An abundant Paddlefish Polyodon spathula population exists in a 0.8 ha pool below a water control structure at Sam D. Hamilton Noxubee National Wildlife Refuge, Mississippi. Managers were concerned that regulated flows from the structure were causing an ecological trap if Paddlefish were being attracted from the larger river downstream during the spawning period, but conditions were not suitable to facilitate reproduction. Between February 2016 to April 2018, 117 Paddlefish were identified and daily abundance was estimated between 18 and 75 fish. Telemetry study of 59 fish suggests a mixed population structure where some remain in the pool year-round and other emigrate seasonally, cued by rising spring discharge and water temperature. Reproduction was not documented which suggests a critical component needed for spawning may be missing, at least during this study. Therefore, given the need to remove Paddlefish from the pool, translocation and flow releases may be effective management strategies.

To investigate the density-dependent factors that may be partly responsible for the apparent stability of hemlock woolly adelgid (HWA; Adelges tsugae Annand) populations in central New England, we infested 64 eastern hemlock (Tsuga canadensis Carrière) trees with varying densities of HWA sistens ovisacs in a typical eastern hemlock forest in western Massachusetts. We subsequently documented HWA density, fecundity, and the amount of new growth on experimental trees over two consecutive years. We used a 2 x 2 randomized block design using previously and newly infested hemlocks divided into 1 m tall saplings and branches of mature trees. There was a density-dependent decline in the survival and fecundity of HWA in both the spring and winter generations. This response was a function of both previous infestation by HWA and current years crawler density in the spring generation. Additionally, the production of sexuparae in the spring generation played a key role in the overall density-dependent survival of HWA, suggesting that sexuparae production is strongly linked to developing crawler density. In Chapter 2, varying densities of HWA were manipulated on 16 previously uninfested eastern hemlocks in an open field plantation. In contrast to HWA populations in our forest experiment, there was no evidence of density-dependent survival on a tree-wide basis in the plantation in the springtime progrediens generation. However, there were comparable density-dependent survival of settled crawlers and sexuparae production when samples of the population were examined from branches with high density. Plantation hemlocks had 9.3 times more foliage and ten times lower HWA densities per cm than forest hemlocks. Despite the lack of density-dependence in the progrediens generation of this study, HWA populations of the subsequent sistens generation went extinct on 13 out of the 16 trees. These results show that density-dependent processes may only exist when HWA density/cm reaches a certain threshold, and that high mortality may occur during the late-summer aestivation phase at densities below this threshold, perhaps due to high summertime temperatures in HWA’s sistens generation. These results may help explain the slow process of HWA establishment in our region.

This thesis deals with an endangered large mammal species - snow leopard, its distribution, population dynamics, landscape genetics and connectivity, trophic ecology and human-snow leopard conflicts in the Nepalese Himalaya (Sagarmatha National Park (SNP), Lower Mustang (LM) and Upper Manang (UM) in the Annapurna Conservation Area, during Wet and Dry seasons in 2014-2016. In the case of snow leopard study, we used data obtained from camera traps, scat's genetic analysis and monitoring of fresh pugmarks and scrapes while direct count method was used to study for its main prey, blue sheep and Himalayan tahr. In study 1, we assessed the determinants of habitat suitability of snow leopards using MaxEnt model and mapped the distribution of suitable habitat for snow leopards in Nepal. Altitude and Annual mean temperature are important common factors contributing to snow leopard habitat suitability within the area studied, which is indicated by both the percentage contribution of environmental variables and Jackknife test from MaxEnt model. Some other uncommon factors also seem to play a role, as they were important in at least one of the analyses. These were: distance from road, and precipitation of driest month but their importance has to be considered with caution. In study 2, we present our...

Species have complex and contextual relationships with their environment; both the relative contributions of life-history stages to population growth and the effect of environmental factors on each stage can be different among co-existing species. Timing and extent of reproduction, survival, and mortality determine population growth, species distributions, and assemblage patterns. I evaluate the role of habitat (intact, degraded) and microsite (shrub, leaf litter, bare sand) on population dynamics of Florida scrub herbs. Isolated overgrown shrubs and extensive bare sand areas in degraded scrub were expected to decrease seed predation, reduce competition of herbs with shrubs, and provide larger habitat for recruitment. I provide evidence that habitat and microsite variation influenced demography of five endemic and two common native species through effects on seed removal, emergence, and establishment. Habitat and species affected seed removal: endemic species with large seeds were removed in higher frequency in degraded habitat, likely by vertebrates, while species with small seeds were removed in higher frequency in intact habitat, by invertebrates. There was no evidence of differences in individual seed production between habitats for the two common species, C. fasciculata and B. angustifolia. Invertebrates were primarily responsible for seed removal of both species, although peak season of removal and microsite varied with species. Removal of seeds, emergence, and establishment increased with seed density. Matrix modeling indicated that population growth of C. fasciculata was greater in degraded habitat and greatest in litter microsites, and population growth of B. angustifolia was similar between habitats and greatest in bare sand. Contrasting responses among species to environmental factors in intact and degraded scrub indicated that natural disturbances are not ecologically equivalent to anthropogenic iv disturbances. Idiosyncratic species dynamics in common environments suggest that understanding relationships between life-history traits and environmental conditions will be required to facilitate restoration

Recruitment, the addition of new individuals to a population, must be understood to make predictions about population growth of marine invertebrates. Red abalone (Haliotis rufescens) represent a former important commercial fishery in California, and until recently, supported a major recreational fishery. However, there have been statewide declines since the 1960s due to overfishing, disease, and climatic factors. Thus, understanding population dynamics to inform management and population restoration is critical. Recruitment dynamics of red abalone are poorly understood, with no prior knowledge of seasonal trends. To address this knowledge gap, I assessed monthly (July 2016-June 2017) and annual (2012-2016) settlement rates of red abalone in the Monterey Bay, which has low density abalone populations due to sea otter predation. I evaluated associations between abalone recruitment and oceanographic factors (temperature, wave forces, and upwelling index) and food availability (kelp density) to understand potential predictors of recruitment. Abalone recruitment occurred year round, with generally higher recruitment in late summer to early fall (July-October) and peaks in August and October. This is the first demonstration of year-round abalone recruitment in the field. On a monthly basis, there were no statistically significant relationships between recruitment and oceanographic factors or food availability. Annual abalone recruitment was consistent in all years, with the exception of 2015 when recruitment majorly decreased during the second year of the North Pacific marine heatwave (i.e., warm blob and El Niño Southern Oscillation (ENSO) events). The failure of recruitment during only the second year of warm temperature suggests that prolonged extreme temperatures lead to reproductive failure. The consistent annual recruitment in the Monterey Bay contrasts with sporadic recruitment observed in Sonoma and Mendocino Counties in northern California. This finding was unexpected because red abalone in northern California were twice as dense as those in Monterey Bay at the time of the study. Possible hypotheses behind the observed consistent recruitment in Monterey Bay despite low densities include that: sheltered embayments retain larvae and promote recruitment, predation by sea otters aggregates abalone in crevices and promotes fertilization success, and the perennially present Macrocystis pyrifera kelp forests better support abalone growth and fecundity than northern California forests dominated by annual Nereocystis leutkeana.

We study the fluctuation effects in the seminal cyclic predator-prey model in population dynamics due to Robert May and Warren Leonard both in the zero-dimensional and two-dimensional spatial version. We compute the mean time to extinction of a stable set of coexisting populations driven by large fluctuations. We see that the contribution of large fluctuations to extinction can be captured by a quasi-stationary approximation and the Wentzel–Kramers–Brillouin (WKB) eikonal ansatz. We see that near the Hopf bifurcation, extinctions are fast owing to the flat non-Gaussian distribution whereas away from the bifurcation, extinctions are dominated by large fluctuations of the fat tails of the distribution. We compare our results to Gillespie simulations and a single-species theoretical calculation. In addition, we study the spatio-temporal pattern formation of the stochastic May--Leonard model through the Doi-Peliti coherent state path integral formalism to obtain a coarse-grained Langevin description, i.e. the Complex Ginzburg Landau equation with stochastic noise in one complex field. We see that when one restricts the internal reaction noise to small amplitudes, one can obtain a simple form for the stochastic noise correlations that modify the Complex Ginzburg Landau equation. Finally, we study the effect of coupling a spatially extended May--Leonard model in two dimensions with symmetric predation rates to one with asymmetric rates that is prone to reach extinction. We show that the symmetric region induces otherwise unstable coexistence spiral patterns in the asymmetric May--Leonard lattice. We obtain the stability criterion for this pattern induction as we vary the strength of the extinction inducing asymmetry. This research was sponsored by the Army Research Office and was accomplished under Grant Number W911NF-17-1-0156. / Doctor of Philosophy / In the field of ecology, the cyclic predator-prey patterns in a food web are relevant yet independent to the hierarchical archetype. We study the paradigmatic cyclic May--Leonard model of three species, both analytically and numerically. First, we employ well--established techniques in large-deviation theory to study the extinction of populations induced by large but rare fluctuations. In the zero--dimensional version of the model, we compare the mean time to extinction computed from the theory to numerical simulations. Secondly, we study the stochastic spatial version of the May--Leonard model and show that for values close to the Hopf bifurcation, in the limit of small fluctuations, we can map the coarse-grained description of the model to the Complex Ginsburg Landau Equation, with stochastic noise corrections. Finally, we explore the induction of ecodiversity through spatio-temporal spirals in the asymmetric version of the May--Leonard model, which is otherwise inclined to reach an extinction state. This is accomplished by coupling to a symmetric May-Leonard counterpart on a two-dimensional lattice. The coupled system creates conditions for spiral formation in the asymmetric subsystem, thus precluding extinction.

There are thousands of species of mosquitoes, but only a handful of these species carry pathogens that cause human diseases. Here, we study two species, Aedes albopictus and Aedes aegypti, which transmit infections such as dengue, Zika, Mayaro virus, and La Crosse virus. Curtailing these diseases is a good reason to consider control of mosquito populations. However, mosquitoes are quite hardy and spraying of pesticides is typically a short-term solution. Thus, more long-term solutions require careful thought about mosquito populations, including early juvenile aquatic stages: egg, larva, and pupa. In this dissertation, we examine the factors that affect the dynamics of aquatic stages by creating mathematical models. The goal is to assess what key biological features most impact the total population. Both Aedes albopictus and Aedes aegypti lay eggs in small containers, producing limitations on space and food. We investigate how restricting resources changes development time, survival to adulthood, and body mass at emergence. The interactions between these changes are complicated, so to disentangle their effects we create three different mathematical models. The first model is discrete in time and focuses on the best way to incorporate the influence of larval density. We compare the impact of larval density by inputting seven different functional forms altering survival and development time. Larval density used in the model is determined from the average of the population size over the past one to thirty-six days. The second model is also discrete in time but focuses on the interaction between survival, development time, and mass. This model considers three levels of mass. Here, we use the density-dependent function determined from our first model and fit the maximum value for development time from experimental data. Survival values are fit using constants and a density-dependent function. Finally, growth is built in as a function of food. Food decreases at each time point as a function of the total larvae in the environment. We compare between model formulations with Akaike information criterion. The third model examines the ramifications of constricting resources on growth verses death. We employ a partial differential equation that has three independent variables: time, age, and mass. We find that density dependence is highly influential in the maturation of mosquitoes, and it is more essential to include its impacts on development time than on survival. These findings can be incorporated into a larger framework of disease dynamics, and give insight into better control of mosquitoes and disease spread. / Doctor of Philosophy / There are thousands of species of mosquitoes, but only a handful of these species spread human diseases. We specifically study mosquitoes that transmit diseases such as dengue and Zika, which plague large portions of the world. One way to reduce disease spread by mosquitoes is to eliminate the mosquito population, but mosquitoes are becoming resistant to commonly used insecticides. Thus, additional ways to combat mosquitoes are needed. To do so requires a better understanding of how mosquito populations change. This necessitates incorporating information from all life stages of the mosquito, including the juvenile stages that live in the water. In this dissertation, we examine various factors that affect the population size and characteristics of young mosquitoes by creating mathematical models. The goal is to assess what key biological features most impact the population. As young mosquitoes live in aquatic environments, there are limitations on space and food. We investigate how restricting resources changes the time it takes for mosquitoes to develop into adults, how many survive to adulthood, and what their body mass is as new adults. These outcomes interact in complicated way. To disentangle this, we create three different mathematical models. The first model focuses on the best way to incorporate the influence of limiting space or density on population size. The second model focuses on the interaction between mosquito body mass, survival, and time spent as a juvenile. The third model examines how resources alter growth and death and the ensuing mass of mosquitoes. Models are fit to experimental data and validated based on how accurately they describe known patterns. We find that population density is highly influential in the maturation of juvenile mosquitoes and its most important effect is on time spent as a juvenile mosquito. By correlating growth of juvenile mosquitoes to density and resources, our second model is better able to reproduce data. These findings provide important understanding on mosquito populations, which provides insight into how to better control mosquitoes and the diseases they spread.

Many biological populations reside in increasingly fragmented landscapes, which arise from human activities and natural causes. Landscape characteristics may change abruptly in space and create sharp transitions (interfaces) in landscape quality. How the patchiness of landscapes affects ecosystem diversity and stability depends, among other things, on how individuals move through the landscape. Individuals adjust their movement behavior to local habitat quality and show preferences for some habitat types over others. In this thesis, we focus on how landscape composition and the movement behaviour of individuals at an interface between patches of different quality affect the steady state of a single species. We consider a model of reaction-diffusion equations for the temporal evolution of the density of the population in space. Individual movement is described by a diffusion process, e.g., an uncorrelated random walk. Population net growth is encapsulated in the growth function that considers birth and death of individuals, including nonlinear effects that arise from competition and/or facilitation within the species. We consider the simplest case of two adjacent one-dimensional patches, e.g., two intervals on the real line that share one boundary point. Conditions are homogeneous within a patch but differ between patches. The movement behaviour of individuals between the two patches is incorporated into matching conditions of population flux and density at the interface between patches, i.e., the boundary point that the intervals share. These matching conditions turn out to be continuous in the flux but discontinuous in the density. Several authors have studied similar models recently. Most of these studies consider monostable dynamics on both patches, i.e., logistic growth. Under logistic growth, the net population growth rate is a strictly decreasing function of population density. Logistic population dynamics are very simple: the population extinction state is unstable and a positive steady state is globally asymptotically stable. In this work, we also include bistable dynamics, i.e., an Allee effect. Biologically, an Allee effect occurs when individuals cooperate at some level so that the net population growth rate is increasing with population density for at least some low or intermediate densities. Models with Allee growth typically exhibit bistability: there are two locally stable steady states, one at low density (possibly zero) and one at high density. This bistability makes mathematical analysis more challenging, but leads to more interesting results in return. Mathematically, most existing work on related models is based on linear stability analysis of the extinction state. We focus on the nonlinear models and specifically on positive steady states. We establish the existence, uniqueness and - in some cases - global asymptotic stability of a positive steady state. We classify the shape of these states depending on movement behaviour. We clarify the role of movement in this context. In particular, we investigate the following prior observation: a randomly diffusing population at steady state in a continuously varying habitat can exceed its carrying capacity. Our results clarify when and under which conditions this effect can arise in our two-patch landscape. The analysis of the model with an Allee effect on one of the two patches yields a rich and interesting structure of steady states. Under certain parameter conditions, some of these states are amenable to explicit stability calculations. These yield insights into the possible bifurcations that can occur in our system. Finally, we indicate how the model and analysis here can be extended to systems of reaction-diffusion equations on graphs that represent natural habitats with different geometries, for example watersheds.

Chenopodium album is considered one of the most important weeds adversely affecting agricultural production due to its highly competitive influence on field crops. Chemical herbicides have increased the efficiency of farming, but recently problems of herbicideresistant weed populations and herbicide residues in soil, water, food products and effects on non-target organisms have increased, consequently, other methods of control of weeds by using specific fungi as herbicides have been suggested. The purpose of this research was to evaluate the biological control of the weed Chenopodium album by the fungus Ascochyta caulina. Some of the factors which control dormancy and germination of Chenopodium album seeds have been investigated to understand better the weed population dynamics. The results showed that seeds from two populations (UK and Libya) differ in their response to factors such as light, chilling, and burying in soil. This could have implications for effective control of the weed in different regions. Two formulations of mycoherbicides (Tween 80 and Gelatine based applications) were tested in the laboratory, and showed promise in reducing growth of the weed, especially the formula of Tween 80. There was extensive shoot fresh and dry weight reduction of inoculated Chenopodium album, as well as reduced root growth. Highest disease severity rates were observed on plants in the first three week of life. A field trial revealed similar results but less disease severity was observed, possibly because of dry weather. However, it was concluded that the fungus Ascochyta caulina is a potentially useful biological control agent but many factors still can be modified in relation to application of the mycoherbicide to increase its efficacy. / Libyan Government

This is one of the first time series studies of bacteria in soils supporting actively growing corn crops. Mathematically modeling bacteria population dynamics has the potential as a tool to more precisely assess the economic optimal nitrogen fertilizer rate for farmers. As a first step in this modeling effort, we examine the possibility that the bacteria population growth might be described by a dynamic model developed in the food sciences describing bacteria growth in food meant for human consumption. We make the assumption that air temperature above the soil can be used as an approximation for soil temperature. Also, because there were two rates of data collection (one for bacteria and one for weather), the weather data was averaged between bacteria samples to obtain the same number of samples per data set. It is under these assumptions that we demonstrate in this thesis that this model, developed by McMeekin and Chandler, fails to apply to bacteria in agricultural soils.