Broad-Scale Assessment of Methylmercury in Adult Amphibians

Mercury (Hg) is a toxic contaminant that has been mobilized and distributed worldwide and is a threat to many wildlife species. Amphibians are facing unprecedented global declines due to many threats including contaminants. While the biphasic life history of many amphibians creates a potential nexus for methylmercury (MeHg) exposure in aquatic habitats and subsequent health effects, the broad-scale distribution of MeHg exposure in amphibians remains unknown. We used nonlethal sampling to assess MeHg bioaccumulation in 3,241 juvenile and adult amphibians during 2017-2021. We sampled 26 populations (14 species) across 11 states in the United States, including several imperiled species that could not have been sampled by traditional lethal methods. We examined whether life history traits of species and whether the concentration of total mercury in sediment or dragonflies could be used as indicators of MeHg bioaccumulation in amphibians. Methylmercury contamination was widespread, with a 33-fold difference in concentrations across sites. Variation among years and clustered subsites was less than variation across sites. Life history characteristics such as size, sex, and whether the amphibian was a frog, toad, newt, or other salamander were the factors most strongly associated with bioaccumulation. Total Hg in dragonflies was a reliable indicator of bioaccumulation of MeHg in amphibians (R2 ≥ 0.67), whereas total Hg in sediment was not (R2 ≤ 0.04). Our study, the largest broad-scale assessment of MeHg bioaccumulation in amphibians, highlights methodological advances that allow for nonlethal sampling of rare species and reveals immense variation among species, life histories, and sites. Our findings can help identify sensitive populations and provide environmentally relevant concentrations for future studies to better quantify the potential threats of MeHg to amphibians.

Demographic consequences of phenological asynchrony for North American songbirds

Changes in phenology in response to ongoing climate change have been observed in numerous taxa around the world. Differing rates of phenological shifts across trophic levels have led to concerns that ecological interactions may become increasingly decoupled in time, with potential negative consequences for populations. Despite widespread evidence of phenological change and a broad body of supporting theory, large-scale multitaxa evidence for demographic consequences of phenological asynchrony remains elusive. Using data from a continental-scale bird-banding program, we assess the impact of phenological dynamics on avian breeding productivity in 41 species of migratory and resident North American birds breeding in and around forested areas. We find strong evidence for a phenological optimum where breeding productivity decreases in years with both particularly early or late phenology and when breeding occurs early or late relative to local vegetation phenology. Moreover, we demonstrate that landbird breeding phenology did not keep pace with shifts in the timing of vegetation green-up over a recent 18-y period, even though avian breeding phenology has tracked green-up with greater sensitivity than arrival for migratory species. Species whose breeding phenology more closely tracked green-up tend to migrate shorter distances (or are resident over the entire year) and breed earlier in the season. These results showcase the broadest-scale evidence yet of the demographic impacts of phenological change. Future climate change-associated phenological shifts will likely result in a decrease in breeding productivity for most species, given that bird breeding phenology is failing to keep pace with climate change.

Disentangling direct and indirect effects of extreme events on coastal wetland communities

One of the primary ways in which climate change will impact coastal freshwater wetlands is through changes in the frequency, intensity, timing and distribution of extreme weather events. Disentangling the direct and indirect mechanisms of population- and community-level responses to extreme events is vital to predicting how species composition of coastal wetlands will change under future conditions. We extended static structural equation modelling approaches to incorporate system dynamics in a multi-year multispecies occupancy model to quantify the effects of extreme weather events on a coastal freshwater wetland system. We used data from an 8-year study (2009-2016) on St. Marks National Wildlife Refuge in Florida, USA, to quantify species-specific and community-level changes in amphibian and fish occupancy associated with two flooding events in 2012 and 2013. We examine how physical changes to the landscape, including potential changes in salinity and increased wetland connectivity, may have contributed to or exacerbated the effects of these extreme weather events on the biota of isolated coastal wetlands. We provide evidence that the primary effects of flooding on the amphibian community were through indirect mechanisms via changes in the composition of the sympatric fish community that may have had lethal (i.e. through direct predation) or non-lethal (i.e. through direct or indirect competitive interactions) effects. In addition, we have shown that amphibian species differed in their sensitivity to direct flooding effects and indirect changes in the fish community and wetland-specific conductance, which led to variable responses across the community. These effects led to the overall decline in amphibian species richness from 2009 to 2016, suggesting that wetland-breeding amphibian communities on St. Marks National Wildlife Refuge may not be resilient to predicted changes in coastal disturbance regimes because of climate change. Understanding both direct and indirect effects, as well as species interactions, is important for predicting the effects of a changing climate on individual species, communities and ecosystems.

Diverse aging rates in ectothermic tetrapods provide insights for the evolution of aging and longevity

Comparative studies of mortality in the wild are necessary to understand the evolution of aging; yet, ectothermic tetrapods are underrepresented in this comparative landscape, despite their suitability for testing evolutionary hypotheses. We present a study of aging rates and longevity across wild tetrapod ectotherms, using data from 107 populations (77 species) of nonavian reptiles and amphibians. We test hypotheses of how thermoregulatory mode, environmental temperature, protective phenotypes, and pace of life history contribute to demographic aging. Controlling for phylogeny and body size, ectotherms display a higher diversity of aging rates compared with endotherms and include phylogenetically widespread evidence of negligible aging. Protective phenotypes and life-history strategies further explain macroevolutionary patterns of aging. Analyzing ectothermic tetrapods in a comparative context enhances our understanding of the evolution of aging.

Using interview surveys and multispecies occupancy models to inform vertebrate conservation

Species distribution data are an essential biodiversity variable requiring robust monitoring to inform wildlife conservation. Yet, such data remain inherently sparse because of the logistical challenges of monitoring biodiversity across broad geographic extents. Surveys of people knowledgeable about the occurrence of wildlife provide an opportunity to evaluate species distributions and the ecology of wildlife communities across large spatial scales. We analyzed detection histories of 30 vertebrate species across the Western Ghats biodiversity hotspot in India, obtained from a large-scale interview survey of 2318 people who live and work in the forests of this region. We developed a multispecies occupancy model that simultaneously corrected for false-negative (non-detection) and false-positive (misidentification) errors that interview surveys can be prone to. Using this model, we integrated data across species in composite analyses of the responses of functional species groups (based on disturbance tolerance, diet, and body mass traits) to spatial variation in environmental variables, protection, and anthropogenic pressures. We observed a positive association between forest cover and the occurrence of species with low tolerance of human disturbance. Protected areas were associated with higher occurrence for species across different functional groups compared with unprotected lands. We also observed the occurrence of species with low disturbance tolerance, herbivores, and large-bodied species was negatively associated with developmental pressures, such as human settlements, energy production and mining, and demographic pressures, such as biological resource extraction. For the conservation of threatened vertebrates, our work underscores the importance of maintaining forest cover and reducing deforestation within and outside protected areas, respectively. In addition, mitigating a suite of pervasive human pressures is also crucial for wildlife conservation in one of the world's most densely populated biodiversity hotspots.

Over a decade of field physiology reveals life-history specific strategies to drought in garter snakes (Thamnophis legans)

Changing climates and severe weather events can affect population viability. Individuals need to buffer such negative fitness consequences through physiological plasticity. Whether certain life-history strategies are more conducive to surviving changing climates is unknown, but theory predicts that strategies prioritizing maintenance and survival over current reproduction should be better able to withstand such change. We tested this hypothesis in a meta-population of garter snakes having naturally occurring variation in life-history strategies. We tested whether slow pace-of-life (POL) animals, that prioritize survival over reproduction, are more resilient than fast POL animals as measured by several physiological biomarkers. From 2006 to 2019, which included two multi-year droughts, baseline and stress-induced reactivity of plasma corticosterone and glucose varied annually with directionalities consistent with life-history theory. Slow POL animals exhibited higher baseline corticosterone and lower baseline glucose, relative to fast POL animals. These patterns were also observed in stress-induced measures; thus, reactivity was equivalent between ecotypes. However, in drought years, measures of corticosterone did not differ between different life histories. Immune cell distribution showed annual variation independent of drought or life history. These persistent physiological patterns form a backdrop to several extirpations of fast POL populations, suggesting a limited physiological toolkit to surviving periods of extreme drought.

Sex-related differences in aging rate are associated with sex chromosome system in amphibians

Sex‐related differences in mortality are widespread in the animal kingdom. Although studies have shown that sex determination systems might drive lifespan evolution, sex chromosome influence on aging rates have not been investigated so far, likely due to an apparent lack of demographic data from clades including both XY (with heterogametic males) and ZW (heterogametic females) systems. Taking advantage of a unique collection of capture–recapture datasets in amphibians, a vertebrate group where XY and ZW systems have repeatedly evolved over the past 200 million years, we examined whether sex heterogamy can predict sex differences in aging rates and lifespans. We showed that the strength and direction of sex differences in aging rates (and not lifespan) differ between XY and ZW systems. Sex‐specific variation in aging rates was moderate within each system, but aging rates tended to be consistently higher in the heterogametic sex. This led to small but detectable effects of sex chromosome system on sex differences in aging rates in our models. Although preliminary, our results suggest that exposed recessive deleterious mutations on the X/Z chromosome (the “unguarded X/Z effect”) or repeat‐rich Y/W chromosome (the “toxic Y/W effect”) could accelerate aging in the heterogametic sex in some vertebrate clades.

Current and time-lagged effects of climate on innate immunity in two sympatric snake species

Changing environments result in alterations at all levels of biological organization, from genetics to physiology to demography. The increasing frequency of droughts worldwide is associated with higher temperatures and reduced precipitation that can impact population persistence via effects on individual immune function and survival.We examined the effects of annual climate variation on immunity in two sympatric species of garter snakes from four populations in California over a seven-year period that included the record-breaking drought.We examined three indices of innate immunity: bactericidal competence (BC), natural antibodies (NABs), and complement-mediated lysis (CL).Precipitation was the only climatic variable explaining variation in immune function: spring precipitation of the current year was positively correlated to Thamnophis sirtalis BC and NABs, whereas spring precipitation of the previous year was positively correlated to T. elegans BC and NABs. This suggests that T. elegans experiences a physiological time-lag in response to reduced precipitation, which may reflect lack of capital for investment in immunity in the year following a dry year.In general, our findings demonstrate compelling evidence that climate can influence wild populations through effects on physiological processes, suggesting that physiological indices such as these may offer valuable opportunities for monitoring the effects of climate.

Accommodating the role of site memory in dynamic species distribution models

First-order dynamic occupancy models (FODOMs) are a class of state-space model in which the true state (occurrence) is observed imperfectly. An important assumption of FODOMs is that site dynamics only depend on the current state and that variations in dynamic processes are adequately captured with covariates or random effects. However, it is often difficult to understand and/or measure the covariates that generate ecological data, which are typically spatiotemporally correlated. Consequently, the non-independent error structure of correlated data causes underestimation of parameter uncertainty and poor ecological inference. Here, we extend the FODOM framework with a second-order Markov process to accommodate site memory when covariates are not available. Our modeling framework can be used to make reliable inference about site occupancy, colonization, extinction, turnover, and detection probabilities. We present a series of simulations to illustrate the data requirements and model performance. We then applied our modeling framework to 13 yr of data from an amphibian community in southern Arizona, USA. In this analysis, we found residual temporal autocorrelation of population processes for most species, even after accounting for long-term drought dynamics. Our approach represents a valuable advance in obtaining inference on population dynamics, especially as they relate to metapopulations.

The influence of species life history and distribution characteristics on species responses to habitat fragmentation in an urban landscape

Fragmentation within urbanized environments often leads to a loss of native species diversity; however, variation exists in responses among-species and among-populations within species. We aimed to identify patterns in species biogeography in an urbanized landscape to understand anthropogenic effects on vertebrate communities and identify species that are more sensitive or resilient to landscape change. We investigated patterns in species richness and species responses to fragmentation in southern Californian small vertebrate communities using multispecies occupancy models and determined factors associated with overall commonness and sensitivity to patch size for 45 small vertebrate species both among and within remaining non-developed patches. In general, smaller patches had fewer species, with amphibian species richness being particularly sensitive to patch size effects. Mammals were generally more common, occurring both in a greater proportion of patches and a higher proportion of the sites within occupied patches. Alternatively, amphibians were generally restricted to larger patches but were more ubiquitous within smaller patches when occupied. Species range size was positively correlated with how common a species was across and within patches, even when controlling for only patches that fell within a species' range. We found sensitivity to patch size was greater for more fecund species and depended on where the patch occurred within a species' range. While all taxa were more likely to occur in patches in the warmer portions of their ranges, amphibians and mammals were more sensitive to fragmentation in these warmer areas as compared to the rest of their ranges. Similarly, amphibians occurred at a smaller proportion of sites within patches in drier portions of their ranges. Mammals occurred at a higher proportion of sites that were also in drier portions of their range while reptiles did not differ in their sensitivity to patch size by range position. We demonstrate that taxonomy, life history, range size and range position can predict commonness and sensitivity of species across this highly fragmented yet biodiverse landscape. The impacts of fragmentation on species communities within an urban landscape depend on scale, with differences emerging among and within species and populations.

The untapped potential of reptile biodiversity for understanding how and why animals age

1. The field of comparative aging biology has greatly expanded in the past 20 years. Longitudinal studies of populations of reptiles with a range of maximum lifespans have accumulated and been analyzed for evidence of mortality senescence and reproductive decline. While not as well represented in studies of amniote senescence, reptiles have been the subjects of many recent demographic and mechanistic studies of the biology of aging. 2. We review recent literature on reptile demographic senescence, mechanisms of senescence, and identify unanswered questions. Given the ecophysiological and demographic diversity of reptiles, what is the expected range of reptile senescence rates? Are known mechanisms of aging in reptiles consistent with canonical hallmarks of aging in model systems? What are the knowledge gaps in our understanding of reptile aging? 3. We find ample evidence of increasing mortality with advancing age in many reptiles. Testudines stand out as slower aging than other orders, but data on crocodilians and tuatara are sparse. Sex-specific analyses are generally not available. Studies of female reproduction suggest that reptiles are less likely to have reproductive decline with advancing age than mammals. 4. Reptiles share many physiological and molecular pathways of aging with mammals, birds, and laboratory model organisms. Adaptations related to stress physiology coupled with reptilian ectothermy suggest novel comparisons and contrasts that can be made with canonical aging phenotypes in mammals. These include stem cell and regeneration biology, homeostatic mechanisms, IIS/TOR signaling, and DNA repair. 5. To overcome challenges to the study of reptile aging, we recommend extending and expanding long-term monitoring of reptile populations, developing reptile cell lines to aid cellular biology, conducting more comparative studies of reptile morphology and physiology sampled along relevant life-history axes, and sequencing more reptile genomes for comparative genomics. Given the diversity of reptile life histories and adaptations, achieving these directives will likely greatly benefit all aging biology.

Tourist photographs as a scalable framework for wildlife monitoring in protected areas

Protected areas are critical to conservation efforts in the face of rapid biodiversity declines [1]. Yet the resources for conservation are often limited and shared amongst many competing priorities [2]. As a consequence, even basic monitoring surveys are absent within most protected areas [3]. Although a range of wildlife monitoring methods exist, considerable focused survey effort is often required to yield accurate and precise estimates [4]. This makes monitoring difficult to sustain or replicate, limiting access to the data required for evidence-based conservation decisions. Citizen-scientists have been proposed as an important complement to the finite resources available for basic monitoring within protected areas [5]; however, the full potential of this approach has yet to be realised. Wildlife tourists and guides are especially focussed on encountering and photographing fauna and flora, yet the data collected in these efforts is rarely harnessed for conservation monitoring within protected areas. A detailed understanding of photographic tourism's potential role in wildlife monitoring has been lacking, but is essential for the development of new tools to harness the data being collected through tourism. Here, we demonstrate that tourist-contributed data can aid wildlife monitoring in protected areas by providing population estimates of large carnivores comparable to those from traditional survey methods. Our approach could capitalize upon the immense number of wildlife photographs being taken daily as part of the global > 30-billion USD, wildlife-based tourism industry.

Resolving misaligned spatial data with integrated species distribution models

Advances in species distribution modeling continue to be driven by a need to predict species responses to environmental change coupled with increasing data availability. Recent work has focused on development of methods that integrate multiple streams of data to model species distributions. Combining sources of information increases spatial coverage and can improve accuracy in estimates of species distributions. However, when fusing multiple streams of data, the temporal and spatial resolutions of data sources may be mismatched. This occurs when data sources have fluctuating geographic coverage, varying spatial scales and resolutions, and differing sources of bias and sparsity. It is well documented in the spatial statistics literature that ignoring the misalignment of different data sources will result in bias in both the point estimates and uncertainty. This will ultimately lead to inaccurate predictions of species distributions. Here, we examine the issue of misaligned data as it relates specifically to integrated species distribution models. We then provide a general solution that builds off work in the statistical literature for the change‐of‐support problem. Specifically, we leverage spatial correlation and repeat observations at multiple scales to make statistically valid predictions at the ecologically relevant scale of inference. An added feature of the approach is that addressing differences in spatial resolution between data sets can allow for the evaluation and calibration of lesser‐quality sources in many instances. Using both simulations and data examples, we highlight the utility of this modeling approach and the consequences of not reconciling misaligned spatial data. We conclude with a brief discussion of the upcoming challenges and obstacles for species distribution modeling via data fusion.

The diversity of population responses to environmental change

The current extinction and climate change crises pressure us to predict population dynamics with ever‐greater accuracy. Although predictions rest on the well‐advanced theory of age‐structured populations, two key issues remain poorly explored. Specifically, how the age‐dependency in demographic rates and the year‐to‐year interactions between survival and fecundity affect stochastic population growth rates. We use inference, simulations and mathematical derivations to explore how environmental perturbations determine population growth rates for populations with different age‐specific demographic rates and when ages are reduced to stages. We find that stage‐ vs. age‐based models can produce markedly divergent stochastic population growth rates. The differences are most pronounced when there are survival‐fecundity‐trade‐offs, which reduce the variance in the population growth rate. Finally, the expected value and variance of the stochastic growth rates of populations with different age‐specific demographic rates can diverge to the extent that, while some populations may thrive, others will inevitably go extinct.

Quantifying climate sensitivity and climate-driven change in North American amphibian communities

Changing climate will impact species' ranges only when environmental variability directly impacts the demography of local populations. However, measurement of demographic responses to climate change has largely been limited to single species and locations. Here we show that amphibian communities are responsive to climatic variability, using >500,000 time-series observations for 81 species across 86 North American study areas. The effect of climate on local colonization and persistence probabilities varies among eco-regions and depends on local climate, species life-histories, and taxonomic classification. We found that local species richness is most sensitive to changes in water availability during breeding and changes in winter conditions. Based on the relationships we measure, recent changes in climate cannot explain why local species richness of North American amphibians has rapidly declined. However, changing climate does explain why some populations are declining faster than others. Our results provide important insights into how amphibians respond to climate and a general framework for measuring climate impacts on species richness.

Ecological correlates of the spatial co-occurrence of sympatric mammalian carnivores worldwide

The composition of local mammalian carnivore communities has far-reaching effects on terrestrial ecosystems worldwide. To better understand how carnivore communities are structured, we analysed camera trap data for 108 087 trap days across 12 countries spanning five continents. We estimate local probabilities of co-occurrence among 768 species pairs from the order Carnivora and evaluate how shared ecological traits correlate with probabilities of co-occurrence. Within individual study areas, species pairs co-occurred more frequently than expected at random. Co-occurrence probabilities were greatest for species pairs that shared ecological traits including similar body size, temporal activity pattern and diet. However, co-occurrence decreased as compared to other species pairs when the pair included a large-bodied carnivore. Our results suggest that a combination of shared traits and top-down regulation by large carnivores shape local carnivore communities globally.

Use of field-portable ultrasonography reveals differences in developmental phenology and maternal egg provisioning in two sympatric viviparous snakes

A thorough understanding of the life cycles underlying the demography of wild species is limited by the difficulty of observing hidden life‐history traits, such as embryonic development. Major aspects of embryonic development, such as the rate and timing of development, and maternal–fetal interactions can be critical features of early‐life fitness and may impact population trends via effects on individual survival. While information on development in wild snakes and lizards is particularly limited, the repeated evolution of viviparity and diversity of reproductive mode in this clade make it a valuable subject of study. We used field‐portable ultrasonography to investigate embryonic development in two sympatric garter snake species, Thamnophis sirtalis and Thamnophis elegans in the Sierra Nevada mountains of California. This approach allowed us to examine previously hidden reproductive traits including the timing and annual variation in development and differences in parental investment in young. Both species are viviparous, occupy similar ecological niches, and experience the same annual environmental conditions. We found that T. sirtalis embryos were more developmentally advanced than T. elegans embryos during June of three consecutive years. We also found that eggs increased in volume more substantially across developmental stages in T. elegans than in T. sirtalis, indicating differences in maternal provisioning of embryos via placental transfer of water. These findings shed light on interspecific differences in parental investment and timing of development within the same environmental context and demonstrate the value of field ultrasonography for pursuing questions relating to the evolution of reproductive modes, and the ecology of development.

Range position and climate sensitivity: The structure of among-population demographic responses to climatic variation

Species' distributions will respond to climate change based on the relationship between local demographic processes and climate and how this relationship varies based on range position. A rarely tested demographic prediction is that populations at the extremes of a species' climate envelope (e.g., populations in areas with the highest mean annual temperature) will be most sensitive to local shifts in climate (i.e., warming). We tested this prediction using a dynamic species distribution model linking demographic rates to variation in temperature and precipitation for wood frogs (Lithobates sylvaticus) in North America. Using long-term monitoring data from 746 populations in 27 study areas, we determined how climatic variation affected population growth rates and how these relationships varied with respect to long-term climate. Some models supported the predicted pattern, with negative effects of extreme summer temperatures in hotter areas and positive effects on recruitment for summer water availability in drier areas. We also found evidence of interacting temperature and precipitation influencing population size, such as extreme heat having less of a negative effect in wetter areas. Other results were contrary to predictions, such as positive effects of summer water availability in wetter parts of the range and positive responses to winter warming especially in milder areas. In general, we found wood frogs were more sensitive to changes in temperature or temperature interacting with precipitation than to changes in precipitation alone. Our results suggest that sensitivity to changes in climate cannot be predicted simply by knowing locations within the species' climate envelope. Many climate processes did not affect population growth rates in the predicted direction based on range position. Processes such as species-interactions, local adaptation, and interactions with the physical landscape likely affect the responses we observed. Our work highlights the need to measure demographic responses to changing climate.

Heterogeneous responses of temperate-zone amphibian populations to climate change complicates conservation planning

The pervasive and unabated nature of global amphibian declines suggests common demographic responses to a given driver, and quantification of major drivers and responses could inform broad-scale conservation actions. We explored the influence of climate on demographic parameters (i.e., changes in the probabilities of survival and recruitment) using 31 datasets from temperate zone amphibian populations (North America and Europe) with more than a decade of observations each. There was evidence for an influence of climate on population demographic rates, but the direction and magnitude of responses to climate drivers was highly variable among taxa and among populations within taxa. These results reveal that climate drivers interact with variation in life-history traits and population-specific attributes resulting in a diversity of responses. This heterogeneity complicates the identification of conservation 'rules of thumb' for these taxa, and supports the notion of local focus as the most effective approach to overcome global-scale conservation challenges.

Species interactions and the effects of climate variability on a wetland amphibian metacommunity

Disentangling the role that multiple interacting factors have on species responses to shifting climate poses a significant challenge. However, our ability to do so is of utmost importance to predict the effects of climate change on species distributions. We examined how populations of three species of wetland-breeding amphibians, which varied in life history requirements, responded to a six-year period of extremely variable precipitation. This interval was punctuated by both extensive drought and heavy precipitation and flooding, providing a natural experiment to measure community responses to environmental perturbations. We estimated occurrence dynamics using a discrete hidden Markov modeling approach that incorporated information regarding habitat state and predator-prey interactions. This approach allowed us to measure how metapopulation dynamics of each amphibian species was affected by interactions among weather, wetland hydroperiod, and co-occurrence with fish predators. The pig frog, a generalist, proved most resistant to perturbations, with both colonization and persistence being unaffected by seasonal variation in precipitation or co-occurrence with fishes. The ornate chorus frog, an ephemeral wetland specialist, responded positively to periods of drought owing to increased persistence and colonization rates during periods of low-rainfall. Low probabilities of occurrence of the ornate chorus frog in long-duration wetlands were driven by interactions with predators due to low colonization rates when fishes were present. The mole salamander was most sensitive to shifts in water availability. In our study area, this species never occurred in short-duration wetlands and persistence probabilities decreased during periods of drought. At the same time, negative effects occurred with extreme precipitation because flooding facilitated colonization of fishes to isolated wetlands and mole salamanders did not colonize wetlands once fishes were present. We demonstrate that the effects of changes in water availability depend on interactions with predators and wetland type and are influenced by the life history of each of our species. The dynamic species occurrence modeling approach we used offers promise for other systems when the goal is to disentangle the complex interactions that determine species responses to environmental variability.

Evaluating within-population variability in behavior and demography for the adaptive potential of a dispersal-limited species to climate change

Multiple pathways exist for species to respond to changing climates. However, responses of dispersal‐limited species will be more strongly tied to ability to adapt within existing populations as rates of environmental change will likely exceed movement rates. Here, we assess adaptive capacity in Plethodon cinereus, a dispersal‐limited woodland salamander. We quantify plasticity in behavior and variation in demography to observed variation in environmental variables over a 5‐year period. We found strong evidence that temperature and rainfall influence P. cinereus surface presence, indicating changes in climate are likely to affect seasonal activity patterns. We also found that warmer summer temperatures reduced individual growth rates into the autumn, which is likely to have negative demographic consequences. Reduced growth rates may delay reproductive maturity and lead to reductions in size‐specific fecundity, potentially reducing population‐level persistence. To better understand within‐population variability in responses, we examined differences between two common color morphs. Previous evidence suggests that the color polymorphism may be linked to physiological differences in heat and moisture tolerance. We found only moderate support for morph‐specific differences for the relationship between individual growth and temperature. Measuring environmental sensitivity to climatic variability is the first step in predicting species' responses to climate change. Our results suggest phenological shifts and changes in growth rates are likely responses under scenarios where further warming occurs, and we discuss possible adaptive strategies for resulting selective pressures.

Estimating occupancy dynamics for large-scale monitoring networks: amphibian breeding occupancy across protected areas in the northeast United States

Regional monitoring strategies frequently employ a nested sampling design where a finite set of study areas from throughout a region are selected and intensive sampling occurs within a subset of sites within the individual study areas. This sampling protocol naturally lends itself to a hierarchical analysis to account for dependence among subsamples. Implementing such an analysis using a classic likelihood framework is computationally challenging when accounting for detection errors in species occurrence models. Bayesian methods offer an alternative approach for fitting models that readily allows for spatial structure to be incorporated. We demonstrate a general approach for estimating occupancy when data come from a nested sampling design. We analyzed data from a regional monitoring program of wood frogs (Lithobates sylvaticus) and spotted salamanders (Ambystoma maculatum) in vernal pools using static and dynamic occupancy models. We analyzed observations from 2004 to 2013 that were collected within 14 protected areas located throughout the northeast United States. We use the data set to estimate trends in occupancy at both the regional and individual protected area levels. We show that occupancy at the regional level was relatively stable for both species. However, substantial variation occurred among study areas, with some populations declining and some increasing for both species. In addition, When the hierarchical study design is not accounted for, one would conclude stronger support for latitudinal gradient in trends than when using our approach that accounts for the nested design. In contrast to the model that does not account for nesting, the nested model did not include an effect of latitude in the 95% credible interval. These results shed light on the range‐level population status of these pond‐breeding amphibians, and our approach provides a framework that can be used to examine drivers of local and regional occurrence dynamics.

Swimming against the tide: resilience of a riverine turtle to recurrent extreme environmental events

Extreme environmental events (EEEs) are likely to exert deleterious effects on populations. From 1996 to 2012 we studied the nesting dynamics of a riverine population of painted turtles (Chrysemys picta) that experienced seven years with significantly definable spring floods. We used capture-mark-recapture methods to estimate the relationships between more than 5 m and more than 6 m flood events and population parameters. Contrary to expectations, flooding was not associated with annual differences in survival, recruitment or annual population growth rates of the adult female segment of the population. These findings suggest that female C. picta exhibit resiliency to key EEE, which are expected to increase in frequency under climate change.

Determining Occurrence Dynamics when False Positives Occur: Estimating the Range Dynamics of Wolves from Public Survey Data

Large-scale presence-absence monitoring programs have great promise for many conservation applications. Their value can be limited by potential incorrect inferences owing to observational errors, especially when data are collected by the public. To combat this, previous analytical methods have focused on addressing non-detection from public survey data. Misclassification errors have received less attention but are also likely to be a common component of public surveys, as well as many other data types. We derive estimators for dynamic occupancy parameters (extinction and colonization), focusing on the case where certainty can be assumed for a subset of detections. We demonstrate how to simultaneously account for non-detection (false negatives) and misclassification (false positives) when estimating occurrence parameters for gray wolves in northern Montana from 2007-2010. Our primary data source for the analysis was observations by deer and elk hunters, reported as part of the state's annual hunter survey. This data was supplemented with data from known locations of radio-collared wolves. We found that occupancy was relatively stable during the years of the study and wolves were largely restricted to the highest quality habitats in the study area. Transitions in the occupancy status of sites were rare, as occupied sites almost always remained occupied and unoccupied sites remained unoccupied. Failing to account for false positives led to over estimation of both the area inhabited by wolves and the frequency of turnover. The ability to properly account for both false negatives and false positives is an important step to improve inferences for conservation from large-scale public surveys. The approach we propose will improve our understanding of the status of wolf populations and is relevant to many other data types where false positives are a component of observations.

General methods for sensitivity analysis of equilibrium dynamics in patch occupancy models

Sensitivity analysis is a useful tool for the study of ecological models that has many potential applications for patch occupancy modeling. Drawing from the rich foundation of existing methods for Markov chain models, I demonstrate new methods for sensitivity analysis of the equilibrium state dynamics of occupancy models. Estimates from three previous studies are used to illustrate the utility of the sensitivity calculations: a joint occupancy model for a prey species, its predators, and habitat used by both; occurrence dynamics from a well-known metapopulation study of three butterfly species; and Golden Eagle occupancy and reproductive dynamics. I show how to deal efficiently with multistate models and how to calculate sensitivities involving derived state variables and lower-level parameters. In addition, I extend methods to incorporate environmental variation by allowing for spatial and temporal variability in transition probabilities. The approach used here is concise and general and can fully account for environmental variability in transition parameters. The methods can be used to improve inferences in occupancy studies by quantifying the effects of underlying parameters, aiding prediction of future system states, and identifying priorities for sampling effort.

Experimental investigation of false positive errors in auditory species occurrence surveys

False positive errors are a significant component of many ecological data sets, which in combination with false negative errors, can lead to severe biases in conclusions about ecological systems. We present results of a field experiment where observers recorded observations for known combinations of electronically broadcast calling anurans under conditions mimicking field surveys to determine species occurrence. Our objectives were to characterize false positive error probabilities for auditory methods based on a large number of observers, to determine if targeted instruction could be used to reduce false positive error rates, and to establish useful predictors of among-observer and among-species differences in error rates. We recruited 31 observers, ranging in abilities from novice to expert, who recorded detections for 12 species during 180 calling trials (66,960 total observations). All observers made multiple false positive errors, and on average 8.1% of recorded detections in the experiment were false positive errors. Additional instruction had only minor effects on error rates. After instruction, false positive error probabilities decreased by 16% for treatment individuals compared to controls with broad confidence interval overlap of 0 (95% CI:--46 to 30%). This coincided with an increase in false negative errors due to the treatment (26%;--3 to 61%). Differences among observers in false positive and in false negative error rates were best predicted by scores from an online test and a self-assessment of observer ability completed prior to the field experiment. In contrast, years of experience conducting call surveys was a weak predictor of error rates. False positive errors were also more common for species that were played more frequently but were not related to the dominant spectral frequency of the call. Our results corroborate other work that demonstrates false positives are a significant component of species occurrence data collected by auditory methods. Instructing observers to only report detections they are completely certain are correct is not sufficient to eliminate errors. As a result, analytical methods that account for false positive errors will be needed, and independent testing of observer ability is a useful predictor for among-observer variation in observation error rates.

Joint estimation of habitat dynamics and species interactions: disturbance reduces co-occurrence of non-native predators with an endangered toad

1. Ecologists have long been interested in the processes that determine patterns of species occurrence and co-occurrence. Potential short-comings of many existing empirical approaches that address these questions include a reliance on patterns of occurrence at a single time point, failure to account properly for imperfect detection and treating the environment as a static variable. 2. We fit detection and non-detection data collected from repeat visits using a dynamic site occupancy model that simultaneously accounts for the temporal dynamics of a focal prey species, its predators and its habitat. Our objective was to determine how disturbance and species interactions affect the co-occurrence probabilities of an endangered toad and recently introduced non-native predators in stream breeding habitats. For this, we determined statistical support for alternative processes that could affect co-occurrence frequency in the system. 3. We collected occurrence data at stream segments in two watersheds where streams were largely ephemeral and one watershed dominated by perennial streams. Co-occurrence probabilities of toads with non-native predators were related to disturbance frequency, with low co-occurrence in the ephemeral watershed and high co-occurrence in the perennial watershed. This occurred because once predators were established at a site, they were rarely lost from the site except in cases when the site dried out. Once dry sites became suitable again, toads colonized them much more rapidly than predators, creating a period of predator-free space. 4. We attribute the dynamics to a storage effect, where toads persisting outside the stream environment during periods of drought rapidly colonized sites when they become suitable again. Our results support that even in highly connected stream networks, temporal disturbance can structure frequencies with which breeding amphibians encounter non-native predators. 5. Dynamic multi-state occupancy models are a powerful tool for rigorously examining hypotheses about inter-species and species-habitat interactions. In contrast to previous methods that infer dynamic processes based on static patterns in occupancy, the approach we took allows the dynamic processes that determine species-species and species-habitat interactions to be directly estimated.