and trace their homologues by phylogenetics analysis. We elucidate that most examined tandem repeats are of reasonable quality, but the BAC-sized repeats, 173U1020C (176.46 Kbp) and 5U41068C (205.34 Kbp), are likely over-repeated. These results offer unique insights into the centromeric and pericentromeric regions of the human Y chromosomes.

The spatial relationship between human activities and C, N, P, S in soil based on landscape geochemical interpretation.

PubMed

Yu, Huan; He, Zheng-Wei; Kong, Bo; Weng, Zhong-Yin; Shi, Ze-Ming

2016-04-01

The development and formation of chemical elements in soil are affected not only by parent material, climate, biology, and topology factors, but also by human activities. As the main elements supporting life on earth system, the C, N, P, S cycles in soil have been altered by human activity through land-use change, agricultural intensification, and use of fossil fuels. The present study attempts to analyze whether and how a connection can be made between macroscopical control and microcosmic analysis, to estimate the impacts of human activities on C, N, P, S elements in soil, and to determine a way to describe the spatial relationship between C, N, P, S in soil and human activities, by means of landscape geochemical theories and methods. In addition, the disturbances of human activities on C, N, P, S are explored through the analysis of the spatial relationship between human disturbed landscapes and element anomalies, thereby determining the diversified rules of the effects. The study results show that the rules of different landscapes influencing C, N, P, S elements are diversified, and that the C element is closely related to city landscapes; furthermore, the elements N, P, and S are shown to be closely related to river landscapes; the relationships between mine landscapes and the elements C, N, P, S are apparent; the relationships between the elements C, N, P, S and road landscapes are quite close, which shows that road landscapes have significant effects on these elements. Therefore, the conclusion is drawn that the response mechanism analysis of human disturbance and soil chemical element aggregation is feasible, based on the landscape geochemical theories and methods. The spatial information techniques, such as remote sensing and geographic information systems, are effective for research on soil element migration.

The somatic genomic landscape of chromophobe renal cell carcinoma

PubMed Central

Davis, Caleb F.; Ricketts, Christopher; Wang, Min; Yang, Lixing; Cherniack, Andrew D.; Shen, Hui; Buhay, Christian; Kang, Hyojin; Kim, Sang Cheol; Fahey, Catherine C.; Hacker, Kathryn E.; Bhanot, Gyan; Gordenin, Dmitry A.; Chu, Andy; Gunaratne, Preethi H.; Biehl, Michael; Seth, Sahil; Kaipparettu, Benny A.; Bristow, Christopher A.; Donehower, Lawrence A.; Wallen, Eric M.; Smith, Angela B.; Tickoo, Satish K.; Tamboli, Pheroze; Reuter, Victor; Schmidt, Laura S.; Hsieh, James J.; Choueiri, Toni K.; Hakimi, A. Ari; Chin, Lynda; Meyerson, Matthew; Kucherlapati, Raju; Park, Woong-Yang; Robertson, A. Gordon; Laird, Peter W.; Henske, Elizabeth P.; Kwiatkowski, David J.; Park, Peter J.; Morgan, Margaret; Shuch, Brian; Muzny, Donna; Wheeler, David A.; Linehan, W. Marston; Gibbs, Richard A.; Rathmell, W. Kimryn; Creighton, Chad J.

2014-01-01

Summary We describe the landscape of somatic genomic alterations of 66 chromophobe renal cell carcinomas (ChRCCs) based on multidimensional and comprehensive characterization, including mitochondrial DNA (mtDNA) and whole genome sequencing. The result is consistent that ChRCC originates from the distal nephron compared to other kidney cancers with more proximal origins. Combined mtDNA and gene expression analysis implicates changes in mitochondrial function as a component of the disease biology, while suggesting alternative roles for mtDNA mutations in cancers relying on oxidative phosphorylation. Genomic rearrangements lead to recurrent structural breakpoints within TERT promoter region, which correlates with highly elevated TERT expression and manifestation of kataegis, representing a mechanism of TERT up-regulation in cancer distinct from previously-observed amplifications and point mutations. PMID:25155756

The somatic genomic landscape of chromophobe renal cell carcinoma.

PubMed

Davis, Caleb F; Ricketts, Christopher J; Wang, Min; Yang, Lixing; Cherniack, Andrew D; Shen, Hui; Buhay, Christian; Kang, Hyojin; Kim, Sang Cheol; Fahey, Catherine C; Hacker, Kathryn E; Bhanot, Gyan; Gordenin, Dmitry A; Chu, Andy; Gunaratne, Preethi H; Biehl, Michael; Seth, Sahil; Kaipparettu, Benny A; Bristow, Christopher A; Donehower, Lawrence A; Wallen, Eric M; Smith, Angela B; Tickoo, Satish K; Tamboli, Pheroze; Reuter, Victor; Schmidt, Laura S; Hsieh, James J; Choueiri, Toni K; Hakimi, A Ari; Chin, Lynda; Meyerson, Matthew; Kucherlapati, Raju; Park, Woong-Yang; Robertson, A Gordon; Laird, Peter W; Henske, Elizabeth P; Kwiatkowski, David J; Park, Peter J; Morgan, Margaret; Shuch, Brian; Muzny, Donna; Wheeler, David A; Linehan, W Marston; Gibbs, Richard A; Rathmell, W Kimryn; Creighton, Chad J

2014-09-08

We describe the landscape of somatic genomic alterations of 66 chromophobe renal cell carcinomas (ChRCCs) on the basis of multidimensional and comprehensive characterization, including mtDNA and whole-genome sequencing. The result is consistent that ChRCC originates from the distal nephron compared with other kidney cancers with more proximal origins. Combined mtDNA and gene expression analysis implicates changes in mitochondrial function as a component of the disease biology, while suggesting alternative roles for mtDNA mutations in cancers relying on oxidative phosphorylation. Genomic rearrangements lead to recurrent structural breakpoints within TERT promoter region, which correlates with highly elevated TERT expression and manifestation of kataegis, representing a mechanism of TERT upregulation in cancer distinct from previously observed amplifications and point mutations. Copyright © 2014 Elsevier Inc. All rights reserved.

Landscape scale assessment of soil and water salinization processes in agricultural coastal area.

NASA Astrophysics Data System (ADS)

Elen Bless, Aplena; Follain, Stéphane; Coiln, François; Crabit, Armand

2017-04-01

Soil salinization is among main land degradation process around the globe. It reduces soil quality, disturbs soil function, and has harmful impacts on plant growth that would threaten agricultural sustainability, particularly in coastal areas where mostly susceptible on land degradation because of pressure from anthropogenic activities and at the same time need to preserve soil quality for supporting food production. In this presentation, we present a landscape scale analysis aiming to assess salinization process affecting wine production. This study was carried out at Serignan estuary delta in South of France (Languadoc Roussillon Region, 43˚ 28'N and 3˚ 31'E). It is a sedimentary basin near coastline of Mediterranean Sea. Field survey was design to characterize both space and time variability of soil and water salinity through water electrical conductivity (ECw) and soil 1/5 electrical conductivity (EC1/5). For water measurements, Orb River and groundwater salinity (piezometers) were determined and for soil 1737 samples were randomly collected from different soil depths (20, 50, 80, and 120 cm) between year 2012 and 2016 and measured. In order to connect with agricultural practices observations and interviews with farmers were conducted. We found that some areas combining specific criteria presents higher electrical conductivity: positions with lower elevation (a.s.l), Cambisols (Calcaric) / Fluvisols soil type (WRB) and dominated clay textures. These observations combined with geochemical determination and spatial analysis confirm our first hypothesis of sea salt intrusion as the main driven factor of soil salinity in this region. In this context, identification of salinization process, fine determination of pedological specificities and fine understanding of agricultural practices allowed us to proposed adaptation strategies to restore soil production function. Please fill in your abstract text. Key Words: Salinity, Coastal Agriculture, Landscape, Soil, Water

Characterizing RNA Dynamics at Atomic Resolution Using Solution-state NMR Spectroscopy

PubMed Central

Bothe, Jameson R.; Nikolova, Evgenia N.; Eichhorn, Catherine D.; Chugh, Jeetender; Hansen, Alexandar L.; Al-Hashimi, Hashim M.

2012-01-01

Many recently discovered non-coding RNAs do not fold into a single native conformation, but rather, sample many different conformations along their free energy landscape to carry out their biological function. Unprecedented insights into the RNA dynamic structure landscape are provided by solution-state NMR techniques that measure the structural, kinetic, and thermodynamic characteristics of motions spanning picosecond to second timescales at atomic resolution. From these studies a basic description of the RNA dynamic structure landscape is emerging, bringing new insights into how RNA structures change to carry out their function as well as applications in RNA-targeted drug discovery and RNA bioengineering. PMID:22036746

[Wetlands of priority restoration in Northeast China based on spatial analysis].

PubMed

Dong, Zhang-Yu; Liu, Dian-Wei; Wang, Zong-Ming; Ren, Chun-Ying; Tang, Xu-Guang; Jia, Ming-Ming; Wang, Yan

2013-01-01

By using GIS/RS technology, and from the aspects of landscape structure, river- and road densities, wetness index, geomorphology, and cultivated land productivity, a spatial analysis was made on the potentiality of wetland restoration in Northeast China, with the regions of priority and secondary priority restoration wetlands determined. Then, by using the coordinated development index of crop production and wetland as well as the landscape indices, the wetland restoration effect was verified. In Northeast China, the wetland area of priority restoration was 1.78 x 10(6) hm2, among which, farmland and grassland were the main types for restoration, accounting for 96.7% of the total, and mainly located in the Sanjiang Plain in the northeastern part and the Songnen Plain in the central part of Northeast China. The wetland area of secondary priority restoration was 1.03 x 10(6) hm2. After the restoration of the wetlands, the wetland area in Northeast China would be increased by 37.4%, compared with the present wetland area, and the value of the coordinated development index of crop production and wetland would increase from 0.539 before restoration to 0.733 after restoration. The landscape pattern would be more benefit to the performance of the ecological functions of the wetlands. This study revealed that the restoration scheme of the wetlands in Northeast China based on spatial analysis was practicable, which could provide data support for the implement of wetland restoration and the improvement of ecological environment in Northeast China.

The Energy Landscape Analysis of Cancer Mutations in Protein Kinases

PubMed Central

Dixit, Anshuman; Verkhivker, Gennady M.

2011-01-01

The growing interest in quantifying the molecular basis of protein kinase activation and allosteric regulation by cancer mutations has fueled computational studies of allosteric signaling in protein kinases. In the present study, we combined computer simulations and the energy landscape analysis of protein kinases to characterize the interplay between oncogenic mutations and locally frustrated sites as important catalysts of allostetric kinase activation. While structurally rigid kinase core constitutes a minimally frustrated hub of the catalytic domain, locally frustrated residue clusters, whose interaction networks are not energetically optimized, are prone to dynamic modulation and could enable allosteric conformational transitions. The results of this study have shown that the energy landscape effect of oncogenic mutations may be allosteric eliciting global changes in the spatial distribution of highly frustrated residues. We have found that mutation-induced allosteric signaling may involve a dynamic coupling between structurally rigid (minimally frustrated) and plastic (locally frustrated) clusters of residues. The presented study has demonstrated that activation cancer mutations may affect the thermodynamic equilibrium between kinase states by allosterically altering the distribution of locally frustrated sites and increasing the local frustration in the inactive form, while eliminating locally frustrated sites and restoring structural rigidity of the active form. The energy landsape analysis of protein kinases and the proposed role of locally frustrated sites in activation mechanisms may have useful implications for bioinformatics-based screening and detection of functional sites critical for allosteric regulation in complex biomolecular systems. PMID:21998754

Chapter 4: Overview of the vegetation management treatment economic analysis module in the integrated landscape assessment project

Treesearch

Xiaoping Zhou; Miles A. Hemstrom

2014-01-01

Forest land provides various ecosystem services, including timber, biomass, and carbon sequestration. Estimating trends in these ecosystem services is essential for assessing potential outcomes of landscape management scenarios. However, the state-and transition models used in the Integrated Landscape Assessment Project for simulating landscape changes over time do not...

Landscape genetics of leaf-toed geckos in the tropical dry forest of northern Mexico.

PubMed

Blair, Christopher; Jiménez Arcos, Victor H; Mendez de la Cruz, Fausto R; Murphy, Robert W

2013-01-01

Habitat fragmentation due to both natural and anthropogenic forces continues to threaten the evolution and maintenance of biological diversity. This is of particular concern in tropical regions that are experiencing elevated rates of habitat loss. Although less well-studied than tropical rain forests, tropical dry forests (TDF) contain an enormous diversity of species and continue to be threatened by anthropogenic activities including grazing and agriculture. However, little is known about the processes that shape genetic connectivity in species inhabiting TDF ecosystems. We adopt a landscape genetic approach to understanding functional connectivity for leaf-toed geckos (Phyllodactylus tuberculosus) at multiple sites near the northernmost limit of this ecosystem at Alamos, Sonora, Mexico. Traditional analyses of population genetics are combined with multivariate GIS-based landscape analyses to test hypotheses on the potential drivers of spatial genetic variation. Moderate levels of within-population diversity and substantial levels of population differentiation are revealed by FST and Dest. Analyses using structure suggest the occurrence of from 2 to 9 genetic clusters depending on the model used. Landscape genetic analysis suggests that forest cover, stream connectivity, undisturbed habitat, slope, and minimum temperature of the coldest period explain more genetic variation than do simple Euclidean distances. Additional landscape genetic studies throughout TDF habitat are required to understand species-specific responses to landscape and climate change and to identify common drivers. We urge researchers interested in using multivariate distance methods to test for, and report, significant correlations among predictor matrices that can impact results, particularly when adopting least-cost path approaches. Further investigation into the use of information theoretic approaches for model selection is also warranted.

Geographic applications of ERTS-1 data to landscape change

NASA Technical Reports Server (NTRS)

Rehder, J. B.

1973-01-01

The analysis of landscape change requires large area coverage on a periodic basis in order to analyze aggregate changes over an extended period of time. To date, only the ERTS program can provide this capability. Three avenues of experimentation and analysis are being used in the investigation: (1) a multi-scale sampling procedure utilizing aircraft imagery for ground truth and control; (2) a densitometric and computer analytical experiment for the analysis of gray tone signatures, comparisons and ultimately for landscape change detection and monitoring; and (3) an ERTS image enhancement procedure for the detection and analysis of photomorphic regions.

Mapping the landscape of metabolic goals of a cell

DOE PAGES

Zhao, Qi; Stettner, Arion I.; Reznik, Ed; ...

2016-05-23

Here, genome-scale flux balance models of metabolism provide testable predictions of all metabolic rates in an organism, by assuming that the cell is optimizing a metabolic goal known as the objective function. We introduce an efficient inverse flux balance analysis (invFBA) approach, based on linear programming duality, to characterize the space of possible objective functions compatible with measured fluxes. After testing our algorithm on simulated E. coli data and time-dependent S. oneidensis fluxes inferred from gene expression, we apply our inverse approach to flux measurements in long-term evolved E. coli strains, revealing objective functions that provide insight into metabolic adaptationmore » trajectories.« less

A procedure of landscape services assessment based on mosaics of patches and boundaries.

PubMed

Martín de Agar, Pilar; Ortega, Marta; de Pablo, Carlos L

2016-09-15

We develop a procedure for assessing the environmental value of landscape mosaics that simultaneously considers the values of land use patches and the values of the boundaries between them. These boundaries indicate the ecological interactions between the patches. A landscape mosaic is defined as a set of patches and the boundaries between them and corresponds to a spatial pattern of ecological interactions. The procedure is performed in two steps: (i) an environmental assessment of land use patches by means of a function that integrates values based on the goods and services the patches provide, and (ii) an environmental valuation of mosaics using a function that integrates the environmental values of their patches and the types and frequencies of the boundaries between them. This procedure allows us to measure how changes in land uses or in their spatial arrangement cause variations in the environmental value of landscape mosaics and therefore in that of the whole landscape. The procedure was tested in the Sierra Norte of Madrid (central Spain). The results show that the environmental values of the landscape depend not only on the land use patches but also on the values associated with the pattern of the boundaries within the mosaics. The results also highlight the importance of the boundaries between land use patches as determinants of the goods and services provided by the landscape. Copyright © 2016 Elsevier Ltd. All rights reserved.

Critical thresholds in species` responses to landscape structure

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

With, K.A.; Crist, T.O.

1995-12-01

Critical thresholds are transition ranges across which small changes in spatial pattern produce abrupt shifts in ecological responses. Habitat fragmentation provides a familiar example of a critical threshold. As the landscape becomes dissected into smaller parcels of habitat. landscape connectivity-the functional linkage among habitat patches - may suddenly become disrupted, which may have important consequences for the distribution and persistence of populations. Landscape connectivity depends not only on the abundance and spatial patterning of habitat. but also on the habitat specificity and dispersal abilities of species. Habitat specialists with limited dispersal capabilities presumably have a much lower threshold to habitatmore » fragmentation than highly vagile species, which may perceive the landscape as functionally connected across a greater range of fragmentation severity. To determine where threshold effects in species, responses to landscape structure are likely to occur, a simulation model modified from percolation theory was developed. Our simulations predicted the distributional patterns of populations in different landscape mosaics, which we tested empirically using two grasshopper species (Orthoptera: Acrididae) that occur in the shortgrass prairie of north-central Colorado. The distribution of these two species in this grassland mosaic matched the predictions from our simulations. By providing quantitative predictions of threshold effects, this modelling approach may prove useful in the formulation of conservation strategies and assessment of land-use changes on species` distributional patterns and persistence.« less

Design, development, and application of LANDIS-II, a spatial landscape simulation model with flexible temporal and spatial resolution

Treesearch

Robert M. Scheller; James B. Domingo; Brian R. Sturtevant; Jeremy S. Williams; Arnold Rudy; Eric J. Gustafson; David J. Mladenoff

2007-01-01

We introduce LANDIS-II, a landscape model designed to simulate forest succession and disturbances. LANDIS-II builds upon and preserves the functionality of previous LANDIS forest landscape simulation models. LANDIS-II is distinguished by the inclusion of variable time steps for different ecological processes; our use of a rigorous development and testing process used...

Integrated analysis of RNA-binding protein complexes using in vitro selection and high-throughput sequencing and sequence specificity landscapes (SEQRS).

PubMed

Lou, Tzu-Fang; Weidmann, Chase A; Killingsworth, Jordan; Tanaka Hall, Traci M; Goldstrohm, Aaron C; Campbell, Zachary T

2017-04-15

RNA-binding proteins (RBPs) collaborate to control virtually every aspect of RNA function. Tremendous progress has been made in the area of global assessment of RBP specificity using next-generation sequencing approaches both in vivo and in vitro. Understanding how protein-protein interactions enable precise combinatorial regulation of RNA remains a significant problem. Addressing this challenge requires tools that can quantitatively determine the specificities of both individual proteins and multimeric complexes in an unbiased and comprehensive way. One approach utilizes in vitro selection, high-throughput sequencing, and sequence-specificity landscapes (SEQRS). We outline a SEQRS experiment focused on obtaining the specificity of a multi-protein complex between Drosophila RBPs Pumilio (Pum) and Nanos (Nos). We discuss the necessary controls in this type of experiment and examine how the resulting data can be complemented with structural and cell-based reporter assays. Additionally, SEQRS data can be integrated with functional genomics data to uncover biological function. Finally, we propose extensions of the technique that will enhance our understanding of multi-protein regulatory complexes assembled onto RNA. Copyright © 2016 Elsevier Inc. All rights reserved.

Impact of natural climate change and historical land use on vegetation cover and geomorphological process dynamics in the Serra dos Órgãos mountain range in Rio de Janeiro State, Brazil

NASA Astrophysics Data System (ADS)

Nehren, U.; Sattler, D.; Heinrich, J.

2010-03-01

The Serra dos Órgãos mountain range in the hinterland of Rio de Janeiro contains extensive remnants of the Atlantic Forest (Mata Atlântica) biome, which once covered about 1.5 million km² from Northeast to South Brazil and further inland to Paraguay and Argentina. As a result of historical deforestation and recent land use intensification processes today only 5 to 8% of the original Atlantic Forest remains. Despite the dramatic habitat loss and a high degree of forest fragmentation, the remnants are among the Earth’s most diverse habitats in terms of species richness. Furthermore, they are characterized by a high level of endemism. Therefore, the biome is considered a "hotspot of biodiversity". In the last years many efforts have been taken to investigate the Mata Atlântica biome in different spatial and time scales and from different scientific perspectives. We are working in the Atlantic Forest of Rio de Janeiro since 2004 and focus in our research particularly on Quaternary landscape evolution and landscape history. By means of landscape and soil archives we reconstruct changes in the landscape system, which are mainly the result of Quaternary climate variability, young tectonic uplift and human impact. The findings throw light on paleoecological conditions in the Late Quaternary and the impact of pre-colonial and colonial land use practices on these landscapes. In this context, a main focus is set on climate and human-driven changes of the vegetation cover and its consequences for the geomorphological process dynamics, in particular erosion and sedimentation processes. Research methods include geomorphological field studies, interpretation of satellite images, physical and chemical sediment and soil analyses as well as relative and absolute dating (Feo/Fed ratio and 14C dating). For the Late Quaternary landscape evolution, the findings are compared with results from paleoclimatic and paloecological investigations in Southeast and South Brazil using other dating techniques, such as pollen analysis. The impact of early civilizations on deforestation, forest fragmentation and geomorphological process dynamics is estimated on the basis of archaeological and anthropological findings. Furthermore, historical sources, such as written documents, maps, paintings and photographs, were collected and analysed to get a more detailed picture of the younger landscape history. As a result we present a landscape genetic model for the Late Quaternary in the Serra dos Órgãos mountain range and the Guanabara Basin. Based on a functional analysis of the natural process dynamics we reconstruct the human impact on the vegetation cover and related erosion and sedimentation processes in different time periods. According to this, the polycyclic climate fluctuations in the Pleistocene emerge as periods of stability and instability in the landscape system. During dry and cool periods of the Ice Ages forests drew back and erosion processes increased, causing higher erosion and deposition rates on slopes and stronger incision of river beds, accompanied by a deposition of gravels. The colluvial soils presently found in the mountain region were mainly deposited during the last instability period in the Late Pleistocene (Wisconsin) and Early Holocene. With the return of rainforests from their retreats under wetter climate conditions in the mid Holocene, slopes were stabilized under a dense vegetation cover. In the Late Holocene erosion conditions changed again with human deforestation and land use, which led to high erosion rates in the mountainous landscape. Concerning the human impact on rainforests and geomorphological process dynamics we give an overview of the pre-historical (Sambaqui, Tupi) and historical (colonial exploitation cycles) landscape transformation and degradation processes for different landscape units within the Serra dos Órgãos and its floodplains. The results not only give a detailed picture of historical land use patterns and landscape degradation processes, but also contribute to the understanding of recent changes in the landscape system. Thus, landscape genetic and historical analysis is essential for assessing the present landscape status with respect to degradation, stability, resilience and land use potentials, and moreover it is a reference for the development of future scenarios.

Sensitivity of landscape resistance estimates based on point selection functions to scale and behavioral state: Pumas as a case study

Treesearch

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

2014-01-01

Estimating landscape resistance to animal movement is the foundation for connectivity modeling, and resource selection functions based on point data are commonly used to empirically estimate resistance. In this study, we used GPS data points acquired at 5-min intervals from radiocollared pumas in southern California to model context-dependent point selection...

Geographic applications of ERTS-A imagery to rural landscape change

NASA Technical Reports Server (NTRS)

Rehder, J. B. (Principal Investigator)

1972-01-01

There are no author-identified significant results in this report. The study area, centered on Knoxville, Tennessee, encompasses nearly 20,000 square miles. The Knoxville Test Site, an 11 x 21 mile area over the city of Knoxville and the western portion of Knox County, has been chosen for the analysis of landscape change detection associated with urban growth. The second area, the Cumberland Plateau Test Site, exhibits landscape change through forest alterations and landform disturbances associated with strip mining in the area and was so chosen for its sharp contrasts in physical and human phenomena as well as its change dynamics. Accomplishments since reception of ERTS-1 imagery include: (1) basic cataloging and classifying of the data into a filling system; (2) a densitometer analysis; (3) first look analysis; and (4) preparation of results from the project. Examples of all four bands of the MSS have been received and analyses reveal distinctive positive and negative reactions. Band 5 has been found to be best for landscape analysis of contrasts between urban and rural landscapes, and band 7 for topographic features and water surfaces. Preliminary results are summarized.

Landscape features impact connectivity between soil populations: a comparative study of gene flow in earthworms.

PubMed

Dupont, L; Torres-Leguizamon, M; René-Corail, P; Mathieu, J

2017-06-01

Landscape features are known to alter the spatial genetic variation of aboveground organisms. Here, we tested the hypothesis that the genetic structure of belowground organisms also responds to landscape structure. Microsatellite markers were used to carry out a landscape genetic study of two endogeic earthworm species, Allolobophora chlorotica (N = 440, eight microsatellites) and Aporrectodea icterica (N = 519, seven microsatellites), in an agricultural landscape in the North of France, where landscape features were characterized with high accuracy. We found that habitat fragmentation impacted genetic variation of earthworm populations at the local scale. A significant relationship was observed between genetic diversity (H e , A r ) and several landscape features in A. icterica populations and A. chlorotica. Moreover, a strong genetic differentiation between sites was observed in both species, with a low degree of genetic admixture and high F st values. The landscape connectivity analysis at the regional scale, including isolation by distance, least-cost path and cost-weighted distance approaches, showed that genetic distances were linked to landscape connectivity in A. chlorotica. This indicates that the fragmentation of natural habitats has shaped their dispersal patterns and local effective population sizes. Landscape connectivity analysis confirmed that a priori favourable habitats such as grasslands may constitute dispersal corridors for these species. © 2017 John Wiley & Sons Ltd.

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.

Landscape metrics for three-dimension urban pattern recognition

NASA Astrophysics Data System (ADS)

Liu, M.; Hu, Y.; Zhang, W.; Li, C.

2017-12-01

Understanding how landscape pattern determines population or ecosystem dynamics is crucial for managing our landscapes. Urban areas are becoming increasingly dominant social-ecological systems, so it is important to understand patterns of urbanization. Most studies of urban landscape pattern examine land-use maps in two dimensions because the acquisition of 3-dimensional information is difficult. We used Brista software based on Quickbird images and aerial photos to interpret the height of buildings, thus incorporating a 3-dimensional approach. We estimated the feasibility and accuracy of this approach. A total of 164,345 buildings in the Liaoning central urban agglomeration of China, which included seven cities, were measured. Twelve landscape metrics were proposed or chosen to describe the urban landscape patterns in 2- and 3-dimensional scales. The ecological and social meaning of landscape metrics were analyzed with multiple correlation analysis. The results showed that classification accuracy compared with field surveys was 87.6%, which means this method for interpreting building height was acceptable. The metrics effectively reflected the urban architecture in relation to number of buildings, area, height, 3-D shape and diversity aspects. We were able to describe the urban characteristics of each city with these metrics. The metrics also captured ecological and social meanings. The proposed landscape metrics provided a new method for urban landscape analysis in three dimensions.

[Application of land economic ecological niche in landscape pattern analysis at county level: A case study of Jinghe County in Xinjiang, China].

PubMed

Yu, Hai-yang; Zhang, Fei; Wang, Juan; Zhou, Mei

2015-12-01

The theory of land economic ecological niche was used to analyze the regional landscape pattern in this article, with an aim to provide a new method for the characterization and representation of landscape pattern. The Jinghe County region, which is ecologically fragile, was selected as an example for the study, and the Landsat images of 1990, 1998, 2011 and 2013 were selected as remote sensing data. The land economic ecological niche of land use types calculated by ecostate-ecorole theory, combined with landscape ecology theory, was discussed in application of land economic ecological niche in county landscape pattern analysis. The results showed that, during the study period, the correlations between land economic ecological niche of farmland, construction land, and grassland with the parameters, including landscape patch number (NP), aggregated index (AI), fragmented index (FN) and fractal dimension (FD), were significant. Regional landscape was driven by the changes of land economic ecological niche, and the trend of economic development could be represented by land economic ecological niche change in Jinghe County. Land economic ecological niche was closely related with the land use types which could yield direct economic benefits, which could well explain the landscape pattern characteristics in Jinghe County when combined with the landscape indices.

Understanding the Factors that Influence Perceptions of Post-Wildfire Landscape Recovery Across 25 Wildfires in the Northwestern United States.

PubMed

Kooistra, C; Hall, T E; Paveglio, T; Pickering, M

2018-01-01

Disturbances such as wildfire are important features of forested landscapes. The trajectory of changes following wildfires (often referred to as landscape recovery) continues to be an important research topic among ecologists and wildfire scientists. However, the landscape recovery process also has important social dimensions that may or may not correspond to ecological or biophysical perspectives. Perceptions of landscape recovery may affect people's attitudes and behaviors related to forest and wildfire management. We explored the variables that influence people's perceptions of landscape recovery across 25 fires that occurred in 2011 or 2012 in the United States of Washington, Oregon, Idaho, and Montana and that represented a range of fire behavior characteristics and landscape impacts. Residents near each of the 25 fires were randomly selected to receive questionnaires about their experiences with the nearby fire, including perceived impacts and how the landscape had recovered since the fire. People generally perceived landscapes as recovering, even though only one to two years had passed. Regression analysis suggested that perceptions of landscape recovery were positively related to stronger beliefs about the ecological role of fire and negatively related to loss of landscape attachment, concern about erosion, increasing distance from the fire perimeter, and longer lasting fires. Hierarchical linear modeling (HLM) analysis indicated that the above relationships were largely consistent across fires. These findings highlight that perceptions of post-fire landscape recovery are influenced by more than vegetation changes and include emotional and cognitive factors. We discuss the management implications of these findings.

Understanding the Factors that Influence Perceptions of Post-Wildfire Landscape Recovery Across 25 Wildfires in the Northwestern United States

NASA Astrophysics Data System (ADS)

Kooistra, C.; Hall, T. E.; Paveglio, T.; Pickering, M.

2018-01-01

Disturbances such as wildfire are important features of forested landscapes. The trajectory of changes following wildfires (often referred to as landscape recovery) continues to be an important research topic among ecologists and wildfire scientists. However, the landscape recovery process also has important social dimensions that may or may not correspond to ecological or biophysical perspectives. Perceptions of landscape recovery may affect people's attitudes and behaviors related to forest and wildfire management. We explored the variables that influence people's perceptions of landscape recovery across 25 fires that occurred in 2011 or 2012 in the United States of Washington, Oregon, Idaho, and Montana and that represented a range of fire behavior characteristics and landscape impacts. Residents near each of the 25 fires were randomly selected to receive questionnaires about their experiences with the nearby fire, including perceived impacts and how the landscape had recovered since the fire. People generally perceived landscapes as recovering, even though only one to two years had passed. Regression analysis suggested that perceptions of landscape recovery were positively related to stronger beliefs about the ecological role of fire and negatively related to loss of landscape attachment, concern about erosion, increasing distance from the fire perimeter, and longer lasting fires. Hierarchical linear modeling (HLM) analysis indicated that the above relationships were largely consistent across fires. These findings highlight that perceptions of post-fire landscape recovery are influenced by more than vegetation changes and include emotional and cognitive factors. We discuss the management implications of these findings.

The landscape context of cereal aphid–parasitoid interactions

PubMed Central

Thies, Carsten; Roschewitz, Indra; Tscharntke, Teja

2005-01-01

Analyses at multiple spatial scales may show how important ecosystem services such as biological control are determined by processes acting on the landscape scale. We examined cereal aphid–parasitoid interactions in wheat fields in agricultural landscapes differing in structural complexity (32–100% arable land). Complex landscapes were associated with increased aphid mortality resulting from parasitism, but also with higher aphid colonization, thereby counterbalancing possible biological control by parasitoids and lastly resulting in similar aphid densities across landscapes. Thus, undisturbed perennial habitats appeared to enhance both pests and natural enemies. Analyses at multiple spatial scales (landscape sectors of 0.5–6 km diameter) showed that correlations between parasitism and percentage of arable land were significant at scales of 0.5–2 km, whereas aphid densities responded to percentage of arable land at scales of 1–6 km diameter. Hence, the higher trophic level populations appeared to be determined by smaller landscape sectors owing to dispersal limitation, showing the ‘functional spatial scale’ for species-specific landscape management. PMID:15695212

Effects of Hydrocarbon Extraction on Landscapes of the Appalachian Basin

USGS Publications Warehouse

Slonecker, Terry E.; Milheim, Lesley E.; Roig-Silva, Coral M.; Kalaly, Siddiq S.

2015-09-30

The need for energy resources has created numerous economic opportunities for hydrocarbon extraction in the Appalachian basin. The development of alternative energy natural gas resources from deep-shale drilling techniques, along with conventional natural gas extraction methods, has created a flurry of wells, roads, pipelines, and related infrastructure across many parts of the region. An unintended and sometimes overlooked consequence of these activities is their effect on the structure and function of the landscape and ecosystems. The collective effect of over 100,000 hydrocarbon extraction permits for oil, coal bed methane, Marcellus and Utica Shale natural gas wells, and other types of hydrocarbon gases and their associated infrastructure has saturated much of the landscape and disturbed the natural environment in the Appalachian basin. The disturbance created by the sheer magnitude of the development of these collective wells and infrastructure directly affects how the landscape and ecosystems function and how they provide ecological goods and services. 

Contrasting watershed-scale trends in runoff and sediment yield complicate rangeland water resources planning

NASA Astrophysics Data System (ADS)

Berg, Matthew D.; Marcantonio, Franco; Allison, Mead A.; McAlister, Jason; Wilcox, Bradford P.; Fox, William E.

2016-06-01

Rangelands cover a large portion of the earth's land surface and are undergoing dramatic landscape changes. At the same time, these ecosystems face increasing expectations to meet growing water supply needs. To address major gaps in our understanding of rangeland hydrologic function, we investigated historical watershed-scale runoff and sediment yield in a dynamic landscape in central Texas, USA. We quantified the relationship between precipitation and runoff and analyzed reservoir sediment cores dated using cesium-137 and lead-210 radioisotopes. Local rainfall and streamflow showed no directional trend over a period of 85 years, resulting in a rainfall-runoff ratio that has been resilient to watershed changes. Reservoir sedimentation rates generally were higher before 1963, but have been much lower and very stable since that time. Our findings suggest that (1) rangeland water yields may be stable over long periods despite dramatic landscape changes while (2) these same landscape changes influence sediment yields that impact downstream reservoir storage. Relying on rangelands to meet water needs demands an understanding of how these dynamic landscapes function and a quantification of the physical processes at work.

Calculating landscape surface area from digital elevation models

Treesearch

Jeff S. Jenness

2004-01-01

There are many reasons to want to know the true surface area of the landscape, especially in landscape analysis and studies of wildlife habitat. Surface area provides a better estimate of the land area available to an animal than planimetric area, and the ratio of this surface area to planimetric area provides a useful measure of topographic roughness of the landscape...

Analysis of Landscape Structure in the Southeastern Missouri Ozarks

Treesearch

Ming Xu; Sari C. Saunders; Jiquan. Chen

1997-01-01

We characterized the landscape structure within and surrounding the MOFEP study sites using Landsat TM data and GIS databases. Up to 31 percent of the landscape was within Iiparian zones. Road density was 1.4 km/km2 within the landscape but reached 2.0 km/km2 within 40-m stream buffers. More than 99 percent of the region...

[Landscape and ecological genomics].

PubMed

Tetushkin, E Ia

2013-10-01

Landscape genomics is the modern version of landscape genetics, a discipline that arose approximately 10 years ago as a combination of population genetics, landscape ecology, and spatial statistics. It studies the effects of environmental variables on gene flow and other microevolutionary processes that determine genetic connectivity and variations in populations. In contrast to population genetics, it operates at the level of individual specimens rather than at the level of population samples. Another important difference between landscape genetics and genomics and population genetics is that, in the former, the analysis of gene flow and local adaptations takes quantitative account of landforms and features of the matrix, i.e., hostile spaces that separate species habitats. Landscape genomics is a part of population ecogenomics, which, along with community genomics, is a major part of ecological genomics. One of the principal purposes of landscape genomics is the identification and differentiation of various genome-wide and locus-specific effects. The approaches and computation tools developed for combined analysis of genomic and landscape variables make it possible to detect adaptation-related genome fragments, which facilitates the planning of conservation efforts and the prediction of species' fate in response to expected changes in the environment.

Spatially Explicit Analysis of Metal Transfer to Biota: Influence of Soil Contamination and Landscape

PubMed Central

Fritsch, Clémentine; Cœurdassier, Michaël; Giraudoux, Patrick; Raoul, Francis; Douay, Francis; Rieffel, Dominique; de Vaufleury, Annette; Scheifler, Renaud

2011-01-01

Concepts and developments for a new field in ecotoxicology, referred to as “landscape ecotoxicology,” were proposed in the 1990s; however, to date, few studies have been developed in this emergent field. In fact, there is a strong interest in developing this area, both for renewing the concepts and tools used in ecotoxicology as well as for responding to practical issues, such as risk assessment. The aim of this study was to investigate the spatial heterogeneity of metal bioaccumulation in animals in order to identify the role of spatially explicit factors, such as landscape as well as total and extractable metal concentrations in soils. Over a smelter-impacted area, we studied the accumulation of trace metals (TMs: Cd, Pb and Zn) in invertebrates (the grove snail Cepaea sp and the glass snail Oxychilus draparnaudi) and vertebrates (the bank vole Myodes glareolus and the greater white-toothed shrew Crocidura russula). Total and CaCl2-extractable concentrations of TMs were measured in soils from woody patches where the animals were captured. TM concentrations in animals exhibited a high spatial heterogeneity. They increased with soil pollution and were better explained by total rather than CaCl2-extractable TM concentrations, except in Cepaea sp. TM levels in animals and their variations along the pollution gradient were modulated by the landscape, and this influence was species and metal specific. Median soil metal concentrations (predicted by universal kriging) were calculated in buffers of increasing size and were related to bioaccumulation. The spatial scale at which TM concentrations in animals and soils showed the strongest correlations varied between metals, species and landscapes. The potential underlying mechanisms of landscape influence (community functioning, behaviour, etc.) are discussed. Present results highlight the need for the further development of landscape ecotoxicology and multi-scale approaches, which would enhance our understanding of pollutant transfer and effects in ecosystems. PMID:21655187

DEM-based analysis of landscape organization: 2) Application to catchment comparison

NASA Astrophysics Data System (ADS)

Seibert, J.; McGlynn, B.

2003-04-01

The delineation of homogeneous landscape elements (or "hydrologic response units") is often a prerequisite in field investigations and the application of semi-distributed hydrologic (or coupled hydrologic and biogeochemical) models. Delineation and quantification of dominant landscape elements requires methods to extract the features from digital elevation data or other readily available information. It is often assumed that hillslope and riparian areas constitute the two most important and identifiable landscape units contributing to catchment runoff in upland humid catchments. In addition, we have found that that the degree of hillslope water expression in stormflow is partially a function of riparian to hillslope reservoir ratios and landscape organization. Therefore, we developed a simple approach for quantifying landscape organization and distributed riparian to hillslope area ratios (riparian buffer ratios), as described in the accompanying contribution. Here we use this method as a framework for comparing and classifying diverse catchments located in Europe, the U.S., and New Zealand. Based on the three catchments Maimai (New Zealand), Panola (Georgia) and Sleepers (Vermont) we obtained the following preliminary results: (1) Local area entering the stream channels was most variable at Maimai and consistently diffuse at Sleepers and Panola. Also the median local area entering the channel network was largest at Maimai and smallest at Sleepers and Panola. This demonstrates the degree of landscape dissection (highest for Maimai) and the concentration of hillslope inputs along the stream network. (2) Riparian areas were smallest at Maimai, larger at Sleepers, and largest at Panola. The combination of riparian zone extent and focused (Maimai) versus diffuse (Sleepers and Panola) hillslope inputs to riparian zones controls local riparian to hillslope area ratios (riparian buffer capacities). (3) Area was accumulated to a large extend in the channel heads in all catchments. At Sleepers about 75 percent of all area originated from sub-catchments of less than 5 ha, whereas this proportion was 50 and 40 percent at Panola and Maimai respectively.

Energy landscapes for machine learning

NASA Astrophysics Data System (ADS)

Ballard, Andrew J.; Das, Ritankar; Martiniani, Stefano; Mehta, Dhagash; Sagun, Levent; Stevenson, Jacob D.; Wales, David J.

Machine learning techniques are being increasingly used as flexible non-linear fitting and prediction tools in the physical sciences. Fitting functions that exhibit multiple solutions as local minima can be analysed in terms of the corresponding machine learning landscape. Methods to explore and visualise molecular potential energy landscapes can be applied to these machine learning landscapes to gain new insight into the solution space involved in training and the nature of the corresponding predictions. In particular, we can define quantities analogous to molecular structure, thermodynamics, and kinetics, and relate these emergent properties to the structure of the underlying landscape. This Perspective aims to describe these analogies with examples from recent applications, and suggest avenues for new interdisciplinary research.

Economic Growth and Landscape Change

USGS Publications Warehouse

Prato, Tony; Fagre, Dan

2007-01-01

Sustaining Rocky Mountain Landscapes provides a scientific basis for communities to develop policies for managing the growth and economic transformation of the CCE without sacrificing the quality of life and environment for which the land is renowned. This forthcoming edited volume focuses on five aspects of sustaining mountain landscapes in the CCE and similar regions in the Rocky Mountains. The five aspects are: 1) how social, economic, demographic and environmental forces are transforming ecosystem structure and function, 2) trends in use and conditions for human and environmental resources, 3) activating science, policy and education to enhance sustainable landscape management, 4) challenges to sustainable management of public and private lands, and 5) future prospects for achieving sustainable landscapes.

Dimensions of landscape preferences from pairwise comparisons

Treesearch

F. González Bernaldez; F. Parra

1979-01-01

Analysis of landscape preferences allows the detection of major dimensions as:(1) the opposition between "natural and humanized", (comprising features like vegetation cover, cultivation, pattern of landscape elements, artifacts, excavations, etc.); (2) polarity "precision/ambiguity" (involving opposition between: predominance of straight, vertical...

The clinical trial landscape in oncology and connectivity of somatic mutational profiles to targeted therapies.

PubMed

Patterson, Sara E; Liu, Rangjiao; Statz, Cara M; Durkin, Daniel; Lakshminarayana, Anuradha; Mockus, Susan M

2016-01-16

Precision medicine in oncology relies on rapid associations between patient-specific variations and targeted therapeutic efficacy. Due to the advancement of genomic analysis, a vast literature characterizing cancer-associated molecular aberrations and relative therapeutic relevance has been published. However, data are not uniformly reported or readily available, and accessing relevant information in a clinically acceptable time-frame is a daunting proposition, hampering connections between patients and appropriate therapeutic options. One important therapeutic avenue for oncology patients is through clinical trials. Accordingly, a global view into the availability of targeted clinical trials would provide insight into strengths and weaknesses and potentially enable research focus. However, data regarding the landscape of clinical trials in oncology is not readily available, and as a result, a comprehensive understanding of clinical trial availability is difficult. To support clinical decision-making, we have developed a data loader and mapper that connects sequence information from oncology patients to data stored in an in-house database, the JAX Clinical Knowledgebase (JAX-CKB), which can be queried readily to access comprehensive data for clinical reporting via customized reporting queries. JAX-CKB functions as a repository to house expertly curated clinically relevant data surrounding our 358-gene panel, the JAX Cancer Treatment Profile (JAX CTP), and supports annotation of functional significance of molecular variants. Through queries of data housed in JAX-CKB, we have analyzed the landscape of clinical trials relevant to our 358-gene targeted sequencing panel to evaluate strengths and weaknesses in current molecular targeting in oncology. Through this analysis, we have identified patient indications, molecular aberrations, and targeted therapy classes that have strong or weak representation in clinical trials. Here, we describe the development and disseminate system methods for associating patient genomic sequence data with clinically relevant information, facilitating interpretation and providing a mechanism for informing therapeutic decision-making. Additionally, through customized queries, we have the capability to rapidly analyze the landscape of targeted therapies in clinical trials, enabling a unique view into current therapeutic availability in oncology.

Rare ecomorphological convergence on a complex adaptive landscape: Body size and diet mediate evolution of jaw shape in squirrels (Sciuridae).

PubMed

Zelditch, Miriam Leah; Ye, Ji; Mitchell, Jonathan S; Swiderski, Donald L

2017-03-01

Convergence is widely regarded as compelling evidence for adaptation, often being portrayed as evidence that phenotypic outcomes are predictable from ecology, overriding contingencies of history. However, repeated outcomes may be very rare unless adaptive landscapes are simple, structured by strong ecological and functional constraints. One such constraint may be a limitation on body size because performance often scales with size, allowing species to adapt to challenging functions by modifying only size. When size is constrained, species might adapt by changing shape; convergent shapes may therefore be common when size is limiting and functions are challenging. We examine the roles of size and diet as determinants of jaw shape in Sciuridae. As expected, size and diet have significant interdependent effects on jaw shape and ecomorphological convergence is rare, typically involving demanding diets and limiting sizes. More surprising is morphological without ecological convergence, which is equally common between and within dietary classes. Those cases, like rare ecomorphological convergence, may be consequences of evolving on an adaptive landscape shaped by many-to-many relationships between ecology and function, many-to-one relationships between form and performance, and one-to-many relationships between functionally versatile morphologies and ecology. On complex adaptive landscapes, ecological selection can yield different outcomes. © 2017 The Author(s). Evolution © 2017 The Society for the Study of Evolution.

Proceedings of our national landscape: a conference on applied techniques for analysis and management of the visual resource [Incline Village, Nev., April 23-25, 1979

Treesearch

Gary H. Elsner; Richard C. Smardon; technical coordinators

1979-01-01

These 104 papers were presented at "Our National Landscape: A Conference on Applied Techniques for Analysis and Management of the Visual Resource," Incline Village, Nevada, April 23-25, 1979. Included in this proceedings are state-of-the-art papers on landscape planning. Emphasis is upon planning the visual aspects of the large and wildland areas of the...

[Impact of traditionally managed forest units on the landscape connectivity of Sierra de Los Tuxtlas, Mexico].

PubMed

Aguilar Vásquez, Yunin; Aliphat Fernández, Mario Manuel; Caso Barrera, Laura; Del Amo Rodríguez, Silvia; Sánchez Gómez, Maria De Lourdes; Martínez-Carrera, Daniel

2014-09-01

The ever-increasing establishment of landscape mosaics is expressed as a surrounding matrix of agricultural activities, which frames patches or remnants of the original vegetation cover. Conservation actions should be aimed to establish or to increase those interactive systems, which help to maintain the land- scape flow through linkages. Spaces occupied by traditional management systems retain and support this func- tion. In this paper, we used Geographic Information Systems to evaluate the importance of traditionally managed forest units ('acahuales'-coffee plantations) and to assess landscape connectivity in the indigenous Popoluca area of Sierra de los Tuxtlas, Mexico. The cartographic material used to establish the types of vegetation and their coverture included the period 1991-2008. At landscape level, four indices were used to assess the general situation of the habitat network, and to identify the patches of high priority. Individually, indices evaluated if patches were important for their area, their potential flow or their connecting function. Results showed that the landscape is functioning as a single system, but having low connectivity. Values improved when traditionally managed forest patches were considered as viable habitat. We detected 367 patches of very high priority, 80% belonging to forests managed traditionally. Patches were important for their potential flow (size and topologi- cal relationships). Only 70 patches were significant for their function as biological corridors between largest forests located at the top of the volcanoes, and are mostly managed forest (75%). We concluded that the units of traditionally managed forest play a significant role in landscape connectivity maintenance.

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.

A Study on the Campus Landscape Design of the National University of Singapore

NASA Astrophysics Data System (ADS)

Lin, Lusheng; Dong, Ya

2018-01-01

In this paper, we analyzed the functions, structure, layout, landscape and engineering measure of the campus of NUS by the way of such research methods as present situation research, interview and comparative study. And we get the spatial characteristics of landscape environment affected by political economy, human geography, geographical conditions which will provide a new perspective for building international, modern, high-level research universities.

Fundamental Study about the Landscape Estimation and Analysis by CG

NASA Astrophysics Data System (ADS)

Nakashima, Yoshio; Miyagoshi, Takashi; Takamatsu, Mamoru; Sassa, Kazuhiro

In recent years, the color of advertising signboards or vending machines on the streets should be harmonized with the surrounding landscape. In this study, we investigated how the colors (red and white) of the vending machines virtually installed by CG would affect the traditional landscape. 20 subjects estimated landscape samples in Hida-Furukawa by the SD technique. The result of our experiment shows that the vending machines have great influence on the surrounding landscape. On the other hand, we have confirmed that they can harmonize with the circumference landscape by the color to use.

Approaches to integrating indicators into 3D landscape visualisations and their benefits for participative planning situations.

PubMed

Wissen, Ulrike; Schroth, Olaf; Lange, Eckart; Schmid, Willy A

2008-11-01

In discussing issues of landscape change, the complex relationships in the landscape have to be assessed. In participative planning processes, 3D visualisations have a high potential as an aid in understanding and communicating characteristics of landscape conditions by integrating visual and non-visual landscape information. Unclear is, which design and how much interactivity is required for an indicator visualisation that would suit stakeholders best in workshop situations. This paper describes the preparation and application of three different types of integrated 3D visualisations in workshops conducted in the Entlebuch UNESCO Biosphere Reserve (CH). The results reveal that simple representations of a complex issue created by draping thematic maps on the 3D model can make problematic developments visible at a glance; that diagrams linked to the spatial context can help draw attention to problematic relationships not considered beforehand; and that the size of species as indicators of conditions of the landscape's production and biotope function seems to provide a common language for stakeholders with different perspectives. Overall, the of the indicators the functions required to assist in information processing. Further research should focus on testing the effectiveness of the integrated visualisation tools in participative processes for the general public.

[Dynamic evaluation on landscape connectivity of ecological land: a case study of Shenzhen, Guangdong Province of South China].

PubMed

Wu, Jian-Sheng; Liu, Hong-Meng; Huang, Xiu-Lan; Feng, Zhe

2012-09-01

Ecological land is the most crucial and sensitive land use type in rapidly urbanizing areas. Landscape connectivity can help us to better understand the interactions between landscape structure and landscape function. By using the land use data of Shenzhen from 1996 to 2008 and the graph theory- based integral index of connectivity (IIC), probability index of connectivity (PC), and importance value of patches (dPC), a dynamic evaluation on the landscape connectivity of ecological land in the City was conducted, and a spatial assessment was made to identify the most important patches for maintaining overall landscape connectivity. In combining with the basic ecological controlling line in Shenzhen, the variations of the landscape connectivity of the ecological land inside and outside the basic ecological controlling line were evaluated. From 1996 to 2008, the overall landscape connectivity of the ecological land in Shenzhen displayed a downward trend, the importance and the spatial distribution of the important patches for maintaining the overall landscape connectivity changed, and the basic ecological controlling line played definite roles in maintaining the landscape connectivity of ecological land inside the line.

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

Landscape Conservation of Aquatic Habitats Promotes Watershed-scale Biological, Biogeochemical, and Hydrological Functions

EPA Science Inventory

Wetlands are exceptionally productive landscape features that provide critical habitat for endemic species, threatened/endangered and migratory animals, store floodwaters and maintain baseflows in stream systems, recharge groundwaters, and biogeochemically and physically affect n...

Vulnerability of Oregon hydrologic landscapes and streamflow to climate change

EPA Science Inventory

Hydrologic classification systems can provide a basis for broadscale assessments of the hydrologic functions of landscapes and watersheds and their responses to stressors. Such assessments could be particularly useful in determining hydrologic vulnerability from climate change. ...

A gradient analysis on urban sprawl and urban landscape pattern between 1985 and 2000 in the Pearl River Delta, China

NASA Astrophysics Data System (ADS)

Dai, Erfu; Wu, Zhuo; Du, Xiaodian

2017-04-01

Urbanization is an irreversible trend worldwide, especially in rapidly developing China. Accelerated urbanization has resulted in rapid urban sprawl and urban landscape pattern changes. Quantifying the spatiotemporal dynamics of urban land use and landscape pattern not only can reveal the characteristics of social transfer and economic development, but also can provide insights into the driving mechanisms of land use changes. In this study, we integrated remote sensing (RS), geographic information system (GIS), landscape metrics, and gradient analysis to quantitatively compare the spatiotemporal dynamics of land use, urban sprawl, and landscape pattern for nine cities in the Pearl River Delta from 1985‒2000. For the whole study region, urbanization was obvious. The results show an increase in urban buildup land and shrinkage of cropland in the Pearl River Delta. However, the nine cities differed greatly in terms of the process and magnitude of urban sprawl for both the spatial and temporal dimensions. This was most evident for the cities of Guangzhou and Shenzhen. Gradient analysis on urban landscape changes could deepen understanding of the stages of urban development and provide a scientific foundation for future urban planning and land management strategies in China.

Multiscale assessment of landscape structure in heterogeneous forested area

NASA Astrophysics Data System (ADS)

Simoniello, T.; Pignatti, S.; Carone, M. T.; Fusilli, L.; Lanfredi, M.; Coppola, R.; Santini, F.

2010-05-01

The characterization of landscape structure in space or time is fundamental to infer ecological processes (Ingegnoli, 2002). Landscape pattern arrangements strongly influence forest ecological functioning and biodiversity, as an example landscape fragmentation can induce habitat degradation reducing forest species populations or limiting their recolonization. Such arrangements are spatially correlated and scale-dependent, therefore they have distinctive operational-scales at which they can be best characterized (Wu, 2004). In addition, the detail of the land cover classification can have substantial influences on resulting pattern quantification (Greenberg et al.2001). In order to evaluate the influence of the observational scales and labelling details, we investigated a forested area (Pollino National Park; southern Italy) by analyzing the patch arrangement derived from three remote sensing sensors having different spectral and spatial resolutions. In particular, we elaborated data from the hyperspectral MIVIS (102 bands; ~7m) and Hyperion (220 bands; 30m), and the multispectral Landsat-TM (7 bands; 30m). Moreover, to assess the landscape evolution we investigated the hierarchical structure of the study area (landscape, class, patch) by elaborating two Landsat-TM acquired in 1987 and 1998. Preprocessed data were classified by adopting a supervised procedure based on the Minimum Distance classifier. The obtained labelling correspond to Corine level 5 for the high resolution MIVIS data, to Corine level 4 for Hyperion and to an intermediate level 4-3 for TM data. The analysis was performed by taking into account patch density, diversity and evenness at landscape level; mean patch size and interdispersion at class level; patch structure and perimeter regularity at patch level. The three sensors described a landscape with a quite high level of richness and distribution. The high spectral and spatial resolution of MIVIS data provided the highest diversity level (SHDI = 2.05), even if the results obtained for TM were not so different (1.93), Hyperion showed the lowest value (1.79). The obtained evenness index was similar for all the landscapes (~ 0.72). At class level, the interdispersion increases as the spatial and spectral resolution power decrease. Due to the low labelling detail, TM classes represent an aggregation of MIVIS and Hyperion classes; therefore they result larger and more diffused over the territory favouring higher interspersion values in the computation. The investigation of the patch structure highlighted the highest MIVIS capability in describing the patch articulation; Hyperion and TM showed quite similar situation. The historical analysis based on TM imagery showed a fragmentation process for some forested patches (mainly beeches): an increase of structure complexity (higher FRACT) is coupled with a higher patch number and an extension reduction. On the whole, the obtained results showed that the multispectral Landsat-TM images represent a good data source for supporting studies on landscape structure of forested areas and that for analyzing the articulation of particular species the high spectral resolution needs to be coupled with a high spatial resolution, i.e. Hyperion sampling is not adequate for such a purpose.

Fire risk in the road landscape patterns of the state of Paraná, Brazil - planning grants for the wildland-urban interface

Treesearch

Daniela Biondi; Antonio Carlos Batista; Angeline Martini

2013-01-01

Urban growth worldwide has generated great concern in the planning of the different environments belonging to the wildland-urban interface. One of the problems that arise is the landscape treatment given to roads, which must not only comply with aesthetic and ecological principles, but also be functional, adding functions relating to forest fire prevention and control...

Using IBMs to Investigate Spatially-dependent Processes in Landscape Genetics Theory

EPA Science Inventory

Much of landscape and conservation genetics theory has been derived using non-spatialmathematical models. Here, we use a mechanistic, spatially-explicit, eco-evolutionary IBM to examine the utility of this theoretical framework in landscapes with spatial structure. Our analysis...

Dynamics of Hierarchical Urban Green Space Patches and Implications for Management Policy.

PubMed

Yu, Zhoulu; Wang, Yaohui; Deng, Jinsong; Shen, Zhangquan; Wang, Ke; Zhu, Jinxia; Gan, Muye

2017-06-06

Accurately quantifying the variation of urban green space is the prerequisite for fully understanding its ecosystem services. However, knowledge about the spatiotemporal dynamics of urban green space is still insufficient due to multiple challenges that remain in mapping green spaces within heterogeneous urban environments. This paper uses the city of Hangzhou to demonstrate an analysis methodology that integrates sub-pixel mapping technology and landscape analysis to fully investigate the spatiotemporal pattern and variation of hierarchical urban green space patches. Firstly, multiple endmember spectral mixture analysis was applied to time series Landsat data to derive green space coverage at the sub-pixel level. Landscape metric analysis was then employed to characterize the variation pattern of urban green space patches. Results indicate that Hangzhou has experienced a significant loss of urban greenness, producing a more fragmented and isolated vegetation landscape. Additionally, a remarkable amelioration of urban greenness occurred in the city core from 2002 to 2013, characterized by the significant increase of small-sized green space patches. The green space network has been formed as a consequence of new urban greening strategies in Hangzhou. These strategies have greatly fragmented the built-up areas and enriched the diversity of the urban landscape. Gradient analysis further revealed a distinct pattern of urban green space landscape variation in the process of urbanization. By integrating both sub-pixel mapping technology and landscape analysis, our approach revealed the subtle variation of urban green space patches which are otherwise easy to overlook. Findings from this study will help us to refine our understanding of the evolution of heterogeneous urban environments.

Dynamics of Hierarchical Urban Green Space Patches and Implications for Management Policy

PubMed Central

Yu, Zhoulu; Wang, Yaohui; Deng, Jinsong; Shen, Zhangquan; Wang, Ke; Zhu, Jinxia; Gan, Muye

2017-01-01

Accurately quantifying the variation of urban green space is the prerequisite for fully understanding its ecosystem services. However, knowledge about the spatiotemporal dynamics of urban green space is still insufficient due to multiple challenges that remain in mapping green spaces within heterogeneous urban environments. This paper uses the city of Hangzhou to demonstrate an analysis methodology that integrates sub-pixel mapping technology and landscape analysis to fully investigate the spatiotemporal pattern and variation of hierarchical urban green space patches. Firstly, multiple endmember spectral mixture analysis was applied to time series Landsat data to derive green space coverage at the sub-pixel level. Landscape metric analysis was then employed to characterize the variation pattern of urban green space patches. Results indicate that Hangzhou has experienced a significant loss of urban greenness, producing a more fragmented and isolated vegetation landscape. Additionally, a remarkable amelioration of urban greenness occurred in the city core from 2002 to 2013, characterized by the significant increase of small-sized green space patches. The green space network has been formed as a consequence of new urban greening strategies in Hangzhou. These strategies have greatly fragmented the built-up areas and enriched the diversity of the urban landscape. Gradient analysis further revealed a distinct pattern of urban green space landscape variation in the process of urbanization. By integrating both sub-pixel mapping technology and landscape analysis, our approach revealed the subtle variation of urban green space patches which are otherwise easy to overlook. Findings from this study will help us to refine our understanding of the evolution of heterogeneous urban environments. PMID:28587309

The visual-landscape analysis during the integration of high-rise buildings within the historic urban environment

NASA Astrophysics Data System (ADS)

Akristiniy, Vera A.; Dikova, Elena A.

2018-03-01

The article is devoted to one of the types of urban planning studies - the visual-landscape analysis during the integration of high-rise buildings within the historic urban environment for the purposes of providing pre-design and design studies in terms of preserving the historical urban environment and the implementation of the reconstructional resource of the area. In the article formed and systematized the stages and methods of conducting the visual-landscape analysis taking into account the influence of high-rise buildings on objects of cultural heritage and valuable historical buildings of the city. Practical application of the visual-landscape analysis provides an opportunity to assess the influence of hypothetical location of high-rise buildings on the perception of a historically developed environment and optimal building parameters. The contents of the main stages in the conduct of the visual - landscape analysis and their key aspects, concerning the construction of predicted zones of visibility of the significant historically valuable urban development objects and hypothetically planned of the high-rise buildings are revealed. The obtained data are oriented to the successive development of the planning and typological structure of the city territory and preservation of the compositional influence of valuable fragments of the historical environment in the structure of the urban landscape. On their basis, an information database is formed to determine the permissible urban development parameters of the high-rise buildings for the preservation of the compositional integrity of the urban area.

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.

Learnings from Opportunistic Wetlands: The Role of Substrate and Landscape Position on Reconstructed Landforms in a Sub-humid Climate

NASA Astrophysics Data System (ADS)

Little-Devito, M.; Chasmer, L.; Devito, K.; Kettridge, N.; Lukenbach, M. C.; Mendoza, C. A.

2017-12-01

Wetlands are important features in large-scale reclamation projects, and are integral to sustaining landscape eco-hydrological function and meeting reclamation goals. Despite a sub-humid climate, opportunistic wetlands are appearing on reconstructed landforms, and present an opportunity to understand the requirements for wetland construction, relative wetland succession, and their role in functioning landscapes. The relative importance and relationship between local and landscape-scale factors in determining initial wetland formation, as well as the relative occurrence and wetland type found on newly reclaimed landscapes was studied using both field and active (LiDAR) remote sensing methods. A random transect survey approach was used to characterize vegetation communities, soil and hydrologic characteristics, and local and landscape physiographic position across reconstructed landforms. Transects were also used to validate a broader area LiDAR-based classification. Preliminary findings suggest a higher frequency of opportunistic wetlands than anticipated. Soil texture of constructed landforms was important in determining the significance of local and landscape factors. On fine-textured constructed landforms, regardless of landscape position, wetlands formed on flat areas and in shallow depressions where soils had low water storage that promoted frequent surface saturation. Wetlands were less frequent on coarse-textured landforms and their location was controlled by landscape-scale factors, being restricted to the toes of slopes and areas intersecting the groundwater table. Wetlands found across all material types were predominantly Salix sp. and Carex sp. swamps with Typha sp. marsh complexes. This may indicate a potential initial phase of wetland succession and paludification in the Boreal Plains. These findings have important implications for understanding general wetland development, the initial phase of wetland paludification, and will aid the development of a geomorphic framework to better inform wetland construction and promote sustainable forest-wetland complexes similar to those found in natural landscapes.

Incorporating resource protection constraints in an analysis of landscape fuel-treatment effectiveness in the northern Sierra Nevada, CA, USA

Treesearch

Christopher B. Dow; Brandon M. Collins; Scott L. Stephens

2016-01-01

Finding novel ways to plan and implement landscape-level forest treatments that protect sensitive wildlife and other key ecosystem components, while also reducing the risk of large-scale, high-severity fires, can prove to be difficult. We examined alternative approaches to landscape-scale fuel-treatment design for the same landscape. These approaches included two...

NMR Mapping of Protein Conformational Landscapes using Coordinated Behavior of Chemical Shifts upon Ligand Binding

PubMed Central

Cembran, Alessandro; Kim, Jonggul; Gao, Jiali; Veglia, Gianluigi

2014-01-01

Proteins exist as an ensemble of conformers that are distributed on free energy landscapes resembling folding funnels. While the most stable conformers populate low energy basins, protein function is often carried out through low-populated conformational states that occupy high energy basins. Ligand binding shifts the populations of these states, changing the distribution of these conformers. Understanding how the equilibrium among the states is altered upon ligand binding, interaction with other binding partners, and/or mutations and post-translational modifications is of critical importance for explaining allosteric signaling in proteins. Here, we propose a statistical analysis of the chemical shifts (CONCISE, COordiNated ChemIcal Shifts bEhavior) for the interpretation of protein conformational equilibria following linear trajectories of NMR chemical shifts. CONCISE enables one to quantitatively measure the population shifts associated with ligand titrations and estimate the degree of collectiveness of the protein residues’ response to ligand binding, giving a concise view of the structural transitions. The combination of CONCISE with thermocalorimetric and kinetic data allows one to depict a protein’s approximate conformational energy landscape. We tested this method with the catalytic subunit of cAMP-dependent protein kinase A, a ubiquitous enzyme that undergoes conformational transitions upon both nucleotide and pseudo-substrate binding. When complemented with chemical shift covariance analysis (CHESCA), this new method offers both collective response and residue-specific correlations for ligand binding to proteins. PMID:24604024

Evaluating hydrological response to forecasted land-use change—scenario testing with the automated geospatial watershed assessment (AGWA) tool

USGS Publications Warehouse

Kepner, William G.; Semmens, Darius J.; Hernandez, Mariano; Goodrich, David C.

2009-01-01

Envisioning and evaluating future scenarios has emerged as a critical component of both science and social decision-making. The ability to assess, report, map, and forecast the life support functions of ecosystems is absolutely critical to our capacity to make informed decisions to maintain the sustainable nature of our ecosystem services now and into the future. During the past two decades, important advances in the integration of remote imagery, computer processing, and spatial-analysis technologies have been used to develop landscape information that can be integrated with hydrologic models to determine long-term change and make predictive inferences about the future. Two diverse case studies in northwest Oregon (Willamette River basin) and southeastern Arizona (San Pedro River) were examined in regard to future land use scenarios relative to their impact on surface water conditions (e.g., sediment yield and surface runoff) using hydrologic models associated with the Automated Geospatial Watershed Assessment (AGWA) tool. The base reference grid for land cover was modified in both study locations to reflect stakeholder preferences 20 to 60 yrs into the future, and the consequences of landscape change were evaluated relative to the selected future scenarios. The two studies provide examples of integrating hydrologic modeling with a scenario analysis framework to evaluate plausible future forecasts and to understand the potential impact of landscape change on ecosystem services.

Differences in soil biological activity by terrain types at the sub-field scale in central Iowa US

DOE PAGES

Kaleita, Amy L.; Schott, Linda R.; Hargreaves, Sarah K.; ...

2017-07-07

Soil microbial communities are structured by biogeochemical processes that occur at many different spatial scales, which makes soil sampling difficult. Because soil microbial communities are important in nutrient cycling and soil fertility, it is important to understand how microbial communities function within the heterogeneous soil landscape. In this study, a self-organizing map was used to determine whether landscape data can be used to characterize the distribution of microbial biomass and activity in order to provide an improved understanding of soil microbial community function. Points within a row crop field in south-central Iowa were clustered via a self-organizing map using sixmore » landscape properties into three separate landscape clusters. Twelve sampling locations per cluster were chosen for a total of 36 locations. After the soil samples were collected, the samples were then analysed for various metabolic indicators, such as nitrogen and carbon mineralization, extractable organic carbon, microbial biomass, etc. It was found that sampling locations located in the potholes and toe slope positions had significantly greater microbial biomass nitrogen and carbon, total carbon, total nitrogen and extractable organic carbon than the other two landscape position clusters, while locations located on the upslope did not differ significantly from the other landscape clusters. However, factors such as nitrate, ammonia, and nitrogen and carbon mineralization did not differ significantly across the landscape. Altogether, this research demonstrates the effectiveness of a terrain-based clustering method for guiding soil sampling of microbial communities.« less

Differences in soil biological activity by terrain types at the sub-field scale in central Iowa US

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

Kaleita, Amy L.; Schott, Linda R.; Hargreaves, Sarah K.

Soil microbial communities are structured by biogeochemical processes that occur at many different spatial scales, which makes soil sampling difficult. Because soil microbial communities are important in nutrient cycling and soil fertility, it is important to understand how microbial communities function within the heterogeneous soil landscape. In this study, a self-organizing map was used to determine whether landscape data can be used to characterize the distribution of microbial biomass and activity in order to provide an improved understanding of soil microbial community function. Points within a row crop field in south-central Iowa were clustered via a self-organizing map using sixmore » landscape properties into three separate landscape clusters. Twelve sampling locations per cluster were chosen for a total of 36 locations. After the soil samples were collected, the samples were then analysed for various metabolic indicators, such as nitrogen and carbon mineralization, extractable organic carbon, microbial biomass, etc. It was found that sampling locations located in the potholes and toe slope positions had significantly greater microbial biomass nitrogen and carbon, total carbon, total nitrogen and extractable organic carbon than the other two landscape position clusters, while locations located on the upslope did not differ significantly from the other landscape clusters. However, factors such as nitrate, ammonia, and nitrogen and carbon mineralization did not differ significantly across the landscape. Altogether, this research demonstrates the effectiveness of a terrain-based clustering method for guiding soil sampling of microbial communities.« less

INTRODUCTION TO THE LANDSCAPE ANALYSIS TOOLS ARCVIEW EXTENSION

EPA Science Inventory

Geographic Information Systems (GIS) have become a powerful tool in the field of landscape ecology. A common application of GIS is the generation of landscape indicators, which are quantitative measurements of the status or potential health of an area (e.g. watershed or county). ...

Persistent homology of time-dependent functional networks constructed from coupled time series

NASA Astrophysics Data System (ADS)

Stolz, Bernadette J.; Harrington, Heather A.; Porter, Mason A.

2017-04-01

We use topological data analysis to study "functional networks" that we construct from time-series data from both experimental and synthetic sources. We use persistent homology with a weight rank clique filtration to gain insights into these functional networks, and we use persistence landscapes to interpret our results. Our first example uses time-series output from networks of coupled Kuramoto oscillators. Our second example consists of biological data in the form of functional magnetic resonance imaging data that were acquired from human subjects during a simple motor-learning task in which subjects were monitored for three days during a five-day period. With these examples, we demonstrate that (1) using persistent homology to study functional networks provides fascinating insights into their properties and (2) the position of the features in a filtration can sometimes play a more vital role than persistence in the interpretation of topological features, even though conventionally the latter is used to distinguish between signal and noise. We find that persistent homology can detect differences in synchronization patterns in our data sets over time, giving insight both on changes in community structure in the networks and on increased synchronization between brain regions that form loops in a functional network during motor learning. For the motor-learning data, persistence landscapes also reveal that on average the majority of changes in the network loops take place on the second of the three days of the learning process.

Validation of Pacific Northwest hydrologic landscapes at the catchment scale

EPA Science Inventory

The interaction between the physical properties of a catchment (form) and climatic forcing of precipitation and energy control how water is partitioned, stored, and conveyed through a catchment (function). Hydrologic Landscapes (HLs) were previously developed across Oregon and de...

Topological Landscapes: A Terrain Metaphor for ScientificData

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

Weber, Gunther H.; Bremer, Peer-Timo; Pascucci, Valerio

2007-08-01

Scientific visualization and illustration tools are designed to help people understand the structure and complexity of scientific data with images that are as informative and intuitive as possible. In this context, the use of metaphors plays an important role, since they make complex information easily accessible by using commonly known concepts. In this paper we propose a new metaphor, called 'Topological Landscapes', which facilitates understanding the topological structure of scalar functions. The basic idea is to construct a terrain with the same topology as a given dataset and to display the terrain as an easily understood representation of the actualmore » input data. In this projection from an n-dimensional scalar function to a two-dimensional (2D) model we preserve function values of critical points, the persistence (function span) of topological features, and one possible additional metric property (in our examples volume). By displaying this topologically equivalent landscape together with the original data we harness the natural human proficiency in understanding terrain topography and make complex topological information easily accessible.« less

A hierarchical approach to forest landscape pattern characterization.

PubMed

Wang, Jialing; Yang, Xiaojun

2012-01-01

Landscape spatial patterns have increasingly been considered to be essential for environmental planning and resources management. In this study, we proposed a hierarchical approach for landscape classification and evaluation by characterizing landscape spatial patterns across different hierarchical levels. The case study site is the Red Hills region of northern Florida and southwestern Georgia, well known for its biodiversity, historic resources, and scenic beauty. We used one Landsat Enhanced Thematic Mapper image to extract land-use/-cover information. Then, we employed principal-component analysis to help identify key class-level landscape metrics for forests at different hierarchical levels, namely, open pine, upland pine, and forest as a whole. We found that the key class-level landscape metrics varied across different hierarchical levels. Compared with forest as a whole, open pine forest is much more fragmented. The landscape metric, such as CONTIG_MN, which measures whether pine patches are contiguous or not, is more important to characterize the spatial pattern of pine forest than to forest as a whole. This suggests that different metric sets should be used to characterize landscape patterns at different hierarchical levels. We further used these key metrics, along with the total class area, to classify and evaluate subwatersheds through cluster analysis. This study demonstrates a promising approach that can be used to integrate spatial patterns and processes for hierarchical forest landscape planning and management.

Efficient retrieval of landscape Hessian: Forced optimal covariance adaptive learning

NASA Astrophysics Data System (ADS)

Shir, Ofer M.; Roslund, Jonathan; Whitley, Darrell; Rabitz, Herschel

2014-06-01

Knowledge of the Hessian matrix at the landscape optimum of a controlled physical observable offers valuable information about the system robustness to control noise. The Hessian can also assist in physical landscape characterization, which is of particular interest in quantum system control experiments. The recently developed landscape theoretical analysis motivated the compilation of an automated method to learn the Hessian matrix about the global optimum without derivative measurements from noisy data. The current study introduces the forced optimal covariance adaptive learning (FOCAL) technique for this purpose. FOCAL relies on the covariance matrix adaptation evolution strategy (CMA-ES) that exploits covariance information amongst the control variables by means of principal component analysis. The FOCAL technique is designed to operate with experimental optimization, generally involving continuous high-dimensional search landscapes (≳30) with large Hessian condition numbers (≳104). This paper introduces the theoretical foundations of the inverse relationship between the covariance learned by the evolution strategy and the actual Hessian matrix of the landscape. FOCAL is presented and demonstrated to retrieve the Hessian matrix with high fidelity on both model landscapes and quantum control experiments, which are observed to possess nonseparable, nonquadratic search landscapes. The recovered Hessian forms were corroborated by physical knowledge of the systems. The implications of FOCAL extend beyond the investigated studies to potentially cover other physically motivated multivariate landscapes.

Deforestation Impacts on Bat Functional Diversity in Tropical Landscapes

PubMed Central

García-Morales, Rodrigo; Badano, Ernesto I.; Zuria, Iriana; Galindo-González, Jorge; Rojas-Martínez, Alberto E.; Ávila-Gómez, Eva S.

2016-01-01

Functional diversity is the variability in the functional roles carried out by species within ecosystems. Changes in the environment can affect this component of biodiversity and can, in turn, affect different processes, including some ecosystem services. This study aimed to determine the effect of forest loss on species richness, abundance and functional diversity of Neotropical bats. To this end, we identified six landscapes with increasing loss of forest cover in the Huasteca region of the state of Hidalgo, Mexico. We captured bats in each landscape using mist nets, and calculated functional diversity indices (functional richness and functional evenness) along with species richness and abundance. We analyzed these measures in terms of percent forest cover. We captured 906 bats (Phyllostomidae and Mormoopidae), including 10 genera and 12 species. Species richness, abundance and functional richness per night are positively related with forest cover. Generalized linear models show that species richness, abundance and functional richness per night are significantly related with forest cover, while seasonality had an effect on abundance and functional richness. Neither forest cover nor season had a significant effect on functional evenness. All these findings were consistent across three spatial scales (1, 3 and 5 km radius around sampling sites). The decrease in species, abundance and functional richness of bats with forest loss may have implications for the ecological processes they carry out such as seed dispersal, pollination and insect predation, among others. PMID:27926923

Population structure of the large Japanese field mouse, Apodemus speciosus (Rodentia: Muridae), in suburban landscape, based on mitochondrial D-loop sequences.

PubMed

Hirota, Tadao; Hirohata, Tetsuo; Mashima, Hiroshi; Satoh, Toshiyuki; Obara, Yoshiaki

2004-11-01

Genetic structure of the large Japanese field mouse populations in suburban landscape of West Tokyo, Japan was determined using mitochondrial DNA control region sequence. Samples were collected from six habitats linked by forests and green tract along the Tama River, and from two forests segregated by urban areas from those continuous habitats. Thirty-five haplotypes were detected in 221 animals. Four to eight haplotypes were found within each local population belonging to the continuous landscape. Some haplotypes were shared by two or three adjacent local populations. On the other hand, two isolated habitats were occupied by one or two indigenous haplotypes. Significant genetic differentiation between all pairs of local populations, except for one pair in the continuous habitats, was found by analysis of molecular variance (amova). The geographical distance between habitats did not explain the large variance of pairwise F(ST)-values among local populations. F(ST)-values between local populations segregated by urban areas were higher than those between local populations in the continuous habitat, regardless of geographical distance. The results of this study demonstrated quantitatively that urban areas inhibit the migration of Apodemus speciosus, whereas a linear green tract along a river functions as a corridor. Moreover, it preserves the metapopulation structure of A. speciosus as well as the corridors in suburban landscape.

Qualitative assessment of the medieval fortifications condition with the use of remote sensing data (Republic of Tatarstan)

NASA Astrophysics Data System (ADS)

Gainullin, Iskander I.; Khomyakov, Petr V.; Sitdikov, Airat G.; Usmanov, Bulat M.

2017-09-01

Archaeological monuments are an essential part of the cultural landscape. According to UNESCO directive, the "cultural landscape" is understood not simply as a result of joint creativity of man and nature, but as a purposefully formed natural and cultural territorial complex, which has structural, functional integrity, developing in specific physical and geographical, cultural and historical conditions. This article discusses the modern condition of the archaeological monuments of the Republic of Tatarstan, as a manmade part of the cultural landscape. Fortified settlements, with the system of defensive fortifications, were selected as the objects of study, as they are easily identified by remote sensing data. Identification and evaluation of monuments destruction risks is a priority in the study of medieval settlements. Due to the fact, that most of monuments is located on the small rivers banks, the first task of our study was to assess the risk of their destruction by natural processes. The second objective was to evaluate the role of the human factor in archaeological sites destruction. One of the main used methods is archival and modern remote sensing data analysis that also made able to correct the form of study settlements in comparison with existing plans, as well their size and location in the landscape. The results of research will help to identify trends in the monuments state and quantify the risks of their destruction.

Multiple successional pathways in human-modified tropical landscapes: new insights from forest succession, forest fragmentation and landscape ecology research.

PubMed

Arroyo-Rodríguez, Víctor; Melo, Felipe P L; Martínez-Ramos, Miguel; Bongers, Frans; Chazdon, Robin L; Meave, Jorge A; Norden, Natalia; Santos, Bráulio A; Leal, Inara R; Tabarelli, Marcelo

2017-02-01

Old-growth tropical forests are being extensively deforested and fragmented worldwide. Yet forest recovery through succession has led to an expansion of secondary forests in human-modified tropical landscapes (HMTLs). Secondary forests thus emerge as a potential repository for tropical biodiversity, and also as a source of essential ecosystem functions and services in HMTLs. Such critical roles are controversial, however, as they depend on successional, landscape and socio-economic dynamics, which can vary widely within and across landscapes and regions. Understanding the main drivers of successional pathways of disturbed tropical forests is critically needed for improving management, conservation, and restoration strategies. Here, we combine emerging knowledge from tropical forest succession, forest fragmentation and landscape ecology research to identify the main driving forces shaping successional pathways at different spatial scales. We also explore causal connections between land-use dynamics and the level of predictability of successional pathways, and examine potential implications of such connections to determine the importance of secondary forests for biodiversity conservation in HMTLs. We show that secondary succession (SS) in tropical landscapes is a multifactorial phenomenon affected by a myriad of forces operating at multiple spatio-temporal scales. SS is relatively fast and more predictable in recently modified landscapes and where well-preserved biodiversity-rich native forests are still present in the landscape. Yet the increasing variation in landscape spatial configuration and matrix heterogeneity in landscapes with intermediate levels of disturbance increases the uncertainty of successional pathways. In landscapes that have suffered extensive and intensive human disturbances, however, succession can be slow or arrested, with impoverished assemblages and reduced potential to deliver ecosystem functions and services. We conclude that: (i) succession must be examined using more comprehensive explanatory models, providing information about the forces affecting not only the presence but also the persistence of species and ecological groups, particularly of those taxa expected to be extirpated from HMTLs; (ii) SS research should integrate new aspects from forest fragmentation and landscape ecology research to address accurately the potential of secondary forests to serve as biodiversity repositories; and (iii) secondary forest stands, as a dynamic component of HMTLs, must be incorporated as key elements of conservation planning; i.e. secondary forest stands must be actively managed (e.g. using assisted forest restoration) according to conservation goals at broad spatial scales. © 2015 Cambridge Philosophical Society.

Wildlife tradeoffs based on landscape models of habitat preference

USGS Publications Warehouse

Loehle, C.; Mitchell, M.S.; White, M.

2000-01-01

Wildlife tradeoffs based on landscape models of habitat preference were presented. Multiscale logistic regression models were used and based on these models a spatial optimization technique was utilized to generate optimal maps. The tradeoffs were analyzed by gradually increasing the weighting on a single species in the objective function over a series of simulations. Results indicated that efficiency of habitat management for species diversity could be maximized for small landscapes by incorporating spatial context.

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.

Landscape‐level patterns in fawn survival across North America

USGS Publications Warehouse

Gingery, Tess M.; Diefenbach, Duane R.; Wallingford, Bret D.; Rosenberry, Christopher S.

2018-01-01

A landscape‐level meta‐analysis approach to examining early survival of ungulates may elucidate patterns in survival not evident from individual studies. Despite numerous efforts, the relationship between fawn survival and habitat characteristics remains unclear and there has been no attempt to examine trends in survival across landscape types with adequate replication. In 2015–2016, we radiomarked 98 white‐tailed deer (Odocoileus virginianus) fawns in 2 study areas in Pennsylvania. By using a meta‐analysis approach, we compared fawn survival estimates from across North America using published data from 29 populations in 16 states to identify patterns in survival and cause‐specific mortality related to landscape characteristics, predator communities, and deer population density. We modeled fawn survival relative to percentage of agricultural land cover and deer density. Estimated average survival to 3–6 months of age was 0.414 ± 0.062 (SE) in contiguous forest landscapes (no agriculture) and for every 10% increase in land area in agriculture, fawn survival increased 0.049 ± 0.014. We classified cause‐specific mortality as human‐caused, natural (excluding predation), and predation according to agriculturally dominated, forested, and mixed (i.e., both agricultural and forest cover) landscapes. Predation was the greatest source of mortality in all landscapes. Landscapes with mixed forest and agricultural cover had greater proportions and rates of human‐caused mortalities, and lower proportions and rates of mortality due to predators, when compared to forested landscapes. Proportion and rate of natural deaths did not differ among landscapes. We failed to detect any relationship between fawn survival and deer density. The results highlight the need to consider multiple spatial scales when accounting for factors that influence fawn survival. Furthermore, variation in mortality sources and rates among landscapes indicate the potential for altered landscape mosaics to influence fawn survival rates. Wildlife managers can use the meta‐analysis to identify factors that will facilitate comparisons of results among studies and advance a better understanding of patterns in fawn survival.

Factors affecting plant species composition of hedgerows: relative importance and hierarchy

NASA Astrophysics Data System (ADS)

Deckers, Bart; Hermy, Martin; Muys, Bart

2004-07-01

Although there has been a clear quantitative and qualitative decline in traditional hedgerow network landscapes during last century, hedgerows are crucial for the conservation of rural biodiversity, functioning as an important habitat, refuge and corridor for numerous species. To safeguard this conservation function, insight in the basic organizing principles of hedgerow plant communities is needed. The vegetation composition of 511 individual hedgerows situated within an ancient hedgerow network landscape in Flanders, Belgium was recorded, in combination with a wide range of explanatory variables, including a selection of spatial variables. Non-parametric statistics in combination with multivariate data analysis techniques were used to study the effect of individual explanatory variables. Next, variables were grouped in five distinct subsets and the relative importance of these variable groups was assessed by two related variation partitioning techniques, partial regression and partial canonical correspondence analysis, taking into account explicitly the existence of intercorrelations between variables of different factor groups. Most explanatory variables affected significantly hedgerow species richness and composition. Multivariate analysis showed that, besides adjacent land use, hedgerow management, soil conditions, hedgerow type and origin, the role of other factors such as hedge dimensions, intactness, etc., could certainly not be neglected. Furthermore, both methods revealed the same overall ranking of the five distinct factor groups. Besides a predominant impact of abiotic environmental conditions, it was found that management variables and structural aspects have a relatively larger influence on the distribution of plant species in hedgerows than their historical background or spatial configuration.

ANALYTICAL TOOL INTERFACE FOR LANDSCAPE ASSESSMENTS (ATIILA): AN ARCVIEW EXTENSION FOR THE ANALYSIS OF LANDSCAPE PATTERNS, COMPOSITION, AND STRUCTURE

EPA Science Inventory

Environmental management practices are trending away from simple, local- scale assessments toward complex, multiple-stressor regional assessments. Landscape ecology provides the theory behind these assessments while geographic information systems (GIS) supply the tools to impleme...

Revegetation for aesthetics

Treesearch

Bernard M. Slick

1980-01-01

Surface mining is changing the landscape character of forests in the East. Aesthetic visual aspects of the landscape are considered in the analysis, planning, and design of revegetation strategies. Application of landscape architectural design techniques in the revegetation of surface-mined lands, as well as knowledge of biological characteristics, will enhance the...

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...

Application of Partial Least Square (PLS) Regression to Determine Landscape-Scale Aquatic Resources Vulnerability in the Ozark Mountains

EPA Science Inventory

Partial least squares (PLS) analysis offers a number of advantages over the more traditionally used regression analyses applied in landscape ecology, particularly for determining the associations among multiple constituents of surface water and landscape configuration. Common dat...

Shallow peatland ecohydrology - the control of peat depth on moss productivity

NASA Astrophysics Data System (ADS)

Dixon, Simon; Kettridge, Nicholas; Moore, Paul; Devito, Kevin; Tilak, Amey; Petrone, Rich; Mendoza, Carl; Waddington, Mike

2017-04-01

Northern peatlands represent an important sink in the global carbon cycle. Shallow peatlands and marginal connective wetlands can be essential components of many northern peatland landscape mosaics, playing a vital role in landscape connectivity and wider landscape hydrology. However the ecohydrological function of these shallow, marginal systems has been largely overlooked, with peatland hydrology research focused on relatively deep bog systems. In order to predict landscape scale wetland function and its vulnerability to climate change we need to understand how these shallow connective systems function. The balance between moss productivity and water loss provide a key component of these systems, as water use efficiency controls the rate of moss growth and thus controls the amount of atmospheric carbon sequestered in peat. Understanding how productivity of shallow peatland systems responds to changes in evaporative stress will aid predictions of peatland landscape hydrological function in a changing climate. To determine the factors influencing peat productivity, water balance simulations using Hydrus 1-D were conducted over annual growing seasons for different soil profile depths, compositions and antecedent moisture conditions. Our results demonstrate a bimodal distribution of peatland responses; either primarily conserving water by limiting evapotranspiration or, maximizing productivity. For sustained periods of evaporative stress, shallow marginal systems are least able to buffer periods of evaporative stress due to limited labile water storage, and will limit evaporation, conserve water and be less productive. Conversely, where present, both deep water storage and a shallow initial water table prolong the onset of high vegetative stress, thus maximizing moss productivity. However, a total depth of 0.8 m is identified as the threshold above which increasing peat depth has no further effect on changing vegetative stress response and thus landscape function. These results are important as moss productivity, along with rate of organic matter decay are the two principle factors controlling the build-up of peat, and therefore sequestration of carbon. With a predicted increase in the frequency and size of rain events in northern latitudes our results indicate the productivity of shallow wetland systems may increase, but greater moisture availability will increase the likelihood they remain as wetlands in a changing climate.

An investigation of the neural substrates of mind wandering induced by viewing traditional Chinese landscape paintings.

PubMed

Wang, Tingting; Mo, Lei; Vartanian, Oshin; Cant, Jonathan S; Cupchik, Gerald

2014-01-01

The present study was conducted to investigate whether the calming effect induced by viewing traditional Chinese landscape paintings would make disengagement from that mental state more difficult, as measured by performance on a cognitive control task. In Experiment 1 we examined the subjective experience of viewing traditional Chinese landscape paintings vs. realistic oil landscape paintings in a behavioral study. Our results confirmed that, as predicted, traditional Chinese landscape paintings induce greater levels of relaxation and mind wandering and lower levels of object-oriented absorption and recognition, compared to realistic oil landscape paintings. In Experiment 2 we used functional Magnetic Resonance Imaging to explore the behavioral and neural effects of viewing traditional Chinese landscape paintings on a task requiring cognitive control (i.e., the flanker task)-administered immediately following exposure to paintings. Contrary to our prediction, the behavioral data demonstrated that compared to realistic oil landscape paintings, exposure to traditional Chinese landscape paintings had no effect on performance on the flanker task. However, the neural data demonstrated an interaction effect such that there was greater activation in the inferior parietal cortex and the superior frontal gyrus on incongruent compared with congruent flanker trials when participants switched from viewing traditional Chinese landscape paintings to the flanker task than when they switched from realistic oil landscape paintings. These results suggest that switching from traditional Chinese landscape paintings placed greater demands on the brain's attention and working memory networks during the flanker task than did switching from realistic oil landscape paintings.

Designing agricultural landscapes for biodiversity-based ecosystem services

DOE PAGES

Landis, Douglas A.

2016-07-28

Sustainable and resilient agricultural systems are needed to feed and fuel a growing human population. However, the current model of agricultural intensification which produces high yields has also resulted in a loss of biodiversity, ecological function, and critical ecosystem services in agricultural landscapes. A key consequence of agricultural intensification is landscape simplification, where once heterogeneous landscapes contain increasingly fewer crop and non-crop habitats. Landscape simplification exacerbates biodiversity losses which leads to reductions in ecosystem services on which agriculture depends. In recent decades, considerable research has focused on mitigating these negative impacts, primarily via management of habitats to promote biodiversity andmore » enhance services at the local scale. While it is well known that local and landscape factors interact, modifying overall landscape structure is seldom considered due to logistical constraints. Here, I propose that the loss of ecosystem services due to landscape simplification can only be addressed by a concerted effort to fundamentally redesign agricultural landscapes. Designing agricultural landscapes will require that scientists work with stakeholders to determine the mix of desired ecosystem services, evaluate current landscape structure in light of those goals, and implement targeted modifications to achieve them. I evaluate the current status of landscape design, ranging from fundamental ecological principles to resulting guidelines and socioeconomic tools. Finally, while research gaps remain, the time is right for ecologists to engage with other disciplines, stakeholders, and policymakers in education and advocacy to foster agricultural landscape design for sustainable and resilient biodiversity services.« less

Designing agricultural landscapes for biodiversity-based ecosystem services

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

Landis, Douglas A.

Sustainable and resilient agricultural systems are needed to feed and fuel a growing human population. However, the current model of agricultural intensification which produces high yields has also resulted in a loss of biodiversity, ecological function, and critical ecosystem services in agricultural landscapes. A key consequence of agricultural intensification is landscape simplification, where once heterogeneous landscapes contain increasingly fewer crop and non-crop habitats. Landscape simplification exacerbates biodiversity losses which leads to reductions in ecosystem services on which agriculture depends. In recent decades, considerable research has focused on mitigating these negative impacts, primarily via management of habitats to promote biodiversity andmore » enhance services at the local scale. While it is well known that local and landscape factors interact, modifying overall landscape structure is seldom considered due to logistical constraints. Here, I propose that the loss of ecosystem services due to landscape simplification can only be addressed by a concerted effort to fundamentally redesign agricultural landscapes. Designing agricultural landscapes will require that scientists work with stakeholders to determine the mix of desired ecosystem services, evaluate current landscape structure in light of those goals, and implement targeted modifications to achieve them. I evaluate the current status of landscape design, ranging from fundamental ecological principles to resulting guidelines and socioeconomic tools. Finally, while research gaps remain, the time is right for ecologists to engage with other disciplines, stakeholders, and policymakers in education and advocacy to foster agricultural landscape design for sustainable and resilient biodiversity services.« less

Verification of Hydrologic Landscape Derived Basin-Scale Classifications in the Pacific Northwest

EPA Science Inventory

The interaction between the physical properties of a catchment (form) and climatic forcing of precipitation and energy control how water is partitioned, stored, and conveyed through a catchment (function). Hydrologic Landscapes (HLs) were previously developed across Oregon and de...

Vulnerability of Oregon Hydrologic Landscapes and Streamflow to Climate Change - 5/20/2014

EPA Science Inventory

Hydrologic classification systems can provide a basis for broadscale assessments of the hydrologic functions of landscapes and watersheds and their responses to stressors. Such assessments could be particularly useful in determining hydrologic vulnerability from climate change. A...

The role of landscape-dependent disturbance and dispersal in metapopulation persistence.

PubMed

Elkin, Ché M; Possingham, Hugh

2008-10-01

The fundamental processes that influence metapopulation dynamics (extinction and recolonization) will often depend on landscape structure. Disturbances that increase patch extinction rates will frequently be landscape dependent such that they are spatially aggregated and have an increased likelihood of occurring in some areas. Similarly, landscape structure can influence organism movement, producing asymmetric dispersal between patches. Using a stochastic, spatially explicit model, we examine how landscape-dependent correlations between dispersal and disturbance rates influence metapopulation dynamics. Habitat patches that are situated in areas where the likelihood of disturbance is low will experience lower extinction rates and will function as partial refuges. We discovered that the presence of partial refuges increases metapopulation viability and that the value of partial refuges was contingent on whether dispersal was also landscape dependent. Somewhat counterintuitively, metapopulation viability was reduced when individuals had a preponderance to disperse away from refuges and was highest when there was biased dispersal toward refuges. Our work demonstrates that landscape structure needs to be incorporated into metapopulation models when there is either empirical data or ecological rationale for extinction and/or dispersal rates being landscape dependent.

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.

Quasi-potential landscape in complex multi-stable systems

PubMed Central

Zhou, Joseph Xu; Aliyu, M. D. S.; Aurell, Erik; Huang, Sui

2012-01-01

The developmental dynamics of multicellular organisms is a process that takes place in a multi-stable system in which each attractor state represents a cell type, and attractor transitions correspond to cell differentiation paths. This new understanding has revived the idea of a quasi-potential landscape, first proposed by Waddington as a metaphor. To describe development, one is interested in the ‘relative stabilities’ of N attractors (N > 2). Existing theories of state transition between local minima on some potential landscape deal with the exit part in the transition between two attractors in pair-attractor systems but do not offer the notion of a global potential function that relates more than two attractors to each other. Several ad hoc methods have been used in systems biology to compute a landscape in non-gradient systems, such as gene regulatory networks. Here we present an overview of currently available methods, discuss their limitations and propose a new decomposition of vector fields that permits the computation of a quasi-potential function that is equivalent to the Freidlin–Wentzell potential but is not limited to two attractors. Several examples of decomposition are given, and the significance of such a quasi-potential function is discussed. PMID:22933187

Mapping Candidate Ecological Restoration Areas Using Morphological Spatial Pattern Analysis (MSPA)

EPA Science Inventory

Morphological Spatial Pattern Analysis (MSPA) has been widely adopted by landscape ecologists over the past decade. A few examples of its many uses include: 1) quantifying landscape indicators and fragmentation in continental forest assessments, 2) explaining interior-exterior p...

Applications of ERTS-1 data to landscape change in eastern Tennessee

NASA Technical Reports Server (NTRS)

Rehder, J. B. (Principal Investigator)

1973-01-01

The author has identified the following significant results. The analysis of landscape change in eastern Tennessee from ERTS-1 data is being derived from three avenues of experimentation and analysis: (1) a multi-stage sampling procedure utilizing ground and aircraft imagery for ground truth and control; (2) a densitometric and computer analytical experiment for the analysis of gray tone signatures and comparisons for landscape change detection and monitoring; and (3) an ERTS image enhancement procedure for the detection and analysis of photomorphic regions. Significant results include: maps of strip mining changes and forest inventory, watershed identification and delimitation, and agricultural regions derived from spring plowing patterns appearing on the ERTS-1 imagery.

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.

An approach to analyzing the intensity of the daytime surface urban heat island effect at a local scale.

PubMed

Xu, Shenlai

2009-04-01

A landscape index LI is proposed to evaluate the intensity of the daytime surface urban heat island (SUHI) effect at a local scale. Three aspects of this landscape index are crucial: the source landscape, the sink landscape, and the contribution of source and sink landscapes to the intensity of the SUHI. Source and sink landscape types are identified using the thermo-band of Landsat 7 with a spatial resolution of 60 m, along with appropriate threshold values for the Normalized Difference Vegetation Index, Modified Normalized Difference Water Index, and Normalized Difference Built-up Index. The landscape index was defined as the ratio of the contributions of the source and sink landscapes to the intensity of the SUHI. The intensity of the daytime SUHI is assessed with the help of the landscape index. Our analysis indicates the landscape index can be used to evaluate and compare the intensity of the daytime SUHI for different areas.

Using High Resolution Remote Sensing Images to Investigate Hydrologic Connectivity and Degradation Thresholds along a Precipitation Gradient in Semiarid Australia

NASA Astrophysics Data System (ADS)

Azadi, S.; Saco, P. M.; Moreno-de las Heras, M.; Willgoose, G. R.

2016-12-01

Arid and semiarid landscapes are particularly sensitive to climatic and anthropogenic disturbances. Previous work has identified that these landscapes are prone to undergo critical degradation thresholds above which rehabilitation is difficult to achieve. This threshold behaviour is tightly linked to the overland flow redistribution and an increase in hydrologic connectivity associated with the climatic or anthropogenic disturbances. In fact, disturbances (such as wildfire, overgrazing or harvesting activities) can disrupt the spatial structure of vegetation, increase landscape hydrologic connectivity, trigger erosion and produce a substantial loss of water. All these effects can eventually affect ecosystem functionality (e.g. Rainfall Use Efficiency). In this study, we explore the impact of degradation processes induced by vegetation disturbances (mostly due to grazing pressure) on ecosystem functionality and connectivity along a precipitation gradient (250 mm to 490 mm annual average rainfall) using a combination of remote sensing observations and Digital Elevation Model data. The sites were carefully selected in the Mulga landscapes bioregion (New South Wales, Queensland) and in sites of the Northern Territory in Australia, which display similar vegetation characteristics and good quality rainfall information. Vegetation patterns and the percent of fractional cover were obtained from high resolution remote sensing images (IKONOS, QuickBird and Pleiades). We computed rainfall use efficiency and precipitation marginal response using local precipitation data and MODIS vegetation indices. We estimated mean Flowlength as an indicator of structural hydrologic connectivity using vegetation binary maps and digital elevation models. We compared the trends for several sites along the precipitation gradient, and found that disturbances substantially increase hydrologic connectivity following a threshold behaviour that affects landscape functionality. Though this threshold behaviour is found in all sites, the plots in higher rainfall landscapes show evidence of higher resilience.

Free energy landscapes of RNA/RNA complexes: with applications to snRNA complexes in spliceosomes.

PubMed

Cao, Song; Chen, Shi-Jie

2006-03-17

We develop a statistical mechanical model for RNA/RNA complexes with both intramolecular and intermolecular interactions. As an application of the model, we compute the free energy landscapes, which give the full distribution for all the possible conformations, for U4/U6 and U2/U6 in major spliceosome and U4atac/U6atac and U12/U6atac in minor spliceosome. Different snRNA experiments found contrasting structures, our free energy landscape theory shows why these structures emerge and how they compete with each other. For yeast U2/U6, the model predicts that the two distinct experimental structures, the four-helix junction structure and the helix Ib-containing structure, can actually coexist and specifically compete with each other. In addition, the energy landscapes suggest possible mechanisms for the conformational switches in splicing. For instance, our calculation shows that coaxial stacking is essential for stabilizing the four-helix junction in yeast U2/U6. Therefore, inhibition of the coaxial stacking possibly by protein-binding may activate the conformational switch from the four-helix junction to the helix Ib-containing structure. Moreover, the change of the energy landscape shape gives information about the conformational changes. We find multiple (native-like and misfolded) intermediates formed through base-pairing rearrangements in snRNA complexes. For example, the unfolding of the U2/U6 undergoes a transition to a misfolded state which is functional, while in the unfolding of U12/U6atac, the functional helix Ib is found to be the last one to unfold and is thus the most stable structural component. Furthermore, the energy landscape gives the stabilities of all the possible (functional) intermediates and such information is directly related to splicing efficiency.

The effect of garden designs on mood and heart output in older adults residing in an assisted living facility.

PubMed

Goto, Seiko; Park, Bum-Jin; Tsunetsugu, Yuko; Herrup, Karl; Miyazaki, Yoshifumi

2013-01-01

The objective of this study is to trace short-term changes in mood and heart function in elderly individuals in response to exposure to different landscaped spaces. Nineteen elderly but cognitively intact residents of an assisted living facility participated in the study. They were exposed to three landscaped spaces: a Japanese style garden, an herb garden, and a simple landscaped area planted with a single tree. To assess the effect of different landscaped spaces on older adults, individuals were monitored for mood and cardiac function in response to short exposures to spaces. Mood state was assessed using Profile of Mood States (POMS) before and after viewing the spaces. Cardiac output was assessed using a portable electrocardiograph monitor before and during the viewing. We found that the structured gardens evoked greater responses in all outcome measures. Scores on the POMS improved after observation of the two organized gardens compared to responses to the simple landscaped space with a single tree. During the observation period, heart rate was significantly lower in the Japanese garden than in the other environments, and sympathetic function was significantly lower as well. We conclude that exposure to organized gardens can affect both the mood and cardiac physiology of elderly individuals. Our data further suggest that these effects can differ depending on the types of landscape to which an individual is exposed. Elderly, Japanese garden, herb garden, heart rate, mood, healing environmentPreferred Citation: Goto, S., Park, B-J., Tsunetsugu, Y., Herrup, K., & Miyazaki, Y. (2013). The effect of garden designs on mood and heart output in older adults residing in an assisted living facility. Health Environments Research & Design Journal 6(2), pp 27-42.

The propagation of varied timescale perturbations in landscapes

NASA Astrophysics Data System (ADS)

Bingham, N.; Johnson, K. N.; Bookhagen, B.; Chadwick, O.

2016-12-01

The classic assumption of steady-state landscapes greatly simplifies models of earth-surface processes. Theoretically, steady-state denotes time independence, but in real landscapes steady-state requires a timescale over which to assume (or document) no change. In the past, poor spatiotemporal resolution of eroding landscapes necessitated that shorter timescale perturbations be ignored in favor of regional formulations of rock uplift = erosion, 105, 6 years. Now, novel techniques and technologies provide an opportunity to define local landscape response to various timescales of perturbations; thus, allowing us to consider multiple steady-states on adjacent watersheds or even along a single watershed. This study seeks to identify the physical propagation of varied timescale perturbations in landscapes in order to provide an updated geomorphic context for interpreting critical zone processes. At our study site - Santa Cruz Island (SCI), CA - perturbations include sea level and climate fluctuations over 105 years coupled with pulses of overgrazing and extreme storm events during the last 200 years. Comprehensive knickpoint location maps and dated marine and fill terraces tighten the spatiotemporal constraints on erosion for SCI. In addition, the island hosts a wide range of lithologies, allowing us to compare lithologic effects on landscape response to perturbations. Our study uses lidar point clouds and high resolution (0.25 and 1 m) digital elevation model analysis to segment landscapes by the degree of their response to perturbations. Landscape response is measured by increases in topographic roughness. We ascertain roughness by analyzing the changes in different terrain attributes on multiple spatial scales: catchment, sub-catchments and individual hillslopes. Terrain attributes utilized include slope, curvature, local relief, flowpath length and contributing catchment area. Statistical analysis of these properties indicates narrower ranges in values for regions of relative stability compared to unstable areas. This updated assessment of landscape response leads to a more detailed and nuanced definition of steady-state across landscapes, enabling a finer resolution of process understanding with the critical zone. The classic assumption of steady-state landscapes greatly simplifies models of earth-surface processes. Theoretically, steady-state denotes time independence, but in real landscapes steady-state requires a timescale over which to assume (or document) no change. In the past, poor spatiotemporal resolution of eroding landscapes necessitated that shorter timescale perturbations be ignored in favor of regional formulations of rock uplift = erosion, 105, 6 years. Now, novel techniques and technologies provide an opportunity to define local landscape response to various timescales of perturbations; thus, allowing us to consider multiple steady-states on adjacent watersheds or even along a single watershed. This study seeks to identify the physical propagation of varied timescale perturbations in landscapes in order to provide an updated geomorphic context for interpreting critical zone processes. At our study site - Santa Cruz Island (SCI), CA - perturbations include sea level and climate fluctuations over 105 years coupled with pulses of overgrazing and extreme storm events during the last 200 years. Comprehensive knickpoint location maps and dated marine and fill terraces tighten the spatiotemporal constraints on erosion for SCI. In addition, the island hosts a wide range of lithologies, allowing us to compare lithologic effects on landscape response to perturbations. Our study uses lidar point clouds and high resolution (0.25 and 1 m) digital elevation model analysis to segment landscapes by the degree of their response to perturbations. Landscape response is measured by increases in topographic roughness. We ascertain roughness by analyzing the changes in different terrain attributes on multiple spatial scales: catchment, sub-catchments and individual hillslopes. Terrain attributes utilized include slope, curvature, local relief, flowpath length and contributing catchment area. Statistical analysis of these properties indicates narrower ranges in values for regions of relative stability compared to unstable areas. This updated assessment of landscape response leads to a more detailed and nuanced definition of steady-state across landscapes, enabling a finer resolution of process understanding with the critical zone.

Historic Landscape Inventory for Marietta National Cemetery

DTIC Science & Technology

2017-11-14

development context, a description of current conditions, and an analysis of changes over time to the cultural landscape. All landscape features were...Factors ..................................................................................................... xxiv 1 Methodology ...yards 0.9144 meters ERDC/CERL TR-17-41 1 1 Methodology 1.1 Background The U.S. Congress codified the National Historic Preservation Act of

Chapter 10: Geographic information system landscape analysis using GTR 220 concepts

Treesearch

M. North; R.M. Boynton; P.A. Stine; K.F. Shipley; E.C. Underwood; N.E. Roth; J.H. Viers; J.F. Quinn

2012-01-01

Forest Service General Technical Report "An Ecosystem Management Strategy for Sierran Mixed-Conifer Forests" (hereafter GTR 220) (North et al. 2009) emphasizes increasing forest heterogeneity throughout a range of spatial scales including within-stand microsites, individual stands, watersheds, and entire landscapes. For fuels reduction, various landscape...

ANALYSIS OF LANDSCAPE AND WATER QUALITY IN THE NEW YORK CATSKILL - DELAWARE WATERSHED (1973-1998)

EPA Science Inventory

The primary goal of this study is to improve risk assessment through the development of methods and tools for characterization of landscape and water resource change. Exploring the relationship between landscape pattern and water quality in the Catskill-Delaware basins will impro...

Application of Partial Least Squares (PLS) Regression to Determine Landscape-Scale Aquatic Resource Vulnerability in the Ozark Mountains

EPA Science Inventory

Partial least squares (PLS) analysis offers a number of advantages over the more traditionally used regression analyses applied in landscape ecology to study the associations among constituents of surface water and landscapes. Common data problems in ecological studies include: s...

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 ...

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.

Estimating restorable wetland water storage at landscape scales

USGS Publications Warehouse

Jones, Charles Nathan; Evenson, Grey R.; McLaughlin, Daniel L.; Vanderhoof, Melanie; Lang, Megan W.; McCarty, Greg W.; Golden, Heather E.; Lane, Charles R.; Alexander, Laurie C.

2018-01-01

Globally, hydrologic modifications such as ditching and subsurface drainage have significantly reduced wetland water storage capacity (i.e., volume of surface water a wetland can retain) and consequent wetland functions. While wetland area has been well documented across many landscapes and used to guide restoration efforts, few studies have directly quantified the associated wetland storage capacity. Here, we present a novel raster-based approach to quantify both contemporary and potential (i.e., restorable) storage capacities of individual depressional basins across landscapes. We demonstrate the utility of this method by applying it to the Delmarva Peninsula, a region punctuated by both depressional wetlands and drainage ditches. Across the entire peninsula, we estimated that restoration (i.e., plugging ditches) could increase storage capacity by 80%. Focusing on an individual watershed, we found that over 59% of restorable storage capacity occurs within 20 m of the drainage network, and that 93% occurs within 1 m elevation of the drainage network. Our demonstration highlights widespread ditching in this landscape, spatial patterns of both contemporary and potential storage capacities, and clear opportunities for hydrologic restoration. In Delmarva and more broadly, our novel approach can inform targeted landscape-scale conservation and restoration efforts to optimize hydrologically mediated wetland functions.

Estimating restorable wetland water storage at landscape scales.

PubMed

Jones, Charles Nathan; Evenson, Grey R; McLaughlin, Daniel L; Vanderhoof, Melanie K; Lang, Megan W; McCarty, Greg W; Golden, Heather E; Lane, Charles R; Alexander, Laurie C

2018-01-01

Globally, hydrologic modifications such as ditching and subsurface drainage have significantly reduced wetland water storage capacity (i.e., volume of surface water a wetland can retain) and consequent wetland functions. While wetland area has been well documented across many landscapes and used to guide restoration efforts, few studies have directly quantified the associated wetland storage capacity. Here, we present a novel raster-based approach to quantify both contemporary and potential (i.e., restorable) storage capacities of individual depressional basins across landscapes. We demonstrate the utility of this method by applying it to the Delmarva Peninsula, a region punctuated by both depressional wetlands and drainage ditches. Across the entire peninsula, we estimated that restoration (i.e., plugging ditches) could increase storage capacity by 80%. Focusing on an individual watershed, we found that over 59% of restorable storage capacity occurs within 20 m of the drainage network, and that 93% occurs within 1 m elevation of the drainage network. Our demonstration highlights widespread ditching in this landscape, spatial patterns of both contemporary and potential storage capacities, and clear opportunities for hydrologic restoration. In Delmarva and more broadly, our novel approach can inform targeted landscape-scale conservation and restoration efforts to optimize hydrologically mediated wetland functions.

Common foundations of optimal control across the sciences: evidence of a free lunch

NASA Astrophysics Data System (ADS)

Russell, Benjamin; Rabitz, Herschel

2017-03-01

A common goal in the sciences is optimization of an objective function by selecting control variables such that a desired outcome is achieved. This scenario can be expressed in terms of a control landscape of an objective considered as a function of the control variables. At the most basic level, it is known that the vast majority of quantum control landscapes possess no traps, whose presence would hinder reaching the objective. This paper reviews and extends the quantum control landscape assessment, presenting evidence that the same highly favourable landscape features exist in many other domains of science. The implications of this broader evidence are discussed. Specifically, control landscape examples from quantum mechanics, chemistry and evolutionary biology are presented. Despite the obvious differences, commonalities between these areas are highlighted within a unified mathematical framework. This mathematical framework is driven by the wide-ranging experimental evidence on the ease of finding optimal controls (in terms of the required algorithmic search effort beyond the laboratory set-up overhead). The full scope and implications of this observed common control behaviour pose an open question for assessment in further work. This article is part of the themed issue 'Horizons of cybernetical physics'.

How to handle spatial heterogeneity in hydrological models.

NASA Astrophysics Data System (ADS)

Loritz, Ralf; Neuper, Malte; Gupta, Hoshin; Zehe, Erwin

2017-04-01

The amount of data we observe in our environmental systems is larger than ever. This leads to a new kind of problem where hydrological modelers can have access to large datasets with various quantitative and qualitative observations but are uncertain about the information content with respect to the hydrological functioning of a landscape. For example digital elevation models obviously contain plenty of information about the topography of a landscape; however the question of relevance for Hydrology is how much of this information is important for the hydrological functioning of a landscape. This kind of question is not limited to topography and we can ask similar questions when handling distributed rainfall data or geophysical images. In this study we would like to show how one can separate dominant patterns in the landscape from idiosyncratic system details. We use a 2D numerical hillslope model in combination with an extensive research data set to test a variety of different model setups that are built upon different landscape characteristics and run by different rainfalls measurements. With the help of information theory based measures we can identify and learn how much heterogeneity is really necessary for successful hydrological simulations and how much of it we can neglect.

[Landscape pattern and productivity characteristics of the oasis landscape ecosystem in Linze, Gansu, China].

PubMed

Liu, Xuelu; Ren, Jizhou; Zhang, Zihe

2002-08-01

Oasis landscape ecosystem is composed of 10 landscape elements, i.e., residence land, cultivated land, grassland, forestland, water area, water system, road, rocky desert, sandy desert, and gravel desert. Among the elements, cultivated land formed by human being production covers the most of the area, is most connected, and hence, is the matrix of the oasis landscape ecosystem. Residence land, grassland, forestland, water area, rocky desert, sandy desert, and gravel desert are patches. Residence land and forestland generate from human being production, while rocky desert, gravel desert and sandy desert are the remnant with the human being disturbance. Water region and grassland are the environmental resources remnant after natural disturbance. Water system and road are corridors. Cultivated land dominated in plant production should be utilized with more productive layers through developing animal production other than expanding used-area to maintain the landscape heterogeneity and diversity of the oasis landscape ecosystem. For remnant and environmental resource patches, it should be profitable in preserving and stabilizing landscape heterogeneity and diversity, exploiting the functions of water and soil conservation, tourism, windbreak and sand fixation. For landscape elements remnant only, it should be fruitful in avoiding degeneration of the landscape pattern to explore their preceding plant production with moderate plant production.

[Relationships of wetland landscape fragmentation with climate change in middle reaches of Heihe River, China].

PubMed

Jiang, Peng-Hui; Zhao, Rui-Feng; Zhao, Hai-Li; Lu, Li-Peng; Xie, Zuo-Lun

2013-06-01

Based on the 1975-2010 multi-temporal remotely sensed TM and ETM images and meteorological data, in combining with wavelet analysis, trend surface simulation, and interpolation method, this paper analyzed the meteorological elements' spatial distribution and change characteristics in the middle reaches of Heihe River, and elucidated the process of wetland landscape fragmentation in the study area by using the landscape indices patch density (PD), mean patch size (MPS), and patch shape fragment index (FS). The relationships between the wetland landscape fragmentation and climate change were also approached through correlation analysis and multiple stepwise regression analysis. In 1975-2010, the overall distribution patterns of precipitation and temperature in the study area were low precipitation in high temperature regions and high precipitation in low temperature regions, and the main characteristics of climate change were the conversion from dry to wet and from cold to warm. In the whole study period, the wetland landscape fragmentation was mainly manifested in the decrease of MPS, with a decrement of 48.95 hm2, and the increase of PD, with an increment of 0.006 ind x hm(-2).

Population genetic structure in a social landscape: barley in a traditional Ethiopian agricultural system

PubMed Central

Samberg, Leah H; Fishman, Lila; Allendorf, Fred W

2013-01-01

Conservation strategies are increasingly driven by our understanding of the processes and patterns of gene flow across complex landscapes. The expansion of population genetic approaches into traditional agricultural systems requires understanding how social factors contribute to that landscape, and thus to gene flow. This study incorporates extensive farmer interviews and population genetic analysis of barley landraces (Hordeum vulgare) to build a holistic picture of farmer-mediated geneflow in an ancient, traditional agricultural system in the highlands of Ethiopia. We analyze barley samples at 14 microsatellite loci across sites at varying elevations and locations across a contiguous mountain range, and across farmer-identified barley types and management strategies. Genetic structure is analyzed using population-based and individual-based methods, including measures of population differentiation and genetic distance, multivariate Principal Coordinate Analysis, and Bayesian assignment tests. Phenotypic analysis links genetic patterns to traits identified by farmers. We find that differential farmer management strategies lead to markedly different patterns of population structure across elevation classes and barley types. The extent to which farmer seed management appears as a stronger determinant of spatial structure than the physical landscape highlights the need for incorporation of social, landscape, and genetic data for the design of conservation strategies in human-influenced landscapes. PMID:24478796

Stonehenge's Greater Cursus

NASA Astrophysics Data System (ADS)

Burley, Paul; Mooers, Howard D.

2016-01-01

Archaeological investigations have emphasized relationships between solar and lunar phenomena and architectural features of prehistoric sites located on the Stonehenge ritual landscape. However, no over-riding landscape design has been identified to explain the purpose of placing hundreds of Neolithic through Iron Age burial sites upon the landscape. Our research and analysis shows the mid-4th millennium BC (mid-Neolithic) landscape represents an 'above, so below' cosmo-geographical relationship. Type, shape, size and orientation of specific elements (such as long barrows, henges, cursus and topography) created a hierotopy representing the Winter Hexagon asterism, Milky Way, ecliptic and other stellar features. The resulting pattern of ritual sites represents translocation of the astronomical Otherworld - the Spirit World - onto the plain. Results of the analysis create a new paradigm of purpose for the built landscape circa 3500 BC, and identifies the reason why Stonehenge is located where it is with respect to other contemorary monuments.

Analysis of umbu (Spondias tuberosa Arruda (Anacardiaceae)) in different landscape management regimes: a process of incipient domestication?

PubMed

Lins Neto, Ernani Machado de Freitas; Peroni, Nivaldo; Maranhão, Christine Maria Carneiro; Maciel, Maria Inês Sucupira; de Albuquerque, Ulysses Paulino

2012-07-01

Plant domestication is an evolutionary process guided by human groups who modify the landscape for their needs. The objective of this study was to evaluate the phenotypic variations between populations of Spondias tuberosa Arruda (umbuzeiro) when subjected to different local landscape management strategies. The influence of the landscape management system on these populations was evaluated in five identified regional units (mountains, base of mountains, pastures, cultivated areas and home gardens). Ten individuals were randomly selected from each region and subjected to morphological and chemical fruit analysis. The diversity index, based on Simpson's index, was determined for the different populations. We then evaluated the morphological differences between the individual fruits from the distinct landscape areas. We observed no significant differences in morphological diversity between the areas studied. Our data suggest that the umbuzeiro specimens in this region may be in the process of incipient domestication.

Landscape Phage: Evolution from Phage Display to Nanobiotechnology.

PubMed

Petrenko, Valery A

2018-06-07

The development of phage engineering technology has led to the construction of a novel type of phage display library-a collection of nanofiber materials with diverse molecular landscapes accommodated on the surface of phage particles. These new nanomaterials, called the "landscape phage", serve as a huge resource of diagnostic/detection probes and versatile construction materials for the preparation of phage-functionalized biosensors and phage-targeted nanomedicines. Landscape-phage-derived probes interact with biological threat agents and generate detectable signals as a part of robust and inexpensive molecular recognition interfaces introduced in mobile detection devices. The use of landscape-phage-based interfaces may greatly improve the sensitivity, selectivity, robustness, and longevity of these devices. In another area of bioengineering, landscape-phage technology has facilitated the development and testing of targeted nanomedicines. The development of high-throughput phage selection methods resulted in the discovery of a variety of cancer cell-associated phages and phage proteins demonstrating natural proficiency to self-assemble into various drug- and gene-targeting nanovehicles. The application of this new "phage-programmed-nanomedicines" concept led to the development of a number of cancer cell-targeting nanomedicine platforms, which demonstrated anticancer efficacy in both in vitro and in vivo experiments. This review was prepared to attract the attention of chemical scientists and bioengineers seeking to develop functionalized nanomaterials and use them in different areas of bioscience, medicine, and engineering.

Project visual analysis for the Allegheny National Forest

Treesearch

Gary W. Kell

1979-01-01

The Project Visual Analysis is a landscape assessment procedure involving forest vegetative manipulation. A logical step by step analysis leads the user to a specific set of landscape management guidelines to be used as an aid in designing a project or in evaluating whether the proposed project impacts will meet visual objectives. Key elements within the procedure are...

Use of Chemotypes for Profiling and Exploring the ToxCast Chemical-Assay Landscape (ACS Spring meeting)

EPA Science Inventory

EPA's ToxCast chemical library, currently exceeding 4000 unique chemicals, has successfully captured a broad diversity of chemical use-types, functionality, and structures and features potentially relevant to toxicity and environmental exposure landscapes. Chemical diversity in ...

Proceedings of the First Landscape State-and-Transition Simulation Modeling Conference, June 14–16, 2011, Portland, Oregon

Treesearch

Becky K. Kerns; Ayn J. Shlisky; Colin J. Daniel

2012-01-01

The first ever Landscape State-and-Transition Simulation Modeling Conference was held from June 14–16, 2011, in Portland Oregon. The conference brought together over 70 users of state-and-transition simulation modeling tools—the Vegetation Dynamics Development Tool (VDDT), the Tool for Exploratory Landscape Analysis (TELSA) and the Path Landscape Model. The goal of the...

Landscape Characterization of Arctic Ecosystems Using Data Mining Algorithms and Large Geospatial Datasets

NASA Astrophysics Data System (ADS)

Langford, Z. L.; Kumar, J.; Hoffman, F. M.

2015-12-01

Observations indicate that over the past several decades, landscape processes in the Arctic have been changing or intensifying. A dynamic Arctic landscape has the potential to alter ecosystems across a broad range of scales. Accurate characterization is useful to understand the properties and organization of the landscape, optimal sampling network design, measurement and process upscaling and to establish a landscape-based framework for multi-scale modeling of ecosystem processes. This study seeks to delineate the landscape at Seward Peninsula of Alaska into ecoregions using large volumes (terabytes) of high spatial resolution satellite remote-sensing data. Defining high-resolution ecoregion boundaries is difficult because many ecosystem processes in Arctic ecosystems occur at small local to regional scales, which are often resolved in by coarse resolution satellites (e.g., MODIS). We seek to use data-fusion techniques and data analytics algorithms applied to Phased Array type L-band Synthetic Aperture Radar (PALSAR), Interferometric Synthetic Aperture Radar (IFSAR), Satellite for Observation of Earth (SPOT), WorldView-2, WorldView-3, and QuickBird-2 to develop high-resolution (˜5m) ecoregion maps for multiple time periods. Traditional analysis methods and algorithms are insufficient for analyzing and synthesizing such large geospatial data sets, and those algorithms rarely scale out onto large distributed- memory parallel computer systems. We seek to develop computationally efficient algorithms and techniques using high-performance computing for characterization of Arctic landscapes. We will apply a variety of data analytics algorithms, such as cluster analysis, complex object-based image analysis (COBIA), and neural networks. We also propose to use representativeness analysis within the Seward Peninsula domain to determine optimal sampling locations for fine-scale measurements. This methodology should provide an initial framework for analyzing dynamic landscape trends in Arctic ecosystems, such as shrubification and disturbances, and integration of ecoregions into multi-scale models.

Spatial pattern enhances ecosystem functioning in an African savanna.

PubMed

Pringle, Robert M; Doak, Daniel F; Brody, Alison K; Jocqué, Rudy; Palmer, Todd M

2010-05-25

The finding that regular spatial patterns can emerge in nature from local interactions between organisms has prompted a search for the ecological importance of these patterns. Theoretical models have predicted that patterning may have positive emergent effects on fundamental ecosystem functions, such as productivity. We provide empirical support for this prediction. In dryland ecosystems, termite mounds are often hotspots of plant growth (primary productivity). Using detailed observations and manipulative experiments in an African savanna, we show that these mounds are also local hotspots of animal abundance (secondary and tertiary productivity): insect abundance and biomass decreased with distance from the nearest termite mound, as did the abundance, biomass, and reproductive output of insect-eating predators. Null-model analyses indicated that at the landscape scale, the evenly spaced distribution of termite mounds produced dramatically greater abundance, biomass, and reproductive output of consumers across trophic levels than would be obtained in landscapes with randomly distributed mounds. These emergent properties of spatial pattern arose because the average distance from an arbitrarily chosen point to the nearest feature in a landscape is minimized in landscapes where the features are hyper-dispersed (i.e., uniformly spaced). This suggests that the linkage between patterning and ecosystem functioning will be common to systems spanning the range of human management intensities. The centrality of spatial pattern to system-wide biomass accumulation underscores the need to conserve pattern-generating organisms and mechanisms, and to incorporate landscape patterning in efforts to restore degraded habitats and maximize the delivery of ecosystem services.

An ex-post evaluation approach to assess the impacts of accomplished urban structure shift on landscape connectivity.

PubMed

Huang, Junlong; He, Jianhua; Liu, Dianfeng; Li, Chun; Qian, Jing

2018-05-01

Many studies have been conducted to evaluate the effects of different urban structures on landscape connectivity, and most of them rely on the comparison approach or ex-ante scenario analysis. However, we still lack an ex-post method to capture the consequences of accomplished urban structure shift (from monocentric to polycentric), which is guided by the land use planning. To fill this gap, we develop an ex-post evaluation approach which integrates counterfactual analysis and landscape graphs. Counterfactual analysis is combined with cellular automata simulation model, to uncover what the city might look like, if it had continued to expand in a monocentric structure; and the landscape graphs enable us to reveal the possible landscape connectivity in actual and counterfactual scenarios. We select Nanjing city as the study area and 4 target species, to delve into the varying impacts of the urban structure shift on different taxonomic groups. Our case study demonstrates that: (1) the impact of urban structure shift is more relevant to the long disperser; (2) the actual landscape (polycentric) would facilitate the bird's dispersal, while (3) forest mammals have higher connectivity in the counterfactual scenario (monocentric), and the possible reasons are discussed. Finally, we demonstrate that the urban structure shift might not necessarily cause the connectivity decline, on condition that the key connectivity providers are identified by integrating ecological network analysis into the land use planning, and well preserved in the shift. Copyright © 2017 Elsevier B.V. All rights reserved.

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.

Landscape Context Mediates Avian Habitat Choice in Tropical Forest Restoration

PubMed Central

Reid, J. Leighton; Mendenhall, Chase D.; Rosales, J. Abel; Zahawi, Rakan A.; Holl, Karen D.

2014-01-01

Birds both promote and prosper from forest restoration. The ecosystem functions birds perform can increase the pace of forest regeneration and, correspondingly, increase the available habitat for birds and other forest-dependent species. The aim of this study was to learn how tropical forest restoration treatments interact with landscape tree cover to affect the structure and composition of a diverse bird assemblage. We sampled bird communities over two years in 13 restoration sites and two old-growth forests in southern Costa Rica. Restoration sites were established on degraded farmlands in a variety of landscape contexts, and each included a 0.25-ha plantation, island treatment (trees planted in patches), and unplanted control. We analyzed four attributes of bird communities including frugivore abundance, nectarivore abundance, migrant insectivore richness, and compositional similarity of bird communities in restoration plots to bird communities in old-growth forests. All four bird community variables were greater in plantations and/or islands than in control treatments. Frugivore and nectarivore abundance decreased with increasing tree cover in the landscape surrounding restoration plots, whereas compositional similarity to old-growth forests was greatest in plantations embedded in landscapes with high tree cover. Migrant insectivore richness was unaffected by landscape tree cover. Our results agree with previous studies showing that increasing levels of investment in active restoration are positively related to bird richness and abundance, but differences in the effects of landscape tree cover on foraging guilds and community composition suggest that trade-offs between biodiversity conservation and bird-mediated ecosystem functioning may be important for prioritizing restoration sites. PMID:24595233

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

Relationships between landscape pattern and land surface temperature and their applications to the study of West Nile Virus: As case studies in cities of Indianapolis and Chicago, United States

NASA Astrophysics Data System (ADS)

Liu, Hua

A new synthesis of remote sensing and landscape ecology approaches was developed to establish relationships between the landscape patterns and land surface temperatures (LST) in the city of Indianapolis, Indiana, United States. Land use and land cover (LULC) and LST images were derived from Terra Satellite's Advanced Spaceborne Thermal Emission and Reflection Radiometer (ASTER) imagery. An analytical procedure using landscape metrics was developed, applying configuration analysis of landscape patterns and land surface temperature zones. Detailed landscape pattern analyses at the landscape and class scales were conducted using landscape metrics in the City of Indianapolis. The effects of spatial resolution on the identification of the relationship were examined in the same city. The best level of equalization between the LULC and LST maps was determined based on minimum distance analysis in landscape metrics space. The analyses of relationships between the landscape patterns and land surface temperatures, and scaling effects were applied to the spread of West Nile Virus (WNV) in the City of Chicago, Illinois. Results show that urban, forest, and grassland were the main landscape components in Indianapolis. They possessed relatively higher fractal dimensions but lower spatial aggregation levels in April 5, 2004, June 16, 2001, and October 3, 2000, but not in February 6, 2006. Obvious seasonal differences existed with the most distinct landscape pattern detected on February 6, 2006. Urban was the dominant LULC type in high-temperature zones, while water and vegetation mainly fell in low-temperature zones. For each individual date, the metrics of LST zones apparently corresponded to the metrics of LULC types. In the study of scaling-up effect analysis, Patch Percentage, Patch Density, and Landscape Shape index were found to be able to effectively quantify the spatial changes of LULC types and temperature zones at different scales without contradiction. Urban, forest, and grassland in each season were more easily affected by the process in Patch Density and Landscape Shape index. Ninety meters was believed to be the optimal spatial resolution to examine relationships between landscape patterns and LSTs in the City of Indianapolis. In the study of the spread of West Nile Virus in the City of Chicago, WNV was found to have been spread throughout all of Cook County since 2001. Landscape factors, like landscape aggregation index and areas of urban, grass, and water showed a strong correlation with the number of WNV infections. Socioeconomic conditions, like population above 65 years old also showed a strong relationship with the spread of WNV in Cook County. Thermal conditions of water had a lower but still significant correlation to the spread of WNV. This research offers an opportunity to explore the mechanism of interaction between urban landscape patterns and land surface temperatures at different spatial scales, and show the effects of landscape pattern and land surface temperature on the spread of West Nile Virus. This study can be useful for urban planning and environmental management practices in the studied areas. It also contributes to public health management and protection.

Peculiarities of high-altitude landscapes formation in the Small Caucasus mountains

NASA Astrophysics Data System (ADS)

Trifonova, Tatiana

2014-05-01

Various mountain systems differ in character of landscapes and soil. Basic problem of present research: conditions and parameters determining the development of various landscapes and soils in mountain areas. Our research object is the area of Armenia where Small Caucasus, a part of Armenian upland is located. The specific character of the area is defined by the whole variety of all mountain structures like fold, block folding mountain ridges, volcanic upland, individual volcanoes, and intermountain depressions. As for the climate, the area belongs to dry subtropics. We have studied the peculiarities of high-altitude landscapes formation and mountain river basins development. We have used remote sensing data and statistic database of climatic parameters in this research. Field observations and landscape pictures analysis of space images allow distinguishing three types of mountain geosystems clearly: volcanic massifs, fold mountainous structures and closed high mountain basins - area of the lakes. The distribution of precipitation according to altitude shows some peculiarities. It has been found that due to this factor the investigated mountain area may be divided into three regions: storage (fold) mountainous area; Ararat volcanic area (southern macro exposure); closed high mountainous basin-area of the lake Sevan. The mountainous nature-climatic vertical landscapes appear to be horizontally oriented and they are more or less equilibrium (stable) geosystems, where the stable functional relationship between the landscape components is formed. Within their limits, definite bioclimatic structure of soil is developed. Along the slopes of fold mountains specific landscape shapes like litho-drainage basins are formed. They are intensively developing like relatively independent vertical geosystems. Mechanism of basin formation is versatile resulting in formation of the polychronous soil mantle structure. Landscapes and soils within the basin are of a different age, since the permanent exogenic processes favor regular rejuvenation of the slope soils. The basin structure determines the soilscape, and morphological elements of the basin are also different. The factors playing the significant part in the formation of soil-mantle composition in the basin can be identified. It is shown that landscapes formation and soil structure in mountains are controlled by two superimposed natural processes, i.e. the formation of vertical zonality and the development of river lithodrainage basins. References Trifonova T.A., 2008. River drainage basin as self-regulated natural geosistem. Izv. Russian of Academy of Sciences, Series on geography, 1: 28-36. Trifonova T.A., 2005. Development of basin approach in pedological and ecological studies. Eurasian Soil Science, 9: 931-937

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.

Impaired protein conformational landscapes as revealed in anomalous Arrhenius prefactors.

PubMed

Nagel, Zachary D; Dong, Ming; Bahnson, Brian J; Klinman, Judith P

2011-06-28

A growing body of data supports a role for protein motion in enzyme catalysis. In particular, the ability of enzymes to sample catalytically relevant conformational substates has been invoked to model kinetic and spectroscopic data. However, direct experimental links between rapidly interconverting conformations and the chemical steps of catalysis remain rare. We report here on the kinetic analysis and characterization of the hydride transfer step catalyzed by a series of mutant thermophilic alcohol dehydrogenases (ht-ADH), presenting evidence for Arrhenius prefactor values that become enormously elevated above an expected value of approximately 10(13) s(-1) when the enzyme operates below its optimal temperature range. Restoration of normal Arrhenius behavior in the ht-ADH reaction occurs at elevated temperatures. A simple model, in which reduced temperature alters the ability of the ht-ADH variants to sample the catalytically relevant region of conformational space, can reproduce the available data. These findings indicate an impaired landscape that has been generated by the combined condition of reduced temperature and mutation at a single, active-site hydrophobic side chain. The broader implication is that optimal enzyme function requires the maintenance of a relatively smooth landscape that minimizes low energy traps.

Impaired protein conformational landscapes as revealed in anomalous Arrhenius prefactors

PubMed Central

Nagel, Zachary D.; Dong, Ming; Bahnson, Brian J.; Klinman, Judith P.

2011-01-01

A growing body of data supports a role for protein motion in enzyme catalysis. In particular, the ability of enzymes to sample catalytically relevant conformational substates has been invoked to model kinetic and spectroscopic data. However, direct experimental links between rapidly interconverting conformations and the chemical steps of catalysis remain rare. We report here on the kinetic analysis and characterization of the hydride transfer step catalyzed by a series of mutant thermophilic alcohol dehydrogenases (ht-ADH), presenting evidence for Arrhenius prefactor values that become enormously elevated above an expected value of approximately 1013 s-1 when the enzyme operates below its optimal temperature range. Restoration of normal Arrhenius behavior in the ht-ADH reaction occurs at elevated temperatures. A simple model, in which reduced temperature alters the ability of the ht-ADH variants to sample the catalytically relevant region of conformational space, can reproduce the available data. These findings indicate an impaired landscape that has been generated by the combined condition of reduced temperature and mutation at a single, active-site hydrophobic side chain. The broader implication is that optimal enzyme function requires the maintenance of a relatively smooth landscape that minimizes low energy traps. PMID:21670258

Species richness and biomass explain spatial turnover in ecosystem functioning across tropical and temperate ecosystems.

PubMed

Barnes, Andrew D; Weigelt, Patrick; Jochum, Malte; Ott, David; Hodapp, Dorothee; Haneda, Noor Farikhah; Brose, Ulrich

2016-05-19

Predicting ecosystem functioning at large spatial scales rests on our ability to scale up from local plots to landscapes, but this is highly contingent on our understanding of how functioning varies through space. Such an understanding has been hampered by a strong experimental focus of biodiversity-ecosystem functioning research restricted to small spatial scales. To address this limitation, we investigate the drivers of spatial variation in multitrophic energy flux-a measure of ecosystem functioning in complex communities-at the landscape scale. We use a structural equation modelling framework based on distance matrices to test how spatial and environmental distances drive variation in community energy flux via four mechanisms: species composition, species richness, niche complementarity and biomass. We found that in both a tropical and a temperate study region, geographical and environmental distance indirectly influence species richness and biomass, with clear evidence that these are the dominant mechanisms explaining variability in community energy flux over spatial and environmental gradients. Our results reveal that species composition and trait variability may become redundant in predicting ecosystem functioning at the landscape scale. Instead, we demonstrate that species richness and total biomass may best predict rates of ecosystem functioning at larger spatial scales. © 2016 The Author(s).

Free Energy Landscape of Protein-Protein Encounter Resulting from Brownian Dynamics Simulations of Barnase:Barstar.

PubMed

Spaar, Alexander; Helms, Volkhard

2005-07-01

Over the past years Brownian dynamics (BD) simulations have been proven to be a suitable tool for the analysis of protein-protein association. The computed rates and relative trends for protein mutants and different ionic strength are generally in good agreement with experimental results, e.g. see ref 1. By design, BD simulations correspond to an intensive sampling over energetically favorable states, rather than to a systematic sampling over all possible states which is feasible only at rather low resolution. On the example of barnase and barstar, a well characterized model system of electrostatically steered diffusional encounter, we report here the computation of the 6-dimensional free energy landscape for the encounter process of two proteins by a novel, careful analysis of the trajectories from BD simulations. The aim of these studies was the clarification of the encounter state. Along the trajectories, the individual positions and orientations of one protein (relative to the other) are recorded and stored in so-called occupancy maps. Since the number of simulated trajectories is sufficiently high, these occupancy maps can be interpreted as a probability distribution which allows the calculation of the entropy landscape by the use of a locally defined entropy function. Additionally, the configuration dependent electrostatic and desolvation energies are recorded in separate maps. The free energy landscape of protein-protein encounter is finally obtained by summing the energy and entropy contributions. In the free energy profile along the reaction path, which is defined as the path along the minima in the free energy landscape, a minimum shows up suggesting this to be used as the definition of the encounter state. This minimum describes a state of reduced diffusion velocity where the electrostatic attraction is compensated by the repulsion due to the unfavorable desolvation of the charged residues and the entropy loss due to the increasing restriction of the motional freedom. In the simulations the orientational degrees of freedom at the encounter state are found to be less restricted than the translational degrees of freedom. Therefore, the orientational alignment of the two binding partners seems to take place beyond this free energy minimum. The free energy profiles along the reaction pathway are compared for different ionic strength and temperature. This novel analysis technique facilitates mechanistic interpretation of protein-protein encounter pathways which should be useful for interpretation of experimental results as well.

A LANDSCAPE ECOLOGY APPROACH TO IDENTIFYING ECOLOGICAL VULNERABILITY IN GEOGRAPHICALLY ISOLATED WETLANDS

EPA Science Inventory

U.S. EPA 's Office of Research and Development is using a landscape approach to assess the ecological/hydrologic functions of geographically isolated wetlands in the mid-western, southern, and western regions of the United States. Geographically isolated wetlands are considered t...

LAND-COVER CHARACTERIZATION AND CHANGE DETECTION USING MULTI-TEMPORAL MODIS NDIV DATA

EPA Science Inventory

Land-cover (LC) composition and conversions are important factors that affect ecosystem condition and function. These data are frequently used as a primary data source to generate landscape-based metrics to assess landscape condition at multiple assessment scales. The use of sate...

Prototype Protein-Based Three-Dimensional Memory

DTIC Science & Technology

2003-01-01

9 Figure 3.2: Hypothetical mutational landscape ...to explore the genetic mutational landscape of a protein without any a priori knowledge of structure- function relationships. As such, it explores...native organism, Halobacterium salinarum, the protein acts as a photosynthetic sunlight to chemical energy transducer. Through several billion years of

Global Survey of Anthropogenic Neighborhood Threats to Conservation of Grass-Shrub and Forest Vegetation

EPA Science Inventory

The ecological functions of natural vegetation are threatened when it is subsumed in anthropogenic landscapes. We report the first comparative global survey of anthropogenic landscape threats to forest and grass-shrub vegetation. Using a global land-cover map derived from remote...

A sustainable landscape ecosystem design: a case study.

PubMed

Huang, Lei-Chang; Ye, Shu-Hong; Gu, Xun; Cao, Fu-Cun; Fan, Zheng-Qiu; Wang, Xiang-Rong; Wu, Ya-Sheng; Wang, Shou-Bing

2010-05-01

Landscape planning is clearly ecologically and socially relevant. Concern about sustainability between human and environment is now a driving paradigm for this professional. However, the explosion of the sustainable landscape in China is a very recent phenomenon. What is the sustainable landscape? How is this realized in practice? In this article, on the basis of the reviews of history and perplexities of Chinese landscape and nature analysis of sustainable landscape, the ecothinking model, an implemental tool for sustainable landscape, was developed, which applies ecothinking in vision, culture, conservation and development of site, and the process of public participation for a harmonious relationship between human and environment. And a case study of the south entrance of TongNiuling Scenic Area was carried out, in which the most optimum scenario was chosen from among three models according to the ecothinking model, to illustrate the construction of the ecothinking model and how to achieve a sustainable landscape.

ASSESSING THE PREDICTIVE CAPABILITY OF LANDSCAPE SAMPLING UNITS OF VARYING SCALE IN THE ANALYSIS OF ESTUARINE CONDITION

EPA Science Inventory

Landscape structure metrics are often used to predict water and sediment quality of lakes, streams, and estuaries; however, the sampling units used to generate the landscape metrics are often at an irrelevant spatial scale. They are either too large (i.e., an entire watershed) or...

Predicting landscape connectivity for the Asian elephant in its largest remaining subpopulation

Treesearch

J.-P. Puyravaud; Samuel Cushman; P. Davidar; D. Madappa

2016-01-01

Landscape connectivity between protected areas is crucial for the conservation of megafauna. But often, corridor identification relies on expert knowledge that is subjective and not spatially synoptic. Landscape analysis allows generalization of expert knowledge when satellite tracking or genetic data are not available. The Nilgiri Biosphere Reserve in southern India...

FRAGSTATS: spatial pattern analysis program for quantifying landscape structure.

Treesearch

Kevin McGarigal; Barbara J. Marks

1995-01-01

This report describes a program, FRAGSTATS, developed to quantify landscape structure. FRAGSTATS offers a comprehensive choice of landscape metrics and was designed to be as versatile as possible. The program is almost completely automated and thus requires little technical training. Two separate versions of FRAGSTATS exist: one for vector images and one for raster...

Phenotypic and genotypic analysis of a U.S. native fine-leaved Festuca population portends its potential use for low-input urban landscapes

USDA-ARS?s Scientific Manuscript database

Continued reduction in limited natural resources worldwide increasingly necessitates the incorporation of low maintenance and input plant materials into urban landscapes. Although some fine-leaved Festuca grass species have been utilized in formal gardens and native urban landscapes because of thei...

Landscape-level analysis of mountain goat population connectivity in Washington and southern British Columbia

Treesearch

Leslie C. Parks; David O. Wallin; Samuel A. Cushman; Brad H. McRae

2015-01-01

Habitat fragmentation and habitat loss diminish population connectivity, reducing genetic diversity and increasing extinction risk over time. Improving connectivity is widely recommended to preserve the long-term viability of populations, but this requires accurate knowledge of how landscapes influence connectivity. Detectability of landscape effects on gene...

Chapter 6. Landscape Analysis for Habitat Monitoring

Treesearch

Samuel A. Cushman; Kevin McGarigal; Kevin S. McKelvey; Christina D. Vojta; Claudia M. Regan

2013-01-01

The primary objective of this chapter is to describe standardized methods for measur¬ing and monitoring attributes of landscape pattern in support of habitat monitoring. This chapter describes the process of monitoring categorical landscape maps in which either selected habitat attributes or different classes of habitat quality are represented as different patch types...

Prescribing habitat layouts: Analysis of optimal placement for landscape planning [Chapter 23

Treesearch

Curtis H. Flather; Michael Bevers; John Hof

2002-01-01

Physical restructuring of landscapes by humans is a prominent stress on ecological systems (Rapport et al. 1985). Landscape restructuring occurs primarily through land-use conversions or alteration of native habitats through natural resource management. A common faunal response to such land-use intensification is an increased dominance of opportunistic species leading...

Tools for understanding landscapes: combining large-scale surveys to characterize change. Chapter 9.

Treesearch

W. Keith Moser; Janine Bolliger; Don C. Bragg; Mark H. Hansen; Mark A. Hatfield; Timothy A. Nigh; Lisa A. Schulte

2008-01-01

All landscapes change continuously. Since change is perceived and interpreted through measures of scale, any quantitative analysis of landscapes must identify and describe the spatiotemporal mosaics shaped by large-scale structures and processes. This process is controlled by core influences, or "drivers," that shape the change and affect the outcome...

The effect of landscape complexity and microclimate on the thermal tolerance of a pest insect.

PubMed

Alford, Lucy; Tougeron, Kévin; Pierre, Jean-Sébastien; Burel, Françoise; van Baaren, Joan

2017-03-21

Landscape changes are known to exacerbate the impacts of climate change. As such, understanding the combined effect of climate and landscape on agroecosystems is vital if we are to maintain the function of agroecosystems. This study aimed to elucidate the effects of agricultural landscape complexity on the microclimate and thermal tolerance of an aphid pest to better understand how landscape and climate may interact to affect the thermal tolerance of pest species within the context of global climate change. Meteorological data were measured at the landscape level, and cereal aphids (Sitobion avenae, Metopolophium dirhodum and Rhopalosiphum padi) sampled, from contrasting landscapes (simple and complex) in winter 2013/2014 and spring 2014 in cereal fields of Brittany, France. Aphids were returned to the laboratory and the effect of landscape of origin on aphid cold tolerance (as determined by CT min ) was investigated. Results revealed that local landscape complexity significantly affected microclimate, with simple homogenous landscapes being on average warmer, but with greater temperature variation. Landscape complexity was shown to impact aphid cold tolerance, with aphids from complex landscapes being more cold tolerant than those from simple landscapes in both winter and spring, but with differences among species. This study highlights that future changes to land use could have implications for the thermal tolerance and adaptability of insects. Furthermore, not all insect species respond in a similar way to microhabitat and microclimate, which could disrupt important predator-prey relationships and the ecosystem service they provide. © 2017 Institute of Zoology, Chinese Academy of Sciences.

An investigation of the neural substrates of mind wandering induced by viewing traditional Chinese landscape paintings

PubMed Central

Wang, Tingting; Mo, Lei; Vartanian, Oshin; Cant, Jonathan S.; Cupchik, Gerald

2015-01-01

The present study was conducted to investigate whether the calming effect induced by viewing traditional Chinese landscape paintings would make disengagement from that mental state more difficult, as measured by performance on a cognitive control task. In Experiment 1 we examined the subjective experience of viewing traditional Chinese landscape paintings vs. realistic oil landscape paintings in a behavioral study. Our results confirmed that, as predicted, traditional Chinese landscape paintings induce greater levels of relaxation and mind wandering and lower levels of object-oriented absorption and recognition, compared to realistic oil landscape paintings. In Experiment 2 we used functional Magnetic Resonance Imaging to explore the behavioral and neural effects of viewing traditional Chinese landscape paintings on a task requiring cognitive control (i.e., the flanker task)—administered immediately following exposure to paintings. Contrary to our prediction, the behavioral data demonstrated that compared to realistic oil landscape paintings, exposure to traditional Chinese landscape paintings had no effect on performance on the flanker task. However, the neural data demonstrated an interaction effect such that there was greater activation in the inferior parietal cortex and the superior frontal gyrus on incongruent compared with congruent flanker trials when participants switched from viewing traditional Chinese landscape paintings to the flanker task than when they switched from realistic oil landscape paintings. These results suggest that switching from traditional Chinese landscape paintings placed greater demands on the brain’s attention and working memory networks during the flanker task than did switching from realistic oil landscape paintings. PMID:25610386

Complexity of the Alternative Splicing Landscape in Plants[C][W][OPEN

PubMed Central

Reddy, Anireddy S.N.; Marquez, Yamile; Kalyna, Maria; Barta, Andrea

2013-01-01

Alternative splicing (AS) of precursor mRNAs (pre-mRNAs) from multiexon genes allows organisms to increase their coding potential and regulate gene expression through multiple mechanisms. Recent transcriptome-wide analysis of AS using RNA sequencing has revealed that AS is highly pervasive in plants. Pre-mRNAs from over 60% of intron-containing genes undergo AS to produce a vast repertoire of mRNA isoforms. The functions of most splice variants are unknown. However, emerging evidence indicates that splice variants increase the functional diversity of proteins. Furthermore, AS is coupled to transcript stability and translation through nonsense-mediated decay and microRNA-mediated gene regulation. Widespread changes in AS in response to developmental cues and stresses suggest a role for regulated splicing in plant development and stress responses. Here, we review recent progress in uncovering the extent and complexity of the AS landscape in plants, its regulation, and the roles of AS in gene regulation. The prevalence of AS in plants has raised many new questions that require additional studies. New tools based on recent technological advances are allowing genome-wide analysis of RNA elements in transcripts and of chromatin modifications that regulate AS. Application of these tools in plants will provide significant new insights into AS regulation and crosstalk between AS and other layers of gene regulation. PMID:24179125

Hierarchical Regularity in Multi-Basin Dynamics on Protein Landscapes

NASA Astrophysics Data System (ADS)

Matsunaga, Yasuhiro; Kostov, Konstatin S.; Komatsuzaki, Tamiki

2004-04-01

We analyze time series of potential energy fluctuations and principal components at several temperatures for two kinds of off-lattice 46-bead models that have two distinctive energy landscapes. The less-frustrated "funnel" energy landscape brings about stronger nonstationary behavior of the potential energy fluctuations at the folding temperature than the other, rather frustrated energy landscape at the collapse temperature. By combining principal component analysis with an embedding nonlinear time-series analysis, it is shown that the fast fluctuations with small amplitudes of 70-80% of the principal components cause the time series to become almost "random" in only 100 simulation steps. However, the stochastic feature of the principal components tends to be suppressed through a wide range of degrees of freedom at the transition temperature.

Adapting Landscape Mosaics of medIteranean Rainfed Agrosystems for a sustainable management of crop production, water and soil resources: the ALMIRA project.

NASA Astrophysics Data System (ADS)

Jacob, Frédéric; Mekki, Insaf; Chikhaoui, Mohamed

2014-05-01

In the context of mitigating the pressures induced by global change combined with demography and market pressures, there is increasing societal demand and scientific need to understand the functioning of Mediterranean Rainfed Agrosystems (MRAs) for their potential to provide various environmental and economic services of importance such as food production, preservation of employment and local knowhow, downstream water delivery or mitigation of rural exodus. Efficient MRAs management strategies that allow for compromises between economic development and natural resources preservation are needed. Such strategies require innovative system based research, integration across approaches and scales. One of the major challenges is to make all contributions from different disciplines converging towards a reproducible transdisciplinary approach. The objective of this communication is to present the ALMIRA project, a Tunisian - Moroccan - French project which lasts four years (2014 - 2017). The communication details the societal context, the scientific positioning and the related work hypothesis, the study areas, the project structure, the expected outcomes and the partnership which capitalizes on long term collaborations. ALMIRA aims to explore the modulation of landscape mosaics within MRAs to optimize landscape services. To explore this new lever, ALMIRA proposes to design, implement and test a new Integrated Assessment Modelling approach that explicitly i) includes innovations and action means into prospective scenarii for landscape evolutions, and ii) addresses landscape mosaics and processes of interest from the agricultural field to the resource governance catchment. This requires tackling methodological challenges in relation to i) the design of spatially explicit landscape evolution scenarii, ii) the coupling of biophysical processes related to agricultural catchment hydrology, iii) the digital mapping of landscape properties and iv) the economic assessment of the landscape services. The new Integrated Assessment Modelling approach is implemented and tested within three catchments located in Tunisia, France, and Morocco. Beyond the obtaining of significant advances in the aforementioned methodological domains, and the understanding of landscape functioning and services for the considered catchments, outcomes are expected to help in revisiting former recommendations at the levels of agricultural field and resource governance catchment, and in identifying new levers that improve MRA management at the intermediate level of landscape mosaics.

Tool-effect: Controls on Landscape Persistence

NASA Astrophysics Data System (ADS)

Willenbring, J. K.; Brocard, G. Y.; Salles, T.; Harrison, E. J.

2017-12-01

The ability of rivers to cut through rock and to remove former land surfaces sets the pace of landscape response to mountain uplift. Because of associations between tectonism, river incision, erosion, carbon burial and silicate weathering, high rates of rock uplift are thought to initiate a cascade of processes that are linked to sequestration of CO2 over geologic timescales. However, even in some cases of landscapes experiencing rapid uplift, some portions of landscapes remain unchanged or `relict' for long periods and the fluxes of chemical weathering and physical erosion do not reflect the new tectonic regime-sometimes for millions of years following uplift. These relict portions of the landscape are often composed of subdued topography with thick soils. River incision is achieved by various processes, but one of the main contributors is bedrock abrasion by bedload. Here, we show how the presence of flat, relict landscapes in headwaters can lead to reduced incision rates and low erosion fluxes. We use a known pulse of uplift in Puerto Rico and track the river response to the uplift over time to illustrate a how landscapes in hot, humid climates can persist for millions of years even after rapid mountain uplift. We run experiments on simplified topography using numerical landscape evolution models. Typically, numerical landscape evolution models apply a standard stream power law model, whereby river incision is proportional to basal shear stress or unit stream power, and is not affected by gravel flux. We implement a formulation of the tool and cover effect model, and then we added a reinforcing effect of weathering on this process, by implementing a gravel production function. This function simulates the effect of the residence time of rocks in soil, which is expected to affect the grain-size distribution of the particles in the soil, with lower erosion rates, and longer residence time further decreasing the proportion of gravel delivered to the streams. We find that the presence of rock fragments in a landscape acts as a stream attractor and fine-grained materials retard stream incision. Thus, a relict surface with thick soils composed of sand and clays effectively protects itself from dissection.

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...

Hacked Landscapes: Tensions, Borders, and Positionality in Spatial Literacy

ERIC Educational Resources Information Center

Schmidt, Sandra J.

2017-01-01

By focusing on critical geographies, landscape, and spatial literacy, this article evaluates a semester-long spatial justice project conducted in a preservice teacher education program. The analysis recognizes the limitations of reading the products literally as a means of comprehending spatial representation. It expands the analysis by hacking…

Big Cats in Our Backyards: Persistence of Large Carnivores in a Human Dominated Landscape in India

PubMed Central

Athreya, Vidya; Odden, Morten; Linnell, John D. C.; Krishnaswamy, Jagdish; Karanth, Ullas

2013-01-01

Protected areas are extremely important for the long term viability of biodiversity in a densely populated country like India where land is a scarce resource. However, protected areas cover only 5% of the land area in India and in the case of large carnivores that range widely, human use landscapes will function as important habitats required for gene flow to occur between protected areas. In this study, we used photographic capture recapture analysis to assess the density of large carnivores in a human-dominated agricultural landscape with density >300 people/km2 in western Maharashtra, India. We found evidence of a wide suite of wild carnivores inhabiting a cropland landscape devoid of wilderness and wild herbivore prey. Furthermore, the large carnivores; leopard (Panthera pardus) and striped hyaena (Hyaena hyaena) occurred at relatively high density of 4.8±1.2 (sd) adults/100 km2 and 5.03±1.3 (sd) adults/100 km2 respectively. This situation has never been reported before where 10 large carnivores/100 km2 are sharing space with dense human populations in a completely modified landscape. Human attacks by leopards were rare despite a potentially volatile situation considering that the leopard has been involved in serious conflict, including human deaths in adjoining areas. The results of our work push the frontiers of our understanding of the adaptability of both, humans and wildlife to each other’s presence. The results also highlight the urgent need to shift from a PA centric to a landscape level conservation approach, where issues are more complex, and the potential for conflict is also very high. It also highlights the need for a serious rethink of conservation policy, law and practice where the current management focus is restricted to wildlife inside Protected Areas. PMID:23483933

Chapter 7 - Mapping potential vegetation type for the LANDFIRE Prototype Project

Treesearch

Tracey S. Frescino; Matthew G. Rollins

2006-01-01

Mapped potential vegetation functioned as a key component in the Landscape Fire and Resource Management Planning Tools Prototype Project (LANDFIRE Prototype Project). Disturbance regimes, vegetation response and succession, and wildland fuel dynamics across landscapes are controlled by patterns of the environmental factors (biophysical settings) that entrain the...

Supplementing forest ecosystem health projects on the ground

Treesearch

Cathy Barbouletos; Lynette Z. Morelan

1995-01-01

Understanding the functions and processes of ecosystems is critical before implementing forest ecosystem health projects on the landscape. Silvicultural treatments such as thinning, prescribed fire, and reforestation can simulate disturbance regimes and landscape patterns that have regulated forest ecosystems for centuries. As land managers we need to understand these...

Advances in forest hydrology: challenges and opportunities

Treesearch

D.M. Amatya; K.R. Douglas-Mankin; T.M. Williams; R.W. Skaggs; J.E. Nettles

2011-01-01

Forests are an integral component of the landscape, and maintaining their functional integrity is fundamental for the sustainability of ecosystems and societies alike. Tools, innovations, and practices, analogous to those developed to improve agricultural production and quantify environmental impacts, are needed to ensure the sustainability of these forested landscapes...

Spatial distribution of hemlock woolly adelgid induced hemlock mortality in the Southern Appalachians

Treesearch

Tuula Kantola; Päivi Lyytikäinen-Saarenmaa; Robert N. Coulson; Sheryl Strauch; Maria D. Tchakerian; Markus Holopainen; Hannu Saarenmaa; Douglas A. Streett

2014-01-01

Hemlock woolly adelgid (Adelges tsugae Annand, HWA) outbreaks are posing a major threat to eastern hemlock (Tsuga canadensis L. Carr.) and Carolina hemlock (Tsuga caroliniana Engelm.) forest landscapes in the eastern USA. As foundation species, hemlocks play a variety of functional roles in forest landscapes....

LANDSCAPE ECOLOGY APPROACHES FOR DETECTING, MAPPING, AND ASSESSING THE VULNERABILITY OF DEPRESSIONAL WETLANDS

EPA Science Inventory

U.S. EPA is using a landscape ecology approach to assess the ecological/hydrologic functions and related human values of depressional wetlands along coastal Texas, considered to be vulnerable to human disturbance. Many of those wetlands may be at high risk because of recent court...

US EPA'S LANDSCAPE ECOLOGY RESEARCH: ASSESSING TRENDS FOR WETLANDS AND SURFACE WATERS USING REMORE SENSING, GIS, AND FIELD-BASED TECHNIQUES

EPA Science Inventory

The US EPA, Environmental Sciences Division-Las Vegas is using a variety of geopspatical and statistical modeling approaches to locate and assess the complex functions of wetland ecosystems. These assessments involve measuring landscape characteristrics and change, at multiple s...

IMPLICATIONS OF INVASION BY JUNIPERUS VIRGINIANA ON SMALL MAMMALS IN THE SOUTHERN GREAT PLAINS

EPA Science Inventory

Changes in landscape cover in the Great Plains are resulting from the range expansion and invasion of eastern red cedar (Juniperus virginiana). By altering the landscape and local vegetation, red cedar is changing the structure and function of habitat for small mammals. We exam...

Guidelines for Developing Habitat-Based Threatened and Endangered Species Population Goals on Army Installations

DTIC Science & Technology

2005-10-01

Many plants have both sexual and vegetative reproduction, and this may be best handled with separate classes that reflect meaningful differ- ences in... Transmutation and functional representation of heterogeneous landscapes.” Landscape Ecology 5: 239-253. LaGro, J.Jr. 1991. “Assessing patch

Diversity in Riparian Landscapes

Treesearch

Thomas R. Crow; Matthew E. Baker; Burton V. Barnes

2000-01-01

Therefore, in this chapter we focus on ecosystem diversity, defined as the number, kind, and pattern of landscape and waterscape ecosystems in a specified area and the ecological processes that are associated with these patterns (Lapin and Barnes 1995). One can then characterize eeosysterns as to their composition, structure, and function -- the attributes Of...

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.

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.