In this thesis the effects of individual and multiple environmental stressors (physical and chemical) are examined in inbred and outbred zebrafish (Danio rerio, Hamilton), a model species used in ecotoxicology and environmental risk assessment (ERA). The central question addressed is, are inbred laboratory animals representative and protective of wild populations? That is, are inbred fish equally or more sensitive to chemicals and other stressors compared with more outbred (wild) fish? A combination of tools and approaches incorporating traditional (eco)toxicology and population genetics have been employed, together with more contemporary molecular genetics and population modelling, to compare and contrast a range of responses in inbred and outbred zebrafish exposed to the endocrine disrupting chemical clotrimazole and/or temperature elevation in the laboratory. The choice of test species was based on our broad understanding of its basic biology, extending from the molecular level to the population level, and its wide use as a model organism in (eco)toxicology. Selection of the test chemical clotrimazole and temperature was based on a shared mode of action, aromatase inhibition, and therefore their ability to block oestrogen production, impair reproduction, promote male development and skew population sex ratios in zebrafish. A cascade of responses were compared in inbred and outbred zebrafish, including changes in the levels of expression of genes for gonadal aromatase and other steroidogenic enzymes, circulating sex steroid hormones, gonadal sex differentiation and development (via gonadal histopathology) and reproductive fitness (female fecundity, paternity and viability of embryos). Amongst the most striking results were directional skews in sex ratio towards males in response to clotrimazole (Chapter 5) and elevated temperature exposure (Chapter 7). Inbred fish were generally more responsive compared to outbreds, which showed evidence of physiological and developmental compensation, resulting in lower male-sex skews and superior fitness in terms of male reproductive success (paternity and viability of embryos). The greater effects observed in inbred fish were attributed to inbreeding×environment interactions and the amplification of inbreeding depression. Although no empirical genetic evidence of this mechanism is presented (loss of heterozygosity at quantitative trait loci and concomitant loss of heterosis and/or the expression of recessive, deleterious alleles in homozygotes), supporting evidence was provided by increased phenotypic variance in some apical endpoints in inbred fish, including specific growth rate and fecundity. This increased variance also has the potential to counteract the higher levels of response observed in inbreds, because the power to detect statistically significant changes in responses is reduced. This trade-off was demonstrated for specific growth rate. Crucially, significant male-sex ratio skews (>80%) were induced at substantially lower clotrimazole exposure concentrations (1.7 µg l-1) in combination with elevated temperature (33°C), compared with exposure concentrations (43.7 µg l-1) generating similar sex ratio skews at the standard test temperature of 28°C. These temperatures represent current and predicted 2100 (elevated) mean temperatures in the zebrafish’s native India and Bangladesh. Although the lowest observed effect concentration was an order of magnitude above the predicted environmental concentration for clotrimazole, it is conceivable that combined environmental exposures to similarly acting chemicals (e.g. other azole compounds used in crop protection, veterinary and human medicine) could produce similar effects to those we observed. The consequent effects of sex ratios skews and reduced fitness (fecundity and embryo viability) on per capita population growth rate (r) and extinction probability were predicted in inbred versus outbred zebrafish populations using stochastic population viability analysis. The results showed that the observed male-skews >80% threaten small zebrafish populations with fewer than 100 breeding adults (<20 adult females). However, small reductions of 2-3% in embryo-juvenile (age 0+) survivorship (including simulated inbreeding depression) were more influential on r and extinction probability than large sex ratio skews and/or reduced female fecundity. The results presented in this thesis support the contention that chemical effects may be exacerbated by other environmental stressors, but also illustrate the importance of considering biological (genetic), as well as physical and chemical interactions in cumulative ERA. Greater sensitivity of inbred versus outbred organisms to the effects of environmental stressors on sexual differentiation and reproductive fitness offers a margin of safety to ERA and the protection of wildlife populations (excluding those that are severely inbred and critically endangered). This is because, as originally stated, laboratory organisms used in ERA are generally more inbred than their wild counterparts. Nevertheless, more attention should be paid to the origin, breeding history and genetics of laboratory strains. This will help to ensure consistency between studies and testing laboratories and provide more confidence in extrapolating the results to wild populations.

Marine turtles produce many offspring which offsets the high mortality experienced by turtles during early development. Juvenile mortality might be reduced by evolving effective behavioral as well as morphological anti-predator defenses. Body proportions of three species (Caretta caretta, Chelonia mydas, Dermochelys coriacea) of turtles were measured in the first fourteen weeks of development to examine how growth may mitigate predation by gape-limited predators. Growth was categorized as isometric if shape did not change during development or allometric if body shape did change. All three species showed allometric growth in carapace width; however it was less pronounced in the larger D. coriacea turtles. Allometric growth in carapace width decreased as all three species grew in size. When high predation occurs in early development, many species will favor rapid growth into a size refuge. Juvenile sea turtles may optimize their survival by growing allometrically when predation risk is the greatest. / Includes bibliography. / Thesis (M.S.)--Florida Atlantic University, 2014. / FAU Electronic Theses and Dissertations Collection

Sotalia guianensis é um pequeno cetáceo costeiro encontrado ao longo do Oceano Atlântico Sul-Ocidental. Está exposta a inúmeras ameaças, tais como captura acidental em redes de pesca, tráfego de embarcações e turismo. A análise de viabilidade populacional (AVP) é uma forma de prever as flutuações e a probabilidade de persistência ou extinção de uma espécie ou população ao longo do tempo, incorporando dados demográficos, ecológicos e ambientais de populações reais em simulações computacionais de modelos estocásticos e determinísticos. O presente estudo teve como objetivos estimar densidade, abundância e realizar uma AVP para S. guianensis no Complexo Estuarino-Lagunar de Cananéia, São Paulo. Estimativas de abundância e densidade foram obtidas entre 2011 e 2012, utilizando o método de transecção linear com amostragem de distâncias, com 1.339,91 km percorridos e 83h05min em esforço. Avistou-se 241 grupos, compostos por 1 a 20 indivíduos. O programa Distance, com modelo half-normal e ajuste coseno e menor valor de AIC, estimou uma abundância de 193 indivíduos (95%IC: 158 - 237) e densidade de 2,5538 ind/km2 (95%IC: 2,0812 - 3,1337). A média de tamanho de grupo é 4,1504 indivíduos (95%IC: 3,7666 - 4,5734). De forma geral, a espécie apresenta grandes variações ao longo de sua distribuição com relação ao tamanho populacional, densidade, tamanho de grupos, distribuição nos habitats e residência. Tais diferenças estão associadas possivelmente às características físicas e ambientais de cada habitat, que interferem direta ou indiretamente na distribuição e dinâmica populacional da espécie e suas presas. Para a AVP a população foi tratada como não suplementada, sem dispersão, sem remoção, sem depressão endogâmica e a extinção foi definida como a permanência de apenas um sexo. O valor inicial da população é 193 indivíduos e demais parâmetros demográficos e reprodutivos foram estimados com base na literatura disponível. Variações de parâmetros específicos (mortalidade, capacidade de suporte do ambiente (K), variação ambiental na reprodução e catástrofe) foram inseridas nos cenários para avaliar as tendências populacionais sob diferentes ameças. Utilizou-se o programa VORTEX 9.99b. A AVP apontou para o declínio e extinção (P(E) = 1,000) da população em menos de 300 anos em todos os cenários, com taxas de crescimento de -0,082 (SD = 0,120), - 0,049 (SD = 0,107) e -0,086 (SD = 0,062), para os cenários 1, 2 e 3 respectivamente. O tempo médio para extinção foi estimado em 39,6 anos para o cenário 1, 57,3 anos para o cenário 2 e 3,3 anos para o cenário 3. As projeções geradas pela AVP apontaram cenários pessimistas, o que pode estar relacionado ao pequeno tamanho da população. As análises mostram que variações no tamanho populacional, mortalidade, K e catástrofes podem influenciar fortemente a persistência de pequenas populações. O estuário de Cananéia é um ambiente favorável e bem preservado que oferece recursos suficientes para S. guianensis, entretanto, o aumento das atividades antrópicas na área pode levar a mudanças na dinâmica populacional e alterações no habitat, comprometendo sua persistência ao longo do tempo. / Sotalia guianensis is a small coastal cetacean found along the south-western Atlantic Ocean. Through its range, is exposed to numerous threats, such as bycatch in fishing nets, vessel traffic and tourism. Population viability analysis (PVA) is a way to predict the trends and the probability of persistence or extinction of a species or population over time, incorporating demographic, ecological and environmental data of real populations in computer simulations of stochastic and deterministic models. The present study aimed to estimate density, abundance and population viability of S. guianensis in the estuarine-lagoon complex. Estimates of abundance and density were obtained between 2011 and 2012, using the distance sampling method and linear transects, with 1,339 .91 km and 83h05min in effort. It were recorded 241 groups (n) with group size between 1 to 20 individuals. The Distance program, with half-normal model and adjust cosine with the lowest AIC, estimated an abundance of 193 individuals (95% CI: 158-237) and density of 2.5538 ind/km2 (95% CI: 2.0812 - 3.1337). The average group size is 4.1504 individuals (95% IC: 3.7666-4.5734). In general, the species presents large variations throughout its distribution regarding population size, density, groups size, distribution in habitat and residence. Such differences are possibly associated with the physical characteristics of each habitat and environmental conditions that interfere directly or indirectly in the distribution and population dynamics of the species and its prey. For the PVA population was treated as not supplemented, without dispersion, without removal, without inbreeding depression, and extinction was defined as the presence of only one sex. The initial population size was 193 individuals and other demographic and reproductive parameters were estimated based on available literature for the species. Variations of specific parameters (mortality, carrying capacity of the environment, environmental variation on reproduction and catastrophe) were used to evaluate population trends under different threats and scenarios. It was used the VORTEX program v. 9.99 b. AVP pointed to the decline and extinction (P(E) = 1,000) of the population in less than 300 years in all scenarios, with growth rates of -0.082 (SD = 0.120), -0.049 (SD = 0.107) and - 0.086 (SD = 0.062), for scenarios 1, 2 and 3 respectively. The average time to extinction was estimated at 39.6 years for scenario 1, 57.3 years for scenario 2 and 3.3 years for scenario 3. The projections generated by the AVP showed pessimistic scenarios, which may be related to the small size of the population. The analyses show that variations in population size, mortality, carrying capacity and disasters can strongly influence the persistence of small populations. Cananéia estuary is a well preserved environment that offers sufficient resources to S. guianensis, however, the increase in anthropogenic activities in the estuary may lead to changes in population dynamics and habitat quality, compromising their persistence over time.

Effective conservation strategies for imperiled species require an understanding of processes that influence fitness throughout the organism's life cycle and across the range of habitats needed to complete that cycle. I evaluated factors that affect population viability of bull trout Salvelinus confluentus, a threatened freshwater char species, throughout individual life stages and over the entire life cycle. I assessed the relationship between bull trout egg incubation success and environmental variables. Egg survival was negatively related to the percent of fine sediment in redds and positively related to hydraulic conductivity and the strength of downwelling. Next, I quantified juvenile bull trout survival rates and described movement patterns for this life stage. Juvenile bull trout emigrated from natal headwaters into larger rivers throughout the entire year and across a range of sizes. Estimates of juvenile survival rates improved dramatically when emigration was incorporated into the analysis. I integrated my observations of bull trout survival, growth, and movement to create a life-cycle model, which I used to better understand how populations respond to changes in specific demographic rates. Bull trout populations were particularly sensitive to changes in juvenile growth and survival. The relative effect of changes to fertility rates and adult survival varied depending upon whether a population was composed primarily of large, migratory, or smaller, resident individuals. Dispersal helped to lower the probability of extinction for small or declining populations when neighboring populations were stable. My research demonstrates that bull trout require access to habitats throughout entire watersheds to maintain population viability. My results suggest that limiting anthropogenic sources of fine sediment and maintaining areas of channel complexity that promote downwelling can be important for bull trout embryo survival. Management decisions should also consider the diverse behavior of juvenile bull trout and the wide range of habitat they use. Additionally, connectivity between populations is likely to be important for declining populations to persist. The diversity of life-history strategies expressed by bull trout helps maintain demographic stability within and among populations. As such, preservation of habitat integrity and full life-history diversity is imperative for conservation and recovery of bull trout populations range-wide.

<p>Population viability analysis (PVA) is commonly used in conservation biology to predict population viability in terms of population growth rate and risk of extinction. However, large data requirements limit the use of PVA for many rare and threatened species. This thesis examines the possibility of conducting a matrix model-based PVA for plants with limited data and provides some practical recommendations for reducing the amount of work required. Moreover, the thesis applies different forms of matrix population models to species with different life histories. Matrix manipulations on 37 plant species revealed that the amount of demographic data required can often be reduced using a smaller matrix dimensionality. Given that an individual’s fitness is affected by plant density, linear matrix models are unlikely to predict population dynamics correctly. Estimates of population size of the herb <i>Melampyrum sylvaticum</i> were sensitive to the strength of density dependence operating at different life stages, suggesting that in addition to identifying density-dependent life stages, it is important to estimate the strength of density dependence precisely. When a small number of matrices are available for stochastic matrix population models, the precision of population estimates may depend on the stochastic method used. To optimize the precision of population estimates and the amount of calculation effort in stochastic matrix models, selection of matrices and Tuljapurkar’s approximation are preferable methods to assess population viability. Overall, these results emphasize that in a matrix model-based PVA, the selection of a stage classification and a model is essential because both factors significantly affect the amount of data required as well as the precision of population estimates. By integrating population dynamics into different environmental and genetic factors, matrix population models may be used more effectively in conservation biology and ecology in the future.</p>

Population viability analysis (PVA) is commonly used in conservation biology to predict population viability in terms of population growth rate and risk of extinction. However, large data requirements limit the use of PVA for many rare and threatened species. This thesis examines the possibility of conducting a matrix model-based PVA for plants with limited data and provides some practical recommendations for reducing the amount of work required. Moreover, the thesis applies different forms of matrix population models to species with different life histories. Matrix manipulations on 37 plant species revealed that the amount of demographic data required can often be reduced using a smaller matrix dimensionality. Given that an individual’s fitness is affected by plant density, linear matrix models are unlikely to predict population dynamics correctly. Estimates of population size of the herb Melampyrum sylvaticum were sensitive to the strength of density dependence operating at different life stages, suggesting that in addition to identifying density-dependent life stages, it is important to estimate the strength of density dependence precisely. When a small number of matrices are available for stochastic matrix population models, the precision of population estimates may depend on the stochastic method used. To optimize the precision of population estimates and the amount of calculation effort in stochastic matrix models, selection of matrices and Tuljapurkar’s approximation are preferable methods to assess population viability. Overall, these results emphasize that in a matrix model-based PVA, the selection of a stage classification and a model is essential because both factors significantly affect the amount of data required as well as the precision of population estimates. By integrating population dynamics into different environmental and genetic factors, matrix population models may be used more effectively in conservation biology and ecology in the future.

Effective conservation strategies for imperiled species require an understanding of processes that influence fitness throughout the organism's life cycle and across the range of habitats needed to complete that cycle. I evaluated factors that affect population viability of bull trout Salvelinus confluentus, a threatened freshwater char species, throughout individual life stages and over the entire life cycle. I assessed the relationship between bull trout egg incubation success and environmental variables. Egg survival was negatively related to the percent of fine sediment in redds and positively related to hydraulic conductivity and the strength of downwelling. Next, I quantified juvenile bull trout survival rates and described movement patterns for this life stage. Juvenile bull trout emigrated from natal headwaters into larger rivers throughout the entire year and across a range of sizes. Estimates of juvenile survival rates improved dramatically when emigration was incorporated into the analysis. I integrated my observations of bull trout survival, growth, and movement to create a life-cycle model, which I used to better understand how populations respond to changes in specific demographic rates. Bull trout populations were particularly sensitive to changes in juvenile growth and survival. The relative effect of changes to fertility rates and adult survival varied depending upon whether a population was composed primarily of large, migratory, or smaller, resident individuals. Dispersal helped to lower the probability of extinction for small or declining populations when neighboring populations were stable. My research demonstrates that bull trout require access to habitats throughout entire watersheds to maintain population viability. My results suggest that limiting anthropogenic sources of fine sediment and maintaining areas of channel complexity that promote downwelling can be important for bull trout embryo survival. Management decisions should also consider the diverse behavior of juvenile bull trout and the wide range of habitat they use. Additionally, connectivity between populations is likely to be important for declining populations to persist. The diversity of life-history strategies expressed by bull trout helps maintain demographic stability within and among populations. As such, preservation of habitat integrity and full life-history diversity is imperative for conservation and recovery of bull trout populations range-wide.

Management of big wildlife such as bears can be a difficult task, especially in the face of human-wildlife conflict and demands of the hunting industry. The Brown Bear (Ursus arctos) population at Yusufeli County (Artvin, northeastern Turkey) has recently been the focus of scientific, social and economic concerns. This study population of c. 140 individuals occurs within 800 km2 of forested and alpine land. Legal hunting of male bears was allowed in 2007 after an interval of four years. This study aims to find out through a population viability analysis the level and frequency of trophy hunting this population can tolerate for the next 50 years. A matrix model with six age-classes for each sex was constructed using observed and literature-based parameter values. RAMAS Metapop was used to simulate four different scenarios where numbers of hunted bears and hunting frequency changes. The model was highly sensitive to maximum growth rate and adult survival. Interval extinction probabilities for the next 50 years ranged between 0% and 26% depending on the scenario. Viable scenarios (with an extinction probability &lt / 0.05) were only possible with either no trophy hunting or hunting of 4 subadult/adult males and 1 adult female every other year. Legal and illegal hunting jointly impact the bear population in a strong way, and when they occur simultaneously every year, they lead to extinction in the long run. Avoidance of illegal killing and a close supervision of trophy hunting are crucial in the management of this bear population.

Centaurea tchihatcheffii Fisch. &amp / Mey. is a critically endangered annual endemic plant found only in Ankara. This study aimed to determine its distributional range, metapopulation status, the effects of agricultural activities, and assess conservation options. Occurrences and population size estimates were carried out by ground surveys. Two adjacent subpopulations were intensively studied during 2004-2008. Plant and seed demographic data were collected in the field and by laboratory tests. Field experiments simulated the effects of agricultural practices. Risks of extinction and possible impacts of different management actions were investigated through a population viability analysis (PVA) by constructing a two-stage stochastic model. Six scenarios involving different management actions were run with 10,000 replications each using RAMAS Metapop. A total of 14 patchily distributed subpopulations were found to have an extent of occurrence of &gt / 700 km2. Herbicide applications caused extreme mortality and reduced germination success, and were shown to be the major anthropogenic threat against long-term survival of C. tchihatcheffii. Tillage led to an increase in density and reproductive success in the following year. PVA simulations for most scenarios predicted extinction of both subpopulations within 4 to 95 years, but a conservation management scenario involving delayed tillage ensured viable populations with a combined size of 21 million individuals. PVA results demonstrated that timing and frequency of tillage is crucial. Therefore, we propose tillage to be carried out after seed set every other year for protected subpopulations to ensure their long term persistence. Alternatively, unprotected subpopulations elsewhere can benefit from organic or nature-friendly farming.

Goitered gazelle (Gazella subgutturosa) is an Asian antelope species and it is classified as Vulnerable by IUCN. They have an economic, esthetic and cultural value / therefore, they had been hunted and domesticated for a long time. Additional human disturbance over years nearly led goitered gazelle populations in Turkey to extinction. Today in Turkey, only natural population of goitered gazelle lives in Sanlurfa. In this theses, demographic structure and population parameters of natural population goitered gazelle in Sanliurfa is studied. Line transect and regular surveys are performed to collect data about demographic structure of the population such as sex ratio and group composition. Line transect sampling, which is a distance sampling technique, is used to estimate population size and density of the population. GPS collared goitered gazelles are monitored for fecundity and survival rate. Data is collected for 18 from July 2008 to December 2009 during 32 field surveys. Four main transect samplings have been performed and including transect samplings that are done during regular surveys, 90 line transects are walked. Population sizes and densities were estimated to be (average &plusmn / standard error) 242 &plusmn / 184 and 2.302 &plusmn / 1.590 individual per km2 for July 2008 / 365 &plusmn / 179 and 3.476 &plusmn / 1.707 individual per km2 for January 2009 / 319 &plusmn / 111 and 3.039 &plusmn / 1.059 individual per km2 for June 2009 and lastly, 317 &plusmn / 243 and 3.019 &plusmn / 2.315 for November 2009. Survival rate is estimated to be 0.276, 0.540 and 0.585 for calves, 1 year old and 2+ years olds respectivelty, and fecundity is estimated to be 0.4. This preliminary study shows that according to Population Viability Analysis results, natural goitered gazelle population in Turkey will be extinct in next 10 years if more effective conservation is not performed.