[Dynamic evolution of landscape spatial pattern in Taihu Lake basin, China].

PubMed

Wang, Fang; Xie, Xiao Ping; Chen, Zhi Cong

2017-11-01

Based on the land-use satellite image datasets of 2000, 2010 and 2015, the landscape index, dynamic change model, landscape transfer matrix and CLUE-S model were integrated to analyze the dynamic evolution of the landscape spatial pattern of Taihu Lake basin. The results showed that the landscape type of the basin was dominated by cultivated land and construction land, and the degree of landscape fragmentation was strengthened from 2000 to 2015, and the distribution showed a uniform trend. From the point of transfer dynamic change, the cultivated land and construction land changed significantly, which was reduced by 6761 km 2 (2.1%) and increased by 6615.33 km 2 (8.4%), respectively. From the landscape transfer, it could be seen that the main change direction of the cultivated land reduction was the construction land, and the cultivated land with 7866.30 km 2 was converted into construction land, accounting for 91.6% of the cultivated land change, and the contribution to the construction land was 96.5%. The trend of dynamic changes of cultivated and construction land in the counties and cities was the same as that of the whole Taihu Lake basin. For Shanghai Central Urban, as well as Pudong District, Lin'an City, Baoshan District, Minhang District, Jiading District and Changzhou City, the area of the cultivated land and construction land changed more prominently. However, compared with the CLUE-S model for the landscape pattern change in 2030, the change of cultivated and construction lands would be the largest in the natural development scenario. Under the ecological protection scenario, the area of grassland would increase and the dynamic degree would reach 54.5%. Under the situation of cultivated land protection, the conversion of cultivated land to construction land would be decreased.

Recent developments in computer modeling add ecological realism to landscape genetics

EPA Science Inventory

Background / Question / Methods A factor limiting the rate of progress in landscape genetics has been the shortage of spatial models capable of linking life history attributes such as dispersal behavior to complex dynamic landscape features. The recent development of new models...

How fuel treatment types, locations, and amounts impact landscape-scale fire behavior and carbon dynamics

Treesearch

Christopher A. Dicus; Kevin J. Osborne

2015-01-01

When managing for fire across a large landscape, the types of fuel treatments, the locations of treatments, and the percentage of the landscape being treated should all interact to impact not only potential fire size, but also carbon dynamics across that landscape. To investigate these interactions, we utilized a forest growth model (FVS-FFE) and fire simulation...

Critical zone evolution and the origins of organised complexity in watersheds

NASA Astrophysics Data System (ADS)

Harman, C.; Troch, P. A.; Pelletier, J.; Rasmussen, C.; Chorover, J.

2012-04-01

The capacity of the landscape to store and transmit water is the result of a historical trajectory of landscape, soil and vegetation development, much of which is driven by hydrology itself. Progress in geomorphology and pedology has produced models of surface and sub-surface evolution in soil-mantled uplands. These dissected, denuding modeled landscapes are emblematic of the kinds of dissipative self-organized flow structures whose hydrologic organization may also be understood by low-dimensional hydrologic models. They offer an exciting starting-point for examining the mapping between the long-term controls on landscape evolution and the high-frequency hydrologic dynamics. Here we build on recent theoretical developments in geomorphology and pedology to try to understand how the relative rates of erosion, sediment transport and soil development in a landscape determine catchment storage capacity and the relative dominance of runoff process, flow pathways and storage-discharge relationships. We do so by using a combination of landscape evolution models, hydrologic process models and data from a variety of sources, including the University of Arizona Critical Zone Observatory. A challenge to linking the landscape evolution and hydrologic model representations is the vast differences in the timescales implicit in the process representations. Furthermore the vast array of processes involved makes parameterization of such models an enormous challenge. The best data-constrained geomorphic transport and soil development laws only represent hydrologic processes implicitly, through the transport and weathering rate parameters. In this work we propose to avoid this problem by identifying the relationship between the landscape and soil evolution parameters and macroscopic climate and geological controls. These macroscopic controls (such as the aridity index) have two roles: 1) they express the water and energy constraints on the long-term evolution of the landscape system, and 2) they bound the range of plausible short-term hydroclimatic regimes that may drive a particular landscape's hydrologic dynamics. To ensure that the hydrologic dynamics implicit in the evolutionary parameters are compatible with the dynamics observed in the hydrologic modeling, a set of consistency checks based on flow process dominance are developed.

Constraining climatic controls on hillslope dynamics using a coupled model for the transport of soil and tracers: Application to loess-mantled hillslopes, Charwell River, South Island, New Zealand

Treesearch

J.J. Roering; P. Almond; P. Tonkin; J. McKean

2004-01-01

Landscapes reflect a legacy of tectonic and climatic forcing as modulated by surface processes. Because the morphologic characteristics of landscapes often do not allow us to uniquely define the relative roles of tectonic deformation and climate, additional constraints are required to interpret and predict landscape dynamics. Here we describe a coupled model for the...

A modeling framework for the establishment and spread of invasive species in heterogeneous environments.

PubMed

Lustig, Audrey; Worner, Susan P; Pitt, Joel P W; Doscher, Crile; Stouffer, Daniel B; Senay, Senait D

2017-10-01

Natural and human-induced events are continuously altering the structure of our landscapes and as a result impacting the spatial relationships between individual landscape elements and the species living in the area. Yet, only recently has the influence of the surrounding landscape on invasive species spread started to be considered. The scientific community increasingly recognizes the need for broader modeling framework that focuses on cross-study comparisons at different spatiotemporal scales. Using two illustrative examples, we introduce a general modeling framework that allows for a systematic investigation of the effect of habitat change on invasive species establishment and spread. The essential parts of the framework are (i) a mechanistic spatially explicit model (a modular dispersal framework-MDIG) that allows population dynamics and dispersal to be modeled in a geographical information system (GIS), (ii) a landscape generator that allows replicated landscape patterns with partially controllable spatial properties to be generated, and (iii) landscape metrics that depict the essential aspects of landscape with which dispersal and demographic processes interact. The modeling framework provides functionality for a wide variety of applications ranging from predictions of the spatiotemporal spread of real species and comparison of potential management strategies, to theoretical investigation of the effect of habitat change on population dynamics. Such a framework allows to quantify how small-grain landscape characteristics, such as habitat size and habitat connectivity, interact with life-history traits to determine the dynamics of invasive species spread in fragmented landscape. As such, it will give deeper insights into species traits and landscape features that lead to establishment and spread success and may be key to preventing new incursions and the development of efficient monitoring, surveillance, control or eradication programs.

What determines area burned in large landscapes? Insights from a decade of comparative landscape-fire modelling

Treesearch

Geoffrey J. Cary; Robert E. Keane; Mike D. Flannigan; Ian D. Davies; Russ A. Parsons

2015-01-01

Understanding what determines area burned in large landscapes is critical for informing wildland fire management in fire-prone environments and for representing fire activity in Dynamic Global Vegetation Models. For the past ten years, a group of landscape-fire modellers have been exploring the relative influence of key determinants of area burned in temperate and...

Unfolding and melting of DNA (RNA) hairpins: the concept of structure-specific 2D dynamic landscapes.

PubMed

Lin, Milo M; Meinhold, Lars; Shorokhov, Dmitry; Zewail, Ahmed H

2008-08-07

A 2D free-energy landscape model is presented to describe the (un)folding transition of DNA/RNA hairpins, together with molecular dynamics simulations and experimental findings. The dependence of the (un)folding transition on the stem sequence and the loop length is shown in the enthalpic and entropic contributions to the free energy. Intermediate structures are well defined by the two coordinates of the landscape during (un)zipping. Both the free-energy landscape model and the extensive molecular dynamics simulations totaling over 10 mus predict the existence of temperature-dependent kinetic intermediate states during hairpin (un)zipping and provide the theoretical description of recent ultrafast temperature-jump studies which indicate that hairpin (un)zipping is, in general, not a two-state process. The model allows for lucid prediction of the collapsed state(s) in simple 2D space and we term it the kinetic intermediate structure (KIS) model.

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

NASA Astrophysics Data System (ADS)

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

2013-04-01

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

Simulating forest landscape disturbances as coupled human and natural systems

USGS Publications Warehouse

Wimberly, Michael; Sohl, Terry L.; Liu, Zhihua; Lamsal, Aashis

2015-01-01

Anthropogenic disturbances resulting from human land use affect forest landscapes over a range of spatial and temporal scales, with diverse influences on vegetation patterns and dynamics. These processes fall within the scope of the coupled human and natural systems (CHANS) concept, which has emerged as an important framework for understanding the reciprocal interactions and feedbacks that connect human activities and ecosystem responses. Spatial simulation modeling of forest landscape change is an important technique for exploring the dynamics of CHANS over large areas and long time periods. Landscape models for simulating interactions between human activities and forest landscape dynamics can be grouped into two main categories. Forest landscape models (FLMs) focus on landscapes where forests are the dominant land cover and simulate succession and natural disturbances along with forest management activities. In contrast, land change models (LCMs) simulate mosaics of different land cover and land use classes that include forests in addition to other land uses such as developed areas and agricultural lands. There are also several examples of coupled models that combine elements of FLMs and LCMs. These integrated models are particularly useful for simulating human–natural interactions in landscapes where human settlement and agriculture are expanding into forested areas. Despite important differences in spatial scale and disciplinary scope, FLMs and LCMs have many commonalities in conceptual design and technical implementation that can facilitate continued integration. The ultimate goal will be to implement forest landscape disturbance modeling in a CHANS framework that recognizes the contextual effects of regional land use and other human activities on the forest ecosystem while capturing the reciprocal influences of forests and their disturbances on the broader land use mosaic.

Understanding coupled natural and human systems on fire prone landscapes: integrating wildfire simulation into an agent based planning system.

NASA Astrophysics Data System (ADS)

Barros, Ana; Ager, Alan; Preisler, Haiganoush; Day, Michelle; Spies, Tom; Bolte, John

2015-04-01

Agent-based models (ABM) allow users to examine the long-term effects of agent decisions in complex systems where multiple agents and processes interact. This framework has potential application to study the dynamics of coupled natural and human systems where multiple stimuli determine trajectories over both space and time. We used Envision, a landscape based ABM, to analyze long-term wildfire dynamics in a heterogeneous, multi-owner landscape in Oregon, USA. Landscape dynamics are affected by land management policies, actors decisions, and autonomous processes such as vegetation succession, wildfire, or at a broader scale, climate change. Key questions include: 1) How are landscape dynamics influenced by policies and institutions, and 2) How do land management policies and actor decisions interact to produce intended and unintended consequences with respect to wildfire on fire-prone landscapes. Applying Envision to address these questions required the development of a wildfire module that could accurately simulate wildfires on the heterogeneous landscapes within the study area in terms of replicating historical fire size distribution, spatial distribution and fire intensity. In this paper we describe the development and testing of a mechanistic fire simulation system within Envision and application of the model on a 3.2 million fire prone landscape in central Oregon USA. The core fire spread equations use the Minimum Travel Time algorithm developed by M Finney. The model operates on a daily time step and uses a fire prediction system based on the relationship between energy release component and historical fires. Specifically, daily wildfire probabilities and sizes are generated from statistical analyses of historical fires in relation to daily ERC values. The MTT was coupled with the vegetation dynamics module in Envision to allow communication between the respective subsystem and effectively model fire effects and vegetation dynamics after a wildfire. Canopy and surface fuels are modeled in a state and transition framework that accounts for succession, fire effects, and fuels management. Fire effects are modeled using simulated fire intensity (flame length) to calculate expected vegetation impacts for each vegetation state. This talk will describe the mechanics of the simulation system along with initial results of Envision simulations for the Central Oregon study area that explore the dynamics of wildfire, fuel management, and succession over time.

Ecohydro-geomorphic implications of orographic precipitation on landform evolution using a landscape evolution model

NASA Astrophysics Data System (ADS)

Yetemen, O.; Saco, P. M.

2016-12-01

Orography induced precipitation and its implications on vegetation dynamics and landscape morphology have long been documented in the literature. However a numerical framework that integrates a range of ecohydrologic and geomorphic processes to explore the coupled ecohydro-geomorphic landscape response of catchments where pronounced orographic precipitation prevails has been missing. In this study, our aim is to realistically represent orographic-precipitation-driven ecohydrologic dynamics in a landscape evolution model (LEM). The model is used to investigate how ecohydro-geomorphic differences caused by differential precipitation patterns on the leeward and windward sides of low-relief landscapes lead to differences in the organization of modelled topography, soil moisture and plant biomass. We use the CHILD LEM equipped with a vegetation dynamics component that explicitly tracks above- and below-ground biomass, and a precipitation forcing component that simulates rainfall as a function of elevation and orientation. The preliminary results of the model show how the competition between an increased shear stress through runoff production and an enhanced resistance force due to denser canopy cover shape the landscape. Moreover, orographic precipitation leads to not only the migration of the divide between leeward and windward slopes but also a change in the concavity of streams. These results clearly demonstrate the strong coupling between landform evolution and climate processes.

Modeling Coupled Landscape Evolution and Soil Organic Carbon Dynamics in Intensively Management Landscapes

NASA Astrophysics Data System (ADS)

Yan, Q.; Kumar, P.

2017-12-01

Soil is the largest reservoir of carbon in the biosphere but in agricultural areas it is going through rapid erosion due disturbance arising from crop harvest, tillage, and tile drainage. Identifying whether the production of soil organic carbon (SOC) from the crops can compensate for the loss due to erosion is critical to ensure our food security and adapt to climate change. In the U.S. Midwest where large areas of land are intensively managed for agriculture practices, predicting soil quantity and quality are critical for maintaining crop yield and other Critical Zone services. This work focuses on modeling the coupled landscape evolutions soil organic carbon dynamics in agricultural fields. It couples landscape evolution, surface water runoff, organic matter transformation, and soil moisture dynamics to understand organic carbon gain and loss due to natural forcing and farming practices, such as fertilizer application and tillage. A distinctive feature of the model is the coupling of surface ad subsurface processes that predicts both surficial changes and transport along with the vertical transport and dynamics. Our results show that landscape evolution and farming practices play dominant roles in soil organic carbon (SOC) dynamics both above- and below-ground. Contrary to the common assumption that a vertical profile of SOC concentration decreases exponentially with depth, we find that in many situations SOC concentration below-ground could be higher than that at the surface. Tillage plays a complex role in organic matter dynamics. On one hand, tillage would accelerate the erosion rate, on the other hand, it would improve carbon storage by burying surface SOC into below ground. Our model consistently reproduces the observed above- and below-ground patterns of SOC in the field sites of Intensively Managed Landscapes Critical Zone Observatory (IMLCZO). This model bridges the gaps between the landscape evolution, below- and above-ground hydrologic cycle, and biogeochemical processes. This study not only helps us understand the coupled carbon-nitrogen cycle, but also serve as an instrument to develop practical approaches for reducing soil erosion and carbon loss when the landscape is affected by human activities.

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...

An object-oriented forest landscape model and its representation of tree species

Treesearch

Hong S. He; David J. Mladenoff; Joel Boeder

1999-01-01

LANDIS is a forest landscape model that simulates the interaction of large landscape processes and forest successional dynamics at tree species level. We discuss how object-oriented design (OOD) approaches such as modularity, abstraction and encapsulation are integrated into the design of LANDIS. We show that using OOD approaches, model decisions (olden as model...

Dynamics of coupled human-landscape systems

NASA Astrophysics Data System (ADS)

Werner, B. T.; McNamara, D. E.

2007-11-01

A preliminary dynamical analysis of landscapes and humans as hierarchical complex systems suggests that strong coupling between the two that spreads to become regionally or globally pervasive should be focused at multi-year to decadal time scales. At these scales, landscape dynamics is dominated by water, sediment and biological routing mediated by fluvial, oceanic, atmospheric processes and human dynamics is dominated by simplifying, profit-maximizing market forces and political action based on projection of economic effect. Also at these scales, landscapes impact humans through patterns of natural disasters and trends such as sea level rise; humans impact landscapes by the effect of economic activity and changes meant to mitigate natural disasters and longer term trends. Based on this analysis, human-landscape coupled systems can be modeled using heterogeneous agents employing prediction models to determine actions to represent the nonlinear behavior of economic and political systems and rule-based routing algorithms to represent landscape processes. A cellular model for the development of New Orleans illustrates this approach, with routing algorithms for river and hurricane-storm surge determining flood extent, five markets (home, labor, hotel, tourism and port services) connecting seven types of economic agents (home buyers/laborers, home developers, hotel owners/ employers, hotel developers, tourists, port services developer and port services owners/employers), building of levees or a river spillway by political agents and damage to homes, hotels or port services within cells determined by the passage or depth of flood waters. The model reproduces historical aspects of New Orleans economic development and levee construction and the filtering of frequent small-scale floods at the expense of large disasters.

Calibrating a forest landscape model to simulate frequent fire in Mediterranean-type shrublands

USGS Publications Warehouse

Syphard, A.D.; Yang, J.; Franklin, J.; He, H.S.; Keeley, J.E.

2007-01-01

In Mediterranean-type ecosystems (MTEs), fire disturbance influences the distribution of most plant communities, and altered fire regimes may be more important than climate factors in shaping future MTE vegetation dynamics. Models that simulate the high-frequency fire and post-fire response strategies characteristic of these regions will be important tools for evaluating potential landscape change scenarios. However, few existing models have been designed to simulate these properties over long time frames and broad spatial scales. We refined a landscape disturbance and succession (LANDIS) model to operate on an annual time step and to simulate altered fire regimes in a southern California Mediterranean landscape. After developing a comprehensive set of spatial and non-spatial variables and parameters, we calibrated the model to simulate very high fire frequencies and evaluated the simulations under several parameter scenarios representing hypotheses about system dynamics. The goal was to ensure that observed model behavior would simulate the specified fire regime parameters, and that the predictions were reasonable based on current understanding of community dynamics in the region. After calibration, the two dominant plant functional types responded realistically to different fire regime scenarios. Therefore, this model offers a new alternative for simulating altered fire regimes in MTE landscapes. ?? 2007 Elsevier Ltd. All rights reserved.

Phase Transitions in Geomorphology

NASA Astrophysics Data System (ADS)

Ortiz, C. P.; Jerolmack, D. J.

2015-12-01

Landscapes are patterns in a dynamic steady-state, due to competing processes that smooth or sharpen features over large distances and times. Geomorphic transport laws have been developed to model the mass-flux due to different processes, but are unreasonably effective at recovering the scaling relations of landscape features. Using a continuum approximation to compare experimental landscapes and the observed landscapes of the earth, one finds they share similar morphodynamics despite a breakdown of classical dynamical similarity between the two. We propose the origin of this effectiveness is a different kind of dynamic similarity in the statistics of initiation and cessation of motion of groups of grains, which is common to disordered systems of grains under external driving. We will show how the existing data of sediment transport points to common signatures with dynamical phase transitions between "mobile" and "immobile" phases in other disordered systems, particularly granular materials, colloids, and foams. Viewing landscape evolution from the lens of non-equilibrium statistical physics of disordered systems leads to predictions that the transition of bulk measurements such as particle flux is continuous from one phase to another, that the collective nature of the particle dynamics leads to very slow aging of bulk properties, and that the dynamics are history-dependent. Recent results from sediment transport experiments support these predictions, suggesting that existing geomorphic transport laws may need to be replaced by a new generation of stochastic models with ingredients based on the physics of disordered phase transitions. We discuss possible strategies for extracting the necessary information to develop these models from measurements of geomorphic transport noise by connecting particle-scale collective dynamics and space-time fluctuations over landscape features.

Modeling fluvial incision and transient landscape evolution: Influence of dynamic channel adjustment

NASA Astrophysics Data System (ADS)

Attal, M.; Tucker, G. E.; Whittaker, A. C.; Cowie, P. A.; Roberts, G. P.

2008-09-01

Channel geometry exerts a fundamental control on fluvial processes. Recent work has shown that bedrock channel width depends on a number of parameters, including channel slope, and is not solely a function of drainage area as is commonly assumed. The present work represents the first attempt to investigate the consequences of dynamic, gradient-sensitive channel adjustment for drainage-basin evolution. We use the Channel-Hillslope Integrated Landscape Development (CHILD) model to analyze the response of a catchment to a given tectonic perturbation, using, as a template, the topography of a well-documented catchment in the footwall of an active normal fault in the Apennines (Italy) that is known to be undergoing a transient response to tectonic forcing. We show that the observed transient response can be reproduced to first order with a simple detachment-limited fluvial incision law. Transient landscape is characterized by gentler gradients and a shorter response time when dynamic channel adjustment is allowed. The differences in predicted channel geometry between the static case (width dependent solely on upstream area) and dynamic case (width dependent on both drainage area and channel slope) lead to contrasting landscape morphologies when integrated at the scale of a whole catchment, particularly in presence of strong tilting and/or pronounced slip-rate acceleration. Our results emphasize the importance of channel width in controlling fluvial processes and landscape evolution. They stress the need for using a dynamic hydraulic scaling law when modeling landscape evolution, particularly when the relative uplift field is nonuniform.

Dynamic Shade and Irradiance Simulation of Aquatic Landscapes and Watersheds

EPA Science Inventory

Penumbra is a landscape shade and irradiance simulation model that simulates how solar energy spatially and temporally interacts within dynamic ecosystems such as riparian zones, forests, and other terrain that cast topological shadows. Direct and indirect solar energy accumulate...

Determining landscape extent for succession and disturbance simulation modeling

Treesearch

Eva C. Karau; Robert E. Keane

2007-01-01

Dividing regions into manageable landscape units presents special problems in landscape ecology and land management. Ideally, a landscape should be large enough to capture a broad range of vegetation, environmental and disturbance dynamics, but small enough to be useful for focused management objectives. The purpose of this study was to determine the optimal landscape...

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

Lammert, Heiko; Noel, Jeffrey K.; Haglund, Ellinor

The diversity in a set of protein nuclear magnetic resonance (NMR) structures provides an estimate of native state fluctuations that can be used to refine and enrich structure-based protein models (SBMs). Dynamics are an essential part of a protein’s functional native state. The dynamics in the native state are controlled by the same funneled energy landscape that guides the entire folding process. SBMs apply the principle of minimal frustration, drawn from energy landscape theory, to construct a funneled folding landscape for a given protein using only information from the native structure. On an energy landscape smoothed by evolution towards minimalmore » frustration, geometrical constraints, imposed by the native structure, control the folding mechanism and shape the native dynamics revealed by the model. Native-state fluctuations can alternatively be estimated directly from the diversity in the set of NMR structures for a protein. Based on this information, we identify a highly flexible loop in the ribosomal protein S6 and modify the contact map in a SBM to accommodate the inferred dynamics. By taking into account the probable native state dynamics, the experimental transition state is recovered in the model, and the correct order of folding events is restored. Our study highlights how the shared energy landscape connects folding and function by showing that a better description of the native basin improves the prediction of the folding mechanism.« less

Strategies for control of sudden oak death in Humboldt County-informed guidance based on a parameterized epidemiological model

Treesearch

João A. N. Filipe; Richard C. Cobb; David M. Rizzo; Ross K. Meentemeyer; Christopher A. Gilligan

2010-01-01

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

Influence of dynamic topography on landscape evolution and passive continental margin stratigraphy

NASA Astrophysics Data System (ADS)

Ding, Xuesong; Salles, Tristan; Flament, Nicolas; Rey, Patrice

2017-04-01

Quantifying the interaction between surface processes and tectonics/deep Earth processes is one important aspect of landscape evolution modelling. Both observations and results from numerical modelling indicate that dynamic topography - a surface expression of time-varying mantle convection - plays a significant role in shaping landscape through geological time. Recent research suggests that dynamic topography also has non-negligible effects on stratigraphic architecture by modifying accommodation space available for sedimentation. In addition, dynamic topography influences the sediment supply to continental margins. We use Badlands to investigate the evolution of a continental-scale landscape in response to transient dynamic uplift or subsidence, and to model the stratigraphic development on passive continental margins in response to sea-level change, thermal subsidence and dynamic topography. We consider a circularly symmetric landscape consisting of a plateau surrounded by a gently sloping continental plain and a continental margin, and a linear wave of dynamic topography. We analyze the evolution of river catchments, of longitudinal river profiles and of the χ values to evaluate the dynamic response of drainage systems to dynamic topography. We calculate the amount of cumulative erosion and deposition, and sediment flux at shoreline position, as a function of precipitation rate and erodibility coefficient. We compute the stratal stacking pattern and Wheeler diagram on vertical cross-sections at the continental margin. Our results indicate that dynamic topography 1) has a considerable influence on drainage reorganization; 2) contributes to shoreline migration and the distribution of depositional packages by modifying the accommodation space; 3) affects sediment supply to the continental margin. Transient dynamic topography contributes to the migration of drainage divides and to the migration of the mainstream in a drainage basin. The dynamic uplift (respectively subsidence) of the source area results in an increase (respectively decrease) of sediment supply, while the dynamic uplift (respectively subsidence) of the continental margin leads to a decrease (respectively increase) in sedimentation.

From soilscapes to landscapes: A landscape-oriented approach to simulate soil organic carbon dynamics in intensively managed landscapes

USDA-ARS?s Scientific Manuscript database

Most available biogeochemical models focus within a soil profile and cannot adequately resolve contributions of the lighter size fractions of organic rich soils for Enrichment Ratio (ER) estimates, thereby causing unintended errors in Soil Organic Carbon (SOC) storage predictions. These models set E...

Dynamics of sea level rise and coastal flooding on a changing landscape

NASA Astrophysics Data System (ADS)

Bilskie, M. V.; Hagen, S. C.; Medeiros, S. C.; Passeri, D. L.

2014-02-01

Standard approaches to determining the impacts of sea level rise (SLR) on storm surge flooding employ numerical models reflecting present conditions with modified sea states for a given SLR scenario. In this study, we advance this paradigm by adjusting the model framework so that it reflects not only a change in sea state but also variations to the landscape (morphologic changes and urbanization of coastal cities). We utilize a numerical model of the Mississippi and Alabama coast to simulate the response of hurricane storm surge to changes in sea level, land use/land cover, and land surface elevation for past (1960), present (2005), and future (2050) conditions. The results show that the storm surge response to SLR is dynamic and sensitive to changes in the landscape. We introduce a new modeling framework that includes modification of the landscape when producing storm surge models for future conditions.

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

PubMed

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

2014-08-01

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

Local disturbance cycles and the maintenance of heterogeneity across scales in marine metapopulations.

PubMed

Gouhier, Tarik C; Guichard, Frédéric

2007-03-01

In marine systems, the occurrence and implications of disturbance-recovery cycles have been revealed at the landscape level, but only in demographically open or closed systems where landscape-level dynamics are assumed to have no feedback effect on regional dynamics. We present a mussel metapopulation model to elucidate the role of landscape-level disturbance cycles for regional response of mussel populations to onshore productivity and larval transport. Landscape dynamics are generated through spatially explicit rules, and each landscape is connected to its neighbor through unidirectional larval dispersal. The role of landscape disturbance cycles in the regional system behavior is elucidated (1) in demographically open vs. demographically coupled systems, in relation to (2) onshore reproductive output and (3) the temporal scale of landscape disturbance dynamics. By controlling for spatial structure at the landscape and metapopulation levels, we first demonstrate the interaction between landscape and oceanographic connectivity. The temporal scale of disturbance cycles, as controlled by mussel colonization rate, plays a critical role in the regional behavior of the system. Indeed, fast disturbance cycles are responsible for regional synchrony in relation to onshore reproductive output. Slow disturbance cycles, however, lead to increased robustness to changes in productivity and to demographic coupling. These testable predictions indicate that the occurrence and temporal scale of local disturbance-recovery dynamics can drive large-scale variability in demographically open systems, and the response of metapopulations to changes in nearshore productivity.

Modeling the Influence of Dynamic Zoning of Forest Harvesting on Ecological Succession in a Northern Hardwoods Landscape

Treesearch

Patrick A. Zollner; Eric J. Gustafson; Hong S. He; Volker C. Radeloff; David J. Mladenoff

2005-01-01

Dynamic zoning (systematic alteration in the spatial and temporal allocation of even-aged forest management practices) has been proposed as a means to change the spatial pattern of timber harvest across a landscape to maximize forest interior habitat while holding timber harvest levels constant. Simulation studies have established that dynamic zoning strategies...

Dynamical analysis of cellular ageing by modeling of gene regulatory network based attractor landscape.

PubMed

Chong, Ket Hing; Zhang, Xiaomeng; Zheng, Jie

2018-01-01

Ageing is a natural phenomenon that is inherently complex and remains a mystery. Conceptual model of cellular ageing landscape was proposed for computational studies of ageing. However, there is a lack of quantitative model of cellular ageing landscape. This study aims to investigate the mechanism of cellular ageing in a theoretical model using the framework of Waddington's epigenetic landscape. We construct an ageing gene regulatory network (GRN) consisting of the core cell cycle regulatory genes (including p53). A model parameter (activation rate) is used as a measure of the accumulation of DNA damage. Using the bifurcation diagrams to estimate the parameter values that lead to multi-stability, we obtained a conceptual model for capturing three distinct stable steady states (or attractors) corresponding to homeostasis, cell cycle arrest, and senescence or apoptosis. In addition, we applied a Monte Carlo computational method to quantify the potential landscape, which displays: I) one homeostasis attractor for low accumulation of DNA damage; II) two attractors for cell cycle arrest and senescence (or apoptosis) in response to high accumulation of DNA damage. Using the Waddington's epigenetic landscape framework, the process of ageing can be characterized by state transitions from landscape I to II. By in silico perturbations, we identified the potential landscape of a perturbed network (inactivation of p53), and thereby demonstrated the emergence of a cancer attractor. The simulated dynamics of the perturbed network displays a landscape with four basins of attraction: homeostasis, cell cycle arrest, senescence (or apoptosis) and cancer. Our analysis also showed that for the same perturbed network with low DNA damage, the landscape displays only the homeostasis attractor. The mechanistic model offers theoretical insights that can facilitate discovery of potential strategies for network medicine of ageing-related diseases such as cancer.

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.

Ecohydrologic role of solar radiation on landscape evolution

NASA Astrophysics Data System (ADS)

Yetemen, Omer; Istanbulluoglu, Erkan; Flores-Cervantes, J. Homero; Vivoni, Enrique R.; Bras, Rafael L.

2015-02-01

Solar radiation has a clear signature on the spatial organization of ecohydrologic fluxes, vegetation patterns and dynamics, and landscape morphology in semiarid ecosystems. Existing landscape evolution models (LEMs) do not explicitly consider spatially explicit solar radiation as model forcing. Here, we improve an existing LEM to represent coupled processes of energy, water, and sediment balance for semiarid fluvial catchments. To ground model predictions, a study site is selected in central New Mexico where hillslope aspect has a marked influence on vegetation patterns and landscape morphology. Model predictions are corroborated using limited field observations in central NM and other locations with similar conditions. We design a set of comparative LEM simulations to investigate the role of spatially explicit solar radiation on landscape ecohydro-geomorphic development under different uplift scenarios. Aspect-control and network-control are identified as the two main drivers of soil moisture and vegetation organization on the landscape. Landscape-scale and long-term implications of these short-term ecohdrologic patterns emerged in modeled landscapes. As north facing slopes (NFS) get steeper by continuing uplift they support erosion-resistant denser vegetation cover which leads to further slope steepening until erosion and uplift attains a dynamic equilibrium. Conversely, on south facing slopes (SFS), as slopes grow with uplift, increased solar radiation exposure with slope supports sparser biomass and shallower slopes. At the landscape scale, these differential erosion processes lead to asymmetric development of catchment forms, consistent with regional observations. Understanding of ecohydrogeomorphic evolution will improve to assess the impacts of past and future climates on landscape response and morphology.

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.

[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.

On modeling the organization of landscapes and vegetation patterns controlled by solar radiation

NASA Astrophysics Data System (ADS)

Istanbulluoglu, E.; Yetemen, O.

2014-12-01

Solar radiation is a critical driver of ecohydrologic processes and vegetation dynamics. Patterns of runoff generation and vegetation dictate landscape geomorphic response. Distinct patterns in the organization of soil moisture, vegetation type, and landscape morphology have been documented in close relation to aspect in a range of climates. Within catchments, from north to south facing slopes, studies have shown ecotone shifts from forest to shrub species, and steep diffusion-dominated landforms to fluvial landforms. Over the long term differential evolution of ecohydrology and geomorphology leads to observed asymmetric structure in the planform of channel network and valley morphology. In this talk we present examples of coupled modeling of ecohydrology and geomorphology driven by solar radiation. In a cellular automata model of vegetation dynamics we will first show how plants organize in north and south facing slopes and how biodiversity changes with elevation. When vegetation-erosion feedbacks are coupled emergent properties of the coupled system are observed in the modeled elevation and vegetation fields. Integrating processes at a range of temporal and spatial scales, coupled models of ecohydrologic and geomorphic dynamics enable examination of global change impacts on landscapes and ecosystems.

Dynamic Shade and Irradiance Simulation of Aquatic ...

EPA Pesticide Factsheets

Penumbra is a landscape shade and irradiance simulation model that simulates how solar energy spatially and temporally interacts within dynamic ecosystems such as riparian zones, forests, and other terrain that cast topological shadows. Direct and indirect solar energy accumulates across landscapes and is the main energy driver for increasing aquatic and landscape temperatures at both local and holistic scales. Landscape disturbances such as landuse change, clear cutting, and fire can cause significant variations in the resulting irradiance reaching particular locations. Penumbra can simulate solar angles and irradiance at definable temporal grains as low as one minute while simulating landscape shadowing up to an entire year. Landscapes can be represented at sub-meter resolutions with appropriate spatial data inputs, such as field data or elevation and surface object heights derived from light detection and ranging (LiDAR) data. This work describes Penumbra’s framework and methodology, external model integration capability, and appropriate model application for a variety of watershed restoration project types. First, an overview of Penumbra’s framework reveals what this model adds to the existing ecological modeling domain. Second, Penumbra’s stand-alone and integration modes are explained and demonstrated. Stand-alone modeling results are showcased within the 3-D visualization tool VISTAS (VISualizing Terrestrial-Aquatic Systems), which fluently summariz

A method to efficiently apply a biogeochemical model to a landscape.

Treesearch

Robert E. Kennedy; David P. Turner; Warren B. Cohen; Michael Guzy

2006-01-01

Biogeochemical models offer an important means of understanding carbon dynamics, but the computational complexity of many models means that modeling all grid cells on a large landscape is computationally burdensome. Because most biogeochemical models ignore adjacency effects between cells, however, a more efficient approach is possible. Recognizing that spatial...

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

PubMed

Gilpin, William; Feldman, Marcus W

2017-07-01

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

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

Treesearch

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

2010-01-01

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

Experimental Beetle Metapopulations Respond Positively to Dynamic Landscapes and Reduced Connectivity

PubMed Central

Govindan, Byju N.; Swihart, Robert K.

2012-01-01

Interactive effects of multiple environmental factors on metapopulation dynamics have received scant attention. We designed a laboratory study to test hypotheses regarding interactive effects of factors affecting the metapopulation dynamics of red flour beetle, Tribolium castaneum. Within a four-patch landscape we modified resource level (constant and diminishing), patch connectivity (high and low) and patch configuration (static and dynamic) to conduct a 23 factorial experiment, consisting of 8 metapopulations, each with 3 replicates. For comparison, two control populations consisting of isolated and static subpopulations were provided with resources at constant or diminishing levels. Longitudinal data from 22 tri-weekly counts of beetle abundance were analyzed using Bayesian Poisson generalized linear mixed models to estimate additive and interactive effects of factors affecting abundance. Constant resource levels, low connectivity and dynamic patches yielded greater levels of adult beetle abundance. For a given resource level, frequency of colonization exceeded extinction in landscapes with dynamic patches when connectivity was low, thereby promoting greater patch occupancy. Negative density dependence of pupae on adults occurred and was stronger in landscapes with low connectivity and constant resources; these metapopulations also demonstrated greatest stability. Metapopulations in control landscapes went extinct quickly, denoting lower persistence than comparable landscapes with low connectivity. When landscape carrying capacity was constant, habitat destruction coupled with low connectivity created asynchronous local dynamics and refugia within which cannibalism of pupae was reduced. Increasing connectivity may be counter-productive and habitat destruction/recreation may be beneficial to species in some contexts. PMID:22509314

Integrating the landscape epidemiology and genetics of RNA viruses: rabies in domestic dogs as a model.

PubMed

Brunker, K; Hampson, K; Horton, D L; Biek, R

2012-12-01

Landscape epidemiology and landscape genetics combine advances in molecular techniques, spatial analyses and epidemiological models to generate a more real-world understanding of infectious disease dynamics and provide powerful new tools for the study of RNA viruses. Using dog rabies as a model we have identified how key questions regarding viral spread and persistence can be addressed using a combination of these techniques. In contrast to wildlife rabies, investigations into the landscape epidemiology of domestic dog rabies requires more detailed assessment of the role of humans in disease spread, including the incorporation of anthropogenic landscape features, human movements and socio-cultural factors into spatial models. In particular, identifying and quantifying the influence of anthropogenic features on pathogen spread and measuring the permeability of dispersal barriers are important considerations for planning control strategies, and may differ according to cultural, social and geographical variation across countries or continents. Challenges for dog rabies research include the development of metapopulation models and transmission networks using genetic information to uncover potential source/sink dynamics and identify the main routes of viral dissemination. Information generated from a landscape genetics approach will facilitate spatially strategic control programmes that accommodate for heterogeneities in the landscape and therefore utilise resources in the most cost-effective way. This can include the efficient placement of vaccine barriers, surveillance points and adaptive management for large-scale control programmes.

Looking for the optimal rate of recombination for evolutionary dynamics

NASA Astrophysics Data System (ADS)

Saakian, David B.

2018-01-01

We consider many-site mutation-recombination models of evolution with selection. We are looking for situations where the recombination increases the mean fitness of the population, and there is an optimal recombination rate. We found two fitness landscapes supporting such nonmonotonic behavior of the mean fitness versus the recombination rate. The first case is related to the evolution near the error threshold on a neutral-network-like fitness landscape, for moderate genome lengths and large population. The more realistic case is the second one, in which we consider the evolutionary dynamics of a finite population on a rugged fitness landscape (the smooth fitness landscape plus some random contributions to the fitness). We also give the solution to the horizontal gene transfer model in the case of asymmetric mutations. To obtain nonmonotonic behavior for both mutation and recombination, we need a specially designed (ideal) fitness landscape.

APPLYING THE PATUXENT LANDSCAPE UNIT MODEL TO HUMAN DOMINATED ECOSYSTEMS: THE CASE OF AGRICULTURE. (R827169)

EPA Science Inventory

Non-spatial dynamics are core to landscape simulations. Unit models simulate system interactions aggregated within one space unit of resolution used within a spatial model. For unit models to be applicable to spatial simulations they have to be formulated in a general enough w...

Assessing knowledge ambiguity in the creation of a model based on expert knowledge and comparison with the results of a landscape succession model in central Labrador. Chapter 10.

Treesearch

Frederik Doyon; Brian Sturtevant; Michael J. Papaik; Andrew Fall; Brian Miranda; Daniel D. Kneeshaw; Christian Messier; Marie-Josee Fortin; Patrick M.A. James

2012-01-01

Sustainable forest management (SFM) recognizes that the spatial and temporal patterns generated at different scales by natural landscape and stand dynamics processes should serve as a guide for managing the forest within its range of natural variability. Landscape simulation modeling is a powerful tool that can help encompass such complexity and support SFM planning....

Alternative future analysis for assessing the potential impact of climate change on urban landscape dynamics.

PubMed

He, Chunyang; Zhao, Yuanyuan; Huang, Qingxu; Zhang, Qiaofeng; Zhang, Da

2015-11-01

Assessing the impact of climate change on urban landscape dynamics (ULD) is the foundation for adapting to climate change and maintaining urban landscape sustainability. This paper demonstrates an alternative future analysis by coupling a system dynamics (SD) and a cellular automata (CA) model. The potential impact of different climate change scenarios on ULD from 2009 to 2030 was simulated and evaluated in the Beijing-Tianjin-Tangshan megalopolis cluster area (BTT-MCA). The results suggested that the integrated model, which combines the advantages of the SD and CA model, has the strengths of spatial quantification and flexibility. Meanwhile, the results showed that the influence of climate change would become more severe over time. In 2030, the potential urban area affected by climate change will be 343.60-1260.66 km(2) (5.55 -20.37 % of the total urban area, projected by the no-climate-change-effect scenario). Therefore, the effects of climate change should not be neglected when designing and managing urban landscape. Copyright © 2015 Elsevier B.V. All rights reserved.

Simulation Based Exploration of Critical Zone Dynamics in Intensively Managed Landscapes

NASA Astrophysics Data System (ADS)

Kumar, P.

2017-12-01

The advent of high-resolution measurements of topographic and (vertical) vegetation features using areal LiDAR are enabling us to resolve micro-scale ( 1m) landscape structural characteristics over large areas. Availability of hyperspectral measurements is further augmenting these LiDAR data by enabling the biogeochemical characterization of vegetation and soils at unprecedented spatial resolutions ( 1-10m). Such data have opened up novel opportunities for modeling Critical Zone processes and exploring questions that were not possible before. We show how an integrated 3-D model at 1m grid resolution can enable us to resolve micro-topographic and ecological dynamics and their control on hydrologic and biogeochemical processes over large areas. We address the computational challenge of such detailed modeling by exploiting hybrid CPU and GPU computing technologies. We show results of moisture, biogeochemical, and vegetation dynamics from studies in the Critical Zone Observatory for Intensively managed Landscapes (IMLCZO) in the Midwestern United States.

State-and-transition simulation models: a framework for forecasting landscape change

USGS Publications Warehouse

Daniel, Colin; Frid, Leonardo; Sleeter, Benjamin M.; Fortin, Marie-Josée

2016-01-01

SummaryA wide range of spatially explicit simulation models have been developed to forecast landscape dynamics, including models for projecting changes in both vegetation and land use. While these models have generally been developed as separate applications, each with a separate purpose and audience, they share many common features.We present a general framework, called a state-and-transition simulation model (STSM), which captures a number of these common features, accompanied by a software product, called ST-Sim, to build and run such models. The STSM method divides a landscape into a set of discrete spatial units and simulates the discrete state of each cell forward as a discrete-time-inhomogeneous stochastic process. The method differs from a spatially interacting Markov chain in several important ways, including the ability to add discrete counters such as age and time-since-transition as state variables, to specify one-step transition rates as either probabilities or target areas, and to represent multiple types of transitions between pairs of states.We demonstrate the STSM method using a model of land-use/land-cover (LULC) change for the state of Hawai'i, USA. Processes represented in this example include expansion/contraction of agricultural lands, urbanization, wildfire, shrub encroachment into grassland and harvest of tree plantations; the model also projects shifts in moisture zones due to climate change. Key model output includes projections of the future spatial and temporal distribution of LULC classes and moisture zones across the landscape over the next 50 years.State-and-transition simulation models can be applied to a wide range of landscapes, including questions of both land-use change and vegetation dynamics. Because the method is inherently stochastic, it is well suited for characterizing uncertainty in model projections. When combined with the ST-Sim software, STSMs offer a simple yet powerful means for developing a wide range of models of landscape dynamics.

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.

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

Treesearch

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

2011-01-01

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

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

Treesearch

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

2016-01-01

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

Simulated cavity tree dynamics under alternative timber harvest regimes

Treesearch

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

2004-01-01

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

Integration of climatic water deficit and fine-scale physiography in process-based modeling of forest landscape resilience to large-scale tree mortality

NASA Astrophysics Data System (ADS)

Yang, J.; Weisberg, P.; Dilts, T.

2016-12-01

Climate warming can lead to large-scale drought-induced tree mortality events and greatly affect forest landscape resilience. Climatic water deficit (CWD) and its physiographic variations provide a key mechanism in driving landscape dynamics in response to climate change. Although CWD has been successfully applied in niche-based species distribution models, its application in process-based forest landscape models is still scarce. Here we present a framework incorporating fine-scale influence of terrain on ecohydrology in modeling forest landscape dynamics. We integrated CWD with a forest landscape succession and disturbance model (LANDIS-II) to evaluate how tree species distribution might shift in response to different climate-fire scenarios across an elevation-aspect gradient in a semi-arid montane landscape of northeastern Nevada, USA. Our simulations indicated that drought-intolerant tree species such as quaking aspen could experience greatly reduced distributions in the more arid portions of their existing ranges due to water stress limitations under future climate warming scenarios. However, even at the most xeric portions of its range, aspen is likely to persist in certain environmental settings due to unique and often fine-scale combinations of resource availability, species interactions and disturbance regime. The modeling approach presented here allowed identification of these refugia. In addition, this approach helped quantify how the direction and magnitude of fire influences on species distribution would vary across topoclimatic gradients, as well as furthers our understanding on the role of environmental conditions, fire, and inter-specific competition in shaping potential responses of landscape resilience to climate change.

The past and future of modeling forest dynamics: from growth and yield curves to forest landscape models

Treesearch

Stephen R. Shifley; Hong S. He; Heike Lischke; Wen J. Wang; Wenchi Jin; Eric J. Gustafson; Jonathan R. Thompson; Frank R. Thompson; William D. Dijak; Jian Yang

2017-01-01

Context. Quantitative models of forest dynamics have followed a progression toward methods with increased detail, complexity, and spatial extent. Objectives. We highlight milestones in the development of forest dynamics models and identify future research and application opportunities. Methods. We reviewed...

The invasive species Ulex europaeus (Fabaceae) shows high dynamism in a fragmented landscape of south-central Chile.

PubMed

Altamirano, Adison; Cely, Jenny Paola; Etter, Andrés; Miranda, Alejandro; Fuentes-Ramirez, Andres; Acevedo, Patricio; Salas, Christian; Vargas, Rodrigo

2016-08-01

Ulex europaeus (gorse) is an invasive shrub deemed as one of the most invasive species in the world. U. europaeus is widely distributed in the south-central area of Chile, which is considered a world hotspot for biodiversity conservation. In addition to its negative effects on the biodiversity of natural ecosystems, U. europaeus is one of the most severe pests for agriculture and forestry. Despite its importance as an invasive species, U. europaeus has been little studied. Although information exists on the potential distribution of the species, the interaction of the invasion process with the spatial dynamic of the landscape and the landscape-scale factors that control the presence or absence of the species is still lacking. We studied the spatial and temporal dynamics of the landscape and how these relate to U. europaeus invasion in south-central Chile. We used supervised classification of satellite images to determine the spatial distribution of the species and other land covers for the years 1986 and 2003, analysing the transitions between the different land covers. We used logistic regression for modelling the increase, decrease and permanence of U. europaeus invasion considering landscape variables. Results showed that the species covers only around 1 % of the study area and showed a 42 % reduction in area for the studied period. However, U. europaeus was the cover type which presented the greatest dynamism in the landscape. We found a strong relationship between changes in land cover and the invasion process, especially connected with forest plantations of exotic species, which promotes the displacement of U. europaeus. The model of gorse cover increase presented the best performance, and the most important predictors were distance to seed source and landscape complexity index. Our model predicted high spread potential of U. europaeus in areas of high conservation value. We conclude that proper management for this invasive species must take into account the spatial dynamics of the landscape within the invaded area in order to address containment, control or mitigation of the invasion.

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

Linking river management to species conservation using dynamic landscape scale models

USGS Publications Warehouse

Freeman, Mary C.; Buell, Gary R.; Hay, Lauren E.; Hughes, W. Brian; Jacobson, Robert B.; Jones, John W.; Jones, S.A.; LaFontaine, Jacob H.; Odom, Kenneth R.; Peterson, James T.; Riley, Jeffrey W.; Schindler, J. Stephen; Shea, C.; Weaver, J.D.

2013-01-01

Efforts to conserve stream and river biota could benefit from tools that allow managers to evaluate landscape-scale changes in species distributions in response to water management decisions. We present a framework and methods for integrating hydrology, geographic context and metapopulation processes to simulate effects of changes in streamflow on fish occupancy dynamics across a landscape of interconnected stream segments. We illustrate this approach using a 482 km2 catchment in the southeastern US supporting 50 or more stream fish species. A spatially distributed, deterministic and physically based hydrologic model is used to simulate daily streamflow for sub-basins composing the catchment. We use geographic data to characterize stream segments with respect to channel size, confinement, position and connectedness within the stream network. Simulated streamflow dynamics are then applied to model fish metapopulation dynamics in stream segments, using hypothesized effects of streamflow magnitude and variability on population processes, conditioned by channel characteristics. The resulting time series simulate spatially explicit, annual changes in species occurrences or assemblage metrics (e.g. species richness) across the catchment as outcomes of management scenarios. Sensitivity analyses using alternative, plausible links between streamflow components and metapopulation processes, or allowing for alternative modes of fish dispersal, demonstrate large effects of ecological uncertainty on model outcomes and highlight needed research and monitoring. Nonetheless, with uncertainties explicitly acknowledged, dynamic, landscape-scale simulations may prove useful for quantitatively comparing river management alternatives with respect to species conservation.

The effects of landscape modifications on the long-term persistence of animal populations.

PubMed

Nabe-Nielsen, Jacob; Sibly, Richard M; Forchhammer, Mads C; Forbes, Valery E; Topping, Christopher J

2010-01-28

The effects of landscape modifications on the long-term persistence of wild animal populations is of crucial importance to wildlife managers and conservation biologists, but obtaining experimental evidence using real landscapes is usually impossible. To circumvent this problem we used individual-based models (IBMs) of interacting animals in experimental modifications of a real Danish landscape. The models incorporate as much as possible of the behaviour and ecology of four species with contrasting life-history characteristics: skylark (Alauda arvensis), vole (Microtus agrestis), a ground beetle (Bembidion lampros) and a linyphiid spider (Erigone atra). This allows us to quantify the population implications of experimental modifications of landscape configuration and composition. Starting with a real agricultural landscape, we progressively reduced landscape complexity by (i) homogenizing habitat patch shapes, (ii) randomizing the locations of the patches, and (iii) randomizing the size of the patches. The first two steps increased landscape fragmentation. We assessed the effects of these manipulations on the long-term persistence of animal populations by measuring equilibrium population sizes and time to recovery after disturbance. Patch rearrangement and the presence of corridors had a large effect on the population dynamics of species whose local success depends on the surrounding terrain. Landscape modifications that reduced population sizes increased recovery times in the short-dispersing species, making small populations vulnerable to increasing disturbance. The species that were most strongly affected by large disturbances fluctuated little in population sizes in years when no perturbations took place. Traditional approaches to the management and conservation of populations use either classical methods of population analysis, which fail to adequately account for the spatial configurations of landscapes, or landscape ecology, which accounts for landscape structure but has difficulty predicting the dynamics of populations living in them. Here we show how realistic and replicable individual-based models can bridge the gap between non-spatial population theory and non-dynamic landscape ecology. A major strength of the approach is its ability to identify population vulnerabilities not detected by standard population viability analyses.

Simulating dynamic and mixed-severity fire regimes: a process-based fire extension for LANDIS-II

Treesearch

Brian R. Sturtevant; Robert M. Scheller; Brian R. Miranda; Douglas Shinneman; Alexandra Syphard

2009-01-01

Fire regimes result from reciprocal interactions between vegetation and fire that may be further affected by other disturbances, including climate, landform, and terrain. In this paper, we describe fire and fuel extensions for the forest landscape simulation model, LANDIS-II, that allow dynamic interactions among fire, vegetation, climate, and landscape structure, and...

Comprehensive Representation of Hydrologic and Geomorphic Process Coupling in Numerical Models: Internal Dynamics and Basin Evolution

NASA Astrophysics Data System (ADS)

Istanbulluoglu, E.; Vivoni, E. R.; Ivanov, V. Y.; Bras, R. L.

2005-12-01

Landscape morphology has an important control on the spatial and temporal organization of basin hydrologic response to climate forcing, affecting soil moisture redistribution as well as vegetation function. On the other hand, erosion, driven by hydrology and modulated by vegetation, produces landforms over geologic time scales that reflect characteristic signatures of the dominant land forming process. Responding to extreme climate events or anthropogenic disturbances of the land surface, infrequent but rapid forms of erosion (e.g., arroyo development, landsliding) can modify topography such that basin hydrology is significantly influenced. Despite significant advances in both hydrologic and geomorphic modeling over the past two decades, the dynamic interactions between basin hydrology, geomorphology and terrestrial ecology are not adequately captured in current model frameworks. In order to investigate hydrologic-geomorphic-ecologic interactions at the basin scale we present initial efforts in integrating the CHILD landscape evolution model (Tucker et al. 2001) with the tRIBS hydrology model (Ivanov et al. 2004), both developed in a common software environment. In this talk, we present preliminary results of the numerical modeling of the coupled evolution of basin hydro-geomorphic response and resulting landscape morphology in two sets of examples. First, we discuss the long-term evolution of both the hydrologic response and the resulting basin morphology from an initially uplifted plateau. In the second set of modeling experiments, we implement changes in climate and land-use to an existing topography and compare basin hydrologic response to the model results when landscape form is fixed (e.g. no coupling between hydrology and geomorphology). Model results stress the importance of internal basin dynamics, including runoff generation mechanisms and hydrologic states, in shaping hydrologic response as well as the importance of employing comprehensive conceptualizations of hydrology in modeling landscape evolution.

Predicting landscape vegetation dynamics using state-and-transition simulation models

Treesearch

Colin J. Daniel; Leonardo Frid

2012-01-01

This paper outlines how state-and-transition simulation models (STSMs) can be used to project changes in vegetation over time across a landscape. STSMs are stochastic, empirical simulation models that use an adapted Markov chain approach to predict how vegetation will transition between states over time, typically in response to interactions between succession,...

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

PubMed

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

2017-09-01

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

Landscape matrix mediates occupancy dynamics of Neotropical avian insectivores

USGS Publications Warehouse

Kennedy, Christina M.; Campbell Grant, Evan H.; Neel, Maile C.; Fagan, William F.; Marpa, Peter P.

2011-01-01

In addition to patch-level attributes (i.e., area and isolation), the nature of land cover between habitat patches (the matrix) may drive colonization and extinction dynamics in fragmented landscapes. Despite a long-standing recognition of matrix effects in fragmented systems, an understanding of the relative impacts of different types of land cover on patterns and dynamics of species occurrence remains limited. We employed multi-season occupancy models to determine the relative influence of patch area, patch isolation, within-patch vegetation structure, and landscape matrix on occupancy dynamics of nine Neotropical nsectivorous birds in 99 forest patches embedded in four matrix types (agriculture, suburban evelopment, bauxite mining, and forest) in central Jamaica. We found that within-patch vegetation structure and the matrix type between patches were more important than patch area and patch isolation in determining local colonization and local extinction probabilities, and that the effects of patch area, isolation, and vegetation structure on occupancy dynamics tended to be matrix and species dependent. Across the avian community, the landscape matrix influenced local extinction more than local colonization, indicating that extinction processes, rather than movement, likely drive interspecific differences in occupancy dynamics. These findings lend crucial empirical support to the hypothesis that species occupancy dynamics in fragmented systems may depend greatly upon the landscape context.

Modeling Evolution on Nearly Neutral Network Fitness Landscapes

NASA Astrophysics Data System (ADS)

Yakushkina, Tatiana; Saakian, David B.

2017-08-01

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

Fixation, transient landscape, and diffusion dilemma in stochastic evolutionary game dynamics

NASA Astrophysics Data System (ADS)

Zhou, Da; Qian, Hong

2011-09-01

Agent-based stochastic models for finite populations have recently received much attention in the game theory of evolutionary dynamics. Both the ultimate fixation and the pre-fixation transient behavior are important to a full understanding of the dynamics. In this paper, we study the transient dynamics of the well-mixed Moran process through constructing a landscape function. It is shown that the landscape playing a central theoretical “device” that integrates several lines of inquiries: the stable behavior of the replicator dynamics, the long-time fixation, and continuous diffusion approximation associated with asymptotically large population. Several issues relating to the transient dynamics are discussed: (i) multiple time scales phenomenon associated with intra- and inter-attractoral dynamics; (ii) discontinuous transition in stochastically stationary process akin to Maxwell construction in equilibrium statistical physics; and (iii) the dilemma diffusion approximation facing as a continuous approximation of the discrete evolutionary dynamics. It is found that rare events with exponentially small probabilities, corresponding to the uphill movements and barrier crossing in the landscape with multiple wells that are made possible by strong nonlinear dynamics, plays an important role in understanding the origin of the complexity in evolutionary, nonlinear biological systems.

Site-level model intercomparison of high latitude and high altitude soil thermal dynamics in tundra and barren landscapes

NASA Astrophysics Data System (ADS)

Ekici, A.; Chadburn, S.; Chaudhary, N.; Hajdu, L. H.; Marmy, A.; Peng, S.; Boike, J.; Burke, E.; Friend, A. D.; Hauck, C.; Krinner, G.; Langer, M.; Miller, P. A.; Beer, C.

2015-07-01

Modeling soil thermal dynamics at high latitudes and altitudes requires representations of physical processes such as snow insulation, soil freezing and thawing and subsurface conditions like soil water/ice content and soil texture. We have compared six different land models: JSBACH, ORCHIDEE, JULES, COUP, HYBRID8 and LPJ-GUESS, at four different sites with distinct cold region landscape types, to identify the importance of physical processes in capturing observed temperature dynamics in soils. The sites include alpine, high Arctic, wet polygonal tundra and non-permafrost Arctic, thus showing how a range of models can represent distinct soil temperature regimes. For all sites, snow insulation is of major importance for estimating topsoil conditions. However, soil physics is essential for the subsoil temperature dynamics and thus the active layer thicknesses. This analysis shows that land models need more realistic surface processes, such as detailed snow dynamics and moss cover with changing thickness and wetness, along with better representations of subsoil thermal dynamics.

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

PubMed Central

2017-01-01

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

Spatially Distributed Assimilation of Remotely Sensed Leaf Area Index and Potential Evapotranspiration for Hydrologic Modeling in Wetland Landscapes

EPA Science Inventory

Evapotranspiration (ET), a highly dynamic flux in wetland landscapes, regulates the accuracy of surface/sub-surface runoff simulation in a hydrologic model. However, considerable uncertainty in simulating ET-related processes remains, including our limited ability to incorporate ...

Free energy landscapes of small peptides in an implicit solvent model determined by force-biased multicanonical molecular dynamics simulation

NASA Astrophysics Data System (ADS)

Watanabe, Yukihisa S.; Kim, Jae Gil; Fukunishi, Yoshifumi; Nakamura, Haruki

2004-12-01

In order to investigate whether the implicit solvent (GB/SA) model could reproduce the free energy landscapes of peptides, the potential of mean forces (PMFs) of eight tripeptides was examined and compared with the PMFs of the explicit water model. The force-biased multicanonical molecular dynamics method was used for the enhanced conformational sampling. Consequently, the GB/SA model reproduced almost all the global and local minima in the PMFs observed with the explicit water model. However, the GB/SA model overestimated frequencies of the structures that are stabilized by intra-peptide hydrogen bonds.

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

PubMed Central

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

2017-01-01

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

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.

The effects of wind disturbance on temperate rain forest structure and dynamics of southeast Alaska.

Treesearch

Gregory J. Nowacki; Marc G. Kramer

1998-01-01

Wind disturbance plays a fundamental role in shaping forest dynamics in southeast Alaska. Recent studies have increased our appreciation for the effects of wind at both large and small scales. Current thinking is that wind disturbance characteristics change over a continuum dependent on landscape features (e.g., exposure, landscape position, topography). Data modeling...

Approaches to incorporating climate change effects in state and transition simulation models of vegetation

Treesearch

Becky K. Kerns; Miles A. Hemstrom; David Conklin; Gabriel I. Yospin; Bart Johnson; Dominique Bachelet; Scott Bridgham

2012-01-01

Understanding landscape vegetation dynamics often involves the use of scientifically-based modeling tools that are capable of testing alternative management scenarios given complex ecological, management, and social conditions. State-and-transition simulation model (STSM) frameworks and software such as PATH and VDDT are commonly used tools that simulate how landscapes...

The Ancient Maya Landscape: Facing the Challenges and Embracing the Promise of Integrating Archaeology, Remote Sensing, Soil Science and Hydrologic Modeling for Coupled Natural and Human Systems.

NASA Astrophysics Data System (ADS)

Murtha, T., Jr.; Duffy, C.; Cook, B. D.; Schroder, W.; Webster, D.; French, K. D.; Alcover, O.; Golden, C.; Balzotti, C.; Shaffer, D.

2016-12-01

Relying on a niche inheritance perspective, this paper discusses the long-term spatial and temporal dynamics of land-use management, agricultural decision making and patterns of resource availability in the tropical lowlands of Central America. We introduce and describe ongoing research that addresses a series of long standing questions about coupled natural and human history dynamics in the Central Maya lowlands, emphasizing the role of landscape and region to address these questions. First, we summarize the results of a CNH pilot study focused on the evolution of the regional landscape of Tikal, Guatemala. Particular attention is centered on how we integrated landscape survey, traditional archaeology and soil studies to understand the spatial and temporal dynamics of agricultural land use and intensification over a two thousand period. Additionally, we discuss how these results were integrated into remote sensing, hydrological and erosion models to better understand how past changes in available water and productive land compare to what we know about settlement patterns in the Tikal Region over that same time period. We not only describe how the Maya transformed this landscape, but also how the region influenced changing patterns of settlement and land use. We finish this section with a discussion of some of the unique challenges integrating archaeological information to study CNH dynamics during this pilot study. Second, we introduce a new project designed to `scale up' the pilot study for a macro-regional analysis of the lowland Maya landscape. The new project leverages a uniquely sampled LIDAR data set designed to refine measurements of above ground carbon storage. Our new project quantitatively examines these data for evidence for past human activity. Preliminary results offer a promising path for tightly integrating archaeology, natural science, remote sensing and modeling for studying CNH dynamics in the deep and recent past.

Persistence and diversity of directional landscape connectivity improves biomass pulsing in expanding and contracting wetlands

USGS Publications Warehouse

Yurek, Simeon; DeAngelis, Donald L.; Trexler, Joel C.; Klassen, Stephen; Larsen, Laurel G.

2016-01-01

In flood-pulsed ecosystems, hydrology and landscape structure mediate transfers of energy up the food chain by expanding and contracting in area, enabling spatial expansion and growth of fish populations during rising water levels, and subsequent concentration during the drying phase. Connectivity of flooded areas is dynamic as waters rise and fall, and is largely determined by landscape geomorphology and anisotropy. We developed a methodology for simulating fish dispersal and concentration on spatially-explicit, dynamic floodplain wetlands with pulsed food web dynamics, to evaluate how changes in connectivity through time contribute to the concentration of fish biomass that is essential for higher trophic levels. The model also tracks a connectivity index (DCI) over different compass directions to see if fish biomass dynamics can be related in a simple way to topographic pattern. We demonstrate the model for a seasonally flood-pulsed, oligotrophic system, the Everglades, where flow regimes have been greatly altered. Three dispersing populations of functional fish groups were simulated with empirically-based dispersal rules on two landscapes, and two twelve-year time series of managed water levels for those areas were applied. The topographies of the simulations represented intact and degraded ridge-and-slough landscapes (RSL). Simulation results showed large pulses of biomass concentration forming during the onset of the drying phase, when water levels were falling and fish began to converge into the sloughs. As water levels fell below the ridges, DCI declined over different directions, closing down dispersal lanes, and fish density spiked. Persistence of intermediate levels of connectivity on the intact RSL enabled persistent concentration events throughout the drying phase. The intact landscape also buffered effects of wet season population growth. Water level reversals on both landscapes negatively affected fish densities by depleting fish populations without allowing enough time for them to regenerate. Testable, spatiotemporal predictions of the timing, location, duration, and magnitude of fish concentration pulses were produced by the model, and can be applied to restoration planning.

An extended patch-dynamic framework for food chains in fragmented landscapes

PubMed Central

Liao, Jinbao; Chen, Jiehong; Ying, Zhixia; Hiebeler, David E.; Nijs, Ivan

2016-01-01

Habitat destruction, a key determinant of species loss, can be characterized by two components, patch loss and patch fragmentation, where the former refers to the reduction in patch availability, and the latter to the division of the remaining patches. Classical metacommunity models have recently explored how food web dynamics respond to patch loss, but the effects of patch fragmentation have largely been overlooked. Here we develop an extended patch-dynamic model that tracks the patch occupancy of the various trophic links subject to colonization-extinction-predation dynamics by incorporating species dispersal with patch connectivity. We found that, in a simple food chain, species at higher trophic level become extinct sooner with increasing patch loss and fragmentation due to the constraint in resource availability, confirming the trophic rank hypothesis. Yet, effects of fragmentation on species occupancy are largely determined by patch loss, with maximal fragmentation effects occurring at intermediate patch loss. Compared to the spatially explicit simulations that we also performed, the current model with pair approximation generates similar community patterns especially in spatially clustered landscapes. Overall, our extended framework can be applied to model more complex food webs in fragmented landscapes, broadening the scope of existing metacommunity theory. PMID:27608823

Exploring an Ecologically Sustainable Scheme for Landscape Restoration of Abandoned Mine Land: Scenario-Based Simulation Integrated Linear Programming and CLUE-S Model

PubMed Central

Zhang, Liping; Zhang, Shiwen; Huang, Yajie; Cao, Meng; Huang, Yuanfang; Zhang, Hongyan

2016-01-01

Understanding abandoned mine land (AML) changes during land reclamation is crucial for reusing damaged land resources and formulating sound ecological restoration policies. This study combines the linear programming (LP) model and the CLUE-S model to simulate land-use dynamics in the Mentougou District (Beijing, China) from 2007 to 2020 under three reclamation scenarios, that is, the planning scenario based on the general land-use plan in study area (scenario 1), maximal comprehensive benefits (scenario 2), and maximal ecosystem service value (scenario 3). Nine landscape-scale graph metrics were then selected to describe the landscape characteristics. The results show that the coupled model presented can simulate the dynamics of AML effectively and the spatially explicit transformations of AML were different. New cultivated land dominates in scenario 1, while construction land and forest land account for major percentages in scenarios 2 and 3, respectively. Scenario 3 has an advantage in most of the selected indices as the patches combined most closely. To conclude, reclaiming AML by transformation into more forest can reduce the variability and maintain the stability of the landscape ecological system in study area. These findings contribute to better mapping AML dynamics and providing policy support for the management of AML. PMID:27023575

Exploring an Ecologically Sustainable Scheme for Landscape Restoration of Abandoned Mine Land: Scenario-Based Simulation Integrated Linear Programming and CLUE-S Model.

PubMed

Zhang, Liping; Zhang, Shiwen; Huang, Yajie; Cao, Meng; Huang, Yuanfang; Zhang, Hongyan

2016-03-24

Understanding abandoned mine land (AML) changes during land reclamation is crucial for reusing damaged land resources and formulating sound ecological restoration policies. This study combines the linear programming (LP) model and the CLUE-S model to simulate land-use dynamics in the Mentougou District (Beijing, China) from 2007 to 2020 under three reclamation scenarios, that is, the planning scenario based on the general land-use plan in study area (scenario 1), maximal comprehensive benefits (scenario 2), and maximal ecosystem service value (scenario 3). Nine landscape-scale graph metrics were then selected to describe the landscape characteristics. The results show that the coupled model presented can simulate the dynamics of AML effectively and the spatially explicit transformations of AML were different. New cultivated land dominates in scenario 1, while construction land and forest land account for major percentages in scenarios 2 and 3, respectively. Scenario 3 has an advantage in most of the selected indices as the patches combined most closely. To conclude, reclaiming AML by transformation into more forest can reduce the variability and maintain the stability of the landscape ecological system in study area. These findings contribute to better mapping AML dynamics and providing policy support for the management of AML.

Modeling the influence of long term human-induced land use conversion on sediment fluxes and carbon dynamics at the catchment scale

NASA Astrophysics Data System (ADS)

Bouchoms, Samuel; Van Oost, Kristof; Vanacker, Veerle

2014-05-01

Over the past 20 years, there has been increasing evidence of the strong impact of human activities on the landscape, specifically on soil erosion due to the removal of natural vegetation cover for agricultural and urban purposes. The results question the widespread hypothesis of a steady state landscape since it appears that the balance between soil production and erosion may be broken altering the interactions between chemical, physical and biological processes in both soil and landscape system. Yet, the relationship between this accelerated erosion and the carbon dynamics at the landscape scale remains an important area of investigation. Recent attempts to combine geomorphic models, soil redistribution and carbon dynamic has proved themselves valuable in term of supporting the importance of lateral fluxes as a crucial control of carbon dynamic at the landscape scale. We use the SPEROS LT model, a modified version of SPEROS-C which includes dynamic land use and soil physical properties, to assess the impact of historical land use conversion on sediment and carbon fluxes in the Dijle catchment. This particular location has experienced a significant human impact since the Roman period, undergoing heavy deforestation and expansion of agricultural lands followed by a period of abandonment. The last 400 to 500 years saw a dramatic increase in the intensity of land use conversion associated to population growth leading to forest cleaning and urbanization. Our main objective is to validate the combined geomorphic and soil carbon turnover process descriptions of the model. Historical land use proportions are based on existing literature estimations and spatial assignation of the land conversion relies on simple allocation rules based on criteria such as slope or soil texture. Land use scenarios are constructed for the last 2000 years. We confront the model results with observations and perform a sensitivity analysis. The results indicate that the general trends in sediment production and deposition, as well as soil carbon storage are well predicted by the model. We discuss the key-parameters of the model and the implications of past erosion-deposition for the future C budget of the Dijle catchment.

Integration of a Physically based Distributed Hydrological Model with a Model of Carbon and Nitrogen Cycling: A Case Study at the Luquillo Critical Zone Observatory, Puerto Rico

NASA Astrophysics Data System (ADS)

Bastola, S.; Dialynas, Y. G.; Bras, R. L.; Arnone, E.; Noto, L. V.

2015-12-01

The dynamics of carbon and nitrogen cycles, increasingly influenced by human activities, are the key to the functioning of ecosystems. These cycles are influenced by the composition of the substrate, availability of nitrogen, the population of microorganisms, and by environmental factors. Therefore, land management and use, climate change, and nitrogen deposition patterns influence the dynamics of these macronutrients at the landscape scale. In this work a physically based distributed hydrological model, the tRIBS model, is coupled with a process-based multi-compartment model of the biogeochemical cycle to simulate the dynamics of carbon and nitrogen (CN) in the Mameyes River basin, Puerto Rico. The model includes a wide range of processes that influence the movement, production, alteration of nutrients in the landscape and factors that affect the CN cycling. The tRIBS integrates geomorphological and climatic factors that influence the cycling of CN in soil. Implementing the decomposition module into tRIBS makes the model a powerful complement to a biogeochemical observation system and a forecast tool able to analyze the influences of future changes on ecosystem services. The soil hydrologic parameters of the model were obtained using ranges of published parameters and observed streamflow data at the outlet. The parameters of the decomposition module are based on previously published data from studies conducted in the Luquillio CZO (budgets of soil organic matter and CN ratio for each of the dominant vegetation types across the landscape). Hydrological fluxes, wet depositon of nitrogen, litter fall and its corresponding CN ratio drive the decomposition model. The simulation results demonstrate a strong influence of soil moisture dynamics on the spatiotemporal distribution of nutrients at the landscape level. The carbon in the litter pool and the nitrate and ammonia pool respond quickly to soil moisture content. Moreover, the CN ratios of the plant litter have significant influence in the dynamics of CN cycling.

Invasion complexity at large spatial scales is an emergent property of interactions among landscape characteristics and invader traits

PubMed Central

Jordan, Nicholas R.; Forester, James D.

2018-01-01

Invasion potential should be part of the evaluation of candidate species for any species introduction. However, estimating invasion risks remains a challenging problem, particularly in complex landscapes. Certain plant traits are generally considered to increase invasive potential and there is an understanding that landscapes influence invasions dynamics, but little research has been done to explore how those drivers of invasions interact. We evaluate the relative roles of, and potential interactions between, plant invasiveness traits and landscape characteristics on invasions with a case study using a model parameterized for the potentially invasive biomass crop, Miscanthus × giganteus. Using that model we simulate invasions on 1000 real landscapes to evaluate how landscape characteristics, including both composition and spatial structure, affect invasion outcomes. We conducted replicate simulations with differing strengths of plant invasiveness traits (dispersal ability, establishment ability, population growth rate, and the ability to utilize dispersal corridors) to evaluate how the importance of landscape characteristics for predicting invasion patterns changes depending on the invader details. Analysis of simulations showed that the presence of highly suitable habitat (e.g., grasslands) is generally the strongest determinant of invasion dynamics but that there are also more subtle interactions between landscapes and invader traits. These effects can also vary between different aspects of invasion dynamics (short vs. long time scales and population size vs. spatial extent). These results illustrate that invasions are complex emergent processes with multiple drivers and effective management needs to reflect the ecology of the species of interest and the particular goals or risks for which efforts need to be optimized. PMID:29771923

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

USGS Publications Warehouse

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

2017-01-01

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

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

PubMed

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

2004-10-01

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

Linking state-and-transition simulation and timber supply models for forest biomass production scenarios

USGS Publications Warehouse

Costanza, Jennifer; Abt, Robert C.; McKerrow, Alexa; Collazo, Jaime

2015-01-01

We linked state-and-transition simulation models (STSMs) with an economics-based timber supply model to examine landscape dynamics in North Carolina through 2050 for three scenarios of forest biomass production. Forest biomass could be an important source of renewable energy in the future, but there is currently much uncertainty about how biomass production would impact landscapes. In the southeastern US, if forests become important sources of biomass for bioenergy, we expect increased land-use change and forest management. STSMs are ideal for simulating these landscape changes, but the amounts of change will depend on drivers such as timber prices and demand for forest land, which are best captured with forest economic models. We first developed state-and-transition model pathways in the ST-Sim software platform for 49 vegetation and land-use types that incorporated each expected type of landscape change. Next, for the three biomass production scenarios, the SubRegional Timber Supply Model (SRTS) was used to determine the annual areas of thinning and harvest in five broad forest types, as well as annual areas converted among those forest types, agricultural, and urban lands. The SRTS output was used to define area targets for STSMs in ST-Sim under two scenarios of biomass production and one baseline, business-as-usual scenario. We show that ST-Sim output matched SRTS targets in most cases. Landscape dynamics results indicate that, compared with the baseline scenario, forest biomass production leads to more forest and, specifically, more intensively managed forest on the landscape by 2050. Thus, the STSMs, informed by forest economics models, provide important information about potential landscape effects of bioenergy production.

Extracting temporal and spatial information from remotely sensed data for mapping wildlife habitat: Tucson

USGS Publications Warehouse

Wallace, Cynthia S.A.; Advised by Marsh, Stuart E.

2002-01-01

The research accomplished in this dissertation used both mathematical and statistical techniques to extract and evaluate measures of landscape temporal dynamics and spatial structure from remotely sensed data for the purpose of mapping wildlife habitat. By coupling the landscape measures gleaned from the remotely sensed data with various sets of animal sightings and population data, effective models of habitat preference were created.Measures of temporal dynamics of vegetation greenness as measured by National Oceanographic and Atmospheric Administration’s Advanced Very High Resolution Radiometer (AVHRR) satellite were used to effectively characterize and map season specific habitat of the Sonoran pronghorn antelope, as well as produce preliminary models of potential yellow-billed cuckoo habitat in Arizona. Various measures that capture different aspects of the temporal dynamics of the landscape were derived from AVHRR Normalized Difference Vegetation Index composite data using three main classes of calculations: basic statistics, standardized principal components analysis, and Fourier analysis. Pronghorn habitat models based on the AVHRR measures correspond visually and statistically to GIS-based models produced using data that represent detailed knowledge of ground-condition.Measures of temporal dynamics also revealed statistically significant correlations with annual estimates of elk population in selected Arizona Game Management Units, suggesting elk respond to regional environmental changes that can be measured using satellite data. Such relationships, once verified and established, can be used to help indirectly monitor the population.Measures of landscape spatial structure derived from IKONOS high spatial resolution (1-m) satellite data using geostatistics effectively map details of Sonoran pronghorn antelope habitat. Local estimates of the nugget, sill, and range variogram parameters calculated within 25 x 25-meter image windows describe the spatial autocorrelation of the image, permitting classification of all pixels into coherent units whose signature graphs exhibit a classic variogram shape. The variogram parameters captured in these signatures have been shown in previous studies to discriminate between different species-specific vegetation associations.The synoptic view of the landscape provided by satellite data can inform resource management efforts. The ability to characterize the spatial structure and temporal dynamics of habitat using repeatable remote sensing data allows closer monitoring of the relationship between a species and its landscape.

Modeling Fluvial Incision and Transient Landscape Evolution: Influence of Dynamic Channel Adjustment

NASA Astrophysics Data System (ADS)

Attal, M.; Tucker, G. E.; Cowie, P. A.; Whittaker, A. C.; Roberts, G. P.

2007-12-01

Channel geometry exerts a fundamental control on fluvial processes. Recent work has shown that bedrock channel width (W) depends on a number of parameters, including channel slope, and is not only a function of drainage area (A) as is commonly assumed. The present work represents the first attempt to investigate the consequences, for landscape evolution, of using a static expression of channel width (W ~ A0.5) versus a relationship that allows channels to dynamically adjust to changes in slope. We consider different models for the evolution of the channel geometry, including constant width-to-depth ratio (after Finnegan et al., Geology, v. 33, no. 3, 2005), and width-to-depth ratio varying as a function of slope (after Whittaker et al., Geology, v. 35, no. 2, 2007). We use the Channel-Hillslope Integrated Landscape Development (CHILD) model to analyze the response of a catchment to a given tectonic disturbance. The topography of a catchment in the footwall of an active normal fault in the Apennines (Italy) is used as a template for the study. We show that, for this catchment, the transient response can be fairly well reproduced using a simple detachment-limited fluvial incision law. We also show that, depending on the relationship used to express channel width, initial steady-state topographies differ, as do transient channel width, slope, and the response time of the fluvial system. These differences lead to contrasting landscape morphologies when integrated at the scale of a whole catchment. Our results emphasize the importance of channel width in controlling fluvial processes and landscape evolution. They stress the need for using a dynamic hydraulic scaling law when modeling landscape evolution, particularly when the uplift field is non-uniform.

Metapopulation modelling of riparian tree species persistence in river networks under climate change.

PubMed

Van Looy, Kris; Piffady, Jérémy

2017-11-01

Floodplain landscapes are highly fragmented by river regulation resulting in habitat degradation and flood regime perturbation, posing risks to population persistence. Climate change is expected to pose supplementary risks in this context of fragmented landscapes, and especially for river systems adaptation management programs are developed. The association of habitat quality and quantity with the landscape dynamics and resilience to human-induced disturbances is still poorly understood in the context of species survival and colonization processes, but essential to prioritize conservation and restoration actions. We present a modelling approach that elucidates network connectivity and landscape dynamics in spatial and temporal context to identify vital corridors and conservation priorities in the Loire river and its tributaries. Alteration of flooding and flow regimes is believed to be critical to population dynamics in river ecosystems. Still, little is known of critical levels of alteration both spatially and temporally. We applied metapopulation modelling approaches for a dispersal-limited tree species, white elm; and a recruitment-limited tree species, black poplar. In different model steps the connectivity and natural dynamics of the river landscape are confronted with physical alterations (dams/dykes) to species survival and then future scenarios for climatic changes and potential adaptation measures are entered in the model and translated in population persistence over the river basin. For the two tree species we highlighted crucial network zones in relation to habitat quality and connectivity. Where the human impact model already shows currently restricted metapopulation development, climate change is projected to aggravate this persistence perspective substantially. For both species a significant drawback to the basin population is observed, with 1/3 for elm and ¼ for poplar after 25 years already. But proposed adaptation measures prove effective to even bring metapopulation strength and persistence up to a level above the current level. Copyright © 2016 Elsevier Ltd. All rights reserved.

A Model with Darwinian Dynamics on a Rugged Landscape

NASA Astrophysics Data System (ADS)

Brotto, Tommaso; Bunin, Guy; Kurchan, Jorge

2017-02-01

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

A sub-grid, mixture-fraction-based thermodynamic equilibrium model for gas phase combustion in FIRETEC: development and results

Treesearch

M. M. Clark; T. H. Fletcher; R. R. Linn

2010-01-01

The chemical processes of gas phase combustion in wildland fires are complex and occur at length-scales that are not resolved in computational fluid dynamics (CFD) models of landscape-scale wildland fire. A new approach for modelling fire chemistry in HIGRAD/FIRETEC (a landscape-scale CFD wildfire model) applies a mixture– fraction model relying on thermodynamic...

Integrating remote sensing, GIS and dynamic models for landscape-level simulation of forest insect disturbance

USDA-ARS?s Scientific Manuscript database

Cellular automata (CA) is a powerful tool in modeling the evolution of macroscopic scale phenomena as it couples time, space, and variable together while remaining in a simplified form. However, such application has remained challenging in landscape-level chronic forest insect epidemics due to the h...

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...

Simulation modeling of forest landscape disturbances: Where do we go from here?

Treesearch

Ajith H. Perera; Brian R. Sturtevant; Lisa J. Buse

2015-01-01

It was nearly a quarter-century ago when Turner and Gardner (1991) drew attention to methods of quantifying landscape patterns and processes, including simulation modeling. The many authors who contributed to that seminal text collectively signaled the emergence of a new field—spatially explicit simulation modeling of broad-scale ecosystem dynamics. Of particular note...

A Smoluchowski model of crystallization dynamics of small colloidal clusters

NASA Astrophysics Data System (ADS)

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

2011-10-01

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

Towards integrated modelling of soil organic carbon cycling at landscape scale

NASA Astrophysics Data System (ADS)

Viaud, V.

2009-04-01

Soil organic carbon (SOC) is recognized as a key factor of the chemical, biological and physical quality of soil. Numerous models of soil organic matter turnover have been developed since the 1930ies, most of them dedicated to plot scale applications. More recently, they have been applied to national scales to establish the inventories of carbon stocks directed by the Kyoto protocol. However, only few studies consider the intermediate landscape scale, where the spatio-temporal pattern of land management practices, its interactions with the physical environment and its impacts on SOC dynamics can be investigated to provide guidelines for sustainable management of soils in agricultural areas. Modelling SOC cycling at this scale requires accessing accurate spatially explicit input data on soils (SOC content, bulk density, depth, texture) and land use (land cover, farm practices), and combining both data in a relevant integrated landscape representation. The purpose of this paper is to present a first approach to modelling SOC evolution in a small catchment. The impact of the way landscape is represented on SOC stocks in the catchment was more specifically addressed. This study was based on the field map, the soil survey, the crop rotations and land management practices of an actual 10-km² agricultural catchment located in Brittany (France). RothC model was used to drive soil organic matter dynamics. Landscape representation in the form of a systematic regular grid, where driving properties vary continuously in space, was compared to a representation where landscape is subdivided into a set of homogeneous geographical units. This preliminary work enabled to identify future needs to improve integrated soil-landscape modelling in agricultural areas.

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.

A Biologically Informed, Mechanistic Model of Desert Shrub Population Dynamics Bearing on Arid Landscape Evolution

NASA Astrophysics Data System (ADS)

Worman, Stacey; Furbish, David; Fathel, Siobhan

2014-05-01

In arid landscapes, desert shrubs individually and collectively modify how sediment is transported (e.g by wind, overland-flow, and rain-splash). Addressing how desert shrubs modify landscapes on geomorphic timescales therefore necessitates spanning multiple shrub lifetimes and accounting for how processes affecting shrub dynamics on these longer timescales (e.g. fire, grazing, drought, and climate change) may in turn impact sediment transport. To fulfill this need, we present a mechanistic model of the spatiotemporal dynamics of a desert-shrub population that uses a simple accounting framework and tracks individual shrubs as they enter, age, and exit the population (via recruitment, growth, and mortality). Our model is novel insomuch as it (1) features a strong biophysical foundation, (2) mimics well-documented aspects of how shrub populations respond to changes in precipitation, and (3) possesses the process granularity appropriate for use in geomorphic simulations. In a complimentary abstract (Fathel et al. 2014), we demonstrate the potential of this biological model by coupling it to a physical model of rain-splash sediment transport: We mechanistically reproduce the empirical observation that the erosion rate of a hillslope decreases as its vegetation coverage increases and we predict erosion rates under different climate-change scenarios.

Extinction risk in successional landscapes subject to catastrophic disturbances.

Treesearch

David Boughton; Urmila Malvadkar

2002-01-01

We explore the thesis that stochasticity in successional-disturbance systems can be an agent of species extinction. The analysis uses a simple model of patch dynamics for seral stages in an idealized landscape; each seral stage is assumed to support a specialist biota. The landscape as a whole is characterized by a mean patch birth rate, mean patch size, and mean...

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

Treesearch

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

2015-01-01

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

Exploring the fitness landscape of poliovirus

NASA Astrophysics Data System (ADS)

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

2012-02-01

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

Land use, water and Mediterranean landscapes: modelling long-term dynamics of complex socio-ecological systems.

PubMed

Barton, C Michael; Ullah, Isaac I; Bergin, Sean

2010-11-28

The evolution of Mediterranean landscapes during the Holocene has been increasingly governed by the complex interactions of water and human land use. Different land-use practices change the amount of water flowing across the surface and infiltrating the soil, and change water's ability to move surface sediments. Conversely, water amplifies the impacts of human land use and extends the ecological footprint of human activities far beyond the borders of towns and fields. Advances in computational modelling offer new tools to study the complex feedbacks between land use, land cover, topography and surface water. The Mediterranean Landscape Dynamics project (MedLand) is building a modelling laboratory where experiments can be carried out on the long-term impacts of agropastoral land use, and whose results can be tested against the archaeological record. These computational experiments are providing new insights into the socio-ecological consequences of human decisions at varying temporal and spatial scales.

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.

Mapping landscape phenology preference of yellow-billed cuckoo with AVHRR data

USGS Publications Warehouse

Wallace, Cynthia S.A.; Villarreal, Miguel; van Riper, Charles

2013-01-01

We mapped habitat for threatened Yellow-billed Cuckoo (Coccycus americanus occidentalis) in the State of Arizona using the temporal greenness dynamics of the landscape, or the landscape phenology. Landscape phenometrics were derived from Advanced Very High Resolution Radiometer (AVHRR) Normalized Difference Vegetation Index (NDVI) data for 1998 and 1999 by using Fourier harmonic analysis to analyze the waveform of the annual NDVI profile at each pixel. We modeled the spatial distribution of Yellow-billed Cuckoo habitat by coupling the field data of Cuckoo presence or absence and point-based samples of riparian and cottonwood-willow vegetation types with satellite phenometrics for 1998. Models were validated using field and satellite data collected in 1999. The results indicate that Yellow-billed Cuckoo occupy locations within their preferred habitat that exhibit peak greenness after the start of the summer monsoon and are greener and more dynamic than “average” habitat. Identification of preferred phenotypes within recognized habitat areas can be used to refine habitat models, inform predictions of habitat response to climate change, and suggest adaptation strategies.

Do rising temperatures always increase forest productivity? Interacting effects of temperature, precipitation, cloudiness and soil texture on tree species growth and competition

Treesearch

Eric J. Gustafson; Brian R. Miranda; Arjan M.G. De Bruijn; Brian R. Sturtevant; Mark E. Kubiske

2017-01-01

Forest landscape models (FLM) are increasingly used to project the effects of climate change on forested landscapes, yet most use phenomenological approaches with untested assumptions about future forest dynamics. We used a FLM that relies on first principles to mechanistically simulate growth (LANDIS-II with PnET-Succession) to systematically explore how landscapes...

Toward more robust projections of forest landscape dynamics under novel environmental conditions: embedding PnET within LANDIS-II

Treesearch

A. De Bruijn; E.J. Gustafson; B.R. Sturtevant; J.R. Foster; B.R. Miranda; N.I. Lichti; D.F. Jacobs

2014-01-01

Ecological models built on phenomenological relationships and behavior of the past may not be robustunder novel conditions of the future because global changes are producing environmental conditions that forests have not experienced historically. We developed a new succession extension for the LANDIS-II forest landscape model, PnET-Succession, to simulate forest growth...

Epidemiological modeling of invasion in heterogeneous landscapes: Spread of sudden oak death in California (1990-2030)

Treesearch

R.K. Meentemeyer; N.J. Cunniffe; A.R. Cook; J.A.N. Filipe; R.D. Hunter; D.M. Rizzo; C.A. Gilligan

2011-01-01

The spread of emerging infectious diseases (EIDs) in natural environments poses substantial risks to biodiversity and ecosystem function. As EIDs and their impacts grow, landscape- to regional-scale models of disease dynamics are increasingly needed for quantitative prediction of epidemic outcomes and design of practicable strategies for control. Here we use spatio-...

The effects of seed dispersal on the simulation of long-term forest landscape change

Treesearch

Hong S. He; David J. Mladenoff

1999-01-01

The study of forest landscape change requires an understanding of the complex interactions of both spatial and temporal factors. Traditionally, forest gap models have been used to simulate change on small and independent plots. While gap models are useful in examining forest ecological dynamics across temporal scales, large, spatial processes, such as seed dispersal,...

A hierarchical fire frequency model to simulate temporal patterns of fire regimes in LANDIS

Treesearch

Jian Yang; Hong S. He; Eric J. Gustafson

2004-01-01

Fire disturbance has important ecological effects in many forest landscapes. Existing statistically based approaches can be used to examine the effects of a fire regime on forest landscape dynamics. Most examples of statistically based fire models divide a fire occurrence into two stages--fire ignition and fire initiation. However, the exponential and Weibull fire-...

Vacuum selection on axionic landscapes

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

Wang, Gaoyuan; Battefeld, Thorsten, E-mail: gaoyuan.wang@stud.uni-goettingen.de, E-mail: tbattefe@astro.physik.uni-goettingen.de

2016-04-01

We compute the distribution of minima that are reached dynamically on multi-field axionic landscapes, both numerically and analytically. Such landscapes are well suited for inflationary model building due to the presence of shift symmetries and possible alignment effects (the KNP mechanism). The resulting distribution of dynamically reached minima differs considerably from the naive expectation based on counting all vacua. These differences are more pronounced in the presence of many fields due to dynamical selection effects: while low lying minima are preferred as fields roll down the potential, trajectories are also more likely to get trapped by one of the manymore » nearby minima. We show that common analytic arguments based on random matrix theory in the large D-limit to estimate the distribution of minima are insufficient for quantitative arguments pertaining to the dynamically reached ones. This discrepancy is not restricted to axionic potentials. We provide an empirical expression for the expectation value of such dynamically reached minimas' height and argue that the cosmological constant problem is not alleviated in the absence of anthropic arguments. We further comment on the likelihood of inflation on axionic landscapes in the large D-limit.« less

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...

Simulating effects of fire on northern Rocky Mountain landscapes with the ecological process model FIRE-BGC.

PubMed

Keane, R E; Ryan, K C; Running, S W

1996-03-01

A mechanistic, biogeochemical succession model, FIRE-BGC, was used to investigate the role of fire on long-term landscape dynamics in northern Rocky Mountain coniferous forests of Glacier National Park, Montana, USA. FIRE-BGC is an individual-tree model-created by merging the gap-phase process-based model FIRESUM with the mechanistic ecosystem biogeochemical model FOREST-BGC-that has mixed spatial and temporal resolution in its simulation architecture. Ecological processes that act at a landscape level, such as fire and seed dispersal, are simulated annually from stand and topographic information. Stand-level processes, such as tree establishment, growth and mortality, organic matter accumulation and decomposition, and undergrowth plant dynamics are simulated both daily and annually. Tree growth is mechanistically modeled based on the ecosystem process approach of FOREST-BGC where carbon is fixed daily by forest canopy photosynthesis at the stand level. Carbon allocated to the tree stem at the end of the year generates the corresponding diameter and height growth. The model also explicitly simulates fire behavior and effects on landscape characteristics. We simulated the effects of fire on ecosystem characteristics of net primary productivity, evapotranspiration, standing crop biomass, nitrogen cycling and leaf area index over 200 years for the 50,000-ha McDonald Drainage in Glacier National Park. Results show increases in net primary productivity and available nitrogen when fires are included in the simulation. Standing crop biomass and evapotranspiration decrease under a fire regime. Shade-intolerant species dominate the landscape when fires are excluded. Model tree increment predictions compared well with field data.

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

PubMed

Zhuravlev, Pavel I; Papoian, Garegin A

2010-08-01

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

How interactions between animal movement and landscape processes modify range dynamics and extinction risk

EPA Science Inventory

Range dynamics models now incorporate many of the mechanisms and interactions that drive species distributions. However, connectivity continues to be studied using overly simple distance-based dispersal models with little consideration of how the individual behavior of dispersin...

Dynamic colloidal assembly pathways via low dimensional models

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

Yang, Yuguang; Bevan, Michael A., E-mail: mabevan@jhu.edu; Thyagarajan, Raghuram

2016-05-28

Here we construct a low-dimensional Smoluchowski model for electric field mediated colloidal crystallization using Brownian dynamic simulations, which were previously matched to experiments. Diffusion mapping is used to infer dimensionality and confirm the use of two order parameters, one for degree of condensation and one for global crystallinity. Free energy and diffusivity landscapes are obtained as the coefficients of a low-dimensional Smoluchowski equation to capture the thermodynamics and kinetics of microstructure evolution. The resulting low-dimensional model quantitatively captures the dynamics of different assembly pathways between fluid, polycrystal, and single crystals states, in agreement with the full N-dimensional data as characterizedmore » by first passage time distributions. Numerical solution of the low-dimensional Smoluchowski equation reveals statistical properties of the dynamic evolution of states vs. applied field amplitude and system size. The low-dimensional Smoluchowski equation and associated landscapes calculated here can serve as models for predictive control of electric field mediated assembly of colloidal ensembles into two-dimensional crystalline objects.« less

[Dynamic evolution of wetland landscape spatial pattern in Nansi Lake, China].

PubMed

Chen, Zhi Cong; Xie, Xiao Ping; Bai, Mao Wei

2016-10-01

Based on Landsat images in 1987, 2002 and 2014 from Nansi Lake located in Shandong Province, landscape pattern index, dynamic index, landscape gradient and gridding model were used for analysis of the wetland distribution in the lake. The results showed that the landscape contagion index and aggregation index gradually decreased from 1987 to 2014, while the landscape diversity index and evenness index gradually increased. The distribution of landscape area was more uniform while its patterns trended to be fragmented. Human activities impacted Nansi wetland distribution and the disturbance presented an increasing trend. The total area of Nansi wetland gradually increased during the study period. The area of lake first decreased then increased, and the area reached the maximum in 2014. The area of the ponds along the riparian zone had increased gradually, but the increasing speed slowed down. The area of the rivers remained stable, while the area of the swamps decreased continually during the period. The change of landscape pattern of Nansi Lake wetland mainly resulted from agricultural activities, establishment of Nansi Lake Natural Reserve, and the South-to-North Water Diversion Project.

Forecasting climate change impacts on plant populations over large spatial extents

DOE PAGES

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

2016-10-24

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

Forecasting climate change impacts on plant populations over large spatial extents

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

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

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

Forecasting climate change impacts on plant populations over large spatial extents

USGS Publications Warehouse

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

2016-01-01

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

Forest forming process and dynamic vegetation models under global change

Treesearch

A. Shvidenko; E. Gustafson

2009-01-01

The paper analyzes mathematical models that are used to project the dynamics of forest ecosystems on different spatial and temporal scales. Landscape disturbance and succession models (LDSMs) are of a particular interest for studying the forest forming process in Northern Eurasia. They have a solid empirical background and are able to model ecological processes under...

Glassy dynamics of landscape evolution

PubMed Central

Ortiz, Carlos P.; Jerolmack, Douglas J.

2018-01-01

Soil creeps imperceptibly downhill, but also fails catastrophically to create landslides. Despite the importance of these processes as hazards and in sculpting landscapes, there is no agreed-upon model that captures the full range of behavior. Here we examine the granular origins of hillslope soil transport by discrete element method simulations and reanalysis of measurements in natural landscapes. We find creep for slopes below a critical gradient, where average particle velocity (sediment flux) increases exponentially with friction coefficient (gradient). At critical gradient there is a continuous transition to a dense-granular flow rheology. Slow earthflows and landslides thus exhibit glassy dynamics characteristic of a wide range of disordered materials; they are described by a two-phase flux equation that emerges from grain-scale friction alone. This glassy model reproduces topographic profiles of natural hillslopes, showing its promise for predicting hillslope evolution over geologic timescales. PMID:29686102

Multiple coupled landscapes and non-adiabatic dynamics with applications to self-activating genes.

PubMed

Chen, Cong; Zhang, Kun; Feng, Haidong; Sasai, Masaki; Wang, Jin

2015-11-21

Many physical, chemical and biochemical systems (e.g. electronic dynamics and gene regulatory networks) are governed by continuous stochastic processes (e.g. electron dynamics on a particular electronic energy surface and protein (gene product) synthesis) coupled with discrete processes (e.g. hopping among different electronic energy surfaces and on and off switching of genes). One can also think of the underlying dynamics as the continuous motion on a particular landscape and discrete hoppings among different landscapes. The main difference of such systems from the intra-landscape dynamics alone is the emergence of the timescale involved in transitions among different landscapes in addition to the timescale involved in a particular landscape. The adiabatic limit when inter-landscape hoppings are fast compared to continuous intra-landscape dynamics has been studied both analytically and numerically, but the analytical treatment of the non-adiabatic regime where the inter-landscape hoppings are slow or comparable to continuous intra-landscape dynamics remains challenging. In this study, we show that there exists mathematical mapping of the dynamics on 2(N) discretely coupled N continuous dimensional landscapes onto one single landscape in 2N dimensional extended continuous space. On this 2N dimensional landscape, eddy current emerges as a sign of non-equilibrium non-adiabatic dynamics and plays an important role in system evolution. Many interesting physical effects such as the enhancement of fluctuations, irreversibility, dissipation and optimal kinetics emerge due to non-adiabaticity manifested by the eddy current illustrated for an N = 1 self-activator. We further generalize our theory to the N-gene network with multiple binding sites and multiple synthesis rates for discretely coupled non-equilibrium stochastic physical and biological systems.

Global Langevin model of multidimensional biomolecular dynamics.

PubMed

Schaudinnus, Norbert; Lickert, Benjamin; Biswas, Mithun; Stock, Gerhard

2016-11-14

Molecular dynamics simulations of biomolecular processes are often discussed in terms of diffusive motion on a low-dimensional free energy landscape F(). To provide a theoretical basis for this interpretation, one may invoke the system-bath ansatz á la Zwanzig. That is, by assuming a time scale separation between the slow motion along the system coordinate x and the fast fluctuations of the bath, a memory-free Langevin equation can be derived that describes the system's motion on the free energy landscape F(), which is damped by a friction field and driven by a stochastic force that is related to the friction via the fluctuation-dissipation theorem. While the theoretical formulation of Zwanzig typically assumes a highly idealized form of the bath Hamiltonian and the system-bath coupling, one would like to extend the approach to realistic data-based biomolecular systems. Here a practical method is proposed to construct an analytically defined global model of structural dynamics. Given a molecular dynamics simulation and adequate collective coordinates, the approach employs an "empirical valence bond"-type model which is suitable to represent multidimensional free energy landscapes as well as an approximate description of the friction field. Adopting alanine dipeptide and a three-dimensional model of heptaalanine as simple examples, the resulting Langevin model is shown to reproduce the results of the underlying all-atom simulations. Because the Langevin equation can also be shown to satisfy the underlying assumptions of the theory (such as a delta-correlated Gaussian-distributed noise), the global model provides a correct, albeit empirical, realization of Zwanzig's formulation. As an application, the model can be used to investigate the dependence of the system on parameter changes and to predict the effect of site-selective mutations on the dynamics.

Global Langevin model of multidimensional biomolecular dynamics

NASA Astrophysics Data System (ADS)

Schaudinnus, Norbert; Lickert, Benjamin; Biswas, Mithun; Stock, Gerhard

2016-11-01

Molecular dynamics simulations of biomolecular processes are often discussed in terms of diffusive motion on a low-dimensional free energy landscape F ( 𝒙 ) . To provide a theoretical basis for this interpretation, one may invoke the system-bath ansatz á la Zwanzig. That is, by assuming a time scale separation between the slow motion along the system coordinate x and the fast fluctuations of the bath, a memory-free Langevin equation can be derived that describes the system's motion on the free energy landscape F ( 𝒙 ) , which is damped by a friction field and driven by a stochastic force that is related to the friction via the fluctuation-dissipation theorem. While the theoretical formulation of Zwanzig typically assumes a highly idealized form of the bath Hamiltonian and the system-bath coupling, one would like to extend the approach to realistic data-based biomolecular systems. Here a practical method is proposed to construct an analytically defined global model of structural dynamics. Given a molecular dynamics simulation and adequate collective coordinates, the approach employs an "empirical valence bond"-type model which is suitable to represent multidimensional free energy landscapes as well as an approximate description of the friction field. Adopting alanine dipeptide and a three-dimensional model of heptaalanine as simple examples, the resulting Langevin model is shown to reproduce the results of the underlying all-atom simulations. Because the Langevin equation can also be shown to satisfy the underlying assumptions of the theory (such as a delta-correlated Gaussian-distributed noise), the global model provides a correct, albeit empirical, realization of Zwanzig's formulation. As an application, the model can be used to investigate the dependence of the system on parameter changes and to predict the effect of site-selective mutations on the dynamics.

When relationships estimated in the past cannot be used to predict the future: using mechanistic models to predict landscape ecological dynamics in a changing world

Treesearch

Eric J. Gustafson

2013-01-01

Researchers and natural resource managers need predictions of how multiple global changes (e.g., climate change, rising levels of air pollutants, exotic invasions) will affect landscape composition and ecosystem function. Ecological predictive models used for this purpose are constructed using either a mechanistic (process-based) or a phenomenological (empirical)...

Spatial occurrence of a habitat-tracking saproxylic beetle inhabiting a managed forest landscape.

PubMed

Schroeder, L Martin; Ranius, Thomas; Ekbom, Barbara; Larsson, Stig

2007-04-01

Because of the dynamic nature of many managed habitats, proper evaluation of conservation efforts calls for models that take into account both spatial and temporal habitat dynamics. We develop a metapopulation model for successional-type systems, in which habitat quality changes over time in a predictable fashion. The occupancy and recruitment of the predatory saproxylic (dependent on dead wood) beetle Harminius undulatus was studied in a managed boreal forest landscape, covering 24,449 ha, in central Sweden. In a first step, we analyzed the beetle's occupancy pattern in relation to stand characteristics, and the amounts of present and past habitat in the surrounding landscape. Managed forest is suitable habitat when > or =60 years old, and immediately after cutting, but not between the ages of 10 and 60 years. The observed occupancy of H. undulatus was positively correlated with the stand's age as habitat. We used a metapopulation model to predict the current probability of occurrence in each forest stand, given the spatiotemporal distribution of suitable forest stands during the last 50 years. Metapopulation parameters were estimated by matching predicted spatial distributions with observed spatial distributions. The model predicted observed spatial distributions better than a similar model that assumed constant habitat quality of each forest stand. Thus, metapopulation models for successional-type systems, such as dead wood dependent organisms in managed forest landscapes, should include habitat dynamics. An estimated 82% of the landscape-wide recruitment took place in managed stands, which covered 87% of the forest area, in comparison with 18% in unmanaged stands, which covered 13% of the forest area. Among the managed stand types, > or =60-year-old stands and 3-7-year-old clear-cuttings contributed to 79% of the total recruitment while 8-59-year-old stands only contributed 3%. The results suggest the following guidelines to improve conditions for H. undulatus and other species with similar habitat requirements: (1) the proportion of the landscape constituted by younger stands should not be allowed to grow too large, (2) the rotation period of managed stands should not be allowed to be too short, and (3) dead wood should be retained and created at final cutting.

Memory-efficient RNA energy landscape exploration

PubMed Central

Mann, Martin; Kucharík, Marcel; Flamm, Christoph; Wolfinger, Michael T.

2014-01-01

Motivation: Energy landscapes provide a valuable means for studying the folding dynamics of short RNA molecules in detail by modeling all possible structures and their transitions. Higher abstraction levels based on a macro-state decomposition of the landscape enable the study of larger systems; however, they are still restricted by huge memory requirements of exact approaches. Results: We present a highly parallelizable local enumeration scheme that enables the computation of exact macro-state transition models with highly reduced memory requirements. The approach is evaluated on RNA secondary structure landscapes using a gradient basin definition for macro-states. Furthermore, we demonstrate the need for exact transition models by comparing two barrier-based approaches, and perform a detailed investigation of gradient basins in RNA energy landscapes. Availability and implementation: Source code is part of the C++ Energy Landscape Library available at http://www.bioinf.uni-freiburg.de/Software/. Contact: mmann@informatik.uni-freiburg.de Supplementary information: Supplementary data are available at Bioinformatics online. PMID:24833804

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

PubMed Central

2012-01-01

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

Using LANDIS II to study the effects of global change in Siberia

Treesearch

Eric J. Gustafson; Brian R. Sturtevant; Anatoly Z. Shvidenko; Robert M. Scheller

2010-01-01

Landscape dynamics are characterized by complex interactions among multiple disturbance regimes, anthropogenic use and management, and the mosaic of diverse ecological conditions. LANDIS-IT is a landscape forest succession and disturbance model that independently simulates multiple ecological and disturbance processes, accounting for complex interactions to predict...

Estimating density of a territorial species in a dynamic landscape

Treesearch

Elizabeth M. Glenn; Damon B. Lesmeister; Raymond J. Davis; Bruce Hollen; Anne Poopatanapong

2017-01-01

Context Conservation planning for at-risk species requires understanding of where species are likely to occur, how many individuals are likely to be supported on a given landscape, and the ability to monitor those changes through time. Objectives We developed a distribution model for northern spotted owls that...

[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.

IMPACTS OF LANDSCAPE CHANGE ON WOLF RESTORATION SUCCESS: PLANNING A REINTRODUCTION PROGRAM USING STATIC AND DYNAMIC SPATIAL MODELS

EPA Science Inventory

Mammalian carnivores are increasingly the focus of reintroduction attempts in areas from which
they have been extirpated by historic persecution. We used static and dynamic spatial models to evaluate whether a proposed wolf reintroduction to the southern Rocky Mountain region ...

Spin glass model for cell reprogramming

NASA Astrophysics Data System (ADS)

Pusuluri, Sai Teja; Castillo, Horacio E.

2014-03-01

Recent experiments show that differentiated cells can be reprogrammed to become pluripotent stem cells. The possible cell fates can be modeled as attractors in a dynamical system, the ``epigenetic landscape.'' Both cellular differentiation and reprogramming can be described in the landscape picture as motion from one attractor state to another attractor state. We use a simple model based on spin glass theory that can construct a simulated epigenetic landscape starting from the experimental genomic data. We modify the model to incorporate experimental reprogramming protocols. Our simulations successfully reproduce several reprogramming experiments. We probe the robustness of the results against random changes in the model, explore the importance of asymmetric interactions between transcription factors and study the importance of histone modification errors in reprogramming.

Studying Wildlife at Local and Landscape Scales: Bachman's Sparrow at the Savannah River Site

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

Dunning, J.B.; Danielson, B.J.; Watts, B.D.

2000-10-01

Mutual interests between land managers at SRS and scientists resulted in a landscape ecology study of Bachman's sparrow. The species is declining throughout it's range. The distribution of suitable habitats across the landscape may provide an explanation. The species occupies early successional and late successional savanna habitat. Modeling was closely linked to field observations to demonstrate how the species demographics change with the distribution and dynamics of habitats.

Modeling the effect of pathogenic mutations on the conformational landscape of protein kinases.

PubMed

Saladino, Giorgio; Gervasio, Francesco Luigi

2016-04-01

Most proteins assume different conformations to perform their cellular functions. This conformational dynamics is physiologically regulated by binding events and post-translational modifications, but can also be affected by pathogenic mutations. Atomistic molecular dynamics simulations complemented by enhanced sampling approaches are increasingly used to probe the effect of mutations on the conformational dynamics and on the underlying conformational free energy landscape of proteins. In this short review we discuss recent successful examples of simulations used to understand the molecular mechanism underlying the deregulation of physiological conformational dynamics due to non-synonymous single point mutations. Our examples are mostly drawn from the protein kinase family. Copyright © 2016 Elsevier Ltd. All rights reserved.

Glassy dynamics of landscape evolution.

PubMed

Ferdowsi, Behrooz; Ortiz, Carlos P; Jerolmack, Douglas J

2018-05-08

Soil creeps imperceptibly downhill, but also fails catastrophically to create landslides. Despite the importance of these processes as hazards and in sculpting landscapes, there is no agreed-upon model that captures the full range of behavior. Here we examine the granular origins of hillslope soil transport by discrete element method simulations and reanalysis of measurements in natural landscapes. We find creep for slopes below a critical gradient, where average particle velocity (sediment flux) increases exponentially with friction coefficient (gradient). At critical gradient there is a continuous transition to a dense-granular flow rheology. Slow earthflows and landslides thus exhibit glassy dynamics characteristic of a wide range of disordered materials; they are described by a two-phase flux equation that emerges from grain-scale friction alone. This glassy model reproduces topographic profiles of natural hillslopes, showing its promise for predicting hillslope evolution over geologic timescales. Copyright © 2018 the Author(s). Published by PNAS.

Role of small oligomers on the amyloidogenic aggregation free-energy landscape.

PubMed

He, Xianglan; Giurleo, Jason T; Talaga, David S

2010-01-08

We combine atomic-force-microscopy particle-size-distribution measurements with earlier measurements on 1-anilino-8-naphthalene sulfonate, thioflavin T, and dynamic light scattering to develop a quantitative kinetic model for the aggregation of beta-lactoglobulin into amyloid. We directly compare our simulations to the population distributions provided by dynamic light scattering and atomic force microscopy. We combine species in the simulation according to structural type for comparison with fluorescence fingerprint results. The kinetic model of amyloidogenesis leads to an aggregation free-energy landscape. We define the roles of and propose a classification scheme for different oligomeric species based on their location in the aggregation free-energy landscape. We relate the different types of oligomers to the amyloid cascade hypothesis and the toxic oligomer hypothesis for amyloid-related diseases. We discuss existing kinetic mechanisms in terms of the different types of oligomers. We provide a possible resolution to the toxic oligomer-amyloid coincidence.

Simulating forest fuel and fire risk dynamics across landscapes--LANDIS fuel module design

Treesearch

Hong S. He; Bo Z. Shang; Thomas R. Crow; Eric J. Gustafson; Stephen R. Shifley

2004-01-01

Understanding fuel dynamics over large spatial (103-106 ha) and temporal scales (101-103 years) is important in comprehensive wildfire management. We present a modeling approach to simulate fuel and fire risk dynamics as well as impacts of alternative fuel treatments. The...

Exploring the folding free energy landscape of a β-hairpin miniprotein, chignolin, using multiscale free energy landscape calculation method.

PubMed

Harada, Ryuhei; Kitao, Akio

2011-07-14

The folding process for a β-hairpin miniprotein, chignolin, was investigated by free energy landscape (FEL) calculations using the recently proposed multiscale free energy landscape calculation method (MSFEL). First, coarse-grained molecular dynamics simulations searched a broad conformational space, then multiple independent, all-atom molecular dynamics simulations with explicit solvent determined the detailed local FEL using massively distributed computing. The combination of the two models enabled efficient calculation of the free energy landscapes. The MSFEL analysis showed that chignolin has an intermediate state as well as a misfolded state. The folding process is initiated by the formation of a β-hairpin turn, followed by the formation of contacts in the hydrophobic core between Tyr2 and Trp9. Furthermore, mutation of Tyr2 shifts the population to the misfolded conformation. The results indicate that the hydrophobic core plays an important role in stabilizing the native state of chignolin. © 2011 American Chemical Society

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

USGS Publications Warehouse

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

2015-01-01

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

Testing Lithospheric versus Deep-Mantle Dynamics on Post-100 Ma Evolution of Western U.S. using Landscape Evolution Modeling

NASA Astrophysics Data System (ADS)

Chang, C.; Liu, L.

2017-12-01

Driving mechanisms of the topographic evolution of central-western North America from the Cretaceous Western Interior Seaway (WIS) to its present-day high elevation remain ellusive. Quantifying the effects of lithospheric deformation versus deep-mantle induced topography on the landscape evolution of the region is a key to better constraining the history of North American tectonics and mantle dynamics. One way to tackle this problem is through running landscape evolution simulation coupled with uplift histories characteristic to these tectonic processes. We then use available surface observations, e.g., sedimentation records, land erosion, and drainage evolution, to infer the likely lithospheric and mantle processes that formed the WIS, the subsequent Laramide orogeny, and the present-day high topography of central-western North America. In practice, we use BadLands to simulate the evolution of surface process. To validate a given uplift history, we quantitatively compare model predictions with onshore and offshore stratigraphy data from the literature. Furthermore, critical forcings of landscape evolution, such as climate, lithology and sea level, will also be examined to better attest the effects of different uplift scenarios. Preliminary results demonstrate that only with geographically migratory subsidence, as predicted by an inverse mantle convection model, can we re-produce large scale tilted strata and shifting sediment deposition observed in the WIS basins. Ongoing work will also look into styles of Cenozoic uplift events that ended the WIS and produced the landscape features today. Eventually, we hope to place new constraints on the evolution and properties of lithospheric and deep-mantle dynamics of North American and to locate the best-fit scenario of its coresponding surface evolution since 100 Ma.

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.

Forest dynamics in Oregon landscapes: Evaluation and application of an individual-based model

USGS Publications Warehouse

Busing, R.T.; Solomon, A.M.; McKane, R.B.; Burdick, C.A.

2007-01-01

The FORCLIM model of forest dynamics was tested against field survey data for its ability to simulate basal area and composition of old forests across broad climatic gradients in western Oregon, USA. The model was also tested for its ability to capture successional trends in ecoregions of the west Cascade Range. It was then applied to simulate present and future (1990-2050) forest landscape dynamics of a watershed in the west Cascades. Various regimes of climate change and harvesting in the watershed were considered in the landscape application. The model was able to capture much of the variation in forest basal area and composition in western Oregon even though temperature and precipitation were the only inputs that were varied among simulated sites. The measured decline in total basal area from tall coastal forests eastward to interior steppe was matched by simulations. Changes in simulated forest dominants also approximated those in the actual data. Simulated abundances of a few minor species did not match actual abundances, however. Subsequent projections of climate change and harvest effects in a west Cascades landscape indicated no change in forest dominance as of 2050. Yet, climate-driven shifts in the distributions of some species were projected. The simulation of both stand-replacing and partial-stand disturbances across western Oregon improved agreement between simulated and actual data. Simulations with fire as an agent of partial disturbance suggested that frequent fires of low severity can alter forest composition and structure as much or more than severe fires at historic frequencies. ?? 2007 by the Ecological Society of America.

Sources, Sinks, and Model Accuracy

EPA Science Inventory

Spatial demographic models are a necessary tool for understanding how to manage landscapes sustainably for animal populations. These models, therefore, must offer precise and testable predications about animal population dynamics and how animal demographic parameters respond to ...

Deformation of Attractor Landscape via Cholinergic Presynaptic Modulations: A Computational Study Using a Phase Neuron Model

PubMed Central

Kanamaru, Takashi; Fujii, Hiroshi; Aihara, Kazuyuki

2013-01-01

Corticopetal acetylcholine (ACh) is released transiently from the nucleus basalis of Meynert (NBM) into the cortical layers and is associated with top-down attention. Recent experimental data suggest that this release of ACh disinhibits layer 2/3 pyramidal neurons (PYRs) via muscarinic presynaptic effects on inhibitory synapses. Together with other possible presynaptic cholinergic effects on excitatory synapses, this may result in dynamic and temporal modifications of synapses associated with top-down attention. However, the system-level consequences and cognitive relevance of such disinhibitions are poorly understood. Herein, we propose a theoretical possibility that such transient modifications of connectivity associated with ACh release, in addition to top-down glutamatergic input, may provide a neural mechanism for the temporal reactivation of attractors as neural correlates of memories. With baseline levels of ACh, the brain returns to quasi-attractor states, exhibiting transitive dynamics between several intrinsic internal states. This suggests that top-down attention may cause the attention-induced deformations between two types of attractor landscapes: the quasi-attractor landscape (Q-landscape, present under low-ACh, non-attentional conditions) and the attractor landscape (A-landscape, present under high-ACh, top-down attentional conditions). We present a conceptual computational model based on experimental knowledge of the structure of PYRs and interneurons (INs) in cortical layers 1 and 2/3 and discuss the possible physiological implications of our results. PMID:23326520

An individual-based process model to simulate landscape-scale forest ecosystem dynamics

Treesearch

Rupert Seidl; Werner Rammer; Robert M. Scheller; Thomas Spies

2012-01-01

Forest ecosystem dynamics emerges from nonlinear interactions between adaptive biotic agents (i.e., individual trees) and their relationship with a spatially and temporally heterogeneous abiotic environment. Understanding and predicting the dynamics resulting from these complex interactions is crucial for the sustainable stewardship of ecosystems, particularly in the...

Classifying and comparing spatial models of fire dynamics

Treesearch

Geoffrey J. Cary; Robert E. Keane; Mike D. Flannigan

2007-01-01

Wildland fire is a significant disturbance in many ecosystems worldwide and the interaction of fire with climate and vegetation over long time spans has major effects on vegetation dynamics, ecosystem carbon budgets, and patterns of biodiversity. Landscape-Fire-Succession Models (LFSMs) that simulate the linked processes of fire and vegetation development in a spatial...

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.

From spatially variable streamflow to distributed hydrological models: Analysis of key modeling decisions

NASA Astrophysics Data System (ADS)

Fenicia, Fabrizio; Kavetski, Dmitri; Savenije, Hubert H. G.; Pfister, Laurent

2016-02-01

This paper explores the development and application of distributed hydrological models, focusing on the key decisions of how to discretize the landscape, which model structures to use in each landscape element, and how to link model parameters across multiple landscape elements. The case study considers the Attert catchment in Luxembourg—a 300 km2 mesoscale catchment with 10 nested subcatchments that exhibit clearly different streamflow dynamics. The research questions are investigated using conceptual models applied at hydrologic response unit (HRU) scales (1-4 HRUs) on 6 hourly time steps. Multiple model structures are hypothesized and implemented using the SUPERFLEX framework. Following calibration, space/time model transferability is tested using a split-sample approach, with evaluation criteria including streamflow prediction error metrics and hydrological signatures. Our results suggest that: (1) models using geology-based HRUs are more robust and capture the spatial variability of streamflow time series and signatures better than models using topography-based HRUs; this finding supports the hypothesis that, in the Attert, geology exerts a stronger control than topography on streamflow generation, (2) streamflow dynamics of different HRUs can be represented using distinct and remarkably simple model structures, which can be interpreted in terms of the perceived dominant hydrologic processes in each geology type, and (3) the same maximum root zone storage can be used across the three dominant geological units with no loss in model transferability; this finding suggests that the partitioning of water between streamflow and evaporation in the study area is largely independent of geology and can be used to improve model parsimony. The modeling methodology introduced in this study is general and can be used to advance our broader understanding and prediction of hydrological behavior, including the landscape characteristics that control hydrologic response, the dominant processes associated with different landscape types, and the spatial relations of catchment processes. This article was corrected on 14 MAR 2016. See the end of the full text for details.

Early Holocene to present landscape dynamics of the tectonic lakes of west-central Mexico

NASA Astrophysics Data System (ADS)

Castillo, Miguel; Muñoz-Salinas, Esperanza; Arce, José Luis; Roy, Priyadarsi

2017-12-01

Paleoclimatic reconstructions from lake sediments of central Mexico indicate that the environmental conditions in the Holocene have oscillated from cool-dry to warm-wet, thus, landscape erosion rates have been modified accordingly. The Cenozoic tectonics and volcanic activity of west-central Mexico have produced a set of lakes in warmer and drier conditions compared to lakes of central Mexico. Nevertheless, the Holocene landscape dynamics for this area remains understudied. Using age-depth models, OSL and multi-element chemistry analysis of sediments in the lakes of San Marcos and Sayula we explore the landscape dynamics from early Holocene present of west-central Mexico. Our results indicate that the sedimentation rates in San Marcos Lake notably increased from 240 yr BP to the present. Since AD 1950 the sedimentation rate in Sayula Lake rose fourfold the rates of the last 2000 years. Analysis of OSL and chemistry of major elements of sediments indicates that IRSL/BLSL strongly correlates with Ti/Al (R2 = 0.93) and with the mean monthly rainfall (R2 = 0.70). We propose that the IRSL/BLSL can be used as a proxy to infer past changes in landscape dynamics. Analysis of climatic data from the 1950s to present indicates that rainfall, and consequently water runoff, is enhanced in summers free of ENSO conditions. Extreme one-day rainfall can, however, exceed mean seasonal rainfall and occur in all phases of ENSO. Droughts are particularly severe in the phase of La Niña. Our results indicate that the erosion rate in San Marcos Lake was high from ∼8000 to ∼7000 yr BP in a period coinciding with the advance and recession of glaciers in Central Mexico, however, the erosion rates in the last 165 years have surpassed the rates of the early to mid-Holocene. By constraining the age of sediment and using environmental proxies such as the Ti/Al and IRSL/BLSL from lake sediments of Sayula and San Marcos we present the first model of landscape dynamics of this part of Mexico from the Early Holocene to present times.

Multidimensional spatial characterization of plant invasions in 'El Pinacate y Gran Desierto de Altar' Biosphere Reserve

NASA Astrophysics Data System (ADS)

Sanchez Flores, Erick

Invasive species are considered an agent of ecological change with more significant effects than global warming. Exotic plant invasions threaten biodiversity and ecosystem viability worldwide. Their effects in the Sonoran Desert ecosystems are a growing concern among ecologists and land managers. We hypothesized that highly dynamic desert environments are unstable, therefore more vulnerable to invasion by exotic plant species. To test this hypothesis we used a multidimensional approach to assess the spatial distribution of two exotic species: Brassica tournefortii (Saharan mustard) and Schismus arabicus (Arabian grass), in a portion of 'El Pinacate y Gran Desierto de Altar' Biosphere Reserve (PBR) in northwestern Sonora, Mexico. This approach combined genetic algorithms, geographic information systems, field methods, statistical analysis, and remote sensing modeling at multiple spatial and temporal scales to predict and test the current and potential distribution of the invasives over dynamic landscapes. Predicted probability of invasion was influenced strongly by human factors: Road networks were the strongest predictors of presence, revealing the potential importance of humans as vectors of invasiveness. Dynamic landscapes, associated mostly with vegetation losses, were detected spectrally in the eastern portion of the study area, very likely associated with past agricultural and current grazing activity. Combined models of high probability for invasion by B. tournefortii and S. arabicus over dynamic landscapes were tested against confirmed locations of the invasives and land cover types associated with invasion. Results confirmed the hypothesis of the study and suggest that more dynamic landscapes are more prone to invasion by these two exotic plants in the PBR. B. tournefortii was found associated mostly with landscapes occupied by microphyllous desert scrub and grassland, as well as sarcocaulescent desert scrub. S. arabicus was found more abundantly in the flat low lands occupied by microphyllous and crassicaulescent desert scrub. These relationships cannot, however, be conclusive and require further investigation due to the complex ecology of these invasives.

Simulating vegetation dynamics in Chile from 21ka BP to present: Effects of climate change on vegetation functions and cover

NASA Astrophysics Data System (ADS)

Werner, Christian; Liakka, Johan; Schmid, Manuel; Fuentes, Juan-Pablo; Ehlers, Todd A.; Hickler, Thomas

2017-04-01

Vegetation composition and establishment is strongly dependent on climate conditions but also a result of vegetation dynamics (competition for light, water and nutrients). In addition, vegetation exerts control over the development of landscapes as it mediates the climatic and hydrological forces shaping the terrain via hillslope and fluvial processes. At the same time, topography as well as soil texture and soil depth affect the microclimate, soil water storage and rooting space that is defining the environmental envelope for vegetation development. Within the EarthShape research program (www.earthshape.net) we evaluate these interactions by simulating the co-evolution of landscape and vegetation with a dynamic vegetation model (LPJ-GUESS) and a landscape evolution model (LandLab). LPJ-GUESS is a mechanistic model driven by daily or monthly weather data and explicitly simulates vegetation physiology, succession, competition and water and nutrient cycling. Here we present the results of first transient vegetation simulations from 21kyr BP to present-day using the TraCE-21ka climate dataset for four focus sites along the coastal cordillera of Chile that are exposed to a substantial meridional climate gradient (ranging from hyper-arid to humid-temperate conditions). We show that the warming occurring in the region from LGM to present, in addition to the increase of atmospheric CO2 concentrations, led to a shift in vegetation composition and surface cover. Future work will show how these changes resonate in the dynamics of hillslope and fluvial erosion and ultimately bi-directional feedback mechanisms of vegetation development and landscape evolution/ soil formation (see also companion presentation by Schmid et al., this session).

Higher temporal variability of forest breeding bird communities in fragmented landscapes

USGS Publications Warehouse

Boulinier, T.; Nichols, J.D.; Hines, J.E.; Sauer, J.R.; Flather, C.H.; Pollock, K.H.

1998-01-01

Understanding the relationship between animal community dynamics and landscape structure has become a priority for biodiversity conservation. In particular, predicting the effects of habitat destruction that confine species to networks of small patches is an important prerequisite to conservation plan development. Theoretical models that predict the occurrence of species in fragmented landscapes, and relationships between stability and diversity do exist. However, reliable empirical investigations of the dynamics of biodiversity have been prevented by differences in species detection probabilities among landscapes. Using long-term data sampled at a large spatial scale in conjunction with a capture-recapture approach, we developed estimates of parameters of community changes over a 22-year period for forest breeding birds in selected areas of the eastern United States. We show that forest fragmentation was associated not only with a reduced number of forest bird species, but also with increased temporal variability in the number of species. This higher temporal variability was associated with higher local extinction and turnover rates. These results have major conservation implications. Moreover, the approach used provides a practical tool for the study of the dynamics of biodiversity.

Towards a microscopic description of the free-energy landscape of water.

PubMed

Prada-Gracia, Diego; Shevchuk, Roman; Hamm, Peter; Rao, Francesco

2012-10-14

Free-energy landscape theory is often used to describe complex molecular systems. Here, a microscopic description of water structure and dynamics based on configuration-space-networks and molecular dynamics simulations of the TIP4P/2005 model is applied to investigate the free-energy landscape of water. The latter is built on top of a large set of water microstates describing the kinetic stability of local hydrogen-bond arrangements up to the second solvation shell. In temperature space, the landscape displays three different regimes. At around ambient conditions, the free-energy surface is characterized by many short-lived basins of attraction which are structurally well-defined (inhomogeneous regime). At lower temperatures instead, the liquid rapidly becomes homogeneous. In this regime, the free energy is funneled-like, with fully coordinated water arrangements at the bottom of the funnel. Finally, a third regime develops below the temperature of maximal compressibility (Widom line) where the funnel becomes steeper with few interconversions between microstates other than the fully coordinated ones. Our results present a way to manage the complexity of water structure and dynamics, connecting microscopic properties to its ensemble behavior.

Satellite remote sensing of landscape freeze/thaw state dynamics for complex Topography and Fire Disturbance Areas Using multi-sensor radar and SRTM digital elevation models

NASA Technical Reports Server (NTRS)

Podest, Erika; McDonald, Kyle; Kimball, John; Randerson, James

2003-01-01

We characterize differences in radar-derived freeze/thaw state, examining transitions over complex terrain and landscape disturbance regimes. In areas of complex terrain, we explore freezekhaw dynamics related to elevation, slope aspect and varying landcover. In the burned regions, we explore the timing of seasonal freeze/thaw transition as related to the recovering landscape, relative to that of a nearby control site. We apply in situ biophysical measurements, including flux tower measurements to validate and interpret the remotely sensed parameters. A multi-scale analysis is performed relating high-resolution SAR backscatter and moderate resolution scatterometer measurements to assess trade-offs in spatial and temporal resolution in the remotely sensed fields.

From Particles and Point Clouds to Voxel Models: High Resolution Modeling of Dynamic Landscapes in Open Source GIS

NASA Astrophysics Data System (ADS)

Mitasova, H.; Hardin, E. J.; Kratochvilova, A.; Landa, M.

2012-12-01

Multitemporal data acquired by modern mapping technologies provide unique insights into processes driving land surface dynamics. These high resolution data also offer an opportunity to improve the theoretical foundations and accuracy of process-based simulations of evolving landforms. We discuss development of new generation of visualization and analytics tools for GRASS GIS designed for 3D multitemporal data from repeated lidar surveys and from landscape process simulations. We focus on data and simulation methods that are based on point sampling of continuous fields and lead to representation of evolving surfaces as series of raster map layers or voxel models. For multitemporal lidar data we present workflows that combine open source point cloud processing tools with GRASS GIS and custom python scripts to model and analyze dynamics of coastal topography (Figure 1) and we outline development of coastal analysis toolbox. The simulations focus on particle sampling method for solving continuity equations and its application for geospatial modeling of landscape processes. In addition to water and sediment transport models, already implemented in GIS, the new capabilities under development combine OpenFOAM for wind shear stress simulation with a new module for aeolian sand transport and dune evolution simulations. Comparison of observed dynamics with the results of simulations is supported by a new, integrated 2D and 3D visualization interface that provides highly interactive and intuitive access to the redesigned and enhanced visualization tools. Several case studies will be used to illustrate the presented methods and tools and demonstrate the power of workflows built with FOSS and highlight their interoperability.Figure 1. Isosurfaces representing evolution of shoreline and a z=4.5m contour between the years 1997-2011at Cape Hatteras, NC extracted from a voxel model derived from series of lidar-based DEMs.

Integrating Ecosystem Carbon Dynamics into State-and-Transition Simulation Models of Land Use/Land Cover Change

NASA Astrophysics Data System (ADS)

Sleeter, B. M.; Daniel, C.; Frid, L.; Fortin, M. J.

2016-12-01

State-and-transition simulation models (STSMs) provide a general approach for incorporating uncertainty into forecasts of landscape change. Using a Monte Carlo approach, STSMs generate spatially-explicit projections of the state of a landscape based upon probabilistic transitions defined between states. While STSMs are based on the basic principles of Markov chains, they have additional properties that make them applicable to a wide range of questions and types of landscapes. A current limitation of STSMs is that they are only able to track the fate of discrete state variables, such as land use/land cover (LULC) classes. There are some landscape modelling questions, however, for which continuous state variables - for example carbon biomass - are also required. Here we present a new approach for integrating continuous state variables into spatially-explicit STSMs. Specifically we allow any number of continuous state variables to be defined for each spatial cell in our simulations; the value of each continuous variable is then simulated forward in discrete time as a stochastic process based upon defined rates of change between variables. These rates can be defined as a function of the realized states and transitions of each cell in the STSM, thus providing a connection between the continuous variables and the dynamics of the landscape. We demonstrate this new approach by (1) developing a simple IPCC Tier 3 compliant model of ecosystem carbon biomass, where the continuous state variables are defined as terrestrial carbon biomass pools and the rates of change as carbon fluxes between pools, and (2) integrating this carbon model with an existing LULC change model for the state of Hawaii, USA.

Colonizing Dynamic Alluvial and Coastal Landscapes in the Holocene

NASA Astrophysics Data System (ADS)

Kidder, T.; Liu, X.; Ervin, K.

2017-12-01

Throughout the Holocene humans have had to adapt to dynamic, rapidly changing alluvial and coastal landscapes. Understanding when people inhabit a given environment is an important starting point for exploring human adaptations, but increasingly we need to consider how, and especially why certain environments are used—or not used— so we can understand the consequences of these human actions. Using four case studies—one from the Yellow River Valley, China, one from coastal Jiangsu, China, one from the Mississippi River Valley (Mississippi, USA) and one from the Mississippi River delta (Louisiana , USA)—we develop a model of how humans at various stages of cultural development colonize new environments. Using archaeological data and ecological modeling we investigate the relationship between the timing of landscape colonization and the ecological richness and predictability of any given environment. As new landscapes emerge and mature humans adopt different strategies for exploiting these novel environments that begins with episodic use and increasingly shifts to stable, long-term habitation. The early phase of landscape colonization appears to be the most significant period because it shapes human environmental practices and sets each culture on a trajectory of socio-cultural development. Thus, human-environment interaction is a critical part of the emergence of cultural patterns that shapes the past, present, and even the future.

Detectability of landscape effects on recolonization increases with regional population density

PubMed Central

Liman, Anna-Sara; Dalin, Peter; Björkman, Christer

2015-01-01

Variation in population size over time can influence our ability to identify landscape-moderated differences in community assembly. To date, however, most studies at the landscape scale only cover snapshots in time, thereby overlooking the temporal dynamics of populations and communities. In this paper, we present data that illustrate how temporal variation in population density at a regional scale can influence landscape-moderated variation in recolonization and population buildup in disturbed habitat patches. Four common insect species, two omnivores and two herbivores, were monitored over 8 years in 10 willow short-rotation coppice bio-energy stands with a four-year disturbance regime (coppice cycle). The population densities in these regularly disturbed stands were compared to densities in 17 undisturbed natural Salix cinerea (grey willow) stands in the same region. A time series approach was used, utilizing the natural variation between years to statistically model recolonization as a function of landscape composition under two different levels of regional density. Landscape composition, i.e. relative amount of forest vs. open agricultural habitats, largely determined the density of re-colonizing populations following willow coppicing in three of the four species. However, the impact of landscape composition was not detectable in years with low regional density. Our results illustrate that landscape-moderated recolonization can change over time and that considering the temporal dynamics of populations may be crucial when designing and evaluating studies at landscape level. PMID:26257881

Detectability of landscape effects on recolonization increases with regional population density.

PubMed

Liman, Anna-Sara; Dalin, Peter; Björkman, Christer

2015-07-01

Variation in population size over time can influence our ability to identify landscape-moderated differences in community assembly. To date, however, most studies at the landscape scale only cover snapshots in time, thereby overlooking the temporal dynamics of populations and communities. In this paper, we present data that illustrate how temporal variation in population density at a regional scale can influence landscape-moderated variation in recolonization and population buildup in disturbed habitat patches. Four common insect species, two omnivores and two herbivores, were monitored over 8 years in 10 willow short-rotation coppice bio-energy stands with a four-year disturbance regime (coppice cycle). The population densities in these regularly disturbed stands were compared to densities in 17 undisturbed natural Salix cinerea (grey willow) stands in the same region. A time series approach was used, utilizing the natural variation between years to statistically model recolonization as a function of landscape composition under two different levels of regional density. Landscape composition, i.e. relative amount of forest vs. open agricultural habitats, largely determined the density of re-colonizing populations following willow coppicing in three of the four species. However, the impact of landscape composition was not detectable in years with low regional density. Our results illustrate that landscape-moderated recolonization can change over time and that considering the temporal dynamics of populations may be crucial when designing and evaluating studies at landscape level.

Assessing Impacts of Climate Change on Forests: The State of Biological Modeling

DOE R&D Accomplishments Database

Dale, V. H.; Rauscher, H. M.

1993-04-06

Models that address the impacts to forests of climate change are reviewed by four levels of biological organization: global, regional or landscape, community, and tree. The models are compared as to their ability to assess changes in greenhouse gas flux, land use, maps of forest type or species composition, forest resource productivity, forest health, biodiversity, and wildlife habitat. No one model can address all of these impacts, but landscape transition models and regional vegetation and land-use models consider the largest number of impacts. Developing landscape vegetation dynamics models of functional groups is suggested as a means to integrate the theory of both landscape ecology and individual tree responses to climate change. Risk assessment methodologies can be adapted to deal with the impacts of climate change at various spatial and temporal scales. Four areas of research development are identified: (1) linking socioeconomic and ecologic models, (2) interfacing forest models at different scales, (3) obtaining data on susceptibility of trees and forest to changes in climate and disturbance regimes, and (4) relating information from different scales.

Modeling landscape net ecosystem productivity (LandNEP) under alternative management regimes

Treesearch

Eugenie S. Euskirchen; Jiquan Chen; Harbin Li; Eric J. Gustafson; Thomas R. Crow

2002-01-01

Forests have been considered as a major carbon sink within the global carbon budget. However, a fragmented forest landscape varies significantly in its composition and age structure, and the amount of carbon sequestered at this level remains generally unknown to the scientific community. More precisely, the temporal dynamics and spatial distribution of net ecosystem...

Chapter 6 - Developing the LANDFIRE Vegetation and Biophysical Settings Map Unit Classifications for the LANDFIRE Prototype Project

Treesearch

Jennifer L. Long; Melanie Miller; James P. Menakis; Robert E. Keane

2006-01-01

The Landscape Fire and Resource Management Planning Tools Prototype Project, or LANDFIRE Prototype Project, required a system for classifying vegetation composition, biophysical settings, and vegetation structure to facilitate the mapping of vegetation and wildland fuel characteristics and the simulation of vegetation dynamics using landscape modeling. We developed...

Comparing modern and presettlement forest dynamics of a subboreal wilderness: Does spruce budworm enhance fire risk?

Treesearch

Brian R Sturtevant; Brian R Miranda; Douglas J Shinneman; Eric J Gustafson; Peter T. Wolter

2012-01-01

Insect disturbance is often thought to increase fire risk through enhanced fuel loadings, particularly in coniferous forest ecosystems. Yet insect disturbances also affect successional pathways and landscape structure that interact with fire disturbances (and vice-versa) over longer time scales. We applied a landscape succession and disturbance model (LANDIS-II) to...

Three decades of landscape change in Alaska documented using spatiotemporal analyses of remote sensing imagery

NASA Astrophysics Data System (ADS)

Pastick, N. J.; Jorgenson, T.; Swanson, D. K.; Jorgenson, J. C.; Goetz, S. J.; Jones, B. M.; Wylie, B. K.; Knight, J. F.; Minsley, B. J.; Helene, G.

2017-12-01

Contemporary climate change in Alaska has resulted in amplified rates of press and pulse disturbances that have significant consequences for socio-environmental systems. With the heightened susceptibility of arctic and boreal landscapes to change, the characterization of landscape dynamics and the identification of environmental drivers of change across northern high latitudes is critical. Here, we characterize the historical sensitivity of Alaska's ecosystems to natural and anthropogenic disturbances using expert knowledge, remote sensing data, spatiotemporal analyses, and modeling. Time-series analysis of moderate- and high-resolution imagery was used to characterize landscape dynamics across Alaska and along randomly sampled change-detection grids (n=312). Expert interpretations of ecological and geomorphological changes were made at each grid using historical air photos and high-resolution satellite imagery (1980s, 2000s, 2010s), and corroborate land surface greening, browning, and wetness/moisture trends derived from peak-growing season (July 1st - August 31st) Landsat imagery acquired from 1984 to 2015. Spectral change metrics, climatic data, maps of biophysical characteristics, and interpretations of change were incorporated into a modeling framework for mapping and understanding change across Alaska. At the landscape scale, substantial increases in remotely sensed vegetation productivity were most pronounced in western and northern foothills of Alaska, which is associated with recent warming-induced shrub expansion and vegetation growth. Significant browning trends in interior Alaska were largely the­­­­ result of recent wildland fires, but browning trends are also driven by increases in evaporative demand and surface water gains that have predominately occurred over warming permafrost landscapes. Increased rates of photosynthetic activity were also associated with stabilization and recovery processes following wildfire, timber harvesting, insect damage, thermokarst, and glacial retreat, as well as lake infilling and drainage events. This study documents historical landscape dynamics and drivers of change, which is important for understanding potential future trajectories of change and for identifying areas most likely vulnerable to change.

Bacterial predator–prey dynamics in microscale patchy landscapes

PubMed Central

Rotem, Or; Jurkevitch, Edouard; Dekker, Cees

2016-01-01

Soil is a microenvironment with a fragmented (patchy) spatial structure in which many bacterial species interact. Here, we explore the interaction between the predatory bacterium Bdellovibrio bacteriovorus and its prey Escherichia coli in microfabricated landscapes. We ask how fragmentation influences the prey dynamics at the microscale and compare two landscape geometries: a patchy landscape and a continuous landscape. By following the dynamics of prey populations with high spatial and temporal resolution for many generations, we found that the variation in predation rates was twice as large in the patchy landscape and the dynamics was correlated over shorter length scales. We also found that while the prey population in the continuous landscape was almost entirely driven to extinction, a significant part of the prey population in the fragmented landscape persisted over time. We observed significant surface-associated growth, especially in the fragmented landscape and we surmise that this sub-population is more resistant to predation. Our results thus show that microscale fragmentation can significantly influence bacterial interactions. PMID:26865299

Exploring Neural Network Models with Hierarchical Memories and Their Use in Modeling Biological Systems

NASA Astrophysics Data System (ADS)

Pusuluri, Sai Teja

Energy landscapes are often used as metaphors for phenomena in biology, social sciences and finance. Different methods have been implemented in the past for the construction of energy landscapes. Neural network models based on spin glass physics provide an excellent mathematical framework for the construction of energy landscapes. This framework uses a minimal number of parameters and constructs the landscape using data from the actual phenomena. In the past neural network models were used to mimic the storage and retrieval process of memories (patterns) in the brain. With advances in the field now, these models are being used in machine learning, deep learning and modeling of complex phenomena. Most of the past literature focuses on increasing the storage capacity and stability of stored patterns in the network but does not study these models from a modeling perspective or an energy landscape perspective. This dissertation focuses on neural network models both from a modeling perspective and from an energy landscape perspective. I firstly show how the cellular interconversion phenomenon can be modeled as a transition between attractor states on an epigenetic landscape constructed using neural network models. The model allows the identification of a reaction coordinate of cellular interconversion by analyzing experimental and simulation time course data. Monte Carlo simulations of the model show that the initial phase of cellular interconversion is a Poisson process and the later phase of cellular interconversion is a deterministic process. Secondly, I explore the static features of landscapes generated using neural network models, such as sizes of basins of attraction and densities of metastable states. The simulation results show that the static landscape features are strongly dependent on the correlation strength and correlation structure between patterns. Using different hierarchical structures of the correlation between patterns affects the landscape features. These results show how the static landscape features can be controlled by adjusting the correlations between patterns. Finally, I explore the dynamical features of landscapes generated using neural network models such as the stability of minima and the transition rates between minima. The results from this project show that the stability depends on the correlations between patterns. It is also found that the transition rates between minima strongly depend on the type of bias applied and the correlation between patterns. The results from this part of the dissertation can be useful in engineering an energy landscape without even having the complete information about the associated minima of the landscape.

Structure and Dynamics of Solvent Landscapes in Charge-Transfer Reactions

NASA Astrophysics Data System (ADS)

Leite, Vitor B. Pereira

The dynamics of solvent polarization plays a major role in the control of charge transfer reactions. The success of Marcus theory describing the solvent influence via a single collective quadratic polarization coordinate has been remarkable. Onuchic and Wolynes have recently proposed (J. Chem Phys 98 (3) 2218, 1993) a simple model demonstrating how a many-dimensional-complex model composed by several dipole moments (representing solvent molecules or polar groups in proteins) can be reduced under the appropriate limits into the Marcus Model. This work presents a dynamical study of the same model, which is characterized by two parameters, an average dipole-dipole interaction as a term associated with the potential energy landscape roughness. It is shown why the effective potential, obtained using a thermodynamic approach, is appropriate for the dynamics of the system. At high temperatures, the system exhibits effective diffusive one-dimensional dynamics, where the Born-Marcus limit is recovered. At low temperatures, a glassy phase appears with a slow non-self-averaging dynamics. At intermediate temperatures, the concept of equivalent diffusion paths and polarization dependence effects are discussed. This approach is extended to treat more realistic solvent models. Real solvents are discussed in terms of simple parameters described above, and an analysis of how different regimes affect the rate of charge transfer is presented. Finally, these ideas are correlated to analogous problems in other areas.

Dynamic, spatial models of parasite transmission in wildlife: Their structure, applications and remaining challenges.

PubMed

White, Lauren A; Forester, James D; Craft, Meggan E

2018-05-01

Individual differences in contact rate can arise from host, group and landscape heterogeneity and can result in different patterns of spatial spread for diseases in wildlife populations with concomitant implications for disease control in wildlife of conservation concern, livestock and humans. While dynamic disease models can provide a better understanding of the drivers of spatial spread, the effects of landscape heterogeneity have only been modelled in a few well-studied wildlife systems such as rabies and bovine tuberculosis. Such spatial models tend to be either purely theoretical with intrinsic limiting assumptions or individual-based models that are often highly species- and system-specific, limiting the breadth of their utility. Our goal was to review studies that have utilized dynamic, spatial models to answer questions about pathogen transmission in wildlife and identify key gaps in the literature. We begin by providing an overview of the main types of dynamic, spatial models (e.g., metapopulation, network, lattice, cellular automata, individual-based and continuous-space) and their relation to each other. We investigate different types of ecological questions that these models have been used to explore: pathogen invasion dynamics and range expansion, spatial heterogeneity and pathogen persistence, the implications of management and intervention strategies and the role of evolution in host-pathogen dynamics. We reviewed 168 studies that consider pathogen transmission in free-ranging wildlife and classify them by the model type employed, the focal host-pathogen system, and their overall research themes and motivation. We observed a significant focus on mammalian hosts, a few well-studied or purely theoretical pathogen systems, and a lack of studies occurring at the wildlife-public health or wildlife-livestock interfaces. Finally, we discuss challenges and future directions in the context of unprecedented human-mediated environmental change. Spatial models may provide new insights into understanding, for example, how global warming and habitat disturbance contribute to disease maintenance and emergence. Moving forward, better integration of dynamic, spatial disease models with approaches from movement ecology, landscape genetics/genomics and ecoimmunology may provide new avenues for investigation and aid in the control of zoonotic and emerging infectious diseases. © 2017 The Authors. Journal of Animal Ecology published by John Wiley & Sons Ltd on behalf of British Ecological Society.

Interactions between landslides and landscape evolution using a sediment flux-dependent bedrock incision model incorporating bed macro-roughness

NASA Astrophysics Data System (ADS)

Kwang, J. S.; Parker, G.

2017-12-01

Many landscape evolution models incorporate sediment removal as a quasi-equilibrium process via the Stream Power Incision Model, or otherwise incorporate sediment supply to mixed bedrock-alluvial channels according to a quasi-steady relation between channel incision and hillslope production. Yet in actively uplifting landscapes, hillslope production is often a highly punctuated phenomenon governed by landslides. We investigate the following key question: how does a landscape subject to punctuated sediment supply differ from one with a steady supply at the same rate? To do this, we incorporate punctuated supply into the Macro Roughness Saltation Abrasion Alluviation model [Zhang et al., 2015], a descendant of the Capacity Saltation Abrasion model [Sklar and Dietrich, 2004, 2006], that is specifically designed to capture unsteady alluvial morphodynamics. Our model has three modules: a) a bedrock-alluvial channel module, b) a hillslope diffusion module, and c) a stochastically-driven landslide supply module. Sediment in bedrock channels plays two roles in incision: 1) as an abrasive agent that incises the bed via collisions and 2) as a protector that inhibits collisions of sediment on the bed. The abrasion rate is proportional to a bedload transport rate times the areal fraction of bedrock surface that is exposed. The transport rate is equal to the capacity transport rate times the areal fraction of bedrock surface that is covered with alluvium, i.e. cover factor. Here, the incision rate vanishes with either vanishing cover (no tools) or complete cover (no bedrock exposed for abrasion). The properties of and amount of sediment delivered to the channel heavily depend on hillslope dynamics. Therefore, hillslope dynamics are important in determining the rate of incision of bedrock channels. Conversely, bedrock incision drives the production of sediment by lowering the base of hillslopes, creating a feedback. We explore this feedback in our landscape evolution model by adjusting our landslide model so that it supplies sediment at a steady rate or according to a stochastic algorithm chosen to characterize landslide size and frequency in such settings as Taiwan or Sichuan near the 2008 Wenchuan Earthquake epicenter. We use our model to study the signature of punctuated sediment delivery on the landscape.

Accelerated molecular dynamics and protein conformational change: a theoretical and practical guide using a membrane embedded model neurotransmitter transporter.

PubMed

Gedeon, Patrick C; Thomas, James R; Madura, Jeffry D

2015-01-01

Molecular dynamics simulation provides a powerful and accurate method to model protein conformational change, yet timescale limitations often prevent direct assessment of the kinetic properties of interest. A large number of molecular dynamic steps are necessary for rare events to occur, which allow a system to overcome energy barriers and conformationally transition from one potential energy minimum to another. For many proteins, the energy landscape is further complicated by a multitude of potential energy wells, each separated by high free-energy barriers and each potentially representative of a functionally important protein conformation. To overcome these obstacles, accelerated molecular dynamics utilizes a robust bias potential function to simulate the transition between different potential energy minima. This straightforward approach more efficiently samples conformational space in comparison to classical molecular dynamics simulation, does not require advanced knowledge of the potential energy landscape and converges to the proper canonical distribution. Here, we review the theory behind accelerated molecular dynamics and discuss the approach in the context of modeling protein conformational change. As a practical example, we provide a detailed, step-by-step explanation of how to perform an accelerated molecular dynamics simulation using a model neurotransmitter transporter embedded in a lipid cell membrane. Changes in protein conformation of relevance to the substrate transport cycle are then examined using principle component analysis.

BEEHAVE: a systems model of honeybee colony dynamics and foraging to explore multifactorial causes of colony failure

PubMed Central

Becher, Matthias A; Grimm, Volker; Thorbek, Pernille; Horn, Juliane; Kennedy, Peter J; Osborne, Juliet L

2014-01-01

A notable increase in failure of managed European honeybee Apis mellifera L. colonies has been reported in various regions in recent years. Although the underlying causes remain unclear, it is likely that a combination of stressors act together, particularly varroa mites and other pathogens, forage availability and potentially pesticides. It is experimentally challenging to address causality at the colony scale when multiple factors interact. In silico experiments offer a fast and cost-effective way to begin to address these challenges and inform experiments. However, none of the published bee models combine colony dynamics with foraging patterns and varroa dynamics. We have developed a honeybee model, BEEHAVE, which integrates colony dynamics, population dynamics of the varroa mite, epidemiology of varroa-transmitted viruses and allows foragers in an agent-based foraging model to collect food from a representation of a spatially explicit landscape. We describe the model, which is freely available online (www.beehave-model.net). Extensive sensitivity analyses and tests illustrate the model's robustness and realism. Simulation experiments with various combinations of stressors demonstrate, in simplified landscape settings, the model's potential: predicting colony dynamics and potential losses with and without varroa mites under different foraging conditions and under pesticide application. We also show how mitigation measures can be tested. Synthesis and applications. BEEHAVE offers a valuable tool for researchers to design and focus field experiments, for regulators to explore the relative importance of stressors to devise management and policy advice and for beekeepers to understand and predict varroa dynamics and effects of management interventions. We expect that scientists and stakeholders will find a variety of applications for BEEHAVE, stimulating further model development and the possible inclusion of other stressors of potential importance to honeybee colony dynamics. PMID:25598549

BEEHAVE: a systems model of honeybee colony dynamics and foraging to explore multifactorial causes of colony failure.

PubMed

Becher, Matthias A; Grimm, Volker; Thorbek, Pernille; Horn, Juliane; Kennedy, Peter J; Osborne, Juliet L

2014-04-01

A notable increase in failure of managed European honeybee Apis mellifera L. colonies has been reported in various regions in recent years. Although the underlying causes remain unclear, it is likely that a combination of stressors act together, particularly varroa mites and other pathogens, forage availability and potentially pesticides. It is experimentally challenging to address causality at the colony scale when multiple factors interact. In silico experiments offer a fast and cost-effective way to begin to address these challenges and inform experiments. However, none of the published bee models combine colony dynamics with foraging patterns and varroa dynamics.We have developed a honeybee model, BEEHAVE, which integrates colony dynamics, population dynamics of the varroa mite, epidemiology of varroa-transmitted viruses and allows foragers in an agent-based foraging model to collect food from a representation of a spatially explicit landscape.We describe the model, which is freely available online (www.beehave-model.net). Extensive sensitivity analyses and tests illustrate the model's robustness and realism. Simulation experiments with various combinations of stressors demonstrate, in simplified landscape settings, the model's potential: predicting colony dynamics and potential losses with and without varroa mites under different foraging conditions and under pesticide application. We also show how mitigation measures can be tested. Synthesis and applications . BEEHAVE offers a valuable tool for researchers to design and focus field experiments, for regulators to explore the relative importance of stressors to devise management and policy advice and for beekeepers to understand and predict varroa dynamics and effects of management interventions. We expect that scientists and stakeholders will find a variety of applications for BEEHAVE, stimulating further model development and the possible inclusion of other stressors of potential importance to honeybee colony dynamics.

Modelling hydrological processes in mountainous permafrost basin in North-East of Russia

NASA Astrophysics Data System (ADS)

Makarieva, Olga; Lebedeva, Lyudmila; Nesterova, Natalia

2017-04-01

The studies of hydrological processes in continuous permafrost and the projections of their changes in future have been receiving a lot of attention in the recent years. They are limited by the availability of long-term joint observational data on permafrost dynamic and river runoff which would allow revealing the mechanisms of interaction, tracking the dynamic in historical period and projecting changes in future. The Kolyma Water-Balance Station (KWBS), the Kontaktovy Creek watershed with an area of 22 km2, is situated in the zone of continuous permafrost in the upper reaches of the Kolyma River (Magadan district of Russia). The topography at KWBS is mountainous with the elevations up to 1700 m. Permafrost thickness ranges from 100 to 400 m with temperature -4...-6 °C. Detailed observations of river runoff, active layer dynamics and water balance were carried out at the KWBS from 1948 to 1997. After that permafrost studies were ceased but runoff gauges have been in use and have continuous time series of observations up to 68 years. The hydrological processes at KWBS are representative for the vast NE region of Russia where standard observational network is very scarce. We aim to study and model the mechanisms of interactions between permafrost and runoff, including water flow paths in different landscapes of mountainous permafrost based on detailed historical data of KWBS and the analysis of stable isotopes composition from water samples collected at KWBS in 2016. Mathematical modelling of soil temperature, active layer properties and dynamics, flow formation and interactions between ground and surface water is performed by the means of Hydrograph model (Vinogradov et al. 2011, Semenova et al. 2013). The model algorithms combine process-based and conceptual approaches, which allows for maintaining a balance between the complexity of model design and the use of limited input information. The method for modeling heat dynamics in soil was integrated into Hydrograph model (Semenova et al., 2015; Lebedeva et al., 2015). Small watersheds of KWBS with areas less than 0.5 km2 presenting rocky talus, mountainous tundra and moist larch-forest landscapes were modelled with satisfactory results. The dependence of surface and subsurface flow formation on thawing depth and landscape characteristics is parametrically described. Process analysis and modelling in permafrost regions, including ungauged basins, is suggested, with observable properties of landscapes being used as model parameters, combined with an appropriate level of physically-based conceptualization. The study is partially supported by Russian foundation of basic research, projects 16-35-50151 and 17-05-01138.

Exploring the Free Energy Landscape: From Dynamics to Networks and Back

PubMed Central

Prada-Gracia, Diego; Gómez-Gardeñes, Jesús; Echenique, Pablo; Falo, Fernando

2009-01-01

Knowledge of the Free Energy Landscape topology is the essential key to understanding many biochemical processes. The determination of the conformers of a protein and their basins of attraction takes a central role for studying molecular isomerization reactions. In this work, we present a novel framework to unveil the features of a Free Energy Landscape answering questions such as how many meta-stable conformers there are, what the hierarchical relationship among them is, or what the structure and kinetics of the transition paths are. Exploring the landscape by molecular dynamics simulations, the microscopic data of the trajectory are encoded into a Conformational Markov Network. The structure of this graph reveals the regions of the conformational space corresponding to the basins of attraction. In addition, handling the Conformational Markov Network, relevant kinetic magnitudes as dwell times and rate constants, or hierarchical relationships among basins, completes the global picture of the landscape. We show the power of the analysis studying a toy model of a funnel-like potential and computing efficiently the conformers of a short peptide, dialanine, paving the way to a systematic study of the Free Energy Landscape in large peptides. PMID:19557191

Exploring the free energy landscape: from dynamics to networks and back.

PubMed

Prada-Gracia, Diego; Gómez-Gardeñes, Jesús; Echenique, Pablo; Falo, Fernando

2009-06-01

Knowledge of the Free Energy Landscape topology is the essential key to understanding many biochemical processes. The determination of the conformers of a protein and their basins of attraction takes a central role for studying molecular isomerization reactions. In this work, we present a novel framework to unveil the features of a Free Energy Landscape answering questions such as how many meta-stable conformers there are, what the hierarchical relationship among them is, or what the structure and kinetics of the transition paths are. Exploring the landscape by molecular dynamics simulations, the microscopic data of the trajectory are encoded into a Conformational Markov Network. The structure of this graph reveals the regions of the conformational space corresponding to the basins of attraction. In addition, handling the Conformational Markov Network, relevant kinetic magnitudes as dwell times and rate constants, or hierarchical relationships among basins, completes the global picture of the landscape. We show the power of the analysis studying a toy model of a funnel-like potential and computing efficiently the conformers of a short peptide, dialanine, paving the way to a systematic study of the Free Energy Landscape in large peptides.

The FireBGCv2 landscape fire and succession model: a research simulation platform for exploring fire and vegetation dynamics

Treesearch

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

2011-01-01

Fire management faces important emergent issues in the coming years such as climate change, fire exclusion impacts, and wildland-urban development, so new, innovative means are needed to address these challenges. Field studies, while preferable and reliable, will be problematic because of the large time and space scales involved. Therefore, landscape simulation...

The dynamical landscape of marine phytoplankton diversity

PubMed Central

Lévy, Marina; Jahn, Oliver; Dutkiewicz, Stephanie; Follows, Michael J.; d'Ovidio, Francesco

2015-01-01

Observations suggest that the landscape of marine phytoplankton assemblage might be strongly heterogeneous at the dynamical mesoscale and submesoscale (10–100 km, days to months), with potential consequences in terms of global diversity and carbon export. But these variations are not well documented as synoptic taxonomic data are difficult to acquire. Here, we examine how phytoplankton assemblage and diversity vary between mesoscale eddies and submesoscale fronts. We use a multi-phytoplankton numerical model embedded in a mesoscale flow representative of the North Atlantic. Our model results suggest that the mesoscale flow dynamically distorts the niches predefined by environmental contrasts at the basin scale and that the phytoplankton diversity landscape varies over temporal and spatial scales that are one order of magnitude smaller than those of the basin-scale environmental conditions. We find that any assemblage and any level of diversity can occur in eddies and fronts. However, on a statistical level, the results suggest a tendency for larger diversity and more fast-growing types at fronts, where nutrient supplies are larger and where populations of adjacent water masses are constantly brought into contact; and lower diversity in the core of eddies, where water masses are kept isolated long enough to enable competitive exclusion. PMID:26400196

Evaluation of Dynamic Coastal Response to Sea-level Rise Modifies Inundation Likelihood

NASA Technical Reports Server (NTRS)

Lentz, Erika E.; Thieler, E. Robert; Plant, Nathaniel G.; Stippa, Sawyer R.; Horton, Radley M.; Gesch, Dean B.

2016-01-01

Sea-level rise (SLR) poses a range of threats to natural and built environments, making assessments of SLR-induced hazards essential for informed decision making. We develop a probabilistic model that evaluates the likelihood that an area will inundate (flood) or dynamically respond (adapt) to SLR. The broad-area applicability of the approach is demonstrated by producing 30x30m resolution predictions for more than 38,000 sq km of diverse coastal landscape in the northeastern United States. Probabilistic SLR projections, coastal elevation and vertical land movement are used to estimate likely future inundation levels. Then, conditioned on future inundation levels and the current land-cover type, we evaluate the likelihood of dynamic response versus inundation. We find that nearly 70% of this coastal landscape has some capacity to respond dynamically to SLR, and we show that inundation models over-predict land likely to submerge. This approach is well suited to guiding coastal resource management decisions that weigh future SLR impacts and uncertainty against ecological targets and economic constraints.

Collective degrees of freedom involved in absorption and desorption of surfactant molecules in spherical non-ionic micelles

NASA Astrophysics Data System (ADS)

Ahn, Yong Nam; Mohan, Gunjan; Kopelevich, Dmitry I.

2012-10-01

Dynamics of absorption and desorption of a surfactant monomer into and out of a spherical non-ionic micelle is investigated by coarse-grained molecular dynamics (MD) simulations. It is shown that these processes involve a complex interplay between the micellar structure and the monomer configuration. A quantitative model for collective dynamics of these degrees of freedom is developed. This is accomplished by reconstructing a multi-dimensional free energy landscape of the surfactant-micelle system using constrained MD simulations in which the distance between the micellar and monomer centers of mass is held constant. Results of this analysis are verified by direct (unconstrained) MD simulations of surfactant absorption in the micelle. It is demonstrated that the system dynamics is likely to deviate from the minimum energy path on the energy landscape. These deviations create an energy barrier for the monomer absorption and increase an existing barrier for the monomer desorption. A reduced Fokker-Planck equation is proposed to model these effects.

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

NASA Astrophysics Data System (ADS)

Hart, Gregory; Ferguson, Andrew

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

The Sadder the Story, the Bigger the Check: Reciprocity as an Answer to Organizational Deficit Models

ERIC Educational Resources Information Center

Gindlesparger, Kathryn Johnson

2010-01-01

This ethnographic study argues that reciprocity--the attempt to equalize the power dynamics that occur in working relationships--is a way to counteract the widely-used but rarely-critiqued deficit models that dominate the nonprofit landscape. If community work is not done with a near constant attention to power dynamics, programming that is…

Endangered Butterflies as a Model System for Managing Source Sink Dynamics on Department of Defense Lands

DTIC Science & Technology

patches to cycle from sink to source status and back.Objective: Through a combination of field studies and state-of-the-art quantitative models, we...landscapes with dynamic changes in habitat quality due to management. We also validated our general approach by comparing patterns in our focal species to general, cross-taxa, patterns.

Landslide Hazard Probability Derived from Inherent and Dynamic Determinants

NASA Astrophysics Data System (ADS)

Strauch, Ronda; Istanbulluoglu, Erkan

2016-04-01

Landslide hazard research has typically been conducted independently from hydroclimate research. We unify these two lines of research to provide regional scale landslide hazard information for risk assessments and resource management decision-making. Our approach combines an empirical inherent landslide probability with a numerical dynamic probability, generated by combining routed recharge from the Variable Infiltration Capacity (VIC) macro-scale land surface hydrologic model with a finer resolution probabilistic slope stability model run in a Monte Carlo simulation. Landslide hazard mapping is advanced by adjusting the dynamic model of stability with an empirically-based scalar representing the inherent stability of the landscape, creating a probabilistic quantitative measure of geohazard prediction at a 30-m resolution. Climatology, soil, and topography control the dynamic nature of hillslope stability and the empirical information further improves the discriminating ability of the integrated model. This work will aid resource management decision-making in current and future landscape and climatic conditions. The approach is applied as a case study in North Cascade National Park Complex, a rugged terrain with nearly 2,700 m (9,000 ft) of vertical relief, covering 2757 sq km (1064 sq mi) in northern Washington State, U.S.A.

Solution landscapes in nematic microfluidics

NASA Astrophysics Data System (ADS)

Crespo, M.; Majumdar, A.; Ramos, A. M.; Griffiths, I. M.

2017-08-01

We study the static equilibria of a simplified Leslie-Ericksen model for a unidirectional uniaxial nematic flow in a prototype microfluidic channel, as a function of the pressure gradient G and inverse anchoring strength, B. We numerically find multiple static equilibria for admissible pairs (G , B) and classify them according to their winding numbers and stability. The case G = 0 is analytically tractable and we numerically study how the solution landscape is transformed as G increases. We study the one-dimensional dynamical model, the sensitivity of the dynamic solutions to initial conditions and the rate of change of G and B. We provide a physically interesting example of how the time delay between the applications of G and B can determine the selection of the final steady state.

Simulating the effects of the southern pine beetle on regional dynamics 60 years into the future

Treesearch

Jennifer K. Costanza; Jiri Hulcr; Frank H. Koch; Todd Earnhardt; Alexa J. McKerrow; Rob R. Dunn; Jaime A. Collazo

2012-01-01

We developed a spatially explicit model that simulated future southern pine beetle (Dendroctonus frontalis, SPB) dynamics and pine forest management for a real landscape over 60 years to inform regional forest management. The SPB has a considerable effect on forest dynamics in the Southeastern United States, especially in loblolly pine (...

SEARCH: Spatially Explicit Animal Response to Composition of Habitat.

PubMed

Pauli, Benjamin P; McCann, Nicholas P; Zollner, Patrick A; Cummings, Robert; Gilbert, Jonathan H; Gustafson, Eric J

2013-01-01

Complex decisions dramatically affect animal dispersal and space use. Dispersing individuals respond to a combination of fine-scale environmental stimuli and internal attributes. Individual-based modeling offers a valuable approach for the investigation of such interactions because it combines the heterogeneity of animal behaviors with spatial detail. Most individual-based models (IBMs), however, vastly oversimplify animal behavior and such behavioral minimalism diminishes the value of these models. We present program SEARCH (Spatially Explicit Animal Response to Composition of Habitat), a spatially explicit, individual-based, population model of animal dispersal through realistic landscapes. SEARCH uses values in Geographic Information System (GIS) maps to apply rules that animals follow during dispersal, thus allowing virtual animals to respond to fine-scale features of the landscape and maintain a detailed memory of areas sensed during movement. SEARCH also incorporates temporally dynamic landscapes so that the environment to which virtual animals respond can change during the course of a simulation. Animals in SEARCH are behaviorally dynamic and able to respond to stimuli based upon their individual experiences. Therefore, SEARCH is able to model behavioral traits of dispersing animals at fine scales and with many dynamic aspects. Such added complexity allows investigation of unique ecological questions. To illustrate SEARCH's capabilities, we simulated case studies using three mammals. We examined the impact of seasonally variable food resources on the weight distribution of dispersing raccoons (Procyon lotor), the effect of temporally dynamic mortality pressure in combination with various levels of behavioral responsiveness in eastern chipmunks (Tamias striatus), and the impact of behavioral plasticity and home range selection on disperser mortality and weight change in virtual American martens (Martes americana). These simulations highlight the relevance of SEARCH for a variety of applications and illustrate benefits it can provide for conservation planning.

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

USGS Publications Warehouse

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

2016-01-01

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

Using graph approach for managing connectivity in integrative landscape modelling

NASA Astrophysics Data System (ADS)

Rabotin, Michael; Fabre, Jean-Christophe; Libres, Aline; Lagacherie, Philippe; Crevoisier, David; Moussa, Roger

2013-04-01

In cultivated landscapes, a lot of landscape elements such as field boundaries, ditches or banks strongly impact water flows, mass and energy fluxes. At the watershed scale, these impacts are strongly conditionned by the connectivity of these landscape elements. An accurate representation of these elements and of their complex spatial arrangements is therefore of great importance for modelling and predicting these impacts.We developped in the framework of the OpenFLUID platform (Software Environment for Modelling Fluxes in Landscapes) a digital landscape representation that takes into account the spatial variabilities and connectivities of diverse landscape elements through the application of the graph theory concepts. The proposed landscape representation consider spatial units connected together to represent the flux exchanges or any other information exchanges. Each spatial unit of the landscape is represented as a node of a graph and relations between units as graph connections. The connections are of two types - parent-child connection and up/downstream connection - which allows OpenFLUID to handle hierarchical graphs. Connections can also carry informations and graph evolution during simulation is possible (connections or elements modifications). This graph approach allows a better genericity on landscape representation, a management of complex connections and facilitate development of new landscape representation algorithms. Graph management is fully operational in OpenFLUID for developers or modelers ; and several graph tools are available such as graph traversal algorithms or graph displays. Graph representation can be managed i) manually by the user (for example in simple catchments) through XML-based files in easily editable and readable format or ii) by using methods of the OpenFLUID-landr library which is an OpenFLUID library relying on common open-source spatial libraries (ogr vector, geos topologic vector and gdal raster libraries). OpenFLUID-landr library has been developed in order i) to be used with no GIS expert skills needed (common gis formats can be read and simplified spatial management is provided), ii) to easily develop adapted rules of landscape discretization and graph creation to follow spatialized model requirements and iii) to allow model developers to manage dynamic and complex spatial topology. Graph management in OpenFLUID are shown with i) examples of hydrological modelizations on complex farmed landscapes and ii) the new implementation of Geo-MHYDAS tool based on the OpenFLUID-landr library, which allows to discretize a landscape and create graph structure for the MHYDAS model requirements.

Temporally dynamic habitat suitability predicts genetic relatedness among caribou.

PubMed

Yannic, Glenn; Pellissier, Loïc; Le Corre, Maël; Dussault, Christian; Bernatchez, Louis; Côté, Steeve D

2014-10-07

Landscape heterogeneity plays a central role in shaping ecological and evolutionary processes. While species utilization of the landscape is usually viewed as constant within a year, the spatial distribution of individuals is likely to vary in time in relation to particular seasonal needs. Understanding temporal variation in landscape use and genetic connectivity has direct conservation implications. Here, we modelled the daily use of the landscape by caribou in Quebec and Labrador, Canada and tested its ability to explain the genetic relatedness among individuals. We assessed habitat selection using locations of collared individuals in migratory herds and static occurrences from sedentary groups. Connectivity models based on habitat use outperformed a baseline isolation-by-distance model in explaining genetic relatedness, suggesting that variations in landscape features such as snow, vegetation productivity and land use modulate connectivity among populations. Connectivity surfaces derived from habitat use were the best predictors of genetic relatedness. The relationship between connectivity surface and genetic relatedness varied in time and peaked during the rutting period. Landscape permeability in the period of mate searching is especially important to allow gene flow among populations. Our study highlights the importance of considering temporal variations in habitat selection for optimizing connectivity across heterogeneous landscape and counter habitat fragmentation. © 2014 The Author(s) Published by the Royal Society. All rights reserved.

Advances in global sensitivity analyses of demographic-based species distribution models to address uncertainties in dynamic landscapes.

PubMed

Naujokaitis-Lewis, Ilona; Curtis, Janelle M R

2016-01-01

Developing a rigorous understanding of multiple global threats to species persistence requires the use of integrated modeling methods that capture processes which influence species distributions. Species distribution models (SDMs) coupled with population dynamics models can incorporate relationships between changing environments and demographics and are increasingly used to quantify relative extinction risks associated with climate and land-use changes. Despite their appeal, uncertainties associated with complex models can undermine their usefulness for advancing predictive ecology and informing conservation management decisions. We developed a computationally-efficient and freely available tool (GRIP 2.0) that implements and automates a global sensitivity analysis of coupled SDM-population dynamics models for comparing the relative influence of demographic parameters and habitat attributes on predicted extinction risk. Advances over previous global sensitivity analyses include the ability to vary habitat suitability across gradients, as well as habitat amount and configuration of spatially-explicit suitability maps of real and simulated landscapes. Using GRIP 2.0, we carried out a multi-model global sensitivity analysis of a coupled SDM-population dynamics model of whitebark pine (Pinus albicaulis) in Mount Rainier National Park as a case study and quantified the relative influence of input parameters and their interactions on model predictions. Our results differed from the one-at-time analyses used in the original study, and we found that the most influential parameters included the total amount of suitable habitat within the landscape, survival rates, and effects of a prevalent disease, white pine blister rust. Strong interactions between habitat amount and survival rates of older trees suggests the importance of habitat in mediating the negative influences of white pine blister rust. Our results underscore the importance of considering habitat attributes along with demographic parameters in sensitivity routines. GRIP 2.0 is an important decision-support tool that can be used to prioritize research, identify habitat-based thresholds and management intervention points to improve probability of species persistence, and evaluate trade-offs of alternative management options.

Advances in global sensitivity analyses of demographic-based species distribution models to address uncertainties in dynamic landscapes

PubMed Central

Curtis, Janelle M.R.

2016-01-01

Developing a rigorous understanding of multiple global threats to species persistence requires the use of integrated modeling methods that capture processes which influence species distributions. Species distribution models (SDMs) coupled with population dynamics models can incorporate relationships between changing environments and demographics and are increasingly used to quantify relative extinction risks associated with climate and land-use changes. Despite their appeal, uncertainties associated with complex models can undermine their usefulness for advancing predictive ecology and informing conservation management decisions. We developed a computationally-efficient and freely available tool (GRIP 2.0) that implements and automates a global sensitivity analysis of coupled SDM-population dynamics models for comparing the relative influence of demographic parameters and habitat attributes on predicted extinction risk. Advances over previous global sensitivity analyses include the ability to vary habitat suitability across gradients, as well as habitat amount and configuration of spatially-explicit suitability maps of real and simulated landscapes. Using GRIP 2.0, we carried out a multi-model global sensitivity analysis of a coupled SDM-population dynamics model of whitebark pine (Pinus albicaulis) in Mount Rainier National Park as a case study and quantified the relative influence of input parameters and their interactions on model predictions. Our results differed from the one-at-time analyses used in the original study, and we found that the most influential parameters included the total amount of suitable habitat within the landscape, survival rates, and effects of a prevalent disease, white pine blister rust. Strong interactions between habitat amount and survival rates of older trees suggests the importance of habitat in mediating the negative influences of white pine blister rust. Our results underscore the importance of considering habitat attributes along with demographic parameters in sensitivity routines. GRIP 2.0 is an important decision-support tool that can be used to prioritize research, identify habitat-based thresholds and management intervention points to improve probability of species persistence, and evaluate trade-offs of alternative management options. PMID:27547529

Learning To Fold Proteins Using Energy Landscape Theory

PubMed Central

Schafer, N.P.; Kim, B.L.; Zheng, W.; Wolynes, P.G.

2014-01-01

This review is a tutorial for scientists interested in the problem of protein structure prediction, particularly those interested in using coarse-grained molecular dynamics models that are optimized using lessons learned from the energy landscape theory of protein folding. We also present a review of the results of the AMH/AMC/AMW/AWSEM family of coarse-grained molecular dynamics protein folding models to illustrate the points covered in the first part of the article. Accurate coarse-grained structure prediction models can be used to investigate a wide range of conceptual and mechanistic issues outside of protein structure prediction; specifically, the paper concludes by reviewing how AWSEM has in recent years been able to elucidate questions related to the unusual kinetic behavior of artificially designed proteins, multidomain protein misfolding, and the initial stages of protein aggregation. PMID:25308991

Forward and backward evolution of the Calhoun CZO: the effect of natural and anthropogenic disturbances

NASA Astrophysics Data System (ADS)

Bonetti, S.; Porporato, A. M.

2017-12-01

The time evolution of a landscape topography through erosional and depositional mechanisms is modified by both human and natural disturbances. This is particularly evident in the Calhoun Critical Zone Observatory, where decades of land-use resulted in a distinct topography with gullies, interfluves, hillslopes and significantly eroded areas. Understanding the role of different geomorphological processes that led to these conditions is crucial to reconstruct sediment and soil carbon fluxes, predict critical conditions of landscape degradation, and implement strategies of land recovery. To model these dynamics, an analytical theory of the drainage area (which represents a surrogate for water surface runoff responsible for fluvial incision) is used to evolve ridge and valley lines. Furthermore, the coupled dynamics of surface water runoff and landscape evolution is analyzed theoretically and numerically to detect thresholds leading to either stable landscape configurations or critical conditions of land erosion. Observed erosional cycles due to vegetation disturbances are explored and used to predict future evolutions under various levels of anthropogenic disturbance.

Integrating landscape ecology and geoinformatics to decipher landscape dynamics for regional planning.

PubMed

Dikou, Angela; Papapanagiotou, Evangelos; Troumbis, Andreas

2011-09-01

We used remote sensing and GIS in conjunction with multivariate statistical methods to: (i) quantify landscape composition (land cover types) and configuration (patch density, diversity, fractal dimension, contagion) for five coastal watersheds of Kalloni gulf, Lesvos Island, Greece, in 1945, 1960, 1971, 1990 and 2002/2003, (ii) evaluate the relative importance of physical (slope, geologic substrate, stream order) and human (road network, population density) variables on landscape composition and configuration, and (iii) characterize processes that led to land cover changes through land cover transitions between these five successive periods in time. Distributions of land cover types did not differ among the five time periods at the five watersheds studied because the largest cumulative changes between 1945 and 2002/2003 did not take place at dominant land cover types. Landscape composition related primarily to the physical attributes of the landscape. Nevertheless, increase in population density and the road network were found to increase heterogeneity of the landscape mosaic (patchiness), complexity of patch shape (fractal dimension), and patch disaggregation (contagion). Increase in road network was also found to increase landscape diversity due to the creation of new patches. The main processes involved in land cover changes were plough-land abandonment and ecological succession. Landscape dynamics during the last 50 years corroborate the ecotouristic-agrotouristic model for regional development to reverse trends in agricultural land abandonment and human population decline and when combined with hypothetical regulatory approaches could predict how this landscape could develop in the future, thus, providing a valuable tool to regional planning.

AN INDICATOR OF FOREST DYNAMICS USING A SHIFTING LANDSCAPE MOSAIC

EPA Science Inventory

The composition of a landscape is a fundamental indicator in land-cover pattern assessments. The objective of this paper was to evaluate a landscape composition indicator called ‘landscape mosaic’ as a framework for interpreting land-cover dynamics over a 9-year period in a 360,...

Modeling the spatiotemporal variability in subsurface thermal regimes across a low-relief polygonal tundra landscape

DOE PAGES

Kumar, Jitendra; Collier, Nathan; Bisht, Gautam; ...

2016-09-27

Vast carbon stocks stored in permafrost soils of Arctic tundra are under risk of release to the atmosphere under warming climate scenarios. Ice-wedge polygons in the low-gradient polygonal tundra create a complex mosaic of microtopographic features. This microtopography plays a critical role in regulating the fine-scale variability in thermal and hydrological regimes in the polygonal tundra landscape underlain by continuous permafrost. Modeling of thermal regimes of this sensitive ecosystem is essential for understanding the landscape behavior under the current as well as changing climate. Here, we present an end-to-end effort for high-resolution numerical modeling of thermal hydrology at real-world fieldmore » sites, utilizing the best available data to characterize and parameterize the models. We also develop approaches to model the thermal hydrology of polygonal tundra and apply them at four study sites near Barrow, Alaska, spanning across low to transitional to high-centered polygons, representing a broad polygonal tundra landscape. A multiphase subsurface thermal hydrology model (PFLOTRAN) was developed and applied to study the thermal regimes at four sites. Using a high-resolution lidar digital elevation model (DEM), microtopographic features of the landscape were characterized and represented in the high-resolution model mesh. The best available soil data from field observations and literature were utilized to represent the complex heterogeneous subsurface in the numerical model. Simulation results demonstrate the ability of the developed modeling approach to capture – without recourse to model calibration – several aspects of the complex thermal regimes across the sites, and provide insights into the critical role of polygonal tundra microtopography in regulating the thermal dynamics of the carbon-rich permafrost soils. Moreover, areas of significant disagreement between model results and observations highlight the importance of field-based observations of soil thermal and hydraulic properties for modeling-based studies of permafrost thermal dynamics, and provide motivation and guidance for future observations that will help address model and data gaps affecting our current understanding of the system.« less

Metadynamics Enhanced Markov Modeling of Protein Dynamics.

PubMed

Biswas, Mithun; Lickert, Benjamin; Stock, Gerhard

2018-05-31

Enhanced sampling techniques represent a versatile approach to account for rare conformational transitions in biomolecules. A particularly promising strategy is to combine massive parallel computing of short molecular dynamics (MD) trajectories (to sample the free energy landscape of the system) with Markov state modeling (to rebuild the kinetics from the sampled data). To obtain well-distributed initial structures for the short trajectories, it is proposed to employ metadynamics MD, which quickly sweeps through the entire free energy landscape of interest. Being only used to generate initial conformations, the implementation of metadynamics can be simple and fast. The conformational dynamics of helical peptide Aib 9 is adopted to discuss various technical issues of the approach, including metadynamics settings, minimal number and length of short MD trajectories, and the validation of the resulting Markov models. Using metadynamics to launch some thousands of nanosecond trajectories, several Markov state models are constructed that reveal that previous unbiased MD simulations of in total 16 μs length cannot provide correct equilibrium populations or qualitative features of the pathway distribution of the short peptide.

Rapid evolution accelerates plant population spread in fragmented experimental landscapes.

PubMed

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

2016-07-29

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

Bridging the gap between habitat-modeling research and bird conservation with dynamic landscape and population models

Treesearch

Frank R., III Thompson

2009-01-01

Habitat models are widely used in bird conservation planning to assess current habitat or populations and to evaluate management alternatives. These models include species-habitat matrix or database models, habitat suitability models, and statistical models that predict abundance. While extremely useful, these approaches have some limitations.

Threshold of coexistence and critical behavior of a predator-prey stochastic model in a fractal landscape

NASA Astrophysics Data System (ADS)

Argolo, C.; Barros, P.; Tomé, T.; Arashiro, E.; Gleria, Iram; Lyra, M. L.

2016-08-01

We investigate a stochastic lattice model describing a predator-prey system in a fractal scale-free landscape, mimicked by the fractal Sierpinski carpet. We determine the threshold of species coexistence, that is, the critical phase boundary related to the transition between an active state, where both species coexist and an absorbing state where one of the species is extinct. We show that the predators must live longer in order to persist in a fractal habitat. We further performed a finite-size scaling analysis in the vicinity of the absorbing-state phase transition to compute a set of stationary and dynamical critical exponents. Our results indicate that the transition belongs to the directed percolation universality class exhibited by the usual contact process model on the same fractal landscape.

Landscape modeling for Everglades ecosystem restoration

USGS Publications Warehouse

DeAngelis, D.L.; Gross, L.J.; Huston, M.A.; Wolff, W.F.; Fleming, D.M.; Comiskey, E.J.; Sylvester, S.M.

1998-01-01

A major environmental restoration effort is under way that will affect the Everglades and its neighboring ecosystems in southern Florida. Ecosystem and population-level modeling is being used to help in the planning and evaluation of this restoration. The specific objective of one of these modeling approaches, the Across Trophic Level System Simulation (ATLSS), is to predict the responses of a suite of higher trophic level species to several proposed alterations in Everglades hydrology. These include several species of wading birds, the snail kite, Cape Sable seaside sparrow, Florida panther, white-tailed deer, American alligator, and American crocodile. ATLSS is an ecosystem landscape-modeling approach and uses Geographic Information System (GIS) vegetation data and existing hydrology models for South Florida to provide the basic landscape for these species. A method of pseudotopography provides estimates of water depths through time at 28 ?? 28-m resolution across the landscape of southern Florida. Hydrologic model output drives models of habitat and prey availability for the higher trophic level species. Spatially explicit, individual-based computer models simulate these species. ATLSS simulations can compare the landscape dynamic spatial pattern of the species resulting from different proposed water management strategies. Here we compare the predicted effects of one possible change in water management in South Florida with the base case of no change. Preliminary model results predict substantial differences between these alternatives in some biotic spatial patterns. ?? 1998 Springer-Verlag.

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

USGS Publications Warehouse

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

2018-01-01

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

Landscape dynamics of mountain pine beetles

Treesearch

John E. Lundquist; Robin M. Reich

2014-01-01

The magnitude and urgency of current mountain pine beetle outbreaks in the western United States and Canada have resulted in numerous studies of the dynamics and impacts of these insects in forested ecosystems. This paper reviews some of the aspects of the spatial dynamics and landscape ecology of this bark beetle. Landscape heterogeneity influences dispersal patterns...

A wave-mechanical model of incoherent quasielastic scattering in complex systems.

PubMed

Frauenfelder, Hans; Fenimore, Paul W; Young, Robert D

2014-09-02

Quasielastic incoherent neutron scattering (QENS) is an important tool for the exploration of the dynamics of complex systems such as biomolecules, liquids, and glasses. The dynamics is reflected in the energy spectra of the scattered neutrons. Conventionally these spectra are decomposed into a narrow elastic line and a broad quasielastic band. The band is interpreted as being caused by Doppler broadening due to spatial motion of the target molecules. We propose a quantum-mechanical model in which there is no separate elastic line. The quasielastic band is composed of sharp lines with twice the natural line width, shifted from the center by a random walk of the protein in the free-energy landscape of the target molecule. The walk is driven by vibrations and by external fluctuations. We first explore the model with the Mössbauer effect. In the subsequent application to QENS we treat the incoming neutron as a de Broglie wave packet. While the wave packet passes the protons in the protein and the hydration shell it exchanges energy with the protein during the passage time of about 100 ns. The energy exchange broadens the ensemble spectrum. Because the exchange involves the free-energy landscape of the protein, the QENS not only provides insight into the protein dynamics, but it may also illuminate the free-energy landscape of the protein-solvent system.

Protocol for Landsat-Based Monitoring of Landscape Dynamics at North Coast and Cascades Network Parks

USGS Publications Warehouse

Kennedy, Robert E.; Cohen, Warren B.; Kirschbaum, Alan A.; Haunreiter, Erik

2007-01-01

Background and Objectives As part of the National Park Service's larger goal of developing long-term monitoring programs in response to the Natural Resource Challenge of 2000, the parks of the North Coast and Cascades Network (NCCN) have determined that monitoring of landscape dynamics is necessary to track ecosystem health (Weber and others, 2005). Landscape dynamics refer to a broad suite of ecological, geomorphological, and anthropogenic processes occurring across broad spatial scales. The NCCN has sought protocols that would leverage remote-sensing technologies to aid in monitoring landscape dynamics.

Scaling up in the face of uncertainty - controls on trace gas fluxes in heterogeneous landscapes (Invited)

NASA Astrophysics Data System (ADS)

Bernhardt, E. S.; Helton, A. M.; Morse, J. L.; Poole, G. C.

2013-12-01

Wetlands are the dominant natural source of methane to the global atmosphere and can be important sites of either N2O emission or consumption. Changes in the spatial extent or inundation frequency and duration may lead to substantial shifts in the contribution of wetland ecosystems to global CH4 and N2O emissions. Trace gases are produced at the scale of individual microbes, each of which respond dynamically to the local availability of electron donors and acceptors. Within landscape patches, substrate supply and redox conditions are strongly controlled by variation in water table elevation and vertical hydrologic exchange. At the landscape scale, lateral exchange between patches and the extent and duration of inundation. Accurate estimates of trace gas emissions from wetlands are hard to estimate given the dynamic patterns of redox potential within the soil column and across the landscape that redistribute electron donors and acceptors both vertically and laterally. In five years of trace gas flux measurement and modeling at TOWER, a 440 ha restored wetland in coastal NC, we have developed both simulation and statistical models to estimate landscape level trace gas fluxes. Yet, because trace gas emissions are highly variable in both time and space, our qualitative and quantitative attempts at upscaling trace gas emissions typically generate estimates with extremely high uncertainty. In this talk we will explore the challenges inherent to the estimation of landscape scale trace gas fluxes at the scale of our individual ecosystem as well as the difficulties in extrapolating across multiple ecosystem studies.

Co-evolution of landforms and vegetation under the influence of orographic precipitation

NASA Astrophysics Data System (ADS)

Yetemen, Omer; Srivastava, Ankur; Saco, Patricia M.

2017-04-01

Landforms are controlled by the interaction between tectonics, climate, and vegetation. Orography induced precipitation not only has implications on erosion resistance through vegetation dynamics but also affects erosive forces through modifying runoff production. The implications of elevated precipitation due to orography on landscape morphology requires a numerical framework that integrates a range of ecohydrologic and geomorphic processes to explore the competition between erosive and resisting forces in catchments where pronounced orographic precipitation prevails. In this study, our aim was to realistically represent ecohydrology driven by orographic precipitation and explore its implications on landscape evolution through a numerical model. The model was used to investigate how ecohydro-geomorphic differences caused by differential precipitation patterns as a result of orographic influence and rain-shadow effect lead to differences in the organization of modelled topography, soil moisture, and plant biomass. We use the CHILD landscape evolution model equipped with a vegetation dynamics component that explicitly tracks above- and below-ground biomass, and a precipitation forcing component that simulates rainfall as a function of elevation and orientation. The preliminary results of the model have shown how the competition between an increased shear stress through runoff production and an enhanced resistance force due to denser canopy cover, shape the landscape. Hillslope asymmetry between polar- and equator-facing hillslopes are enhanced (diminished) when they coincide with windward (leeward) side of the mountain series. The mountain divide accommodates itself by migrating toward the windward direction to increase (decrease) hillslope gradients on windward (leeward) slopes. These results clearly demonstrate the strong coupling between landform evolution and climate processes.

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.

Quasisaddles as relevant points of the potential energy surface in the dynamics of supercooled liquids

NASA Astrophysics Data System (ADS)

Angelani, L.; Di Leonardo, R.; Ruocco, G.; Scala, A.; Sciortino, F.

2002-06-01

The supercooled dynamics of a Lennard-Jones model liquid is numerically investigated studying relevant points of the potential energy surface, i.e., the minima of the square gradient of total potential energy V. The main findings are (i) the number of negative curvatures n of these sampled points appears to extrapolate to zero at the mode coupling critical temperature Tc; (ii) the temperature behavior of n(T) has a close relationship with the temperature behavior of the diffusivity; (iii) the potential energy landscape shows a high regularity in the distances among the relevant points and in their energy location. Finally we discuss a model of the landscape, previously introduced by Madan and Keyes [J. Chem. Phys. 98, 3342 (1993)], able to reproduce the previous findings.

Dynamics of a molecular glass former: Energy landscapes for diffusion in ortho-terphenyl

NASA Astrophysics Data System (ADS)

Niblett, S. P.; de Souza, V. K.; Stevenson, J. D.; Wales, D. J.

2016-07-01

Relaxation times and transport processes of many glass-forming supercooled liquids exhibit a super-Arrhenius temperature dependence. We examine this phenomenon by computer simulation of the Lewis-Wahnström model for ortho-terphenyl. We propose a microscopic definition for a single-molecule cage-breaking transition and show that, when correlation behaviour is taken into account, these rearrangements are sufficient to reproduce the correct translational diffusion constants over an intermediate temperature range in the supercooled regime. We show that super-Arrhenius behaviour can be attributed to increasing negative correlation in particle movement at lower temperatures and relate this to the cage-breaking description. Finally, we sample the potential energy landscape of the model and show that it displays hierarchical ordering. Substructures in the landscape, which may correspond to metabasins, have boundaries defined by cage-breaking transitions. The cage-breaking formulation provides a direct link between the potential energy landscape and macroscopic diffusion behaviour.

Modulation of a protein free-energy landscape by circular permutation.

PubMed

Radou, Gaël; Enciso, Marta; Krivov, Sergei; Paci, Emanuele

2013-11-07

Circular permutations usually retain the native structure and function of a protein while inevitably perturbing its folding dynamics. By using simulations with a structure-based model and a rigorous methodology to determine free-energy surfaces from trajectories, we evaluate the effect of a circular permutation on the free-energy landscape of the protein T4 lysozyme. We observe changes which, although subtle, largely affect the cooperativity between the two subdomains. Such a change in cooperativity has been previously experimentally observed and recently also characterized using single molecule optical tweezers and the Crooks relation. The free-energy landscapes show that both the wild type and circular permutant have an on-pathway intermediate, previously experimentally characterized, in which one of the subdomains is completely formed. The landscapes, however, differ in the position of the rate-limiting step for folding, which occurs before the intermediate in the wild type and after in the circular permutant. This shift of transition state explains the observed change in the cooperativity. The underlying free-energy landscape thus provides a microscopic description of the folding dynamics and the connection between circular permutation and the loss of cooperativity experimentally observed.

Hierarchical folding free energy landscape of HP35 revealed by most probable path clustering.

PubMed

Jain, Abhinav; Stock, Gerhard

2014-07-17

Adopting extensive molecular dynamics simulations of villin headpiece protein (HP35) by Shaw and co-workers, a detailed theoretical analysis of the folding of HP35 is presented. The approach is based on the recently proposed most probable path algorithm which identifies the metastable states of the system, combined with dynamical coring of these states in order to obtain a consistent Markov state model. The method facilitates the construction of a dendrogram associated with the folding free-energy landscape of HP35, which reveals a hierarchical funnel structure and shows that the native state is rather a kinetic trap than a network hub. The energy landscape of HP35 consists of the entropic unfolded basin U, where the prestructuring of the protein takes place, the intermediate basin I, which is connected to U via the rate-limiting U → I transition state reflecting the formation of helix-1, and the native basin N, containing a state close to the NMR structure and a native-like state that exhibits enhanced fluctuations of helix-3. The model is in line with recent experimental observations that the intermediate and native states differ mostly in their dynamics (locked vs unlocked states). Employing dihedral angle principal component analysis, subdiffusive motion on a multidimensional free-energy surface is found.

The role of momentum transfer during incoherent neutron scattering is explained by the energy landscape model

PubMed Central

Frauenfelder, Hans; Young, Robert D.; Fenimore, Paul W.

2017-01-01

We recently introduced a model of incoherent quasielastic neutron scattering (QENS) that treats the neutrons as wave packets of finite length and the protein as a random walker in the free energy landscape. We call the model ELM for “energy landscape model.” In ELM, the interaction of the wave packet with a proton in a protein provides the dynamic information. During the scattering event, the momentum Q(t) is transferred by the wave packet to the struck proton and its moiety, exerting the force F(t)=dQ(t)/dt. The resultant energy E⋆ is stored elastically and returned to the neutron as it exits. The energy is given by E⋆=kB(T0+χQ), where T0 is the ambient temperature and χ (≈ 91 K Å) is a new elastobaric coefficient. Experiments yield the scattering intensity (dynamic structure factor) S(Q;T) as a function of Q and T. To test our model, we use published data on proteins where only thermal vibrations are active. ELM competes with the currently accepted theory, here called the spatial motion model (SMM), which explains S(Q,T) by motions in real space. ELM is superior to SMM: It can explain the experimental angular and temperature dependence, whereas SMM cannot do so. PMID:28461503

Processes on the emergent landscapes of biochemical reaction networks and heterogeneous cell population dynamics: differentiation in living matters

PubMed Central

Li, Fangting

2017-01-01

The notion of an attractor has been widely employed in thinking about the nonlinear dynamics of organisms and biological phenomena as systems and as processes. The notion of a landscape with valleys and mountains encoding multiple attractors, however, has a rigorous foundation only for closed, thermodynamically non-driven, chemical systems, such as a protein. Recent advances in the theory of nonlinear stochastic dynamical systems and its applications to mesoscopic reaction networks, one reaction at a time, have provided a new basis for a landscape of open, driven biochemical reaction systems under sustained chemostat. The theory is equally applicable not only to intracellular dynamics of biochemical regulatory networks within an individual cell but also to tissue dynamics of heterogeneous interacting cell populations. The landscape for an individual cell, applicable to a population of isogenic non-interacting cells under the same environmental conditions, is defined on the counting space of intracellular chemical compositions x = (x1,x2, … ,xN) in a cell, where xℓ is the concentration of the ℓth biochemical species. Equivalently, for heterogeneous cell population dynamics xℓ is the number density of cells of the ℓth cell type. One of the insights derived from the landscape perspective is that the life history of an individual organism, which occurs on the hillsides of a landscape, is nearly deterministic and ‘programmed’, while population-wise an asynchronous non-equilibrium steady state resides mostly in the lowlands of the landscape. We argue that a dynamic ‘blue-sky’ bifurcation, as a representation of Waddington's landscape, is a more robust mechanism for a cell fate decision and subsequent differentiation than the widely pictured pitch-fork bifurcation. We revisit, in terms of the chemostatic driving forces upon active, living matter, the notions of near-equilibrium thermodynamic branches versus far-from-equilibrium states. The emergent landscape perspective permits a quantitative discussion of a wide range of biological phenomena as nonlinear, stochastic dynamics. PMID:28490602

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

Kumar, Jitendra; Collier, Nathan; Bisht, Gautam

Vast carbon stocks stored in permafrost soils of Arctic tundra are under risk of release to the atmosphere under warming climate scenarios. Ice-wedge polygons in the low-gradient polygonal tundra create a complex mosaic of microtopographic features. This microtopography plays a critical role in regulating the fine-scale variability in thermal and hydrological regimes in the polygonal tundra landscape underlain by continuous permafrost. Modeling of thermal regimes of this sensitive ecosystem is essential for understanding the landscape behavior under the current as well as changing climate. Here, we present an end-to-end effort for high-resolution numerical modeling of thermal hydrology at real-world fieldmore » sites, utilizing the best available data to characterize and parameterize the models. We also develop approaches to model the thermal hydrology of polygonal tundra and apply them at four study sites near Barrow, Alaska, spanning across low to transitional to high-centered polygons, representing a broad polygonal tundra landscape. A multiphase subsurface thermal hydrology model (PFLOTRAN) was developed and applied to study the thermal regimes at four sites. Using a high-resolution lidar digital elevation model (DEM), microtopographic features of the landscape were characterized and represented in the high-resolution model mesh. The best available soil data from field observations and literature were utilized to represent the complex heterogeneous subsurface in the numerical model. Simulation results demonstrate the ability of the developed modeling approach to capture – without recourse to model calibration – several aspects of the complex thermal regimes across the sites, and provide insights into the critical role of polygonal tundra microtopography in regulating the thermal dynamics of the carbon-rich permafrost soils. Moreover, areas of significant disagreement between model results and observations highlight the importance of field-based observations of soil thermal and hydraulic properties for modeling-based studies of permafrost thermal dynamics, and provide motivation and guidance for future observations that will help address model and data gaps affecting our current understanding of the system.« less

The influence of landscape's dynamics on the Oriental Migratory Locust habitat change based on the time-series satellite data.

PubMed

Shi, Yue; Huang, Wenjiang; Dong, Yingying; Peng, Dailiang; Zheng, Qiong; Yang, Puyun

2018-07-15

Landscape structure and vegetation coverage are important habitat conditions for Oriental Migratory Locust infestation in East Asia. Characterizing the landscape's dynamics of locust habitat is meaningful for reducing the occupation of locusts and limiting potential risks. To better understand causes and consequences of landscape pattern and locust habitat, it is not enough to simply detect locust habitat of each year. Rather, landcover transitions causing the change of locust habitat area must also be explored. This paper proposes an integrated implement to quantify the influence of landscape's dynamics on locust habitat changes based on three tenets: 1) temporal context can provide insight into the land cover transitions, 2) the detection of locust habitat area is operated on patches rather than pixels with full consideration of landscape's ecology, 3) the modeling must be flexible and unsupervised. These ideas have not been previously explored in demonstrating the possible role of changes in landscape characteristics to drive locust habitat transitions. The case study focuses on the Dagang district, a hot spot of locust infestation of China, from 2000 to 2015. Firstly, the seasonal characteristics of typical landcovers in NDVI, TVI, and LST were extracted from fused Landsat-MODIS surface reflectance imagery. Subsequently, a landscape membership-based random forest (LMRF) algorithm was proposed to quantify the landscape structure and hydrological regimen of locust habitat at the patch level. Finally, we investigated the correlations between the specific landcover transitions and habitat changes. Within the 16 years observations, our findings suggest that the sparse reeds and weeds in the vicinity of beach land, riverbanks, and wetlands are the dominant landscape structure associated with locust habitat change (R 2  > 0.68), and the fluctuation in the water level is a key ecological factor to facilitate the locust habitat change (R 2  > 0.61). These results are instrumental for developing precision pesticide use to reduce environmental degradation, and providing positive perspectives for ecological management and transformation of locust habitats. Copyright © 2018 Elsevier Ltd. All rights reserved.

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.

Local and landscape associations between wintering dabbling ducks and wetland complexes in Mississippi

USGS Publications Warehouse

Pearse, Aaron T.; Kaminski, Richard M.; Reinecke, Kenneth J.; Dinsmore, Stephen J.

2012-01-01

Landscape features influence distribution of waterbirds throughout their annual cycle. A conceptual model, the wetland habitat complex, may be useful in conservation of wetland habitats for dabbling ducks (Anatini). The foundation of this conceptual model is that ducks seek complexes of wetlands containing diverse resources to meet dynamic physiological needs. We included flooded croplands, wetlands and ponds, public-land waterfowl sanctuary, and diversity of habitats as key components of wetland habitat complexes and compared their relative influence at two spatial scales (i.e., local, 0.25-km radius; landscape, 4-km) on dabbling ducks wintering in western Mississippi, USA during winters 2002–2004. Distribution of mallard (Anas platyrhynchos) groups was positively associated with flooded cropland at local and landscape scales. Models representing flooded croplands at the landscape scale best explained occurrence of other dabbling ducks. Habitat complexity measured at both scales best explained group size of other dabbling ducks. Flooded croplands likely provided food that had decreased in availability due to conversion of wetlands to agriculture. Wetland complexes at landscape scales were more attractive to wintering ducks than single or structurally simple wetlands. Conservation of wetland complexes at large spatial scales (≥5,000 ha) on public and private lands will require coordination among multiple stakeholders.

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

PubMed

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

2012-12-01

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

Flow resistance interactions on hillslopes with heterogeneous attributes: Effects on runoff hydrograph characteristics

USDA-ARS?s Scientific Manuscript database

An improved modeling framework for capturing the effects of dynamic resistance to overland flow is developed for intensively managed landscapes. The framework builds on the WEPP model but it removes the limitations of the “equivalent” plane and static roughness assumption. The enhanced model therefo...

Mapping sources, sinks, and connectivity using a simulation model of northern spotted owls- 5/20/2014

EPA Science Inventory

Source-sink dynamics are an emergent property of complex species- landscape interactions. A better understanding of how human activities affect source-sink dynamics has the potential to inform and improve the management of species of conservation concern. Here we use a study of t...

Evaluation of dynamic coastal response to sea-level rise modifies inundation likelihood

USGS Publications Warehouse

Lentz, Erika E.; Thieler, E. Robert; Plant, Nathaniel G.; Stippa, Sawyer R.; Horton, Radley M.; Gesch, Dean B.

2016-01-01

Sea-level rise (SLR) poses a range of threats to natural and built environments1, 2, making assessments of SLR-induced hazards essential for informed decision making3. We develop a probabilistic model that evaluates the likelihood that an area will inundate (flood) or dynamically respond (adapt) to SLR. The broad-area applicability of the approach is demonstrated by producing 30 × 30 m resolution predictions for more than 38,000 km2 of diverse coastal landscape in the northeastern United States. Probabilistic SLR projections, coastal elevation and vertical land movement are used to estimate likely future inundation levels. Then, conditioned on future inundation levels and the current land-cover type, we evaluate the likelihood of dynamic response versus inundation. We find that nearly 70% of this coastal landscape has some capacity to respond dynamically to SLR, and we show that inundation models over-predict land likely to submerge. This approach is well suited to guiding coastal resource management decisions that weigh future SLR impacts and uncertainty against ecological targets and economic constraints.

A distributed analysis of Human impact on global sediment dynamics

NASA Astrophysics Data System (ADS)

Cohen, S.; Kettner, A.; Syvitski, J. P.

2012-12-01

Understanding riverine sediment dynamics is an important undertaking for both socially-relevant issues such as agriculture, water security and infrastructure management and for scientific analysis of landscapes, river ecology, oceanography and other disciplines. Providing good quantitative and predictive tools in therefore timely particularly in light of predicted climate and landuse changes. Ever increasing human activity during the Anthropocene have affected sediment dynamics in two major ways: (1) an increase is hillslope erosion due to agriculture, deforestation and landscape engineering and (2) trapping of sediment in dams and other man-made reservoirs. The intensity and dynamics between these man-made factors vary widely across the globe and in time and are therefore hard to predict. Using sophisticated numerical models is therefore warranted. Here we use a distributed global riverine sediment flux and water discharge model (WBMsed) to compare a pristine (without human input) and disturbed (with human input) simulations. Using these 50 year simulations we will show and discuss the complex spatial and temporal patterns of human effect on riverine sediment flux and water discharge.

Historical fire and vegetation dynamics in dry forests of the interior Pacific Northwest, USA, and relationships to northern spotted owl (Strix occidentalis caurina) habitat conservation

Treesearch

Rebecca S.H. Kennedy; Michael C. Wimberly

2009-01-01

Regional conservation planning frequently relies on general assumptions about historical disturbance regimes to inform decisions about landscape restoration, reserve allocations, and landscape management. Spatially explicit simulations of landscape dynamics provide quantitative estimates of landscape structure and allow for the testing of alternative scenarios. We used...

Inflation with a graceful exit in a random landscape

NASA Astrophysics Data System (ADS)

Pedro, F. G.; Westphal, A.

2017-03-01

We develop a stochastic description of small-field inflationary histories with a graceful exit in a random potential whose Hessian is a Gaussian random matrix as a model of the unstructured part of the string landscape. The dynamical evolution in such a random potential from a small-field inflation region towards a viable late-time de Sitter (dS) minimum maps to the dynamics of Dyson Brownian motion describing the relaxation of non-equilibrium eigenvalue spectra in random matrix theory. We analytically compute the relaxation probability in a saddle point approximation of the partition function of the eigenvalue distribution of the Wigner ensemble describing the mass matrices of the critical points. When applied to small-field inflation in the landscape, this leads to an exponentially strong bias against small-field ranges and an upper bound N ≪ 10 on the number of light fields N participating during inflation from the non-observation of negative spatial curvature.

Interactions of forest disturbance-recovery dynamics with a changing climate

NASA Astrophysics Data System (ADS)

Anderson-Teixeira, K. J.; Miller, A. D.; Tepley, A. J.; Bennett, A. C.; Wang, M.

2015-12-01

As the climate changes, altered disturbance-recovery dynamics in forests worldwide are likely to result in significant biogeochemical and biophysical feedbacks to the climate system. Climate shapes forest disturbance events including tree mortality and fire, with consequent climate feedbacks. For instance, in forests globally, drought increases tree mortality rates, having a stronger impact on larger trees and resulting in greater feedbacks to climate change than would occur if drought sensitivities were equal across tree size classes. Forest regeneration and associated biogeochemical and biophysical feedbacks are also shaped by climate: across the tropics the rate of biomass accumulation is faster in everwet than in seasonally dry climates, and in the Klamath region (N California / S Oregon), post-fire vegetation dynamics and microclimate are shaped by aridity. Forest recovery dynamics will be affected by elevated CO2 and climate change; for instance, models predict that forest regeneration rate, successional dynamics, and climate feedbacks will all be altered under elevated CO2. In combination, climatic impacts on disturbance and recovery can result in dramatic shifts in forest cover on the landscape level. For instance, in fire-prone forested landscapes, forest cover decreases with increasing frequency of high-severity fire and decreasing forest recovery rate, both of which could be altered by climate change, producing rapid loss of forest on the landscape level. Such effects may be amplified by the existence of alternative stable states, which can cause systems to experience non-reversible changes in cover type. Critical transitions in landscape-level forest cover would have significant biogeochemical and biophysical feedbacks. Thus, altered disturbance-recovery dynamics under a changing climate may have sudden and dramatic impacts on forest-climate interactions.

Simulating ungulate herbivory across forest landscapes: A browsing extension for LANDIS-II

USGS Publications Warehouse

DeJager, Nathan R.; Drohan, Patrick J.; Miranda, Brian M.; Sturtevant, Brian R.; Stout, Susan L.; Royo, Alejandro; Gustafson, Eric J.; Romanski, Mark C.

2017-01-01

Browsing ungulates alter forest productivity and vegetation succession through selective foraging on species that often dominate early succession. However, the long-term and large-scale effects of browsing on forest succession are not possible to project without the use of simulation models. To explore the effects of ungulates on succession in a spatially explicit manner, we developed a Browse Extension that simulates the effects of browsing ungulates on the growth and survival of plant species cohorts within the LANDIS-II spatially dynamic forest landscape simulation model framework. We demonstrate the capabilities of the new extension and explore the spatial effects of ungulates on forest composition and dynamics using two case studies. The first case study examined the long-term effects of persistently high white-tailed deer browsing rates in the northern hardwood forests of the Allegheny National Forest, USA. In the second case study, we incorporated a dynamic ungulate population model to simulate interactions between the moose population and boreal forest landscape of Isle Royale National Park, USA. In both model applications, browsing reduced total aboveground live biomass and caused shifts in forest composition. Simulations that included effects of browsing resulted in successional patterns that were more similar to those observed in the study regions compared to simulations that did not incorporate browsing effects. Further, model estimates of moose population density and available forage biomass were similar to previously published field estimates at Isle Royale and in other moose-boreal forest systems. Our simulations suggest that neglecting effects of browsing when modeling forest succession in ecosystems known to be influenced by ungulates may result in flawed predictions of aboveground biomass and tree species composition.

The van Hove distribution function for Brownian hard spheres: Dynamical test particle theory and computer simulations for bulk dynamics

NASA Astrophysics Data System (ADS)

Hopkins, Paul; Fortini, Andrea; Archer, Andrew J.; Schmidt, Matthias

2010-12-01

We describe a test particle approach based on dynamical density functional theory (DDFT) for studying the correlated time evolution of the particles that constitute a fluid. Our theory provides a means of calculating the van Hove distribution function by treating its self and distinct parts as the two components of a binary fluid mixture, with the "self " component having only one particle, the "distinct" component consisting of all the other particles, and using DDFT to calculate the time evolution of the density profiles for the two components. We apply this approach to a bulk fluid of Brownian hard spheres and compare to results for the van Hove function and the intermediate scattering function from Brownian dynamics computer simulations. We find good agreement at low and intermediate densities using the very simple Ramakrishnan-Yussouff [Phys. Rev. B 19, 2775 (1979)] approximation for the excess free energy functional. Since the DDFT is based on the equilibrium Helmholtz free energy functional, we can probe a free energy landscape that underlies the dynamics. Within the mean-field approximation we find that as the particle density increases, this landscape develops a minimum, while an exact treatment of a model confined situation shows that for an ergodic fluid this landscape should be monotonic. We discuss possible implications for slow, glassy, and arrested dynamics at high densities.

Tree-, stand- and site-specific controls on landscape-scale patterns of transpiration

NASA Astrophysics Data System (ADS)

Hassler, Sibylle; Markus, Weiler; Theresa, Blume

2017-04-01

Transpiration is a key process in the hydrological cycle and a sound understanding and quantification of transpiration and its spatial variability is essential for management decisions as well as for improving the parameterisation of hydrological and soil-vegetation-atmosphere transfer models. For individual trees, transpiration is commonly estimated by measuring sap flow. Besides evaporative demand and water availability, tree-specific characteristics such as species, size or social status control sap flow amounts of individual trees. Within forest stands, properties such as species composition, basal area or stand density additionally affect sap flow, for example via competition mechanisms. Finally, sap flow patterns might also be influenced by landscape-scale characteristics such as geology, slope position or aspect because they affect water and energy availability; however, little is known about the dynamic interplay of these controls. We studied the relative importance of various tree-, stand- and site-specific characteristics with multiple linear regression models to explain the variability of sap velocity measurements in 61 beech and oak trees, located at 24 sites spread over a 290 km2-catchment in Luxembourg. For each of 132 consecutive days of the growing season of 2014 we modelled the daily sap velocities of these 61 trees and determined the importance of the different predictors. Results indicate that a combination of tree-, stand- and site-specific factors controls sap velocity patterns in the landscape, namely tree species, tree diameter, the stand density, geology and aspect. Compared to these predictors, spatial variability of atmospheric demand and soil moisture explains only a small fraction of the variability in the daily datasets. However, the temporal dynamics of the explanatory power of the tree-specific characteristics, especially species, are correlated to the temporal dynamics of potential evaporation. Thus, transpiration estimates at the landscape scale would benefit from not only considering hydro-meteorological drivers, but also including tree, stand and site characteristics in order to improve the spatial representation of transpiration for hydrological and soil-vegetation-atmosphere transfer models.

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.

The movement ecology and dynamics of plant communities in fragmented landscapes.

PubMed

Damschen, Ellen I; Brudvig, Lars A; Haddad, Nick M; Levey, Douglas J; Orrock, John L; Tewksbury, Joshua J

2008-12-09

A conceptual model of movement ecology has recently been advanced to explain all movement by considering the interaction of four elements: internal state, motion capacity, navigation capacities, and external factors. We modified this framework to generate predictions for species richness dynamics of fragmented plant communities and tested them in experimental landscapes across a 7-year time series. We found that two external factors, dispersal vectors and habitat features, affected species colonization and recolonization in habitat fragments and their effects varied and depended on motion capacity. Bird-dispersed species richness showed connectivity effects that reached an asymptote over time, but no edge effects, whereas wind-dispersed species richness showed steadily accumulating edge and connectivity effects, with no indication of an asymptote. Unassisted species also showed increasing differences caused by connectivity over time, whereas edges had no effect. Our limited use of proxies for movement ecology (e.g., dispersal mode as a proxy for motion capacity) resulted in moderate predictive power for communities and, in some cases, highlighted the importance of a more complete understanding of movement ecology for predicting how landscape conservation actions affect plant community dynamics.

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.

Landscapes of human evolution: models and methods of tectonic geomorphology and the reconstruction of hominin landscapes.

PubMed

Bailey, Geoffrey N; Reynolds, Sally C; King, Geoffrey C P

2011-03-01

This paper examines the relationship between complex and tectonically active landscapes and patterns of human evolution. We show how active tectonics can produce dynamic landscapes with geomorphological and topographic features that may be critical to long-term patterns of hominin land use, but which are not typically addressed in landscape reconstructions based on existing geological and paleoenvironmental principles. We describe methods of representing topography at a range of scales using measures of roughness based on digital elevation data, and combine the resulting maps with satellite imagery and ground observations to reconstruct features of the wider landscape as they existed at the time of hominin occupation and activity. We apply these methods to sites in South Africa, where relatively stable topography facilitates reconstruction. We demonstrate the presence of previously unrecognized tectonic effects and their implications for the interpretation of hominin habitats and land use. In parts of the East African Rift, reconstruction is more difficult because of dramatic changes since the time of hominin occupation, while fossils are often found in places where activity has now almost ceased. However, we show that original, dynamic landscape features can be assessed by analogy with parts of the Rift that are currently active and indicate how this approach can complement other sources of information to add new insights and pose new questions for future investigation of hominin land use and habitats. Copyright © 2010 Elsevier Ltd. All rights reserved.

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

NASA Astrophysics Data System (ADS)

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

2015-04-01

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

An indicator of forest dynamics using a shifting landscape mosaic

Treesearch

Kurt H. Riitters; James D. Wickham; Timothy G. Wade

2009-01-01

The composition of a landscape is a fundamental indicator in land-cover pattern assessments. The objective of this paper was to evaluate a landscape composition indicator called ‘landscape mosaic’ as a framework for interpreting land-cover dynamics over a 9-year period in a 360,000 km2 study area in the southern United States. The indicator...

Coupling Landform Evolution and Soil Pedogenesis - Initial Results From the SSSPAM5D Model

NASA Astrophysics Data System (ADS)

Willgoose, G. R.; Welivitiya, W. D. D. P.; Hancock, G. R.; Cohen, S.

2015-12-01

Evolution of soil on a dynamic landform is a crucial next step in landscape evolution modelling. Some attempts have been taken such as MILESD by Vanwalleghem et al. to develop a first model which is capable of simultaneously evolving both the soil profile and the landform. In previous work we have presented physically based models for soil pedogenesis, mARM and SSSPAM. In this study we present the results of coupling a landform evolution model with our SSSPAM5D soil pedogenesis model. In previous work the SSSPAM5D soil evolution model was used to identify trends of the soil profile evolution on a static landform. Two pedogenetic processes, namely (1) armouring due to erosion, and (2) physical and chemical weathering were used in those simulations to evolve the soil profile. By incorporating elevation changes (due to erosion and deposition) we have advanced the SSSPAM5D modelling framework into the realm of landscape evolution. Simulations have been run using elevation and soil grading data of the engineered landform (spoil heap) at the Ranger Uranium Mine, Northern Territory, Australia. The results obtained for the coupled landform-soil evolution simulations predict the erosion of high slope areas, development of rudimentary channel networks in the landform and deposition of sediments in lowland areas, and qualitatively consistent with landform evolution models on their own. Examination of the soil profile characteristics revealed that hill crests are weathering dominated and tend to develop a thick soil layer. The steeper hillslopes at the edge of the landform are erosion dominated with shallow soils while the foot slopes are deposition dominated with thick soil layers. The simulation results of our coupled landform and soil evolution model provide qualitatively correct and timely characterization of the soil evolution on a dynamic landscape. Finally we will compare the characteristics of erosion and deposition predicted by the coupled landform-soil SSSPAM landscape simulator, with landform evolution simulations using a static soil.

Coffee Agroforests Remain Beneficial for Neotropical Bird Community Conservation across Seasons

PubMed Central

Peters, Valerie E.; Cooper, Robert J.; Carroll, C. Ron

2013-01-01

Coffee agroforestry systems and secondary forests have been shown to support similar bird communities but comparing these habitat types are challenged by potential biases due to differences in detectability between habitats. Furthermore, seasonal dynamics may influence bird communities differently in different habitat types and therefore seasonal effects should be considered in comparisons. To address these issues, we incorporated seasonal effects and factors potentially affecting bird detectability into models to compare avian community composition and dynamics between coffee agroforests and secondary forest fragments. In particular, we modeled community composition and community dynamics of bird functional groups based on habitat type (coffee agroforest vs. secondary forest) and season while accounting for variation in capture probability (i.e. detectability). The models we used estimated capture probability to be similar between habitat types for each dietary guild, but omnivores had a lower capture probability than frugivores and insectivores. Although apparent species richness was higher in coffee agroforest than secondary forest, model results indicated that omnivores and insectivores were more common in secondary forest when accounting for heterogeneity in capture probability. Our results largely support the notion that shade-coffee can serve as a surrogate habitat for secondary forest with respect to avian communities. Small coffee agroforests embedded within the typical tropical countryside matrix of secondary forest patches and small-scale agriculture, therefore, may host avian communities that resemble those of surrounding secondary forest, and may serve as viable corridors linking patches of forest within these landscapes. This information is an important step toward effective landscape-scale conservation in Neotropical agricultural landscapes. PMID:24058437

Development of Return Period Inundation Maps In A Changing Climate Using a Systems of Systems Approach

NASA Astrophysics Data System (ADS)

Bilskie, M. V.; Hagen, S. C.; Alizad, K.; Passeri, D. L.; Irish, J. L.

2016-12-01

Worldwide, coastal land margins are experiencing increased vulnerability from natural and manmade disasters [Nicholls et al., 1999]. Specifically, coastal flooding is expected to increase due to the effects of climate change, and sea level rise (SLR) in particular. A systems of systems (SoS) approach has been implemented to better understand the dynamic and nonlinear effects of SLR on tropical cyclone-induced coastal flooding along a low-gradient coastal landscape (northern Gulf of Mexico [NGOM]). The backbone of the SoS framework is a high-resolution, physics-based, tide, wind-wave, and hurricane storm surge model [Bilskie et al., 2016a] that includes systems of SLR scenarios [Parris et al., 2012], shoreline morphology [Passeri et al., 2016; Plant et al., 2016], marsh evolution [Alizad et al., 2016], and population dynamics driven by carbon emission scenarios [Bilskie et al., 2016b]. Prior to considering future conditions, the storm surge model was comprehensively validated for present-day conditions [Bilskie et al., 2016a]. The present-day model was then modified to represent the potential future landscape based on four SLR scenarios prescribed by Parris et al. [2012] linked to carbon emissions scenarios for the year 2100. Numerical simulations forced by hundreds of synthetic tropical cyclones were performed and the results facilitate the development of return period inundation maps across the NGOM that reflect changes to the coastal landscape. The SoS approach allows new patterns and properties to emerge (i.e. nonlinear and dynamic effects of SLR) that would otherwise be unobserved using a static SLR model.

Spatiotemporal dynamics of landscape pattern and hydrologic process in watershed systems

NASA Astrophysics Data System (ADS)

Randhir, Timothy O.; Tsvetkova, Olga

2011-06-01

SummaryLand use change is influenced by spatial and temporal factors that interact with watershed resources. Modeling these changes is critical to evaluate emerging land use patterns and to predict variation in water quantity and quality. The objective of this study is to model the nature and emergence of spatial patterns in land use and water resource impacts using a spatially explicit and dynamic landscape simulation. Temporal changes are predicted using a probabilistic Markovian process and spatial interaction through cellular automation. The MCMC (Monte Carlo Markov Chain) analysis with cellular automation is linked to hydrologic equations to simulate landscape patterns and processes. The spatiotemporal watershed dynamics (SWD) model is applied to a subwatershed in the Blackstone River watershed of Massachusetts to predict potential land use changes and expected runoff and sediment loading. Changes in watershed land use and water resources are evaluated over 100 years at a yearly time step. Results show high potential for rapid urbanization that could result in lowering of groundwater recharge and increased storm water peaks. The watershed faces potential decreases in agricultural and forest area that affect open space and pervious cover of the watershed system. Water quality deteriorated due to increased runoff which can also impact stream morphology. While overland erosion decreased, instream erosion increased from increased runoff from urban areas. Use of urban best management practices (BMPs) in sensitive locations, preventive strategies, and long-term conservation planning will be useful in sustaining the watershed system.

Brownian motion on random dynamical landscapes

NASA Astrophysics Data System (ADS)

Suñé Simon, Marc; Sancho, José María; Lindenberg, Katja

2016-03-01

We present a study of overdamped Brownian particles moving on a random landscape of dynamic and deformable obstacles (spatio-temporal disorder). The obstacles move randomly, assemble, and dissociate following their own dynamics. This landscape may account for a soft matter or liquid environment in which large obstacles, such as macromolecules and organelles in the cytoplasm of a living cell, or colloids or polymers in a liquid, move slowly leading to crowding effects. This representation also constitutes a novel approach to the macroscopic dynamics exhibited by active matter media. We present numerical results on the transport and diffusion properties of Brownian particles under this disorder biased by a constant external force. The landscape dynamics are characterized by a Gaussian spatio-temporal correlation, with fixed time and spatial scales, and controlled obstacle concentrations.

Modeling the effects of fire on the long-term dynamics and restoration of yellow pine and oak forests in the Southern Appalachian Mountains

Treesearch

Charles W. Lafon; John D. Waldron; David M. Cairns; Maria D. Tchakerian; Robert N. Coulson; Kier D. Klepzig

2007-01-01

We used LANDIS, a model of forest disturbance and succession, to simulate successional dynamics of forests in the southern Appalachian Mountains. The simulated environments are based on the Great Smoky Mountains landscapes studied by Whittaker. We focused on the consequences of two contrasting disturbance regimes—fire exclusion versus frequent burning—for the Yellow...

Metapopulation responses to patch connectivity and quality are masked by successional habitat dynamics.

PubMed

Hodgson, Jenny A; Moilanen, Atte; Thomas, Chris D

2009-06-01

Many species have to track changes in the spatial distribution of suitable habitat from generation to generation. Understanding the dynamics of such species will likely require spatially explicit models, and patch-based metapopulation models are potentially appropriate. However, relatively little attention has been paid to developing metapopulation models that include habitat dynamics, and very little to testing the predictions of these models. We tested three predictions from theory about the differences between dynamic habitat metapopulations and their static counterparts using long-term survey data from two metapopulations of the butterfly Plebejus argus. As predicted, we showed first that the metapopulation inhabiting dynamic habitat had a lower level of habitat occupancy, which could not be accounted for by other differences between the metapopulations. Secondly, we found that patch occupancy did not significantly increase with increasing patch connectivity in dynamic habitat, whereas there was a strong positive connectivity-occupancy relationship in static habitat. Thirdly, we found no significant relationship between patch occupancy and patch quality in dynamic habitat, whereas there was a strong, positive quality-occupancy relationship in static habitat. Modeling confirmed that the differences in mean patch occupancy and connectivity-occupancy slope could arise without changing the species' metapopulation parameters-importantly, without changing the dependence of colonization upon connectivity. We found that, for a range of landscape scenarios, successional simulations always produced a lower connectivity-occupancy slope than comparable simulations with static patches, whether compared like-for-like or controlling for mean occupancy. We conclude that landscape-scale studies may often underestimate the importance of connectivity for species occurrence and persistence because habitat turnover can obscure the connectivity-occupancy relationship in commonly available snapshot data.

Landscape anthropogenic disturbance in the Mediterranean ecosystem: is the current landscape sustainable?

NASA Astrophysics Data System (ADS)

Biondi, Guido; D'Andrea, Mirko; Fiorucci, Paolo; Franciosi, Chiara; Lima, Marco

2013-04-01

Mediterranean landscape during the last centuries has been subject to strong anthropogenic disturbances who shifted natural vegetation cover in a cultural landscape. Most of the natural forest were destroyed in order to allow cultivation and grazing activities. In the last century, fast growing conifer plantations were introduced in order to increase timber production replacing slow growing natural forests. In addition, after the Second World War most of the grazing areas were changed in unmanaged mediterranean conifer forest frequently spread by fires. In the last decades radical socio economic changes lead to a dramatic abandonment of the cultural landscape. One of the most relevant result of these human disturbances, and in particular the replacement of deciduous forests with coniferous forests, has been the increasing in the number of forest fires, mainly human caused. The presence of conifers and shrubs, more prone to fire, triggered a feedback mechanism that makes difficult to return to the stage of potential vegetation causing huge economic, social and environmental damages. The aim of this work is to investigate the sustainability of the current landscape. A future landscape scenario has been simulated considering the natural succession in absence of human intervention assuming the current fire regime will be unaltered. To this end, a new model has been defined, implementing an ecological succession model coupled with a simply Forest Fire Model. The ecological succession model simulates the vegetation dynamics using a rule-based approach discrete in space and time. In this model Plant Functional Types (PFTs) are used to describe the landscape. Wildfires are randomly ignited on the landscape, and their propagation is simulated using a stochastic cellular automata model. The results show that the success of the natural succession toward a potential vegetation cover is prevented by the frequency of fire spreading. The actual landscape is then unsustainable because of the high cost of fire fighting activities. The right path to success consists in development of suitable land use planning and forest management to mitigate the consequences of past anthropogenic disturbances.

Topography and vegetation alter soil nitrogen availability and loss in tropical and temperate ecosystems

NASA Astrophysics Data System (ADS)

Weintraub, S. R.

2016-12-01

A dominant paradigm in ecosystem ecology holds that nitrogen (N) cycles as an excess nutrient in old tropical landscapes but is a scarce, limiting resource in young, temperate ecosystems. However, recent work suggests that both biotic and abiotic state factors can promote unexpected patterns of N cycling across complex landscapes. Here, I present two case studies demonstrating how topography and vegetation shape patterns of N cycling and loss in heterogeneous terrain. In a geomorphically dynamic, high-diversity tropical rainforest, flat ridge tops display open N cycling, yet eroding hillslopes are surprisingly N-poor with multiple indicators implying conservative N cycling. Soil mineralogy indicates slope soils are less developed than adjacent flat ridge counterparts, and the accumulation of cosmogenic 10Be in surface soil suggests residence times are only half as long. Together, these observations suggest erosion resets soil development, with constant N-removal promoting tight N-cycling. Further, soil δ15N is negatively correlated with slope angle across the landscape, and mass balance modeling supports an increasing role for erosive N loss in steep regions. In a temperate montane landscape with lower physical erosion rates, vegetation interacts with hydro-topographic position to mediate local N dynamics. Upslope, forests display conservative N-cycling, yet in adjacent herbaceous areas, multiple indicators point toward an open N cycle. Downslope, both vegetation types show an increase in N-richness. In downslope forests, this is confined to the near-surface, stemming from higher foliar N content due to lateral N transport and uptake. In herbaceous sites, deeper vadose-zone N transport occurs but with no change in foliar N, implying differences in the degree of N limitation between vegetation types. In this landscape, soil nitrate leaching rates track N availability, though δ15N-NO3- does not suggest a similar pattern for gaseous losses, instead reflecting nitrification and/or transport dynamics. Pervasive human alteration of the N cycle underscores the need to unravel these state-factor controls on N availability and loss in order to predict and model ecosystem biogeochemical dynamics in the face of global change.

Dynamics of internal models in game players

NASA Astrophysics Data System (ADS)

Taiji, Makoto; Ikegami, Takashi

1999-10-01

A new approach for the study of social games and communications is proposed. Games are simulated between cognitive players who build the opponent’s internal model and decide their next strategy from predictions based on the model. In this paper, internal models are constructed by the recurrent neural network (RNN), and the iterated prisoner’s dilemma game is performed. The RNN allows us to express the internal model in a geometrical shape. The complicated transients of actions are observed before the stable mutually defecting equilibrium is reached. During the transients, the model shape also becomes complicated and often experiences chaotic changes. These new chaotic dynamics of internal models reflect the dynamical and high-dimensional rugged landscape of the internal model space.

Biological signatures of dynamic river networks from a coupled landscape evolution and neutral community model

NASA Astrophysics Data System (ADS)

Stokes, M.; Perron, J. T.

2017-12-01

Freshwater systems host exceptionally species-rich communities whose spatial structure is dictated by the topology of the river networks they inhabit. Over geologic time, river networks are dynamic; drainage basins shrink and grow, and river capture establishes new connections between previously separated regions. It has been hypothesized that these changes in river network structure influence the evolution of life by exchanging and isolating species, perhaps boosting biodiversity in the process. However, no general model exists to predict the evolutionary consequences of landscape change. We couple a neutral community model of freshwater organisms to a landscape evolution model in which the river network undergoes drainage divide migration and repeated river capture. Neutral community models are macro-ecological models that include stochastic speciation and dispersal to produce realistic patterns of biodiversity. We explore the consequences of three modes of speciation - point mutation, time-protracted, and vicariant (geographic) speciation - by tracking patterns of diversity in time and comparing the final result to an equilibrium solution of the neutral model on the final landscape. Under point mutation, a simple model of stochastic and instantaneous speciation, the results are identical to the equilibrium solution and indicate the dominance of the species-area relationship in forming patterns of diversity. The number of species in a basin is proportional to its area, and regional species richness reaches its maximum when drainage area is evenly distributed among sub-basins. Time-protracted speciation is also modeled as a stochastic process, but in order to produce more realistic rates of diversification, speciation is not assumed to be instantaneous. Rather, each new species must persist for a certain amount of time before it is considered to be established. When vicariance (geographic speciation) is included, there is a transient signature of increased regional diversity after river capture. The results indicate that the mode of speciation and the rate of speciation relative to the rate of divide migration determine the evolutionary signature of river capture.

SIMPPLLE, version 2.5 user's guide

Treesearch

Jimmie D. Chew; Kirk Moeller; Christine Stalling

2012-01-01

SIMPPLLE is a spatially-interactive, dynamic landscape modeling system for projecting temporal changes in the spatial distribution of vegetation in response to insects, disease, wildland fire, and other natural and management-caused disturbances. SIMPPLLE is designed to provide a balance between incorporating enough complexity and interactions in modeling ecosystem...

Anomalous glassy dynamics in simple models of dense biological tissue

NASA Astrophysics Data System (ADS)

Sussman, Daniel M.; Paoluzzi, M.; Marchetti, M. Cristina; Manning, M. Lisa

2018-02-01

In order to understand the mechanisms for glassy dynamics in biological tissues and shed light on those in non-biological materials, we study the low-temperature disordered phase of 2D vertex-like models. Recently it has been noted that vertex models have quite unusual behavior in the zero-temperature limit, with rigidity transitions that are controlled by residual stresses and therefore exhibit very different scaling and phenomenology compared to particulate systems. Here we investigate the finite-temperature phase of two-dimensional Voronoi and Vertex models, and show that they have highly unusual, sub-Arrhenius scaling of dynamics with temperature. We connect the anomalous glassy dynamics to features of the potential energy landscape associated with zero-temperature inherent states.

Activated aging dynamics and effective trap model description in the random energy model

NASA Astrophysics Data System (ADS)

Baity-Jesi, M.; Biroli, G.; Cammarota, C.

2018-01-01

We study the out-of-equilibrium aging dynamics of the random energy model (REM) ruled by a single spin-flip Metropolis dynamics. We focus on the dynamical evolution taking place on time-scales diverging with the system size. Our aim is to show to what extent the activated dynamics displayed by the REM can be described in terms of an effective trap model. We identify two time regimes: the first one corresponds to the process of escaping from a basin in the energy landscape and to the subsequent exploration of high energy configurations, whereas the second one corresponds to the evolution from a deep basin to the other. By combining numerical simulations with analytical arguments we show why the trap model description does not hold in the former but becomes exact in the second.

Debris Flow Process and Climate Controls on Steepland Valley Form and Evolution

NASA Astrophysics Data System (ADS)

Struble, W.; Roering, J. J.

2017-12-01

In unglaciated mountain ranges, steepland bedrock valleys often dominate relief structure and dictate landscape response to perturbations in tectonics or climate; drainage divides have been shown to be dynamic and drainage capture is common. Landscape evolution models often use the stream power model to simulate morphologic changes, but steepland valley networks exhibit trends that deviate from predictions of this model. The prevalence of debris flows in steep channels has motivated approaches that account for commonly observed curvature of slope-area data at small drainage areas. Debris flow deposits correspond with observed curvature in slope-area data, wherein slope increases slowly as drainage area decreases; debris flow incision is implied upstream of deposits. In addition, shallow landslides and in-channel sediment entrainment in humid and arid regions, respectively, have been identified as likely debris flow triggering mechanisms, but the extent to which they set the slope of steep channels is unclear. While an untested model exists for humid landscape debris flows, field observations and models are lacking for regions with lower mean annual precipitation. The Oregon Coastal Ranges are an ideal humid setting for observing how shallow landslide-initiated debris flows abrade channel beds and/or drive exposure-driven weathering. Preliminary field observations in the Lost River Range and the eastern Sierra Nevada - semi-arid and unglaciated environments - suggest that debris flows are pervasive in steep reaches. Evidence for fluvial incision is lacking and the presence of downstream debris flow deposits and a curved morphologic signature in slope-area space suggests stream power models are insufficient for predicting and interpreting landscape dynamics. Investigation of debris flow processes in both humid and arid sites such as these seeks to identify the linkage between sediment transport and the characteristic form of steepland valleys. Bedrock weathering, fracture density, recurrence interval, bulking, and grain size may determine process-form linkages in humid and arid settings. Evaluation of debris flow processes in sites of varying climate presents the opportunity to quantify the role of debris flow incision in the evolution of steepland valleys and improve landscape evolution models.

Cascade model for fluvial geomorphology

NASA Technical Reports Server (NTRS)

Newman, W. I.; Turcotte, D. L.

1990-01-01

Erosional landscapes are generally scale invariant and fractal. Spectral studies provide quantitative confirmation of this statement. Linear theories of erosion will not generate scale-invariant topography. In order to explain the fractal behavior of landscapes a modified Fourier series has been introduced that is the basis for a renormalization approach. A nonlinear dynamical model has been introduced for the decay of the modified Fourier series coefficients that yield a fractal spectra. It is argued that a physical basis for this approach is that a fractal (or nearly fractal) distribution of storms (floods) continually renews erosional features on all scales.

Autonomous oscillation in supramolecular assemblies: Role of free energy landscape and fluctuations

NASA Astrophysics Data System (ADS)

Sereda, Yuriy V.; Ortoleva, Peter J.

2015-11-01

Molecular dynamics studies demonstrated that a supramolecular assembly can express autonomous structural oscillations about equilibrium. It is demonstrated here that for nanosystems such oscillations can result from the interplay of free energy landscape and structural fluctuations. Furthermore, these oscillations have intermittent character, reflecting the conflict between a tendency to oscillate due to features in the free energy landscape, and the Second Law's repression of perpetual oscillation in an isothermal, equilibrium system. The demonstration system is a T = 1 icosahedral structure constituted of 12 protein pentamers in contact with a bath at fixed temperature. The oscillations are explained in terms of a Langevin model accounting for interactions among neighboring pentamers. The model is based on a postulated free energy landscape in the 24-dimensional space of variables describing the centrifugal and rotational motion of each pentamer. The model includes features such as basins of attraction and low free energy corridors. When the system is driven slightly out of equilibrium, the oscillations are transformed into a limit cycle, as expressed in terms of power spectrum narrowing.

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

PubMed

Zhao, Lei; Wang, Jin

2016-11-01

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

Landscape Pattern Dynamic Change Research of Harbin Songbei Based on GIS Technology

NASA Astrophysics Data System (ADS)

Chenyang, Ding; Kun, Wang; Kang, Li Kang

2018-05-01

With the rapid development of social economy in the Songhua River basin, there are big dynamic change of the landscape of the new area beside the river bank, which is represented by Harbin Songbei. This paper selects 13 representative indexes from landscape and patch level, analyzes the cause and process of the change of landscape pattern in Songbei during 2005-2015, and probes into the characteristics of the change based on the principle of landscape ecology, using remote sensing and GIS technology and Fragstats3.3 software data statistics.

Phenology and density-dependent dispersal predict patterns of mountain pine beetle (Dendroctonus ponderosae) impact

Treesearch

James A. Powell; Barbara J. Bentz

2014-01-01

For species with irruptive population behavior, dispersal is an important component of outbreak dynamics. We developed and parameterized a mechanistic model describing mountain pine beetle (Dendroctonus ponderosae Hopkins) population demographics and dispersal across a landscape. Model components include temperature-dependent phenology, host tree colonization...

Comparing spatial diversification and meta-population models in the Indo-Australian Archipelago

PubMed Central

Chalmandrier, Loïc; Albouy, Camille; Descombes, Patrice; Sandel, Brody; Faurby, Soren; Svenning, Jens-Christian; Zimmermann, Niklaus E.

2018-01-01

Reconstructing the processes that have shaped the emergence of biodiversity gradients is critical to understand the dynamics of diversification of life on Earth. Islands have traditionally been used as model systems to unravel the processes shaping biological diversity. MacArthur and Wilson's island biogeographic model predicts diversity to be based on dynamic interactions between colonization and extinction rates, while treating islands themselves as geologically static entities. The current spatial configuration of islands should influence meta-population dynamics, but long-term geological changes within archipelagos are also expected to have shaped island biodiversity, in part by driving diversification. Here, we compare two mechanistic models providing inferences on species richness at a biogeographic scale: a mechanistic spatial-temporal model of species diversification and a spatial meta-population model. While the meta-population model operates over a static landscape, the diversification model is driven by changes in the size and spatial configuration of islands through time. We compare the inferences of both models to floristic diversity patterns among land patches of the Indo-Australian Archipelago. Simulation results from the diversification model better matched observed diversity than a meta-population model constrained only by the contemporary landscape. The diversification model suggests that the dynamic re-positioning of islands promoting land disconnection and reconnection induced an accumulation of particularly high species diversity on Borneo, which is central within the island network. By contrast, the meta-population model predicts a higher diversity on the mainlands, which is less compatible with empirical data. Our analyses highlight that, by comparing models with contrasting assumptions, we can pinpoint the processes that are most compatible with extant biodiversity patterns. PMID:29657753

Comparing spatial diversification and meta-population models in the Indo-Australian Archipelago.

PubMed

Chalmandrier, Loïc; Albouy, Camille; Descombes, Patrice; Sandel, Brody; Faurby, Soren; Svenning, Jens-Christian; Zimmermann, Niklaus E; Pellissier, Loïc

2018-03-01

Reconstructing the processes that have shaped the emergence of biodiversity gradients is critical to understand the dynamics of diversification of life on Earth. Islands have traditionally been used as model systems to unravel the processes shaping biological diversity. MacArthur and Wilson's island biogeographic model predicts diversity to be based on dynamic interactions between colonization and extinction rates, while treating islands themselves as geologically static entities. The current spatial configuration of islands should influence meta-population dynamics, but long-term geological changes within archipelagos are also expected to have shaped island biodiversity, in part by driving diversification. Here, we compare two mechanistic models providing inferences on species richness at a biogeographic scale: a mechanistic spatial-temporal model of species diversification and a spatial meta-population model. While the meta-population model operates over a static landscape, the diversification model is driven by changes in the size and spatial configuration of islands through time. We compare the inferences of both models to floristic diversity patterns among land patches of the Indo-Australian Archipelago. Simulation results from the diversification model better matched observed diversity than a meta-population model constrained only by the contemporary landscape. The diversification model suggests that the dynamic re-positioning of islands promoting land disconnection and reconnection induced an accumulation of particularly high species diversity on Borneo, which is central within the island network. By contrast, the meta-population model predicts a higher diversity on the mainlands, which is less compatible with empirical data. Our analyses highlight that, by comparing models with contrasting assumptions, we can pinpoint the processes that are most compatible with extant biodiversity patterns.

Folding free-energy landscape of villin headpiece subdomain from molecular dynamics simulations.

PubMed

Lei, Hongxing; Wu, Chun; Liu, Haiguang; Duan, Yong

2007-03-20

High-accuracy ab initio folding has remained an elusive objective despite decades of effort. To explore the folding landscape of villin headpiece subdomain HP35, we conducted two sets of replica exchange molecular dynamics for 200 ns each and three sets of conventional microsecond-long molecular dynamics simulations, using AMBER FF03 force field and a generalized-Born solvation model. The protein folded consistently to the native state; the lowest C(alpha)-rmsd from the x-ray structure was 0.46 A, and the C(alpha)- rmsd of the center of the most populated cluster was 1.78 A at 300 K. ab initio simulations have previously not reached this level. The folding landscape of HP35 can be partitioned into the native, denatured, and two intermediate-state regions. The native state is separated from the major folding intermediate state by a small barrier, whereas a large barrier exists between the major folding intermediate and the denatured states. The melting temperature T(m) = 339 K extracted from the heat-capacity profile was in close agreement with the experimentally derived T(m) = 342 K. A comprehensive picture of the kinetics and thermodynamics of HP35 folding emerges when the results from replica exchange and conventional molecular dynamics simulations are combined.

Encounter success of free-ranging marine predator movements across a dynamic prey landscape.

PubMed

Sims, David W; Witt, Matthew J; Richardson, Anthony J; Southall, Emily J; Metcalfe, Julian D

2006-05-22

Movements of wide-ranging top predators can now be studied effectively using satellite and archival telemetry. However, the motivations underlying movements remain difficult to determine because trajectories are seldom related to key biological gradients, such as changing prey distributions. Here, we use a dynamic prey landscape of zooplankton biomass in the north-east Atlantic Ocean to examine active habitat selection in the plankton-feeding basking shark Cetorhinus maximus. The relative success of shark searches across this landscape was examined by comparing prey biomass encountered by sharks with encounters by random-walk simulations of 'model' sharks. Movements of transmitter-tagged sharks monitored for 964 days (16754 km estimated minimum distance) were concentrated on the European continental shelf in areas characterized by high seasonal productivity and complex prey distributions. We show movements by adult and sub-adult sharks yielded consistently higher prey encounter rates than 90% of random-walk simulations. Behavioural patterns were consistent with basking sharks using search tactics structured across multiple scales to exploit the richest prey areas available in preferred habitats. Simple behavioural rules based on learned responses to previously encountered prey distributions may explain the high performances. This study highlights how dynamic prey landscapes enable active habitat selection in large predators to be investigated from a trophic perspective, an approach that may inform conservation by identifying critical habitat of vulnerable species.

Tropical forest landscape dynamics: Population consequences for neotropical lianas, genus Passiflora

NASA Astrophysics Data System (ADS)

Plowes, Robert Merrick

Treefall gaps in rainforest landscapes play a crucial role in providing opportunities for establishment and growth of rare, light-demanding plants such as Passifora vines in Corcovado rainforests, Costa Rica. This study considers the interplay of landscape dynamics with plant life history traits and strategies in an ephemeral patch network. In Chapter One, I show how patch quality dynamics and propagule dispersal affect colonization of treefall gaps by Passifora vitifolia. Recruitment required high patch quality, exceeding 3 hours of sunlight and patches closed after about 6 years. Colonization by seed dispersal (80%) was constrained by patch quality and isolation, while clonal growth from dormant plants (20%) was limited to rare adjacent patches. Since patch turnover is critical in these systems, Chapter Two is focused on factors affecting canopy structure. I showed that prior landuse altered the dynamics of frequent, small-scale disturbances during succession following a single, large deforestation event. Here, I used Landsat subpixel analysis, aerial photographs and field surveys to demonstrate major changes in dynamics of regenerating canopies following release from agricultural activity in 1975. Little work has considered the role of life history traits in persistence of patchy populations, and so in Chapter Three I asked what life history strategies are used by 9 Passiflora species that occur in these transient forest gaps. Although Passiflora species exhibited differences in dormancy or dispersal strategies, abundance was not associated with any one strategy. Elasticities of vital rates (stasis, growth and fecundity) of P. vitifolia differed empirically in old growth and regenerating forests. To explore population responses to changes in landscape parameters or life history strategies, I created a spatially-explicit individual-based model. Simulations indicate that plant types with a dormancy phase have a greater suite of responses since they persist after patch extinction with potential to contribute later through both sexual and asexual dispersal. Plants that rely only on high dispersal were extinction prone in low connectivity landscapes. This novel approach of jointly analyzing spatially-explicit patch parameters and life history traits offers a comprehensive framework for further understanding the effects of patch dynamics on populations.

Lithologic controls on landscape dynamics and aquatic species evolution in post-orogenic mountains

NASA Astrophysics Data System (ADS)

Gallen, Sean F.

2018-07-01

Determining factors that modify Earth's topography is essential for understanding continental mass and nutrient fluxes, and the evolution and diversity of species. Contrary to the paradigm of slow, steady topographic decay after orogenesis ceases, nearly all ancient mountain belts exhibit evidence of unsteady landscape evolution at large spatial scales. External forcing from uplift from dynamic mantle processes or climate change is commonly invoked to explain the unexpected dynamics of dead orogens, yet direct evidence supporting such inferences is generally lacking. Here I use quantitative analysis of fluvial topography in the southern Appalachian Mountains to show that the exhumation of rocks of variable erosional resistance exerts a fundamental, autogenic control on the evolution of post-orogenic landscapes that continually reshapes river networks. I characterize the spatial pattern of erodibility associated with individual rock-types, and use inverse modeling of river profiles to document a ∼150 m base level fall event at 9 ± 3 Ma in the Upper Tennessee drainage basin. This analysis, combined with existing geological and biological data, demonstrates that base level fall was triggered by capture of the Upper Tennessee River basin by the Lower Tennessee River basin in the Late Miocene. I demonstrate that rock-type triggered changes in river network topology gave rise to the modern Tennessee River system and enhanced erosion rates, changed sediment flux and dispersal patterns, and altered bio-evolutionary pathways in the southeastern U.S.A., a biodiversity hotspot. These findings suggest that variability observed in the stratigraphic, geomorphic, and biologic archives of tectonically quiescent regions does not require external drivers, such as geodynamic or climate forcing, as is typically the interpretation. Rather, my findings lead to a new model of inherently unsteady evolution of ancient mountain landscapes due to the geologic legacy of plate tectonics.

Yardang evolution from maturity to demise

NASA Astrophysics Data System (ADS)

Barchyn, Thomas E.; Hugenholtz, Chris H.

2015-07-01

Yardangs are enigmatic wind-parallel ridges sculpted by aeolian processes that are found extensively in arid environments on Earth and Mars. No general theory exists to explain the long-term evolution of yardangs, curtailing modeling of landscape evolution and dynamics of suspended sediment release. We present a hypothesis of yardang evolution using relative rates of sediment flux, interyardang corridor downcutting, yardang denudation, substrate erodibility, and substrate clast content. To develop and sustain yardangs, corridor downcutting must exceed yardang vertical denudation and deflation. However, erosion of substrate yields considerable quantities of sediment that shelters corridors, slowing downcutting. We model the evolution of yardangs through various combinations of rates and substrate compositions, demonstrating the life span, suspended sediment release, and resulting landscape evolution. We find that yardangs have a distinct and predictable evolution, with inevitable demise and unexpectedly dynamic and autogenic erosion rates driven by subtle differences in substrate clast composition.

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

Wu, Wei; Wang, Jin, E-mail: jin.wang.1@stonybrook.edu; State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, 130022 Changchun, China and College of Physics, Jilin University, 130021 Changchun

We have established a general non-equilibrium thermodynamic formalism consistently applicable to both spatially homogeneous and, more importantly, spatially inhomogeneous systems, governed by the Langevin and Fokker-Planck stochastic dynamics with multiple state transition mechanisms, using the potential-flux landscape framework as a bridge connecting stochastic dynamics with non-equilibrium thermodynamics. A set of non-equilibrium thermodynamic equations, quantifying the relations of the non-equilibrium entropy, entropy flow, entropy production, and other thermodynamic quantities, together with their specific expressions, is constructed from a set of dynamical decomposition equations associated with the potential-flux landscape framework. The flux velocity plays a pivotal role on both the dynamic andmore » thermodynamic levels. On the dynamic level, it represents a dynamic force breaking detailed balance, entailing the dynamical decomposition equations. On the thermodynamic level, it represents a thermodynamic force generating entropy production, manifested in the non-equilibrium thermodynamic equations. The Ornstein-Uhlenbeck process and more specific examples, the spatial stochastic neuronal model, in particular, are studied to test and illustrate the general theory. This theoretical framework is particularly suitable to study the non-equilibrium (thermo)dynamics of spatially inhomogeneous systems abundant in nature. This paper is the second of a series.« less

Temporal bird community dynamics are strongly affected by landscape fragmentation in a Central American tropical forest region

USGS Publications Warehouse

Blandón, A.C.; Perelman, S.B.; Ramírez, M.; López, A.; Javier, O.; Robbins, Chandler S.

2016-01-01

Habitat loss and fragmentation are considered the main causes of species extinctions, particularly in tropical ecosystems. The objective of this work was to evaluate the temporal dynamics of tropical bird communities in landscapes with different levels of fragmentation in eastern Guatemala. We evaluated five bird community dynamic parameters for forest specialists and generalists: (1) species extinction, (2) species turnover, (3) number of colonizing species, (4) relative species richness, and (5) a homogeneity index. For each of 24 landscapes, community dynamic parameters were estimated from bird point count data, for the 1998–1999 and 2008–2009 periods, accounting for species’ detection probability. Forest specialists had higher extinction rates and a smaller number of colonizing species in landscapes with higher fragmentation, thus having lower species richness in both time periods. Alternatively, forest generalists elicited a completely different pattern, showing a curvilinear association to forest fragmentation for most parameters. Thus, greater community dynamism for forest generalists was shown in landscapes with intermediate levels of fragmentation. Our study supports general theory regarding the expected negative effects of habitat loss and fragmentation on the temporal dynamics of biotic communities, particularly for forest specialists, providing strong evidence from understudied tropical bird communities.

Aging, memory, and nonhierarchical energy landscape of spin jam

NASA Astrophysics Data System (ADS)

Samarakoon, Anjana; Sato, Taku J.; Chen, Tianran; Chern, Gai-Wei; Yang, Junjie; Klich, Israel; Sinclair, Ryan; Zhou, Haidong; Lee, Seung-Hun

2016-10-01

The notion of complex energy landscape underpins the intriguing dynamical behaviors in many complex systems ranging from polymers, to brain activity, to social networks and glass transitions. The spin glass state found in dilute magnetic alloys has been an exceptionally convenient laboratory frame for studying complex dynamics resulting from a hierarchical energy landscape with rugged funnels. Here, we show, by a bulk susceptibility and Monte Carlo simulation study, that densely populated frustrated magnets in a spin jam state exhibit much weaker memory effects than spin glasses, and the characteristic properties can be reproduced by a nonhierarchical landscape with a wide and nearly flat but rough bottom. Our results illustrate that the memory effects can be used to probe different slow dynamics of glassy materials, hence opening a window to explore their distinct energy landscapes.

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

Carbon dynamics in the future forest: the importance of long-term successional legacy and climate–fire interactions

Treesearch

Louise Loudermilk; Robert Scheller; Peter Weisberg; Jian Yang; Thomas Dilts; Sarah Karam; Carl Skinner

2013-01-01

Understanding how climate change may influence forest carbon (C) budgets requires knowledge of forest growth relationships with regional climate, long-term forest succession, and past and future disturbances, such as wildfires and timber harvesting events. We used a landscape-scale model of forest succession, wildfire, and C dynamics (LANDIS-II) to evaluate the effects...

Simulation of Long-Term Landscape-Level Fuel Treatment Effects on Large Wildfires

Treesearch

Mark A. Finney; Rob C. Seli; Charles W. McHugh; Alan A. Ager; Berni Bahro; James K. Agee

2006-01-01

A simulation system was developed to explore how fuel treatments placed in random and optimal spatial patterns affect the growth and behavior of large fires when implemented at different rates over the course of five decades. The system consists of a forest/fuel dynamics simulation module (FVS), logic for deriving fuel model dynamics from FVS output, a spatial fuel...

Amazon forest carbon dynamics predicted by profiles of canopy leaf area and light environment

Treesearch

S. C. Stark; V. Leitold; J. L. Wu; M. O. Hunter; C. V. de Castilho; F. R. C. Costa; S. M. McMahon; G. G. Parker; M. Takako Shimabukuro; M. A. Lefsky; M. Keller; L. F. Alves; J. Schietti; Y. E. Shimabukuro; D. O. Brandao; T. K. Woodcock; N. Higuchi; P. B de Camargo; R. C. de Oliveira; S. R. Saleska

2012-01-01

Tropical forest structural variation across heterogeneous landscapes may control above-ground carbon dynamics. We tested the hypothesis that canopy structure (leaf area and light availability) – remotely estimated from LiDAR – control variation in above-ground coarse wood production (biomass growth). Using a statistical model, these factors predicted biomass growth...

The influence of agroforestry and other land-use types on the persistence of a Sumatran tiger (Panthera tigris sumatrae) population: an individual-based model approach.

PubMed

Imron, Muhammad Ali; Herzog, Sven; Berger, Uta

2011-08-01

The importance of preserving both protected areas and their surrounding landscapes as one of the major conservation strategies for tigers has received attention over recent decades. However, the mechanism of how land-use surrounding protected areas affects the dynamics of tiger populations is poorly understood. We developed Panthera Population Persistence (PPP)--an individual-based model--to investigate the potential mechanism of the Sumatran tiger population dynamics in a protected area and under different land-use scenarios surrounding the reserve. We tested three main landscape compositions (single, combined and real land-uses of Tesso-Nilo National Park and its surrounding area) on the probability of and time to extinction of the Sumatran tiger over 20 years in Central Sumatra. The model successfully explains the mechanisms behind the population response of tigers under different habitat landscape compositions. Feeding and mating behaviours of tigers are key factors, which determined population persistence in a heterogeneous landscape. All single land-use scenarios resulted in tiger extinction but had a different probability of extinction within 20 years. If tropical forest was combined with other land-use types, the probability of extinction was smaller. The presence of agroforesty and logging concessions adjacent to protected areas encouraged the survival of tiger populations. However, with the real land-use scenario of Tesso-Nilo National Park, tigers could not survive for more than 10 years. Promoting the practice of agroforestry systems surrounding the park is probably the most reasonable way to steer land-use surrounding the Tesso-Nilo National Park to support tiger conservation.

Peptoid conformational free energy landscapes from implicit-solvent molecular simulations in AMBER.

PubMed

Voelz, Vincent A; Dill, Ken A; Chorny, Ilya

2011-01-01

To test the accuracy of existing AMBER force field models in predicting peptoid conformation and dynamics, we simulated a set of model peptoid molecules recently examined by Butterfoss et al. (JACS 2009, 131, 16798-16807) using QM methods as well as three peptoid sequences with experimentally determined structures. We found that AMBER force fields, when used with a Generalized Born/Surface Area (GBSA) implicit solvation model, could accurately reproduce the peptoid torsional landscape as well as the major conformers of known peptoid structures. Enhanced sampling by replica exchange molecular dynamics (REMD) using temperatures from 300 to 800 K was used to sample over cis-trans isomerization barriers. Compared to (Nrch)5 and cyclo-octasarcosyl, the free energy of N-(2-nitro-3-hydroxyl phenyl)glycine-N-(phenyl)glycine has the most "foldable" free energy landscape, due to deep trans-amide minima dictated by N-aryl sidechains. For peptoids with (S)-N (1-phenylethyl) (Nspe) side chains, we observe a discrepancy in backbone dihedral propensities between molecular simulations and QM calculations, which may be due to force field effects or the inability to capture n --> n* interactions. For these residues, an empirical phi-angle biasing potential can "rescue" the backbone propensities seen in QM. This approach can serve as a general strategy for addressing force fields without resorting to a complete reparameterization. Overall, this study demonstrates the utility of implicit-solvent REMD simulations for efficient sampling to predict peptoid conformational landscapes, providing a potential tool for first-principles design of sequences with specific folding properties.

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.

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

Fuel dynamics by using Landscape Ecology Indices in the Alto Mijares, Spain

NASA Astrophysics Data System (ADS)

Iqbal, J.; Garcia, C. V.

2009-04-01

Land abandonment in Mediterranean regions has brought about a number of management problems, being an increased wildfire activity prevalent among them. Agricultural neglect in highlands resulted in reduced anthropogenic disturbances and greater landscape homogeneity in areas such as the Alto Mijares in Spain. It is widely accepted that processes like forest fires, influence structure of the landscape and vice versa. Fire-prone Mediterranean flora is well adapted to this disturbance, exhibiting excellent succession capabilities; but higher fuel loads and homogeneous conditions may ally to promote vegetation recession when the fire regime is altered by land abandonment. Both succession and recession make changes to the landscape structure and configuration. However, these changes are difficult to quantify and characterize. If landscape restoration of these forests is a management objective, then developing a quantitative knowledge base for landscape fuel dynamics is a prerequisite. Four classified LandsatTM satellite images were compared to quantify changes in landscape structure between 1984 and 1998. An attempt is made to define landscape level dynamics for fuel development after reduced disturbance and fuel accumulation that leads to catastrophic fires by using landscape ecology indices. By doing so, indices that best describe the fuel dynamics are pointed. The results indicate that low-level disturbance increases heterogeneity, thus lowers fire hazard. No disturbance or severe disturbance increases homogeneity because of vegetation succession and may lead to devastating fires. These fires could be avoided by human induced disturbance like controlled burning, harvesting, mechanical works for fuel reduction and other silviculture measures; thus bringing in more heterogeneity in the region. The Alto Mijares landscape appears to be in an unstable equilibrium where succession and recession are at tug of war. The effects are evident in the general absence of the climax species of Quercus ilex. It have also been recognised that just one index is rarely sufficient to describe the complex dynamics in any landscape; it is usually a group of indices that needs to be consulted in order to perceive the wider picture. The study indicates that there is a need for landscape and social restoration in areas like Alto Mijares to make best use of available resources and avoid catastrophic fires.

Evaluating the Effect of Autogenic Sedimentation on the Preservation of Climate Proxy Records: Modeling and Examples from the Paleocene Eocene Thermal Maximum

NASA Astrophysics Data System (ADS)

Trampush, S. M.; Hajek, E. A.

2016-12-01

The stratigraphic record provides a vital opportunity to investigate how changes in climate can impact many different landscapes and seascapes. However, the inherent variability in sedimentation within many depositional environments may mask or remove the signature of climate change. A common solution is to use geochemical proxies - usually collected at regular stratigraphic intervals - to independently identify climate events. This approach doesn't account for the potentially significant variability in deposition and erosion time series resulting from autogenic landscape dynamics. In order to explore how geochemical proxy records could be overprinted by landscape dynamics, we use a 1D stochastic sedimentation model where we mimic fluvial, lacustrine, shallow marine, and deep marine environmental dynamics by varying the frequency-magnitude distributions of sedimentation rates. We find that even conservative estimates of the frequency and magnitude of stochastic sedimentation variability can heavily modify proxy records in characteristic ways by alternately removing, compressing, and expanding portions of the record, regardless of the magnitude or duration of the climatic event. Our model results are consistent with observations of the carbon isotope excursions of the Paleocene Eocene Thermal Maximum (PETM) preserved within both fluvial (e.g. the Bighorn Basin, Wyoming and the Piceance Basin, Colorado) and shallow marine (e.g. the New Jersey shelf) deposits. Our results suggest that we may be able to use existing geochemical proxy records within well studied, global climate events, such as the PETM, to constrain the variability in sedimentation present within different depositional environments.

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

Measurement of energy landscape roughness of folded and unfolded proteins

PubMed Central

Milanesi, Lilia; Waltho, Jonathan P.; Hunter, Christopher A.; Shaw, Daniel J.; Beddard, Godfrey S.; Reid, Gavin D.; Dev, Sagarika; Volk, Martin

2012-01-01

The dynamics of protein conformational changes, from protein folding to smaller changes, such as those involved in ligand binding, are governed by the properties of the conformational energy landscape. Different techniques have been used to follow the motion of a protein over this landscape and thus quantify its properties. However, these techniques often are limited to short timescales and low-energy conformations. Here, we describe a general approach that overcomes these limitations. Starting from a nonnative conformation held by an aromatic disulfide bond, we use time-resolved spectroscopy to observe nonequilibrium backbone dynamics over nine orders of magnitude in time, from picoseconds to milliseconds, after photolysis of the disulfide bond. We find that the reencounter probability of residues that initially are in close contact decreases with time following an unusual power law that persists over the full time range and is independent of the primary sequence. Model simulations show that this power law arises from subdiffusional motion, indicating a wide distribution of trapping times in local minima of the energy landscape, and enable us to quantify the roughness of the energy landscape (4–5 kBT). Surprisingly, even under denaturing conditions, the energy landscape remains highly rugged with deep traps (>20 kBT) that result from multiple nonnative interactions and are sufficient for trapping on the millisecond timescale. Finally, we suggest that the subdiffusional motion of the protein backbone found here may promote rapid folding of proteins with low contact order by enhancing contact formation between nearby residues. PMID:23150572

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

PubMed Central

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

2015-01-01

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

How fragmentation and corridors affect wind dynamics and seed dispersal in open habitats

PubMed Central

Damschen, Ellen I.; Baker, Dirk V.; Bohrer, Gil; Nathan, Ran; Orrock, John L.; Turner, Jay R.; Brudvig, Lars A.; Haddad, Nick M.; Levey, Douglas J.; Tewksbury, Joshua J.

2014-01-01

Determining how widespread human-induced changes such as habitat loss, landscape fragmentation, and climate instability affect populations, communities, and ecosystems is one of the most pressing environmental challenges. Critical to this challenge is understanding how these changes are affecting the movement abilities and dispersal trajectories of organisms and what role conservation planning can play in promoting movement among remaining fragments of suitable habitat. Whereas evidence is mounting for how conservation strategies such as corridors impact animal movement, virtually nothing is known for species dispersed by wind, which are often mistakenly assumed to not be limited by dispersal. Here, we combine mechanistic dispersal models, wind measurements, and seed releases in a large-scale experimental landscape to show that habitat corridors affect wind dynamics and seed dispersal by redirecting and bellowing airflow and by increasing the likelihood of seed uplift. Wind direction interacts with landscape orientation to determine when corridors provide connectivity. Our results predict positive impacts of connectivity and patch shape on species richness of wind-dispersed plants, which we empirically illustrate using 12 y of data from our experimental landscapes. We conclude that habitat fragmentation and corridors strongly impact the movement of wind-dispersed species, which has community-level consequences. PMID:24567398

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

PubMed

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

2015-03-01

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

How fragmentation and corridors affect wind dynamics and seed dispersal in open habitats.

PubMed

Damschen, Ellen I; Baker, Dirk V; Bohrer, Gil; Nathan, Ran; Orrock, John L; Turner, Jay R; Brudvig, Lars A; Haddad, Nick M; Levey, Douglas J; Tewksbury, Joshua J

2014-03-04

Determining how widespread human-induced changes such as habitat loss, landscape fragmentation, and climate instability affect populations, communities, and ecosystems is one of the most pressing environmental challenges. Critical to this challenge is understanding how these changes are affecting the movement abilities and dispersal trajectories of organisms and what role conservation planning can play in promoting movement among remaining fragments of suitable habitat. Whereas evidence is mounting for how conservation strategies such as corridors impact animal movement, virtually nothing is known for species dispersed by wind, which are often mistakenly assumed to not be limited by dispersal. Here, we combine mechanistic dispersal models, wind measurements, and seed releases in a large-scale experimental landscape to show that habitat corridors affect wind dynamics and seed dispersal by redirecting and bellowing airflow and by increasing the likelihood of seed uplift. Wind direction interacts with landscape orientation to determine when corridors provide connectivity. Our results predict positive impacts of connectivity and patch shape on species richness of wind-dispersed plants, which we empirically illustrate using 12 y of data from our experimental landscapes. We conclude that habitat fragmentation and corridors strongly impact the movement of wind-dispersed species, which has community-level consequences.

Application of Spaceborne Scatterometer for Mapping Freeze-Thaw State in Northern Landscapes as a Measure of Ecological and Hydrological Processes

NASA Technical Reports Server (NTRS)

McDonald, Kyle; Kimball, John; Zimmermann, Reiner; Way, JoBea; Frolking, Steve; Running, Steve

1994-01-01

Landscape freeze/thaw transitions coincide with marked shifts in albedo, surface energy and mass exchange, and associated snow dynamics. monitoring landscape freeze/thaw dynamics would improve our ability to quantify the interannual variability of boreal hydrology and river runoff/flood dynamics, The annual duration of frost-free period also bounds the period of photosynthetic activity in borel and arctic regions thus affecting the carbon budget and the interannual variability fo regional carbon fluxes.

Landscape Pattern Determines Neighborhood Size and Structure within a Lizard Population

PubMed Central

Ryberg, Wade A.; Hill, Michael T.; Painter, Charles W.; Fitzgerald, Lee A.

2013-01-01

Although defining population structure according to discrete habitat patches is convenient for metapopulation theories, taking this approach may overlook structure within populations continuously distributed across landscapes. For example, landscape features within habitat patches direct the movement of organisms and define the density distribution of individuals, which can generate spatial structure and localized dynamics within populations as well as among them. Here, we use the neighborhood concept, which describes population structure relative to the scale of individual movements, to illustrate how localized dynamics within a population of lizards (Sceloporus arenicolus) arise in response to variation in landscape pattern within a continuous habitat patch. Our results emphasize links between individual movements at small scales and the emergence of spatial structure within populations which resembles metapopulation dynamics at larger scales. We conclude that population dynamics viewed in a landscape context must consider the explicit distribution and movement of individuals within continuous habitat as well as among habitat patches. PMID:23441217

The movement ecology and dynamics of plant communities in fragmented landscapes

DOE PAGES

Damschen, Ellen I.; Brudvig, Lars A.; Haddad, Nick M.; ...

2008-12-05

A conceptual model of movement ecology has recently been advanced to explain all movement by considering the interaction of four elements: internal state, motion capacity, navigation capacities,and external factors. We modified this framework togenerate predictions for species richness dynamics of fragmented plant communities and tested them in experimental landscapes across a 7-year time series. We found that two external factors, dispersal vectors and habitat features, affected species colonization and recolonization in habitat fragments and their effects varied and depended on motion capacity. Bird-dispersed species richness showed connectivity effects that reached an asymptote over time, but no edge effects, whereas wind-dispersedmore » species richness showed steadily accumulating edge and connectivity effects, with no indication of an asymptote. Unassisted species also showed increasing differences caused by connectivity over time,whereas edges had no effect. Our limited use of proxies for movement ecology (e.g., dispersal mode as a proxy for motion capacity) resulted in moderate predictive power for communities and, in some cases, highlighted the importance of a more complete understanding of movement ecology for predicting how landscape conservation actions affect plant community dynamics.« less

Social network models predict movement and connectivity in ecological landscapes

USGS Publications Warehouse

Fletcher, R.J.; Acevedo, M.A.; Reichert, Brian E.; Pias, Kyle E.; Kitchens, W.M.

2011-01-01

Network analysis is on the rise across scientific disciplines because of its ability to reveal complex, and often emergent, patterns and dynamics. Nonetheless, a growing concern in network analysis is the use of limited data for constructing networks. This concern is strikingly relevant to ecology and conservation biology, where network analysis is used to infer connectivity across landscapes. In this context, movement among patches is the crucial parameter for interpreting connectivity but because of the difficulty of collecting reliable movement data, most network analysis proceeds with only indirect information on movement across landscapes rather than using observed movement to construct networks. Statistical models developed for social networks provide promising alternatives for landscape network construction because they can leverage limited movement information to predict linkages. Using two mark-recapture datasets on individual movement and connectivity across landscapes, we test whether commonly used network constructions for interpreting connectivity can predict actual linkages and network structure, and we contrast these approaches to social network models. We find that currently applied network constructions for assessing connectivity consistently, and substantially, overpredict actual connectivity, resulting in considerable overestimation of metapopulation lifetime. Furthermore, social network models provide accurate predictions of network structure, and can do so with remarkably limited data on movement. Social network models offer a flexible and powerful way for not only understanding the factors influencing connectivity but also for providing more reliable estimates of connectivity and metapopulation persistence in the face of limited data.

Separation of Dynamics in the Free Energy Landscape

NASA Astrophysics Data System (ADS)

Ekimoto, Toru; Odagaki, Takashi; Yoshimori, Akira

2008-02-01

The dynamics of a representative point in a model free energy landscape (FEL) is analyzed by the Langevin equation with the FEL as the driving potential. From the detailed analysis of the generalized susceptibility, fast, slow and Johari-Goldstein (JG) processes are shown to be well described by the FEL. Namely, the fast process is determined by the stochastic motion confined in a basin of the FEL and the relaxation time is related to the curvature of the FEL at the bottom of the basin. The jump motion among basins gives rise to the slow relaxation whose relaxation time is determined by the distribution of the barriers in the FEL and the JG process is produced by weak modulation of the FEL.

Energy barriers, entropy barriers, and non-Arrhenius behavior in a minimal glassy model.

PubMed

Du, Xin; Weeks, Eric R

2016-06-01

We study glassy dynamics using a simulation of three soft Brownian particles confined to a two-dimensional circular region. If the circular region is large, the disks freely rearrange, but rearrangements are rarer for smaller system sizes. We directly measure a one-dimensional free-energy landscape characterizing the dynamics. This landscape has two local minima corresponding to the two distinct disk configurations, separated by a free-energy barrier that governs the rearrangement rate. We study several different interaction potentials and demonstrate that the free-energy barrier is composed of a potential-energy barrier and an entropic barrier. The heights of both of these barriers depend on temperature and system size, demonstrating how non-Arrhenius behavior can arise close to the glass transition.

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

NASA Astrophysics Data System (ADS)

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

2010-12-01

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

Evolution and Extinction Dynamics in Rugged Fitness Landscapes

NASA Astrophysics Data System (ADS)

Sibani, Paolo; Brandt, Michael; Alstrøm, Preben

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

Homogenization techniques for population dynamics in strongly heterogeneous landscapes.

PubMed

Yurk, Brian P; Cobbold, Christina A

2018-12-01

An important problem in spatial ecology is to understand how population-scale patterns emerge from individual-level birth, death, and movement processes. These processes, which depend on local landscape characteristics, vary spatially and may exhibit sharp transitions through behavioural responses to habitat edges, leading to discontinuous population densities. Such systems can be modelled using reaction-diffusion equations with interface conditions that capture local behaviour at patch boundaries. In this work we develop a novel homogenization technique to approximate the large-scale dynamics of the system. We illustrate our approach, which also generalizes to multiple species, with an example of logistic growth within a periodic environment. We find that population persistence and the large-scale population carrying capacity is influenced by patch residence times that depend on patch preference, as well as movement rates in adjacent patches. The forms of the homogenized coefficients yield key theoretical insights into how large-scale dynamics arise from the small-scale features.

Mapping sources, sinks, and connectivity using a simulation model of Northern Spotted Owls

EPA Science Inventory

This is a study of source-sink dynamics at a landscape scale. In conducting the study, we make use of a mature simulation model for the northern spotted owl (Strix occidentalis caurina) that was developed as part of the US Fish and Wildlife Service’s most recent recovery plannin...

Resource selection by an ectothermic predator in a dynamic thermal landscape

Treesearch

Andrew D. George; Grant M. Connette; Frank R. Thompson; John Faaborg

2017-01-01

Predicting the effects of global climate change on species interactions has remained difficult because there is a spatiotemporal mismatch between regional climate models and microclimates experienced by organisms. We evaluated resource selection in a predominant ectothermic predator using a modeling approach that permitted us to assess the importance of habitat...

Representing climate, disturbance, and vegetation interactions in landscape models

Treesearch

Robert E. Keane; Donald McKenzie; Donald A. Falk; Erica A.H. Smithwick; Carol Miller; Lara-Karena B. Kellogg

2015-01-01

The prospect of rapidly changing climates over the next century calls for methods to predict their effects on myriad, interactive ecosystem processes. Spatially explicit models that simulate ecosystem dynamics at fine (plant, stand) to coarse (regional, global) scales are indispensable tools for meeting this challenge under a variety of possible futures. A special...

A landscape based, systems dynamic model for assessing impacts of urban development on water quality for sustainable seagrass growth in Tampa Bay, Florida

EPA Science Inventory

We present an integrated assessment model to predict potential unintended consequences of urban development on the sustainability of seagrasses and preservation of ecosystem services, such as catchable fish, in Tampa Bay. Ecosystem services are those ecological functions and pro...

Spatial Stochastic Intracellular Kinetics: A Review of Modelling Approaches.

PubMed

Smith, Stephen; Grima, Ramon

2018-05-21

Models of chemical kinetics that incorporate both stochasticity and diffusion are an increasingly common tool for studying biology. The variety of competing models is vast, but two stand out by virtue of their popularity: the reaction-diffusion master equation and Brownian dynamics. In this review, we critically address a number of open questions surrounding these models: How can they be justified physically? How do they relate to each other? How do they fit into the wider landscape of chemical models, ranging from the rate equations to molecular dynamics? This review assumes no prior knowledge of modelling chemical kinetics and should be accessible to a wide range of readers.

Aging, memory, and nonhierarchical energy landscape of spin jam

PubMed Central

Samarakoon, Anjana; Sato, Taku J.; Chen, Tianran; Chern, Gai-Wei; Yang, Junjie; Klich, Israel; Sinclair, Ryan; Zhou, Haidong; Lee, Seung-Hun

2016-01-01

The notion of complex energy landscape underpins the intriguing dynamical behaviors in many complex systems ranging from polymers, to brain activity, to social networks and glass transitions. The spin glass state found in dilute magnetic alloys has been an exceptionally convenient laboratory frame for studying complex dynamics resulting from a hierarchical energy landscape with rugged funnels. Here, we show, by a bulk susceptibility and Monte Carlo simulation study, that densely populated frustrated magnets in a spin jam state exhibit much weaker memory effects than spin glasses, and the characteristic properties can be reproduced by a nonhierarchical landscape with a wide and nearly flat but rough bottom. Our results illustrate that the memory effects can be used to probe different slow dynamics of glassy materials, hence opening a window to explore their distinct energy landscapes. PMID:27698141

Robbing Peter to Pay Paul: Modeling the Dynamic Evolution of the Coastal Carbon Sink Across Multiple Landforms

NASA Astrophysics Data System (ADS)

Herbert, E. R.; Walters, D.; Windham-Myers, L.; Kirwan, M. L.

2016-12-01

Evaluating the strength and long-term stability of the coastal carbon sink requires a consideration of the spatial evolution of coastal landscapes in both the horizontal and vertical dimensions. We present a model of the transformation and burial of carbon along a bay-marsh-upland forest complex to explore the response of the coastal carbon sink to sea level rise (SLR) and anthropogenic activity. We establish a carbon mass-balance by coupling dynamic biogeochemically-based models of soil carbon burial in aquatic, intertidal, and upland environments with a physically-based model of marsh edge erosion, vertical growth and migration into adjacent uplands. The modeled increase in marsh vertical growth and carbon burial at moderate rates of sea level rise (3-10 mm/yr) is consistent with a synthesis of 219 field measurements of marsh carbon accumulation that show a significant (p<0.0001) positive correlation with local SLR rates. The model suggests that at moderate SLR rates in low topographic relief landscapes, net marsh expansion into upland forest concomitant with increased carbon burial rates are sufficient to mitigate the associated loss of forest carbon stocks. Coastlines with high relief or barriers to wetland migration can become sources of carbon through the erosion of buried carbon stocks, but we show that the recapture of eroded carbon through vertical growth can be an important mechanism for reducing carbon loss. Overall, we show that the coastal carbon balance must be evaluated in a landscape context to account for changes in the size and magnitude of both the stocks and sinks of marsh carbon and for the transfers of carbon between coastal habitats. These results may help inform current efforts to appraise coastal carbon sinks that are beset by issues of landscape heterogeneity and the provenance of buried carbon.

Wake Dynamics in the Atmospheric Boundary Layer Over Complex Terrain

NASA Astrophysics Data System (ADS)

Markfort, Corey D.

The goal of this research is to advance our understanding of atmospheric boundary layer processes over heterogeneous landscapes and complex terrain. The atmospheric boundary layer (ABL) is a relatively thin (˜ 1 km) turbulent layer of air near the earth's surface, in which most human activities and engineered systems are concentrated. Its dynamics are crucially important for biosphere-atmosphere couplings and for global atmospheric dynamics, with significant implications on our ability to predict and mitigate adverse impacts of land use and climate change. In models of the ABL, land surface heterogeneity is typically represented, in the context of Monin-Obukhov similarity theory, as changes in aerodynamic roughness length and surface heat and moisture fluxes. However, many real landscapes are more complex, often leading to massive boundary layer separation and wake turbulence, for which standard models fail. Trees, building clusters, and steep topography produce extensive wake regions currently not accounted for in models of the ABL. Wind turbines and wind farms also generate wakes that combine in complex ways to modify the ABL. Wind farms are covering an increasingly significant area of the globe and the effects of large wind farms must be included in regional and global scale models. Research presented in this thesis demonstrates that wakes caused by landscape heterogeneity must be included in flux parameterizations for momentum, heat, and mass (water vapor and trace gases, e.g. CO2 and CH4) in ABL simulation and prediction models in order to accurately represent land-atmosphere interactions. Accurate representation of these processes is crucial for the predictions of weather, air quality, lake processes, and ecosystems response to climate change. Objectives of the research reported in this thesis are: 1) to investigate turbulent boundary layer adjustment, turbulent transport and scalar flux in wind farms of varying configurations and develop an improved modeling framework for wind farm - atmosphere interaction, 2) to determine how heterogeneous patches of forest affect the structure of the ABL and its interactions with clearings and water bodies, 3) to investigate how landscape heterogeneity, including wakes, may be parameterized in regional-scale weather and climate models to improve the representation of surface fluxes, e.g. from lakes/wetlands and forest clearings. To achieve these objectives, this research employs an interdisciplinary strategy, utilizing concepts and methods from fluid mechanics, micrometeorology, ecosystem ecology and environmental sciences, and combines laboratory and field experiments. In particular, a) wind tunnel experiments of flow through and over model wind farms and model forest canopies were used to improve our fundamental understanding of how wakes affect land-atmosphere coupling, including surface fluxes, after wind farm installation and for heterogeneous landscapes of canopies and clearings or lakes, and b) extensive field studies over lakes and wetlands were undertaken to study the effects of wakes downwind of forest canopies and the effect of wind sheltering on lake stratification dynamics and gas fluxes. These experiments were also used to improve and validate numerical simulation techniques for the atmospheric boundary layer, specifically the large eddy simulation technique, which is used to simulate flow in wind farms and flow over heterogeneous terrain.

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.

Modeling vulnerability to thermokarst disturbance and its consequences on regional land cover dynamic in boreal Alaska

NASA Astrophysics Data System (ADS)

Genet, H.; Lara, M. J.; Bolton, W. R.; McGuire, A. D.

2016-12-01

Estimation of the magnitude and consequences of permafrost degradation in high latitude is one of the most urgent research challenges related to contemporary and future climate change. In addition to widespread vertical degradation, ice-rich permafrost can thaw laterally, often triggering abrupt subsidence of the ground surface called thermokart. In this depression, permafrost plateau vegetation will transition to wetlands or lakes, while surface water of the surrounding landscape may drain towards it. These abrupt changes in land cover and hydrology can have dramatic consequences from wildlife habitat and biogeochemical cycles. Although recent studies have documented an acceleration of the rates of thermokarst formation in boreal and arctic peatlands, the importance of thermokarst at the regional level is still poorly understood. To better understand the vulnerability of the landscape to thermokarst disturbance in Alaska, we developed the Alaska Thermokarst Model (ATM), a state-and-transition model designed to simulate land cover change associated with thermokarst disturbance. In boreal regions, the model simulates transitions from permafrost plateau forest to thermokarst lake, bog or fen, as a function of climate and fire dynamics, permafrost characteristics and physiographic information. This model is designed and parameterized based on existing literature and a new repeated imagery analysis we conducted in a major wetland complex in boreal Alaska. We will present simulation and validation of thermokarst dynamic and associated land cover change in two wetland complexes in boreal Alaska, from 2000 to 2100 for six climate scenarios associating three AR5 emission scenarios and two global circulation model simulations. By 2100, ATM is predicting decrease between 3.5 and 9.1 % in the extent of permafrost plateau forest, mostly to the benefit of thermokarst fen, and lake. This analysis allowed us to assess the importance of thermokarst dynamics and landscape evolution associated with permafrost thaw in vulnerable regions of boreal Alaska during the 21st century and could be used as a baseline for managers to incorporate projected land cover changes in designing land management strategies.

Modeling the impacts of phenological and inter-annual changes in landscape metrics on local biodiversity of agricultural lands of Eastern Ontario using multi-spatial and multi-temporal remote sensing data

NASA Astrophysics Data System (ADS)

Alavi-Shoushtari, N.; King, D.

2017-12-01

Agricultural landscapes are highly variable ecosystems and are home to many local farmland species. Seasonal, phenological and inter-annual agricultural landscape dynamics have potential to affect the richness and abundance of farmland species. Remote sensing provides data and techniques which enable monitoring landscape changes in multiple temporal and spatial scales. MODIS high temporal resolution remote sensing images enable detection of seasonal and phenological trends, while Landsat higher spatial resolution images, with its long term archive enables inter-annual trend analysis over several decades. The objective of this study to use multi-spatial and multi-temporal remote sensing data to model the response of farmland species to landscape metrics. The study area is the predominantly agricultural region of eastern Ontario. 92 sample landscapes were selected within this region using a protocol designed to maximize variance in composition and configuration heterogeneity while controlling for amount of forest and spatial autocorrelation. Two sample landscape extents (1×1km and 3×3km) were selected to analyze the impacts of spatial scale on biodiversity response. Gamma diversity index data for four taxa groups (birds, butterflies, plants, and beetles) were collected during the summers of 2011 and 2012 within the cropped area of each landscape. To extract the seasonal and phenological metrics a 2000-2012 MODIS NDVI time-series was used, while a 1985-2012 Landsat time-series was used to model the inter-annual trends of change in the sample landscapes. The results of statistical modeling showed significant relationships between farmland biodiversity for several taxa and the phenological and inter-annual variables. The following general results were obtained: 1) Among the taxa groups, plant and beetles diversity was most significantly correlated with the phenological variables; 2) Those phenological variables which are associated with the variability in the start of season date across the sample landscapes and the variability in the corresponding NDVI values at that date showed the strongest correlation with the biodiversity indices; 3) The significance of the models improved when using 3×3km site extent both for MODIS and Landsat based models due most likely to the larger sample size over 3x3km.

The Landlab v1.0 OverlandFlow component: a Python tool for computing shallow-water flow across watersheds

NASA Astrophysics Data System (ADS)

Adams, Jordan M.; Gasparini, Nicole M.; Hobley, Daniel E. J.; Tucker, Gregory E.; Hutton, Eric W. H.; Nudurupati, Sai S.; Istanbulluoglu, Erkan

2017-04-01

Representation of flowing water in landscape evolution models (LEMs) is often simplified compared to hydrodynamic models, as LEMs make assumptions reducing physical complexity in favor of computational efficiency. The Landlab modeling framework can be used to bridge the divide between complex runoff models and more traditional LEMs, creating a new type of framework not commonly used in the geomorphology or hydrology communities. Landlab is a Python-language library that includes tools and process components that can be used to create models of Earth-surface dynamics over a range of temporal and spatial scales. The Landlab OverlandFlow component is based on a simplified inertial approximation of the shallow water equations, following the solution of de Almeida et al.(2012). This explicit two-dimensional hydrodynamic algorithm simulates a flood wave across a model domain, where water discharge and flow depth are calculated at all locations within a structured (raster) grid. Here, we illustrate how the OverlandFlow component contained within Landlab can be applied as a simplified event-based runoff model and how to couple the runoff model with an incision model operating on decadal timescales. Examples of flow routing on both real and synthetic landscapes are shown. Hydrographs from a single storm at multiple locations in the Spring Creek watershed, Colorado, USA, are illustrated, along with a map of shear stress applied on the land surface by flowing water. The OverlandFlow component can also be coupled with the Landlab DetachmentLtdErosion component to illustrate how the non-steady flow routing regime impacts incision across a watershed. The hydrograph and incision results are compared to simulations driven by steady-state runoff. Results from the coupled runoff and incision model indicate that runoff dynamics can impact landscape relief and channel concavity, suggesting that, on landscape evolution timescales, the OverlandFlow model may lead to differences in simulated topography in comparison with traditional methods. The exploratory test cases described within demonstrate how the OverlandFlow component can be used in both hydrologic and geomorphic applications.

Urban growth and landscape connectivity threats assessment at Saguaro National Park, Arizona, USA

USGS Publications Warehouse

Perkl, Ryan; Norman, Laura M.; Mitchell, David; Feller, Mark R.; Smith, Garrett; Wilson, Natalie R.

2018-01-01

Urban and exurban expansion results in habitat and biodiversity loss globally. We hypothesize that a coupled-model approach could connect urban planning for future cities with landscape ecology to consider wildland habitat connectivity. Our work combines urban growth simulations with models of wildlife corridors to examine how species will be impacted by development to test this hypothesis. We leverage a land use change model (SLEUTH) with structural and functional landscape-connectivity modeling techniques to ascertain the spatial extent and locations of connectivity related threats to a national park in southern Arizona, USA, and describe how protected areas might be impacted by urban expansion. Results of projected growth significantly altered structural connectivity (80%) when compared to current (baseline) corridor conditions. Moreover, projected growth impacted functional connectivity differently amongst species, indicating resilience of some species and near-complete displacement of others. We propose that implementing a geospatial-design-based model will allow for a better understanding of the impacts management decisions have on wildlife populations. The application provides the potential to understand both human and environmental impacts of land-system dynamics, critical for long-term sustainability.

Variable flushing mechanisms and landscape structure control stream DOC export during snowmelt in a set of nested catchments

Treesearch

Vincent J. Pacific; Kelsey G. Jencso; Brian L. McGlynn

2010-01-01

Stream DOC dynamics during snowmelt have been the focus of much research, and numerous DOC mobilization and delivery mechanisms from riparian and upland areas have been proposed. However, landscape structure controls on DOC export from riparian and upland landscape elements remains poorly understood. We investigated stream and groundwater DOC dynamics across three...

Analytical approximation of a stochastic, spatial simulation model of fire and forest landscape dynamics

Treesearch

A.J. Tepley; E.A. Thomann

2012-01-01

Recent increases in computation power have prompted enormous growth in the use of simulation models in ecological research. These models are valued for their ability to account for much of the ecological complexity found in field studies, but this ability usually comes at the cost of losing transparency into how the models work. In order to foster greater understanding...

Importance of ecotone type to landscape dynamics at biome transition zones

USDA-ARS?s Scientific Manuscript database

Landscapes in biome transition zones consist of a mosaic of patches dominated or codominated by species from adjacent biomes. Shifts in the vegetation composition and dynamics of a biome transition zone depend upon the underlying patch dynamics of the ecotones between these dominant species. Landsc...

Predictors of breeding site occupancy by amphibians in montane landscapes

USGS Publications Warehouse

Groff, Luke A.; Loftin, Cynthia S.; Calhoun, Aram J.K.

2017-01-01

Ecological relationships and processes vary across species’ geographic distributions, life stages and spatial, and temporal scales. Montane landscapes are characterized by low wetland densities, rugged topographies, and cold climates. Consequently, aquatic-dependent and low-vagility ectothermic species (e.g., pool-breeding amphibians) may exhibit unique ecological associations in montane landscapes. We evaluated the relative importance of breeding- and landscape-scale features associated with spotted salamander (Ambystoma maculatum) and wood frog (Lithobates sylvaticus) wetland occupancy in Maine's Upper Montane-Alpine Zone ecoregion, and we determined whether models performed better when the inclusive landscape-scale covariates were estimated with topography-weighted or circular buffers. We surveyed 135 potential breeding sites during May 2013–June 2014 and evaluated environmental relationships with multi-season implicit dynamics occupancy models. Breeding site occupancy by both species was influenced solely by breeding-scale habitat features. Spotted salamander occupancy probabilities increased with previous or current beaver (Castor canadensis) presence, and models generally were better supported when the inclusive landscape-scale covariates were estimated with topography-weighted rather than circular buffers. Wood frog occupancy probabilities increased with site area and percent shallows, but neither buffer type was better supported than the other. Model rank order and support varied between buffer types, but model inferences did not. Our results suggest pool-breeding amphibian conservation in montane Maine include measures to maintain beaver populations and large wetlands with proportionally large areas of shallows ≤1-m deep. Inconsistencies between our study and previous studies substantiate the value of region-specific research for augmenting species’ conservation management plans and suggest the application of out-of-region inferences may promote ineffective conservation. 

The interaction between land use change, sediment fluxes and carbon dynamics: evaluating an integrated soil-landscape model at the millennial time-scale.

NASA Astrophysics Data System (ADS)

Bouchoms, Samuel; Van Oost, Kristof; Vanacker, Veerle

2015-04-01

Soil-landscape modelling has received growing attention as it allows us to evaluate the interaction between earth surface and soil bio-physical processes. At the landscape scale, human-induced land use change has altered the balance between soil erosion and production, and largely modified sediment fluxes. Intensification in soil redistribution rates affects the interaction between soil chemical, physical and biological processes at the landscape scale. Here, we evaluate the SPEROS-LT model, a spatially explicit 3D model combining a dynamic representation of land use, soil erosion and deposition and the soil carbon cycle. We assess the impact of millennial-scale human-induced land use change on sediment fluxes and carbon dynamics in the Dijle catchement (central Belgium). The watershed has undergone a 3000 years continuous human-induced alteration of the vegetation covers for agricultural characterized by Our study is based on land use reconstructions for the last 3000 years, including massive deforestation for agriculture in Roman Times and the Middle Ages followed by urbanization in the last 150 years. Land use reconstructions rely on simple land use allocation rules based on slope gradients. SPEROS-LT is parametrized for erosion rates against available figures in the literature by changing the transport capacity and the transfer coefficient which defines the amount of flux transferred between different land uses. Carbon content profiles at steady state (i.e. without influence of erosion or deposition) are calibrated for each land use and for the first upper meter of soil by comparing modeled profiles to an averaged observed profiles in stable areas of the pedologic region. We present a model sensitivity analysis and a full validation of the predicted soil carbon storage (horizontally, i.e. in space, and vertically, i.e. with depth) using a large database of observational data. The results indicate (i) a good agreement of the erosion rates. Speros LT modeled erosion and export rates, both modern and averaged over the last millennium, fall into the published range. Mean erosion rate over the last 1000 years equals 4.6 t/ha over the entire catchment while the export rate is 1.2 t/ha. (ii) Carbon content in the erosion areas is well predicted for lower soil layers (from 20 to 80 cm) where no significant differences were found between observational and modeled C content. There is though a significant difference for the top soil where modeled mean is 0.92% compared to the 0.8% in observations. (iii) erosion and deposition's spatial patterns are relatively well represented: correspondence between erosion areas as extracted from the digital soil map and modeled erosion maps higher for slightly truncated areas than in high truncation areas (55% of the modeled erosions pixels correspond to a non-depositional area compared to 37%). Correspondence between the model and the soil map increases with the total deposition ranging from 19% to 30% Yet, the model overestimated the carbon content in depositional areas, where statistical differences between observed and modeled carbon amount were found for each soil layers. This indicates that other factors, not accounted for by the model, influence carbon turnover for these sites. They may have a different dynamic than eroding places, cycling carbon faster or transferring it quicker to higher depth. Overall, the results indicates that the model performs relatively well in predicting sediment fluxes and carbon amount on long time scale during transient simulation. They underline the importance of developing an integrated approach to understand the dynamic and interactions at the landscape scale.

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

USGS Publications Warehouse

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

2014-01-01

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

RESEARCH AREA 7.1: Exploring the Systematics of Controlling Quantum Phenomena

DTIC Science & Technology

2016-10-05

the bottom to the top of the landscape. Computational analyses for simple model quantum systems are performed to ascertain the relative abundance of...SECURITY CLASSIFICATION OF: This research is concerned with the theoretical and experimental control quantum dynamics phenomena. Advances include new...algorithms to accelerate quantum control as well as provide physical insights into the controlled dynamics. The latter research includes the

Using spatiotemporal statistical models to estimate animal abundance and infer ecological dynamics from survey counts

USGS Publications Warehouse

Conn, Paul B.; Johnson, Devin S.; Ver Hoef, Jay M.; Hooten, Mevin B.; London, Joshua M.; Boveng, Peter L.

2015-01-01

Ecologists often fit models to survey data to estimate and explain variation in animal abundance. Such models typically require that animal density remains constant across the landscape where sampling is being conducted, a potentially problematic assumption for animals inhabiting dynamic landscapes or otherwise exhibiting considerable spatiotemporal variation in density. We review several concepts from the burgeoning literature on spatiotemporal statistical models, including the nature of the temporal structure (i.e., descriptive or dynamical) and strategies for dimension reduction to promote computational tractability. We also review several features as they specifically relate to abundance estimation, including boundary conditions, population closure, choice of link function, and extrapolation of predicted relationships to unsampled areas. We then compare a suite of novel and existing spatiotemporal hierarchical models for animal count data that permit animal density to vary over space and time, including formulations motivated by resource selection and allowing for closed populations. We gauge the relative performance (bias, precision, computational demands) of alternative spatiotemporal models when confronted with simulated and real data sets from dynamic animal populations. For the latter, we analyze spotted seal (Phoca largha) counts from an aerial survey of the Bering Sea where the quantity and quality of suitable habitat (sea ice) changed dramatically while surveys were being conducted. Simulation analyses suggested that multiple types of spatiotemporal models provide reasonable inference (low positive bias, high precision) about animal abundance, but have potential for overestimating precision. Analysis of spotted seal data indicated that several model formulations, including those based on a log-Gaussian Cox process, had a tendency to overestimate abundance. By contrast, a model that included a population closure assumption and a scale prior on total abundance produced estimates that largely conformed to our a priori expectation. Although care must be taken to tailor models to match the study population and survey data available, we argue that hierarchical spatiotemporal statistical models represent a powerful way forward for estimating abundance and explaining variation in the distribution of dynamical populations.

Dynamics of Soil Organic Carbon and Microbial Biomass Carbon in Relation to Water Erosion and Tillage Erosion

PubMed Central

Xiaojun, Nie; Jianhui, Zhang; Zhengan, Su

2013-01-01

Dynamics of soil organic carbon (SOC) are associated with soil erosion, yet there is a shortage of research concerning the relationship between soil erosion, SOC, and especially microbial biomass carbon (MBC). In this paper, we selected two typical slope landscapes including gentle and steep slopes from the Sichuan Basin, China, and used the 137Cs technique to determine the effects of water erosion and tillage erosion on the dynamics of SOC and MBC. Soil samples for the determination of 137Cs, SOC, MBC and soil particle-size fractions were collected on two types of contrasting hillslopes. 137Cs data revealed that soil loss occurred at upper slope positions of the two landscapes and soil accumulation at the lower slope positions. Soil erosion rates as well as distribution patterns of the <0.002-mm clay shows that water erosion is the major process of soil redistribution in the gentle slope landscape, while tillage erosion acts as the dominant process of soil redistribution in the steep slope landscape. In gentle slope landscapes, both SOC and MBC contents increased downslope and these distribution patterns were closely linked to soil redistribution rates. In steep slope landscapes, only SOC contents increased downslope, dependent on soil redistribution. It is noticeable that MBC/SOC ratios were significantly lower in gentle slope landscapes than in steep slope landscapes, implying that water erosion has a negative effect on the microbial biomass compared with tillage erosion. It is suggested that MBC dynamics are closely associated with soil redistribution by water erosion but independent of that by tillage erosion, while SOC dynamics are influenced by soil redistribution by both water erosion and tillage erosion. PMID:23717530

Studying the effects of fuel treatment based on burn probability on a boreal forest landscape.

PubMed

Liu, Zhihua; Yang, Jian; He, Hong S

2013-01-30

Fuel treatment is assumed to be a primary tactic to mitigate intense and damaging wildfires. However, how to place treatment units across a landscape and assess its effectiveness is difficult for landscape-scale fuel management planning. In this study, we used a spatially explicit simulation model (LANDIS) to conduct wildfire risk assessments and optimize the placement of fuel treatments at the landscape scale. We first calculated a baseline burn probability map from empirical data (fuel, topography, weather, and fire ignition and size data) to assess fire risk. We then prioritized landscape-scale fuel treatment based on maps of burn probability and fuel loads (calculated from the interactions among tree composition, stand age, and disturbance history), and compared their effects on reducing fire risk. The burn probability map described the likelihood of burning on a given location; the fuel load map described the probability that a high fuel load will accumulate on a given location. Fuel treatment based on the burn probability map specified that stands with high burn probability be treated first, while fuel treatment based on the fuel load map specified that stands with high fuel loads be treated first. Our results indicated that fuel treatment based on burn probability greatly reduced the burned area and number of fires of different intensities. Fuel treatment based on burn probability also produced more dispersed and smaller high-risk fire patches and therefore can improve efficiency of subsequent fire suppression. The strength of our approach is that more model components (e.g., succession, fuel, and harvest) can be linked into LANDIS to map the spatially explicit wildfire risk and its dynamics to fuel management, vegetation dynamics, and harvesting. Copyright © 2012 Elsevier Ltd. All rights reserved.

Carrot or stick? Modelling how landowner behavioural responses can cause incentive-based forest governance to backfire.

PubMed

Henderson, Kirsten A; Anand, Madhur; Bauch, Chris T

2013-01-01

Mitigating the negative impacts of declining worldwide forest cover remains a significant socio-ecological challenge, due to the dominant role of human decision-making. Here we use a Markov chain model of land-use dynamics to examine the impact of governance on forest cover in a region. Each land parcel can be either forested or barren (deforested), and landowners decide whether to deforest their parcel according to perceived value (utility). We focus on three governance strategies: yearly incentive for conservation, one-time penalty for deforestation and one-time incentive for reforestation. The incentive and penalty are incorporated into the expected utility of forested land, which decreases the net gain of deforestation. By analyzing the equilibrium and stability of the landscape dynamics, we observe four possible outcomes: a stationary-forested landscape, a stationary-deforested landscape, an unstable landscape fluctuating near the equilibrium, and a cyclic-forested landscape induced by synchronized deforestation. We find that the two incentive-based strategies often result in highly fluctuating forest cover over decadal time scales or longer, and in a few cases, reforestation incentives actually decrease the average forest cover. In contrast, a penalty for deforestation results in the stable persistence of forest cover (generally >30%). The idea that larger conservation incentives will always yield higher and more stable forest cover is not supported in our findings. The decision to deforest is influenced by more than a simple, "rational" cost-benefit analysis: social learning and myopic, stochastic decision-making also have important effects. We conclude that design of incentive programs may need to account for potential counter-productive long-term effects due to behavioural feedbacks.

Time series evaluation of landscape dynamics using annual Landsat imagery and spatial statistical modeling: Evidence from the Phoenix metropolitan region

NASA Astrophysics Data System (ADS)

Fan, Chao; Myint, Soe W.; Rey, Sergio J.; Li, Wenwen

2017-06-01

Urbanization is a natural and social process involving simultaneous changes to the Earth's land systems, energy flow, demographics, and the economy. Understanding the spatiotemporal pattern of urbanization is increasingly important for policy formulation, decision making, and natural resource management. A combination of satellite remote sensing and patch-based models has been widely adopted to characterize landscape changes at various spatial and temporal scales. Nevertheless, the validity of this type of framework in identifying long-term changes, especially subtle or gradual land modifications is seriously challenged. In this paper, we integrate annual image time series, continuous spatial indices, and non-parametric trend analysis into a spatiotemporal study of landscape dynamics over the Phoenix metropolitan area from 1991 to 2010. We harness local indicators of spatial dependence and modified Mann-Kendall test to describe the monotonic trends in the quantity and spatial arrangement of two important land use land cover types: vegetation and built-up areas. Results suggest that declines in vegetation and increases in built-up areas are the two prevalent types of changes across the region. Vegetation increases mostly occur at the outskirts where new residential areas are developed from natural desert. A sizable proportion of vegetation declines and built-up increases are seen in the central and southeast part. Extensive land conversion from agricultural fields into urban land use is one important driver of vegetation declines. The xeriscaping practice also contributes to part of vegetation loss and an increasingly heterogeneous landscape. The quantitative framework proposed in this study provides a pathway to effective landscape mapping and change monitoring from a spatial statistical perspective.

Landscape Ecology and Epidemiology of Malaria Associated with Rubber Plantations in Thailand: Integrated Approaches to Malaria Ecotoping

PubMed Central

Kaewwaen, Wuthichai

2015-01-01

The agricultural land use changes that are human-induced changes in agroforestry ecosystems and in physical environmental conditions contribute substantially to the potential risks for malaria transmission in receptive areas. Due to the pattern and extent of land use change, the risks or negatively ecosystemic outcomes are the results of the dynamics of malaria transmission, the susceptibility of human populations, and the geographical distribution of malaria vectors. This review focused basically on what are the potential effects of agricultural land use change as a result of the expansion of rubber plantations in Thailand and how significant the ecotopes of malaria-associated rubber plantations (MRP) are. More profoundly, this review synthesized the novel concepts and perspectives on applied landscape ecology and epidemiology of malaria, as well as approaches to determine the degree to which an MRP ecotope as fundamental landscape scale can establish malaria infection pocket(s). Malaria ecotoping encompasses the integrated approaches and tools applied to or used in modeling malaria transmission. The scalability of MRP ecotope depends upon its unique landscape structure as it is geographically associated with the infestation or reinfestation of Anopheles vectors, along with the attributes that are epidemiologically linked with the infections. The MRP ecotope can be depicted as the hotspot such that malaria transmission is modeled upon the MRP factors underlying human settlements and movement activities, health behaviors, land use/land cover change, malaria vector population dynamics, and agrienvironmental and climatic conditions. The systemic and uniform approaches to malaria ecotoping underpin the stratification of the potential risks for malaria transmission by making use of remotely sensed satellite imagery or landscape aerial photography using unmanned aerial vehicle (UAV), global positioning systems (GPS), and geographical information systems (GIS). PMID:25838822

Carrot or Stick? Modelling How Landowner Behavioural Responses Can Cause Incentive-Based Forest Governance to Backfire

PubMed Central

Henderson, Kirsten A.; Anand, Madhur; Bauch, Chris T.

2013-01-01

Mitigating the negative impacts of declining worldwide forest cover remains a significant socio-ecological challenge, due to the dominant role of human decision-making. Here we use a Markov chain model of land-use dynamics to examine the impact of governance on forest cover in a region. Each land parcel can be either forested or barren (deforested), and landowners decide whether to deforest their parcel according to perceived value (utility). We focus on three governance strategies: yearly incentive for conservation, one-time penalty for deforestation and one-time incentive for reforestation. The incentive and penalty are incorporated into the expected utility of forested land, which decreases the net gain of deforestation. By analyzing the equilibrium and stability of the landscape dynamics, we observe four possible outcomes: a stationary-forested landscape, a stationary-deforested landscape, an unstable landscape fluctuating near the equilibrium, and a cyclic-forested landscape induced by synchronized deforestation. We find that the two incentive-based strategies often result in highly fluctuating forest cover over decadal time scales or longer, and in a few cases, reforestation incentives actually decrease the average forest cover. In contrast, a penalty for deforestation results in the stable persistence of forest cover (generally >30%). The idea that larger conservation incentives will always yield higher and more stable forest cover is not supported in our findings. The decision to deforest is influenced by more than a simple, “rational” cost-benefit analysis: social learning and myopic, stochastic decision-making also have important effects. We conclude that design of incentive programs may need to account for potential counter-productive long-term effects due to behavioural feedbacks. PMID:24204942

Natural extension of fast-slow decomposition for dynamical systems

NASA Astrophysics Data System (ADS)

Rubin, J. E.; Krauskopf, B.; Osinga, H. M.

2018-01-01

Modeling and parameter estimation to capture the dynamics of physical systems are often challenging because many parameters can range over orders of magnitude and are difficult to measure experimentally. Moreover, selecting a suitable model complexity requires a sufficient understanding of the model's potential use, such as highlighting essential mechanisms underlying qualitative behavior or precisely quantifying realistic dynamics. We present an approach that can guide model development and tuning to achieve desired qualitative and quantitative solution properties. It relies on the presence of disparate time scales and employs techniques of separating the dynamics of fast and slow variables, which are well known in the analysis of qualitative solution features. We build on these methods to show how it is also possible to obtain quantitative solution features by imposing designed dynamics for the slow variables in the form of specified two-dimensional paths in a bifurcation-parameter landscape.

Evaluating coastal landscape response to sea-level rise in the northeastern United States: approach and methods

USGS Publications Warehouse

Lentz, Erika E.; Stippa, Sawyer R.; Thieler, E. Robert; Plant, Nathaniel G.; Gesch, Dean B.; Horton, Radley M.

2014-02-13

The U.S. Geological Survey is examining effects of future sea-level rise on the coastal landscape from Maine to Virginia by producing spatially explicit, probabilistic predictions using sea-level projections, vertical land movement rates (due to isostacy), elevation data, and land-cover data. Sea-level-rise scenarios used as model inputs are generated by using multiple sources of information, including Coupled Model Intercomparison Project Phase 5 models following representative concentration pathways 4.5 and 8.5 in the Intergovernmental Panel on Climate Change Fifth Assessment Report. A Bayesian network is used to develop a predictive coastal response model that integrates the sea-level, elevation, and land-cover data with assigned probabilities that account for interactions with coastal geomorphology as well as the corresponding ecological and societal systems it supports. The effects of sea-level rise are presented as (1) level of landscape submergence and (2) coastal response type characterized as either static (that is, inundation) or dynamic (that is, landform or landscape change). Results are produced at a spatial scale of 30 meters for four decades (the 2020s, 2030s, 2050s, and 2080s). The probabilistic predictions can be applied to landscape management decisions based on sea-level-rise effects as well as on assessments of the prediction uncertainty and need for improved data or fundamental understanding. This report describes the methods used to produce predictions, including information on input datasets; the modeling approach; model outputs; data-quality-control procedures; and information on how to access the data and metadata online.

Evaluating Coastal Landscape Response to Sea-Level Rise in the Northeastern United States - Approach and Methods

NASA Technical Reports Server (NTRS)

Lentz, Erika E.; Stippa, Sawyer R.; Thieler, E. Robert; Plant, Nathaniel G.; Gesch, Dean B.; Horton, Radley M.

2015-01-01

The U.S. Geological Survey is examining effects of future sea-level rise on the coastal landscape from Maine to Virginia by producing spatially explicit, probabilistic predictions using sea-level projections, vertical land movement rates (due to isostacy), elevation data, and land-cover data. Sea-level-rise scenarios used as model inputs are generated by using multiple sources of information, including Coupled Model Intercomparison Project Phase 5 models following representative concentration pathways 4.5 and 8.5 in the Intergovernmental Panel on Climate Change Fifth Assessment Report. A Bayesian network is used to develop a predictive coastal response model that integrates the sea-level, elevation, and land-cover data with assigned probabilities that account for interactions with coastal geomorphology as well as the corresponding ecological and societal systems it supports. The effects of sea-level rise are presented as (1) level of landscape submergence and (2) coastal response type characterized as either static (that is, inundation) or dynamic (that is, landform or landscape change). Results are produced at a spatial scale of 30 meters for four decades (the 2020s, 2030s, 2050s, and 2080s). The probabilistic predictions can be applied to landscape management decisions based on sea-level-rise effects as well as on assessments of the prediction uncertainty and need for improved data or fundamental understanding. This report describes the methods used to produce predictions, including information on input datasets; the modeling approach; model outputs; data-quality-control procedures; and information on how to access the data and metadata online.

Combining a dispersal model with network theory to assess habitat connectivity.

PubMed

Lookingbill, Todd R; Gardner, Robert H; Ferrari, Joseph R; Keller, Cherry E

2010-03-01

Assessing the potential for threatened species to persist and spread within fragmented landscapes requires the identification of core areas that can sustain resident populations and dispersal corridors that can link these core areas with isolated patches of remnant habitat. We developed a set of GIS tools, simulation methods, and network analysis procedures to assess potential landscape connectivity for the Delmarva fox squirrel (DFS; Sciurus niger cinereus), an endangered species inhabiting forested areas on the Delmarva Peninsula, USA. Information on the DFS's life history and dispersal characteristics, together with data on the composition and configuration of land cover on the peninsula, were used as input data for an individual-based model to simulate dispersal patterns of millions of squirrels. Simulation results were then assessed using methods from graph theory, which quantifies habitat attributes associated with local and global connectivity. Several bottlenecks to dispersal were identified that were not apparent from simple distance-based metrics, highlighting specific locations for landscape conservation, restoration, and/or squirrel translocations. Our approach links simulation models, network analysis, and available field data in an efficient and general manner, making these methods useful and appropriate for assessing the movement dynamics of threatened species within landscapes being altered by human and natural disturbances.

Multi-model comparison on the effects of climate change on tree species in the eastern U.S.: results from an enhanced niche model and process-based ecosystem and landscape models

Treesearch

Louis R. Iverson; Frank R. Thompson; Stephen Matthews; Matthew Peters; Anantha Prasad; William D. Dijak; Jacob Fraser; Wen J. Wang; Brice Hanberry; Hong He; Maria Janowiak; Patricia Butler; Leslie Brandt; Chris Swanston

2016-01-01

Context. Species distribution models (SDM) establish statistical relationships between the current distribution of species and key attributes whereas process-based models simulate ecosystem and tree species dynamics based on representations of physical and biological processes. TreeAtlas, which uses DISTRIB SDM, and Linkages and LANDIS PRO, process...

Impacts of Landscape Context on Patterns of Wind Downfall Damage in a Fragmented Amazonian Landscape

NASA Astrophysics Data System (ADS)

Schwartz, N.; Uriarte, M.; DeFries, R. S.; Gutierrez-Velez, V. H.; Fernandes, K.; Pinedo-Vasquez, M.

2015-12-01

Wind is a major disturbance in the Amazon and has both short-term impacts and lasting legacies in tropical forests. Observed patterns of damage across landscapes result from differences in wind exposure and stand characteristics, such as tree stature, species traits, successional age, and fragmentation. Wind disturbance has important consequences for biomass dynamics in Amazonian forests, and understanding the spatial distribution and size of impacts is necessary to quantify the effects on carbon dynamics. In November 2013, a mesoscale convective system was observed over the study area in Ucayali, Peru, a highly human modified and fragmented forest landscape. We mapped downfall damage associated with the storm in order to ask: how does the severity of damage vary within forest patches, and across forest patches of different sizes and successional ages? We applied spectral mixture analysis to Landsat images from 2013 and 2014 to calculate the change in non-photosynthetic vegetation fraction after the storm, and combined it with C-band SAR data from the Sentinel-1 satellite to predict downfall damage measured in 30 field plots using random forest regression. We then applied this model to map damage in forests across the study area. Using a land cover classification developed in a previous study, we mapped secondary and mature forest, and compared the severity of damage in the two. We found that damage was on average higher in secondary forests, but patterns varied spatially. This study demonstrates the utility of using multiple sources of satellite data for mapping wind disturbance, and adds to our understanding of the sources of variation in wind-related damage. Ultimately, an improved ability to map wind impacts and a better understanding of their spatial patterns can contribute to better quantification of carbon dynamics in Amazonian landscapes.

Energy landscape of LeuT from molecular simulations

NASA Astrophysics Data System (ADS)

Gur, Mert; Zomot, Elia; Cheng, Mary Hongying; Bahar, Ivet

2015-12-01

The bacterial sodium-coupled leucine transporter (LeuT) has been broadly used as a structural model for understanding the structure-dynamics-function of mammalian neurotransmitter transporters as well as other solute carriers that share the same fold (LeuT fold), as the first member of the family crystallographically resolved in multiple states: outward-facing open, outward-facing occluded, and inward-facing open. Yet, a complete picture of the energy landscape of (sub)states visited along the LeuT transport cycle has been elusive. In an attempt to visualize the conformational spectrum of LeuT, we performed extensive simulations of LeuT dimer dynamics in the presence of substrate (Ala or Leu) and co-transported Na+ ions, in explicit membrane and water. We used both conventional molecular dynamics (MD) simulations (with Anton supercomputing machine) and a recently introduced method, collective MD, that takes advantage of collective modes of motions predicted by the anisotropic network model. Free energy landscapes constructed based on ˜40 μs trajectories reveal multiple substates occluded to the extracellular (EC) and/or intracellular (IC) media, varying in the levels of exposure of LeuT to EC or IC vestibules. The IC-facing transmembrane (TM) helical segment TM1a shows an opening, albeit to a smaller extent and in a slightly different direction than that observed in the inward-facing open crystal structure. The study provides insights into the spectrum of conformational substates and paths accessible to LeuT and highlights the differences between Ala- and Leu-bound substates.

Energy landscape of LeuT from molecular simulations.

PubMed

Gur, Mert; Zomot, Elia; Cheng, Mary Hongying; Bahar, Ivet

2015-12-28

The bacterial sodium-coupled leucine transporter (LeuT) has been broadly used as a structural model for understanding the structure-dynamics-function of mammalian neurotransmitter transporters as well as other solute carriers that share the same fold (LeuT fold), as the first member of the family crystallographically resolved in multiple states: outward-facing open, outward-facing occluded, and inward-facing open. Yet, a complete picture of the energy landscape of (sub)states visited along the LeuT transport cycle has been elusive. In an attempt to visualize the conformational spectrum of LeuT, we performed extensive simulations of LeuT dimer dynamics in the presence of substrate (Ala or Leu) and co-transported Na(+) ions, in explicit membrane and water. We used both conventional molecular dynamics (MD) simulations (with Anton supercomputing machine) and a recently introduced method, collective MD, that takes advantage of collective modes of motions predicted by the anisotropic network model. Free energy landscapes constructed based on ∼40 μs trajectories reveal multiple substates occluded to the extracellular (EC) and/or intracellular (IC) media, varying in the levels of exposure of LeuT to EC or IC vestibules. The IC-facing transmembrane (TM) helical segment TM1a shows an opening, albeit to a smaller extent and in a slightly different direction than that observed in the inward-facing open crystal structure. The study provides insights into the spectrum of conformational substates and paths accessible to LeuT and highlights the differences between Ala- and Leu-bound substates.

Energy landscape of LeuT from molecular simulations

PubMed Central

Gur, Mert; Zomot, Elia; Cheng, Mary Hongying; Bahar, Ivet

2015-01-01

The bacterial sodium-coupled leucine transporter (LeuT) has been broadly used as a structural model for understanding the structure-dynamics-function of mammalian neurotransmitter transporters as well as other solute carriers that share the same fold (LeuT fold), as the first member of the family crystallographically resolved in multiple states: outward-facing open, outward-facing occluded, and inward-facing open. Yet, a complete picture of the energy landscape of (sub)states visited along the LeuT transport cycle has been elusive. In an attempt to visualize the conformational spectrum of LeuT, we performed extensive simulations of LeuT dimer dynamics in the presence of substrate (Ala or Leu) and co-transported Na+ ions, in explicit membrane and water. We used both conventional molecular dynamics (MD) simulations (with Anton supercomputing machine) and a recently introduced method, collective MD, that takes advantage of collective modes of motions predicted by the anisotropic network model. Free energy landscapes constructed based on ∼40 μs trajectories reveal multiple substates occluded to the extracellular (EC) and/or intracellular (IC) media, varying in the levels of exposure of LeuT to EC or IC vestibules. The IC-facing transmembrane (TM) helical segment TM1a shows an opening, albeit to a smaller extent and in a slightly different direction than that observed in the inward-facing open crystal structure. The study provides insights into the spectrum of conformational substates and paths accessible to LeuT and highlights the differences between Ala- and Leu-bound substates. PMID:26723619

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

Efficient Parallel Algorithms for Landscape Evolution Modelling

NASA Astrophysics Data System (ADS)

Moresi, L. N.; Mather, B.; Beucher, R.

2017-12-01

Landscape erosion and the deposition of sediments by river systems are strongly controlled bytopography, rainfall patterns, and the susceptibility of the basement to the action ofrunning water. It is well understood that each of these processes depends on the other, for example:topography results from active tectonic processes; deformation, metamorphosis andexhumation alter the competence of the basement; rainfall patterns depend on topography;uplift and subsidence in response to tectonic stress can be amplified by erosionand sediment deposition. We typically gain understanding of such coupled systems through forward models which capture theessential interactions of the various components and attempt parameterise those parts of the individual systemthat are unresolvable at the scale of the interaction. Here we address the problem of predicting erosion and deposition rates at a continental scalewith a resolution of tens to hundreds of metres in a dynamic, Lagrangian framework. This isa typical requirement for a code to interface with a mantle / lithosphere dynamics model anddemands an efficient, unstructured, parallel implementation. We address this through a very general algorithm that treats all parts of the landscape evolution equationsin sparse-matrix form including those for stream-flow accumulation, dam-filling and catchment determination. This givesus considerable flexibility in developing unstructured, parallel code, and in creating a modular packagethat can be configured by users to work at different temporal and spatial scales, but is also has potential advantagesin treating the non-linear parts of the problem in a general manner.

Dynamic response of the scenic beauty value of different forests to various thinning intensities in central eastern China.

PubMed

Deng, Songqiu; Yin, Na; Guan, Qingwei; Katoh, Masato

2014-11-01

Forest management has a significant influence on the preferences of people for forest landscapes. This study sought to evaluate the dynamic effects of thinning intensities on the landscape value of forests over time. Five typical stands in Wuxiangsi National Forest Park in Nanjing, China, were subjected to a thinning experiment designed with four intensities: unthinned, light thinning, moderate thinning, and heavy thinning. People's preferences for landscape photographs taken in plots under various thinning intensities were assessed through scenic beauty estimation (SBE) at 2 and 5 years after thinning. The differences in scenic beauty value between different thinning intensities were then analyzed with a paired samples t test for the two periods. The results indicated that the landscape value of all of the thinned plots significantly exceeded that of the unthinned plots 2 years after thinning (p < 0.01) and that the heavily thinned plots were most appreciated, showing an average improvement of 9.71 % compared with the control plots. Additionally, the heavily thinned plots were judged to be more beautiful than the lightly thinned and moderately thinned plots, whereas there was no significant difference between moderate thinning and light thinning. At 5 years after thinning, however, the moderately thinned plots received the highest preference scores among the four intensities, displaying an average improvement of 11.32 % compared with the unthinned plots. A multiple linear regression (MLR) model indicated that landscape value improved with increases in the average diameter at breast height (DBH) and with the improvement of environmental cleanliness in the stand, whereas the value decreased with an increasing stem density, species diversity, litter coverage, and canopy density. In addition, we found that the performance of a neural network model based on a multilayer perception (MLP) algorithm for predicting scenic beauty was slightly better than that of the MLR model. The findings of our study suggest that moderate to heavy thinning should be recommended to manage forests for the improvement of forest landscape value.

Multiple ecosystem services in a working landscape

PubMed Central

Eastburn, Danny J.; O’Geen, Anthony T.; Tate, Kenneth W.; Roche, Leslie M.

2017-01-01

Policy makers and practitioners are in need of useful tools and models for assessing ecosystem service outcomes and the potential risks and opportunities of ecosystem management options. We utilize a state-and-transition model framework integrating dynamic soil and vegetation properties to examine multiple ecosystem services—specifically agricultural production, biodiversity and habitat, and soil health—across human created vegetation states in a managed oak woodland landscape in a Mediterranean climate. We found clear tradeoffs and synergies in management outcomes. Grassland states maximized agricultural productivity at a loss of soil health, biodiversity, and other ecosystem services. Synergies existed among multiple ecosystem services in savanna and woodland states with significantly larger nutrient pools, more diversity and native plant richness, and less invasive species. This integrative approach can be adapted to a diversity of working landscapes to provide useful information for science-based ecosystem service valuations, conservation decision making, and management effectiveness assessments. PMID:28301475

Understanding soft glassy materials using an energy landscape approach

NASA Astrophysics Data System (ADS)

Hwang, Hyun Joo; Riggleman, Robert A.; Crocker, John C.

2016-09-01

Many seemingly different soft materials--such as soap foams, mayonnaise, toothpaste and living cells--display strikingly similar viscoelastic behaviour. A fundamental physical understanding of such soft glassy rheology and how it can manifest in such diverse materials, however, remains unknown. Here, by using a model soap foam consisting of compressible spherical bubbles, whose sizes slowly evolve and whose collective motion is simply dictated by energy minimization, we study the foam's dynamics as it corresponds to downhill motion on an energy landscape function spanning a high-dimensional configuration space. We find that these downhill paths, when viewed in this configuration space, are, surprisingly, fractal. The complex behaviour of our model, including power-law rheology and non-diffusive bubble motion and avalanches, stems directly from the fractal dimension and energy function of these paths. Our results suggest that ubiquitous soft glassy rheology may be a consequence of emergent fractal geometry in the energy landscapes of many complex fluids.

Multiple ecosystem services in a working landscape.

PubMed

Eastburn, Danny J; O'Geen, Anthony T; Tate, Kenneth W; Roche, Leslie M

2017-01-01

Policy makers and practitioners are in need of useful tools and models for assessing ecosystem service outcomes and the potential risks and opportunities of ecosystem management options. We utilize a state-and-transition model framework integrating dynamic soil and vegetation properties to examine multiple ecosystem services-specifically agricultural production, biodiversity and habitat, and soil health-across human created vegetation states in a managed oak woodland landscape in a Mediterranean climate. We found clear tradeoffs and synergies in management outcomes. Grassland states maximized agricultural productivity at a loss of soil health, biodiversity, and other ecosystem services. Synergies existed among multiple ecosystem services in savanna and woodland states with significantly larger nutrient pools, more diversity and native plant richness, and less invasive species. This integrative approach can be adapted to a diversity of working landscapes to provide useful information for science-based ecosystem service valuations, conservation decision making, and management effectiveness assessments.

Free-energy landscape of a hyperstable RNA tetraloop.

PubMed

Miner, Jacob C; Chen, Alan A; García, Angel E

2016-06-14

We report the characterization of the energy landscape and the folding/unfolding thermodynamics of a hyperstable RNA tetraloop obtained through high-performance molecular dynamics simulations at microsecond timescales. Sampling of the configurational landscape is conducted using temperature replica exchange molecular dynamics over three isochores at high, ambient, and negative pressures to determine the thermodynamic stability and the free-energy landscape of the tetraloop. The simulations reveal reversible folding/unfolding transitions of the tetraloop into the canonical A-RNA conformation and the presence of two alternative configurations, including a left-handed Z-RNA conformation and a compact purine Triplet. Increasing hydrostatic pressure shows a stabilizing effect on the A-RNA conformation and a destabilization of the left-handed Z-RNA. Our results provide a comprehensive description of the folded free-energy landscape of a hyperstable RNA tetraloop and highlight the significant advances of all-atom molecular dynamics in describing the unbiased folding of a simple RNA secondary structure motif.

OpenFLUID: an open-source software environment for modelling fluxes in landscapes

NASA Astrophysics Data System (ADS)

Fabre, Jean-Christophe; Rabotin, Michaël; Crevoisier, David; Libres, Aline; Dagès, Cécile; Moussa, Roger; Lagacherie, Philippe; Raclot, Damien; Voltz, Marc

2013-04-01

Integrative landscape functioning has become a common concept in environmental management. Landscapes are complex systems where many processes interact in time and space. In agro-ecosystems, these processes are mainly physical processes, including hydrological-processes, biological processes and human activities. Modelling such systems requires an interdisciplinary approach, coupling models coming from different disciplines, developed by different teams. In order to support collaborative works, involving many models coupled in time and space for integrative simulations, an open software modelling platform is a relevant answer. OpenFLUID is an open source software platform for modelling landscape functioning, mainly focused on spatial fluxes. It provides an advanced object-oriented architecture allowing to i) couple models developed de novo or from existing source code, and which are dynamically plugged to the platform, ii) represent landscapes as hierarchical graphs, taking into account multi-scale, spatial heterogeneities and landscape objects connectivity, iii) run and explore simulations in many ways : using the OpenFLUID software interfaces for users (command line interface, graphical user interface), or using external applications such as GNU R through the provided ROpenFLUID package. OpenFLUID is developed in C++ and relies on open source libraries only (Boost, libXML2, GLib/GTK, OGR/GDAL, …). For modelers and developers, OpenFLUID provides a dedicated environment for model development, which is based on an open source toolchain, including the Eclipse editor, the GCC compiler and the CMake build system. OpenFLUID is distributed under the GPLv3 open source license, with a special exception allowing to plug existing models licensed under any license. It is clearly in the spirit of sharing knowledge and favouring collaboration in a community of modelers. OpenFLUID has been involved in many research applications, such as modelling of hydrological network transfer, diagnosis and prediction of water quality taking into account human activities, study of the effect of spatial organization on hydrological fluxes, modelling of surface-subsurface water exchanges, … At LISAH research unit, OpenFLUID is the supporting development platform of the MHYDAS model, which is a distributed model for agrosystems (Moussa et al., 2002, Hydrological Processes, 16, 393-412). OpenFLUID web site : http://www.openfluid-project.org

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.

The effect of heterogeneous landscape dynamics on ecotone types at two convergent semi-arid biomes

USDA-ARS?s Scientific Manuscript database

Landscapes in biome transition zones consist of a mosaic of patches dominated or codominated by species from adjacent biomes. Shifts in the vegetation composition and dynamics of a biome transition zone depend upon the underlying patch dynamics of the ecotones between these dominant species. Landsca...

A Transient Landscape: Geospatial Analysis and Numerical Modeling of Coastal Geomorphology in the Outer Banks, North Carolina

NASA Astrophysics Data System (ADS)

Hardin, Eric Jon

Coastal landscapes can be relentlessly dynamic---owing to wave energy, tidal cycles, extreme weather events, and perpetual coastal winds. In these settings, the ever-changing landscape can threaten assets and infrastructure, necessitating costly measures to mitigate associated risks and to repair or maintain the changing landscape. Mapping and monitoring of terrain change, identification of areas susceptible to dramatic change, and understanding the processes that drive landscape change are critical for the development of responsible coastal management strategies and policies. Over the past two decades, LiDAR mapping has been conducted along the U.S. east coast (including the Outer Banks, North Carolina) on a near annual basis---generating a rich time series of topographic data with unprecedented accuracy, resolution, and extent. This time series has captured the response of the landscape to episodic storms, daily forcing of wind and waves, and anthropogenic activities. This work presents raster-based geospatial techniques developed to gain new insights into coastal geomorphology from the time series of available LiDAR. Per-cell statistical techniques derive information that is typically not obtained through the techniques traditionally employed by coastal scientists and engineers. Application of these techniques to study sites along the Outer Banks, NC, revealed substantial spatial and temporal variations in terrain change. Additionally, they identify the foredunes as being the most geomorphologically dynamic coastal features. In addition to per-cell statistical analysis, an approach is presented for the extraction of the dune ridge and dune toe (two features that are essential to standard vulnerability assessment). The approach employs a novel application of least cost path analysis and a physics-based model of an elastic sheet. The spatially distributed nature of the approach achieves a high level of automation and repeatability that semi-automated methods and manual digitization lack. Furthermore, the approach can be fully implemented with standard Geographic Information System (GIS) functionality, resulting in efficiency and ease of implementation. With this approach, a raster-based implementation of the U.S. Geological Survey (USGS) storm impact scale (designed to assess storm vulnerability of barrier islands) was developed. Vulnerability of 4km of the Outer Banks to Hurricane Isabel (2003) was assessed. The demonstrated approach produced vulnerability mapping at the high resolution of the input Digital Elevation Model (DEM)---providing results at the scale needed for local management, in contrast to the USGS approach, which is designed for continental scale vulnerability assessment. However, geospatial techniques cannot fully explain the observed geomorphology. Therefore, we present the Smoothed Particle Hydrodynamics (SPH) implementation of the Sauermann model for wind-driven sand transport. The SPH implementation enables the full nonlinearity of the model to be applied to complex scenarios that are typical of coastal landscapes. Through application of the SPH model and Computational Fluid Dynamics (CFD) modeling of the windborne surface shear stress (which drives sand transport), we present the sediment flux at two study sites along the Outer Banks. Scenarios were tested that involved steady-state surface shear stress as well as scenarios with intermittent variations in the surface shear stress. Results showed that intermittency in the surface shear stress has the potential to greatly influence the resulting flux. However, the degree to which intermittency does alter the flux is highly dependent on wind characteristics and wind direction relative to the orientation of salient topographic features.

Hessian eigenvalue distribution in a random Gaussian landscape

NASA Astrophysics Data System (ADS)

Yamada, Masaki; Vilenkin, Alexander

2018-03-01

The energy landscape of multiverse cosmology is often modeled by a multi-dimensional random Gaussian potential. The physical predictions of such models crucially depend on the eigenvalue distribution of the Hessian matrix at potential minima. In particular, the stability of vacua and the dynamics of slow-roll inflation are sensitive to the magnitude of the smallest eigenvalues. The Hessian eigenvalue distribution has been studied earlier, using the saddle point approximation, in the leading order of 1/ N expansion, where N is the dimensionality of the landscape. This approximation, however, is insufficient for the small eigenvalue end of the spectrum, where sub-leading terms play a significant role. We extend the saddle point method to account for the sub-leading contributions. We also develop a new approach, where the eigenvalue distribution is found as an equilibrium distribution at the endpoint of a stochastic process (Dyson Brownian motion). The results of the two approaches are consistent in cases where both methods are applicable. We discuss the implications of our results for vacuum stability and slow-roll inflation in the landscape.

A 'Turing' Test for Landscape Evolution Models

NASA Astrophysics Data System (ADS)

Parsons, A. J.; Wise, S. M.; Wainwright, J.; Swift, D. A.

2008-12-01

Resolving the interactions among tectonics, climate and surface processes at long timescales has benefited from the development of computer models of landscape evolution. However, testing these Landscape Evolution Models (LEMs) has been piecemeal and partial. We argue that a more systematic approach is required. What is needed is a test that will establish how 'realistic' an LEM is and thus the extent to which its predictions may be trusted. We propose a test based upon the Turing Test of artificial intelligence as a way forward. In 1950 Alan Turing posed the question of whether a machine could think. Rather than attempt to address the question directly he proposed a test in which an interrogator asked questions of a person and a machine, with no means of telling which was which. If the machine's answer could not be distinguished from those of the human, the machine could be said to demonstrate artificial intelligence. By analogy, if an LEM cannot be distinguished from a real landscape it can be deemed to be realistic. The Turing test of intelligence is a test of the way in which a computer behaves. The analogy in the case of an LEM is that it should show realistic behaviour in terms of form and process, both at a given moment in time (punctual) and in the way both form and process evolve over time (dynamic). For some of these behaviours, tests already exist. For example there are numerous morphometric tests of punctual form and measurements of punctual process. The test discussed in this paper provides new ways of assessing dynamic behaviour of an LEM over realistically long timescales. However challenges remain in developing an appropriate suite of challenging tests, in applying these tests to current LEMs and in developing LEMs that pass them.

Biomorphodynamics: Physical-biological feedbacks that shape landscapes

USGS Publications Warehouse

Murray, A.B.; Knaapen, M.A.F.; Tal, M.; Kirwan, M.L.

2008-01-01

Plants and animals affect morphological evolution in many environments. The term "ecogeomorphology" describes studies that address such effects. In this opinion article we use the term "biomorphodynamics" to characterize a subset of ecogeomorphologic studies: those that investigate not only the effects of organisms on physical processes and morphology but also how the biological processes depend on morphology and physical forcing. The two-way coupling precipitates feedbacks, leading to interesting modes of behavior, much like the coupling between flow/sediment transport and morphology leads to rich morphodynamic behaviors. Select examples illustrate how even the basic aspects of some systems cannot be understood without considering biomorphodynamic coupling. Prominent examples include the dynamic interactions between vegetation and flow/sediment transport that can determine river channel patterns and the multifaceted biomorphodynamic feedbacks shaping tidal marshes and channel networks. These examples suggest that the effects of morphology and physical processes on biology tend to operate over the timescale of the evolution of the morphological pattern. Thus, in field studies, which represent a snapshot in the pattern evolution, these effects are often not as obvious as the effects of biology on physical processes. However, numerical modeling indicates that the influences on biology from physical processes can play a key role in shaping landscapes and that even local and temporary vegetation disturbances can steer large-scale, long-term landscape evolution. The prevalence of biomorphodynamic research is burgeoning in recent years, driven by societal need and a confluence of complex systems-inspired modeling approaches in ecology and geomorphology. To make fundamental progress in understanding the dynamics of many landscapes, our community needs to increasingly learn to look for two-way, biomorphodynamic feedbacks and to collect new types of data to support the modeling of such emergent interactions. Copyright 2008 by the American Geophysical Union.

Assessing Potential Future Carbon Dynamics with Climate Change and Fire Management in a Mountainous Landscape on the Olympic Peninsula, Washington, USA

NASA Astrophysics Data System (ADS)

Kennedy, R. S.

2010-12-01

Forests of the mountainous landscapes of the maritime Pacific Northwestern USA may have high carbon sequestration potential via their high productivity and moderate to infrequent fire regimes. With climate change, there may be shifts in incidence and severity of fire, especially in the drier areas of the region, via changes to forest productivity and hydrology, and consequent effects to C sequestration and forest structure. To explore this issue, I assessed potential effects of fire management (little fire suppression/wildland fire management/highly effective fire suppression) under two climate change scenarios on future C sequestration dynamics (amounts and spatial pattern) in Olympic National Park, WA, over a 500-year simulation period. I used the simulation platform FireBGCv2, which contains a mechanistic, individual tree succession model, a spatially explicit climate-based biophysical model that uses daily weather data, and a spatially explicit fire model incorporating ignition, spread, and effects on ecosystem components. C sequestration patterns varied over time and spatial and temporal patterns differed somewhat depending on the climate change scenario applied and the fire management methods employed. Under the more extreme climate change scenario with little fire suppression, fires were most frequent and severe and C sequestration decreased. General trends were similar under the more moderate climate change scenario, as compared to current climate, but spatial patterns differed. Both climate change scenarios under highly effective fire suppression showed about 50% of starting total C after the initial transition phase, whereas with 10% fire suppression both scenarios exhibited about 10% of starting amounts. Areas of the landscape that served as refugia for older forest under increasing frequency of high severity fire were also hotspots for C sequestration in a landscape experiencing increasing frequency of disturbance with climate change.

IMPORTANCE OF MOVEMENT VARIES IN STATIC AND DYNAMIC LANDSCAPES

EPA Science Inventory

The relative sensitivity of spatially explicit population models (SEPMs) to movement parameters is a topic of ongoing debate among theoretical ecologists. In this study, we add additional realism to this debate by examining a SEPM's sensitivity to dispersal ability in static vs....

Modeling apple snail population dynamics on the Everglades landscape

USGS Publications Warehouse

Darby, Phil; DeAngelis, Donald L.; Romañach, Stephanie; Suir, Kevin J.; Bridevaux, Joshua L.

2015-01-01

Comparisons of model output to empirical data indicate the need for more data to better understand, and eventually parameterize, several aspects of snail ecology in support of EverSnail. A primary value of EverSnail is its capacity to describe the relative response of snail abundance to alternative hydrologic scenarios considered for Everglades water management and restoration.

Fractal Landscape Algorithms for Environmental Simulations

NASA Astrophysics Data System (ADS)

Mao, H.; Moran, S.

2014-12-01

Natural science and geographical research are now able to take advantage of environmental simulations that more accurately test experimental hypotheses, resulting in deeper understanding. Experiments affected by the natural environment can benefit from 3D landscape simulations capable of simulating a variety of terrains and environmental phenomena. Such simulations can employ random terrain generation algorithms that dynamically simulate environments to test specific models against a variety of factors. Through the use of noise functions such as Perlin noise, Simplex noise, and diamond square algorithms, computers can generate simulations that model a variety of landscapes and ecosystems. This study shows how these algorithms work together to create realistic landscapes. By seeding values into the diamond square algorithm, one can control the shape of landscape. Perlin noise and Simplex noise are also used to simulate moisture and temperature. The smooth gradient created by coherent noise allows more realistic landscapes to be simulated. Terrain generation algorithms can be used in environmental studies and physics simulations. Potential studies that would benefit from simulations include the geophysical impact of flash floods or drought on a particular region and regional impacts on low lying area due to global warming and rising sea levels. Furthermore, terrain generation algorithms also serve as aesthetic tools to display landscapes (Google Earth), and simulate planetary landscapes. Hence, it can be used as a tool to assist science education. Algorithms used to generate these natural phenomena provide scientists a different approach in analyzing our world. The random algorithms used in terrain generation not only contribute to the generating the terrains themselves, but are also capable of simulating weather patterns.

No Future in the Past? The role of initial topography on landform evolution model predictions

NASA Astrophysics Data System (ADS)

Hancock, G. R.; Coulthard, T. J.; Lowry, J.

2014-12-01

Our understanding of earth surface processes is based on long-term empirical understandings, short-term field measurements as well as numerical models. In particular, numerical landscape evolution models (LEMs) have been developed which have the capability to capture a range of both surface (erosion and deposition), tectonics, as well as near surface or critical zone processes (i.e. pedogenesis). These models have a range of applications for understanding both surface and whole of landscape dynamics through to more applied situations such as degraded site rehabilitation. LEMs are now at the stage of development where if calibrated, can provide some level of reliability. However, these models are largely calibrated based on parameters determined from present surface conditions which are the product of much longer-term geology-soil-climate-vegetation interactions. Here, we assess the effect of the initial landscape dimensions and associated error as well as parameterisation for a potential post-mining landform design. The results demonstrate that subtle surface changes in the initial DEM as well as parameterisation can have a large impact on landscape behaviour, erosion depth and sediment discharge. For example, the predicted sediment output from LEM's is shown to be highly variable even with very subtle changes in initial surface conditions. This has two important implications in that decadal time scale field data is needed to (a) better parameterise models and (b) evaluate their predictions. We question how a LEM using parameters derived from field plots can firstly be employed to examine long-term landscape evolution. Secondly, the potential range of outcomes is examined based on estimated temporal parameter change and thirdly, the need for more detailed and rigorous field data for calibration and validation of these models is discussed.

A multistage decision support framework to guide tree species management under climate change via habitat suitability and colonization models, and a knowledge-based scoring system

Treesearch

Anantha M. Prasad; Louis R. Iverson; Stephen N. Matthews; Matthew P. Peters

2016-01-01

Context. No single model can capture the complex species range dynamics under changing climates--hence the need for a combination approach that addresses management concerns. Objective. A multistage approach is illustrated to manage forested landscapes under climate change. We combine a tree species habitat model--DISTRIB II, a species colonization model--SHIFT, and...

Trade-offs between pasture production and farmland bird conservation: exploration of options using a dynamic farm model.

PubMed

Sabatier, R; Teillard, F; Rossing, W A H; Doyen, L; Tichit, M

2015-05-01

In European grassland landscapes, grazing and mowing play a key role for the maintenance of high-quality habitats that host important bird populations. As grasslands are also key resources for cattle feeding, there is a need to develop management strategies that achieve the double objective of production and biodiversity conservation. The objective of this study was to use a modelling approach to generate recognisable patterns of bird dynamics in farms composed of different land use proportions, and to compare their production and ecological dimensions. We developed a dynamic model, which linked grassland management to bird population dynamics at the field and farm levels. The model was parameterised for two types of suckling farms corresponding to contrasting levels of grassland intensification and for two bird species of high conservation value. A viability algorithm was used to define and assess viable management strategies for production and ecological performance so as to draw the shape of the relationship between both types of performances for the two types of farms. Our results indicated that, at the farm level, there was a farming system effect with a negative and non-linear relationship linking performance. Improving bird population maintenance was less costly in extensive farms compared with intensive farms. At the field level, the model predicted the timing and intensity of land use, maximising either production or ecological performance. The results suggested that multi-objective grassland management would benefit from public policies that consider levels of organisation higher than the field level, such as the farm or the landscape.

Scale Invariance in Landscape Evolution Models Using Stream Power Laws

NASA Astrophysics Data System (ADS)

Kwang, J. S.; Parker, G.

2014-12-01

Landscape evolution models (LEM) commonly utilize stream power laws to simulate river incision with formulations such as E = KAmSn, where E is a vertical incision rate [L/T], K is an erodibility constant [L1-2m/T], A is an upstream drainage area [L2], S is a local channel gradient [-], and m and n are positive exponents that describe the basin hydrology. In our reduced complexity model, the landscape approached equilibrium by balancing an incision rate with a constant, uniform, vertical rock uplift rate at every location in the landscape. From our simulations, for a combination of m and n, the landscape exhibited scale invariance. That is, regardless of the size and scale of the basin, the relief and vertical structure of the landscape remained constant. Therefore, the relief and elevation profile of the landscape at equilibrium were only dependent on the coefficients for erodibility and uplift and an equation that described how upstream area, A, increased as the length of a stream increased. In our analytical 1D models, we utilized two equations that described upslope area, (a) A = Bl, where B is the profile width [L], and l is the stream length from the ridge [L] and (b) A = Clh, Hack's Law, where C is a constant [L2-h] and h is a positive exponent. With these equations, (a) m = n and (b) hm = n resulted in scale invariance. In our numerical 2D models, the relationship between A and l was inherent in the actual structure of the drainage network. From our numerical 2D results, scale invariance occurred when 2m = n. Additionally, using reasonable values from the literature for exponents, n, m and h, resulted in singularities at the ridges in the landscape, which caused truncation error. In consequence, the elevation of the ridge increased as the number of grid cells in the domain increased in the numerical model, and the model was unable to converge. These singularities at the ridges appeared when (a) m ≥ n and (b) hm ≥ n in the analytical model and 2m ≥ n in the numerical model. Here we present (1) 1D analytical solutions and (2) 2D numerical solutions that demonstrate scale invariance in LEMs and (3) the consequences of the singularity in 2D LEM numerical simulations. These results will help provide insight about the structure and dynamics of landscapes and drainage networks and shed light on geomorphological empirical relationships.

Fort Collins Science Center Ecosystem Dynamics branch--interdisciplinary research for addressing complex natural resource issues across landscapes and time

USGS Publications Warehouse

Bowen, Zachary H.; Melcher, Cynthia P.; Wilson, Juliette T.

2013-01-01

The Ecosystem Dynamics Branch of the Fort Collins Science Center offers an interdisciplinary team of talented and creative scientists with expertise in biology, botany, ecology, geology, biogeochemistry, physical sciences, geographic information systems, and remote-sensing, for tackling complex questions about natural resources. As demand for natural resources increases, the issues facing natural resource managers, planners, policy makers, industry, and private landowners are increasing in spatial and temporal scope, often involving entire regions, multiple jurisdictions, and long timeframes. Needs for addressing these issues include (1) a better understanding of biotic and abiotic ecosystem components and their complex interactions; (2) the ability to easily monitor, assess, and visualize the spatially complex movements of animals, plants, water, and elements across highly variable landscapes; and (3) the techniques for accurately predicting both immediate and long-term responses of system components to natural and human-caused change. The overall objectives of our research are to provide the knowledge, tools, and techniques needed by the U.S. Department of the Interior, state agencies, and other stakeholders in their endeavors to meet the demand for natural resources while conserving biodiversity and ecosystem services. Ecosystem Dynamics scientists use field and laboratory research, data assimilation, and ecological modeling to understand ecosystem patterns, trends, and mechanistic processes. This information is used to predict the outcomes of changes imposed on species, habitats, landscapes, and climate across spatiotemporal scales. The products we develop include conceptual models to illustrate system structure and processes; regional baseline and integrated assessments; predictive spatial and mathematical models; literature syntheses; and frameworks or protocols for improved ecosystem monitoring, adaptive management, and program evaluation. The descriptions in this fact sheet provide snapshots of our three research emphases, followed by descriptions of select current projects.

Spatial distribution of tree species governs the spatio-temporal interaction of leaf area index and soil moisture across a forested landscape.

PubMed

Naithani, Kusum J; Baldwin, Doug C; Gaines, Katie P; Lin, Henry; Eissenstat, David M

2013-01-01

Quantifying coupled spatio-temporal dynamics of phenology and hydrology and understanding underlying processes is a fundamental challenge in ecohydrology. While variation in phenology and factors influencing it have attracted the attention of ecologists for a long time, the influence of biodiversity on coupled dynamics of phenology and hydrology across a landscape is largely untested. We measured leaf area index (L) and volumetric soil water content (θ) on a co-located spatial grid to characterize forest phenology and hydrology across a forested catchment in central Pennsylvania during 2010. We used hierarchical Bayesian modeling to quantify spatio-temporal patterns of L and θ. Our results suggest that the spatial distribution of tree species across the landscape created unique spatio-temporal patterns of L, which created patterns of water demand reflected in variable soil moisture across space and time. We found a lag of about 11 days between increase in L and decline in θ. Vegetation and soil moisture become increasingly homogenized and coupled from leaf-onset to maturity but heterogeneous and uncoupled from leaf maturity to senescence. Our results provide insight into spatio-temporal coupling between biodiversity and soil hydrology that is useful to enhance ecohydrological modeling in humid temperate forests.

Experimental rugged fitness landscape in protein sequence space.

PubMed

Hayashi, Yuuki; Aita, Takuyo; Toyota, Hitoshi; Husimi, Yuzuru; Urabe, Itaru; Yomo, Tetsuya

2006-12-20

The fitness landscape in sequence space determines the process of biomolecular evolution. To plot the fitness landscape of protein function, we carried out in vitro molecular evolution beginning with a defective fd phage carrying a random polypeptide of 139 amino acids in place of the g3p minor coat protein D2 domain, which is essential for phage infection. After 20 cycles of random substitution at sites 12-130 of the initial random polypeptide and selection for infectivity, the selected phage showed a 1.7x10(4)-fold increase in infectivity, defined as the number of infected cells per ml of phage suspension. Fitness was defined as the logarithm of infectivity, and we analyzed (1) the dependence of stationary fitness on library size, which increased gradually, and (2) the time course of changes in fitness in transitional phases, based on an original theory regarding the evolutionary dynamics in Kauffman's n-k fitness landscape model. In the landscape model, single mutations at single sites among n sites affect the contribution of k other sites to fitness. Based on the results of these analyses, k was estimated to be 18-24. According to the estimated parameters, the landscape was plotted as a smooth surface up to a relative fitness of 0.4 of the global peak, whereas the landscape had a highly rugged surface with many local peaks above this relative fitness value. Based on the landscapes of these two different surfaces, it appears possible for adaptive walks with only random substitutions to climb with relative ease up to the middle region of the fitness landscape from any primordial or random sequence, whereas an enormous range of sequence diversity is required to climb further up the rugged surface above the middle region.

Experimental Rugged Fitness Landscape in Protein Sequence Space

PubMed Central

Hayashi, Yuuki; Aita, Takuyo; Toyota, Hitoshi; Husimi, Yuzuru; Urabe, Itaru; Yomo, Tetsuya

2006-01-01

The fitness landscape in sequence space determines the process of biomolecular evolution. To plot the fitness landscape of protein function, we carried out in vitro molecular evolution beginning with a defective fd phage carrying a random polypeptide of 139 amino acids in place of the g3p minor coat protein D2 domain, which is essential for phage infection. After 20 cycles of random substitution at sites 12–130 of the initial random polypeptide and selection for infectivity, the selected phage showed a 1.7×104-fold increase in infectivity, defined as the number of infected cells per ml of phage suspension. Fitness was defined as the logarithm of infectivity, and we analyzed (1) the dependence of stationary fitness on library size, which increased gradually, and (2) the time course of changes in fitness in transitional phases, based on an original theory regarding the evolutionary dynamics in Kauffman's n-k fitness landscape model. In the landscape model, single mutations at single sites among n sites affect the contribution of k other sites to fitness. Based on the results of these analyses, k was estimated to be 18–24. According to the estimated parameters, the landscape was plotted as a smooth surface up to a relative fitness of 0.4 of the global peak, whereas the landscape had a highly rugged surface with many local peaks above this relative fitness value. Based on the landscapes of these two different surfaces, it appears possible for adaptive walks with only random substitutions to climb with relative ease up to the middle region of the fitness landscape from any primordial or random sequence, whereas an enormous range of sequence diversity is required to climb further up the rugged surface above the middle region. PMID:17183728

Seasonal source-sink dynamics at the edge of a species' range

USGS Publications Warehouse

Kanda, L.L.; Fuller, T.K.; Sievert, P.R.; Kellogg, R.L.

2009-01-01

The roles of dispersal and population dynamics in determining species' range boundaries recently have received theoretical attention but little empirical work. Here we provide data on survival, reproduction, and movement for a Virginia opossum (Didelphis virginiana) population at a local distributional edge in central Massachusetts (USA). Most juvenile females that apparently exploited anthropogenic resources survived their first winter, whereas those using adjacent natural resources died of starvation. In spring, adult females recolonized natural areas. A life-table model suggests that a population exploiting anthropogenic resources may grow, acting as source to a geographically interlaced sink of opossums using only natural resources, and also providing emigrants for further range expansion to new human-dominated landscapes. In a geographical model, this source-sink dynamic is consistent with the local distribution identified through road-kill surveys. The Virginia opossum's exploitation of human resources likely ameliorates energetically restrictive winters and may explain both their local distribution and their northward expansion in unsuitable natural climatic regimes. Landscape heterogeneity, such as created by urbanization, may result in source-sink dynamics at highly localized scales. Differential fitness and individual dispersal movements within local populations are key to generating regional distributions, and thus species ranges, that exceed expectations. ?? 2009 by the Ecological Society of America.

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 effects of spatial and temporal heterogeneity on the population dynamics of four animal species in a Danish landscape

PubMed Central

Sibly, Richard M; Nabe-Nielsen, Jacob; Forchhammer, Mads C; Forbes, Valery E; Topping, Christopher J

2009-01-01

Background Variation in carrying capacity and population return rates is generally ignored in traditional studies of population dynamics. Variation is hard to study in the field because of difficulties controlling the environment in order to obtain statistical replicates, and because of the scale and expense of experimenting on populations. There may also be ethical issues. To circumvent these problems we used detailed simulations of the simultaneous behaviours of interacting animals in an accurate facsimile of a real Danish landscape. The models incorporate as much as possible of the behaviour and ecology of skylarks Alauda arvensis, voles Microtus agrestis, a ground beetle Bembidion lampros and a linyphiid spider Erigone atra. This allows us to quantify and evaluate the importance of spatial and temporal heterogeneity on the population dynamics of the four species. Results Both spatial and temporal heterogeneity affected the relationship between population growth rate and population density in all four species. Spatial heterogeneity accounted for 23–30% of the variance in population growth rate after accounting for the effects of density, reflecting big differences in local carrying capacity associated with the landscape features important to individual species. Temporal heterogeneity accounted for 3–13% of the variance in vole, skylark and spider, but 43% in beetles. The associated temporal variation in carrying capacity would be problematic in traditional analyses of density dependence. Return rates were less than one in all species and essentially invariant in skylarks, spiders and beetles. Return rates varied over the landscape in voles, being slower where there were larger fluctuations in local population sizes. Conclusion Our analyses estimated the traditional parameters of carrying capacities and return rates, but these are now seen as varying continuously over the landscape depending on habitat quality and the mechanisms of density dependence. The importance of our results lies in our demonstration that the effects of spatial and temporal heterogeneity must be accounted for if we are to have accurate predictive models for use in management and conservation. This is an area which until now has lacked an adequate theoretical framework and methodology. PMID:19549327

Projected effects of vegetation and organic matter on soil carbon dynamics after rainfall in a model basalt landscape.

NASA Astrophysics Data System (ADS)

Van Haren, J. L. M.; Sanchez-Canete, E. P.; Juarez, S.; Howard, E. L.; Dontsova, K.; Le Galliard, J. F.; Barron-Gafford, G.; Volkmann, T.; Troch, P. A.

2017-12-01

Basalt is one of the most important rock types in controlling atmospheric carbon dioxide concentrations on a geologic scale. At the University of Arizona's Biosphere 2 facility, we have built the world's largest geological model system - the Landscape Evolution Observatory (LEO) - to determine the hydrological and biogeochemical changes before and after the addition of plants. LEO consists of three 30x11 m and 1-m deep hillslope landscapes of basaltic tephra ground to homogenous loamy sand inside an environmentally controlled facility. Each landscape contains a sensor network capable of capturing water, carbon, and energy cycling processes at 15-min resolution and sub-meter to whole-landscape scales. At LEO, we measured the soil carbon dynamics in bare soil, with only minimal biological activity, after multiple rainfall events. These measurements consistently showed that rainfall, soil moisture, and soil gas diffusion are strong drivers of carbon uptake in a porous basalt matrix. Our expectation is that the addition of plants will dramatically change the carbon dynamics following rainfall events and produce Birch-effect-like pulses of carbon dioxide following rainfall events. We tested this prediction in smaller-scale and shorter-term experiments done at the CEREEP-ECOTRON lab in Ile de France, France, where we experimented with three different plant species grown in the same LEO soil. Soil carbon responses were similar to the LEO slope irrespective of whether plants were grown in the soil: initial wetting leads to a strong drawdown of carbon dioxide in the soil. However, due to plant activity, the soil carbon dioxide concentration recovered faster in the basalt soil when plants were present. Only in small scale incubations with a mixture of LEO soil with an organic-rich (6.5% carbon) prairie soil did we see the expected pulse of carbon dioxide following the addition of water. The smaller-scale experiments suggest that the occurrence of carbon dioxide fluxes generated by rainfall events will not occur after the addition of plants, but will depend on the development of an organic horizon within the LEO soil.

A Dynamic Flood Inundation Model Framework to Assess Coastal Flood Risk in a Changing Climate

NASA Astrophysics Data System (ADS)

Bilskie, M. V.; Hagen, S. C.; Passeri, D. L.; Alizad, K.; Medeiros, S. C.; Irish, J. L.

2015-12-01

Coastal regions around the world are susceptible to a variety of natural disasters causing extreme inundation. It is anticipated that the vulnerability of coastal cities will increase due to the effects of climate change, and in particular sea level rise (SLR). A novel framework was developed to generate a suite of physics-based storm surge models that include projections of coastal floodplain dynamics under climate change scenarios: shoreline erosion/accretion, dune morphology, salt marsh migration, and population dynamics. First, the storm surge inundation model was extensively validated for present day conditions with respect to astronomic tides and hindcasts of Hurricane Ivan (2004), Dennis (2005), Katrina (2005), and Isaac (2012). The model was then modified to characterize the future outlook of the landscape for four climate change scenarios for the year 2100 (B1, B2, A1B, and A2), and each climate change scenario was linked to a sea level rise of 0.2 m, 0.5 m, 1.2 m, and 2.0 m. The adapted model was then used to simulate hurricane storm surge conditions for each climate scenario using a variety of tropical cyclones as the forcing mechanism. The collection of results shows the intensification of inundation area and the vulnerability of the coast to potential future climate conditions. The methodology developed herein to assess coastal flooding under climate change can be performed across any coastal region worldwide, and results provide awareness of regions vulnerable to extreme flooding in the future. Note: The main theme behind this work is to appear in a future Earth's Future publication. Bilskie, M. V., S. C. Hagen, S. C. Medeiros, and D. L. Passeri (2014), Dynamics of sea level rise and coastal flooding on a changing landscape, Geophysical Research Letters, 41(3), 927-934. Parris, A., et al. (2012), Global Sea Level Rise Scenarios for the United States National Climate AssessmentRep., 37 pp. Passeri, D. L., S. C. Hagen, M. V. Bilskie, and S. C. Medeiros (2014), On the significance of incorporating shoreline changes for evaluating coastal hydrodynamics under sea level rise scenarios, Natural Hazards, 1599-1617. Passeri, D. L., S. C. Hagen, S. C. Medeiros, M. V. Bilskie, K. Alizad, and D. Wang (2015), The dynamic effects of sea level rise on low gradient coastal landscapes: a review, Earth's Future, 3.

A General Model for Estimating Macroevolutionary Landscapes.

PubMed

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

2018-03-01

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

Quantifying Grassland-to-Woodland Transitions and the Implications for Carbon and Nitrogen Dynamics in the Southwest United States

NASA Technical Reports Server (NTRS)

Wessman, Carol A.; Archer, Steven R.; Asner, Gregory P.; Bateson, C. Ann

2004-01-01

Replacement of grasslands and savannas by shrublands and woodlands has been widely reported in tropical, temperate and high-latitude rangelands worldwide (Archer 1994). These changes in vegetation structure may reflect historical shifts in climate and land use; and are likely to influence biodiversity, productivity, above- and below ground carbon and nitrogen sequestration and biophysical aspects of land surface-atmosphere interactions. The goal of our proposed research is to investigate how changes in the relative abundance of herbaceous and woody vegetation affect carbon and nitrogen dynamics across heterogeneous savannas and shrub/woodlands. By linking actual land-cover composition (derived through spectral mixture analysis of AVIRIS, TM, and AVHRR imagery) with a process-based ecosystem model, we will generate explicit predictions of the C and N storage in plants and soils resulting from changes in vegetation structure. Our specific objectives will be to (1) continue development and test applications of spectral mixture analysis across grassland-to-woodland transitions; (2) quantify temporal changes in plant and soil C and N storage and turnover for remote sensing and process model parameterization and verification; and (3) couple landscape fraction maps to an ecosystem simulation model to observe biogeochemical dynamics under changing landscape structure and climatological forcings.

Temperature and chain length dependence of ultrafast vibrational dynamics of thiocyanate in alkylimidazolium ionic liquids: A random walk on a rugged energy landscape.

PubMed

Brinzer, Thomas; Garrett-Roe, Sean

2017-11-21

Ultrafast two-dimensional infrared spectroscopy of a thiocyanate vibrational probe (SCN - ) was used to investigate local dynamics in alkylimidazolium bis-[trifluoromethylsulfonyl]imide ionic liquids ([Im n,1 ][Tf 2 N], n = 2, 4, 6) at temperatures from 5 to 80 °C. The rate of frequency fluctuations reported by SCN - increases with increasing temperature and decreasing alkyl chain length. Temperature-dependent correlation times scale proportionally to temperature-dependent bulk viscosities of each ionic liquid studied. A multimode Brownian oscillator model demonstrates that very low frequency (<10 cm -1 ) modes primarily drive the observed spectral diffusion and that these modes broaden and blue shift on average with increasing temperature. An Arrhenius analysis shows activation barriers for local motions around the probe between 5.5 and 6.5 kcal/mol that are very similar to those for translational diffusion of ions. [Im 6,1 ][Tf 2 N] shows an unexpected decrease in activation energy compared to [Im 4,1 ][Tf 2 N] that may be related to mesoscopically ordered polar and nonpolar domains. A model of dynamics on a rugged potential energy landscape provides a unifying description of the observed Arrhenius behavior and the Brownian oscillator model of the low frequency modes.

Grassland Aboveground Biomass in Inner Mongolia: Dynamics (2001-2016) and Driving force

NASA Astrophysics Data System (ADS)

Li, F.; Zeng, Y.; Chen, J.; Wu, B.

2017-12-01

Plant biomass is the most critical measure of carbon stored in an ecosystem, yet it remains imprecisely modeled for many terrestrial biomes. This lack of modeling capacity for biomass and its change through time and space has impeded scientists from making headway concerning issues in the geographic and social sciences. Satellite remote sensing techniques excel at detecting changes in the Earth's surface; however, accurate estimates of biomass for the heterogeneous biome landscapes based on remote sensing techniques are few and far between, which has led to many repetitive studies. Here, we argued that our ability to assess biomass in a heterogeneous landscape using satellite remote sensing techniques would be effectively enhanced through a stratification of landscapes, i.e homogenizing landscapes. Specifically, above-ground biomass (AGB) for an extended heterogeneous grassland biome over the entirety of Inner Mongolia during the past 16 years (2001-2016) was explored using remote sensing time series data from the Moderate Resolution Imaging Spectroradiometer (MODIS). Massive and extensive in-situ measurement AGB data and pure vegetation index (PVI) models, developed from normal remote sensing vegetation indices such as the normalized difference vegetation index (NDVI) and the enhanced vegetation index (EVI), were highlighted in the accomplishment of this study. Taking into full consideration the landscape heterogeneity for the grassland biome over Inner Mongolia, we achieved a series of AGB models with high R2 (>0.85) and low RMSE ( 20.85 g/m2). The total average amount of fresh AGB for the entirety of Inner Mongolia grasslands over the past 16 years was estimated as 87 Tg with an inter-annual standard deviation of 9 Tg. Overall, the grassland AGB for Inner Mongolia increased sporadically. We found that the dynamics of AGB in the grassland biome of Inner Mongolia were substantially dominated by variation in precipitation despite the accommodation of a huge population of livestock in this area over the past few decades. Concerning the production of grassland AGB for the future, we emphasized that the impacts of the frequently warming-drying climate associated with climate change across the Mongolia Plateau should be paid more attention.

Spatial distribution of erosion and deposition on an agricultural watershed

NASA Astrophysics Data System (ADS)

Pineux, Nathalie; Gilles, Colinet; Degré, Aurore

2013-04-01

To better understand the agricultural landscapes evolution becomes an essential preoccupation and, for this, it is needed to take into account the sediments deposition, in a distributed way. As it is not possible in practice to study all terrestrial surfaces in detail by instrumenting sectors to obtain data, models of prediction are valuable tools to control the current problems, to predict the future tendencies and to provide a scientific base to the political decisions. In our case, a landscape evolution model is needed, which aims at representing both erosion and sedimentation and dynamically adjusts the landscape to erosion and deposition by modifying the initial digital elevation model. The Landsoil model (Landscape design for Soil conservation under soil use and climate change), among others, could fulfil this objective. It has the advantage to take the soil variability into account. This model, designed for the analysis of agricultural landscape, is suitable for simulations from parcel to catchment scale, is spatially distributed and event-based. Observed quantitative data are essential (notably to calibrate the model) but still limited. Particularly, we lack observations spatially distributed on the watershed. For this purpose, we choose a watershed in Belgium (Wallonia) which is a 124 ha agricultural zone in the loamy region. Its slopes range from 0% to 9%. To test the predictions of the model, comparisons will be done with: - sediment measurements which are done with water samplings in four points on the site to compare the net erosion results; - sediment selective measurements (depth variation observed along graduated bares placed on site) to compare the erosion and deposition results; - very accurate DSM's (6,76 cm pixel resolution X-Y) obtained by the drone (Gatewing X100) each winter. Besides planning what the landscape evolution should be, a revision of the soil map (drew in 1958) is organized to compare with the past situation and establish how the landscape moved in 50 years. The first results of the sediment measurements and of the pictures of the drone will be showed in the presentation.

Landscape scale prediction of earthquake-induced landsliding based on seismological and geomorphological parameters.

NASA Astrophysics Data System (ADS)

Marc, O.; Hovius, N.; Meunier, P.; Rault, C.

2017-12-01

In tectonically active areas, earthquakes are an important trigger of landslides with significant impact on hillslopes and river evolutions. However, detailed prediction of landslides locations and properties for a given earthquakes remain difficult.In contrast we propose, landscape scale, analytical prediction of bulk coseismic landsliding, that is total landslide area and volume (Marc et al., 2016a) as well as the regional area within which most landslide must distribute (Marc et al., 2017). The prediction is based on a limited number of seismological (seismic moment, source depth) and geomorphological (landscape steepness, threshold acceleration) parameters, and therefore could be implemented in landscape evolution model aiming at engaging with erosion dynamics at the scale of the seismic cycle. To assess the model we have compiled and normalized estimates of total landslide volume, total landslide area and regional area affected by landslides for 40, 17 and 83 earthquakes, respectively. We have found that low landscape steepness systematically leads to overprediction of the total area and volume of landslides. When this effect is accounted for, the model is able to predict within a factor of 2 the landslide areas and associated volumes for about 70% of the cases in our databases. The prediction of regional area affected do not require a calibration for the landscape steepness and gives a prediction within a factor of 2 for 60% of the database. For 7 out of 10 comprehensive inventories we show that our prediction compares well with the smallest region around the fault containing 95% of the total landslide area. This is a significant improvement on a previously published empirical expression based only on earthquake moment.Some of the outliers seems related to exceptional rock mass strength in the epicentral area or shaking duration and other seismic source complexities ignored by the model. Applications include prediction on the mass balance of earthquakes and this model predicts that only earthquakes generated on a narrow range of fault sizes may cause more erosion than uplift (Marc et al., 2016b), while very large earthquakes are expected to always build topography. The model could also be used to physically calibrate hillslope erosion or perturbations to river network within landscape evolution model.

Direct design of an energy landscape with bistable DNA origami mechanisms.

PubMed

Zhou, Lifeng; Marras, Alexander E; Su, Hai-Jun; Castro, Carlos E

2015-03-11

Structural DNA nanotechnology provides a feasible technique for the design and fabrication of complex geometries even exhibiting controllable dynamic behavior. Recently we have demonstrated the possibility of implementing macroscopic engineering design approaches to construct DNA origami mechanisms (DOM) with programmable motion and tunable flexibility. Here, we implement the design of compliant DNA origami mechanisms to extend from prescribing motion to prescribing an energy landscape. Compliant mechanisms facilitate motion via deformation of components with tunable stiffness resulting in well-defined mechanical energy stored in the structure. We design, fabricate, and characterize a DNA origami nanostructure with an energy landscape defined by two stable states (local energy minima) separated by a designed energy barrier. This nanostructure is a four-bar bistable mechanism with two undeformed states. Traversing between those states requires deformation, and hence mechanical energy storage, in a compliant arm of the linkage. The energy barrier for switching between two states was obtained from the conformational distribution based on a Boltzmann probability function and closely follows a predictive mechanical model. Furthermore, we demonstrated the ability to actuate the mechanism into one stable state via additional DNA inputs and then release the actuation via DNA strand displacement. This controllable multistate system establishes a foundation for direct design of energy landscapes that regulate conformational dynamics similar to biomolecular complexes.

The Ecohydrologic Role of Coexistence and Competition in Semiarid Hillslopes

NASA Astrophysics Data System (ADS)

Soltanjalili, M. J.; Saco, P. M.; Willgoose, G. R.

2015-12-01

Through its influence on runoff and erosion-deposition processes, vegetation remarkably regulates different aspects of landscape dynamics. Here, the influence of different plant functional traits on the coexistence of different species in arid and semi-arid regions with patchy vegetation is investigated using an ecohydrology model. The model simulates coevolving changes in biomass patterns for two species, as well as overland flow and soil moisture dynamics. Vegetation patterns emerge as a result of facilitation (shading and infiltration) and competition mechanisms as well as varying seed dispersal strategies. The results show that the survival of only one species or the coexistence of both species not only strongly depends on environmental stresses, but also on differences in hillslope micro and macro topography. These vegetation patterns have very different hydrologic signatures and the potential to trigger remarkably different geomorphic responses. Based on these results we establish new hypothesis that will be used to further investigate the role of plant interspecific and intraspecific feedbacks on landscape coevolution processes.

Integrating continuous stocks and flows into state-and-transition simulation models of landscape change

USGS Publications Warehouse

Daniel, Colin J.; Sleeter, Benjamin M.; Frid, Leonardo; Fortin, Marie-Josée

2018-01-01

State-and-transition simulation models (STSMs) provide a general framework for forecasting landscape dynamics, including projections of both vegetation and land-use/land-cover (LULC) change. The STSM method divides a landscape into spatially-referenced cells and then simulates the state of each cell forward in time, as a discrete-time stochastic process using a Monte Carlo approach, in response to any number of possible transitions. A current limitation of the STSM method, however, is that all of the state variables must be discrete.Here we present a new approach for extending a STSM, in order to account for continuous state variables, called a state-and-transition simulation model with stocks and flows (STSM-SF). The STSM-SF method allows for any number of continuous stocks to be defined for every spatial cell in the STSM, along with a suite of continuous flows specifying the rates at which stock levels change over time. The change in the level of each stock is then simulated forward in time, for each spatial cell, as a discrete-time stochastic process. The method differs from the traditional systems dynamics approach to stock-flow modelling in that the stocks and flows can be spatially-explicit, and the flows can be expressed as a function of the STSM states and transitions.We demonstrate the STSM-SF method by integrating a spatially-explicit carbon (C) budget model with a STSM of LULC change for the state of Hawai'i, USA. In this example, continuous stocks are pools of terrestrial C, while the flows are the possible fluxes of C between these pools. Importantly, several of these C fluxes are triggered by corresponding LULC transitions in the STSM. Model outputs include changes in the spatial and temporal distribution of C pools and fluxes across the landscape in response to projected future changes in LULC over the next 50 years.The new STSM-SF method allows both discrete and continuous state variables to be integrated into a STSM, including interactions between them. With the addition of stocks and flows, STSMs provide a conceptually simple yet powerful approach for characterizing uncertainties in projections of a wide range of questions regarding landscape change.

Tree-, stand- and site-specific controls on landscape-scale patterns of transpiration

NASA Astrophysics Data System (ADS)

Kathrin Hassler, Sibylle; Weiler, Markus; Blume, Theresa

2018-01-01

Transpiration is a key process in the hydrological cycle, and a sound understanding and quantification of transpiration and its spatial variability is essential for management decisions as well as for improving the parameterisation and evaluation of hydrological and soil-vegetation-atmosphere transfer models. For individual trees, transpiration is commonly estimated by measuring sap flow. Besides evaporative demand and water availability, tree-specific characteristics such as species, size or social status control sap flow amounts of individual trees. Within forest stands, properties such as species composition, basal area or stand density additionally affect sap flow, for example via competition mechanisms. Finally, sap flow patterns might also be influenced by landscape-scale characteristics such as geology and soils, slope position or aspect because they affect water and energy availability; however, little is known about the dynamic interplay of these controls.We studied the relative importance of various tree-, stand- and site-specific characteristics with multiple linear regression models to explain the variability of sap velocity measurements in 61 beech and oak trees, located at 24 sites across a 290 km2 catchment in Luxembourg. For each of 132 consecutive days of the growing season of 2014 we modelled the daily sap velocity and derived sap flow patterns of these 61 trees, and we determined the importance of the different controls.Results indicate that a combination of mainly tree- and site-specific factors controls sap velocity patterns in the landscape, namely tree species, tree diameter, geology and aspect. For sap flow we included only the stand- and site-specific predictors in the models to ensure variable independence. Of those, geology and aspect were most important. Compared to these predictors, spatial variability of atmospheric demand and soil moisture explains only a small fraction of the variability in the daily datasets. However, the temporal dynamics of the explanatory power of the tree-specific characteristics, especially species, are correlated to the temporal dynamics of potential evaporation. We conclude that transpiration estimates on the landscape scale would benefit from not only consideration of hydro-meteorological drivers, but also tree, stand and site characteristics in order to improve the spatial and temporal representation of transpiration for hydrological and soil-vegetation-atmosphere transfer models.

Global attractors and extinction dynamics of cyclically competing species.

PubMed

Rulands, Steffen; Zielinski, Alejandro; Frey, Erwin

2013-05-01

Transitions to absorbing states are of fundamental importance in nonequilibrium physics as well as ecology. In ecology, absorbing states correspond to the extinction of species. We here study the spatial population dynamics of three cyclically interacting species. The interaction scheme comprises both direct competition between species as in the cyclic Lotka-Volterra model, and separated selection and reproduction processes as in the May-Leonard model. We show that the dynamic processes leading to the transient maintenance of biodiversity are closely linked to attractors of the nonlinear dynamics for the overall species' concentrations. The characteristics of these global attractors change qualitatively at certain threshold values of the mobility and depend on the relative strength of the different types of competition between species. They give information about the scaling of extinction times with the system size and thereby the stability of biodiversity. We define an effective free energy as the negative logarithm of the probability to find the system in a specific global state before reaching one of the absorbing states. The global attractors then correspond to minima of this effective energy landscape and determine the most probable values for the species' global concentrations. As in equilibrium thermodynamics, qualitative changes in the effective free energy landscape indicate and characterize the underlying nonequilibrium phase transitions. We provide the complete phase diagrams for the population dynamics and give a comprehensive analysis of the spatio-temporal dynamics and routes to extinction in the respective phases.

The walk is never random: subtle landscape effects shape gene flow in a continuous white-tailed deer population in the Midwestern United States

USGS Publications Warehouse

Robinson, Stacie J.; Samuel, Michael D.; Lopez, Davin L.; Shelton, Paul

2012-01-01

One of the pervasive challenges in landscape genetics is detecting gene flow patterns within continuous populations of highly mobile wildlife. Understanding population genetic structure within a continuous population can give insights into social structure, movement across the landscape and contact between populations, which influence ecological interactions, reproductive dynamics or pathogen transmission. We investigated the genetic structure of a large population of deer spanning the area of Wisconsin and Illinois, USA, affected by chronic wasting disease. We combined multiscale investigation, landscape genetic techniques and spatial statistical modelling to address the complex questions of landscape factors influencing population structure. We sampled over 2000 deer and used spatial autocorrelation and a spatial principal components analysis to describe the population genetic structure. We evaluated landscape effects on this pattern using a spatial autoregressive model within a model selection framework to test alternative hypotheses about gene flow. We found high levels of genetic connectivity, with gradients of variation across the large continuous population of white-tailed deer. At the fine scale, spatial clustering of related animals was correlated with the amount and arrangement of forested habitat. At the broader scale, impediments to dispersal were important to shaping genetic connectivity within the population. We found significant barrier effects of individual state and interstate highways and rivers. Our results offer an important understanding of deer biology and movement that will help inform the management of this species in an area where overabundance and disease spread are primary concerns.

Modeling Climate Change Impacts on Landscape Evolution, Fire, and Hydrology

NASA Astrophysics Data System (ADS)

Sheppard, B. S.; O Connor, C.; Falk, D. A.; Garfin, G. M.

2015-12-01

Landscape disturbances such as wildfire interact with climate variability to influence hydrologic regimes. We coupled landscape, fire, and hydrologic models and forced them using projected climate to demonstrate climate change impacts anticipated at Fort Huachuca in southeastern Arizona, USA. The US Department of Defense (DoD) recognizes climate change as a trend that has implications for military installations, national security and global instability. The goal of this DoD Strategic Environmental Research and Development Program (SERDP) project (RC-2232) is to provide decision making tools for military installations in the southwestern US to help them adapt to the operational realities associated with climate change. For this study we coupled the spatially explicit fire and vegetation dynamics model FireBGCv2 with the Automated Geospatial Watershed Assessment tool (AGWA) to evaluate landscape vegetation change, fire disturbance, and surface runoff in response to projected climate forcing. A projected climate stream for the years 2005-2055 was developed from the Multivariate Adaptive Constructed Analogs (MACA) 4 km statistical downscaling of the CanESM2 GCM using Representative Concentration Pathway (RCP) 8.5. AGWA, an ArcGIS add-in tool, was used to automate the parameterization and execution of the Soil Water Assessment Tool (SWAT) and the KINematic runoff and EROSion2 (KINEROS2) models based on GIS layers. Landscape raster data generated by FireBGCv2 project an increase in fire and drought associated tree mortality and a decrease in vegetative basal area over the years of simulation. Preliminary results from SWAT modeling efforts show an increase to surface runoff during years following a fire, and for future winter rainy seasons. Initial results from KINEROS2 model runs show that peak runoff rates are expected to increase 10-100 fold as a result of intense rainfall falling on burned areas.

Drought-induced shift of a forest–woodland ecotone: Rapid landscape response to climate variation

PubMed Central

Allen, Craig D.; Breshears, David D.

1998-01-01

In coming decades, global climate changes are expected to produce large shifts in vegetation distributions at unprecedented rates. These shifts are expected to be most rapid and extreme at ecotones, the boundaries between ecosystems, particularly those in semiarid landscapes. However, current models do not adequately provide for such rapid effects—particularly those caused by mortality—largely because of the lack of data from field studies. Here we report the most rapid landscape-scale shift of a woody ecotone ever documented: in northern New Mexico in the 1950s, the ecotone between semiarid ponderosa pine forest and piñon–juniper woodland shifted extensively (2 km or more) and rapidly (<5 years) through mortality of ponderosa pines in response to a severe drought. This shift has persisted for 40 years. Forest patches within the shift zone became much more fragmented, and soil erosion greatly accelerated. The rapidity and the complex dynamics of the persistent shift point to the need to represent more accurately these dynamics, especially the mortality factor, in assessments of the effects of climate change. PMID:9843976

Drought-induced shift of a forest-woodland ecotone: Rapid landscape response to climate variation

USGS Publications Warehouse

Allen, Craig D.; Breshears, David D.

1998-01-01

In coming decades, global climate changes are expected to produce large shifts in vegetation distributions at unprecedented rates. These shifts are expected to be most rapid and extreme at ecotones, the boundaries between ecosystems, particularly those in semiarid landscapes. However, current models do not adequately provide for such rapid effects—particularly those caused by mortality—largely because of the lack of data from field studies. Here we report the most rapid landscape-scale shift of a woody ecotone ever documented: in northern New Mexico in the 1950s, the ecotone between semiarid ponderosa pine forest and piñon–juniper woodland shifted extensively (2 km or more) and rapidly (<5 years) through mortality of ponderosa pines in response to a severe drought. This shift has persisted for 40 years. Forest patches within the shift zone became much more fragmented, and soil erosion greatly accelerated. The rapidity and the complex dynamics of the persistent shift point to the need to represent more accurately these dynamics, especially the mortality factor, in assessments of the effects of climate change.

A Coupled SD and CLUE-S Model for Exploring the Impact of Land Use Change on Ecosystem Service Value: A Case Study in Baoshan District, Shanghai, China

NASA Astrophysics Data System (ADS)

Wu, Meng; Ren, Xiangyu; Che, Yue; Yang, Kai

2015-08-01

Most of the cities in developing countries are experiencing rapid urbanization. Land use change driven by urban sprawl, population growth, and intensified socio-economic activities have led to a steep decline of ecosystem service value (ESV) in rapid urbanization areas, and decision-makers often ignore some valuable ecosystem service functions and values in land use planning. In this paper, we attempt to build a modeling framework which integrated System Dynamics model with Conversion of Land Use and its Effects at Small Extent model to simulate the dynamics of ESV of landscape and explore the potential impacts of land use change on ESV. We take Baoshan district of Shanghai as an example which is a fast urbanization area of metropolitan in China. The results of the study indicate that: (1) The integrated methodology can improve the characterization and presentation of the dynamics of ESV, which may give insight into understanding the possible impacts of land use change on ESV and provide information for land use planning. (2) Land use polices can affect the magnitude and location of ESV both directly and indirectly. Land use changes tend to weaken and simplify ecosystem service functions and values of landscape at urban rural fringe where land use change is more intensive. (3) The application of the methodology has proved that the integration of currently existing models within a single modeling framework could be a beneficial exploration, and should be encouraged and enhanced in the future research on the changing dynamics of ESV due to the complexity of ecosystem services and land use system.

A Coupled SD and CLUE-S Model for Exploring the Impact of Land Use Change on Ecosystem Service Value: A Case Study in Baoshan District, Shanghai, China.

PubMed

Wu, Meng; Ren, Xiangyu; Che, Yue; Yang, Kai

2015-08-01

Most of the cities in developing countries are experiencing rapid urbanization. Land use change driven by urban sprawl, population growth, and intensified socio-economic activities have led to a steep decline of ecosystem service value (ESV) in rapid urbanization areas, and decision-makers often ignore some valuable ecosystem service functions and values in land use planning. In this paper, we attempt to build a modeling framework which integrated System Dynamics model with Conversion of Land Use and its Effects at Small Extent model to simulate the dynamics of ESV of landscape and explore the potential impacts of land use change on ESV. We take Baoshan district of Shanghai as an example which is a fast urbanization area of metropolitan in China. The results of the study indicate that: (1) The integrated methodology can improve the characterization and presentation of the dynamics of ESV, which may give insight into understanding the possible impacts of land use change on ESV and provide information for land use planning. (2) Land use polices can affect the magnitude and location of ESV both directly and indirectly. Land use changes tend to weaken and simplify ecosystem service functions and values of landscape at urban rural fringe where land use change is more intensive. (3) The application of the methodology has proved that the integration of currently existing models within a single modeling framework could be a beneficial exploration, and should be encouraged and enhanced in the future research on the changing dynamics of ESV due to the complexity of ecosystem services and land use system.

Measuring urban tree loss dynamics across residential landscapes.

PubMed

Ossola, Alessandro; Hopton, Matthew E

2018-01-15

The spatial arrangement of urban vegetation depends on urban morphology and socio-economic settings. Urban vegetation changes over time because of human management. Urban trees are removed due to hazard prevention or aesthetic preferences. Previous research attributed tree loss to decreases in canopy cover. However, this provides little information about location and structural characteristics of trees lost, as well as environmental and social factors affecting tree loss dynamics. This is particularly relevant in residential landscapes where access to residential parcels for field surveys is limited. We tested whether multi-temporal airborne LiDAR and multi-spectral imagery collected at a 5-year interval can be used to investigate urban tree loss dynamics across residential landscapes in Denver, CO and Milwaukee, WI, covering 400,705 residential parcels in 444 census tracts. Position and stem height of trees lost were extracted from canopy height models calculated as the difference between final (year 5) and initial (year 0) vegetation height derived from LiDAR. Multivariate regression models were used to predict number and height of tree stems lost in residential parcels in each census tract based on urban morphological and socio-economic variables. A total of 28,427 stems were lost from residential parcels in Denver and Milwaukee over 5years. Overall, 7% of residential parcels lost one stem, averaging 90.87 stems per km 2 . Average stem height was 10.16m, though trees lost in Denver were taller compared to Milwaukee. The number of stems lost was higher in neighborhoods with higher canopy cover and developed before the 1970s. However, socio-economic characteristics had little effect on tree loss dynamics. The study provides a simple method for measuring urban tree loss dynamics within and across entire cities, and represents a further step toward high resolution assessments of the three-dimensional change of urban vegetation at large spatial scales. Published by Elsevier B.V.

Landscape genetics of the nonnative red fox of California.

PubMed

Sacks, Benjamin N; Brazeal, Jennifer L; Lewis, Jeffrey C

2016-07-01

Invasive mammalian carnivores contribute disproportionately to declines in global biodiversity. In California, nonnative red foxes (Vulpes vulpes) have significantly impacted endangered ground-nesting birds and native canids. These foxes derive primarily from captive-reared animals associated with the fur-farming industry. Over the past five decades, the cumulative area occupied by nonnative red fox increased to cover much of central and southern California. We used a landscape-genetic approach involving mitochondrial DNA (mtDNA) sequences and 13 microsatellites of 402 nonnative red foxes removed in predator control programs to investigate source populations, contemporary connectivity, and metapopulation dynamics. Both markers indicated high population structuring consistent with origins from multiple introductions and low subsequent gene flow. Landscape-genetic modeling indicated that population connectivity was especially low among coastal sampling sites surrounded by mountainous wildlands but somewhat higher through topographically flat, urban and agricultural landscapes. The genetic composition of populations tended to be stable for multiple generations, indicating a degree of demographic resilience to predator removal programs. However, in two sites where intensive predator control reduced fox abundance, we observed increases in immigration, suggesting potential for recolonization to counter eradication attempts. These findings, along with continued genetic monitoring, can help guide localized management of foxes by identifying points of introductions and routes of spread and evaluating the relative importance of reproduction and immigration in maintaining populations. More generally, the study illustrates the utility of a landscape-genetic approach for understanding invasion dynamics and metapopulation structure of one of the world's most destructive invasive mammals, the red fox.

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

PubMed

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

2015-05-01

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

Langevin Equation for DNA Dynamics

NASA Astrophysics Data System (ADS)

Grych, David; Copperman, Jeremy; Guenza, Marina

Under physiological conditions, DNA oligomers can contain well-ordered helical regions and also flexible single-stranded regions. We describe the site-specific motion of DNA with a modified Rouse-Zimm Langevin equation formalism that describes DNA as a coarse-grained polymeric chain with global structure and local flexibility. The approach has successfully described the protein dynamics in solution and has been extended to nucleic acids. Our approach provides diffusive mode analytical solutions for the dynamics of global rotational diffusion and internal motion. The internal DNA dynamics present a rich energy landscape that accounts for an interior where hydrogen bonds and base-stacking determine structure and experience limited solvent exposure. We have implemented several models incorporating different coarse-grained sites with anisotropic rotation, energy barrier crossing, and local friction coefficients that include a unique internal viscosity and our models reproduce dynamics predicted by atomistic simulations. The models reproduce bond autocorrelation along the sequence as compared to that directly calculated from atomistic molecular dynamics simulations. The Langevin equation approach captures the essence of DNA dynamics without a cumbersome atomistic representation.

Dynamical inversion of the energy landscape promotes non-equilibrium self-assembly of binary mixtures

DOE PAGES

Pestana, Luis Ruiz; Minnetian, Natalie; Lammers, Laura Nielsen; ...

2018-01-02

When driven out of equilibrium, many diverse systems can form complex spatial and dynamical patterns, even in the absence of attractive interactions. Using kinetic Monte Carlo simulations, we investigate the phase behavior of a binary system of particles of dissimilar size confined between semiflexible planar surfaces, in which the nanoconfinement introduces a non-local coupling between particles, which we model as an activation energy barrier to diffusion that decreases with the local fraction of the larger particle. The system autonomously reaches a cyclical non-equilibrium state characterized by the formation and dissolution of metastable micelle-like clusters with the small particles in themore » core and the large ones in the surrounding corona. The power spectrum of the fluctuations in the aggregation number exhibits 1/f noise reminiscent of self-organized critical systems. Finally, we suggest that the dynamical metastability of the micellar structures arises from an inversion of the energy landscape, in which the relaxation dynamics of one of the species induces a metastable phase for the other species.« less

Dynamical inversion of the energy landscape promotes non-equilibrium self-assembly of binary mixtures

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

Pestana, Luis Ruiz; Minnetian, Natalie; Lammers, Laura Nielsen

When driven out of equilibrium, many diverse systems can form complex spatial and dynamical patterns, even in the absence of attractive interactions. Using kinetic Monte Carlo simulations, we investigate the phase behavior of a binary system of particles of dissimilar size confined between semiflexible planar surfaces, in which the nanoconfinement introduces a non-local coupling between particles, which we model as an activation energy barrier to diffusion that decreases with the local fraction of the larger particle. The system autonomously reaches a cyclical non-equilibrium state characterized by the formation and dissolution of metastable micelle-like clusters with the small particles in themore » core and the large ones in the surrounding corona. The power spectrum of the fluctuations in the aggregation number exhibits 1/f noise reminiscent of self-organized critical systems. Finally, we suggest that the dynamical metastability of the micellar structures arises from an inversion of the energy landscape, in which the relaxation dynamics of one of the species induces a metastable phase for the other species.« less

Development and assessment of 30-meter pine density maps for landscape-level modeling of mountain pine beetle dynamics

Treesearch

Benjamin A. Crabb; James A. Powell; Barbara J. Bentz

2012-01-01

Forecasting spatial patterns of mountain pine beetle (MPB) population success requires spatially explicit information on host pine distribution. We developed a means of producing spatially explicit datasets of pine density at 30-m resolution using existing geospatial datasets of vegetation composition and structure. Because our ultimate goal is to model MPB population...

Modeling the spatially dynamic distribution of humans in the Oregon (USA) coast range.

Treesearch

Jeffrey D. Kline; David L. Azuma; Alissa Moses

2003-01-01

A common approach to land use change analyses in multidisciplinary landscape-level studies is to delineate discrete forest and non-forest or urban and non-urban land use categories to serve as inputs into sets of integrated sub-models describing socioeconomic and ecological processes. Such discrete land use categories, however, may be inappropriate when the...

Phase Transition Behavior in a Neutral Evolution Model

NASA Astrophysics Data System (ADS)

King, Dawn; Scott, Adam; Maric, Nevena; Bahar, Sonya

2014-03-01

The complexity of interactions among individuals and between individuals and the environment make agent based modeling ideal for studying emergent speciation. This is a dynamically complex problem that can be characterized via the critical behavior of a continuous phase transition. Concomitant with the main tenets of natural selection, we allow organisms to reproduce, mutate, and die within a neutral phenotype space. Previous work has shown phase transition behavior in an assortative mating model with variable fitness landscapes as the maximum mutation size (μ) was varied (Dees and Bahar, 2010). Similarly, this behavior was recently presented in the work of Scott et al. (2013), even on a completely neutral landscape, for bacterial-like fission as well as for assortative mating. Here we present another neutral model to investigate the `critical' phase transition behavior of three mating types - assortative, bacterial, and random - in a phenotype space as a function of the percentage of random death. Results show two types of phase transitions occurring for the parameters of the population size and the number of clusters (an analogue of species), indicating different evolutionary dynamics for system survival and clustering. This research was supported by funding from: University of Missouri Research Board and James S. McDonnell Foundation.

Beyond the blank slate: routes to learning new coordination patterns depend on the intrinsic dynamics of the learner—experimental evidence and theoretical model

PubMed Central

Kostrubiec, Viviane; Zanone, Pier-Giorgio; Fuchs, Armin; Kelso, J. A. Scott

2012-01-01

Using an approach that combines experimental studies of bimanual movements to visual stimuli and theoretical modeling, the present paper develops a dynamical account of sensorimotor learning, that is, how new skills are acquired and old ones modified. A significant aspect of our approach is the focus on the individual learner as the basic unit of analysis, in particular the quantification of predispositions and capabilities that the individual learner brings to the learning environment. Such predispositions constitute the learner's behavioral repertoire, captured here theoretically as a dynamical landscape (“intrinsic dynamics”). The learning process is demonstrated to not only lead to a relatively permanent improvement of performance in the required task—the usual outcome—but also to alter the individual's entire repertoire. Changes in the dynamical landscape due to learning are shown to result from two basic mechanisms or “routes”: bifurcation and shift. Which mechanism is selected depends the initial individual repertoire before new learning begins. Both bifurcation and shift mechanisms are accommodated by a dynamical model, a relatively straightforward development of the well-established HKB model of movement coordination. Model simulations show that although environmental or task demands may be met equally well using either mechanism, the bifurcation route results in greater stabilization of the to-be-learned behavior. Thus, stability not (or not only) error is demonstrated to be the basis of selection, both of a new pattern of behavior and the path (smooth shift versus abrupt qualitative change) that learning takes. In line with these results, recent neurophysiological evidence indicates that stability is a relevant feature around which brain activity is organized while an individual performs a coordination task. Finally, we explore the consequences of the dynamical approach to learning for theories of biological change. PMID:22876227

Causality, transfer entropy, and allosteric communication landscapes in proteins with harmonic interactions.

PubMed

Hacisuleyman, Aysima; Erman, Burak

2017-06-01

A fast and approximate method of generating allosteric communication landscapes in proteins is presented by using Schreiber's entropy transfer concept in combination with the Gaussian Network Model of proteins. Predictions of the model and the allosteric communication landscapes generated show that information transfer in proteins does not necessarily take place along a single path, but an ensemble of pathways is possible. The model emphasizes that knowledge of entropy only is not sufficient for determining allosteric communication and additional information based on time delayed correlations should be introduced, which leads to the presence of causality in proteins. The model provides a simple tool for mapping entropy sink-source relations into pairs of residues. By this approach, residues that should be manipulated to control protein activity may be determined. This should be of great importance for allosteric drug design and for understanding the effects of mutations on function. The model is applied to determine allosteric communication in three proteins, Ubiquitin, Pyruvate Kinase, and the PDZ domain. Predictions are in agreement with molecular dynamics simulations and experimental evidence. Proteins 2017; 85:1056-1064. © 2017 Wiley Periodicals, Inc. © 2017 Wiley Periodicals, Inc.

Free-energy landscape of a hyperstable RNA tetraloop

PubMed Central

Miner, Jacob C.; Chen, Alan A.; García, Angel E.

2016-01-01

We report the characterization of the energy landscape and the folding/unfolding thermodynamics of a hyperstable RNA tetraloop obtained through high-performance molecular dynamics simulations at microsecond timescales. Sampling of the configurational landscape is conducted using temperature replica exchange molecular dynamics over three isochores at high, ambient, and negative pressures to determine the thermodynamic stability and the free-energy landscape of the tetraloop. The simulations reveal reversible folding/unfolding transitions of the tetraloop into the canonical A-RNA conformation and the presence of two alternative configurations, including a left-handed Z-RNA conformation and a compact purine Triplet. Increasing hydrostatic pressure shows a stabilizing effect on the A-RNA conformation and a destabilization of the left-handed Z-RNA. Our results provide a comprehensive description of the folded free-energy landscape of a hyperstable RNA tetraloop and highlight the significant advances of all-atom molecular dynamics in describing the unbiased folding of a simple RNA secondary structure motif. PMID:27233937

Dissolved organic matter composition of Arctic rivers: Linking permafrost and parent material to riverine carbon

USGS Publications Warehouse

O’Donnell, Jonathan A.; Aiken, George R.; Swanson, David K.; Santosh, Panda; Butler, Kenna D.; Baltensperger, Andrew P.

2016-01-01

Recent climate change in the Arctic is driving permafrost thaw, which has important implications for regional hydrology and global carbon dynamics. Permafrost is an important control on groundwater dynamics and the amount and chemical composition of dissolved organic matter (DOM) transported by high-latitude rivers. The consequences of permafrost thaw for riverine DOM dynamics will likely vary across space and time, due in part to spatial variation in ecosystem properties in Arctic watersheds. Here we examined watershed controls on DOM composition in 69 streams and rivers draining heterogeneous landscapes across a broad region of Arctic Alaska. We characterized DOM using bulk dissolved organic carbon (DOC) concentration, optical properties, and chemical fractionation and classified watersheds based on permafrost characteristics (mapping of parent material and ground ice content, modeling of thermal state) and ecotypes. Parent material and ground ice content significantly affected the amount and composition of DOM. DOC concentrations were higher in watersheds underlain by fine-grained loess compared to watersheds underlain by coarse-grained sand or shallow bedrock. DOC concentration was also higher in rivers draining ice-rich landscapes compared to rivers draining ice-poor landscapes. Similarly, specific ultraviolet absorbance (SUVA254, an index of DOM aromaticity) values were highest in watersheds underlain by fine-grained deposits or ice-rich permafrost. We also observed differences in hydrophobic organic acids, hydrophilic compounds, and DOM fluorescence across watersheds. Both DOC concentration and SUVA254 were negatively correlated with watershed active layer thickness, as determined by high-resolution permafrost modeling. Together, these findings highlight how spatial variations in permafrost physical and thermal properties can influence riverine DOM.

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.

[Homeopathy and structure of water: a physical model].

PubMed

Kratky, K W

2004-02-01

Formerly, the author has suggested a relatively simple water model. There, the dynamical structure of a typical water cluster was investigated, being represented by the movement of a ball in an abstract energy landscape. Now the above-mentioned model is investigated in more detail to answer the following question: Are essential claims of homeopathy concerning potentiation (diluting and shaking) in agreement with science? Equations of motion are employed that represent vibrations of clusters. For the computer experiments, the formalism of Nosé-Hoover is used, the surrounding water being interpreted as a heat bath. Diluting corresponds to a shift of the energy landscape towards the pure solvent (water), shaking is accompanied by an increase of the contact to the heat bath. There is a tendency of the ball to be caught in local valleys of the energy landscape (metastable states) if the temperature is not too high and if the liquid is not shaken. Thus, even for a given landscape there are a variety of structures being durable for some time. The computer experiments suggest that the repeated process of potentiation eventually results in a specific metastable state of the pure solvent. The initial substance helps to obtain this goal, but is no longer necessary at last. Copyright 2004 S. Karger GmbH, Freiburg

Interaction Between Ecohydrologic Dynamics and Microtopographic Variability Under Climate Change

NASA Astrophysics Data System (ADS)

Le, Phong V. V.; Kumar, Praveen

2017-10-01

Vegetation acclimation resulting from elevated atmospheric CO2 concentration, along with response to increased temperature and altered rainfall pattern, is expected to result in emergent behavior in ecologic and hydrologic functions. We hypothesize that microtopographic variability, which are landscape features typically of the length scale of the order of meters, such as topographic depressions, will play an important role in determining this dynamics by altering the persistence and variability of moisture. To investigate these emergent ecohydrologic dynamics, we develop a modeling framework, Dhara, which explicitly incorporates the control of microtopographic variability on vegetation, moisture, and energy dynamics. The intensive computational demand from such a modeling framework that allows coupling of multilayer modeling of the soil-vegetation continuum with 3-D surface-subsurface flow processes is addressed using hybrid CPU-GPU parallel computing framework. The study is performed for different climate change scenarios for an intensively managed agricultural landscape in central Illinois, USA, which is dominated by row-crop agriculture, primarily soybean (Glycine max) and maize (Zea mays). We show that rising CO2 concentration will decrease evapotranspiration, thus increasing soil moisture and surface water ponding in topographic depressions. However, increased atmospheric demand from higher air temperature overcomes this conservative behavior resulting in a net increase of evapotranspiration, leading to reduction in both soil moisture storage and persistence of ponding. These results shed light on the linkage between vegetation acclimation under climate change and microtopography variability controls on ecohydrologic processes.

Spatial and Temporal Dynamics and Value of Nature-Based Recreation, Estimated via Social Media.

PubMed

Sonter, Laura J; Watson, Keri B; Wood, Spencer A; Ricketts, Taylor H

2016-01-01

Conserved lands provide multiple ecosystem services, including opportunities for nature-based recreation. Managing this service requires understanding the landscape attributes underpinning its provision, and how changes in land management affect its contribution to human wellbeing over time. However, evidence from both spatially explicit and temporally dynamic analyses is scarce, often due to data limitations. In this study, we investigated nature-based recreation within conserved lands in Vermont, USA. We used geotagged photographs uploaded to the photo-sharing website Flickr to quantify visits by in-state and out-of-state visitors, and we multiplied visits by mean trip expenditures to show that conserved lands contributed US $1.8 billion (US $0.18-20.2 at 95% confidence) to Vermont's tourism industry between 2007 and 2014. We found eight landscape attributes explained the pattern of visits to conserved lands; visits were higher in larger conserved lands, with less forest cover, greater trail density and more opportunities for snow sports. Some of these attributes differed from those found in other locations, but all aligned with our understanding of recreation in Vermont. We also found that using temporally static models to inform conservation decisions may have perverse outcomes for nature-based recreation. For example, static models suggest conserved land with less forest cover receive more visits, but temporally dynamic models suggest clearing forests decreases, rather than increases, visits to these sites. Our results illustrate the importance of understanding both the spatial and temporal dynamics of ecosystem services for conservation decision-making.

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.

Hysteresis, regime shifts, and non-stationarity in aquifer recharge-storage-discharge systems

NASA Astrophysics Data System (ADS)

Klammler, Harald; Jawitz, James; Annable, Michael; Hatfield, Kirk; Rao, Suresh

2016-04-01

Based on physical principles and geological information we develop a parsimonious aquifer model for Silver Springs, one of the largest karst springs in Florida. The model structure is linear and time-invariant with recharge, aquifer head (storage) and spring discharge as dynamic variables at the springshed (landscape) scale. Aquifer recharge is the hydrological driver with trends over a range of time scales from seasonal to multi-decadal. The freshwater-saltwater interaction is considered as a dynamic storage mechanism. Model results and observed time series show that aquifer storage causes significant rate-dependent hysteretic behavior between aquifer recharge and discharge. This leads to variable discharge per unit recharge over time scales up to decades, which may be interpreted as a gradual and cyclic regime shift in the aquifer drainage behavior. Based on field observations, we further amend the aquifer model by assuming vegetation growth in the spring run to be inversely proportional to stream velocity and to hinder stream flow. This simple modification introduces non-linearity into the dynamic system, for which we investigate the occurrence of rate-independent hysteresis and of different possible steady states with respective regime shifts between them. Results may contribute towards explaining observed non-stationary behavior potentially due to hydrological regime shifts (e.g., triggered by gradual, long-term changes in recharge or single extreme events) or long-term hysteresis (e.g., caused by aquifer storage). This improved understanding of the springshed hydrologic response dynamics is fundamental for managing the ecological, economic and social aspects at the landscape scale.

[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.

Climate change amplifies the interactions between wind and bark beetle disturbances in forest landscapes.

PubMed

Seidl, Rupert; Rammer, Werner

2017-07-01

Growing evidence suggests that climate change could substantially alter forest disturbances. Interactions between individual disturbance agents are a major component of disturbance regimes, yet how interactions contribute to their climate sensitivity remains largely unknown. Here, our aim was to assess the climate sensitivity of disturbance interactions, focusing on wind and bark beetle disturbances. We developed a process-based model of bark beetle disturbance, integrated into the dynamic forest landscape model iLand (already including a detailed model of wind disturbance). We evaluated the integrated model against observations from three wind events and a subsequent bark beetle outbreak, affecting 530.2 ha (3.8 %) of a mountain forest landscape in Austria between 2007 and 2014. Subsequently, we conducted a factorial experiment determining the effect of changes in climate variables on the area disturbed by wind and bark beetles separately and in combination. iLand was well able to reproduce observations with regard to area, temporal sequence, and spatial pattern of disturbance. The observed disturbance dynamics was strongly driven by interactions, with 64.3 % of the area disturbed attributed to interaction effects. A +4 °C warming increased the disturbed area by +264.7 % and the area-weighted mean patch size by +1794.3 %. Interactions were found to have a ten times higher sensitivity to temperature changes than main effects, considerably amplifying the climate sensitivity of the disturbance regime. Disturbance interactions are a key component of the forest disturbance regime. Neglecting interaction effects can lead to a substantial underestimation of the climate change sensitivity of disturbance regimes.

The hills are alive: Earth surface dynamics in the University of Arizona Landscape Evolution Observatory

NASA Astrophysics Data System (ADS)

DeLong, S.; Troch, P. A.; Barron-Gafford, G. A.; Huxman, T. E.; Pelletier, J. D.; Dontsova, K.; Niu, G.; Chorover, J.; Zeng, X.

2012-12-01

To meet the challenge of predicting landscape-scale changes in Earth system behavior, the University of Arizona has designed and constructed a new large-scale and community-oriented scientific facility - the Landscape Evolution Observatory (LEO). The primary scientific objectives are to quantify interactions among hydrologic partitioning, geochemical weathering, ecology, microbiology, atmospheric processes, and geomorphic change associated with incipient hillslope development. LEO consists of three identical, sloping, 333 m2 convergent landscapes inside a 5,000 m2 environmentally controlled facility. These engineered landscapes contain 1 meter of basaltic tephra ground to homogenous loamy sand and contains a spatially dense sensor and sampler network capable of resolving meter-scale lateral heterogeneity and sub-meter scale vertical heterogeneity in moisture, energy and carbon states and fluxes. Each ~1000 metric ton landscape has load cells embedded into the structure to measure changes in total system mass with 0.05% full-scale repeatability (equivalent to less than 1 cm of precipitation), to facilitate better quantification of evapotraspiration. Each landscape has an engineered rain system that allows application of precipitation at rates between3 and 45 mm/hr. These landscapes are being studied in replicate as "bare soil" for an initial period of several years. After this initial phase, heat- and drought-tolerant vascular plant communities will be introduced. Introduction of vascular plants is expected to change how water, carbon, and energy cycle through the landscapes, with potentially dramatic effects on co-evolution of the physical and biological systems. LEO also provides a physical comparison to computer models that are designed to predict interactions among hydrological, geochemical, atmospheric, ecological and geomorphic processes in changing climates. These computer models will be improved by comparing their predictions to physical measurements made in LEO. The main focus of our iterative modeling and measurement discovery cycle is to use rapid data assimilation to facilitate validation of newly coupled open-source Earth systems models. LEO will be a community resource for Earth system science research, education, and outreach. The LEO project operational philosophy includes 1) open and real-time availability of sensor network data, 2) a framework for community collaboration and facility access that includes integration of new or comparative measurement capabilities into existing facility cyberinfrastructure, 3) community-guided science planning and 4) development of novel education and outreach programs.Artistic rendering of the University of Arizona Landscape Evolution Observatory

Dynamic Disturbance Processes Create Dynamic Lek Site Selection in a Prairie Grouse.

PubMed

Hovick, Torre J; Allred, Brady W; Elmore, R Dwayne; Fuhlendorf, Samuel D; Hamilton, Robert G; Breland, Amber

2015-01-01

It is well understood that landscape processes can affect habitat selection patterns, movements, and species persistence. These selection patterns may be altered or even eliminated as a result of changes in disturbance regimes and a concomitant management focus on uniform, moderate disturbance across landscapes. To assess how restored landscape heterogeneity influences habitat selection patterns, we examined 21 years (1991, 1993-2012) of Greater Prairie-Chicken (Tympanuchus cupido) lek location data in tallgrass prairie with restored fire and grazing processes. Our study took place at The Nature Conservancy's Tallgrass Prairie Preserve located at the southern extent of Flint Hills in northeastern Oklahoma. We specifically addressed stability of lek locations in the context of the fire-grazing interaction, and the environmental factors influencing lek locations. We found that lek locations were dynamic in a landscape with interacting fire and grazing. While previous conservation efforts have treated leks as stable with high site fidelity in static landscapes, a majority of lek locations in our study (i.e., 65%) moved by nearly one kilometer on an annual basis in this dynamic setting. Lek sites were in elevated areas with low tree cover and low road density. Additionally, lek site selection was influenced by an interaction of fire and patch edge, indicating that in recently burned patches, leks were located near patch edges. These results suggest that dynamic and interactive processes such as fire and grazing that restore heterogeneity to grasslands do influence habitat selection patterns in prairie grouse, a phenomenon that is likely to apply throughout the Greater Prairie-Chicken's distribution when dynamic processes are restored. As conservation moves toward restoring dynamic historic disturbance patterns, it will be important that siting and planning of anthropogenic structures (e.g., wind energy, oil and gas) and management plans not view lek locations as static points, but rather as sites that shift around the landscape in response to shifting vegetation structure. Acknowledging shifting lek locations in these landscapes will help ensure conservation efforts are successful by targeting the appropriate areas for protection and management.

A coupled vegetation/sediment transport model for dryland environments

NASA Astrophysics Data System (ADS)

Mayaud, Jerome R.; Bailey, Richard M.; Wiggs, Giles F. S.

2017-04-01

Dryland regions are characterized by patchy vegetation, erodible surfaces, and erosive aeolian processes. Understanding how these constituent factors interact and shape landscape evolution is critical for managing potential environmental and anthropogenic impacts in drylands. However, modeling wind erosion on partially vegetated surfaces is a complex problem that has remained challenging for researchers. We present the new, coupled cellular automaton Vegetation and Sediment TrAnsport (ViSTA) model, which is designed to address fundamental questions about the development of arid and semiarid landscapes in a spatially explicit way. The technical aspects of the ViSTA model are described, including a new method for directly imposing oblique wind and transport directions onto a cell-based domain. Verification tests for the model are reported, including stable state solutions, the impact of drought and fire stress, wake flow dynamics, temporal scaling issues, and the impact of feedbacks between sediment movement and vegetation growth on landscape morphology. The model is then used to simulate an equilibrium nebkha dune field, and the resultant bed forms are shown to have very similar size and spacing characteristics to nebkhas observed in the Skeleton Coast, Namibia. The ViSTA model is a versatile geomorphological tool that could be used to predict threshold-related transitions in a range of dryland ecogeomorphic systems.

Free-energy landscape for cage breaking of three hard disks.

PubMed

Hunter, Gary L; Weeks, Eric R

2012-03-01

We investigate cage breaking in dense hard-disk systems using a model of three Brownian disks confined within a circular corral. This system has a six-dimensional configuration space, but can be equivalently thought to explore a symmetric one-dimensional free-energy landscape containing two energy minima separated by an energy barrier. The exact free-energy landscape can be calculated as a function of system size by a direct enumeration of states. Results of simulations show the average time between cage breaking events follows an Arrhenius scaling when the energy barrier is large. We also discuss some of the consequences of using a one-dimensional representation to understand dynamics through a multidimensional space, such as diffusion acquiring spatial dependence and discontinuities in spatial derivatives of free energy.

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

Groundwater-surface water interactions across scales in a boreal landscape investigated using a numerical modelling approach

NASA Astrophysics Data System (ADS)

Jutebring Sterte, Elin; Johansson, Emma; Sjöberg, Ylva; Huseby Karlsen, Reinert; Laudon, Hjalmar

2018-05-01

Groundwater and surface-water interactions are regulated by catchment characteristics and complex inter- and intra-annual variations in climatic conditions that are not yet fully understood. Our objective was to investigate the influence of catchment characteristics and freeze-thaw processes on surface and groundwater interactions in a boreal landscape, the Krycklan catchment in Sweden. We used a numerical modelling approach and sub-catchment evaluation method to identify and evaluate fundamental catchment characteristics and processes. The model reproduced observed stream discharge patterns of the 14 sub-catchments and the dynamics of the 15 groundwater wells with an average accumulated discharge error of 1% (15% standard deviation) and an average groundwater-level mean error of 0.1 m (0.23 m standard deviation). We show how peatland characteristics dampen the effect of intense rain, and how soil freeze-thaw processes regulate surface and groundwater partitioning during snowmelt. With these results, we demonstrate the importance of defining, understanding and quantifying the role of landscape heterogeneity and sub-catchment characteristics for accurately representing catchment hydrological functioning.

Organic fields sustain weed metacommunity dynamics in farmland landscapes.

PubMed

Henckel, Laura; Börger, Luca; Meiss, Helmut; Gaba, Sabrina; Bretagnolle, Vincent

2015-06-07

Agro-ecosystems constitute essential habitat for many organisms. Agricultural intensification, however, has caused a strong decline of farmland biodiversity. Organic farming (OF) is often presented as a more biodiversity-friendly practice, but the generality of the beneficial effects of OF is debated as the effects appear often species- and context-dependent, and current research has highlighted the need to quantify the relative effects of local- and landscape-scale management on farmland biodiversity. Yet very few studies have investigated the landscape-level effects of OF; that is to say, how the biodiversity of a field is affected by the presence or density of organically farmed fields in the surrounding landscape. We addressed this issue using the metacommunity framework, with weed species richness in winter wheat within an intensively farmed landscape in France as model system. Controlling for the effects of local and landscape structure, we showed that OF leads to higher local weed diversity and that the presence of OF in the landscape is associated with higher local weed biodiversity also for conventionally farmed fields, and may reach a similar biodiversity level to organic fields in field margins. Based on these results, we derive indications for improving the sustainable management of farming systems. © 2015 The Author(s) Published by the Royal Society. All rights reserved.

Understanding Broadscale Wildfire Risks in a Human-Dominated Landscape

Treesearch

Jeffrey P. Prestemon; John M. Pye; David T. Butry; Thomas P. Holmes; D. Evan Mercer

2002-01-01

Broadscale statistical evaluations of wildfire incidence can answer policy relevant questions about the effectiveness of microlevel vegetation management and can identify subjects needing further study. A dynamic time series cross-sectional model was used to evaluate the statistical links between forest wildfire and vegetation management, human land use, and climatic...

Simulating the impacts of southern pine beetle and fire on the dynamics of xerophytic pine landscapes in the southern Appalachians

Treesearch

J.D. Waldron; C.W. Lafon; R.N. Coulson; D.M. Cairns; M.D. Tchakerian; A. Birt; K.D. Klepzig

2007-01-01

Question: Can fire be used to maintain Yellow pine (Pinus subgenus Diploxylon) stands disturbed by periodic outbreaks of southern pine beetle?Location: Southern Appalachian Mountains, USA.Methods: We used LANDIS to model vegetation disturbance and succession...

MODELING MERCURY DYNAMICS IN STREAM SYSTEMS WITH WASP7: CHARACTERIZING PROCESSES CONTROLLING SHORT AND LONG TERM RESPONSE

EPA Science Inventory

Mercury transport through stream ecosystems is driven by a complicated set of transport and transformation reactions operating on a variety of scales in the atmosphere, landscape, surface water, and biota. Riverine systems typically have short residence times and can experience l...

Incorporating historical ecosystem diversity into conservation planning efforts in grass and shrub ecosystems

Treesearch

Amy C. Ganguli; Johathan B. Haufler; Carolyn A. Mehl; Jimmie D. Chew

2011-01-01

Understanding historical ecosystem diversity and wildlife habitat quality can provide a useful reference for managing and restoring rangeland ecosystems. We characterized historical ecosystem diversity using available empirical data, expert opinion, and the spatially explicit vegetation dynamics model SIMPPLLE (SIMulating Vegetative Patterns and Processes at Landscape...

Evaluating Effects of Localized Habitat Manipulations on Landscape-level Dynamics of White-footed Mouse Populations

EPA Science Inventory

Due to complex population dynamics and migration behaviors, the well-being of animal populations that host human diseases sometimes varies across landscapes in ways that cannot be deduced from geographic abundance patterns alone. In such cases, efficient management of ecological...

The threshold algorithm: Description of the methodology and new developments

NASA Astrophysics Data System (ADS)

Neelamraju, Sridhar; Oligschleger, Christina; Schön, J. Christian

2017-10-01

Understanding the dynamics of complex systems requires the investigation of their energy landscape. In particular, the flow of probability on such landscapes is a central feature in visualizing the time evolution of complex systems. To obtain such flows, and the concomitant stable states of the systems and the generalized barriers among them, the threshold algorithm has been developed. Here, we describe the methodology of this approach starting from the fundamental concepts in complex energy landscapes and present recent new developments, the threshold-minimization algorithm and the molecular dynamics threshold algorithm. For applications of these new algorithms, we draw on landscape studies of three disaccharide molecules: lactose, maltose, and sucrose.

Mapping, monitoring, and modeling Western Gateway Community landscape dynamics

USGS Publications Warehouse

Hester, David J.

2013-01-01

Federal public lands in the western United States are becoming increasingly surrounded by Gateway Communities. These communities are undergoing landscape change due to population growth, economic growth, and the resulting land-use development. Socioeconomic, demographic, and land-use changes in Gateway Communities are often perceived as threats to Federal land resources, natural amenities, cultural resources, and recreational opportunities. However, land-surface disturbances on Federal public lands, such as conventional and alternative energy development (which impact surrounding Gateway Communities), are also environmental and societal issues that Federal land and adjacent regional community planners need to consider in their long-range land-use planning.

Landscape analysis of methane flux across complex terrain

NASA Astrophysics Data System (ADS)

Kaiser, K. E.; McGlynn, B. L.; Dore, J. E.

2014-12-01

Greenhouse gas (GHG) fluxes into and out of the soil are influenced by environmental conditions resulting in landscape-mediated patterns of spatial heterogeneity. The temporal variability of inputs (e.g. precipitation) and internal redistribution (e.g. groundwater flow) and dynamics (e.g. microbial communities) make predicating these fluxes challenging. Complex terrain can provide a laboratory for improving understanding of the spatial patterns, temporal dynamics, and drivers of trace gas flux rates, requisite to constraining current GHG budgets and future scenarios. Our research builds on previous carbon cycle research at the USFS Tenderfoot Creek Experimental Forest, Little Belt Mountains, Montana that highlighted the relationships between landscape position and seasonal CO2 efflux, induced by the topographic redistribution of water. Spatial patterns and landscape scale mediation of CH4 fluxes in seasonally aerobic soils have not yet been elucidated. We measured soil methane concentrations and fluxes across a full range of landscape positions, leveraging topographic and seasonal gradients, to examine the relationships between environmental variables, hydrologic dynamics, and CH4 production and consumption. We determined that a threshold of ~30% VWC distinguished the direction of flux at individual time points, with the riparian area and uplands having distinct source/sink characteristics respectively. Riparian locations were either strong sources or fluctuated between sink and source behavior, resulting in near neutral seasonal flux. Upland sites however, exhibited significant relationships between sink strength and topographic/energy balance indices. Our results highlight spatial and temporal coherence to landscape scale heterogeneity of CH4 dynamics that can improve estimates of landscape scale CH4 balances and sensitivity to change.

The role of waterfalls in controlling the style and pace of landscape adjustment

NASA Astrophysics Data System (ADS)

DiBiase, R.; Lamb, M. P.; Whipple, K. X.

2013-12-01

Bedrock rivers set the pace of landscape adjustment to tectonic or climatic forcing by transmitting signals of baselevel change upstream through the channel network and ultimately to hillslopes. River incision is typically modeled as a monotonic function of bed shear stress, modulated by sediment tools and cover effects, but these models break down in landscapes where waterfalls are common due to changes in flow dynamics across steep, near-vertical reaches. Here we investigate how waterfalls influence the response times of landscapes to external forcing with a conceptual long-profile model and field observations from the San Gabriel Mountains, California. We show that the transient channel response of rivers with waterfalls can either be 'slow' or 'fast' relative to the response of rivers without waterfalls, and identify a series of field tests to identify which end-member behavior is present for natural waterfalls. We apply this conceptual model to the 300 km2 watershed of Big Tujunga Creek in the San Gabriel Mountains, where we identified over 800 bedrock steps greater than 3m in height from a 1m LiDAR DEM and 20 km of detailed field surveys. Two prominent slope-break knickpoints along the mainstem characterized by numerous waterfalls show contrasting behavior. For the upper knickpoint, waterfalls align with bands of harder rock exposed on adjacent hillslopes, and between waterfalls the channel is mantled by large (>2 m) boulders, suggesting that waterfalls here are stalled and enhance the preservation of an upstream relict landscape. In contrast, the lower knickpoint is characterized by waterfalls within an incised inner gorge, and the intervening reaches are a mixture of gravel and exposed bedrock. These observations, combined with a well-preserved strath terrace level parallel with the modern channel downstream of the inner gorge, indicate that the waterfalls here are retreating rapidly relative to background river incision. Our results highlight the importance of quantifying waterfall development and retreat processes for inclusion in landscape evolution models.

Evolving neural networks with genetic algorithms to study the string landscape

NASA Astrophysics Data System (ADS)

Ruehle, Fabian

2017-08-01

We study possible applications of artificial neural networks to examine the string landscape. Since the field of application is rather versatile, we propose to dynamically evolve these networks via genetic algorithms. This means that we start from basic building blocks and combine them such that the neural network performs best for the application we are interested in. We study three areas in which neural networks can be applied: to classify models according to a fixed set of (physically) appealing features, to find a concrete realization for a computation for which the precise algorithm is known in principle but very tedious to actually implement, and to predict or approximate the outcome of some involved mathematical computation which performs too inefficient to apply it, e.g. in model scans within the string landscape. We present simple examples that arise in string phenomenology for all three types of problems and discuss how they can be addressed by evolving neural networks from genetic algorithms.

Predictive energy landscapes for folding membrane protein assemblies

NASA Astrophysics Data System (ADS)

Truong, Ha H.; Kim, Bobby L.; Schafer, Nicholas P.; Wolynes, Peter G.

2015-12-01

We study the energy landscapes for membrane protein oligomerization using the Associative memory, Water mediated, Structure and Energy Model with an implicit membrane potential (AWSEM-membrane), a coarse-grained molecular dynamics model previously optimized under the assumption that the energy landscapes for folding α-helical membrane protein monomers are funneled once their native topology within the membrane is established. In this study we show that the AWSEM-membrane force field is able to sample near native binding interfaces of several oligomeric systems. By predicting candidate structures using simulated annealing, we further show that degeneracies in predicting structures of membrane protein monomers are generally resolved in the folding of the higher order assemblies as is the case in the assemblies of both nicotinic acetylcholine receptor and V-type Na+-ATPase dimers. The physics of the phenomenon resembles domain swapping, which is consistent with the landscape following the principle of minimal frustration. We revisit also the classic Khorana study of the reconstitution of bacteriorhodopsin from its fragments, which is the close analogue of the early Anfinsen experiment on globular proteins. Here, we show the retinal cofactor likely plays a major role in selecting the final functional assembly.

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

NASA Astrophysics Data System (ADS)

Hart, Gregory; Ferguson, Andrew

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

Universality Classes of Interaction Structures for NK Fitness Landscapes

NASA Astrophysics Data System (ADS)

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

2018-07-01

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

Universality Classes of Interaction Structures for NK Fitness Landscapes

NASA Astrophysics Data System (ADS)

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

2018-02-01

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

Mapping landscape phenology preference of yellow-billed cuckoo with AVHRR data

Treesearch

Cynthia S. A. Wallace; Miguel Villarreal; Charles van Riper

2013-01-01

We mapped habitat for threatened Yellow-billed Cuckoo (Coccycus americanus occidentalis) in the State of Arizona using the temporal greenness dynamics of the landscape, or the landscape phenology. Landscape phenometrics were derived from Advanced Very High Resolution Radiometer (AVHRR) Normalized Difference Vegetation Index (NDVI) data for 1998 and 1999 by using...

[Dynamic changes of landscape pattern during desertification in Duolun County of Inner Mongolia].

PubMed

Aruhan; Yang, Chi

2007-11-01

By using landscape analyzing software Fragstats 3.3 and the interpretation results of remote-sensing images of 1960, 1975, 1987, 1995, 2000 and 2005, this paper analyzed the dynamic changes of landscape pattern during the desertification in Duolun County of Inner Mongolia in 1960-2005. The results showed that in 1960-1995, the desertification area appeared a tendency of increasing first and decreasing then, with a total increase of 212.7 km2. The numbers of desertification landscape patches decreased after an initial increase, landscape diversity and evenness increased, and the shapes of light-, moderate-, and heavy desertification patches tended to be simplex. From 1995 to 2005, the numbers of desertification patches increased greatly, landscape diversity and evenness decreased, and the shapes of light-, moderate-, and heavy desertification patches tended to be complex. Since 1960, the shapes of severe desertification patches had been inclined to complication. In the study period, the whole desertification landscape showed a trend of integrity-broken-integrity-broken, and the broken degree of the patch types of desertification landscape was gradually from light down to severe.

Overcoming potential energy distortions in constrained internal coordinate molecular dynamics simulations.

PubMed

Kandel, Saugat; Salomon-Ferrer, Romelia; Larsen, Adrien B; Jain, Abhinandan; Vaidehi, Nagarajan

2016-01-28

The Internal Coordinate Molecular Dynamics (ICMD) method is an attractive molecular dynamics (MD) method for studying the dynamics of bonded systems such as proteins and polymers. It offers a simple venue for coarsening the dynamics model of a system at multiple hierarchical levels. For example, large scale protein dynamics can be studied using torsional dynamics, where large domains or helical structures can be treated as rigid bodies and the loops connecting them as flexible torsions. ICMD with such a dynamic model of the protein, combined with enhanced conformational sampling method such as temperature replica exchange, allows the sampling of large scale domain motion involving high energy barrier transitions. Once these large scale conformational transitions are sampled, all-torsion, or even all-atom, MD simulations can be carried out for the low energy conformations sampled via coarse grained ICMD to calculate the energetics of distinct conformations. Such hierarchical MD simulations can be carried out with standard all-atom forcefields without the need for compromising on the accuracy of the forces. Using constraints to treat bond lengths and bond angles as rigid can, however, distort the potential energy landscape of the system and reduce the number of dihedral transitions as well as conformational sampling. We present here a two-part solution to overcome such distortions of the potential energy landscape with ICMD models. To alleviate the intrinsic distortion that stems from the reduced phase space in torsional MD, we use the Fixman compensating potential. To additionally alleviate the extrinsic distortion that arises from the coupling between the dihedral angles and bond angles within a force field, we propose a hybrid ICMD method that allows the selective relaxing of bond angles. This hybrid ICMD method bridges the gap between all-atom MD and torsional MD. We demonstrate with examples that these methods together offer a solution to eliminate the potential energy distortions encountered in constrained ICMD simulations of peptide molecules.

Overcoming potential energy distortions in constrained internal coordinate molecular dynamics simulations

NASA Astrophysics Data System (ADS)

Kandel, Saugat; Salomon-Ferrer, Romelia; Larsen, Adrien B.; Jain, Abhinandan; Vaidehi, Nagarajan

2016-01-01

The Internal Coordinate Molecular Dynamics (ICMD) method is an attractive molecular dynamics (MD) method for studying the dynamics of bonded systems such as proteins and polymers. It offers a simple venue for coarsening the dynamics model of a system at multiple hierarchical levels. For example, large scale protein dynamics can be studied using torsional dynamics, where large domains or helical structures can be treated as rigid bodies and the loops connecting them as flexible torsions. ICMD with such a dynamic model of the protein, combined with enhanced conformational sampling method such as temperature replica exchange, allows the sampling of large scale domain motion involving high energy barrier transitions. Once these large scale conformational transitions are sampled, all-torsion, or even all-atom, MD simulations can be carried out for the low energy conformations sampled via coarse grained ICMD to calculate the energetics of distinct conformations. Such hierarchical MD simulations can be carried out with standard all-atom forcefields without the need for compromising on the accuracy of the forces. Using constraints to treat bond lengths and bond angles as rigid can, however, distort the potential energy landscape of the system and reduce the number of dihedral transitions as well as conformational sampling. We present here a two-part solution to overcome such distortions of the potential energy landscape with ICMD models. To alleviate the intrinsic distortion that stems from the reduced phase space in torsional MD, we use the Fixman compensating potential. To additionally alleviate the extrinsic distortion that arises from the coupling between the dihedral angles and bond angles within a force field, we propose a hybrid ICMD method that allows the selective relaxing of bond angles. This hybrid ICMD method bridges the gap between all-atom MD and torsional MD. We demonstrate with examples that these methods together offer a solution to eliminate the potential energy distortions encountered in constrained ICMD simulations of peptide molecules.

The Evolving Urban Community and Military Installations: A Dynamic Spatial Decision Support System for Sustainable Military Communities

DTIC Science & Technology

2007-01-01

focus on identifying growth by income and housing costs. These, and other models are focused on the city itself and deal with growth over the course...2. This model employs a set of econometric models to project future population, household, and employment. The landscape is gridded into one... model in LEAM (LEAMecon) forecasts changes in output, employment and income over time based on changes in the market, technology, productivity and

Species sorting and patch dynamics in harlequin metacommunities affect the relative importance of environment and space.

PubMed

Leibold, Mathew A; Loeuille, Nicolas

2015-12-01

Metacommunity theory indicates that variation in local community structure can be partitioned into components including those related to local environmental conditions vs. spatial effects and that these can be quantified using statistical methods based on variation partitioning. It has been hypothesized that joint associations of community composition with environment and space could be due to patch dynamics involving colonization-extinction processes in environmentally heterogeneous landscapes but this has yet to be theoretically shown. We develop a two-patch, type-two, species competition model in such a "harlequin" landscape (where different patches have different environments) to evaluate how composition is related to environmental and spatial effects as a function of background extinction rate. Using spatially implicit analytical models, we find that the environmental association of community composition declines with extinction rate as expected. Using spatially explicit simulation models, we further find that there is an increase in the spatial structure with extinction due to spatial patterning into clusters that are not related to environmental conditions but that this increase is limited. Natural metacommunities often show both environment and spatial determination even under conditions of relatively high isolation and these could be more easily explained by our model than alternative metacommunity models.

A dynamic landscape model for fish in the Everglades and its application to restoration

USGS Publications Warehouse

Gaff, H.D.; DeAngelis, D.L.; Gross, L.J.; Salinas, R.; Shorrosh, M.

2000-01-01

A model (ALFISH) for fish functional groups in freshwater marshes of the greater Everglades area of southern Florida has been developed. Its main objective is to assess the spatial pattern of fish densities through time across freshwater marshes. This model has the capability of providing a dynamic measure of the spatially-explicit food resources available to wading birds. ALFISH simulates two functional groups, large and small fish, where the larger ones can prey on the small fish type. Both functional groups are size-structured. The marsh landscape is modeled as 500×500 m spatial cells on a grid across southern Florida. A hydrology model predicts water levels in the spatial cells on 5-day time steps. Fish populations spread across the marsh during flooded conditions and either retreat into refugia (alligator ponds), move to other spatial cells, or die if their cell dries out. ALFISH has been applied to the evaluation of alternative water regulation scenarios under the Central and South Florida Comprehensive Project Review Study. The objective of this Review Study is to compare alternative methods for restoring historical ecological conditions in southern Florida. ALFISH has provided information on which plans are most are likely to increase fish biomass and its availability to wading bird populations.

Hierarchical structure of the energy landscape of proteins revisited by time series analysis. I. Mimicking protein dynamics in different time scales

NASA Astrophysics Data System (ADS)

Alakent, Burak; Camurdan, Mehmet C.; Doruker, Pemra

2005-10-01

Time series models, which are constructed from the projections of the molecular-dynamics (MD) runs on principal components (modes), are used to mimic the dynamics of two proteins: tendamistat and immunity protein of colicin E7 (ImmE7). Four independent MD runs of tendamistat and three independent runs of ImmE7 protein in vacuum are used to investigate the energy landscapes of these proteins. It is found that mean-square displacements of residues along the modes in different time scales can be mimicked by time series models, which are utilized in dividing protein dynamics into different regimes with respect to the dominating motion type. The first two regimes constitute the dominance of intraminimum motions during the first 5ps and the random walk motion in a hierarchically higher-level energy minimum, which comprise the initial time period of the trajectories up to 20-40ps for tendamistat and 80-120ps for ImmE7. These are also the time ranges within which the linear nonstationary time series are completely satisfactory in explaining protein dynamics. Encountering energy barriers enclosing higher-level energy minima constrains the random walk motion of the proteins, and pseudorelaxation processes at different levels of minima are detected in tendamistat, depending on the sampling window size. Correlation (relaxation) times of 30-40ps and 150-200ps are detected for two energy envelopes of successive levels for tendamistat, which gives an overall idea about the hierarchical structure of the energy landscape. However, it should be stressed that correlation times of the modes are highly variable with respect to conformational subspaces and sampling window sizes, indicating the absence of an actual relaxation. The random-walk step sizes and the time length of the second regime are used to illuminate an important difference between the dynamics of the two proteins, which cannot be clarified by the investigation of relaxation times alone: ImmE7 has lower-energy barriers enclosing the higher-level energy minimum, preventing the protein to relax and letting it move in a random-walk fashion for a longer period of time.

Lattice model simulation of interchain protein interactions and the folding dynamics and dimerization of the GCN4 Leucine zipper

NASA Astrophysics Data System (ADS)

Liu, Yanxin; Chapagain, Prem P.; Parra, Jose L.; Gerstman, Bernard S.

2008-01-01

The highest level in the hierarchy of protein structure and folding is the formation of protein complexes through protein-protein interactions. We have made modifications to a well established computer lattice model to expand its applicability to two-protein dimerization and aggregation. Based on Brownian dynamics, we implement translation and rotation moves of two peptide chains relative to each other, in addition to the intrachain motions already present in the model. We use this two-chain model to study the folding dynamics of the yeast transcription factor GCN4 leucine zipper. The calculated heat capacity curves agree well with experimental measurements. Free energy landscapes and median first passage times for the folding process are calculated and elucidate experimentally measured characteristics such as the multistate nature of the dimerization process.

Establishing conservation baselines with dynamic distribution models for bat populations facing imminent decline

USGS Publications Warehouse

Rodhouse, Thomas J.; Ormsbee, Patricia C.; Irvine, Kathryn M.; Vierling, Lee A.; Szewczak, Joseph M.; Vierling, Kerri T.

2015-01-01

Landscape keystone structures associated with roosting habitat emerged as regionally important predictors of bat distributions. The challenges of bat monitoring have constrained previous species distribution modelling efforts to temporally static presence-only approaches. Our approach extends to broader spatial and temporal scales than has been possible in the past for bats, making a substantial increase in capacity for bat conservation.

DYNAMICS OF A SUBTIDAL SEAGRASS LANDSCAPE: SEASONAL AND ANNUAL CHANGE IN RELATION TO WATER DEPTH

EPA Science Inventory

The spatial heterogeneity of a subtidal marine landscape and the areal extent of both monospecific and mixed patches of seagrass species were studied in Tampa Bay, FL. Specifically, we examined the temporal dynamics of seagrass distribution and its relationship to water depth an...

Development of the Fully Adaptive Storm Tide (FAST) Model for hurricane induced storm surges and associated inundation

NASA Astrophysics Data System (ADS)

Teng, Y. C.; Kelly, D.; Li, Y.; Zhang, K.

2016-02-01

A new state-of-the-art model (the Fully Adaptive Storm Tide model, FAST) for the prediction of storm surges over complex landscapes is presented. The FAST model is based on the conservation form of the full non-linear depth-averaged long wave equations. The equations are solved via an explicit finite volume scheme with interfacial fluxes being computed via Osher's approximate Riemann solver. Geometric source terms are treated in a high order manner that is well-balanced. The numerical solution technique has been chosen to enable the accurate simulation of wetting and drying over complex topography. Another important feature of the FAST model is the use of a simple underlying Cartesian mesh with tree-based static and dynamic adaptive mesh refinement (AMR). This permits the simulation of unsteady flows over varying landscapes (including localized features such as canals) by locally increasing (or relaxing) grid resolution in a dynamic fashion. The use of (dynamic) AMR lowers the computational cost of the storm surge model whilst retaining high resolution (and thus accuracy) where and when it is required. In additional, the FAST model has been designed to execute in a parallel computational environment with localized time-stepping. The FAST model has already been carefully verified against a series of benchmark type problems (Kelly et al. 2015). Here we present two simulations of the storm tide due to Hurricane Ike(2008) and Hurricane Sandy (2012). The model incorporates high resolution LIDAR data for the major portion of the New York City. Results compare favorably with water elevations measured by NOAA tidal gauges, by mobile sensors deployed and high water marks collected by the USGS.

A stand-alone tree demography and landscape structure module for Earth system models: integration with global forest data

NASA Astrophysics Data System (ADS)

Haverd, V.; Smith, B.; Nieradzik, L. P.; Briggs, P. R.

2014-02-01

Poorly constrained rates of biomass turnover are a key limitation of Earth system models (ESM). In light of this, we recently proposed a new approach encoded in a model called Populations-Order-Physiology (POP), for the simulation of woody ecosystem stand dynamics, demography and disturbance-mediated heterogeneity. POP is suitable for continental to global applications and designed for coupling to the terrestrial ecosystem component of any ESM. POP bridges the gap between first generation Dynamic Vegetation Models (DVMs) with simple large-area parameterisations of woody biomass (typically used in current ESMs) and complex second generation DVMs, that explicitly simulate demographic processes and landscape heterogeneity of forests. The key simplification in the POP approach, compared with second-generation DVMs, is to compute physiological processes such as assimilation at grid-scale (with CABLE or a similar land surface model), but to partition the grid-scale biomass increment among age classes defined at sub grid-scale, each subject to its own dynamics. POP was successfully demonstrated along a savanna transect in northern Australia, replicating the effects of strong rainfall and fire disturbance gradients on observed stand productivity and structure. Here, we extend the application of POP to a range of forest types around the globe, employing paired observations of stem biomass and density from forest inventory data to calibrate model parameters governing stand demography and biomass evolution. The calibrated POP model is then coupled to the CABLE land surface model and the combined model (CABLE-POP) is evaluated against leaf-stem allometry observations from forest stands ranging in age from 3 to 200 yr. Results indicate that simulated biomass pools conform well with observed allometry. We conclude that POP represents a preferable alternative to large-area parameterisations of woody biomass turnover, typically used in current ESMs.

Dynamic Seascapes Predict the Marine Occurrence of an Endangered Species

NASA Astrophysics Data System (ADS)

Breece, M.; Fox, D. A.; Dunton, K. J.; Frisk, M. G.; Jordaan, A.; Oliver, M. J.

2016-02-01

Landscapes are powerful environmental partitions that index complex biogeochemical processes that drive terrestrial species distributions. However, translating landscapes into seascapes requires that the dynamic nature of the fluid environment be reflected in spatial and temporal boundaries such that seascapes can be used in marine species distribution models and conservation decisions. A seascape product derived from satellite ocean color and sea surface temperature partitioned mid-Atlantic coastal waters on scales commensurate with the Atlantic Sturgeon Acipenser oxyrinchus oxyrinchus coastal migration. The seascapes were then matched with acoustic telemetry records of Atlantic Sturgeon to determine seascape selectivity. To test our model, we used real-time satellite seascape maps to normalize the sampling of an autonomous underwater vehicle that resampled similar geographic regions with time varying seascape classifications. We found that Atlantic Sturgeon exhibited preference for one seascape class over those available in the coastal ocean, indicating selection for environmental properties that co-varied with the dynamic seascape class rather than geographical location. The recent listing of Atlantic Sturgeon as Endangered throughout much of their United States range has highlighted the need for improved understanding of their occurrence in marine waters to reduce interactions with various anthropogenic stressors. Narrow dynamic migration corridors may enable seascapes to be used as a daily decision tool by industry and managers to reduce interactions with this Endangered Species during coastal migrations.

Dynamic Seascapes Predict the Marine Occurrence of an Endangered Species

NASA Astrophysics Data System (ADS)

Breece, M.; Fox, D. A.; Dunton, K. J.; Frisk, M. G.; Jordaan, A.; Oliver, M. J.

2016-12-01

Landscapes are powerful environmental partitions that index complex biogeochemical processes that drive terrestrial species distributions. However, translating landscapes into seascapes requires that the dynamic nature of the fluid environment be reflected in spatial and temporal boundaries such that seascapes can be used in marine species distribution models and conservation decisions. A seascape product derived from satellite ocean color and sea surface temperature partitioned mid-Atlantic coastal waters on scales commensurate with the Atlantic Sturgeon Acipenser oxyrinchus oxyrinchus coastal migration. The seascapes were then matched with acoustic telemetry records of Atlantic Sturgeon to determine seascape selectivity. To test our model, we used real-time satellite seascape maps to normalize the sampling of an autonomous underwater vehicle that resampled similar geographic regions with time varying seascape classifications. We found that Atlantic Sturgeon exhibited preference for one seascape class over those available in the coastal ocean, indicating selection for environmental properties that co-varied with the dynamic seascape class rather than geographical location. The recent listing of Atlantic Sturgeon as Endangered throughout much of their United States range has highlighted the need for improved understanding of their occurrence in marine waters to reduce interactions with various anthropogenic stressors. Narrow dynamic migration corridors may enable seascapes to be used as a daily decision tool by industry and managers to reduce interactions with this Endangered Species during coastal migrations.

Towards a landscape scale management of pesticides: ERA using changes in modelled occupancy and abundance to assess long-term population impacts of pesticides.

PubMed

Topping, Chris J; Craig, Peter S; de Jong, Frank; Klein, Michael; Laskowski, Ryszard; Manachini, Barbara; Pieper, Silvia; Smith, Rob; Sousa, José Paulo; Streissl, Franz; Swarowsky, Klaus; Tiktak, Aaldrik; van der Linden, Ton

2015-12-15

Pesticides are regulated in Europe and this process includes an environmental risk assessment (ERA) for non-target arthropods (NTA). Traditionally a non-spatial or field trial assessment is used. In this study we exemplify the introduction of a spatial context to the ERA as well as suggest a way in which the results of complex models, necessary for proper inclusion of spatial aspects in the ERA, can be presented and evaluated easily using abundance and occupancy ratios (AOR). We used an agent-based simulation system and an existing model for a widespread carabid beetle (Bembidion lampros), to evaluate the impact of a fictitious highly-toxic pesticide on population density and the distribution of beetles in time and space. Landscape structure and field margin management were evaluated by comparing scenario-based ERAs for the beetle. Source-sink dynamics led to an off-crop impact even when no pesticide was present off-crop. In addition, the impacts increased with multi-year application of the pesticide whereas current ERA considers only maximally one year. These results further indicated a complex interaction between landscape structure and pesticide effect in time, both in-crop and off-crop, indicating the need for NTA ERA to be conducted at landscape- and multi-season temporal-scales. Use of AOR indices to compare ERA outputs facilitated easy comparison of scenarios, allowing simultaneous evaluation of impacts and planning of mitigation measures. The landscape and population ERA approach also demonstrates that there is a potential to change from regulation of a pesticide in isolation, towards the consideration of pesticide management at landscape scales and provision of biodiversity benefits via inclusion and testing of mitigation measures in authorisation procedures. Copyright © 2015 Elsevier B.V. All rights reserved.

The elastic free energy of a tandem modular protein under force.

PubMed

Valle-Orero, Jessica; Eckels, Edward C; Stirnemann, Guillaume; Popa, Ionel; Berkovich, Ronen; Fernandez, Julio M

2015-05-01

Recent studies have provided a theoretical framework for including entropic elasticity in the free energy landscape of proteins under mechanical force. Accounting for entropic elasticity using polymer physics models has helped explain the hopping behavior seen in single molecule experiments in the low force regime. Here, we expand on the construction of the free energy of a single protein domain under force proposed by Berkovich et al. to provide a free energy landscape for N tandem domains along a continuous polypeptide. Calculation of the free energy of individual domains followed by their concatenation provides a continuous free energy landscape whose curvature is dominated by the worm-like chain at forces below 20 pN. We have validated our free energy model using Brownian dynamics and reproduce key features of protein folding. This free energy model can predict the effects of changes in the elastic properties of a multidomain protein as a consequence of biological modifications such as phosphorylation or the formation of disulfide bonds. This work lays the foundations for the modeling of tissue elasticity, which is largely determined by the properties of tandem polyproteins. Copyright © 2015. Published by Elsevier Inc.

Long-term Evaluation of Landuse Changes On Landscape Water Balance - A Case Study From North-east Germany

NASA Astrophysics Data System (ADS)

Wegehenkel, M.

In this paper, long-term effects of different afforestation scenarios on landscape wa- ter balance will be analyzed taking into account the results of a regional case study. This analysis is based on using a GIS-coupled simulation model for the the spatially distributed calculation of water balance.For this purpose, the modelling system THE- SEUS with a simple GIS-interface will be used. To take into account the special case of change in forest cover proportion, THESEUS was enhanced with a simple for- est growth model. In the regional case study, model runs will be performed using a detailed spatial data set from North-East Germany. This data set covers a mesoscale catchment located at the moraine landscape of North-East Germany. Based on this data set, the influence of the actual landuse and of different landuse change scenarios on water balance dynamics will be investigated taking into account the spatial distributed modelling results from THESEUS. The model was tested using different experimen- tal data sets from field plots as well as obsverded catchment discharge. Additionally to such convential validation techniques, remote sensing data were used to check the simulated regional distribution of water balance components like evapotranspiration in the catchment.

Impact of forestry practices at a landscape scale on the dynamics of amphibian populations.

PubMed

Harper, Elizabeth B; Patrick, David A; Gibbs, James P

2015-12-01

Forest loss is a primary cause of worldwide amphibian decline. Timber harvesting in the United States has caused dramatic changes in quality and extent of forest ecosystems, and intensive forest management still occurs. Although numerous studies have documented substantial reductions in amphibian densities related to timber harvest, subsequent extinctions are rare. To better understand the population dynamics that have allowed so many amphibian species to persist in the face of widespread forest disturbance, we developed spatially explicit metapopulation models for four forest-dependent amphibian species (Lithobates sylvaticus, Ambystoma opacum, A. talpoideum, and A. maculatum) that incorporated demographic and habitat selection data derived from experiments conducted as part of the Land Use Effects on Amphibian Populations Project (LEAP). We projected local and landscape-scale population persistence under 108 different forestry practice scenarios, varying treatment (partial cut, clear-cut with coarse woody debris [CWD] removed, and clearcut with CWD retained), cut patch size (1, 10, or 50 ha), total area cut (10, 20, or 30%), and initial amphibian population size (5, 50, or 500 adult females per local breeding population). Under these scenarios, landscape-scale extinction was highly unlikely, occurring in < 1% of model runs and for only 2 of the 4 species, because landscape-scale populations were able to persist via dispersal even despite frequent local extinctions. Yet for all species, population sizes were reduced to -50% in all clear-cut scenarios, regardless of the size of harvested patches. These findings suggest that debate over timber harvesting on pool-breeding amphibian populations in the United States should focus not on questions of landscape-scale extinction but on the ecological consequences of dramatic reductions in amphibian biomass, including changes in trophic interactions, nutrient cycling, and energy transfer. Additionally, we conclude that amphibian declines and extinctions are far more likely to occur as a result of permanent habitat loss resulting from development than from the temporary degradation of habitat caused by current forestry practices.

Decoding Dynamic Topography: Geologic and Thermochronologic Constraints From Madagascar

NASA Astrophysics Data System (ADS)

Stephenson, S.; White, N.

2017-12-01

Madagascar's topography is characterized by flights of low relief peneplains separated by escarpments. Remarkably, nearly 50% of the landscape is higher than 500 m despite being surrounded by passive margins. Eocene marine limestones crop out at elevations of 400-800 m, staircases of Pleistocene marine terraces fringe the coastline and longitudinal river profiles are disequilibrated. Together, these observations suggest that Madagascar has experienced Neogene epeirogenic uplift. Positive oceanic residual depth anomalies surrounding the island, long wavelength free-air gravity anomalies, Neogene basaltic volcanism and slow sub-plate shear wave velocities show that Neogene uplift is generated by convective circulation within the upper mantle. However, the landscape's erosional response to long wavelength uplift is poorly known. Here, we present 18 apatite fission track and apatite He analyses of granitoid samples from sub-vertical transects in central and northern Madagascar. Apatite fission track ages are 200-250 Ma with mean track lengths of 12 μm. Apatite He ages are highly dispersed in samples from the highlands (i.e. AHe age > 150 Ma) but a narrower, younger range of 30-60 Ma is found on the coastal lowlands. Joint inverse modeling was carried out using the QTQt transdimensional reversible jump Markov Chain Monte Carlo (MCMC) algorithm to determine time-temperature histories. Results show that the coastal lowlands experienced up to 1 km of exhumation during the Neogene Period, whilst the central highlands experienced either very slow or negligible exhumation. This spatial distribution is expected when kinematic waves of incision propagate through a fluvially eroding landscape from coast to interior. Inverse modeling of suites of river profiles and forward landscape simulations support this interpretation. Our results show that the landscape response to modest (i.e. 1 km) regional uplift is diachronous and that thermochronologic observations can be used to detect spatial patterns of denudation. These combined observations help to constrain the fluid dynamical evolution of the upper mantle beneath Madagascar.

Environmental mapping and monitoring of Iceland by remote sensing (EMMIRS)

NASA Astrophysics Data System (ADS)

Pedersen, Gro B. M.; Vilmundardóttir, Olga K.; Falco, Nicola; Sigurmundsson, Friðþór S.; Rustowicz, Rose; Belart, Joaquin M.-C.; Gísladóttir, Gudrun; Benediktsson, Jón A.

2016-04-01

Iceland is exposed to rapid and dynamic landscape changes caused by natural processes and man-made activities, which impact and challenge the country. Fast and reliable mapping and monitoring techniques are needed on a big spatial scale. However, currently there is lack of operational advanced information processing techniques, which are needed for end-users to incorporate remote sensing (RS) data from multiple data sources. Hence, the full potential of the recent RS data explosion is not being fully exploited. The project Environmental Mapping and Monitoring of Iceland by Remote Sensing (EMMIRS) bridges the gap between advanced information processing capabilities and end-user mapping of the Icelandic environment. This is done by a multidisciplinary assessment of two selected remote sensing super sites, Hekla and Öræfajökull, which encompass many of the rapid natural and man-made landscape changes that Iceland is exposed to. An open-access benchmark repository of the two remote sensing supersites is under construction, providing high-resolution LIDAR topography and hyperspectral data for land-cover and landform classification. Furthermore, a multi-temporal and multi-source archive stretching back to 1945 allows a decadal evaluation of landscape and ecological changes for the two remote sensing super sites by the development of automated change detection techniques. The development of innovative pattern recognition and machine learning-based approaches to image classification and change detection is one of the main tasks of the EMMIRS project, aiming to extract and compute earth observation variables as automatically as possible. Ground reference data collected through a field campaign will be used to validate the implemented methods, which outputs are then inferred with geological and vegetation models. Here, preliminary results of an automatic land-cover classification based on hyperspectral image analysis are reported. Furthermore, the EMMIRS project investigates the complex landscape dynamics between geological and ecological processes. This is done through cross-correlation of mapping results and implementation of modelling techniques that simulate geological and ecological processes in order to extrapolate the landscape evolution

Vulnerability and Resilience of Temperate Forest Landscapes to Broad-Scale Deforestation in Response to Changing Fire Regimes and Altered Post-Fire Vegetation Dynamics

NASA Astrophysics Data System (ADS)

Tepley, A. J.; Veblen, T. T.; Perry, G.; Anderson-Teixeira, K. J.

2015-12-01

In the face of on-going climatic warming and land-use change, there is growing concern that temperate forest landscapes could be near a tipping point where relatively small changes to the fire regime or altered post-fire vegetation dynamics could lead to extensive conversion to shrublands or savannas. To evaluate vulnerability and resilience to such conversion, we develop a simple model based on three factors we hypothesize to be key in predicting temperate forest responses to changing fire regimes: (1) the hazard rate (i.e., the probability of burning in the next year given the time since the last fire) in closed-canopy forests, (2) the hazard rate for recently-burned, open-canopy vegetation, and (3) the time to redevelop canopy closure following fire. We generate a response surface representing the proportions of the landscape potentially supporting closed-canopy forest and non-forest vegetation under nearly all combinations of these three factors. We then place real landscapes on this response surface to assess the type and magnitude of changes to the fire regime that would drive extensive forest loss. We show that the deforestation of much of New Zealand that followed initial human colonization and the introduction of a new ignition source ca. 750 years ago was essentially inevitable due to the slow rate of forest recovery after fire and the high flammability of post-fire vegetation. In North America's Pacific Northwest, by contrast, a predominantly forested landscape persisted despite two periods of widespread burning in the recent past due in large part to faster post-fire forest recovery and less pronounced differences in flammability between forests and the post-fire vegetation. We also assess the factors that could drive extensive deforestation in other regions to identify where management could reduce this potential and to guide field and modeling work to better understand the responses and ecological feedbacks to changing fire regimes.

Engineering the entropy-driven free-energy landscape of a dynamic nanoporous protein assembly.

PubMed

Alberstein, Robert; Suzuki, Yuta; Paesani, Francesco; Tezcan, F Akif

2018-04-30

De novo design and construction of stimuli-responsive protein assemblies that predictably switch between discrete conformational states remains an essential but highly challenging goal in biomolecular design. We previously reported synthetic, two-dimensional protein lattices self-assembled via disulfide bonding interactions, which endows them with a unique capacity to undergo coherent conformational changes without losing crystalline order. Here, we carried out all-atom molecular dynamics simulations to map the free-energy landscape of these lattices, validated this landscape through extensive structural characterization by electron microscopy and established that it is predominantly governed by solvent reorganization entropy. Subsequent redesign of the protein surface with conditionally repulsive electrostatic interactions enabled us to predictably perturb the free-energy landscape and obtain a new protein lattice whose conformational dynamics can be chemically and mechanically toggled between three different states with varying porosities and molecular densities.

Belowground Controls on the Dynamics of Plant Communities

NASA Astrophysics Data System (ADS)

Sivandran, G.

2013-12-01

Arid regions are characterized by high variability in the arrival of rainfall, and species found in these areas have adapted mechanisms to ensure the capture of this scarce resource. In particular, the rooting strategies employed by vegetation can be critical to their survival. These rooting strategies also dictate the competitive outcomes within plant communities. A dynamic rooting scheme was incorporated into tRIBS+VEGGIE (a physically-based, distributed ecohydrologic model). The dynamic rooting scheme allows vegetation the freedom to alter its rooting profile in response to changes in rainfall and soil conditions, in a way that more closely mimics observed phenotypic plasticity. A simple competition-colonization model was combined with the new dynamic root scheme to explore the role of root adaptability in plant competition and landscape evolution in semi-arid environments. The influence of model representation of rooting strategy on the long term plant community composition

Range expansion through fragmented landscapes under a variable climate

PubMed Central

Bennie, Jonathan; Hodgson, Jenny A; Lawson, Callum R; Holloway, Crispin TR; Roy, David B; Brereton, Tom; Thomas, Chris D; Wilson, Robert J

2013-01-01

Ecological responses to climate change may depend on complex patterns of variability in weather and local microclimate that overlay global increases in mean temperature. Here, we show that high-resolution temporal and spatial variability in temperature drives the dynamics of range expansion for an exemplar species, the butterfly Hesperia comma. Using fine-resolution (5 m) models of vegetation surface microclimate, we estimate the thermal suitability of 906 habitat patches at the species' range margin for 27 years. Population and metapopulation models that incorporate this dynamic microclimate surface improve predictions of observed annual changes to population density and patch occupancy dynamics during the species' range expansion from 1982 to 2009. Our findings reveal how fine-scale, short-term environmental variability drives rates and patterns of range expansion through spatially localised, intermittent episodes of expansion and contraction. Incorporating dynamic microclimates can thus improve models of species range shifts at spatial and temporal scales relevant to conservation interventions. PMID:23701124

Introduction to special issue on carbon and landscape dynamics

USGS Publications Warehouse

Madej, Mary Ann; Wohl, Ellen E.

2016-01-01

In October, 2013, at the Geological Society of America annual meeting, a theme session focused on carbon and landscape dynamics.  That event led to interest in producing a special issue in ESPL compiling papers on this subject.  The 13 papers collected for this special issue reflect the diversity of recent geomorphic research, across a range of climatic and geomorphic settings, addressing some aspect of carbon dynamics.

High severity fires, positive fire feedbacks and alternative stable states in Athrotaxis rainforest ecosystems in western Tasmania.

NASA Astrophysics Data System (ADS)

Holz, A.; Wood, S.; Fletcher, M. S.; Ward, C.; Hopf, F.; Veblen, T. T.; Bowman, D. M. J. S.

2016-12-01

Recurrent landscape fires present a powerful selective force on plant regeneration strategies that form a continuum between vegetative resprouters and obligate seeders. In the latter case, reduction of the interval between fires, combined with factors that affect plant traits and regeneration dynamics can drive plant population to local extinction. Here we use Athrotaxis selaginoides, a relict fire-sensitive Gondwanan tree species that occurs in western Tasmania, as model system to investigate the putative impacts of climate change and variability and human management of fire. We integrate landscape ecology (island-wide scale), with field survey and dendrochronology (stand-scale) and sedimentary records (watershed and landscape-scales) to garner a better understanding of the timing and impact of landscape fire on the vegetation dynamics of Athrotaxis at multiple scales. Across the species range sedimentary charcoal and pollen concentrations indicate that the recovery time since the last fire has consistently lengthened over the last 10,000 yrs. Stand-scale tree-age and fire-scar reconstructions suggest that populations of the Athrotxis have survive very infrequent landscape fires over the last 4-6 centuries, but that fire severity has increased following European colonization causing population collapse of Athrotaxis and an associate shift in stand structure and composition that favor resprouter species over obligate seeders. Overall our findings suggest that the resistance to fires and postfire recovery of populations of A. selaginoides have gradually declined throughout the Holocene and rapidly declined after Europeans altered fire regimes, a trend that matches the fate other Gondwanan conifers in temperate rainforests elsewhere in the southern Hemisphere.

Probing Protein-Protein Interactions by Dynamic Force Correlation Spectroscopy

NASA Astrophysics Data System (ADS)

Barsegov, V.; Thirumalai, D.

2005-10-01

We develop a formalism for single molecule dynamic force spectroscopy to map the energy landscape of protein-protein complex (P1P2). The joint distribution P(τ1,τ2) of unbinding lifetimes τ1 and τ2, measurable in a compression-tension cycle, which accounts for the internal relaxation dynamics of the proteins under tension, shows that the histogram of τ1 is not Poissonian. The theory is applied to the forced unbinding of protein P1, modeled as a wormlike chain, from P1P2. We propose a new class of experiments which can resolve the effect of internal protein dynamics on the unbinding lifetimes.

Free Energy Landscape of Cellulose as a Driving Factor in the Mobility of Adsorbed Water.

PubMed

Kulasinski, Karol

2017-06-06

The diffusion coefficient of water adsorbed in hydrophilic porous materials, such as noncrystalline cellulose, depends on water activity. Faster diffusion at higher water concentrations is observed in experimental and modeling studies. In this paper, two asymptotic water concentrations, near-vacuum and fully saturated, are investigated at the surface of crystalline cellulose with molecular dynamics simulations. An increasing water concentration leads to significant changes in the free energy landscape due to perturbation of local electrostatic potential. Smoothening of strong energy minima, corresponding to sorption sites, and formation of layered structure facilitates water transport in the vicinity of cellulose. The determined transition probabilities and hydrogen bond stability reflect the changes in the energy landscape. As a result of a concentration increase, the emerging basins of attraction and spreading out of those existing in the diluted state lead to an increase in water entropy. Thermal fluctuations of cellulose are demonstrated to rearrange the landscape in the diluted limit, increase adsorbed water entropy, and decrease the water-cellulose H-bond lifetime.

Survival in patchy landscapes: the interplay between dispersal, habitat loss and fragmentation

PubMed Central

Niebuhr, Bernardo B. S.; Wosniack, Marina E.; Santos, Marcos C.; Raposo, Ernesto P.; Viswanathan, Gandhimohan M.; da Luz, Marcos G. E.; Pie, Marcio R.

2015-01-01

Habitat loss and fragmentation are important factors determining animal population dynamics and spatial distribution. Such landscape changes can lead to the deleterious impact of a significant drop in the number of species, caused by critically reduced survival rates for organisms. In order to obtain a deeper understanding of the threeway interplay between habitat loss, fragmentation and survival rates, we propose here a spatially explicit multi-scaled movement model of individuals that search for habitat. By considering basic ecological processes, such as predation, starvation (outside the habitat area), and competition, together with dispersal movement as a link among habitat areas, we show that a higher survival rate is achieved in instances with a lower number of patches of larger areas. Our results demonstrate how movement may counterbalance the effects of habitat loss and fragmentation in altered landscapes. In particular, they have important implications for conservation planning and ecosystem management, including the design of specific features of conservation areas in order to enhance landscape connectivity and population viability. PMID:26148488

Resilience and Alternative Stable States of Tropical Forest Landscapes under Shifting Cultivation Regimes

PubMed Central

2015-01-01

Shifting cultivation is a traditional agricultural practice in most tropical regions of the world and has the potential to provide for human livelihoods while hosting substantial biodiversity. Little is known about the resilience of shifting cultivation to increasing agricultural demands on the landscape or to unexpected disturbances. To investigate these issues, we develop a simple social-ecological model and implement it with literature-derived ecological parameters for six shifting cultivation landscapes from three continents. Analyzing the model with the tools of dynamical systems analysis, we show that such landscapes exhibit two stable states, one characterized by high forest cover and agricultural productivity, and another with much lower values of these traits. For some combinations of agricultural pressure and ecological parameters both of these states can potentially exist, and the actual state of the forest depends critically on its historic state. In many cases, the landscapes’ ‘ecological resilience’, or amount of forest that could be destroyed without shifting out of the forested stability domain, declined substantially at lower levels of agricultural pressure than would lead to maximum productivity. A measure of ‘engineering resilience’, the recovery time from standardized disturbances, was independent of ecological resilience. These findings suggest that maximization of short-term agricultural output may have counterproductive impacts on the long-term productivity of shifting cultivation landscapes and the persistence of forested areas. PMID:26406907

Towards a systems approach for understanding honeybee decline: a stocktaking and synthesis of existing models

PubMed Central

Becher, Matthias A; Osborne, Juliet L; Thorbek, Pernille; Kennedy, Peter J; Grimm, Volker

2013-01-01

The health of managed and wild honeybee colonies appears to have declined substantially in Europe and the United States over the last decade. Sustainability of honeybee colonies is important not only for honey production, but also for pollination of crops and wild plants alongside other insect pollinators. A combination of causal factors, including parasites, pathogens, land use changes and pesticide usage, are cited as responsible for the increased colony mortality. However, despite detailed knowledge of the behaviour of honeybees and their colonies, there are no suitable tools to explore the resilience mechanisms of this complex system under stress. Empirically testing all combinations of stressors in a systematic fashion is not feasible. We therefore suggest a cross-level systems approach, based on mechanistic modelling, to investigate the impacts of (and interactions between) colony and land management. We review existing honeybee models that are relevant to examining the effects of different stressors on colony growth and survival. Most of these models describe honeybee colony dynamics, foraging behaviour or honeybee – varroa mite – virus interactions. We found that many, but not all, processes within honeybee colonies, epidemiology and foraging are well understood and described in the models, but there is no model that couples in-hive dynamics and pathology with foraging dynamics in realistic landscapes. Synthesis and applications. We describe how a new integrated model could be built to simulate multifactorial impacts on the honeybee colony system, using building blocks from the reviewed models. The development of such a tool would not only highlight empirical research priorities but also provide an important forecasting tool for policy makers and beekeepers, and we list examples of relevant applications to bee disease and landscape management decisions. PMID:24223431

Towards a systems approach for understanding honeybee decline: a stocktaking and synthesis of existing models.

PubMed

Becher, Matthias A; Osborne, Juliet L; Thorbek, Pernille; Kennedy, Peter J; Grimm, Volker

2013-08-01

The health of managed and wild honeybee colonies appears to have declined substantially in Europe and the United States over the last decade. Sustainability of honeybee colonies is important not only for honey production, but also for pollination of crops and wild plants alongside other insect pollinators. A combination of causal factors, including parasites, pathogens, land use changes and pesticide usage, are cited as responsible for the increased colony mortality.However, despite detailed knowledge of the behaviour of honeybees and their colonies, there are no suitable tools to explore the resilience mechanisms of this complex system under stress. Empirically testing all combinations of stressors in a systematic fashion is not feasible. We therefore suggest a cross-level systems approach, based on mechanistic modelling, to investigate the impacts of (and interactions between) colony and land management.We review existing honeybee models that are relevant to examining the effects of different stressors on colony growth and survival. Most of these models describe honeybee colony dynamics, foraging behaviour or honeybee - varroa mite - virus interactions.We found that many, but not all, processes within honeybee colonies, epidemiology and foraging are well understood and described in the models, but there is no model that couples in-hive dynamics and pathology with foraging dynamics in realistic landscapes. Synthesis and applications . We describe how a new integrated model could be built to simulate multifactorial impacts on the honeybee colony system, using building blocks from the reviewed models. The development of such a tool would not only highlight empirical research priorities but also provide an important forecasting tool for policy makers and beekeepers, and we list examples of relevant applications to bee disease and landscape management decisions.

Dynamic reorganization of river basins.

PubMed

Willett, Sean D; McCoy, Scott W; Perron, J Taylor; Goren, Liran; Chen, Chia-Yu

2014-03-07

River networks evolve as migrating drainage divides reshape river basins and change network topology by capture of river channels. We demonstrate that a characteristic metric of river network geometry gauges the horizontal motion of drainage divides. Assessing this metric throughout a landscape maps the dynamic states of entire river networks, revealing diverse conditions: Drainage divides in the Loess Plateau of China appear stationary; the young topography of Taiwan has migrating divides driving adjustment of major basins; and rivers draining the ancient landscape of the southeastern United States are reorganizing in response to escarpment retreat and coastal advance. The ability to measure the dynamic reorganization of river basins presents opportunities to examine landscape-scale interactions among tectonics, erosion, and ecology.

Multiple loop conformations of peptides predicted by molecular dynamics simulations are compatible with nuclear magnetic resonance.

PubMed

Carstens, Heiko; Renner, Christian; Milbradt, Alexander G; Moroder, Luis; Tavan, Paul

2005-03-29

The affinity and selectivity of protein-protein interactions can be fine-tuned by varying the size, flexibility, and amino acid composition of involved surface loops. As a model for such surface loops, we study the conformational landscape of an octapeptide, whose flexibility is chemically steered by a covalent ring closure integrating an azobenzene dye into and by a disulfide bridge additionally constraining the peptide backbone. Because the covalently integrated azobenzene dyes can be switched by light between a bent cis state and an elongated trans state, six cyclic peptide models of strongly different flexibilities are obtained. The conformational states of these peptide models are sampled by NMR and by unconstrained molecular dynamics (MD) simulations. Prototypical conformations and the free-energy landscapes in the high-dimensional space spanned by the phi/psi angles at the peptide backbone are obtained by clustering techniques from the MD trajectories. Multiple open-loop conformations are shown to be predicted by MD particularly in the very flexible cases and are shown to comply with the NMR data despite the fact that such open-loop conformations are missing in the refined NMR structures.

Adaptation and Coevolution on an Emergent Global Competitive Landscape

NASA Astrophysics Data System (ADS)

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

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

Pathways for diffusion in the potential energy landscape of the network glass former SiO2

NASA Astrophysics Data System (ADS)

Niblett, S. P.; Biedermann, M.; Wales, D. J.; de Souza, V. K.

2017-10-01

We study the dynamical behaviour of a computer model for viscous silica, the archetypal strong glass former, and compare its diffusion mechanism with earlier studies of a fragile binary Lennard-Jones liquid. Three different methods of analysis are employed. First, the temperature and time scale dependence of the diffusion constant is analysed. Negative correlation of particle displacements influences transport properties in silica as well as in fragile liquids. We suggest that the difference between Arrhenius and super-Arrhenius diffusive behaviour results from competition between the correlation time scale and the caging time scale. Second, we analyse the dynamics using a geometrical definition of cage-breaking transitions that was proposed previously for fragile glass formers. We find that this definition accurately captures the bond rearrangement mechanisms that control transport in open network liquids, and reproduces the diffusion constants accurately at low temperatures. As the same method is applicable to both strong and fragile glass formers, we can compare correlation time scales in these two types of systems. We compare the time spent in chains of correlated cage breaks with the characteristic caging time and find that correlations in the fragile binary Lennard-Jones system persist for an order of magnitude longer than those in the strong silica system. We investigate the origin of the correlation behaviour by sampling the potential energy landscape for silica and comparing it with the binary Lennard-Jones model. We find no qualitative difference between the landscapes, but several metrics suggest that the landscape of the fragile liquid is rougher and more frustrated. Metabasins in silica are smaller than those in binary Lennard-Jones and contain fewer high-barrier processes. This difference probably leads to the observed separation of correlation and caging time scales.

The Influence of Agroforestry and Other Land-Use Types on the Persistence of a Sumatran Tiger ( Panthera tigris sumatrae) Population: An Individual-Based Model Approach

NASA Astrophysics Data System (ADS)

Imron, Muhammad Ali; Herzog, Sven; Berger, Uta

2011-08-01

The importance of preserving both protected areas and their surrounding landscapes as one of the major conservation strategies for tigers has received attention over recent decades. However, the mechanism of how land-use surrounding protected areas affects the dynamics of tiger populations is poorly understood. We developed Panthera Population Persistence (PPP)—an individual-based model—to investigate the potential mechanism of the Sumatran tiger population dynamics in a protected area and under different land-use scenarios surrounding the reserve. We tested three main landscape compositions (single, combined and real land-uses of Tesso-Nilo National Park and its surrounding area) on the probability of and time to extinction of the Sumatran tiger over 20 years in Central Sumatra. The model successfully explains the mechanisms behind the population response of tigers under different habitat landscape compositions. Feeding and mating behaviours of tigers are key factors, which determined population persistence in a heterogeneous landscape. All single land-use scenarios resulted in tiger extinction but had a different probability of extinction within 20 years. If tropical forest was combined with other land-use types, the probability of extinction was smaller. The presence of agroforesty and logging concessions adjacent to protected areas encouraged the survival of tiger populations. However, with the real land-use scenario of Tesso-Nilo National Park, tigers could not survive for more than 10 years. Promoting the practice of agroforestry systems surrounding the park is probably the most reasonable way to steer land-use surrounding the Tesso-Nilo National Park to support tiger conservation.

The potential and flux landscape theory of evolution.

PubMed

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

2012-08-14

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

Folding domain B of protein A on a dynamically partitioned free energy landscape.

PubMed

Nelson, Erik D; Grishin, Nick V

2008-02-05

The B domain of staphylococcal protein A (BdpA) is a small helical protein that has been studied intensively in kinetics experiments and detailed computer simulations that include explicit water. The simulations indicate that BdpA needs to reorganize in crossing the transition barrier to facilitate folding its C-terminal helix (H3) onto the nucleus formed from helices H1 and H2. This process suggests frustration between two partially ordered forms of the protein, but recent varphi value measurements indicate that the transition structure is relatively constant over a broad range of temperatures. Here we develop a simplistic model to investigate the folding transition in which properties of the free energy landscape can be quantitatively compared with experimental data. The model is a continuation of the Muñoz-Eaton model to include the intermittency of contacts between structured parts of the protein, and the results compare variations in the landscape with denaturant and temperature to varphi value measurements and chevron plots of the kinetic rates. The topography of the model landscape (in particular, the feature of frustration) is consistent with detailed simulations even though variations in the varphi values are close to measured values. The transition barrier is smaller than indicated by the chevron data, but it agrees in order of magnitude with a similar alpha-carbon type of model. Discrepancies with the chevron plots are investigated from the point of view of solvent effects, and an approach is suggested to account for solvent participation in the model.

Spatial dynamics of thermokarst and thermo-erosion at lakes and ponds in North Siberia and Northwest Alaska using high-resolution remote sensing

NASA Astrophysics Data System (ADS)

Grosse, G.; Tillapaugh, M.; Romanovsky, V. E.; Walter, K. M.; Plug, L. J.

2008-12-01

Formation, growth, and drainage of thermokarst lakes in ice-rich permafrost deposits are important factors of landscape dynamics in extent Arctic lowlands. Monitoring of spatial and temporal dynamics of such lakes will allow an assessment of permafrost stability and enhance the capabilities for modelling and quantifying biogeochemical processes related to permafrost degradation in a warming Arctic. In this study we use high-resolution remote sensing and GIS to analyze the development of thermokarst lakes and ponds in two study regions in North Siberia and Northwest Alaska. The sites are 1) the Cherskii region in the Kolyma lowland (Siberia) and 2) the Kitluk River area on the northern Seward Peninsula (Alaska). Both regions are characterized by continuous permafrost, a highly dissected and dynamic thermokarst landscape, uplands of Late Pleistocene permafrost deposits with high excess ice contents, and a large total volume of permafrost-stored carbon. These ice-rich Yedoma or Yedoma-like deposits are highly vulnerable to permafrost degradation forced by climate warming or other surface disturbance. Time series of high- resolution imagery (aerial, Corona, Ikonos, Alos Prism) covering more than 50 years of lake dynamics allow detailed assessments of processes and spatial patterns of thermokarst lake expansion and drainage in continuous permafrost. Time series of high-resolution imagery (aerial, Corona, Ikonos, Alos Prism) covering more than 50 years of lake dynamics allow detailed assessments of processes and spatial patterns of thermokarst lake expansion and drainage in continuous permafrost. Processes identified include thaw slumping, wave undercutting of frozen sediments or peat blocks and subsequent mass wasting, thaw collapse of near-shore zones, sinkhole formation and ice-wedge tunnelling, and gully formation by thermo-erosion. We use GIS-based tools to relate the remote sensing results to field data (ground ice content, topography, lithology, and relative age of landscape units). Results exhibit a very dynamic lake environment at both sites strongly related to landscape history and past cryolithological development. Lake shore erosion rates reach values of more than 1 m per year over the 50 year observation period at some sites. Permafrost degradation processes are identified as a key driver of both lake expansion and drainage.

Synchrony in small mammal community dynamics across a forested landscape

Treesearch

Ryan B. Stephens; Daniel J. Hocking; Mariko Yamasaki; Rebecca J. Rowe

2016-01-01

Long- term studies at local scales indicate that fluctuations in abundance among trophically similar species are often temporally synchronized. Complementary studies on synchrony across larger spatial extents are less common, as are studies that investigate the subsequent impacts on community dynamics across the landscape. We investigate the impact of species...

Energy landscape scheme for an intuitive understanding of complex domain dynamics in ferroelectric thin films

NASA Astrophysics Data System (ADS)

Heon Kim, Tae; Yoon, Jong-Gul; Hyub Baek, Seung; Park, Woong-Kyu; Mo Yang, Sang; Yup Jang, Seung; Min, Taeyuun; Chung, Jin-Seok; Eom, Chang-Beom; Won Noh, Tae

2015-07-01

Fundamental understanding of domain dynamics in ferroic materials has been a longstanding issue because of its relevance to many systems and to the design of nanoscale domain-wall devices. Despite many theoretical and experimental studies, a full understanding of domain dynamics still remains incomplete, partly due to complex interactions between domain-walls and disorder. We report domain-shape-preserving deterministic domain-wall motion, which directly confirms microscopic return point memory, by observing domain-wall breathing motion in ferroelectric BiFeO3 thin film using stroboscopic piezoresponse force microscopy. Spatial energy landscape that provides new insights into domain dynamics is also mapped based on the breathing motion of domain walls. The evolution of complex domain structure can be understood by the process of occupying the lowest available energy states of polarization in the energy landscape which is determined by defect-induced internal fields. Our result highlights a pathway for the novel design of ferroelectric domain-wall devices through the engineering of energy landscape using defect-induced internal fields such as flexoelectric fields.

Energy landscape scheme for an intuitive understanding of complex domain dynamics in ferroelectric thin films.

PubMed

Kim, Tae Heon; Yoon, Jong-Gul; Baek, Seung Hyub; Park, Woong-kyu; Yang, Sang Mo; Yup Jang, Seung; Min, Taeyuun; Chung, Jin-Seok; Eom, Chang-Beom; Noh, Tae Won

2015-07-01

Fundamental understanding of domain dynamics in ferroic materials has been a longstanding issue because of its relevance to many systems and to the design of nanoscale domain-wall devices. Despite many theoretical and experimental studies, a full understanding of domain dynamics still remains incomplete, partly due to complex interactions between domain-walls and disorder. We report domain-shape-preserving deterministic domain-wall motion, which directly confirms microscopic return point memory, by observing domain-wall breathing motion in ferroelectric BiFeO3 thin film using stroboscopic piezoresponse force microscopy. Spatial energy landscape that provides new insights into domain dynamics is also mapped based on the breathing motion of domain walls. The evolution of complex domain structure can be understood by the process of occupying the lowest available energy states of polarization in the energy landscape which is determined by defect-induced internal fields. Our result highlights a pathway for the novel design of ferroelectric domain-wall devices through the engineering of energy landscape using defect-induced internal fields such as flexoelectric fields.

Energy landscape scheme for an intuitive understanding of complex domain dynamics in ferroelectric thin films

PubMed Central

Heon Kim, Tae; Yoon, Jong-Gul; Hyub Baek, Seung; Park, Woong-kyu; Mo Yang, Sang; Yup Jang, Seung; Min, Taeyuun; Chung, Jin-Seok; Eom, Chang-Beom; Won Noh, Tae

2015-01-01

Fundamental understanding of domain dynamics in ferroic materials has been a longstanding issue because of its relevance to many systems and to the design of nanoscale domain-wall devices. Despite many theoretical and experimental studies, a full understanding of domain dynamics still remains incomplete, partly due to complex interactions between domain-walls and disorder. We report domain-shape-preserving deterministic domain-wall motion, which directly confirms microscopic return point memory, by observing domain-wall breathing motion in ferroelectric BiFeO3 thin film using stroboscopic piezoresponse force microscopy. Spatial energy landscape that provides new insights into domain dynamics is also mapped based on the breathing motion of domain walls. The evolution of complex domain structure can be understood by the process of occupying the lowest available energy states of polarization in the energy landscape which is determined by defect-induced internal fields. Our result highlights a pathway for the novel design of ferroelectric domain-wall devices through the engineering of energy landscape using defect-induced internal fields such as flexoelectric fields. PMID:26130159

Determinants of extinction-colonization dynamics in Mediterranean butterflies: the role of landscape, climate and local habitat features.

PubMed

Fernández-Chacón, Albert; Stefanescu, Constantí; Genovart, Meritxell; Nichols, James D; Hines, James E; Páramo, Ferran; Turco, Marco; Oro, Daniel

2014-01-01

Many species are found today in the form of fragmented populations occupying patches of remnant habitat in human-altered landscapes. The persistence of these population networks requires a balance between extinction and colonization events assumed to be primarily related to patch area and isolation, but the contribution of factors such as the characteristics of patch and matrix habitats, the species' traits (habitat specialization and dispersal capabilities) and variation in climatic conditions have seldom been evaluated simultaneously. The identification of environmental variables associated with patch occupancy and turnover may be especially useful to enhance the persistence of multiple species under current global change. However, for robust inference on occupancy and related parameters, we must account for detection errors, a commonly overlooked problem that leads to biased estimates and misleading conclusions about population dynamics. Here, we provide direct empirical evidence of the effects of different environmental variables on the extinction and colonization rates of a rich butterfly community in the western Mediterranean. The analysis was based on a 17-year data set containing detection/nondetection data on 73 butterfly species for 26 sites in north-eastern Spain. Using multiseason occupancy models, which take into account species' detectability, we were able to obtain robust estimates of local extinction and colonization probabilities for each species and test the potential effects of site covariates such as the area of suitable habitat, topographic variability, landscape permeability around the site and climatic variability in aridity conditions. Results revealed a general pattern across species with local habitat composition and landscape features as stronger predictors of occupancy dynamics compared with topography and local aridity. Increasing area of suitable habitat in a site strongly decreased local extinction risks and, for a number of species, both higher amounts of suitable habitat and more permeable landscapes increased colonization rates. Nevertheless, increased topographic variability decreased the extinction risk of bad dispersers, a group of species with significantly lower colonization rates. Our models predicted higher sensitivity of the butterfly assemblages to deterministic changes in habitat features rather than to stochastic weather patterns, with some relationships being clearly dependent on the species' traits. © 2013 The Authors. Journal of Animal Ecology © 2013 British Ecological Society.

Society and Ecosystem Carbon Budget through Life Cycle Assessment: Results from Asian Drylands

NASA Astrophysics Data System (ADS)

Chen, J.

2017-12-01

Land use, land cover changes, and ecosystem-specific management practices are recognized for their roles in mediating the climatic effects on ecosystem structure and function. A major challenge is that our understanding and forecasting of ecosystem functions, such as C fluxes, cannot rely solely on conventional biophysical regulations from the local ecosystem to the global scale. A second challenge lies in quantifying the magnitude of the C fluxes from managed ecosystems and landscapes over the lifetime of the C cycle, and to deduct the various energy inputs during management. Our specific challenge here is to quantify the landscape-scale C footprint of both managed agricultural-forest landscapes and people - the societal input and engagement in ecosystem studies. Using the East Asia Drylands (Chen et al., 2013) and an agricultural watershed in southwestern Michigan as a test bed, the mechanisms (carbon as an example) from both human activities and biophysical changes on ecosystem C dynamics at different temporal and spatial scales are proposed to be explored by modeling total net ecosystem C production (physical and social C fluxes), performing a spatially-explicit life cycle assessment (LCA) on the total C production. Remote sensing technology, available geospatial data, records of management practices, surveys of historical practices, a land surface model, and in situ measurements of C fluxes are all needed to achieve our objectives. Our case study calls for direct involvement of society as both the driver and beneficiary of ecosystem dynamics. Reference Chen, J., Wan, S., Henebry, G., Qi, J., Gutman, G., Sun, G., and Kappas, M. (Eds.) 2013. Dryland East Asia (DEA): Land Dynamics Amid Social And Climate Change. HEP and De Gruyter, 470 pp.

Landscape fragmentation affects responses of avian communities to climate change.

PubMed

Jarzyna, Marta A; Porter, William F; Maurer, Brian A; Zuckerberg, Benjamin; Finley, Andrew O

2015-08-01

Forecasting the consequences of climate change is contingent upon our understanding of the relationship between biodiversity patterns and climatic variability. While the impacts of climate change on individual species have been well-documented, there is a paucity of studies on climate-mediated changes in community dynamics. Our objectives were to investigate the relationship between temporal turnover in avian biodiversity and changes in climatic conditions and to assess the role of landscape fragmentation in affecting this relationship. We hypothesized that community turnover would be highest in regions experiencing the most pronounced changes in climate and that these patterns would be reduced in human-dominated landscapes. To test this hypothesis, we quantified temporal turnover in avian communities over a 20-year period using data from the New York State Breeding Atlases collected during 1980-1985 and 2000-2005. We applied Bayesian spatially varying intercept models to evaluate the relationship between temporal turnover and temporal trends in climatic conditions and landscape fragmentation. We found that models including interaction terms between climate change and landscape fragmentation were superior to models without the interaction terms, suggesting that the relationship between avian community turnover and changes in climatic conditions was affected by the level of landscape fragmentation. Specifically, we found weaker associations between temporal turnover and climatic change in regions with prevalent habitat fragmentation. We suggest that avian communities in fragmented landscapes are more robust to climate change than communities found in contiguous habitats because they are comprised of species with wider thermal niches and thus are less susceptible to shifts in climatic variability. We conclude that highly fragmented regions are likely to undergo less pronounced changes in composition and structure of faunal communities as a result of climate change, whereas those changes are likely to be greater in contiguous and unfragmented habitats. © 2015 John Wiley & Sons Ltd.

Spatiotemporal models for data-anomaly detection in dynamic environmental monitoring campaigns

Treesearch

E.W. Dereszynski; T.G. Dietterich

2011-01-01

The ecological sciences have benefited greatly from recent advances in wireless sensor technologies. These technologies allow researchers to deploy networks of automated sensors, which can monitor a landscape at very fine temporal and spatial scales. However, these networks are subject to harsh conditions, which lead to malfunctions in individual sensors and failures...

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

EPA Science Inventory

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

The Hawaii protocol for scientific monitoring of coffee berry borer: a model for coffee agroecosystems worldwide

USDA-ARS?s Scientific Manuscript database

Coffee Berry Borer (CBB) is the most devastating insect pest for coffee crops worldwide. We developed a scientific monitoring protocol aimed at capturing and quantifying the dynamics and impact of this invasive insect pest as well as the development of its host plant across a heterogeneous landscape...

Emerging Team Leader Dynamics in Contingent Situations: A Doctoral-Level Simulation

ERIC Educational Resources Information Center

Rojas, Ronald

2017-01-01

The literature on how a team leader emerges during the initial stages of a team formation presents a divergent landscape of possibilities. Most of the approaches focus on attributes, personality types, the influence of social tendencies, or relational capabilities. Yet these different theories and models suggest that many questions remain on this…

An integrated view of complex landscapes: a big data-model integration approach to trans-disciplinary science

USDA-ARS?s Scientific Manuscript database

The Earth is a complex system comprised of many interacting spatial and temporal scales. Understanding, predicting, and managing for these dynamics requires a trans-disciplinary integrated approach. Although there have been calls for this integration, a general approach is needed. We developed a Tra...

Homogenous Nucleation and Crystal Growth in a Model Liquid from Direct Energy Landscape Sampling Simulation

NASA Astrophysics Data System (ADS)

Walter, Nathan; Zhang, Yang

Nucleation and crystal growth are understood to be activated processes involving the crossing of free-energy barriers. Attempts to capture the entire crystallization process over long timescales with molecular dynamic simulations have met major obstacles because of molecular dynamics' temporal constraints. Herein, we circumvent this temporal limitation by using a brutal-force, metadynamics-like, adaptive basin-climbing algorithm and directly sample the free-energy landscape of a model liquid Argon. The algorithm biases the system to evolve from an amorphous liquid like structure towards an FCC crystal through inherent structure, and then traces back the energy barriers. Consequently, the sampled timescale is macroscopically long. We observe that the formation of a crystal involves two processes, each with a unique temperature-dependent energy barrier. One barrier corresponds to the crystal nucleus formation; the other barrier corresponds to the crystal growth. We find the two processes dominate in different temperature regimes. Compared to other computation techniques, our method requires no assumptions about the shape or chemical potential of the critical crystal nucleus. The success of this method is encouraging for studying the crystallization of more complex

Free energy landscape of a minimalist salt bridge model.

PubMed

Li, Xubin; Lv, Chao; Corbett, Karen M; Zheng, Lianqing; Wu, Dongsheng; Yang, Wei

2016-01-01

Salt bridges are essential to protein stability and dynamics. Despite the importance, there has been scarce of detailed discussion on how salt bridge partners interact with each other in distinct solvent exposed environments. In this study, employing a recent generalized orthogonal space tempering (gOST) method, we enabled efficient molecular dynamics simulation of repetitive breaking and reforming of salt bridge structures within a minimalist salt-bridge model, the Asp-Arg dipeptide and thereby were able to map its detailed free energy landscape in aqueous solution. Free energy surface analysis shows that although individually-solvated states are more favorable, salt-bridge states still occupy a noticeable portion of the overall population. Notably, the competing forces, e.g. intercharge attractions that drive the formation of salt bridges and solvation forces that pull the charged groups away from each other, are energetically comparable. As the result, the salt bridge stability is highly tunable by local environments; for instance when local water molecules are perturbed to interact more strongly with each other, the population of the salt-bridge states is likely to increase. Our results reveal the critical role of local solvent structures in modulating salt-bridge partner interactions and imply the importance of water fluctuations on conformational dynamics that involves solvent accessible salt bridge formations. © 2015 The Protein Society.

How spatio-temporal habitat connectivity affects amphibian genetic structure.

PubMed

Watts, Alexander G; Schlichting, Peter E; Billerman, Shawn M; Jesmer, Brett R; Micheletti, Steven; Fortin, Marie-Josée; Funk, W Chris; Hapeman, Paul; Muths, Erin; Murphy, Melanie A

2015-01-01

Heterogeneous landscapes and fluctuating environmental conditions can affect species dispersal, population genetics, and genetic structure, yet understanding how biotic and abiotic factors affect population dynamics in a fluctuating environment is critical for species management. We evaluated how spatio-temporal habitat connectivity influences dispersal and genetic structure in a population of boreal chorus frogs (Pseudacris maculata) using a landscape genetics approach. We developed gravity models to assess the contribution of various factors to the observed genetic distance as a measure of functional connectivity. We selected (a) wetland (within-site) and (b) landscape matrix (between-site) characteristics; and (c) wetland connectivity metrics using a unique methodology. Specifically, we developed three networks that quantify wetland connectivity based on: (i) P. maculata dispersal ability, (ii) temporal variation in wetland quality, and (iii) contribution of wetland stepping-stones to frog dispersal. We examined 18 wetlands in Colorado, and quantified 12 microsatellite loci from 322 individual frogs. We found that genetic connectivity was related to topographic complexity, within- and between-wetland differences in moisture, and wetland functional connectivity as contributed by stepping-stone wetlands. Our results highlight the role that dynamic environmental factors have on dispersal-limited species and illustrate how complex asynchronous interactions contribute to the structure of spatially-explicit metapopulations.

Directed Magnetic Particle Transport above Artificial Magnetic Domains Due to Dynamic Magnetic Potential Energy Landscape Transformation.

PubMed

Holzinger, Dennis; Koch, Iris; Burgard, Stefan; Ehresmann, Arno

2015-07-28

An approach for a remotely controllable transport of magnetic micro- and/or nanoparticles above a topographically flat exchange-bias (EB) thin film system, magnetically patterned into parallel stripe domains, is presented where the particle manipulation is achieved by sub-mT external magnetic field pulses. Superparamagnetic core-shell particles are moved stepwise by the dynamic transformation of the particles' magnetic potential energy landscape due to the external magnetic field pulses without affecting the magnetic state of the thin film system. The magnetic particle velocity is adjustable in the range of 1-100 μm/s by the design of the substrate's magnetic field landscape (MFL), the particle-substrate distance, and the magnitude of the applied external magnetic field pulses. The agglomeration of magnetic particles is avoided by the intrinsic magnetostatic repulsion of particles due to the parallel alignment of the particles' magnetic moments perpendicular to the transport direction and parallel to the surface normal of the substrate during the particle motion. The transport mechanism is modeled by a quantitative theory based on the precise knowledge of the sample's MFL and the particle-substrate distance.

Ecological correlates of population genetic structure: a comparative approach using a vertebrate metacommunity.

PubMed

Manier, Mollie K; Arnold, Stevan J

2006-12-07

Identifying ecological factors associated with population genetic differentiation is important for understanding microevolutionary processes and guiding the management of threatened populations. We identified ecological correlates of several population genetic parameters for three interacting species (two garter snakes and an anuran) that occupy a common landscape. Using multiple regression analysis, we found that species interactions were more important in explaining variation in population genetic parameters than habitat and nearest-neighbour characteristics. Effective population size was best explained by census size, while migration was associated with differences in species abundance. In contrast, genetic distance was poorly explained by the ecological correlates that we tested, but geographical distance was prominent in models for all species. We found substantially different population dynamics for the prey species relative to the two predators, characterized by larger effective sizes, lower gene flow and a state of migration-drift equilibrium. We also identified an escarpment formed by a series of block faults that serves as a barrier to dispersal for the predators. Our results suggest that successful landscape-level management should incorporate genetic and ecological data for all relevant species, because even closely associated species can exhibit very different population genetic dynamics on the same landscape.

Thermokarst transformation of permafrost preserved glaciated landscapes.

NASA Astrophysics Data System (ADS)

Kokelj, S.; Tunnicliffe, J. F.; Fraser, R.; Kokoszka, J.; Lacelle, D.; Lantz, T. C.; Lamoureux, S. F.; Rudy, A.; Shakil, S.; Tank, S. E.; van der Sluijs, J.; Wolfe, S.; Zolkos, S.

2017-12-01

Thermokarst is the fundamental mechanism of landscape change and a primary driver of downstream effects in a warming circumpolar world. Permafrost degradation is inherently non-linear because latent heat effects can inhibit thawing. However, once this thermal transition is crossed thermokarst can accelerate due to the interaction of thermal, physical and ecological feedbacks. In this paper we highlight recent climate and precipitation-driven intensification of thaw slumping that is transforming permafrost preserved glaciated landscapes in northwestern Canada. The continental distribution of slump affected terrain reflects glacial extents and recessional positions of the Laurentide Ice sheet. On this basis and in conjunction with intense thermokarst in cold polar environments, we highlight the critical roles of geological legacy and climate history in dictating the sensitivity of permafrost terrain. These glaciated landscapes, maintained in a quasi-stable state throughout much of the late Holocene are now being transformed into remarkably dynamic environments by climate-driven thermokarst. Individual disturbances displace millions of cubic metres of previously frozen material downslope, converting upland sedimentary stores into major source areas. Precipitation-driven evacuation of sediment by fluidized mass flows perpetuates non-linear enlargement of disturbances. The infilling of valleys with debris deposits tens of metres thick increases stream base-levels and promotes rapid valley-side erosion. These processes destabilize adjacent slopes and proliferate disturbance effects. Physically-based modeling of thaw slump development provides insight into the trajectories of landscape change, and the mapping of fluvial linkages portrays the cascade of effects across watershed scales. Post-glacial or "paraglacial" models of landscape evolution provide a useful framework for understanding the nature and magnitude of climate-driven changes in permafrost preserved glaciated landscapes.

Occupancy dynamics in human-modified landscapes in a tropical island: implications for conservation design

USGS Publications Warehouse

Irizarry, Julissa I.; Collazo, Jaime A.; Dinsmore, Stephen J.

2016-01-01

AimAvian communities in human-modified landscapes exhibit varying patterns of local colonization and extinction rates, determinants of species occurrence. Our objective was to model these processes to identify habitat features that might enable movements and account for occupancy patterns in habitat matrices between the Guanica and Susua forest reserves. This knowledge is central to conservation design, particularly in ever changing insular landscapes.LocationSouth-western Puerto Rico.MethodsWe used a multiseason occupancy modelling approach to quantify seasonal estimates of occupancy, and colonization and extinction rates of seven resident avian species surveyed over five seasons from January 2010 to June 2011. We modelled parameters by matrix type, expressions of survey station isolation, quality, amount of forest cover and context (embedded in forest patch).ResultsSeasonal occupancy remained stable throughout the study for all species, consistent with seasonally constant colonization and extinction probabilities. Occupancy was mediated by matrix type, higher in reserves and forested matrix than in the urban and agricultural matrices. This pattern is in accord with the forest affinities of all but an open-habitat specialist. Puerto Rican Spindalis (Spindalis portoricensis) exhibited high occupancy in the urban matrix, highlighting the adaptability of some insular species to novel environments. Highest colonization rates occurred when perching structures were at ≤ 500 m. Survey stations with at least three fruiting tree species and 61% forest cover exhibited lowest seasonal extinction rates.Main conclusionsOur work identified habitat features that influenced seasonal probabilities of colonization and extinction in a human-modified landscape. Conservation design decisions are better informed with increased knowledge about interpatch distances to improve matrix permeability, and habitat features that increase persistence or continued use of habitat stepping stones. A focus on dynamic processes is valuable because conservation actions directly influence colonization and extinction rates, and thus, a quantitative means to gauge their benefit.

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

PubMed Central

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

2015-01-01

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

Climate-driven spatial dynamics of plague among prairie dog colonies.

PubMed

Snäll, T; O'Hara, R B; Ray, C; Collinge, S K

2008-02-01

We present a Bayesian hierarchical model for the joint spatial dynamics of a host-parasite system. The model was fitted to long-term data on regional plague dynamics and metapopulation dynamics of the black-tailed prairie dog, a declining keystone species of North American prairies. The rate of plague transmission between colonies increases with increasing precipitation, while the rate of infection from unknown sources decreases in response to hot weather. The mean annual dispersal distance of plague is about 10 km, and topographic relief reduces the transmission rate. Larger colonies are more likely to become infected, but colony area does not affect the infectiousness of colonies. The results suggest that prairie dog movements do not drive the spread of plague through the landscape. Instead, prairie dogs are useful sentinels of plague epizootics. Simulations suggest that this model can be used for predicting long-term colony and plague dynamics as well as for identifying which colonies are most likely to become infected in a specific year.

Stability, Bistability, and Critical Thresholds in Fire-prone Forested Landscapes: How Frequency and Intensity of Disturbance Interact and Influence Forest Cover

NASA Astrophysics Data System (ADS)

Miller, A. D.

2015-12-01

Many aspects of disturbance processes can have large impacts on the composition of plant communities, and associated changes in land cover type in turn have biogeochemical feedbacks to climate. In particular, changes to disturbance regimes can potentially change the number and stability of equilibrial states, and plant community states can differ dramatically in their carbon (C) dynamics, energy balance, and hydrology. Using the Klamath region of northern California as a model system, we present a theoretical analysis of how changes to climate and associated fire dynamics can disrupt high-carbon, long-lived conifer forests and replace them with shrub-chaparral communities that have much lower biomass and are more pyrogenic. Specifically, we develop a tractable model of plant community dynamics, structured by size class, life-history traits, lottery-type competition, and species-specific responses to disturbance. We assess the stability of different states in terms of disturbance frequency and intensity, and quantitatively partition long-term low-density population growth rates into mechanisms that influence critical transitions from stable to bistable behavior. Our findings show how different aspects of disturbance act and interact to control competitive outcomes and stable states, hence ecosystem-atmosphere C exchange. Forests tend to dominate in low frequency and intensity regimes, while shrubs dominate at high fire frequency and intensity. In other regimes, the system is bistable, and the fate of the system depends both on initial conditions and random chance. Importantly, the system can cross a critical threshold where hysteresis prevents easy return to the prior forested state. We conclude that changes in disturbance-recovery dynamics driven by projected climate change can shift this system away from forest dominated in the direction of shrub-dominated landscape. This will result in a large net C release from the landscape, and alter biophysical ecosystem-climate interactions.