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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]

The article discusses the ecosystem in South Florida. It examines the rainfall frequency, water quality and quantity, wetlands, birds and animal population in the location. It mentions that South Florida has diverse subtropical, coastal and marine areas that are being protected by the South Florida Water Management District (SFWMD). According to the author, authorities are establishing laws such as water policy, flood control and reforestation, to further protect and preserve the ecosystem of South Florida.

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]

While the effects of barriers to dispersal such as population declines, habitat fragmentation, and geographic distance have been well-documented in terrestrial wildlife, factors impeding the dispersal of highly vagile taxa such as seabirds are less well understood. The roseate tern (Sterna dougallii) is a globally distributed seabird species, but populations tend to be both fragmented and small, and the species is declining across most of its range. We evaluated structuring of roseate tern populations in the Northwestern Atlantic, the Caribbean, and the Azores using both microsatellite markers and single-nucleotide polymorphisms generated through targeted sequencing of Ultra-conserved Elements. For both marker types, we found significant genetic differentiation among all 3 populations and evidence for moderate contemporary unidirectional gene flow from the Caribbean to the Azores, but not between other populations. Within the Caribbean population, we found high rates of unidirectional migration from the Virgin Islands to Florida, potentially indicative of movement from source population to sink or an artifact of dispersal among other unsampled populations in the Caribbean region. These observations have significance for species persistence in the Atlantic, as our results indicate that loss of genetic diversity within populations is unlikely to be buffered by inflow of new alleles from other breeding populations. [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]

The Argentine giant tegu, a large lizard native to South America, was first discovered as established in the USA in scrub habitats of west-central Florida in 2006. Invasive populations potentially could occupy an extensive range of habitats and in much of the southern United States and Mexico and threaten many native species. The Argentine giant tegu was recently deemed as having a "highest impact concern" among the invasive reptile species most threatening to Florida ecology. Among the most rewarding research directions identified for this species was "having a reliable and practical method to detect/monitor" them. We address this need by evaluating five methods for monitoring Argentine giant tegus on how well each method detected the species and whether the observations were sufficient to quantitatively assess population abundance using a widely applicable framework for indexing animal populations. Passive tracking plots were the most efficient and effective means for detecting tegus and calculating abundance indices but were best suited for late winter to spring before summer rains compacted tracking substrates. Gopher tortoise burrows are often used by tegus and camera traps on their entrances proved able to obtain data suitable for indexing populations but required more labor and expense than tracking plots. Trapping either at gopher tortoise burrows or along drift fences was ineffective at capturing tegus. Similarly, visual encounter transects were not effective for observing tegus. [ABSTRACT FROM AUTHOR]

I developed a preliminary quadrat-based protocol to survey low density populations of burrows of the Gopher Tortoise (Gopherus polyphemus) and applied the protocol in four upland habitats at Avon Park Air Force Range, Florida in 1997-98. I randomly selected and surveyed 55 1-ha plots in oak scrub, 23 in sand pine scrub, 53 in pine flatwoods, and 17 in oak hammock. Detection probability was maximized by using 10 transects and multiple observers at most quadrats. Oak scrub had the highest density of burrows per ha (1.47) and sand pine scrub had the lowest density (0.17). Spatial distribution of oak scrub burrows fit the negative binomial distribution. Likelihood ratio tests showed that the best model for all four habitats had a dispersion parameter (k) of the negative binomial that did not vary but did have a variable mean (m). This protocol is appropriate to survey low density populations of any object in situations where distance sampling could be inefficient, and can be improved by conducting double-observer surveys at a subset of quadrats to calibrate detection probability. This approach is supported by two subsequent studies that showed that distance sampling is not efficient in cases where densities of burrows are low and that quadrat sampling may offer advantages over other tortoise survey techniques. [ABSTRACT FROM AUTHOR]

Persistent organic pollutants (POPs) are recognized manmade threats to sea turtle populations, but substantial uncertainty exists surrounding their exposure to contaminants and their sensitivity to toxic effects. This uncertainty creates difficulty for conservation managers to make informed decisions for the recovery of these threatened species. To provide baseline concentrations and spatial comparisons, we measured a large suite of POPs in loggerhead sea turtle ( Caretta caretta) egg yolk samples collected from 44 nests in three distinct U.S. locations: North Carolina (NC), eastern Florida (E FL), and western Florida (W FL). The POPs included polychlorinated biphenyls (PCBs), organochlorine pesticides such as dichlorodiphenyltrichloroethanes (DDTs), chlordanes, mirex, dieldin, hexachlorocyclohexanes (HCHs), hexachlorobenzene, and toxaphene congeners, as well as polybrominated diphenyl ether congeners (PBDEs). Persistent organic pollutant concentrations were lowest in W FL, intermediate in E FL, and highest in NC egg samples, with several statistically significant spatial differences. This increasing gradient along the southeast coast around the Florida peninsula to North Carolina was explained partly by the foraging site selection of the nesting females. Data from previous tracking studies show that NC nesting females feed primarily along the U.S. eastern coast, whereas W FL nesting females forage in the Gulf of Mexico and Caribbean Sea. The E FL nesting females forage in areas that overlap these two. The foraging site selection also results in exposure to different patterns of POPs. An unusual PBDE pattern was seen in the NC samples, with nearly equal contributions of PBDE congeners 47, 100, and 154. These findings are important to managers assessing threats among different stocks or subpopulations of this threatened species. Environ. Toxicol. Chem. 2011; 30:1677-1688. © 2011 SETAC [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]

Our primary goal was to determine whether rotenone would be a useful control against introduced populations of Asian swamp eels (family Synbranchidae, genus Monopterus). We report the results of a laboratory experiment comparing the efficacy of various rotenone concentrations (1, 2, 4, and 8 mg of 5% liquid rotenone/L of water) in killing nonindigenous swamp eels of various sizes (1-350 g) from the three known Florida populations. Although most small swamp eels were killed at concentrations of 2 and 4 mg/L, 100% mortality of adult swamp eels was achieved only at 8 mg/L. We conclude that the effective use of rotenone to control established Florida swamp eel populations would be difficult, based on the relatively high concentration of rotenone needed to kill swamp eels; the complexity of the swamp eel's habitat; and our observations of the species' habitat use and behavior, including its widespread distribution and life history characteristics (e.g., burrowing and overland movement) that enhance its invasion and survival in multiple environments. Nevertheless, control of swamp eels may be achieved in certain situations. A combination of rotenone and electroshocking may be an effective way to eradicate swamp eels from small water bodies and to control populations in larger habitats. However, we are cautious in this recommendation and provide details related to the technical aspects of this type of strategy and caveats related to the toxicity of the chemical. [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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The threatened seagrass Halophila johnsonii Eiseman coexists subtidally with H. decipiens Ostenfeld in southeastern Florida, but only H. johnsonii also occurs intertidally. Pulse amplitude modulated fluorometry and fiber-optic spectrometry were used to investigate the photobiology of two populations of H. johnsonii and H. decipiens in an attempt to explain these distribution patterns. Maximum photosynthetic quantum yields (Fv/Fm) were measured in situ as a function of depth distribution within, and between, these two species at two sites (Jupiter Sound, 26°57′N; 80°04′W, and northern Biscayne Bay, 25°55′N; 80°07′W) along the east coast of Florida, USA, during 6–10 March 2001. Reciprocal transplants at the northern site were used to evaluate the plasticity of photosynthetic patterns and pigment absorption spectra and to gain insights into the mechanisms responsible for variations in the observed depth-distribution patterns. Subtidal-population Fv/Fm values were generally higher for H. johnsonii than for H. decipiens, at both sites. At the northern site, intertidal H. johnsonii had significantly lower Fv/Fm (0.494±0.138) than both subtidal H. johnsonii (0.696±0.045) and subtidal H. decipiens (0.668±0.048). In contrast, at the southern site intertidal H. johnsonii had the highest Fv/Fm (0.663±0.047) and were the largest plants. Fv/Fm values of subtidal plants of both species decreased when they were transplanted into shallow, intertidal beds. Correspondingly, Fv/Fm increased for intertidal H. johnsonii transplanted into the subtidal, 2 m deep beds. Rapid light curves indicated that H. decipiens had lower maximum relative electron transport rates (RETRmax) than did H. johnsonii. In addition, the onset of photoinhibition occurred at lower irradiances for H. decipiens (537–820 μmol photons m-2 s-1) compared to H. johnsonii (1141–2670 μmol photons m-2 s-1). RETRmax values decreased for intertidal H. johnsonii transplanted into subtidal beds, but they increased for both species when transplanted from subtidal to intertidal beds. Absorption spectra for the acetone-soluble leaf pigments of intertidal H. johnsonii exhibited a dominant peak near 345 nm; this UV peak was 30% lower for subtidal plants. Pigment absorption spectra for H. decipiens lacked the 345 nm peak and absorbances, normalized to leaf pairs, were lower across the spectrum. Our results indicate that photosynthetic tolerance to higher irradiances and presence of UV-absorbing pigments (UVP) in H. johnsonii may allow this species to exploit the shallowest waters without competition from the closely related, but UVP-lacking H. decipiens. [ABSTRACT FROM AUTHOR]