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Numerous modelling techniques exist to estimate abundance of plant and animal populations. The most accurate methods account for multiple complexities found in ecological data, such as observational biases, spatial autocorrelation, and species correlations. There is, however, a lack of user‐friendly and computationally efficient software to implement the various models, particularly for large data sets.We developed the spAbundance R package for fitting spatially explicit Bayesian single‐species and multi‐species hierarchical distance sampling models, N‐mixture models, and generalized linear mixed models. The models within the package can account for spatial autocorrelation using Nearest Neighbour Gaussian Processes and accommodate species correlations in multi‐species models using a latent factor approach, which enables model fitting for data sets with large numbers of sites and/or species.We provide three vignettes and three case studies that highlight spAbundance functionality. We used spatially explicit multi‐species distance sampling models to estimate density of 16 bird species in Florida, USA, an N‐mixture model to estimate black‐throated blue warbler (Setophaga caerulescens) abundance in New Hampshire, USA, and a spatial linear mixed model to estimate forest above‐ground biomass across the continental USA.spAbundance provides a user‐friendly, formula‐based interface to fit a variety of univariate and multivariate spatially explicit abundance models. The package serves as a useful tool for ecologists and conservation practitioners to generate improved inference and predictions on the spatial drivers of abundance in populations and communities. [ABSTRACT FROM AUTHOR]

Discusses the fate of the panther in southern Florida. Estimated population; Biggest threat to panther's survival; Role of the United States Fish and Wildlife Service, the federal agency charged with using the best available science to make sure the panther has enough habitat to find mates, hunt, disperse to new home ranges, and persist as a population; Formation of a panther recovery subteam; Deconstruction of the panther landscape; Effort to revitalize the panther population.

The last three decades have brought clear recognition that many populations of animals are experiencing severe declines or local and global extinctions. Many examples have become common knowledge to the general public, such as worldwide declines in amphibian populations and extensive loss of coral reefs. The mechanisms underlying these and other changes are poorly understood. However, a growing literature indicates that a wide array of chemical contaminants have the potential to disrupt normal cell-to-cell signaling mechanisms. A global pollutant of most aquatic systems, nitrate has the potential to be an endocrine disrupting contaminant. This paper reviews studies performed on vertebrates demonstrating that nitrate and/or nitrite have the potential to alter endocrine function. Further, a retrospective study of our work on alligators from various lakes in Florida suggests that nitrate could contribute to some of the altered endocrine parameters previously reported in juvenile animals. We propose hypotheses suggesting that nitrate could alter steroidogenesis by 1) conversion to nitrite and nitric oxide in the mitochondria, the site of initial steroid synthesis, 2) altering Cl- ion concentrations in the cell by substituting for Cl- in the membrane transport pump or 3) binding to the heme region of various P450 enzymes associated with steroidogenesis and altering enzymatic action. Future studies are needed to examine the endocrine disruptive action of this ubiquitous pollutant. A growing literature indicates that all biologists studying natural systems, whether they choose to or not, must now consider contaminant exposure as a direct influence on their studies. That is, ubiquitous global contamination has the potential to alter the endocrine, nervous and immune systems of all organisms with resulting changes in gene expression and phenotypes. [ABSTRACT FROM AUTHOR]

Background: Florida's waters are a reservoir for a host of pathogens and toxins. Many of these microorganisms cause water-related diseases in people that are reportable to the Florida Department of Health. Our objective in this review was to ascertain which water-related pathogens and toxins of public health importance have been found in animal populations in Florida over the last twenty years. Methods: Nineteen databases were searched, including PubMed and Web of Science Core Collection, using keywords and search terms for the waterborne diseases, water-related vector-borne diseases, and water-based toxins reportable to the Florida Department of Health. For inclusion, peer-reviewed journal articles were to be written in English, published between January 1, 1999 and December 31, 2019, and contain primary research findings documenting at least one of the water-related pathogens or toxins of interest in an animal population within Florida during this same time frame. Results: Of over eight thousand initial search results, 65 studies were included for final analysis. The most common animal types implicated in the diseases of interest included marine mammals, fish and shellfish, wild birds, and livestock. Toxins or pathogens most often associated with these animals included toxin-producer Karenia brevis, vibriosis, Escherichia coli, and Salmonellosis. Discussion/conclusion: Findings from this review elucidate the water-related disease-causing pathogens and toxins which have been reported within animal populations in recent Florida history. As most of these diseases are zoonotic, our results suggest a One Health approach is necessary to support and maintain healthy water systems throughout the state of Florida for the protection of both human and animal populations. [ABSTRACT FROM AUTHOR]

Wildlife‐vehicle collisions (WVCs) are a major source of wildlife mortality and should affect regional wildlife diversity and abundance, yet most WVC studies are locally scaled. Here, we evaluated biogeographic diversity (i.e., species richness, effective diversity) and abundance of WVCs at state parks across the Florida peninsula to answer two questions aimed to help inform wildlife conservation efforts: which parks have greatest WVC diversity, and why? We processed and compiled 9,254 WVC survey records collected by Florida State Parks personnel at 42 parks during a decade (2005–2015). Data for birds (138 species), mammals (35 species), reptiles (64 species), and all taxa combined were analyzed for patterns among parks (for the first question) and for biogeographic, climatic, ecoregion, and anthropogenic predictors of those patterns (for the second). Predictors represented nonexclusive alternative a priori hypotheses and were evaluated by model comparison. Parks differed widely in WVC diversity and abundance; we identify "hot spot" parks where management may most effectively reduce WVCs. Biogeographic and anthropogenic hypotheses were supported, but climatic and ecoregion hypotheses were not. Models for overall diversity fit data better (R2s > 0.50) than did models for specific taxa (e.g., birds). Larger parks closer to Florida's highly populated Atlantic Coast and with greater park attendance and perhaps faster speeds on adjacent roads have more WVC diversity and numbers. Of these predictors, attendance and speed limits are manageable. Traffic management in and near‐identified "hot spot" parks in Florida can most effectively reduce WVC effects on wildlife populations and diversity amidst a growing human population. [ABSTRACT FROM AUTHOR]

The frequency and intensity of ecological perturbations affecting wild animal populations is expected to increase in the future with animals facing numerous global threats. Seahorse Key is a continental island off mainland Florida that has historically been a major rookery for several species of waterbirds. As a result of an unknown disturbance, the entire rookery abandoned Seahorse Key in April 2015 and shifted nesting activities to nearby Snake Key, resulting in an influx of food resources in the form of fish carrion to resident Florida cottonmouth snakes (Agkistrodon conanti), while snakes on Seahorse Key experienced a drastic reduction in food resources. Our objective was to assess plasma corticosterone concentrations, corticosterone negative feedback using dexamethasone, blood glucose, body condition, packed cell volume, natural antibody agglutination, white blood cell counts and ratios and erythrocyte sedimentation rate to characterize the long-term effects of differential resource availability in these two snake populations 3 years after this major ecological disturbance. We collected blood samples at three time points from cottonmouths on Seahorse Key (n  = 6 individuals) and Snake Key (n  = 13 individuals) in fall 2018. In due consideration of the small sample size, our study shows evidence that 3 years after the shift in waterbird nesting Seahorse Key cottonmouths exhibit a dampened acute stress response and presumptive impaired innate immune functions relative to cottonmouths on Snake Key. These results highlight the context-dependent nature of biomarkers and implicate the significant decrease in food resources on Seahorse Key in altering hormonal stress responses and innate immune functions, possibly leading to unknown long-term downstream effects. This study assessed the response of a wild population of pit viper to ecological disturbance in situ with the aim to improve our understanding of how animals cope with such perturbations and improve our capacity to make informed decisions for conservation. [ABSTRACT FROM AUTHOR]

One of the goals of the Florida panther (Puma concolor coryi) recovery plan is to expand panther range north of the Caloosahatchee River in central Florida. Our objective was to evaluate the potential of that region to support panthers. We used a geographic information system and the Mahalanobis distance statistic to develop a habitat model based on landscape characteristics associated with panther home ranges. We used cross-validation and an independent telemetry data set to test the habitat model. We also conducted a least-cost path analysis to identify potential habitat linkages and to provide a relative measure of connectivity among habitat patches. Variables in our model were paved road density, major highways, human population density, percentage of the area permanently or semipermanently flooded, and percentage of the area in natural land cover. Our model clearly identified habitat typical of that found within panther home ranges based on model testing with recent telemetry data. We identified 4 potential translocation sites that may support a total of approximately 36 panthers. Although we identified potential habitat linkages, our least-cost path analyses highlighted the extreme isolation of panther habitat in portions of the study area. Human intervention will likely be required if the goal is to establish female panthers north of the Caloosahatchee in the near term. [ABSTRACT FROM AUTHOR]

Relocations of gopher tortoises (Gopherus polyphemus) in Florida, USA, are frequently employed as mitigation tools when tortoises occupy land desired for development. Here we present information about retention and health of a relocated population of gopher tortoises 17 years after relocation. We combine our 17-year postrelocation data with earlier surveys 1 year and 2 years postrelocation to examine whether retention rates change over time. We also evaluate whether retention rates vary by age and gender. Of 74 gopher tortoises relocated in 1985, 31 were present in 2002. We found a 1-year retention rate of 42%, with retention rates of 100% each year thereafter, when we used the percentage of relocated individuals captured at each survey. We found a 1-year retention rate of 73%, a retention rate of 92% from year 1 to year 2, and an overall retention rate of 98.5% from year 2 through year 17, based on the assumption that all individuals present in later surveys were present in earlier surveys. We found no significant difference in retention rate over the 17-year period for adults and juveniles and for adult males and females. Relocated gopher tortoises showed natural growth patterns, indicating good health, but 35% of these gopher tortoises had ≥1 symptom of upper respiratory tract disease, a disease associated elsewhere with population declines of tortoises. Thus, retention rates of relocated gopher tortoises change over time, with relatively low retention during the first year postrelocation but nearly 100% retention in subsequent years. In general, our study shows that relocations can successfully lead to long-term retention of gopher tortoises, but we predict that without management (e.g., fire management and predator control) this relocated population is not viable. [ABSTRACT FROM AUTHOR]

1. Using data on breeding birds from a 35-year study of Florida scrub-jays Aphelocoma coerulescens (Bosc 1795), we show that survival probabilities are structured by age, birth cohort, and maternal family, but not by sex. Using both accelerated failure time (AFT) and Cox proportional hazard models, the data are best described by models incorporating variation among birth cohorts and greater mortality hazard with increasing age. AFT models using Weibull distributions with the shape parameter > 1 were always the best-fitting models. 2. Shared frailty models allowing for family structure greatly reduce model deviance. The best-fitting models included a term for frailty shared by maternal families. 3. To ask how long a data set must be to reach qualitatively the same conclusions, we repeated the analyses for all possible truncated data sets of 2 years in length or greater. Length of the data set affects the parameter estimates, but not the qualitative conclusions. In all but three of 337 truncated data sets the best-fitting models pointed to same conclusions as the full data set. Shared frailty models appear to be quite robust. 4. The data are not adequate for testing hypotheses as to whether variation in frailty is heritable. 5. Substantial structured heterogeneity for survival exists in this population. Such structured heterogeneity has been shown to have substantial effects in reducing demographic stochasticity. [ABSTRACT FROM AUTHOR]

We assessed effects of groundwater pumping to elevate lake levels on lake water chemistry and fish population metrics at seven Florida lakes. Following groundwater pumping, lake level fluctuation was reduced and lake water samples increased in mean pH, total alkalinity, total phosphorus, chloride and Secchi depth compared to historical means, indicating a close resemblance to the chemistry of aquifer water in the region. Fish community metrics from the augmented lakes were compared to 36 non-augmented lakes in Florida. The mean values for catch per unit effort, species richness and biomass of harvestable fishes, determined by electrofishing, were lower in augmented lakes compared to non-augmented lakes. Canonical correspondence analysis (CCA) indicated a high probability of a low abundance of individual species in augmented lakes compared to a majority of non-augmented lakes. The augmented lake with the lowest pumping rate exhibited less of a shift in limnological variables from historical values, and had fish population characteristics more closely resembling those of non-augmented lakes. Thus, reduced volumes of groundwater introduction could lower impacts to limnological and fish population characteristics. Augmentation allows for lakes to be utilized for recreational activities, and without augmentation some lakes in central Florida would likely go dry due to groundwater withdrawals for water supply. Therefore, allowing more natural water level fluctuations and possible reductions in total pumpage are recommended to reduce impacts to limnological and fish population characteristics, while still allowing sufficient groundwater pumping to preserve lake habitats. [ABSTRACT FROM AUTHOR]

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