Estimating population impacts via dynamic occupancy analysis of Before-After Control-Impact studies

Wildfire immediately reduces nest and adult survival of greater sage-grouse

Wildfire events are becoming more frequent and severe on a global scale. Rising temperatures, prolonged drought, and the presence of pyrophytic invasive grasses are contributing to the degradation of native vegetation communities. Within the Great Basin region of the western U.S., increasing wildfire frequency is transforming the ecosystem toward a higher degree of homogeneity, one dominated by invasive annual grasses and declining landscape productivity. Greater sage-grouse (Centrocercus urophasianus; hereafter sage-grouse) are a species of conservation concern that rely on large tracts of structurally and functionally diverse sagebrush (Artemisia spp.) communities. Using a 12-year (2008-2019) telemetry dataset, we documented immediate impacts of wildfire on demographic rates of a population of sage-grouse that were exposed to two large wildfire events (Virginia Mountains Fire Complex-2016; Long Valley Fire-2017) near the border of California and Nevada. Spatiotemporal heterogeneity in demographic rates were accounted for using a Before-After Control-Impact Paired Series (BACIPS) study design. Results revealed a 40% reduction in adult survival and a 79% reduction in nest survival within areas impacted by wildfires. Our results indicate that wildfire has strong and immediate impacts to two key life stages of a sagebrush indicator species and underscores the importance of fire suppression and immediate restoration following wildfire events.

The impact of the striped field mouse's range expansion on communities of native small mammals

Understanding species expansion as an element of the dispersal process is crucial to gaining a better comprehension of the functioning of the populations and the communities. Populations of the same species that are native in one area could be considered nonindigenous, naturalised or invasive somewhere else. The striped field mouse has been expanding its range in south-western Slovakia since 2010, although the origin of the spread has still not been clarified. In light of the striped field mouse's life history, the recent range expansion is considered to be the expansion of a native species. This study analyses the impact of the striped field mouse's expansion on the native population and small mammal communities and confronts the documented stages of striped field mouse expansion with the stages of invasion biology. Our research replicates the design and compares results from past research of small mammals prior to this expansion at the same three study areas with the same 20 study sites and control sites. Several years after expansion, the striped field mouse has a 100% frequency of occurrence in all study sites and has become the dominant species in two of the study areas. The native community is significantly affected by the striped field mouse's increasing dominance, specifically: (i) we found a re-ordering of the species rank, mainly in areas with higher dominance, and (ii) an initial positive impact on diversity and evenness during low dominance of the striped field mouse turned markedly negative after crossing the 25% dominance threshold. Results suggested that the variation in the striped field mouse's dominance is affected by the northern direction of its spread. Our findings show that establishment in a new area, spread and impact on the native community are stages possibly shared by both invasive and native species during their range expansion.

Invader removal triggers competitive release in a threatened avian predator

Invasive species can cause extinctions of native species and widespread biodiversity loss. Invader removal is a common management response, but the use of long-term field experiments to characterize effectiveness of removals in benefitting impacted native species is rare. We used a large-scale removal experiment to investigate the demographic response of a threatened native species, the northern spotted owl, to removal of an invasive competitor species, the barred owl. Removal of barred owls had a strong, positive effect on survival of spotted owls, which arrested long-term population declines of spotted owls. The results demonstrate that the long-term persistence of spotted owls will depend heavily on reducing the negative impacts of barred owls while simultaneously addressing other threats, such as habitat loss.

Changes in the distribution and abundance of invasive species can have far-reaching ecological consequences. Programs to control invaders are common but gauging the effectiveness of such programs using carefully controlled, large-scale field experiments is rare, especially at higher trophic levels. Experimental manipulations coupled with long-term demographic monitoring can reveal the mechanistic underpinnings of interspecific competition among apex predators and suggest mitigation options for invasive species. We used a large-scale before–after control–impact removal experiment to investigate the effects of an invasive competitor, the barred owl (Strix varia), on the population dynamics of an iconic old-forest native species, the northern spotted owl (Strix occidentalis caurina). Removal of barred owls had a strong, positive effect on survival of sympatric spotted owls and a weaker but positive effect on spotted owl dispersal and recruitment. After removals, the estimated mean annual rate of population change for spotted owls stabilized in areas with removals (0.2% decline per year), but continued to decline sharply in areas without removals (12.1% decline per year). The results demonstrated that the most substantial changes in population dynamics of northern spotted owls over the past two decades were associated with the invasion, population expansion, and subsequent removal of barred owls. Our study provides experimental evidence of the demographic consequences of competitive release, where a threatened avian predator was freed from restrictions imposed on its population dynamics with the removal of a competitively dominant invasive species.

Impacts of invasive quagga mussels (Dreissena rostriformis bugensis) on reservoir water quality, as revealed by progressive-change BACIPS analysis

Invasive quagga mussels (Dreissena rostriformis bugensis) are an emerging threat to the functioning and management of freshwater ecosystems. Quagga mussels were first recorded in the UK in 2014 and have subsequently established at high densities in a number of major reservoirs. Through implementing a Progressive-Change BACIPS (Before-After-Control-Impact Paired Series) analysis, we found that the following trends were observed following quagga mussel establishment: reduced diatom and cyanobacteria abundances; increased soluble reactive phosphorus and reactive silica concentrations; and reduced abundances of Aphanizomenon sp., a potentially toxic cyanobacterium. We also found reservoirs with established quagga mussel populations experienced slightly increased overall chlorophyll a concentration but no changes in turbidity or Microcystis sp. abundance, which are often considered common indicators of dreissenid invasion. Our results show that Progressive-Change BACIPS analysis is a powerful tool which can be used to interrogate industry standard long-term datasets of water quality metrics in order to identify and quantify the impacts of invasive species when the approximate timeframe of species arrival is known. We also demonstrate that quagga mussels may have had significant effects on reservoir ecosystems which, primarily through their impacts on phytoplankton communities, may have implications for reservoir management.

Linking monitoring and data analysis to predictions and decisions for the range-wide eastern black rail status assessment

The US Fish and Wildlife Service (USFWS) has initiated a re-envisioned approach for providing decision makers with the best available science and synthesis of that information, called the Species Status Assessment (SSA), for endangered species decision making. The SSA report is a descriptive document that provides decision makers with an assessment of the current and predicted future status of a species. These analyses support all manner of decisions under the US Endangered Species Act, such as listing, reclassification, and recovery planning. Novel scientific analysis and predictive modeling in SSAs could be an important part of rooting conservation decisions in current data and cutting edge analytical and modeling techniques. Here, we describe a novel analysis of available data to assess the current condition of eastern black rail Laterallus jamaicensis jamaicensis across its range in a dynamic occupancy analysis. We used the results of the analysis to develop a site occupancy projection model where the model parameters (initial occupancy, site persistence, colonization) were linked to environmental covariates, such as land management and land cover change (sea-level rise, development, etc.). We used the projection model to predict future status under multiple sea-level rise and habitat management scenarios. Occupancy probability and site colonization were low in all analysis units, and site persistence was also low, suggesting low resiliency and redundancy currently. Extinction probability was high for all analysis units in all simulated scenarios except one with significant effort to preserve existing habitat, suggesting low future resiliency and redundancy. With the results of these data analyses and predictive models, the USFWS concluded that protections of the Endangered Species Act were warranted for this subspecies.

Landscape resistance mediates native fish species distribution shifts and vulnerability to climate change in riverscapes

A broader understanding of how landscape resistance influences climate change vulnerability for many species is needed, as is an understanding of how barriers to dispersal may impact vulnerability. Freshwater biodiversity is at particular risk, but previous studies have focused on popular cold-water fishes (e.g., salmon, trout, and char) with relatively large body sizes and mobility. Those fishes may be able to track habitat change more adeptly than less mobile species. Smaller, less mobile fishes are rarely represented in studies demonstrating effects of climate change, but depending on their thermal tolerance, they may be particularly vulnerable to environmental change. By revisiting 280 sites over a 20 year interval throughout a warming riverscape, we described changes in occupancy (i.e., site extirpation and colonization probabilities) and assessed the environmental conditions associated with those changes for four fishes spanning a range of body sizes, thermal and habitat preferences. Two larger-bodied trout species exhibited small changes in site occupancy, with bull trout experiencing a 9.2% (95% CI = 8.3%-10.1%) reduction, mostly in warmer stream reaches, and westslope cutthroat trout experiencing a nonsignificant 1% increase. The small-bodied cool water slimy sculpin was originally distributed broadly throughout the network and experienced a 48.0% (95% CI = 42.0%-54.0%) reduction in site occupancy with declines common in warmer stream reaches and areas subject to wildfire disturbances. The small-bodied comparatively warmer water longnose dace primarily occupied larger streams and increased its occurrence in the lower portions of connected tributaries during the study period. Distribution shifts for sculpin and dace were significantly constrained by barriers, which included anthropogenic water diversions, natural step-pools and cascades in steeper upstream reaches. Our results suggest that aquatic communities exhibit a range of responses to climate change, and that improving passage and fluvial connectivity will be important climate adaptation tactics for conserving aquatic biodiversity.

Dry conifer forest restoration benefits Colorado Front Range avian communities

Fire suppression has increased stand density and risk of severe, stand-replacing wildfire in lower elevation dry conifer forests of western North America, threatening ecological function. The U.S. Forest Service's Collaborative Forest Landscape Restoration Program (CFLRP) aims to mitigate impacts to ecological function, while mandating effectiveness monitoring to verify restoration success. Expected benefits include improved conditions for biodiversity, but relatively few empirical studies evaluate restoration effects on biodiversity. We applied the Integrated Monitoring in Bird Conservation Regions program to survey birds in relation to CFLRP treatments along the Colorado Front Range in 2015-2017. We employed hierarchical models to analyze species occupancy and richness at 1972 points nested within 141 1-km² grid cells. Our objectives were to investigate (1) species occupancy relationships with treatments at local (point) and landscape (grid) spatial scales, (2) potential mechanisms for treatment relationships considering species and treatment relationships with forest structure and composition (i.e., habitat relationships), and (3) treatment and habitat relationships with species richness. The data supported positive and negative point-level treatment relationships, suggesting uneven species distributions between treated and untreated points. At the grid scale, however, we only found positive species relationships with percent area treated, and accordingly, grid-level species richness increased with treatment extent. Potential mechanisms for treatment relationships included treatments generating foraging opportunities for aerial insectivores by opening the canopy, improving conditions for ground-associated species by increasing herbaceous growth, and limiting opportunities for shrub-nesting species by reducing shrub cover. Landscape-scale patterns suggest CFLRP treatments can benefit avian communities by generating habitat for open-forest species without necessarily eliminating habitat for closed-forest species. Our results provide evidence for a commonly expected but rarely verified pattern of increased species richness with forest heterogeneity. We suggest restoration treatments will most benefit forest bird diversity by reducing canopy cover, encouraging herbaceous ground cover, limiting ladder fuel species, and encouraging shrub diversity in canopy openings, while maintaining some dense forest stands on the landscape.

Megafire effects on spotted owls: elucidation of a growing threat and a response to Hanson et al. (2018)

The extent to which wildfire adversely affects spotted owls (Strix occidentalis) is a key consideration for ecosystem restoration efforts in seasonally dry forests of the western United States. Recently, Jones et al. (2016) demonstrated that the 2014 King Fire (a “megafire”) adversely affected a population of individually-marked California spotted owls (S. o. occidentalis) monitored as part of a long-term demographic study in the Sierra Nevada, California, USA because territory occupancy declined substantially at territories burned at high-severity and GPS-tagged spotted owls avoided large patches of high-severity fire. Hanson et al. (2018) attempted to reassess changes in territory occupancy of the Jones et al. (2016) study population and claimed that occupancy declined as a result of post-fire salvage logging not fire per se and suggested that the avoidance of GPS-marked owls from areas that burned at high-severity was due to post-fire logging rather than a response to high-severity fire. Here, we demonstrate that Hanson et al. (2018) used erroneous data, inadequate statistical analyses and faulty inferences to reach their conclusion that the King Fire did not affect spotted owls and, more broadly, that large, high-severity fires do not pose risks to spotted owls in western North American dry forest ecosystems. We also provide further evidence indicating that the King Fire exerted a clear and significant negative effect on our marked study population of spotted owls. Collectively, the additional evidence presented here and in Jones et al. (2016) suggests that large, high-severity fires can pose a threat to spotted owls and that restoration of natural low- to mixed-severity frequent fire regimes would likely benefit both old-forest species and dry forest ecosystems in this era of climate change. Meeting these dual objectives of species conservation and forest restoration will be complex but it is made more challenging by faulty science that does not acknowledge the full range of wildfire effects on spotted owls.

Nonconsumptive effects of hunting on a nontarget game bird

Human hunting activity and disturbance can significantly impact prey species through both consumptive and nonconsumptive effects. The nonconsumptive effects of rabbit hunting on Northern Bobwhite (Colinus virginianus; hereafter, bobwhite) are currently unknown. Increased perceived risk of predation by bobwhite during rabbit hunting events may elicit antipredator responses among bobwhite that impact fitness via changes in behavior that ultimately impact population growth.We estimated the nonconsumptive effects of rabbit hunting on bobwhite behavior using telemetry across varying rabbit hunting intensities. Movements were analyzed using Bayesian hierarchical modeling with a before-after-control-impact (BACI) design to determine the effect of rabbit hunting on bobwhite.We observed an overall reduction in bobwhite movement in the presence of rabbit hunting, with a 38% (Posterior Overlap = 0.01) increase in bobwhite step length in the absence of rabbit hunting. We also observed bobwhite maintaining closer proximity to hardwood and escape cover under high rabbit hunting intensity, with a 59% (Posterior Overlap = 0.03) increase in distance from hardwood and a 28% (Posterior Overlap = 0.14) increase in distance from escape cover when rabbit hunting was removed. Synthesis and applications. Heightened antipredator behavior through decreased movement may assist with bobwhite predator avoidance. However, decreased movement and increased use of poor habitats may also have negative effects as a result of reduced foraging time or increased susceptibility to other predators. Future research should attempt to quantify the effect of decreased movement on bobwhite fitness through the evaluation of foraging time and survival in order to continue to improve management efforts for the species.

Megafire effects on spotted owls: elucidation of a growing threat and a response to Hanson et al. (2018)

The extent to which wildfire adversely affects spotted owls (Strixoccidentalis) is a key consideration for ecosystem restoration efforts in seasonally dry forests of the western United States. Recently, Jones et al. (2016) demonstrated that the 2014 King Fire (a “megafire”) adversely affected a population of individually-marked California spotted owls (S.o.occidentalis) monitored as part of a long-term demographic study in the Sierra Nevada, California, USA because territory occupancy declined substantially at territories burned at high-severity and GPS-tagged spotted owls avoided large patches of high-severity fire. Hanson et al. (2018) attempted to reassess changes in territory occupancy of the Jones et al. (2016) study population and claimed that occupancy declined as a result of post-fire salvage logging not fire per se and suggested that the avoidance of GPS-marked owls from areas that burned at high-severity was due to post-fire logging rather than a response to high-severity fire. Here, we demonstrate that Hanson et al. (2018) used erroneous data, inadequate statistical analyses and faulty inferences to reach their conclusion that the King Fire did not affect spotted owls and, more broadly, that large, high-severity fires do not pose risks to spotted owls in western North American dry forest ecosystems. We also provide further evidence indicating that the King Fire exerted a clear and significant negative effect on our marked study population of spotted owls. Collectively, the additional evidence presented here and in Jones et al. (2016) suggests that large, high-severity fires can pose a threat to spotted owls and that restoration of natural low- to mixed-severity frequent fire regimes would likely benefit both old-forest species and dry forest ecosystems in this era of climate change. Meeting these dual objectives of species conservation and forest restoration will be complex but it is made more challenging by faulty science that does not acknowledge the full range of wildfire effects on spotted owls.

New measures for evaluation of environmental perturbations using Before-After-Control-Impact analyses

Before-After-Control-Impact (BACI) designs are powerful tools to derive inferences about environmental perturbations (e.g., hurricanes, restoration programs) when controlled experimental designs are unfeasible. Applications of BACI designs mostly rely on testing for a significant interaction between periods and treatments (so-called BACI contrast) to demonstrate the effects of the perturbation. However, significant interactions can emerge for several reasons, including when changes are larger in control sites, such that additional diagnostics must be performed to determine the full complexity of system changes. We propose two measures that detail the nature of change implied by BACI contrasts, along with its uncertainty. CI-divergence (Control-Impact divergence) quantifies to what extent control and impact sites have diverged between the after and the before period, whereas CI-contribution (Control-Impact contribution) quantifies to what extent the change between periods is stronger in impact sites relative to control sites. To illustrate how these two CI measures can be combined with BACI contrast to gain insights about effects of environmental perturbations, we used count data from the Swedish Breeding Bird Survey to investigate how hurricane Gudrun affected the long-term abundances of four bird species in forested areas of southern Sweden. Before-After-Control-Impact contrasts suggested the hurricane affected all four species. However, the values of the two CI measures strongly differed, even among species showing similar BACI contrasts. Those differences highlight qualitatively distinct population trajectories between periods and treatments requiring different ecological explanations. Overall, we show that BACI contrasts do not provide the full story in assessing the effects of environmental perturbations. The two CI measures can be used to assist ecological interpretations, or to specify detailed hypotheses about effects of restoration actions to allow stronger confirmatory inference about their outcomes. By providing a framework to develop more detailed explanations and hypotheses about ecological changes, the two CI measures can improve conclusions and strengthen evidence of effects of conservation actions and impact assessments under BACI designs.

Dynamic multi-species occupancy models reveal individualistic habitat preferences in a high-altitude grassland bird community

Moist, high-altitude grasslands of eastern South African harbour rich avian diversity and endemism. This area is also threatened by increasingly intensive agriculture and land conversion for energy production. This conflict is particularly evident at Ingula, an Important Bird and Biodiversity Area located within the least conserved high-altitude grasslands and which is also the site of a new Pumped Storage Scheme. The new management seeks to maximise biodiversity through manipulation of the key habitat variables: grass height and grass cover through burning and grazing to make habitat suitable for birds. However, different species have individual habitat preferences, which further vary through the season. We used a dynamic multi-species occupancy model to examine the seasonal occupancy dynamics of 12 common grassland bird species and their habitat preferences. We estimated monthly occupancy, colonisation and persistence in relation to grass height and grass cover throughout the summer breeding season of 2011/12. For majority of these species, at the beginning of the season occupancy increased with increasing grass height and decreased with increasing grass cover. Persistence and colonisation decreased with increasing grass height and cover. However, the 12 species varied considerably in their responses to grass height and cover. Our results suggest that management should aim to provide plots which vary in grass height and cover to maximise bird diversity. We also conclude that the decreasing occupancy with increasing grass cover and low colonisation with increasing grass height and cover is a results of little grazing on our study site. We further conclude that some of the 12 selected species are good indicators of habitat suitability more generally because they represent a range of habitat needs and are relatively easy to monitor.

Evaluating the efficacy of a landscape scale feral cat control program using camera traps and occupancy models

The impact of introduced predators is a major factor limiting survivorship and recruitment of many native Australian species. In particular, the feral cat and red fox have been implicated in range reductions and population declines of many conservation dependent species across Australia, including ground-nesting birds and small to medium-sized mammals. The impact of predation by feral cats since their introduction some 200 years ago has altered the structure of native fauna communities and led to the development of landscape-scale threat abatement via baiting programs with the feral cat bait, Eradicat. Demonstrating the effectiveness of broad-scale programs is essential for managers to fine tune delivery and timing of baiting. Efficacy of feral cat baiting at the Fortescue Marsh in the Pilbara, Western Australia was tested using camera traps and occupancy models. There was a significant decrease in probability of site occupancy in baited sites in each of the five years of this study, demonstrating both the effectiveness of aerial baiting for landscape-scale removal of feral cats, and the validity of camera trap monitoring techniques for detecting changes in feral cat occupancy during a five-year baiting program.

Evaluating impacts using a BACI design, ratios, and a Bayesian approach with a focus on restoration

Before-after-control-impact (BACI) designs are an effective method to evaluate natural and human-induced perturbations on ecological variables when treatment sites cannot be randomly chosen. While effect sizes of interest can be tested with frequentist methods, using Bayesian Markov chain Monte Carlo (MCMC) sampling methods, probabilities of effect sizes, such as a ≥20 % increase in density after restoration, can be directly estimated. Although BACI and Bayesian methods are used widely for assessing natural and human-induced impacts for field experiments, the application of hierarchal Bayesian modeling with MCMC sampling to BACI designs is less common. Here, we combine these approaches and extend the typical presentation of results with an easy to interpret ratio, which provides an answer to the main study question-"How much impact did a management action or natural perturbation have?" As an example of this approach, we evaluate the impact of a restoration project, which implemented beaver dam analogs, on survival and density of juvenile steelhead. Results indicated the probabilities of a ≥30 % increase were high for survival and density after the dams were installed, 0.88 and 0.99, respectively, while probabilities for a higher increase of ≥50 % were variable, 0.17 and 0.82, respectively. This approach demonstrates a useful extension of Bayesian methods that can easily be generalized to other study designs from simple (e.g., single factor ANOVA, paired t test) to more complicated block designs (e.g., crossover, split-plot). This approach is valuable for estimating the probabilities of restoration impacts or other management actions.