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At least 199 records · Page 11Linked to original sources
USGS2015

Evaluating abundance and trends in a Hawaiian avian community using state-space analysis

Estimating population abundances and patterns of change over time are important in both ecology and conservation. Trend assessment typically entails fitting a regression to a time series of abundances to estimate population trajectory. However, changes in abundance estimates from year-to-year across time are due to both true variation in population size (process variation) and variation due to imperfect sampling and model fit. State-space models are a relatively new method that can be used to partition the error components and quantify trends based only on process variation. We compare a state-space modelling approach with a more traditional linear regression approach to assess trends in uncorrected raw counts and detection-corrected abundance estimates of forest birds at Hakalau Forest National Wildlife Refuge, Hawai‘i. Most species demonstrated similar trends using either method. In general, evidence for trends using state-space models was less strong than for linear regression, as measured by estimates of precision. However, while the state-space models may sacrifice precision, the expectation is that these estimates provide a better representation of the real world biological processes of interest because they are partitioning process variation (environmental and demographic variation) and observation variation (sampling and model variation). The state-space approach also provides annual estimates of abundance which can be used by managers to set conservation strategies, and can be linked to factors that vary by year, such as climate, to better understand processes that drive population trends.

Hawai'i↗
USGS2000

Geographic analysis of species richness and community attributes of forest birds from survey data in the mid-Atlantic integrated assessment region

Species richness of local communities is a state variable commonly used in community ecology and conservation biology. Investigation of spatial and temporal variations in richness and identification of factors associated with these variations form a basis for specifying management plans, evaluating these plans, and for testing hypotheses of theoretical interest. However, estimation of species richness is not trivial: species can be missed by investigators during sampling sessions. Sampling artifacts can lead to erroneous conclusions on spatial and temporal variation in species richness. Here we use data from the North American Breeding Bird Survey to estimate parameters describing the state of bird communities in the Mid-Atlantic Assessment (MAIA) region: species richness, extinction probability, turnover and relative species richness. We use a recently developed approach to estimation of species richness and related parameters that does not require the assumption that all the species are detected during sampling efforts. The information presented here is intended to visualize the state of bird communities in the MAIA region. We provide information on 1975 and 1990. We also quantified the changes between these years. We summarized and mapped the community attributes at a scale of management interest (watershed units).

Delaware, Maryland, Pennsylvania, Virginia, West V↗
USGS2026

Individual encounter data of six African carnivore species optimized for multi-species density estimation

The ability to estimate abundances of multiple wildlife species within an area is valuable for both conservation and ecological inquiry. Spatially explicit capture–recapture (SCR) methods are commonly used to obtain reliable population size estimates, particularly for low-density and individually identifiable carnivore species. However, estimating abundance within multi-species communities poses a methodological challenge as survey designs and analytical tools are primarily tailored for single target species. Here, we present a dataset of spatially referenced individual encounter histories of six carnivore species with varying space requirements (lion, Panthera leo ; leopard, Panthera pardus ; spotted hyena, Crocuta crocuta ; cheetah, Acinonyx jubatus ; serval, Leptailurus serval ; large-spotted genet, Genetta tigrina ). These data were collected in a South African game reserve using a camera trap array optimized for multi-species density estimation using SCR methods. This dataset will be a valuable resource for studying spatial processes among potentially interacting carnivores without the common pitfalls that come with by-catch data of non-target species, and will provide a much-needed case study for the further development of multi-species statistical method development.

Munywana Conservancy↗
USGS2004

Tigers and their prey: Predicting carnivore densities from prey abundance

The goal of ecology is to understand interactions that determine the distribution and abundance of organisms. In principle, ecologists should be able to identify a small number of limiting resources for a species of interest, estimate densities of these resources at different locations across the landscape, and then use these estimates to predict the density of the focal species at these locations. In practice, however, development of functional relationships between abundances of species and their resources has proven extremely difficult, and examples of such predictive ability are very rare. Ecological studies of prey requirements of tigers Panthera tigris led us to develop a simple mechanistic model for predicting tiger density as a function of prey density. We tested our model using data from a landscape-scale long-term (1995-2003) field study that estimated tiger and prey densities in 11 ecologically diverse sites across India. We used field techniques and analytical methods that specifically addressed sampling and detectability, two issues that frequently present problems in macroecological studies of animal populations. Estimated densities of ungulate prey ranged between 5.3 and 63.8 animals per km 2 . Estimated tiger densities (3.2-16.8 tigers per 100 km 2 ) were reasonably consistent with model predictions. The results provide evidence of a functional relationship between abundances of large carnivores and their prey under a wide range of ecological conditions. In addition to generating important insights into carnivore ecology and conservation, the study provides a potentially useful model for the rigorous conduct of macroecological science.

Proceedings of the National Academy of Sciences↗
USGS2024

Landscape fragmentation overturns classical metapopulation thinking

Habitat loss and isolation caused by landscape fragmentation represent a growing threat to global biodiversity. Existing theory suggests that the process will lead to a decline in metapopulation viability. However, since most metapopulation models are restricted to simple networks of discrete habitat patches, the effects of real landscape fragmentation, particularly in stochastic environments, are not well understood. To close this major gap in ecological theory, we developed a spatially explicit, individual-based model applicable to realistic landscape structures, bridging metapopulation ecology and landscape ecology. This model reproduced classical metapopulation dynamics under conventional model assumptions, but on fragmented landscapes, it uncovered general dynamics that are in stark contradiction to the prevailing views in the ecological and conservation literature. Notably, fragmentation can give rise to a series of dualities: a) positive and negative responses to environmental noise, b) relative slowdown and acceleration in density decline, and c) synchronization and desynchronization of local population dynamics. Furthermore, counter to common intuition, species that interact locally (“residents”) were often more resilient to fragmentation than long-ranging “migrants.” This set of findings signals a need to fundamentally reconsider our approach to ecosystem management in a noisy and fragmented world.

PNAS↗
USGS2016

Planning and setting objectives in field studies: Chapter 2

This chapter enumerates the steps required in designing and planning field studies on the ecology and conservation of reptiles, as these involve a high level of uncertainty and risk. To this end, the chapter differentiates between goals (descriptions of what one intends to accomplish) and objectives (the measurable steps required to achieve the established goals). Thus, meeting a specific goal may require many objectives. It may not be possible to define some of them until certain experiments have been conducted; often evaluations of sampling protocols are needed to increase certainty in the biological results. And if sampling locations are fixed and sampling events are repeated over time, then both study-specific covariates and sampling-specific covariates should exist. Additionally, other critical design considerations for field study include obtaining permits, as well as researching ethics and biosecurity issues.

Book chapter↗
USGS2022

African penguins and localized fisheries management: Response to Butterworth and Ross-Gillespie

We present a response to Butterworth and Ross-Gillespie's (2022) comment on our perspectives on how forage fish fisheries are impacting the endangered African penguin ( Sphenicus demersus ), and corresponding management options. Butterworth and Ross-Gillespie overstate model uncertainties and downplay the clear ecological and conservation significance of the fisheries closure experiment. We demonstrate that their criticism of “pseudo-replication” is weak, and not in line with their own analyses nor with the interpretations of many international scientific review panels commissioned by the government of South Africa to evaluate experimental results. Their comment does not alter our fundamental conclusions that forage fisheries operating near penguin breeding colonies compete with the birds for food resources, are detrimental to the penguin's population health, and are impeding recovery. Given that sardines are depleted (DFFE, 2021) and the African penguin is approaching a conservation crisis, we reiterate our position that continuing the precautionary approach of closures at the local scale of central-place foraging penguins is warranted to facilitate their population growth under fisheries management goals to conserve and maintain ecosystem functions.

ICES Journal of Marine Science↗
USGS2024

Metagenomic sequencing sheds light on microbes putatively associated with pneumonia-related fatalities of white-tailed deer (Odocoileus virginianus)

With emerging infectious disease outbreaks in human, domestic and wild animal populations on the rise, improvements in pathogen characterization and surveillance are paramount for the protection of human and animal health, as well as the conservation of ecologically and economically important wildlife. Genomics offers a range of suitable tools to meet these goals, with metagenomic sequencing facilitating the characterization of whole microbial communities associated with emerging and endemic disease outbreaks. Here, we use metagenomic sequencing in a case-control study to identify microbes in lung tissue associated with newly observed pneumonia-related fatalities in 34 white-tailed deer ( Odocoileus virginianus ) in Wisconsin, USA. We identified 20 bacterial species that occurred in more than a single individual. Of these, only Clostridium novyi was found to substantially differ (in number of detections) between case and control sample groups; however, this difference was not statistically significant. We also detected several bacterial species associated with pneumonia and/or other diseases in ruminants ( Mycoplasma ovipneumoniae , Trueperella pyogenes , Pasteurella multocida , Anaplasma phagocytophilum , Fusobacterium necrophorum ); however, these species did not substantially differ between case and control sample groups. On average, we detected a larger number of bacterial species in case samples than controls, supporting the potential role of polymicrobial infections in this system. Importantly, we did not detect DNA of viruses or fungi, suggesting that they are not significantly associated with pneumonia in this system. Together, these results highlight the utility of metagenomic sequencing for identifying disease-associated microbes. This preliminary list of microbes will help inform future research on pneumonia-associated fatalities of white-tailed deer.

Microbial Genomics↗
USGS2017

Estimating occupancy and abundance using aerial images with imperfect detection

Species distribution and abundance are critical population characteristics for efficient management, conservation, and ecological insight. Point process models are a powerful tool for modelling distribution and abundance, and can incorporate many data types, including count data, presence-absence data, and presence-only data. Aerial photographic images are a natural tool for collecting data to fit point process models, but aerial images do not always capture all animals that are present at a site. Methods for estimating detection probability for aerial surveys usually include collecting auxiliary data to estimate the proportion of time animals are available to be detected. We developed an approach for fitting point process models using an N -mixture model framework to estimate detection probability for aerial occupancy and abundance surveys. Our method uses multiple aerial images taken of animals at the same spatial location to provide temporal replication of sample sites. The intersection of the images provide multiple counts of individuals at different times. We examined this approach using both simulated and real data of sea otters ( Enhydra lutris kenyoni ) in Glacier Bay National Park, southeastern Alaska. Using our proposed methods, we estimated detection probability of sea otters to be 0.76, the same as visual aerial surveys that have been used in the past. Further, simulations demonstrated that our approach is a promising tool for estimating occupancy, abundance, and detection probability from aerial photographic surveys. Our methods can be readily extended to data collected using unmanned aerial vehicles, as technology and regulations permit. The generality of our methods for other aerial surveys depends on how well surveys can be designed to meet the assumptions of N -mixture models.

Methods in Ecology and Evolution↗
USGS2022

Pursuing best practices for minimizing wild bee captures to support biological research

Bees are important pollinators of wild and domesticated flowering plant species. Over the last 30 years, an increasing number of scientific articles have been published on the ecology and conservation of wild bees. To achieve research goals, many studies have pursued the lethal take of wild bees. Although the impact of lethal take for scientific pursuits is likely negligible compared to the negative impacts of human-mediated phenomena such as climate change, urbanization, and agricultural intensification, it is important to evaluate the history of lethal take on scientific endeavors. In our study, we evaluated a random sample of 30 years of scientific publications on wild bees. Across 1426 surveyed publications, 536 reported the lethal take of wild bees. We found that 61% of these studies lethally captured wild bees primarily for species identification. Furthermore, we determined passive sampling of wild bees resulted in substantially more lethal collections than active methods per study. However, combined approaches of passive and active collection resulted in the greatest lethal take of wild bees per study. Finally, we determined that 64% of the studies did not provide deposition information for their samples, hindering additional research that could be done with them. The increasing availability of video and photographic devices and artificial intelligence approaches to identification, the development of low and noninvasive molecular methods, and the ease of sharing information, allow for a timely discussion on alternative routes and potentially new best practices in bee research. We focus our discussion on alternative methods for minimizing lethal captures for identification purposes and through passive methods, and for maximizing the utility of the data collected. Finally, we provide a framework for continued engagement among researchers and managers to develop strategies that can contribute to reducing our impact on wild bee communities and making the most of collected specimens.

Conservation Science and Practice↗
USGS2006

Linking the concept of scale to studies of biological diversity: evolving approaches and tools.

Although the concepts of scale and biological diversity independently have received rapidly increasing attention in the scientific literature since the 1980s, the rate at which the two concepts have been investigated jointly has grown much more slowly. We find that scale considerations have been incorporated explicitly into six broad areas of investigation related to biological diversity: (1) heterogeneity within and among ecosystems, (2) disturbance ecology, (3) conservation and restoration, (4) invasion biology, (5) importance of temporal scale for understanding processes, and (6) species responses to environmental heterogeneity. In addition to placing the papers of this Special Feature within the context of brief summaries of the expanding literature on these six topics, we provide an overview of tools useful for integrating scale considerations into studies of biological diversity. Such tools include hierarchical and structural-equation modelling, kriging, variable-width buffers, k -fold cross-validation, and cascading graph diagrams, among others. Finally, we address some of the major challenges and research frontiers that remain, and conclude with a look to the future.

Diversity and Distributions↗
USGS2011

The cost of fear

What should parents do when they detect indications of more predators nearby that might eat their babies? This scenario is commonly faced by parents in the wild, and the consequences are important. The number of offspring that organisms produce has a major influence on fitness and, when averaged across a population, affects whether this population will increase or decrease. Offspring production thus has critical implications for evolution via fitness, and ecology and conservation via demography. On page 1398 of this issue, Zanette et al. ( 1 ) show that the fear of predation can, by itself, strongly affect the number of offspring produced over an annual cycle by song sparrows (see the figure).

Science↗
USGS2019

Testing theoretical metapopulation conditions with genotypic data from Boreal Chorus Frogs (Pseudacris maculata)

The metapopulation concept has far-reaching implications in ecology and conservation biology. Hanski’s criteria operationally define metapopulations, yet testing them is hindered by logistical and financial constraints inherent to the collection of long-term demographic data. Hence, ecologists and conservationists often assume metapopulation existence for dispersal-limited species that occupy patchy habitats. To advance understanding of metapopulation theory and improve conservation of metapopulations, we used population and landscape genetic tools to develop a methodological framework for evaluating Hanski’s criteria. We used genotypic data (11 microsatellite loci) from a purported metapopulation of Boreal Chorus Frogs ( Pseudacris maculata (Agassiz, 1850)) in Colorado, U.S.A., to test Hanski’s four criteria. We found support for each criterion: (1) significant genetic differentiation between wetlands, suggesting distinct breeding populations; (2) wetlands had small effective population sizes and recent bottlenecks, suggesting populations do not experience long-term persistence; (3) population graphs provided evidence of gene flow between patches, indicating potential for recolonization; and (4) multiscale bottleneck analyses suggest asynchrony, indicating that simultaneous extinction of all populations was unlikely. Our methodological framework provides a logistically and financially feasible alternative to long-term demographic data for identifying amphibian metapopulations.

Colorado↗
USGS2024

Smaller body size under warming is not due to gill-oxygen limitation in a coldwater salmonid

Declining body size in fishes and other aquatic ectotherms associated with anthropogenic climate warming has significant implications for future fisheries yields, stock assessments and aquatic ecosystem stability. One proposed mechanism seeking to explain such body-size reductions, known as the gill oxygen limitation (GOL) hypothesis, has recently been used to model future impacts of climate warming on fisheries but has not been robustly empirically tested. We used brook trout ( Salvelinus fontinalis ), a fast-growing, cold-water salmonid species of broad economic, conservation and ecological value, to examine the GOL hypothesis in a long-term experiment quantifying effects of temperature on growth, resting metabolic rate (RMR), maximum metabolic rate (MMR) and gill surface area (GSA). Despite significantly reduced growth and body size at an elevated temperature, allometric slopes of GSA were not significantly different than 1.0 and were above those for RMR and MMR at both temperature treatments (15°C and 20°C), contrary to GOL expectations. We also found that the effect of temperature on RMR was time-dependent, contradicting the prediction that heightened temperatures increase metabolic rates and reinforcing the importance of longer-term exposures (e.g. >6 months) to fully understand the influence of acclimation on temperature–metabolic rate relationships. Our results indicate that although oxygen limitation may be important in some aspects of temperature–body size relationships and constraints on metabolic supply may contribute to reduced growth in some cases, it is unlikely that GOL is a universal mechanism explaining temperature–body size relationships in aquatic ectotherms. We suggest future research focus on alternative mechanisms underlying temperature–body size relationships, and that projections of climate change impacts on fisheries yields using models based on GOL assumptions be interpreted with caution.

Journal of Experimental Biology↗
USGS2014

The southern megalopolis: using the past to predict the future of urban sprawl in the Southeast U.S.

The future health of ecosystems is arguably as dependent on urban sprawl as it is on human-caused climatic warming. Urban sprawl strongly impacts the urban ecosystems it creates and the natural and agro-ecosystems that it displaces and fragments. Here, we project urban sprawl changes for the next 50 years for the fast-growing Southeast U.S. Previous studies have focused on modeling population density, but the urban extent is arguably as important as population density per se in terms of its ecological and conservation impacts. We develop simulations using the SLEUTH urban growth model that complement population-driven models but focus on spatial pattern and extent. To better capture the reach of low-density suburban development, we extend the capabilities of SLEUTH by incorporating street-network information. Our simulations point to a future in which the extent of urbanization in the Southeast is projected to increase by 101% to 192%. Our results highlight areas where ecosystem fragmentation is likely, and serve as a benchmark to explore the challenging tradeoffs between ecosystem health, economic growth and cultural desires.

PLoS ONE↗
USGS2005

Predicted sex ratio of juvenile Kemp's Ridley sea turtles captured near Steinhatchee, Florida

The Kemp's Ridley ( Lepidochelys kempii ) is one of the most endangered sea turtles in the world, and it possesses temperature-dependent sex determination (TSD). Sex ratios produced under TSD can vary widely and can affect the reproductive ecology of a population. Therefore, sex ratios produced from TSD are of ecological and conservation interest. The current study validated and utilized a testosterone radioimmunoassay (RIA) to examine the sex ratio of juvenile Kemp's Ridleys inhabiting the waters near Steinhatchee, Florida. Testosterone levels were measured in blood samples collected from juvenile Kemp's Ridleys captured over a three-year period. Results of this study indicate that a significant female bias (approximately 3.7:1) occurs in the aggregation of juvenile Kemp's Ridleys inhabiting the waters near Steinhatchee.

Copeia↗
USGS2003

Predicted sex ratio of juvenile Hawksbill Seaturtles inhabiting Buck Island Reef national monument, U.S. Virgin Islands

Hawksbill Seaturtles have temperature-dependent sex determination. As such, the resulting sex ratios are of conservational and ecological significance. Buck Island Reef is an interesting location for sex ratio studies since it represents a natural and unexploited foraging ground for hawksbills in the Caribbean. To examine sex ratios, blood samples were obtained from juvenile Hawksbill Seaturtles captured on Buck Island Reef over a four-year period. We used a radioimmunoassay to determine testosterone levels in those samples and compared those values to testosterone levels of juvenile hawksbills from the Caribbean whose sex has been verified by laparoscopy. The results of this study reveal a significantly female-biased sex ratio (approximately 80% female) occurs in this juvenile aggregation inhabiting Buck Island Reef .

U.S. Virgin Islands↗
USGS2021

Decision analysis of barrier placement and targeted removal to control invasive carp in the Tennessee River Basin

Controlling range expansion of invasive carp (specifically Hypophthalmichthys spp.) on the Tennessee River is important to conserve the ecological and economic benefits provided by the river. We collaborated with State and Federal agencies (the stakeholder group) to develop a decision framework and decision support model to evaluate strategies to control carp expansion in the Tennessee River. Using this decision framework, we assessed the efficacy of various barrier strategies (technologies and locations) on reducing bigheaded carp (Hypophthalmichthys nobilis [bighead carp] and Hypophthalmichthys molitrix [silver carp]) relative abundance under different patterns and magnitudes of population growth and movement. We also assessed whether or not these strategies induced tradeoffs between reducing bigheaded carp relative abundance and other considerations for public satisfaction, effects on lock operation, and native species. For the purpose of comparing options to control carp in a quantitative framework, we codeveloped a carp population dynamics model with the stakeholder group. We then used the model to compare invasive carp management options within the Tennessee River system. The actions we considered included barrier placement at lock and dam systems and targeted removal through harvest, which were believed to impede upstream carp spread and establishment. To account for the uncertainty in carp population growth and movement rates, the group developed four population models that varied in the underlying population dynamics and population growth rates. The models affected population growth through either the stock-recruitment relation or intrinsic density-dependent growth rate. We then tasked the stakeholder group to test various strategies using the model. We then developed a more formal optimization framework and solved for strategies that performed well under scenarios of barrier effectiveness, movement rate, recruitment frequency, fishing mortality, and variation in population growth rate. The results of our qualitative and quantitative analyses indicated that strategies designed to first protect reservoirs just above the leading edge of carp invasion by installing barriers and removing fish below that point would perform best; however, this depended on barrier effectiveness. When barrier effectiveness was high, simply cutting off the presumed source of carp and blocking the leading the edge was enough to stop carp invasion; however, lower effectiveness meant that more barriers would be needed to slow, but not completely stop, carp invasion. We discuss what these findings mean in terms of future monitoring and management efforts to reduce the potential for expanding carp invasion.

Kentucky↗