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At least 865 records · Page 48Linked to original sources
USGS2024

Thinking beyond the closure assumption: Designing surveys for estimating biological truth with occupancy models

Occupancy models estimate distributions of imperfectly detected species, but violations of the closure assumption can bias results. However, researchers working with mobile animals may find it impossible to eliminate such violations. Here, we tested the hypothesis that occupancy models fit to realistic sampling data can generate unbiased occupancy estimates for an itinerant Wood Thrush ( Hylocichla mustelina ) population. In 2013 and 2014, we tracked movements of 41 breeding Wood Thrush males. We modelled territory shift probabilities using logistic exposure models and within-territory movements using continuous-time stochastic process models. We then constructed an individual-based model, simulated (1000 iterations) spatiotemporal locations for individuals and simulated sampling these populations using 162 different point count protocols with variable spatial (sampling radius and point placement method), and temporal (survey length, between-survey intervals and number of surveys) characteristics. We compared occupancy estimates with true values of instantaneous, daily and seasonal occupancy from the simulations. We parameterized continuous time stochastic process models based on movements within 34 unique territories and estimated a daily territory shift probability of 0.0099 (95% CI: 0.0060, 0.0152). Simulated data indicated that estimates of occupancy ranged from 0.18 (0.06, 1.00) to 0.80 (0.71, 0.89) depending on protocol characteristics. Occupancy estimates increased with increasing survey radius, survey length and between-survey interval. Protocols using shorter surveys and between-survey intervals were good estimators for instantaneous occupancy (low bias and mean-squared error) but poor estimators for daily and seasonal occupancy; longer surveys and intervals generated unbiased estimators of daily occupancy but underestimated seasonal occupancy. Logistic regression models that ignored imperfect detection outperformed occupancy models for estimating instantaneous occupancy but not daily or seasonal occupancy. For mobile animals, occupancy of sampling sites changes in space and time. Consequently, the spatial and temporal aspects of a sampling protocol have strong, but predictable, effects on occupancy model parameter estimates. Our results demonstrate that how these factors interact is critical for designing surveys that produce occupancy estimates representative of the biological process of interest to a researcher.

Methods in Ecology and Evolution↗
USGS2011

Spatial capture-recapture models for search-encounter data

1. Spatial capture–recapture models make use of auxiliary data on capture location to provide density estimates for animal populations. Previously, models have been developed primarily for fixed trap arrays which define the observable locations of individuals by a set of discrete points. 2. Here, we develop a class of models for 'search-encounter' data, i.e. for detections of recognizable individuals in continuous space, not restricted to trap locations. In our hierarchical model, detection probability is related to the average distance between individual location and the survey path. The locations are allowed to change over time owing to movements of individuals, and individual locations are related formally by a model describing individual activity or home range centre which is itself regarded as a latent variable in the model. We provide a Bayesian analysis of the model in WinBUGS, and develop a custom MCMC algorithm in the R language. 3. The model is applied to simulated data and to territory mapping data for the Willow Tit from the Swiss Breeding Bird Survey MHB. While the observed density was 15 territories per nominal 1 km 2 plot of unknown effective sample area, the model produced a density estimate of 21∙12 territories per square km (95% posterior interval: 17–26). 4. Spatial capture–recapture models are relevant to virtually all animal population studies that seek to estimate population size or density, yet existing models have been proposed mainly for conventional sampling using arrays of traps. Our model for search-encounter data, where the spatial pattern of searching can be arbitrary and may change over occasions, greatly expands the scope and utility of spatial capture–recapture models.

Methods in Ecology and Evolution↗
USGS2013

Animal migration amid shifting patterns of phenology and predation: Lessons from a Yellowstone elk herd

Migration is a striking behavioral strategy by which many animals enhance resource acquisition while reducing predation risk. Historically, the demographic benefits of such movements made migration common, but in many taxa the phenomenon is considered globally threatened. Here we describe a long-term decline in the productivity of elk ( Cervus elaphus ) that migrate through intact wilderness areas to protected summer ranges inside Yellowstone National Park, USA. We attribute this decline to a long-term reduction in the demographic benefits that ungulates typically gain from migration. Among migratory elk, we observed a 21-year, 70% reduction in recruitment and a 4-year, 19% depression in their pregnancy rate largely caused by infrequent reproduction of females that were young or lactating. In contrast, among resident elk, we have recently observed increasing recruitment and a high rate of pregnancy. Landscape-level changes in habitat quality and predation appear to be responsible for the declining productivity of Yellowstone migrants. From 1989 to 2009, migratory elk experienced an increasing rate and shorter duration of green-up coincident with warmer spring–summer temperatures and reduced spring precipitation, also consistent with observations of an unusually severe drought in the region. Migrants are also now exposed to four times as many grizzly bears ( Ursus arctos ) and wolves ( Canis lupus ) as resident elk. Both of these restored predators consume migratory elk calves at high rates in the Yellowstone wilderness but are maintained at low densities via lethal management and human disturbance in the year-round habitats of resident elk. Our findings suggest that large-carnivore recovery and drought, operating simultaneously along an elevation gradient, have disproportionately influenced the demography of migratory elk. Many migratory animals travel large geographic distances between their seasonal ranges. Changes in land use and climate that disparately influence such seasonal ranges may alter the ecological basis of migratory behavior, representing an important challenge for, and a powerful lens into, the ecology and conservation of migratory taxa.

Idaho, Montana, Wyoming↗
USGS2011

Inference about density and temporary emigration in unmarked populations

Few species are distributed uniformly in space, and populations of mobile organisms are rarely closed with respect to movement, yet many models of density rely upon these assumptions. We present a hierarchical model allowing inference about the density of unmarked populations subject to temporary emigration and imperfect detection. The model can be fit to data collected using a variety of standard survey methods such as repeated point counts in which removal sampling, double‐observer sampling, or distance sampling is used during each count. Simulation studies demonstrated that parameter estimators are unbiased when temporary emigration is either “completely random” or is determined by the size and location of home ranges relative to survey points. We also applied the model to repeated removal sampling data collected on Chestnut‐sided Warblers ( Dendroica pensylvancia ) in the White Mountain National Forest, USA. The density estimate from our model, 1.09 birds/ha, was similar to an estimate of 1.11 birds/ha produced by an intensive spot‐mapping effort. Our model is also applicable when processes other than temporary emigration affect the probability of being available for detection, such as in studies using cue counts. Functions to implement the model have been added to the R package unmarked .

New Hampshire↗
USGS2019

Quantifying source and sink habitats and pathways in spatially structured populations: A generalized modelling approach

The ability to classify habitats and movement pathways as sources or sinks is an important part of the decision making process for the conservation of spatially structured populations. Diverse approaches have been used to quantify the importance of habitats and pathways in a spatial network, however these approaches have been limited by a lack of general applicability across life histories and movement strategies. In this paper we develop a generalized per-capita contribution metric, the C-metric, for quantifying habitat and pathway quality. This metric is novel in that it can be applied broadly to both metapopulations and migratory species. It allows for any number of age and sex classes, unlimited number of seasons or time intervals within the annual cycle, and for density-dependent parameters. We demonstrate the flexibility of the metric with four case studies: a hypothetical metapopulation, elk of the Greater Yellowstone Ecosystem, northern pintail ducks in North America, and the eastern population of the monarch butterfly. General computer code to calculate the per-capita contribution metric is provided. We demonstrate that the C-metric is useful for identifying source and sink habitats in a network and suggest that the C-metric could be supplemented by some measure of network structure for a more robust description of habitat or pathway importance.

Ecological Modelling↗
USGS2010

The effects of road crossings on prairie stream habitat and function

Improperly designed stream crossing structures may alter the form and function of stream ecosystems and habitat and prohibit the movement of aquatic organisms. Stream sections adjoining five concrete box culverts, five low-water crossings (concrete slabs vented by one or multiple culverts), and two large, single corrugated culvert vehicle crossings in eastern Kansas streams were compared to reference reaches using a geomorphologic survey and stream classification. Stream reaches were also compared upstream and downstream of crossings, and crossing measurements were used to determine which crossing design best mimicked the natural dimensions of the adjoining stream. Four of five low-water crossings, three of five box culverts, and one of two large, single corrugated pipe culverts changed classification from upstream to downstream of the crossings. Mean riffle spacing upstream at low-water crossings (8.6 bankfull widths) was double that of downstream reaches (mean 4.4 bankfull widths) but was similar upstream and downstream of box and corrugated pipe culverts. There also appeared to be greater deposition of fine sediments directly upstream of these designs. Box and corrugated culverts were more similar to natural streams than low-water crossings at transporting water, sediments, and debris during bankfull flows.

Journal of Freshwater Ecology↗
USGS2014

Preliminary geologic map of Black Canyon and surrounding region, Nevada and Arizona

Thermal springs in Black Canyon of the Colorado River, downstream of Hoover Dam, are important recreational, ecological, and scenic features of the Lake Mead National Recreation Area. This report presents the results from a U.S. Geological Survey study of the geologic framework of the springs. The study was conducted in cooperation with the National Park Service and funded by both the National Park Service and National Cooperative Geologic Mapping Program of the U.S. Geological Survey. The report has two parts: A, a 1:48,000-scale geologic map created from existing geologic maps and augmented by new geologic mapping and geochronology; and B, an interpretive report that presents results based on a collection of fault kinematic data near springs within Black Canyon and construction of 1:100,000-scale geologic cross sections that extend across the western Lake Mead region. Exposures in Black Canyon are mostly of Miocene volcanic rocks, underlain by crystalline basement composed of Miocene plutonic rocks or Proterozoic metamorphic rocks. The rocks are variably tilted and highly faulted. Faults strike northwest to northeast and include normal and strike-slip faults. Spring discharge occurs along faults intruded by dacite dikes and plugs; weeping walls and seeps extend away from the faults in highly fractured rock or relatively porous volcanic breccias, or both. Results of kinematic analysis of fault data collected along tributaries to the Colorado River indicate two episodes of deformation, consistent with earlier studies. The earlier episode formed during east-northeast-directed extension, and the later during east-southeast-directed extension. At the northern end of the study area, pre-existing fault blocks that formed during the first episode were rotated counterclockwise along the left-lateral Lake Mead Fault System. The resulting fault pattern forms a complex arrangement that provides both barriers and pathways for groundwater movement within and around Black Canyon. Regional cross sections in this report show that thick Paleozoic carbonate aquifer rocks of east-central Nevada do not extend into the Black Canyon area and generally are terminated to the south at a major tectonic boundary defined by the northeast-striking Lake Mead Fault System and the northwest-striking Las Vegas Valley shear zone. Faults to the west of Black Canyon strike dominantly north-south and form a complicated pattern that may inhibit easterly groundwater movement from Eldorado Valley. To the east of Black Canyon, crystalline Proterozoic rocks locally overlain by Tertiary volcanic rocks in the Black Mountains are bounded by steep north-south normal faults. These faults may also inhibit westerly groundwater movement from Detrital Valley toward Black Canyon. Finally, the cross sections show clearly that Proterozoic basement rocks and (or) Tertiary plutonic rocks are shallow in the Black Canyon area (at the surface to a few hundred meters depth) and are cut by several major faults that discharge most of the springs in the Black Canyon. Therefore, the faults most likely provide groundwater pathways to sufficient depths that the groundwater is heated to the observed temperatures of up to 55 °C.

Arizona, Nevada↗
USGS2014

Geologic framework of thermal springs, Black Canyon, Nevada and Arizona

Thermal springs in Black Canyon of the Colorado River, downstream of Hoover Dam, are important recreational, ecological, and scenic features of the Lake Mead National Recreation Area. This report presents the results from a U.S. Geological Survey study of the geologic framework of the springs. The study was conducted in cooperation with the National Park Service and funded by both the National Park Service and National Cooperative Geologic Mapping Program of the U.S. Geological Survey. The report has two parts: A, a 1:48,000-scale geologic map created from existing geologic maps and augmented by new geologic mapping and geochronology; and B, an interpretive report that presents results based on a collection of fault kinematic data near springs within Black Canyon and construction of 1:100,000-scale geologic cross sections that extend across the western Lake Mead region. Exposures in Black Canyon are mostly of Miocene volcanic rocks, underlain by crystalline basement composed of Miocene plutonic rocks or Proterozoic metamorphic rocks. The rocks are variably tilted and highly faulted. Faults strike northwest to northeast and include normal and strike-slip faults. Spring discharge occurs along faults intruded by dacite dikes and plugs; weeping walls and seeps extend away from the faults in highly fractured rock or relatively porous volcanic breccias, or both. Results of kinematic analysis of fault data collected along tributaries to the Colorado River indicate two episodes of deformation, consistent with earlier studies. The earlier episode formed during east-northeast-directed extension, and the later during east-southeast-directed extension. At the northern end of the study area, pre-existing fault blocks that formed during the first episode were rotated counterclockwise along the left-lateral Lake Mead Fault System. The resulting fault pattern forms a complex arrangement that provides both barriers and pathways for groundwater movement within and around Black Canyon. Regional cross sections in this report show that thick Paleozoic carbonate aquifer rocks of east-central Nevada do not extend into the Black Canyon area and generally are terminated to the south at a major tectonic boundary defined by the northeast-striking Lake Mead Fault System and the northwest-striking Las Vegas Valley shear zone. Faults to the west of Black Canyon strike dominantly north-south and form a complicated pattern that may inhibit easterly groundwater movement from Eldorado Valley. To the east of Black Canyon, crystalline Proterozoic rocks locally overlain by Tertiary volcanic rocks in the Black Mountains are bounded by steep north-south normal faults. These faults may also inhibit westerly groundwater movement from Detrital Valley toward Black Canyon. Finally, the cross sections show clearly that Proterozoic basement rocks and (or) Tertiary plutonic rocks are shallow in the Black Canyon area (at the surface to a few hundred meters depth) and are cut by several major faults that discharge most of the springs in the Black Canyon. Therefore, the faults most likely provide groundwater pathways to sufficient depths that the groundwater is heated to the observed temperatures of up to 55 °C.

Arizona, Nevada↗
USGS2017

Altitudinal migration and the future of an iconic Hawaiian honeycreeper in response to climate change and management

Altitudinal movement by tropical birds to track seasonally variable resources can move them from protected areas to areas of increased vulnerability. In Hawaiʻi, historical reports suggest that many Hawaiian honeycreepers such as the ‘I‘iwi ( Drepanis coccinea ) once undertook seasonal migrations, but the existence of such movements today is unclear. Because Hawaiian honeycreepers are highly susceptible to avian malaria, currently minimal in high-elevation forests, understanding the degree to which honeycreepers visit lower elevation forests may be critical to predict the current impact of malaria on population dynamics and how susceptible bird populations may respond to climate change and mitigation scenarios. Using radio telemetry data, we demonstrate for the first time that a large fraction of breeding adult and juvenile ‘I‘iwi originating from an upper-elevation (1,920 m) population at Hakalau Forest National Wildlife Refuge exhibit post-breeding movements well below the upper elevational limit for mosquitoes. Bloom data suggest seasonal variation in floral resources is the primary driver of seasonal movement for ‘I‘iwi. To understand the demographic implications of such movement, we developed a spatial individual-based model calibrated using previously published and original data. ʻI‘iwi dynamics were simulated backward in time, to estimate population levels in the absence of avian malaria, and forward in time, to assess the impact of climate warming as well as two potential mitigation actions. Even in disease-free ‘refuge’ populations, we found that breeding densities failed to reach the estimated carrying capacity, suggesting the existence of a seasonal “migration load” as a result of travel to disease-prevalent areas. We predict that ‘I‘iwi may be on the verge of extinction in 2100, with the total number of pairs reaching only ~ 0.2–12.3% of the estimated pre-malaria density, based on an optimistic climate change scenario. The probability of extinction of ‘I‘iwi populations, as measured by population estimates for 2100, is strongly related to their estimated migration propensity. Long-term conservation strategies likely will require a multi-pronged response including a reduction of malaria threats, habitat restoration and continued landscape-level access to seasonally variable nectar resources.

Ecological Monographs↗
USGS2026

Waterfowl move less in heterogeneous and human-populated landscapes, with implications for spread of avian influenza viruses

Animal movements contribute to the spread of infectious diseases and are driven in part by environmental conditions. We investigated the links among the environment, animal movement, and infectious disease dynamics in waterfowl, which are among the primary wildlife hosts of avian influenza viruses. By combining telemetry data on 4606 individuals from 26 waterfowl species with data on land cover, weather, and vegetation, we found that waterfowl moved less in areas of higher land cover heterogeneity and higher human population density. Moreover, predicted waterfowl movement distances were weakly but positively correlated with distances between detections of H5N1 highly pathogenic avian influenza in wild waterfowl, suggesting that environmental conditions might contribute to the spread of this disease via their effects on bird movements. By considering wildlife movements alongside other drivers of infectious disease dynamics, such as livestock production and human mobility, we move closer to predicting outbreaks and informing interventions.

Ecology Letters↗
USGS2026

Habitat restoration efforts increase patch retention times in migratory mule deer (Odocoileus hemionus)

Mule deer ( Odocoileus hemionus ) populations have been declining across much of their range, often due to habitat alteration. Habitat alterations, including the introduction of non-native annual grasses and the expansion of pinyon–juniper (PJ) forests on sagebrush ecosystems, are changing resource availability compared to historical conditions. Extensive habitat restoration has been completed across the State of Utah to foster plant communities that better reflect historical conditions and optimal mule deer habitat. We investigated how patch retention times differ on eight different habitat restoration treatment types and random locations during summer and winter across the State of Utah, to evaluate the efficacy of restoration treatments for migratory mule deer, as retention time is expected to reflect resource availability. We developed seasonal moving-window Brownian Bridge Movement Models for individual mule deer ( n = 593 animals), and intersected occurrence distributions (OD) with habitat restoration treatments and randomly generated background landscape polygons. We quantified patch retention time as the number of days individuals’ OD overlapped treatment or random polygons during each season, using a Poisson regression. In winter sites treated to remove PJ, both with (56.5 days, 95% CI [29.3, 108.0]) and without seeding (55.3 days, 95% CI [29.1, 105.8]), as well as sagebrush restoration sites (59.0 days, 95% CI [30.6, 114.8]), had increased retention times when compared to the landscape average (41.9 days, 95% CI [20.7, 84.1]), with effects decreasing 5+ years post-treatment. Retention times in summer were longer across all treatment types in the 2–4-year post-treatment age class (37.5 days, 95% CI [26.3, 53.1]) compared to the landscape average (28.6 days, 95% CI [25.7, 31.8]). Our results demonstrate the positive effects of habitat restoration through increased patch retention times on mule deer winter and summer range and may suggest follow-up treatment 5+ years after initial treatment to maximize mule deer use.

Utah↗
USGS2012

Modelling effects of chemical exposure on birds wintering in agricultural landscapes: The western burrowing owl ( Athene cunicularia hypugaea ) as a case study

We describe an ecotoxicological model that simulates the sublethal and lethal effects of chronic, low-level, chemical exposure on birds wintering in agricultural landscapes. Previous models estimating the impact on wildlife of chemicals used in agro-ecosystems typically have not included the variety of pathways, including both dermal and oral, by which individuals are exposed. The present model contains four submodels simulating (1) foraging behavior of individual birds, (2) chemical applications to crops, (3) transfers of chemicals among soil, insects, and small mammals, and (4) transfers of chemicals to birds via ingestion and dermal exposure. We demonstrate use of the model by simulating the impacts of a variety of commonly used herbicides, insecticides, growth regulators, and defoliants on western burrowing owls ( Athene cunicularia hypugaea ) that winter in agricultural landscapes in southern Texas, United States. The model generated reasonable movement patterns for each chemical through soil, water, insects, and rodents, as well as into the owl via consumption and dermal absorption. Sensitivity analysis suggested model predictions were sensitive to uncertainty associated with estimates of chemical half-lives in birds, soil, and prey, sensitive to parameters associated with estimating dermal exposure, and relatively insensitive to uncertainty associated with details of chemical application procedures (timing of application, amount of drift). Nonetheless, the general trends in chemical accumulations and the relative impacts of the various chemicals were robust to these parameter changes. Simulation results suggested that insecticides posed a greater potential risk to owls of both sublethal and lethal effects than do herbicides, defoliants, and growth regulators under crop scenarios typical of southern Texas, and that use of multiple indicators, or endpoints provided a more accurate assessment of risk due to agricultural chemical exposure. The model should prove useful in helping prioritize the chemicals and transfer pathways targeted in future studies and also, as these new data become available, in assessing the relative danger to other birds of exposure to different types of agricultural chemicals.

Texas↗
USGS2016

Bioenergetic evaluation of diel vertical migration by bull trout (Salvelinus confluentus) in a thermally stratified reservoir

Many species living in deeper lentic ecosystems exhibit daily movements that cycle through the water column, generally referred to as diel vertical migration (DVM). In this study, we applied bioenergetics modelling to evaluate growth as a hypothesis to explain DVM by bull trout ( Salvelinus confluentus ) in a thermally stratified reservoir (Ross Lake, WA, USA) during the peak of thermal stratification in July and August. Bioenergetics model parameters were derived from observed vertical distributions of temperature, prey and bull trout. Field sampling confirmed that bull trout prey almost exclusively on recently introduced redside shiner ( Richardsonius balteatus ). Model predictions revealed that deeper (>25 m) DVMs commonly exhibited by bull trout during peak thermal stratification cannot be explained by maximising growth. Survival, another common explanation for DVM, may have influenced bull trout depth use, but observations suggest there may be additional drivers of DVM. We propose these deeper summertime excursions may be partly explained by an alternative hypothesis: the importance of colder water for gametogenesis. In Ross Lake, reliance of bull trout on warm water prey (redside shiner) for consumption and growth poses a potential trade-off with the need for colder water for gametogenesis.

Washington↗
USGS2021

How to increase the supply of native seed to improve restoration success: The US native seed development process

With the United Nations Decade on Ecosystem Restoration, restoration of damaged ecosystems is turning into a global movement. Restoration actions that are not based on science and an understanding of ecosystem function can thwart desired restoration outcomes at best and cause further damage to ecosystems at worst. Restoration often includes revegetation using seed. Where we source seed for restoration can make a difference for species establishment, restoration outcomes, and recovery of ecosystem function. However, sourcing seeds of native species, let alone genetically appropriate seed, is not currently possible for many restoration projects. The process of increasing and sourcing suitable seed for restoration includes many steps that need to be addressed typically years before a restoration project is initiated. These steps of seed collection, evaluation and development, field establishment, production, certification and procurement, storage, and finally restoration, need to be considered ideally at a scale larger than individual restoration projects and with research conducted in each step. We describe these steps as implemented in the United States, the challenges therein, and provide suggestions and examples of how groups can make efficient and effective progress toward getting the right seed in the right place at the right time.

Restoration Ecology↗
USGS2021

Toward improved decision-support tools for Delta Smelt management actions

The Collaborative Science and Adaptive Management Program (CSAMP) has endorsed a goal of reversing the recent downward trajectory of the Delta Smelt population within 5-10 generations, with the long-term aim of establishing a self-sustaining population. An ambitious agenda of management actions is planned, and more management actions are being considered. This White Paper furthers one of the recommendations in the 2019 Delta Smelt Science Plan – the need to predict the potential ecological effects of taking a management action. Existing statistical models can be highly informative in assessing the response of Delta Smelt to changing system conditions and management actions. However, management actions can shift or alter conditions in ways that models based on analysis of historical data may not be able to represent, and short-term or localized effects may be missed with models designed to assess effects at the population level. Decision support tools (DSTs) are computer-based tools developed to assist decision-making, often combining computationally intensive analysis and spatial mapping of environmental relationships. DSTs can be used in planning processes that evaluate an array of actions, such as in Structured Decision Making (SDM), where DSTs are needed to compare among alternatives. DSTs can also be used to explore the potential effects of different approaches to implementing management actions. The goal of this White Paper is to identify plausible options for DSTs that could be developed for future use to evaluate management actions that seek to either reverse the decline of Delta Smelt or minimize or mitigate the effects of other water management actions. Different types of management actions lead to different needs for DSTs. This White Paper was developed using three types of actions currently being considered to enhance the Delta Smelt population: Supplementation with Hatchery Fish, Summer-Fall Habitat, and Food Enhancement actions. These three management actions target different parts of the estuary and different processes, with a variety of possible metrics to gauge performance. Three DSTs are proposed that collectively address management questions related to the management actions considered, with each requiring a slightly different set of processes to be included and producing an array of outputs at varying spatial and temporal scales: DST 1. Modeling Fish Movement, Survival, and Reproduction Across Their Range. This DST can address management questions that require information about Delta Smelt spatial distribution and movement. • DST 1 could be used to compare conditions with and without management actions in place, how the management action performs among different types of water years (with varied flow and associated abiotic conditions), and to assess relative change with different variations and strategies of the management actions. • DST 2. Changes in Habitat Conditions and Delta Smelt Response. This DST is intended to evaluate combinations of conditions that are considered to provide suitable habitat for Delta Smelt, and Delta Smelt response. Delta Smelt habitat is generally described as open water with low salinity (0 to 6), turbidity of at least 12 NTU, suitable temperature conditions, and sufficient food availability to support growth. • DST 3. Regional Effects of Food Subsidy. This DSTs seeks to evaluate effectiveness of food enhancement actions by providing information on responses of the immediate targets of the action (i.e., phytoplankton or zooplankton) and tracing those to projected growth responses of Delta Smelt. There is not a single DST that adequately addresses management questions relevant to all management actions, although there is some overlap in the management questions each of the three DSTs can address. For each of the DSTs a substantial foundation of models and approaches already exists and modeling has already been applied to several of the management actions described. However, a number of outstanding issues remain for further development of the proposed DSTs. These are summarized in this White Paper together with potential approaches that could be applied or tested. Some components for the DSTs are already available and thus development could be relatively easy. However, for several of the topics identified there are gaps in knowledge that currently limit formulation of model structure and process representations. This presents challenges to readily incorporate some needed mechanisms into the models. Eleven next steps, aligned with relevant DSTs, are outlined. The next steps vary in their complexity or technical ‘lift’ required. Many build on existing work, or methods and approaches that have already been developed or are underway, while others require additional thinking to establish a viable approach. Some interim utility for decisions could be gained during initial development of the DSTs with further features added over time. Development of a DST requires engagement of both managers and scientists. Identifying the outputs and resolution needed for management purposes early in development of any DST is essential for effective pursuit of next steps and suitable approaches to address challenges. Dialog between managers and technical experts also informs what process-based simulation can do, and what tradeoffs are acceptable to meet a given purpose. To further develop the DSTs outlined here for application in the estuary requires: - Engagement of a committed group of technical experts with appropriate expertise. - The development of a coordinated workplan including appropriate project management and tracking. - Dialog between potential users (i.e., managers and policy makers) and technical experts. - Resources to pursue DST development including personnel and computational resources. This White Paper demonstrates the potential for moving toward DSTs for a variety of management actions in support of Delta Smelt that include mechanistic representations of physical and biological processes. Through focused effort from technical experts, managers and policy makers, DSTs can be developed to provide quantitative predictions of management effects on the ecosystem, targeting the changes the management actions seek to achieve, how these effects compare to ambient conditions, and how the effects vary among water year types or with timing and location of actions. Importantly, solid foundations exist which can be leveraged, refined, and built upon to specifically inform current and future management decisions.

White Paper↗
USGS2017

Landscape complementation revealed through bipartite networks: An example with the Florida manatee

Context Landscape complementation, or how landscapes that contain two or more non-substitutable and spatially separated resources facilitate resource use, is critical for many populations. Implicit to the problem of landscape complementation is the movement of individuals to access multiple resources. Conventional measures of complementation, such as habitat area or distance between habitats, do not consider the spatial configuration of resources or how landscape features impede movement. Objectives We advanced a bipartite network approach to capture the spatial configuration and connectivity of two habitat types and contrasted this framework to conventional approaches in a habitat selection model. Methods Using satellite-telemetry of the Florida manatee (Trichechus manatus latirostris), a marine mammal that relies on two distinct, spatially separate habitats for foraging and thermoregulating, we parameterized and compared mixed conditional logistic models with covariates describing classic habitat selection metrics, conventional measures of landscape complementation, and bipartite network metrics. Results The models best supported included habitat area, resistance distance between habitats, and the bipartite network metric eigenvector centrality. The connectivity between habitats and the spatial configuration of one habitat type relative to other types better described habitat selection than conventional measures of landscape complementation alone. The type of habitat, i.e. seagrass or thermal refuge, influenced both the direction and magnitude of the response. Conclusions Landscape complementation is an important predictor of selection and thus classic complementation measures are not sufficient in describing the process. Formalization of complementation with bipartite network can therefor reveal effects potentially missed with conventional measures.

Florida↗
USGS2008

A comparison of seed banks across a sand dune successional gradient at Lake Michigan dunes (Indiana, USA)

In habitats where disturbance is frequent, seed banks are important for the regeneration of vegetation. Sand dune systems are dynamic habitats in which sand movement provides intermittent disturbance. As succession proceeds from bare sand to forest, the disturbance decreases. At Indiana Dunes National Lakeshore, we examined the seed banks of three habitat types across a successional gradient: foredunes, secondary dunes, and oak savanna. There were differences among the types of species that germinated from each of the habitats. The mean seed bank density increased across the successional gradient by habitat, from 376 to 433 to 968 seeds m -2 , but with foredune and secondary dune seed bank densities being significantly lower than the savanna seed bank density. The number of seeds germinated was significantly correlated with soil organic carbon, demonstrating for this primary successional sequence that seed density increases with stage and age. The seed bank had much lower species richness than that of the aboveground vegetation across all habitats. Among sites within a habitat type, the similarity of species germinated from the seed banks was very low, illustrating the variability of the seed bank even in similar habitat types. These results suggest that restoration of these habitats cannot rely on seed banks alone. ?? 2008 Springer Science+Business Media B.V.

Plant Ecology↗
USGS2008

Multi-scale occupancy estimation and modelling using multiple detection methods

Occupancy estimation and modelling based on detection–nondetection data provide an effective way of exploring change in a species’ distribution across time and space in cases where the species is not always detected with certainty. Today, many monitoring programmes target multiple species, or life stages within a species, requiring the use of multiple detection methods. When multiple methods or devices are used at the same sample sites, animals can be detected by more than one method. We develop occupancy models for multiple detection methods that permit simultaneous use of data from all methods for inference about method-specific detection probabilities. Moreover, the approach permits estimation of occupancy at two spatial scales: the larger scale corresponds to species’ use of a sample unit, whereas the smaller scale corresponds to presence of the species at the local sample station or site. We apply the models to data collected on two different vertebrate species: striped skunks Mephitis mephitis and red salamanders Pseudotriton ruber . For striped skunks, large-scale occupancy estimates were consistent between two sampling seasons. Small-scale occupancy probabilities were slightly lower in the late winter/spring when skunks tend to conserve energy, and movements are limited to males in search of females for breeding. There was strong evidence of method-specific detection probabilities for skunks. As anticipated, large- and small-scale occupancy areas completely overlapped for red salamanders. The analyses provided weak evidence of method-specific detection probabilities for this species. Synthesis and applications. Increasingly, many studies are utilizing multiple detection methods at sampling locations. The modelling approach presented here makes efficient use of detections from multiple methods to estimate occupancy probabilities at two spatial scales and to compare detection probabilities associated with different detection methods. The models can be viewed as another variation of Pollock's robust design and may be applicable to a wide variety of scenarios where species occur in an area but are not always near the sampled locations. The estimation approach is likely to be especially useful in multispecies conservation programmes by providing efficient estimates using multiple detection devices and by providing device-specific detection probability estimates for use in survey design.

Journal of Applied Ecology↗