Acoustic telemetry is an important tool when studying the spatial ecology of marine animals. First, it is important to identify the challenges of using this tool in shallow tropical marine environments before tracking marine animals. One significant issue that can influence the effectiveness of acoustic telemetry is the efficiency or detectability of acoustic signals by receivers. Understanding factors influencing detection efficiency of acoustic tags is especially important for fine-scale positioning systems (such as the VEMCO positioning system, VPS) that use detections in an overlapping receiver network to calculate geographic positions of tagged fish. I modelled the efficiency of an acoustic array in a tropical reef flat in Culebra, Puerto Rico and then tested the capability of detecting and positioning tagged permit (Trachinotus falcatus) and great barracuda (Sphyraena barracuda). Detection efficiencies were analyzed for a fine-scale array comprised of 25 receivers and 17 sync tags deployed as a fine-scale array for nearly three years. I used a generalized linear mixed-effect model Template Builder Model (glmmTMB) that helped elucidate the environmental variables that play a role in influencing the ability to detect transmitter signals. Then, I evaluated how well the fine- scale array was at detecting tagged permit (n=1) and great barracuda (n=4) using the reef flat. Once, the model was created, it was used to predict the likeliness of hourly detections of sync tags and tagged animals. Finally, the fine-scale and broad-scale array consisting of 59 receivers were used to determine the spatial movement patterns of permit and great barracuda. A glmmTMB was created to determine what environmental variables were present when each species visited the fine-scale array in the coral reef flat. The dynamic Brownian-Bridge Movement Model (DBBMM) was used to determine the fishes’ home range within the coral reef flat using X Y locations. Network connectivity was used to determine each fishes’ spatial movement patterns and community structure related to the receivers they visited. Lastly, spatial patterns throughout each diel period and season were determined. Collectively, this study revealed the benefits and limitations of using fine-scale acoustic telemetry in shallow coral reef ecosystems.

Elk (Cervus canadensis) are known to exhibit high movement strategy diversity compared to other ungulate species. Most elk populations are migratory or partially migratory, presenting unique conservation and management challenges. For example, successful maintenance of multiple seasonal ranges and connectivity between them is necessary to conserve populations with migratory behaviors. Further study of the structure and maintenance of movement strategy diversity within partially migratory populations is needed to assist management and refine fundamental ecological theory. Improved understanding of the determinants of elk migratory timing is also important, with the dynamics of significant drivers likely to shift under future climate change and anthropogenic expansion. I investigated strategy-specific environmental responses in multiple Rocky Mountain elk populations and found evidence for a differentiation in resource use and selection among sympatric individuals using differing strategies. This result suggests a potential mechanism for the reduction of intraspecific competition and heightened population densities in partially migratory herds. However, the nature and strength of differentiation was found to be context dependent. I found that elk avoid human development and seasonally select for forage quantity over quality at relatively fine scales, highlighting some consistent selection responses as well. Overall, this analysis demonstrated intrapopulation response heterogeneity in partially migratory elk populations and characterized strategy-specific patterns of resource use and selection.I investigated how spring migratory timing and duration relate to spatiotemporal forage dynamics, finding that departure dates are affected by vegetative green-up along migratory corridors, while the duration of migration is influenced by the timing of green-up at the summer range. These results highlight a form of migratory plasticity, wherein migrants modulate both their departure date and the duration of their migration as a function of vegetative phenology. Additionally, I present a framework to quantify optimality of migratory movements in relation to peak forage conditions. On average, elk were found to exhibit high optimality, with interindividual variability along a gradient. My findings suggest a variety of responses to green-wave phenology, with optimality of movements differing as a function of individual and study area. This work contributes to the growing understanding of migratory plasticity as multidimensional and highlights the variability of migratory behavior within and among populations.

An elasmobranch survey conducted from 2013-2018 in the waters adjacent to Pinellas County, Florida, was used for a baseline assessment of the local shark population. ArcGIS and Boosted Regression Trees were used to identify hot spots of abundance and links between environmental predictors and distribution, as well as create species distribution models. A diverse assemblage of sharks, dominated by five species: nurse shark, bonnethead, Atlantic sharpnose shark, blacktip shark, and blacknose shark, was identified. A large proportion of captures (~42%) were immature sharks. Results indicate areas characterized by seagrass and “No Internal Combustion Engine” zones correlate with greater diversity and abundance, particularly for immature sharks. BRT results underscored the importance of seagrass bottoms, as well as warm (>31℃) and shallow (< 6m) waters as essential habitat. By identifying spatially explicit areas and environmental conditions suited for shark abundance, this study provides practical resources for managing and protecting Florida’s sharks.

No description available.

A regional IPM project was initiated with four rounds of sampling for white grubs on the fairways of nine golf courses located on the Lower Peninsula of eastern Virginia, from 2000 through 2002. Fifteen regressor variables were collected and measured that included local-scale variables, golf course management practices and spatial pattern metrics derived from satellite images that underwent two methods of a supervised classification of six land-cover types (turf, woods, wetland, urban, bare soil and water) on four landscape scales derived from 10 km x 10 km buffer zones surrounding each golf course. Pearson's correlation coefficients were calculated to reduce the number of variables to a few that were highly correlated with white grub densities. Mallow's C(p) calculations were performed on the reduced variable sets to extract those that would be highly predictive. A multiple linear regression was performed using the Mallow's variables to develop eight regression equations (two classification methods x four landscape scales) that were used to predict regional white grub presence and abundance in 2003 on six additional golf courses located on the Lower Peninsula. The best model was the 6 km x 6 km buffer zones model from the second classification method, which included one local-scale variable (golf course age) and three spatial pattern metrics (total turf area, total turf area-to-total urban area ratio, and a woods interspersion-juxtaposition index). The mean difference between actual and predicted values was -0.15, standard deviation = 0.79, R2 = 81.38%. Additionally, a study was conducted to determine whether the number of white grubs collected from transects of sampled golf course fairways was significantly different from those found in the roughs. White grub counts from the roughs were significantly higher (mean = 0.283 grubs/transect, standard error = 0.0135) than those from fairways (mean = 0.146 grubs/transect, standard error = 0.0188); t = -4.31, df = 735, P = 0.0001. / Ph. D.

Wild pigs (Sus scrofa) are among the world's most destructive mammalian invasive species, and mitigating farther range expansion will require a thorough understanding of movement behavior, diel activity patterns, space use, and resource selection. Currently, limited empirical evidence is available on the ecology of wild pigs in Southwest Florida. Therefore, I examined how wild pigs behaviorally modified their movements and diel activity patterns in response to individual and environmental covariates. I investigated space use dynamics (e.g., home range size and seasonal variation) and evaluated how individual and environmental variation influenced home range size. Next, I determined how fine-scale movement patterns and resource selection of wild pigs are affected by temperature and time of day, and how those resources changed at broad and fine-scales, given their availability. I found that as temperature increased, the probability of foraging increased while the probability of traveling decreased. Foraging behavior occurred predominately between 8:00 and 17:00, and traveling behavior occurred predominately between 18:00 and 7:00, thereby indicating wild pigs were cathemeral. Home range size ranged from 2.6 to 35.8 km2 and averaged 13.0 km2 (n=16). Finally, home range size increased as the proportion of pasture increased and decreased as the proportion of wetlands increased, indicating that resources in agricultural areas were more diffuse than in natural habitats. At the broad (i.e., home range selection) and fine-scale (i.e., within home range) wild pigs selected for wetlands, forests, and pastures. Wild pig movement tended to be tortuous in forested and cropland habitats, but more directed in pasture habitats. Slower movements (i.e., smaller steps) and more directed (i.e., fewer turning) steps were observed during warmer temperatures, particularly avoiding croplands when temperatures were warmer. Wild pigs avoided wetland habitats during dusk and night hours and cropland habitats during dawn hours. Wild pigs selected for forested habitats during night and dawn hours, possibly in response to human activity. In addition, I found that wild pigs were less likely to step into a location with a daily temperature of 35.7°C than 16.1 C°. Wild pigs were less likely to choose warmer locations and more likely to select intermediate temperatures, thus avoiding locations with extremely low or high daily temperatures. Also, I found that wild pigs were more likely to select home ranges nearer to wetlands, forests, and pastures, while avoiding areas near cropland habitats. However, within their home ranges they were more likely to select habitats farther from croplands, forests, and wetlands. My findings reinforce the importance of wetlands, forests and pastures to wild pig selection of home ranges, where they likely utilize these landcover types for thermoregulation (e.g. forests and wetlands) and for foraging resources (e.g. pastures). Within their home ranges wild pigs may avoid forests and wetlands due to perceived predation risk being higher in those habitats, thus causing wild pigs to forgo higher quality resources to reduce risk. These results contribute information useful to wildlife managers to better predict which landcover types provide refuge (e.g., wetlands and forests) or potential movement corridors (e.g., pasture and cropland habitats) for wild pigs. In Southwest Florida, wild pigs have broad inter-individual variation in home range size, are strongly regulated by temperature, and are largely dependent on wetlands and forests to meet their energetic demands. / Doctor of Philosophy / Wild pigs are one of the world's most destructive invasive species. Although, hunters often oppose efforts to reduce wild pig populations, agricultural and natural resource managers support reduction efforts because they cause major economic and ecological damage. In addition, wild pigs carry a plethora of diseases and pose direct health risks to livestock, wildlife, and humans. Therefore, a better understanding of how environmental and landscape factors influence wild pig movements and space use is of broad interest to multiple stakeholder groups. I found that wild pigs mostly foraged during daytime and traveled at night, indicative of irregular activity patterns. Home range size averaged 13.0 km2 across 16 individuals and tended to increase as the proportion of pasture habitat increased and decreased as herbaceous wetlands increased. This indicated that resources were more abundant in natural habitats. Wild pigs preferred wetlands, forests, and pastures, and avoided croplands. However, they were more likely to forage in forests and croplands, and travel in pastures. Wild pigs avoided wetlands during dusk and night hours and croplands at dawn, while selecting forests during night and dawn hours. Wild pigs tended to move slower with less turning during warmer temperatures, particularly avoiding croplands when temperatures were hot. In general, wild pigs avoided locations with extremely low or high daily temperatures. I found wild pigs were more likely to select home ranges nearer to wetlands, forests, and pastures, while avoiding areas near cropland habitats. Wild pigs likely utilized these landcover types for thermoregulation (e.g. forests and wetlands) and for foraging resources (e.g. pastures), while avoiding open areas (e.g. croplands) due to a lack of shade. However, within their home ranges they were more likely to select habitats farther from croplands, forests, and wetlands, possibly because they perceived these areas to have higher predation risk. I highlight differences in space use among individuals and identify habitat types that are most likely to meet energetic demands. By understanding how environmental factors (e.g., habitat type and temperature) influence home range movement behaviors of wild pigs, land managers can focus on scale-dependent population control efforts. My results will aid land managers in better predicting which landcover types are providing refuge (e.g., wetlands and forests) or serving as potential movement corridors (e.g., pasture and cropland habitats).

Metapopulation ecology has developed to explain the population dynamics that occur in spatially structured landscapes. In this study, I combined an empirical laboratory approach, using metapopulation microcosms of Callosobruchus maculatus and its endospecific parasitoid Anisopteromalus calandrae, with mathematical population models in order to investigate several fundamental metapopulation processes. Population dynamics in these systems can be studied at two scales; the local patch-wise scale and the regional metapopulation scale. Here I demonstrate that in both homogeneous and heterogeneous landscapes knowledge of local scale demographic processes is necessary in order to understand regional metapopulation dynamics. The differences in the rate and net direction of dispersal between patches as a result of the permeability of the matrix in homogeneous systems and density-dependent dispersal in heterogeneous systems were also explored. Metapopulation dynamics rely on a balance between local extinctions and recolonisations. Therefore, increasing local mortality rates is likely to be detrimental to the persistence of the system. Here, the impact of several common harvesting strategies on the persistence of a host-parasitoid metapopulation was examined. Contrary to expectation I discovered that harvesting in these systems increased both local and regional population sizes. The increased population size as a result of increased mortality was explained in terms of a hydra effect, where harvesting relaxed density-dependence acting on local host populations. The results presented in this thesis are relevant for the monitoring, management and conservation of natural metapopulations and the development of sustainable harvesting strategies in structured landscapes.

Coral reefs have one of the highest levels of biodiversity of all ecosystems in the world and are important for both human livelihood and food security throughout many tropical countries. However, due to increased anthropogenic pressure on marine ecosystems, especially during the last couple of decades, coral reefs have become critically over-fished, and many reefs are now in a degraded state and are facing additional future threats due to further over-exploitation, chemical pollution, sedimentation, and effects of climate change. The main aim of this PhD thesis was to understand effects of anthropogenic disturbances on tropical coastal ecosystems and fish connectivity for coastal management purposes. Therefore, linkages between anthropogenic disturbance and corals were investigated (Paper I), as well as interactions between coral reef habitat and associated fish assemblage (Paper II). Furthermore, connectivity between coral reefs and other tropical coastal ecosystems was explored (Paper III), as well as fish migration to reproduction sites (Paper IV), and evaluations of spatial ecology methods (Paper V). The result showed that coral reefs that are already exposed to disturbances, such as freshwater and nutrient run-offs, may be more sensitive to climate change, in terms of increased sea surface temperatures (Paper I). In addition, there were also clear linkages between coral reef quality, in terms of coral coverage, and fish assemblages, which displayed high spatial variability and suggesting patchy recovery after the 1997/1998 bleaching and subsequent coral mass mortality event (Paper II). This highlights the importance of understanding effects of disturbances on corals, especially in terms of synergistic effects between increased water temperatures and other coastal stressors such as decreased salinity and increased nutrients; and the indirect effects of habitat degradation on the fish community. Linkages between fish and different coastal habitats were further explored. The results showed that coral reefs were strongly connected with mangrove and seagrass beds, through ontogenetic migration of fish (Paper III). Migrations to spawning sites of groupers were related to lunar activities when thousands of fish gather for reproduction purposes during new moon, which increases the risk of over-exploitation (Paper IV). The results emphasises the importance of protecting key areas such as nursing grounds and reproduction sites. Furthermore, acoustic telemetry has become an increasingly common method in studies of fish movement, and the results showed that efficiency of acoustic arrays may increase depending on deployment strategies and habitat characteristics (Paper V). In conclusion, the results from this PhD thesis emphasises the importance of protecting coral reef habitats, as well as identifying related susceptible tropical coastal areas, such as nursing grounds and reproduction sites. Indeed, a better scientific understanding of coral reef ecology and indirect and direct effects on fish assemblages are needed for efficient and accurate coastal management decisions. / <p>At the time of the doctoral defense, the following paper was unpublished and had a status as follows: Paper 5: Manuscript.</p>

A dissertation submitted to the Faculty of Science, University of the Witwatersrand, in fulfilment of the requirements for the degree of Master of Science. Johannesburg, 2017. / With an increase in opportunistically-collected data, statistical methods that can accommodate unstructured designs are increasingly useful. Spatial capturerecapture (SCR) has such potential, but its applicability for species that are strongly gregarious is uncertain. It assumes that average animal locations are spatially random and independent, which is violated for gregarious species. I used a data set for African elephants (Loxodonta africana) and data simulation to assess bias and precision of SCR population density estimates given violations in location independence. I found that estimates were negatively biased and likely too precise if non-independence was ignored. Encounter heterogeneity models produced more realistic precision but density estimates were positively biased. Lowest bias was achieved by estimating density of groups, group size, and then multiplying to estimate overall population density. Such findings have important implications for the reliability of population density estimates where data are collected by unstructured means. / LG2017

As populações de veado-campeiro vêm sofrendo constantes ameaças, principalmente pela caça excessiva e destruição de seu habitat. A escassez de conhecimento sobre a biologia da espécie dificulta a elaboração de diferentes formas de manejo. Assim, há necessidade de estudos básicos para a instituição de programas para a conservação do veado-campeiro, principalmente no Brasil. O presente estudo teve como objetivos estimar o tamanho da área de vida de fêmeas de veado-campeiro, além de quantificar e comparar o uso de habitat pelas mesmas nos períodos reprodutivos e não-reprodutivos no Pantanal Sul-Matogrossense. Foram utilizadas quatro fêmeas de veado-campeiro em vida livre marcadas com colares de GPS modelo ATS® G2110, as quais tiveram suas localizações registradas a cada 13 horas por um período de aproximadamente 12 meses. Os cálculos para área de vida foram feitos através do programa ArcView® GIS versão 3 Extensão Animal Movement, usando os métodos do Mínimo Polígono Convexo (MPC) com 100% das localizações, e Kernel fixo com 95%, 70% e 50% de probabilidade de uso, sendo os dois últimos para estimativas dos centros de atividade. As fêmeas tiveram uma área de vida anual média de 549,88ha ± 124,76 quando estimado pelo MPC e 258,69ha ± 34,54 quando estimado por Kernel com 95% de probabilidade de uso. Quanto às áreas de uso mensais por status reprodutivo, não houve diferença significativa entre os meses (p > 0,05), evidenciando apenas uma pequena diminuição no tamanho das áreas de vida durante o período de aleitamento e um aumento nas épocas de acasalamento. Os habitats foram estabelecidos pelo tipo de vegetação predominante na área e foram caracterizados por imagem de satélite Landsat-5 e verificação in loco da região de estudo. Para verificar se houve uso desproporcional entre as categorias de habitats em relação à disponibilidade em suas respectivas áreas de vida foi usado o teste qui-quadrado de qualidade de ajustamento (chi-square goodness-of-fit test) e posterior estimativa do intervalo simultâneo de confiança de Bonferroni. Na análise anual, os habitats campo e baía foram selecionados, apesar deste último ser o menos abundante, enquanto floresta e caronal foram evitados pelas fêmeas de veado-campeiro. No entanto, ao analisarmos a seleção de habitat mensalmente para comparar o uso entre os diferentes status reprodutivos, o habitat campo tendeu a ser preferido, mas seu uso foi igual ao disponível em todos os períodos. Sendo assim, este estudo elucidou algumas informações sobre a ecologia do veado-campeiro, a fim de facilitar o desenvolvimento de programas de conservação para a espécie. / The pampas deer populations have been under constant threats, mainly by excessive hunting and habitat destruction. The lack of knowledge about the biology of the species hampers the development of different forms of management. Thus, there is a need for basic studies of establishment of conservation programs, mainly in Brazil. This study aimed to estimate the size of home-range, to quantify and compare the habitat use by females in reproductive and non-reproductive periods rights in Pantanal Sul-Matogrossense. Four females of pampas deer were marked with GPS collars, model ATS® G2110, which had recorded their locations every 13 hours for approximately 12 months. The calculations for home-range were made using the Arcview® GIS version 3 Extension Animal Movement, using the methods of the minimum convex polygon (MPC) with 100% of the locations, and fixed Kernel 95%, 70% and 50% of probability, being the last two for estimating the activity centers. The females had an annual home-range average of 549.88 ± 124.76 ha when estimated by MPC and 258.69 ± 34.54 ha when estimated by Kernel with 95% of probability. For the monthly home-ranges for reproductive status, no significant difference among months (p > 0.05), showing only a slight decrease in the size of home-range during the suckling period, increasing in the mating seasons. The habitats were established by the type of dominant vegetation and characterized by landsat-5 imaging satellite and in loco verification of the study area. To determine if there was disproportionate use of habitats between the categories regarding availability in their respective home-range, was used the chi-square goodness-of-fit test and subsequent estimation of Bonferroni simultaneous confidence intervals. In annual analysis, field and bay habitats were selected, despite the last being the less abundant, while forest and caronal were avoided by females of pampas deer. However, when analyzing the monthly habitat selection to compare the use between the different reproductive status, the habitat field tended to be preferred, but its use was equal to that available in all periods. Thus, this study clarified some informations about the ecology of pampas-deer, facilitating conservation programs development for the species.