EolPop, a R-shiny tool for quantifying the demographic impact of species exposed to fatalities: Application to bird collisions with wind turbines

Quantifying the demographic impact of anthropogenic fatalities on animal populations is a key component of wildlife conservation. However, such quantification remains rare in environmental impact assessments (EIA) of large-infrastructure projects, partly because of the complexity of implementing demographic models. Providing user-friendly demographic tools is thus an important step to fill this gap. We developed an application called EolPop to run demographic simulations and assess population-level impacts of fatalities. This tool, freely available online, is easy to use and requires minimal input data from the user. As an output, it provides an estimate, with associated uncertainty, of the relative deficit in population size at a given time horizon. Because this impact metric is relative to a baseline scenario without fatalities, it is robust to uncertainties. We showcase the tool using examples on two species that are affected by collisions with wind turbines: Lesser kestrel (Falco naumanni) and Eurasian skylark (Alauda arvensis). After 30 years, the kestrel's population is expected to suffer a deficit of ca. 48%. In contrast, the impact on skylarks, which are already declining in France, is estimated to be fairly low (ca. 7%). EolPop aims at providing a robust quantification of the relative impact of fatalities. This tool was originally built for windfarm EIA, with a focus on birds, but it can be used to assess the demographic consequences of any type of fatalities on any species.

BatTool: projecting bat populations facing multiple stressors using a demographic model

Bats provide ecologically and agriculturally important ecosystem services but are currently experiencing population declines caused by multiple environmental stressors, including mortality from white-nose syndrome and wind energy development. Analyses of the current and future health and viability of these species may support conservation management decision making. Demographic modeling provides a quantitative tool for decision makers and conservation managers to make more informed decisions, but widespread adoption of these tools can be limited because of the complexity of the mathematical, statistical, and computational components involved in implementing these models. In this work, we provide an exposition of the BatTool R package, detailing the primary components of the matrix projection model, a publicly accessible graphical user interface ( https://rconnect.usgs.gov/battool ) facilitating user-defined scenario analyses, and its intended uses and limitations (Wiens et al., US Geol Surv Data Release 2022; Wiens et al., US Geol Surv Softw Release 2022). We present a case study involving wind energy permitting, weighing the effects of potential mortality caused by a hypothetical wind energy facility on the projected abundance of four imperiled bat species in the Midwestern United States.

Quantifying the impacts of predation by Great Black-backed Gulls Larus marinus on an Atlantic Puffin Fratercula arctica population: Implications for conservation management and impact assessments

The management of predator-prey conflicts can be a key aspect of species conservation. For management approaches to be effective, a robust understanding of the predator-prey relationship is needed, particularly when both predator and prey are species of conservation concern. On the Isle of May, Firth of Forth, Scotland, numbers of breeding Great Black-backed Gulls Larus marinus, a generalist predator, have been increasing since the 1980s, which has led to increasing numbers of sympatrically breeding Atlantic Puffins Fratercula arctica being predated during the breeding season. This may have consequences for species management on the Isle of May and impact assessments of offshore windfarms in the wider Firth of Forth area. We used population viability analysis to quantify under what predation pressure the Atlantic Puffin population may decline and become locally extinct over a three-generation period. The predation level empirically estimated in 2017 (1120 Puffins per year) was not sufficient to drive a decline in the Puffin population. Rather, an increase to approximately 3000 Puffins per year would be required to cause a population decline, and >4000 to drive the population to quasi-extinction within 66 years. We discuss the likelihood of such a scenario being reached on the Isle of May, and we recommend that where predator-prey conflicts occur, predation-driven mortality should be regularly quantified to inform conservation management and population viability analyses associated with impact assessments.

Make flying-fox hunting sustainable again: Comparing expected demographic effectiveness and hunters' acceptance of more restrictive regulations

Hunting is a major threat to many species of wildlife. However, managing hunting systems to ensure their sustainability requires a thorough demographic knowledge about the impact of hunting. Here we develop a framework integrating ecological, modelling and sociological data to achieve a sustainability assessment of flying-fox hunting in New Caledonia and assess the relative merits of alternative management policies. Using age-specific stochastic population models, we found that the current annual hunting rate [5.5-8.5%] is likely to lead to a severe decline (- 79%) of Pteropus populations over the next 30 years. However, a majority of hunters surveyed (60%) were willing to soften their practices, offering an opportunity for adaptive management. Recurrent temporary hunting ban (at least 1 year out of 2) in combination with protected areas (≥ 25%) appears as the most effective and most accepted management option. Our integrative approach appears to be a promising method for ensuring that traditional hunting systems can remain sustainable in a rapidly changing world.

Climate change complicates efforts to ensure survival and recovery of St. Lawrence Estuary beluga

Decades after a ban on hunting, and despite focused management interventions, the endangered St. Lawrence Estuary (SLE) beluga (Delphinapterus leucas) population has failed to recover. We applied a population viability analysis to simulate the responses of the SLE beluga population across a wide range of variability and uncertainty under current and projected changes in environmental and climate-mediated conditions. Three proximate threats to recovery were explored: ocean noise; contaminants; and prey limitation. Even the most optimistic scenarios failed to achieve the reliable positive population growth needed to meet current recovery targets. Here we show that predicted effects of climate change may be a more significant driver of SLE beluga population dynamics than the proximate threats we considered. Aggressive mitigation of all three proximate threats will be needed to build the population's resilience and allow the population to persist long enough for global actions to mitigate climate change to take effect.

Assessing Ecological and Social Dimensions of Success in a Community-based Sustainable Harvest Program

Community-based conservation and resource management (CBCRM) programs often incorporate the dual goals of poverty alleviation and conservation. However, robust assessments of CBCRM program outcomes are relatively scarce. This study uses a multidisciplinary, systems approach to assess the ecological and social dimensions of success of an internationally acclaimed CBCRM program. This program, located in one of the largest protected areas in the Peruvian Amazon (Pacaya-Samiria National Reserve), strives for the sustainable harvest and trade of a turtle species (Podocnemis unifilis). We used mixed methods analysis, including interviews and population viability modeling, to understand three elements: how local perceptions of changes in the managed population compare to changes inferred by ecological analyses, the indicators stakeholders use to measure success, and the barriers to long-term program success and social-ecological system sustainability. We find that stakeholders perceive a growth trend in the managed turtle population, but this perception may diverge from our ecological understanding of the system under current management. Population viability analyses with a 1:1 sex ratio suggested population size will decline under two of three management scenarios (different degrees of harvest). Yet this and similar studies are plagued by a lack of species- and site-specific population parameters that could improve understanding of the system. Significant vulnerabilities exist for system sustainability, notably the recent decrease in foreign demand for the traded resource. Identifying a sustainable species-specific harvest rate, developing locally-grounded ecological and social indicators, and focusing on data-driven adaptive management will facilitate the identification of key leverage points for future management interventions.

Extinction risk assessment of a Patagonian ungulate using population dynamics models under climate change scenarios

Climate change affects population cycles of several species, threatening biodiversity. However, there are few long-term studies on species with conservation issues and restricted distributions. Huemul is a deer endemic to the southern Andes in South America and it is considered endangered mostly due to a 50% reduction of its distribution over the last 500 years. To assess environmental variables potentially affecting huemul population viability and the impact of climate change, we developed population dynamics models. We used a 14-year survey data from Bernardo O'Higgins National Park, coastal Chilean Patagonia. We used Ricker models considering winter and spring temperatures and precipitation as variables influencing huemul population dynamics. We used the Bayesian information criterion (BIC) to select models with the greatest predictive power. The two best models (ΔBIC < 2) included winter temperature and density-dependence population growth drivers. The best model considered a lateral effect, where winter temperature influences carrying capacity and the second best a vertical effect with winter temperature influencing R_max and carrying capacity. Population viability was evaluated using those models, projecting them over a 100-year period: (a) under current conditions and (b) under conditions estimated by Global Climate Models for 2050 and 2070. The extinction risk and quasi-extinction were estimated for this population considering two critical huemul abundance levels (15 and 30 individuals) for persistence. The population is currently in a quasi-extinction process, with extinction probabilities increasing with climate change. These results are crucial for conservation of species like huemul that have low densities and are threatened by climate change.

Multiple stressors and data deficient populations; a comparative life-history approach sheds new light on the extinction risk of the highly vulnerable Baltic harbour porpoises (Phocoena phocoena)

Many endangered marine mammal populations are difficult to study, spread out over large areas, and capturing them for branding and research purposes would be unethical. Yet, they are in urgent need for assessment and conservation actions. We suggest collecting data from other more abundant populations of the same species, with careful consideration of body size, age at sexual maturity, and ecological conditions to produce scientifically sound best approximations of vital rates of data deficient endangered populations. The genetically distinct Baltic Sea harbour porpoise population amounts to about 500 animals and is classified as 'Critically Endangered' according to the IUCN red list. Data deficiency on nearly all demographic parameters have precluded systematic investigations of the relative importance of stressors affecting population viability. We took a comparative life history approach and investigated the phenotypic plasticity in somatic and demographic vital rates of seven larger, well studied North Atlantic harbour porpoise populations, enabling us to approximate the missing pieces of the life history of the Baltic population. We parameterized a stochastic, individual-based population model, and performed a population viability analysis for a range of biologically realistic parameter values and scenarios of environmental stressors. The baseline scenario was based on the most representative samples of healthy harbour porpoise populations and challenged with three different levels of bycatches. Due to high levels of endocrine disruptive contaminants observed in Baltic harbour porpoises, we also investigated the effect of a possible reduction in fecundity. Subsequently, the combined effects of bycatches and reduced fecundity were investigated in terms of population growth rate and quasi-extinction risk. The Baltic harbour porpoise population is viable in the baseline scenario without anthropogenic stressors. However, even the lowest estimated bycatch level of 7 individuals per year will lead to a population collapse to ≤50 animals with high probability (0.4-1.0) over the next century, assuming an intermediate or low (<73%) fecundity. Adult survival is of critical importance and mitigation of fishery impacts and reduction of anthropogenic disturbances in the identified main breeding areas are recommended.

Adapting population models for application in pesticide risk assessment: A case study with Mead's milkweed

Population models can facilitate assessment of potential impacts of pesticides on populations or species rather than individuals and have been identified as important tools for pesticide risk assessment of nontarget species including those listed under the Endangered Species Act. Few examples of population models developed for this specific purpose are available; however, population models are commonly used in conservation science as a tool to project the viability of populations and the long-term outcomes of management actions. We present a population model for Mead's milkweed (Asclepias meadii), a species listed as threatened under the Endangered Species Act throughout its range across the Midwestern United States. We adapted a published population model based on demographic field data for application in pesticide risk assessment. Exposure and effects were modeled as reductions of sets of vital rates in the transition matrices, simulating both lethal and sublethal effects of herbicides. Two herbicides, atrazine and mesotrione, were used as case study examples to evaluate a range of assumptions about potential exposure-effects relationships. In addition, we assessed buffers (i.e., setback distances of herbicide spray applications from the simulated habitat) as hypothetical mitigation scenarios and evaluated their influence on population-level effects in the model. The model results suggest that buffers can be effective at reducing risk from herbicide drift to plant populations. These case studies demonstrate that existing population models can be adopted and integrated with exposure and effects information for use in pesticide risk assessment. Environ Toxicol Chem 2018;37:2235-2245. © 2018 SETAC.

Predicted effects of landscape change, sea level rise, and habitat management on the extirpation risk of the Hawaiian common gallinule (Gallinula galeata sandvicensis) on the island of O'ahu

We conducted a spatially explicit, stochastic, individually based population viability analysis for the Hawaiian common gallinule (Gallinula galeata sandvicensis), an endangered subspecies of waterbird endemic to fragmented coastal wetlands in Hawai'i. This subspecies persists on two islands, with no apparent movement between them. We assessed extirpation risk for birds on O'ahu, where the resident gallinule population is made up of several fragmented subpopulations. Data on genetic differentiation were used to delineate subpopulations and estimate dispersal rates between them. We used sensitivity analyses to gauge the impact of current uncertainty of vital rate parameters on population projections, to ascertain the relative importance of gallinule vital rates to population persistence, and to compare the efficacy of potential management strategies. We used available sea level rise projections to examine the relative vulnerability of O'ahu's gallinule population to habitat loss arising from this threat. Our model predicted persistence of the island's gallinule population at 160 years (∼40 generations), but with high probabilities of extirpation for small subpopulations. Sensitivity analyses highlighted the importance of juvenile and adult mortality to population persistence in Hawaiian gallinules, justifying current predator control efforts and suggesting the need for additional research on chick and fledgling survival. Subpopulation connectivity from dispersal had little effect on the persistence of the island-wide population, but strong effects on the persistence of smaller subpopulations. Our model also predicted island-wide population persistence under predicted sea level rise scenarios, but with O'ahu's largest gallinule populations losing >40% of current carrying capacity.

Density and population viability of coastal marten: a rare and geographically isolated small carnivore

Pacific martens (Martes caurina humboldtensis) in coastal forests of Oregon and northern California in the United States are rare and geographically isolated, prompting a petition for listing under the Endangered Species Act. If listed, regulations have the potential to influence land-use decisions on public and private lands, but no estimates of population size, density, or viability of remnant marten populations are available for evaluating their conservation status. We used GPS and VHF telemetry and spatial mark-resight to estimate home ranges, density, and population size of Pacific martens in the Oregon Dunes National Recreation Area, central coast Oregon, USA. We then estimated population viability at differing levels of human-caused mortality (e.g., vehicle mortality). Marten home ranges were small on average (females = 0.8 km², males 1.5 km²) and density (1.13 martens/1 km²) was the highest reported for North American populations (M. caurina, M. americana). We estimated 71 adult martens (95% CRI [41–87]) across two subpopulations separated by a large barrier (Umpqua River). Using population viability analysis, extinction risk for a subpopulation of 30 martens, approximately the size of the subpopulation south of the Umpqua River, ranged from 32% to 99% with two or three annual human-caused mortalities within 30 years. Absent population expansion, limiting human-caused mortalities will likely have the greatest conservation impact.

Modelling Population Viability of Three Independent Javan Gibbon (Hylobates moloch) Populations on Java, Indonesia

Population viability analysis is a predictive procedure that uses a combination of different modelling approaches to estimate species vulnerability to extinction. Javan gibbons (Hylobates moloch) are vulnerable to local extinction primarily due to loss of habitat and hunting for the illegal pet trade. Using the modelling software VORTEX, we assessed the status of Javan gibbons in 3 areas (Ujung Kulon National Park, Halimun-Salak National Park, and Dieng Mountains) which hold over half of the remaining estimated number of gibbons on Java. Ujung Kulon and Halimun-Salak are long-time protected areas, whereas Dieng Mountains remain unprotected. For each area, we calculated the probability of extinction over a 100-year time period by testing different area-specific scenarios (e.g., hunting, deforestation, and increase in carrying capacity). Our modelling suggests each of the populations has a high chance of becoming extinct within the next 100 years if hunting and deforestation persist. If these threats are eliminated, the model shows each of the populations are large enough to persist in the long term whilst maintaining high levels of current genetic diversity. We conclude that specific actions should be implemented to develop more inclusive conservation management practices, especially improving awareness regarding the illegal wildlife trade and increased protection of wild populations and their habitats.

HexSim: a modeling environment for ecology and conservation

CONTEXT

Simulation models are increasingly used in both theoretical and applied studies to explore system responses to natural and anthropogenic forcing functions, develop defensible predictions of future conditions, challenge simplifying assumptions that facilitated past research, and to train students in scientific concepts and technology. Researcher's increased use of simulation models has created a demand for new platforms that balance performance, utility, and flexibility.

OBJECTIVES

We describe HexSim, a powerful new spatially-explicit, individual-based modeling framework that will have applications spanning diverse landscape settings, species, stressors, and disciplines (e.g. ecology, conservation, genetics, epidemiology). We begin with a model overview and follow-up with a discussion of key formative studies that influenced HexSim's development. We then describe specific model applications of relevance to readers of Landscape Ecology. Our goal is to introduce readers to this new modeling platform, and to provide examples characterizing its novelty and utility.

CONCLUSIONS

With this publication, we conclude a >10 year development effort, and assert that our HexSim model is mature, robust, extremely well tested, and ready for adoption by the research community. The HexSim model, documentation, worked examples, and other materials can be freely obtained from the website www.hexsim.net.

A habitat-based framework to predict the effects of agricultural drain maintenance on imperiled fishes

One third of the total global land viable for agricultural production has artificial drainage systems. These drainage systems can provide important habitat for fishes and, in some cases, imperiled fish species vulnerable to impact by drainage maintenance activities. A framework to provide quantitative assessments of the effects of maintenance activities on imperiled fish species is needed. In this study, a six-step habitat-based framework was developed to predict suitable habitat for two at-risk species in an agricultural drain: the Endangered Pugnose Shiner (Notropis anogenus) and the Special Concern Blackstripe Topminnow (Fundulus notatus). Using the framework, spatial models were developed to assess the effects of proposed drain maintenance on the overall amount of suitable habitat, habitat patch size, and connectivity of habitat patches. Maintenance had a significant impact on habitat connectivity, but did not significantly reduce the habitat size of isolated patches. The amount of suitable habitat available after maintenance fell below the minimum area for population viability (MAPV) for the Pugnose Shiner, but not the Blackstripe Topminnow. Future impact assessments of drain maintenance should incorporate population viability analysis, coupled with habitat patch analysis (patch size and connectivity), to quantitatively test consequences of proposed alteration to the viability of spatially structured populations.

Implicit assumptions underlying simple harvest models of marine bird populations can mislead environmental management decisions

Assessing the potential impact of additional mortality from anthropogenic causes on animal populations requires detailed demographic information. However, these data are frequently lacking, making simple algorithms, which require little data, appealing. Because of their simplicity, these algorithms often rely on implicit assumptions, some of which may be quite restrictive. Potential Biological Removal (PBR) is a simple harvest model that estimates the number of additional mortalities that a population can theoretically sustain without causing population extinction. However, PBR relies on a number of implicit assumptions, particularly around density dependence and population trajectory that limit its applicability in many situations. Among several uses, it has been widely employed in Europe in Environmental Impact Assessments (EIA), to examine the acceptability of potential effects of offshore wind farms on marine bird populations. As a case study, we use PBR to estimate the number of additional mortalities that a population with characteristics typical of a seabird population can theoretically sustain. We incorporated this level of additional mortality within Leslie matrix models to test assumptions within the PBR algorithm about density dependence and current population trajectory. Our analyses suggest that the PBR algorithm identifies levels of mortality which cause population declines for most population trajectories and forms of population regulation. Consequently, we recommend that practitioners do not use PBR in an EIA context for offshore wind energy developments. Rather than using simple algorithms that rely on potentially invalid implicit assumptions, we recommend use of Leslie matrix models for assessing the impact of additional mortality on a population, enabling the user to explicitly define assumptions and test their importance.

Assessing the risks of pesticides to threatened and endangered species using population modeling: A critical review and recommendations for future work

United States legislation requires the US Environmental Protection Agency to ensure that pesticide use does not cause unreasonable adverse effects on the environment, including species listed under the Endangered Species Act (ESA; hereafter referred to as listed species). Despite a long history of population models used in conservation biology and resource management and a 2013 report from the US National Research Council recommending their use, application of population models for pesticide risk assessments under the ESA has been minimal. The pertinent literature published from 2004 to 2014 was reviewed to explore the availability of population models and their frequency of use in listed species risk assessments. The models were categorized in terms of structure, taxonomic coverage, purpose, inputs and outputs, and whether the models included density dependence, stochasticity, or risk estimates, or were spatially explicit. Despite the widespread availability of models and an extensive literature documenting their use in other management contexts, only 2 of the approximately 400 studies reviewed used population models to assess the risks of pesticides to listed species. This result suggests that there is an untapped potential to adapt existing models for pesticide risk assessments under the ESA, but also that there are some challenges to do so for listed species. Key conclusions from the analysis are summarized, and priorities are recommended for future work to increase the usefulness of population models as tools for pesticide risk assessments. Environ Toxicol Chem 2016;35:1904-1913. © 2016 SETAC.

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

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.

Metapopulation viability of an endangered shorebird depends on dispersal and human-created habitats: piping plovers (Charadrius melodus) and prairie rivers

BACKGROUND

Many species are distributed as metapopulations in dynamic landscapes, where habitats change through space and time. Individuals locate habitat through dispersal, and the relationship between a species and landscape characteristics can have profound effects on population persistence. Despite the importance of connectivity in dynamic environments, few empirical studies have examined temporal variability in dispersal or its effect on metapopulation dynamics. In response to this knowledge gap, we studied the dispersal, demography, and viability of a metapopulation of an endangered, disturbance-dependent shorebird. We examined three subpopulations of piping plovers (Charadrius melodus) on the lower Platte and Missouri rivers from 2008-2013. High flow events from an upstream dam on the Missouri River in 2010 and 2011 allowed us to assess the effect of total habitat loss and the subsequent creation of new habitat associated with a large disturbance at one 'natural' study location. The other two sites within the metapopulation, which were maintained by anthropogenic activities (e.g., mining, development, habitat restoration), were largely unaffected by this disturbance, resulting in a controlled natural experiment.

RESULTS

High flow events were associated with increased emigration, decreased immigration, and decreased survival in the subpopulation that experienced high flows. Following the high flow event, immigration into that subpopulation increased. Dispersal rates among subpopulations were negatively correlated with distance. The metapopulation had a low probability of extinction over 100 years (0 %) under the current disturbance interval and associated dispersal and survival rates. However, persistence depended on relatively stable, human-created habitats, not the dynamic, natural habitat (47.7 % extinction probability for this subpopulation).

CONCLUSIONS

We found that functional connectivity, as measured by the rate of dispersal among subpopulations, increased as a result of the high flow event in our study metapopulation. Plovers also increased reproductive output following this event. Although the study metapopulation had a low overall probability of extinction, metapopulation persistence depended on anthropogenically created habitats that provided a small but stable source of nesting habitat and dispersers through time. However, all subpopulations remained small, even if persistent, making them individually vulnerable to extinction through stochastic events. Given the highly dynamic nature of habitat availability in this system, maintaining several subpopulations within the metapopulation and stable sources of habitat will be critical, and this species will likely remain conservation-reliant.