DIMACS/MBI Workshop in Quantitative Landscape Ecology and Environmental Sustainability

Workshop July 3 - 7, 2012 (with optional pre-meeting July 1 - 2 and optional field trip July 7 - 11, 2012 )
University of KwaZulu-Natal, Durban, South Africa

Barend Erasmus, University of the Witwatersrand, Barend.Erasmus at wits.ac.za
Holly Gaff, Old Dominion University, Virginia, hgaff at odu.edu
Wayne Getz, UC Berkeley, wgetz at berkeley.edu
Marty Golubitsky, Mathematical Biosciences Institute - Ohio State University, mg at mbi.osu.edu
Victoria Goodall, SAEON, Cape Town, South Africa, victoria at saeon.ac.za
Kesh Govinder, School of Mathematics, Statistics, and Computer Science, UKZN, Durban, govinder at ukzn.ac.za
Fred Roberts, Rutgers University, froberts at dimacs.rutgers.edu
Sadie Ryan, SUNY Syracuse, sjryan at esf.edu

Presented under the auspices of the DIMACS/MBI US-African BioMathematics Initiative.

This Workshop is jointly sponsored by:


Brian Clough, School of Environmental & Biological Sciences, Department of Ecology & Evolution, Rutgers, The State University of New Jersey

Title: Evaluation of several interpolation methods for mapping soil organic carbon at the regional scale

Accurate estimation of soil organic carbon (SOC) stocks at broad spatial scales is crucial to the development of a global carbon accounting effort, but reducing uncertainty in these estimates to a level acceptable to policy makers remains a difficult task. Geostatistical interpolation has received increased attention as a preferred approach for mapping SOC distribution. However, there is no single agreed upon interpolation method, and models may differ substantially in how well they account for spatial error. Our objective is to evaluate the performance of several popular interpolation models in mapping SOC distribution for forests of the coastal plain region of New Jersey. Four interpolation procedures are used: ordinary kriging (OK), universal kriging (UK), maximum likelihood interpolation, and spatial Bayesian hierarchical interpolation (i.e. -F!Bayesian kriging"). Both SOC stock and aboveground biomass have been measured for 150 sampling locations across the region, and these data are applied to map soil organic carbon using each of the aforementioned interpolation models. An additional set of sampling locations (n=50) is used for validation, and the models are evaluated by comparing mean, mean squared, and absolute error. By directly comparing the performance of several interpolation methods for a single dataset, the results of this study contribute to the development of a coherent statistical framework for obtaining regional estimates of SOC stocks

Mia T. Comeros-Raynal, John Howard Choat, Beth A. Polidoro, Kendall D. Clements, Rene Abesamis, Matthew T. Craig, Muhammad Erdi Lazuardi, Jennifer McIlwain, Andreas Muljadi, Robert F. Myers, Cleto L. Na-Aqola, Jr., Shinta Pardede, Luiz A. Rocha, Barry Russell, Jonnell C. Sanciangco, Brian Stockwell Heather Harwell, Kent E. Carpenter

Title: Conservation status of key players in coral reef ecosystems: the parrotfishes and surgeonfishes

Parrotfishes and surgeonfishes are iconic reef inhabitants that perform important functional roles in the dynamics of coral reef systems. This is a consequence of their varied feeding behaviors ranging from targeted consumption of living plant material (primarily surgeonfishes) to feeding on detrital aggregates that are either scraped from the reef surface or excavated from the deeper reef substratum (primarily parrotfishes). Increased fishing pressure and widespread habitat destruction have led to population declines for several species of these two groups. Therefore, species-specific data on global distribution, population status, life history characteristics, and major threats were compiled for each of the 179 known species of parrotfishes and surgeonfishes to determine the likelihood of extinction of each species under the Categories and Criteria of the IUCN Red List of Threatened Species. Due in part to the extensive distributions of most species and the life history traits exhibited in these two families, only three (1.7%) of the species are listed at an elevated risk of global extinction. The majority of the parrotfishes and surgeonfishes (86%) are listed as Least Concern, 10% are listed as Data Deficient and 1% are listed as Near Threatened. The risk of localized extinction, however, is higher in some areas, particularly in the Coral Triangle region. This region of highest biodiversity for the parrotfishes and surgeonfishes is highly impacted by a multitude of threats including overfishing, pollution and rampant coral reef area loss and degradation. Other geographical areas of concern include Oceania and the Western Indian Ocean where a high percentage of species is threatened by exploitation. Globally, the relatively low proportion of species globally listed in threatened Categories is highly encouraging, and some conservation successes are attributed to concentrated conservation efforts. However, with the growing realization of man-F"s profound impact on the planet, conservation actions such as improved marine reserve networks, more stringent fishing regulations, and continued monitoring of the population status at the species and community levels are imperative for the prevention of species loss in these groups of important and iconic coral reef fishes.

Sarah E Haas, Mevin B Hooten, David Rizzo, Ross K Meentemeyer, Department of Geography & Earth Sciences, University of North Carolina

Title: Landscape epidemiology of biodiversity-disease risk relationships in a multihost plant pathogen invasion


Mounting evidence indicates that biodiversity loss can increase infectious disease transmission1. Although effects of species diversity on disease risk have been reasonably well-studied in a range of host-pathogen systems, our understanding of the diversity-disease hypothesis for generalist plant pathogens in natural ecosystems is limited. We use a landscape epidemiological approach with observational data to examine two scenarios regarding species diversity effects on the emerging plant pathogen Phytophthora ramorum across a broad, heterogeneous ecoregion of coastal California (n=280 plots): (1) an 'amplification effect' exists in which disease risk is higher in areas with greater plant diversity due to the pathogen's wide host range, or (2) a 'dilution effect' where disease risk is reduced with increasing plant diversity due to lower competency of alternative hosts. P. ramorum, etiological agent of the forest disease Sudden Oak Death, is a generalist pathogen that infects dozens of plant species in the Pacific Northwest of the USA, yet varies in its ability to infect, sporulate on, and cause mortality of infected hosts. In addition to species diversity, quantified as both species richness and evenness, we also account for the potentially-confounding effects of host density and landscape heterogeneity on disease risk. To accommodate inherent spatial effects of the invasion process across the landscape, we compare inference among a set of Bayesian hierarchical models with varying complexity: (1) a binomial generalized linear model (GLM), (2) a zero-inflated binomial GLM, and (3) a zero-inflated binomial GLM with a spatial random effect.


A total of 10152 hosts among 279 plots were assessed for P. ramorum symptoms. Of these, 23% of hosts across 152 plots were considered infected following laboratory confirmation of P. ramorum in the respective plot. We find evidence for pathogen dilution, whereby disease risk is lower in sites with higher plant diversity, after accounting for host density and landscape context. The zero-inflated binomial GLM with the spatial effect had better model fit based on DIC criterion compared to the simpler zero-inflated binomial GLM and binomial GLM. Our finding of a dilution effect suggests that although nearly all plants in the ecosystem are hosts, the less-competent, alternative hosts may dilute disease transmission by competent hosts, thereby buffering forest health from infectious disease2.

1. Keesing et al. (2010). Impacts of biodiversity on the emergence and transmission of infectious diseases. Nature, 468, 647652. 
2. Haas et al. (2011). Forest species diversity reduces disease risk in a generalist plant pathogen invasion. Ecology Letters, 14: 11081116

Hemanta Kafley, Graduate student, Department of Fisheries and Wildlife Sciences, University of Missouri-Columbia

Title: An ecology-based landscape conservation prioritization approach to tiger (Panthera tigris tigris) conservation in Nepal

Habitat fragmentation and isolation is a major threat to the persistence of wildlife. It can be particularly detrimental to the conservation of large carnivores because their large home ranges make them susceptible to causes of mortality that are especially prevalent towards the edges and outside of protected areas. Nepal"s terai habitat has witnessed such severe fragmentation. With an objective to identify functional tiger corridor addressing the issues of landscape permeability, we use a GIS-based modeling approach to evaluate habitat connectivity and identify best movement corridors for tigers in the TAL of Nepal.

The royal bengal tiger is one of the most threatened large carnivores to extinction in the world, and its numbers are decreasing rapidly in many areas. This trend has been attributed to the range collapse that confines tiger in a mere 7 percent of the historic range. As territorial top carnivores, tigers require large, possibly intact, spaces. However severe habitat fragmentation and loss along with the consequent prey depletion coupled with the impact of poaching on tigers have exerted tremendous adverse effect in the existence of tigers. This study attempts to blend ecology-based landscape approach to explore tiger use of corridors in the terai arc landscape (TAL) of Nepal to identify the functional corridors and recommend the strategies to enhance the quality of available but unused habitat.

Ecological data on habitat occupancy for carnivores were collected by the remotely triggered camera traps and Patch occupancy survey based on animal signs. We surveyed 96 grids of size 5km-AW5km in the Chitwan National Park and adjoining corridor towards the western end of the park. We employed one paired cameras and a single camera in each grid for 7-8 nights. Simultaneously two 2km long transects were walked by 2-3 expert field technicians in each grid. Ground-truth data were collected using hand-held GPS for supervised classification of the image. Point-centered-quarter method was adopted to collect other vegetation data required for incorporating into the final model.

Preliminary analyses shows that probability of occupancy of tiger is very low (<0.5) in the park and even lower (<0.2) in the corridor based on the patch occupancy survey. We hypothesize that the significantly low prey density in the corridor might have rendered corridor unused by tigers in addition to other factors such as habitat fragmentation and various other forms of direct human disturbance. Camera trapping results also did not provide any evidence of tiger using the corridor despite of available habitat. These results also suggest us to consider developing an ecology-based connectivity model. Conventional least-cost corridor analyses models based on mere physical habitat features might produce erroneous results. Therefore, our future work will also include habitat suitability metrics for tigers and its major prey species, prey density data and certain index for direct human induced disturbances to delineate more plausible tiger movement corridor.

Thus, landscape-scale GIS modeling techniques will be used to evaluate tiger habitat connectivity. Resistance posed to tiger movement due to habitat alteration will be used along with the results of occupancy studies to identify major habitat barriers and delineate best movement corridors. The method we use can be readily adapted to prioritize conservation actions in the landscape to improve conservation strategies for ensuring perpetual existence of Tigers. We believe that the management intervention in the delineated corridor based on this technique will have higher confidence to aid in restoring tiger habitat in the landscape and thus better serves in tiger conservation initiatives.

Rebecca C. S. Levine, Daniel G. Mead, Gabriel L. Hamer, Paula Marcet, David Hedeen, Meghan W. Hedeen, Christopher Showalter, James Ballance, Juanette Willis, and Uriel D. Kitron, Emory University, Department of Environmental Studies

Title: Urban Eco-Epidemiology of West Nile Virus in Atlanta, Georgia

Since its introduction in 1999, West Nile Virus (WNV) has become the most important mosquito-borne disease in the USA. WNV activity in the mosquito vectors and reservoir hosts (birds) is clustered in space and time, with transmission focused in certain urban centers (in the East and Midwest) during the summer. However, not all urban areas with intensive enzootic activity see corresponding human cases of disease. In Georgia, substantial WNV presence in the vector and host species has not translated into a large number of human cases, reflecting a similar pattern seen throughout the Southeast, one that is in sharp contrast to some urban areas in the Northeast and Midwest. In a study conducted in Atlanta, Georgia's major urban center, we are addressing the question: in the face of abundant reservoir hosts, disease vectors, and viral presence, why is spillover transmission of WNV (beyond the enzootic) suppressed? We perform comprehensive avian and mosquito sampling in a variety of urban microhabitats, over multiple seasons, to determine the distribution, density, and prevalence of WNV infection in the host and vector species of Atlanta. We focus on sampling in four habitat types within the urban center: mixed-use parks, old-growth forest patches, residential areas, and outdoor animal-holding facilities. Fine-resolution aerial imagery is used to characterize habitat types, percent tree cover, and height of the tree canopy. Avian point counts are conducted at each site to estimate bird species richness and abundance. Using these data, we evaluate the role of Atlanta's diverse urban habitats in disease transmission, focusing on differences in percent tree cover and height of the tree canopy in constraining WNV transmission in time and space. We also explore the extent to which the diversity of avian host species in Atlanta contributes to a WNV "dilution effect." This study targets some of the complex ecological factors governing vector-borne disease transmission in urban settings, combining ecological, epidemiological, and general public health approaches.

James MacCarthy, Graduate Student, State University of New York College of Environmental Science and Forestry (SUNY-ESF)
Dr. Sadie Ryan, Assistant Professor, SUNY-ESF
Dr. Ellen Pehek, Principal Research Ecologist, New York City Parks and Recreation
Dr. Jason Munshi-South, Assistant Professor, City University of New York Baruch College

Title: The influence of habitat fragmentation in urban environments: A phylogeographic analysis of northern two-lined salamanders in New York City

As cities across the world continue to increase in terms of population size, the importance of studying the effects of urbanization on wildlife becomes ever more important. Working in collaboration with NYC Parks and Recreation scientists at the Urban Field Station, I will use existing genetic data from 25-35 salamanders in two historically isolated populations in Queens and two in the Bronx this summer. Fieldwork will be conducted to collect another 25-35 samples from up to four recently isolated populations on Staten Island for genetic analysis at Baruch College, City University of New York (CUNY). Salamanders from which samples are taken will also be marked in the field to determine if their movement corresponds to genetic differences. Using spatially explicit data in a Geographic Information System (GIS)maps of historical streams, habitat variables such as tree cover, stream quality measures, and the results of genetic analyses I will evaluate how patterns of connectivity in the urban environment have shaped the evolutionary history of these populations and influenced urban biodiversity.

Orion Weldon, Graduate Student, Rutgers University, Ecology and Evolution GraduateProgram
Dr. Olaf Jensen, Assistant Professor, Rutgers University - Institute of Marine and Coastal Sciences
Dr. Julie Lockwood, Professor I, Rutgers University - Ecology and Evolution Graduate Program

Title: Landscape scale analysis of vegetation structure preference by early successional and mature forest breeding birds using lidar

Forest breeding birds are a highly threatened group in the Northeast US, with many species such as Golden-winged Warbler (Vermivora chrysoptera) and Cerulean Warbler (Dendroica cerulea) suffering from habitat loss. Conservation and restoration efforts have been hindered by our poor understanding of the forest structure and composition required by these species. Previously, exploring such relationships at a landscape scale would have required a prohibitively large data collection effort. Here we combine vegetation structure metrics extracted from lidar data that were collected across northern New Jersey and eastern Pennsylvania with abundance data for twelve species from the Breeding Bird Survey. Of these, six species were early successional breeding birds, and six were mature forest breeding birds. We used a bayesian hierarchical model to define relationships between habitat characteristics and abundance. Lidar data allowed us to define forest vegetation structure in much greater detail than would have been possible from the available coarse land-use land-cover maps. Lidar-based habitat descriptions resulted in substantially improved habit models for several species with respect to structural resolution and spatial extent. These results provide specific guidance on ways that land-owners might manage forest characteristics to benefit threatened forest breeding bird species.

Irene Zager, Rutgers University, Laura C. Schneider, Rutgers University and John Rogan, Clark University

Title: Forest Fragmentation And Increased Vulnerability To Hurricane Impacts In The Sian Ka'an-Calakmul Biological Corridor In The Yucatan Peninsula, Mexico

The Sian Ka'an-Calakmul biological corridor in the Yucatan Peninsula connects two of Mexico's main Biosphere Reserves and contains one of the largest areas of continuous seasonally dry forest left in Mesoamerica. However, land use and land cover changes are still common both within and outside the reserves, and ongoing deforestation and fragmentation are a main concern for the persistence of the corridor. Here, we explore the changes in forest extent and spatial configuration within the Sian Ka'an Calakuml corridor over the last four decades. We conducted a morphological spatial pattern analysis using land cover maps from 1976, 2000 and 2007. Results show that since 1976, over 400,000 ha of contiguous forest have been transformed into non forested areas (including agriculture, pastures and urban land use) across the corridor. Furthermore, the proportion of forest edge and number of isolated forest patches has increased in detriment of the areas of contiguous forest, a process that has occurred at a much higher rate in the last decade. This high rate in forest fragmentation might severely increase the forests vulnerability to both hurricanes and agricultural wildfires that seasonally affect the region, as well as compromise their effectiveness as a biological corridor and their ability to provide ecosystem services. Ongoing efforts aim to explore the effect of the fragmentation patterns on forest damage and initial recovery after hurricane Dean hit in 2007, based on field data recorded within 28 permanent plots of 500 m2 each, distributed across the corridor.

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Document last modified on July 13, 2012.