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At least 235 records · Page 13Linked to original sources
USGS2025

Short-term ecological effects of solar energy development depend on plant community, soil type, and disturbance intensity

Solar energy is rapidly growing to decarbonize the electrical grid. Maintaining ecosystem function with solar energy generation can be promoted through construction methods that minimize negative impacts on soils and vegetation. However, the disturbance created by less-impactful construction methods at utility-scale solar energy (USSE) facilities and the ecosystem responses remain relatively unknown. We monitored soils and vegetation before and after the USSE build-out to assess the short-term impacts of construction on soils and vegetation at the Gemini Solar Project in the Mojave Desert. The facility was constructed with methods intended to be less impactful than traditional techniques. Our goal was to answer three questions: (1) What are the short-term effects of construction on soils and vegetation? (2) Do construction effects vary by the initial plant community and soil type? and (3) Does disturbance intensity from construction affect soil and vegetation response? We found strong evidence that the construction of the Gemini facility increased bare soil and soil compaction, and decreased dark biocrust cover and soil stability in the short term. For every 1% increase in disturbance intensity, we found a 0.23% increase in bare soil cover and a 0.10% decrease in dark biocrust cover. Plant responses varied more than soil responses and depended on the initial plant community and soil type, with decreases in plant canopy cover highest in sandy soils dominated by creosote bush ( Larrea tridentata ) and white bursage ( Ambrosia dumosa ) shrubs. Synthesis and applications : Many impacts of USSE facility construction depend on the underlying vegetation and soils and the level of disturbance intensity. The use of less-impactful construction methods, including a combination of overland travel and drive-and-crush examined in our study, can ameliorate negative effects relative to traditional construction practices and provide a pathway to maintain ecosystem function.

Journal of Applied Ecology↗
USGS1979

Population ecology of house mice in unstable habitats

(1) The relationships between habitat change and house mouse populations were studied by monthly live trapping in a corn-wheat-hay rotation on a small Maryland farm. (2) Population density reached 53.0/ha in a wheat/hay field in October and 25.4/ha in corn in September. Populations increased by immigration as wheat or corn grew and ripened and decreased by emigration as hay became tall and dense. (3) Survival rates were high in winter in the relatively stable habitat of the wheat/hay field; they were low throughout the summer in both fields, and were reduced by corn harvest, less so by wheat harvest. If they were related to population density or increase, or to breeding condition, the relationships were obscured by the overriding influence of habitat change. (4) In the spring, when the population in the hay field `crashed,' essentially the entire population moved from long-established ranges in the hay field to the field of ripening wheat, where new ranges were established. In the new field, fewer than 30% of the old associations between individuals persisted. (5) Individual mice maintained home ranges (88.1 +- 6.1 m in length) in the same general area during their residence in a field. Ranges shifted from month to month, perhaps in response to changes in populations and habitat; exploratory travels and other movements also modified home range behaviour. (6) Minimum life expectancy (residence time) was greater from November (4-5 months) than from June/July (1-2 months). Maximum individual age was 17 months. (7) The demographic pattern fell at the r extreme of the r-K continuum. Mice bred from May to October, matured and produced litters rapidly, produced several litters in a season, and had a high turnover rate. (8) It was concluded that migration was a primary mechanism of population regulation in the cropfield mosaic and that it was driven by habitat change, a system in contrast to those described for house mice in confined conditions.

Journal of Animal Ecology↗
USGS2011

Compensatory effects of recruitment and survival when amphibian populations are perturbed by disease

The need to increase our understanding of factors that regulate animal population dynamics has been catalysed by recent, observed declines in wildlife populations worldwide. Reliable estimates of demographic parameters are critical for addressing basic and applied ecological questions and understanding the response of parameters to perturbations (e.g. disease, habitat loss, climate change). However, to fully assess the impact of perturbation on population dynamics, all parameters contributing to the response of the target population must be estimated. We applied the reverse‐time model of Pradel in Program mark to 6 years of capture–recapture data from two populations of Anaxyrus boreas (boreal toad) populations, one with disease and one without. We then assessed a priori hypotheses about differences in survival and recruitment relative to local environmental conditions and the presence of disease. We further explored the relative contribution of survival probability and recruitment rate to population growth and investigated how shifts in these parameters can alter population dynamics when a population is perturbed. High recruitment rates (0·41) are probably compensating for low survival probability (range 0·51–0·54) in the population challenged by an emerging pathogen, resulting in a relatively slow rate of decline. In contrast, the population with no evidence of disease had high survival probability (range 0·75–0·78) but lower recruitment rates (0·25). Synthesis and applications. We suggest that the relationship between survival and recruitment may be compensatory, providing evidence that populations challenged with disease are not necessarily doomed to extinction. A better understanding of these interactions may help to explain, and be used to predict, population regulation and persistence for wildlife threatened with disease. Further, reliable estimates of population parameters such as recruitment and survival can guide the formulation and implementation of conservation actions such as repatriations or habitat management aimed to improve recruitment.

Journal of Applied Ecology↗
USGS2025

Temporal and spatial equivalence in demographic responses of emperor penguins (Aptenodytes forsteri) to environmental change

1. Population ecology and biogeography applications often necessitate the transfer of models across spatial and/or temporal dimensions to make predictions outside the bounds of the data used for model fitting. However, ecological data are often spatiotemporally unbalanced such that the spatial or the temporal dimension tends to contain more data than the other. This unbalance frequently leads model transfers to become substitutions, which are predictions to a different dimension than the predictive model was built on. Despite the prevalence of substitutions in ecology, studies validating their performance and their underlying assumptions are scarce. 2. Here, we present a successful case study demonstrating both space-for-time and time-for-space substitutions using emperor penguins (Aptenodytes forsteri) as the focal species. Using abundance-based species distribution models (aSDM) of adult emperor penguins in attendance during spring across 50 colonies, we predict long-term annual fluctuations in fledgling abundance and breeding success at a single colony, Pointe Géologie. Subsequently, we construct statistical models from time series of extended counts on Pointe Géologie to predict average fledgling abundance across 50 colonies. 3. Our analysis reveals that distance to nearest open water (NOW) exhibits the strongest association with both temporal and spatial data. aSDM’s space-for-time substitution performance, as measured by Pearson correlation coefficient was 0.63 and 0.56 when predicting breeding success and fledgling abundance time series, respectively. Linear regression of fledgling abundance on NOW yields similar time-for-space substitution performance when predicting abundance distribution of emperor penguin colonies with a correlation coefficient of 0.58. 4. We posit that such space-time equivalence arises because: 1) emperor penguins colonies conform to their existing fundamental niche; 2) there is not yet any environmental novelty when comparing the spatial vs temporal variation of distance to nearest open water; and 3) models of more specific components of life histories, such as fledgling abundance, rather than occurrence or total population abundance, are more transferable. Identifying these conditions empirically can enhance the qualitative validation of substitutions in cases where direct validation data are lacking.

Journal of Animal Ecology↗
USGS2021

Integrating socioecological suitability with human-wildlife conflict risk: Case study for translocation of a large ungulate

Translocations are essential for re-establishing wildlife populations. As they sometimes fail, it is critical to assess factors that influence their success pre-translocation. Socioecological suitability models (SESMs) integrate social acceptance and ecological suitability to enable identification of areas where wildlife populations will expand, which makes it likely that SESMs will also be useful for predicting translocation success. To inform site selection for potential elk Cervus canadensis reintroduction to north-eastern Minnesota, United States, we developed broadscale maps of social acceptance from surveys of local residents and landowners, animal use equivalence (AUE) from forage measured in the field and empirical conflict risk from geospatial data. Resulting SESMs integrated social acceptance favourability scores, AUE and conflict risk, and weighted SESMs showed the relative influences of acceptance and conflict. Social acceptance was positive for local residents and landowners (mean ≥ 5.4; scale of 1–7). AUE (scaled to an elk home range) ranged between 1 and 9 elk/16 km 2 during winter, and from 14 to 83 elk/16 km 2 during summer. Human–elk conflict risk was low (mean ≤ 0.10; scaled 0–1), increasing from north to south. Geographical distributions differed for social acceptance, AUE and conflict risk, and weighted SESMs revealed unsuitable areas that were otherwise obscured. Synthesis and applications . Integrating human–wildlife conflict risk into SESMs shows where social acceptance of translocated species is likely to erode, even where viewed favourably pre-translocation, to inform translocation planning by highlighting interactions between key factors. Such integrated models supplement existing reintroduction biology frameworks by supporting decision-making and knowledge development. In north-eastern Minnesota, natural resource managers who are considering elk reintroductions are using SESMs reported here to identify where human–elk conflict is unlikely to result in an isolated elk population and where addressing concerns for area residents about conflict risk is essential.

Minnesota↗
USGS2026

Disease-associated mortality drives reduction in Yukon River Chinook salmon escapement: A novel method for quantifying the negative impacts of ‘misfit’ parasites to improve fisheries management

Parasites can suppress host populations through parasite-induced mortality. However, the negative effects of parasites are difficult to measure in wild populations and we have few tools for quantifying the magnitude of parasite-induced mortality. This is especially true for many ‘misfit’ parasites that do not fit into standard classifications (e.g. fungal-like parasites and myxozoans). As such, we are limited in our ability to include the effects of parasites in fish and wildlife management strategies. Chinook salmon ( Oncorhynchus tshawytscha ) are a species of immense cultural and ecological significance but populations are declining across much of their range. In the Yukon River, Alaska, USA, episodic outbreaks of the ichthyosporean parasite Ichthyophonus have been linked to declines, but population-level effects of Ichthyophonus on Yukon Chinook salmon remain largely unknown. We developed a novel model that leverages changes in parasite intensity distributions to quantify the magnitude of disease-induced mortality occurring in host populations. We used it to address two questions to inform management of Yukon Chinook salmon: (i) Is parasite-induced mortality occurring in Chinook salmon and at what magnitude? (ii) What are the drivers of spatio-temporal variability in parasite-induced mortality? Using 3 years of surveys, we quantified the evidence for the presence, magnitude, and variability in Ichthyophonus -induced mortality in Chinook salmon. Our model predicted that Ichthyophonus was responsible for between 8% and 15% mortality of the migrating Chinook salmon population prior to reaching the Canadian border and could describe nearly 35% of unaccounted for mortality at the border. The model predicted that variability in mortality among years could largely be explained by differences in parasite acquisition in the marine environment rather than differences in infection dynamics in the river. Synthesis and applications . Alaska Department of Fish and Game is implementing an annual monitoring program at the mouth of the Yukon River where our model will estimate the proportion of fish at risk from parasite-induced mortality to inform annual management. Moreover, the model is broadly applicable to other fungal-like and myxozoan parasites of conservation concern, where improved estimates of parasite-induced mortality could be used to predict parasite suppression of wild and managed host populations.

Alaska↗
USGS2024

Droughts reshape apex predator space use and intraguild overlap

1. Droughts are increasing in frequency and severity globally due to climate change, leading to changes in resource availability that may have cascading effects on animal ecology. Resource availability is a key driver of animal space use, which in turn influences interspecific interactions like intraguild competition. Understanding how climate-induced changes in resource availability influence animal space use, and how species-specific responses scale up to affect intraguild dynamics, is necessary for predicting broader community-level responses to climatic changes. 2. Although several studies have demonstrated the ecological impacts of drought, the behavioral responses of individuals that scale up to these broader-scale effects are not well known, particularly among animals in top trophic levels, such as large carnivores. Furthermore, we currently lack understanding of how the impacts of climate variability on individual carnivore behavior are linked to intraguild dynamics, in part because multi-species datasets collected at timescales relevant to climatic changes are rare. 3. Using 11 years of GPS data from four sympatric large carnivore species in southern Africa – lions ( Panthera leo ), leopards ( Panthera pardus ), African wild dogs ( Lycaon pictus) , and cheetahs ( Acinonyx jubatus ) – spanning 4 severe drought events, we test whether drought conditions impact 1) large carnivore space use, 2) broad-scale intraguild spatial overlap, and 3) fine-scale intraguild interactions. 4. Drought conditions expanded space use across species, with carnivores increasing their monthly home range sizes by 35% (wild dogs) to 66% (leopards). Drought conditions increased the amount of spatial overlap between lions and subordinate felids (cheetahs and leopards) by up to 119%, but only lion-cheetah encounter rates were affected by these changes, declining in response to drought. 5. Our findings reveal that drought has a clear signature on the space use of multiple sympatric large carnivore species, which can alter spatiotemporal partitioning between competing species. Our study thereby illuminates the links between environmental change, animal behavior, and intraguild dynamics. While fine-scale avoidance strategies may facilitate intraguild coexistence during periodic droughts, large carnivore conservation may require considerable expansion of protected areas or revised human-carnivore coexistence strategies to accommodate the likely long-term increased space demands of large carnivores under projected increases in drought intensity.

Okavango Delta↗
USGS2003

Long-term fitness consequences of early conditions in the kittiwake

1. The long - term fitness consequences of conditions during development are receiving growing attention: they are at the interface between ecological and evolutionary processes. We addressed the influence of the length of the rearing period and 'rank' on fitness components in a long -lived seabird species with deferred breeding: the kittiwake (Rissa tridactyla). Rank, which depends on hatching order, was used as a surrogate for dominance status in the brood. Rank could be viewed as a random factor affecting individuals regardless of their possible 'intrinsic quality' at birth. The length of the rearing period was used as a surrogate for parental effort. It reflects the interaction between numerous factors such as environmental conditions , parental quality, reproductive decisions and effort, and also offspring decisions and intrinsic quality at birth. 2. There was evidence of an influence of the length of the rearing period on local survival before recruitment. Individuals with shorter rearing periods had lower local survival during the first winter (e.g. the relationship was positive). They may incur higher mortality. In rank 1 prebreeders, this relationship was negative in older age-classes. Longer rearing periods and better condition at independence may be associated with stronger migrating ability, and prebreeders that have not yet made settlement decisions may emigrate permanently to distant locations. Such a complex pattern may reflect age-related changes in the relative contribution of mortality and permanent emigration to local survival. 3. The length of the rearing period had long - term consequences on reproductive performance. The relationship was positive but the rate of increase decreased slightly at higher values of the covariate. 4. There was an unambiguously negative influence of rank on survival before recruitment and recruitment probability, but not on demographic parameters specific to the reproductive stage. Juniors recruited later than elder siblings. The disadvantage of juniors may be expressed mainly in terms of higher mortality and disappearance from the population before recruitment.

Journal of Animal Ecology↗
USGS2013

Evaluating a multispecies adaptive management framework: Must uncertainty impede effective decision-making?

Application of adaptive management to complex natural resource systems requires careful evaluation to ensure that the process leads to improved decision-making. As part of that evaluation, adaptive policies can be compared with alternative nonadaptive management scenarios. Also, the value of reducing structural (ecological) uncertainty to achieving management objectives can be quantified. A multispecies adaptive management framework was recently adopted by the Atlantic States Marine Fisheries Commission for sustainable harvest of Delaware Bay horseshoe crabs Limulus polyphemus, while maintaining adequate stopover habitat for migrating red knots Calidris canutus rufa , the focal shorebird species. The predictive model set encompassed the structural uncertainty in the relationships between horseshoe crab spawning, red knot weight gain and red knot vital rates. Stochastic dynamic programming was used to generate a state-dependent strategy for harvest decisions given that uncertainty. In this paper, we employed a management strategy evaluation approach to evaluate the performance of this adaptive management framework. Active adaptive management was used by including model weights as state variables in the optimization and reducing structural uncertainty by model weight updating. We found that the value of information for reducing structural uncertainty is expected to be low, because the uncertainty does not appear to impede effective management. Harvest policy responded to abundance levels of both species regardless of uncertainty in the specific relationship that generated those abundances. Thus, the expected horseshoe crab harvest and red knot abundance were similar when the population generating model was uncertain or known, and harvest policy was robust to structural uncertainty as specified. Synthesis and applications . The combination of management strategy evaluation with state-dependent strategies from stochastic dynamic programming was an informative approach to evaluate adaptive management performance and value of learning. Although natural resource decisions are characterized by uncertainty, not all uncertainty will cause decisions to be altered substantially, as we found in this case. It is important to incorporate uncertainty into the decision framing and evaluate the effect of reducing that uncertainty on achieving the desired outcomes

Journal of Applied Ecology↗
USGS2021

Tree mortality response to drought-density interactions suggests opportunities to enhance drought resistance

The future of dry forests around the world is uncertain given predictions that rising temperatures and enhanced aridity will increase drought-induced tree mortality. Using forest management and ecological restoration to reduce density and competition for water offers one of the few pathways that forests managers can potentially minimize drought-induced tree mortality. Competition for water during drought leads to elevated tree mortality in dense stands, although the influence of density on heat-induced stress, and the durations of hot or dry conditions that most impact mortality, remain unclear. Understanding how competition interacts with hot-drought stress is essential to recognize how, where, and how much reducing density can help sustain dry forests in a rapidly changing world. Here, we integrated repeat measurements of 28,881 ponderosa pine trees across the western US (2000-2017) with soil moisture estimates from a water balance model to examine how annual mortality responds to competition, temperature and soil moisture conditions. Tree mortality responded most strongly to basal area, and was elevated in places with high mean temperatures, unusually hot 7-year high temperature anomalies, and unusually dry 8-year low soil moisture anomalies. Mortality was also lower in places that experienced unusually wet 3-year soil moisture anomalies between measurements. Importantly, we found that basal area interacts with temperature and soil moisture, exacerbating mortality during times of stress imposed by high temperature or low moisture. Synthesis and Applications: Our results imply that a 50% reduction in forest basal area could reduce drought-driven tree mortality by 20-80%. The largest impacts of density reduction are seen in areas with high current basal area and places that experience high temperatures and/or severe multiyear droughts. These interactions between competition and drought are critical to understand past and future patterns of tree mortality in the context of climate change, and provide information for resource managers seeking to enhance dry forest drought resistance.

Journal of Applied Ecology.↗
USGS2016

Overwintering strategies of migratory birds: a novel approach for estimating seasonal movement patterns of residents and transients

Our understanding of movement patterns in wildlife populations has played an important role in current ecological knowledge and can inform landscape conservation decisions. Direct measures of movement can be obtained using marked individuals, but this requires tracking individuals across a landscape or multiple sites. We demonstrate how movements can be estimated indirectly using single-site, capture–mark–recapture (CMR) data with a multi-state open robust design with state uncertainty model (MSORD-SU). We treat residence and transience as two phenotypic states of overwintering migrants and use time- and state-dependent probabilities of site entry and persistence as indirect measures of movement. We applied the MSORD-SU to data on eight species of overwintering Neotropical birds collected in 14 countries between 2002 and 2011. In addition to entry and persistence probabilities, we estimated the proportions of residents at a study site and mean residence times. We identified overwintering movement patterns and residence times that contrasted with prior categorizations of territoriality. Most species showed an evidence of residents entering sites at multiple time intervals, with transients tending to enter between peak resident movement times. Persistence and the proportion of residents varied by latitude, but were not always positively correlated for a given species. Synthesis and applications . Our results suggest that migratory songbirds commonly move among habitats during the overwintering period. Substantial proportions of populations appear to be comprised of transient individuals, and residents tend to persist at specific sites for relatively short periods of time. This information on persistence and movement patterns should be explored for specific habitats to guide landscape management on the wintering grounds, such as determining which habitats are conserved or restored as part of certification programmes of tropical agroforestry crops. We suggest that research and conservation efforts on Neotropical migrant songbirds focus on identifying landscape configurations and regional habitat networks that support these diverse overwintering strategies to secure full life cycle conservation.

Journal of Applied Ecology↗
USGS2009

Trend estimation in populations with imperfect detection

1. Trends of animal populations are of great interest in ecology but cannot be directly observed owing to imperfect detection. Binomial mixture models use replicated counts to estimate abundance, corrected for detection, in demographically closed populations. Here, we extend these models to open populations and illustrate them using sand lizard Lacerta agilis counts from the national Dutch reptile monitoring scheme. 2. Our model requires replicated counts from multiple sites in each of several periods, within which population closure is assumed. Counts are described by a hierarchical generalized linear model, where the state model deals with spatio-temporal patterns in true abundance and the observation model with imperfect counts, given that true state. We used WinBUGS to fit the model to lizard counts from 208 transects with 1–10 (mean 3) replicate surveys during each spring 1994–2005. 3. Our state model for abundance contained two independent log-linear Poisson regressions on year for coastal and inland sites, and random site effects to account for unexplained heterogeneity. The observation model for detection of an individual lizard contained effects of region, survey date, temperature, observer experience and random survey effects. 4. Lizard populations increased in both regions but more steeply on the coast. Detectability increased over the first few years of the study, was greater on the coast and for the most experienced observers, and highest around 1 June. Interestingly, the population increase inland was not detectable when the observed counts were analysed without account of detectability. The proportional increase between 1994 and 2005 in total lizard abundance across all sites was estimated at 86% (95% CRI 35–151). 5. Synthesis and applications . Open-population binomial mixture models are attractive for studying true population dynamics while explicitly accounting for the observation process, i.e. imperfect detection. We emphasize the important conceptual benefit provided by temporal replicate observations in terms of the interpretability of animal counts.

Journal of Applied Ecology↗
USGS2018

Trophic implications of a phenological paradigm shift: Bald eagles and salmon in a changing climate

Climate change influences apex predators in complex ways, due to their important trophic position, capacity for resource plasticity, and sensitivity to numerous anthropogenic stressors. Bald eagles, an ecologically and culturally significant apex predator, congregate seasonally in high densities on salmon spawning rivers across the Pacific Northwest. One of the largest eagle concentrations is in the Skagit River watershed, which connects the montane wilderness of North Cascades National Park to the Puget Sound. Using multiple long‐term datasets, we evaluated local bald eagle abundance in relation to chum and coho salmon availability; salmon phenology; and the number and timing of flood events in the Skagit. We analysed changes over time as a reflection of climate change impacts, as well as differences between managed and unmanaged portions of the river. We found that peaks in chum salmon and bald eagle presence have advanced at remarkably similar rates ( c . 0.45 days/year), suggesting synchronous phenological responses within this trophic relationship. Yet the temporal relationship between chum salmon spawning and flood events, which remove salmon carcasses from the system, has not remained constant. This has resulted in a paradigm shift whereby the peak of chum spawning now occurs before the first flood event of the season rather than after. The interval between peak chum and first flood event was a significant predictor of bald eagle presence: as this interval grew over time (by nearly one day per year), bald eagle counts declined, with a steady decrease in bald eagle observations since 2002. River section was also an important factor, with fewer flood events, and more eagle observations occurring in the river section experiencing direct hydroelectric flow management. Synthesis and applications . The effects of climate change and hydroelectric management contribute to a complex human footprint in the North Cascades National Park, an otherwise largely natural ecosystem. By accounting for the differential phenological impacts of climate change on bald eagles, salmon, and flood events, Park managers and the operators of the hydroelectric system can more effectively ensure the resilience of the eagle–salmon relationship along the Skagit River.

Washington↗
USGS2005

Designing occupancy studies: General advice and allocating survey effort

1. The fraction of sampling units in a landscape where a target species is present (occu pancy) is an extensively used concept in ecology. Yet in many applications the species will not always be detected in a sampling unit even when present, resulting in biased estimates of occupancy. Given that sampling units are surveyed repeatedly within a r elatively short timeframe, a number of similar methods have now been developed to provide unbiased occupancy estimates. However, practical guidance on the efficient design of occupancy studies has been lacking. 2. In this paper we comment on a number of general issues related to designing occu pancy studies, including the need for clear objectives that are explicitly linked to science or management, selection of sampling units, timing of repeat surveys and allocation of survey effort. Advice on the number of repeat surveys per sampling unit is considered in terms of the variance of the occupancy estimator, for three possible study designs. 3. We r ecommend that sampling units should be surveyed a minimum of three times w hen detection probability is high (> 0·5 survey − 1 ), unless a removal design is used. 4. We f ound that an optimal removal design will generally be the most efficient, but we suggest it may be less robust to assumption violations than a standard design. 5. Our results suggest that for a rare species it is more efficient to survey more sampling units less intensively, while for a common species fewer sampling units should be surveyed more intensively. 6. Synthesis and applications . Reliable inferences can only result from quality data. To ma ke the best use of logistical resources, study objectives must be clearly defined; sampling units must be selected, and repeated surveys timed appropriately; and a sufficient n umber of repeated surveys must be conducted. Failure to do so may compromise the integrity of the study. The guidance given here on study design issues is particularly a pplicable to studies of species occurrence and distribution, habitat selection and modelling, metapopulation studies and monitoring programmes.

Journal of Applied Ecology↗
USGS2013

Modelling interactions of toxicants and density dependence in wildlife populations

1. A major challenge in the conservation of threatened and endangered species is to predict population decline and design appropriate recovery measures. However, anthropogenic impacts on wildlife populations are notoriously difficult to predict due to potentially nonlinear responses and interactions with natural ecological processes like density dependence. 2. Here, we incorporated both density dependence and anthropogenic stressors in a stage-based matrix population model and parameterized it for a density-dependent population of peregrine falcons Falco peregrinus exposed to two anthropogenic toxicants [dichlorodiphenyldichloroethylene (DDE) and polybrominated diphenyl ethers (PBDEs)]. Log-logistic exposure–response relationships were used to translate toxicant concentrations in peregrine falcon eggs to effects on fecundity. Density dependence was modelled as the probability of a nonbreeding bird acquiring a breeding territory as a function of the current number of breeders. 3. The equilibrium size of the population, as represented by the number of breeders, responded nonlinearly to increasing toxicant concentrations, showing a gradual decrease followed by a relatively steep decline. Initially, toxicant-induced reductions in population size were mitigated by an alleviation of the density limitation, that is, an increasing probability of territory acquisition. Once population density was no longer limiting, the toxicant impacts were no longer buffered by an increasing proportion of nonbreeders shifting to the breeding stage, resulting in a strong decrease in the equilibrium number of breeders. 4. Median critical exposure concentrations, that is, median toxicant concentrations in eggs corresponding with an equilibrium population size of zero, were 33 and 46 μg g −1 fresh weight for DDE and PBDEs, respectively. 5. Synthesis and applications. Our modelling results showed that particular life stages of a density-limited population may be relatively insensitive to toxicant impacts until a critical threshold is crossed. In our study population, toxicant-induced changes were observed in the equilibrium number of nonbreeding rather than breeding birds, suggesting that monitoring efforts including both life stages are needed to timely detect population declines. Further, by combining quantitative exposure–response relationships with a wildlife demographic model, we provided a method to quantify critical toxicant thresholds for wildlife population persistence.

California↗
USGS2011

Exploring sensitivity of a multistate occupancy model to inform management decisions

1. Dynamic occupancy models are often used to investigate questions regarding the processes that influence patch occupancy and are prominent in the fields of population and community ecology and conservation biology. Recently, multistate occupancy models have been developed to investigate dynamic systems involving more than one occupied state, including reproductive states, relative abundance states and joint habitat‐occupancy states. Here we investigate the sensitivities of the equilibrium‐state distribution of multistate occupancy models to changes in transition rates. 2. We develop equilibrium occupancy expressions and their associated sensitivity metrics for dynamic multistate occupancy models. To illustrate our approach, we use two examples that represent common multistate occupancy systems. The first example involves a three‐state dynamic model involving occupied states with and without successful reproduction (California spotted owl Strix occidentalis occidentalis ), and the second involves a novel way of using a multistate occupancy approach to accommodate second‐order Markov processes (wood frog Lithobates sylvatica breeding and metamorphosis). 3. In many ways, multistate sensitivity metrics behave in similar ways as standard occupancy sensitivities. When equilibrium occupancy rates are low, sensitivity to parameters related to colonisation is high, while sensitivity to persistence parameters is greater when equilibrium occupancy rates are high. Sensitivities can also provide guidance for managers when estimates of transition probabilities are not available. 4. Synthesis and applications. Multistate models provide practitioners a flexible framework to define multiple, distinct occupied states and the ability to choose which state, or combination of states, is most relevant to questions and decisions about their own systems. In addition to standard multistate occupancy models, we provide an example of how a second‐order Markov process can be modified to fit a multistate framework. Assuming the system is near equilibrium, our sensitivity analyses illustrate how to investigate the sensitivity of the system‐specific equilibrium state(s) to changes in transition rates. Because management will typically act on these transition rates, sensitivity analyses can provide valuable information about the potential influence of different actions and when it may be prudent to shift the focus of management among the various transition rates.

Journal of Applied Ecology↗
USGS2017

Effects of host species and environment on the skin microbiome of Plethodontid salamanders

The amphibian skin microbiome is recognized for its role in defence against pathogens, including the deadly fungal pathogen Batrachochytrium dendrobatidis (Bd). Yet, we have little understanding of evolutionary and ecological processes that structure these communities, especially for salamanders and closely related species. We investigated patterns in the distribution of bacterial communities on Plethodon salamander skin across host species and environments. Quantifying salamander skin microbiome structure contributes to our understanding of how host-associated bacteria are distributed across the landscape, among host species, and their putative relationship with disease. We characterized skin microbiome structure (alpha-diversity, beta-diversity and bacterial operational taxonomic unit [OTU] abundances) using 16S rRNA gene sequencing for co-occurring Plethodon salamander species (35 Plethodon cinereus , 17 Plethodon glutinosus , 10 Plethodon cylindraceus ) at three localities to differentiate the effects of host species from environmental factors on the microbiome. We sampled the microbiome of P. cinereus along an elevational gradient ( n = 50, 700–1,000 m a.s.l.) at one locality to determine whether elevation predicts microbiome structure. Finally, we quantified prevalence and abundance of putatively anti-Bd bacteria to determine if Bd-inhibitory bacteria are dominant microbiome members. Co-occurring salamanders had similar microbiome structure, but among sites salamanders had dissimilar microbiome structure for beta-diversity and abundance of 28 bacterial OTUs. We found that alpha-diversity increased with elevation, beta-diversity and the abundance of 17 bacterial OTUs changed with elevation (16 OTUs decreasing, 1 OTU increasing). We detected 11 putatively anti-Bd bacterial OTUs that were present on 90% of salamanders and made up an average relative abundance of 83% ( SD ± 8.5) per salamander. All salamanders tested negative for Bd. We conclude that environment is more influential in shaping skin microbiome structure than host differences in these congeneric species, and suggest that environmental characteristics that covary with elevation influence microbiome structure. High prevalence and abundance of anti-Bd bacteria may contribute to low Bd levels in these populations of Plethodon salamanders.

Journal of Animal Ecology↗
USGS2015

Predictive modelling of habitat use by marine predators with respect to the abundance and depth distribution of pelagic prey

Understanding the ecological processes that underpin species distribution patterns is a fundamental goal in spatial ecology. However, developing predictive models of habitat use is challenging for species that forage in marine environments, as both predators and prey are often highly mobile and difficult to monitor. Consequently, few studies have developed resource selection functions for marine predators based directly on the abundance and distribution of their prey. We analysed contemporaneous data on the diving locations of two seabird species, the shallow-diving Peruvian Booby ( Sula variegata ) and deeper diving Guanay Cormorant ( Phalacrocorax bougainvilliorum ), and the abundance and depth distribution of their main prey, Peruvian anchoveta ( Engraulis ringens ). Based on this unique data set, we developed resource selection functions to test the hypothesis that the probability of seabird diving behaviour at a given location is a function of the relative abundance of prey in the upper water column. For both species, we show that the probability of diving behaviour is mostly explained by the distribution of prey at shallow depths. While the probability of diving behaviour increases sharply with prey abundance at relatively low levels of abundance, support for including abundance in addition to the depth distribution of prey is weak, suggesting that prey abundance was not a major factor determining the location of diving behaviour during the study period. The study thus highlights the importance of the depth distribution of prey for two species of seabird with different diving capabilities. The results complement previous research that points towards the importance of oceanographic processes that enhance the accessibility of prey to seabirds. The implications are that locations where prey is predictably found at accessible depths may be more important for surface foragers, such as seabirds, than locations where prey is predictably abundant. Analysis of the relative importance of abundance and accessibility is essential for the design and evaluation of effective management responses to reduced prey availability for seabirds and other top predators in marine systems.

Gulf of Guinea↗