The primary objectives of this study were: 1) to evaluate the movement patterns, habitat use, and survival of triploid grass carp Ctenopharyngodon idella stocked to control hydrilla Hydrilla verticillata in a riverine reservoir (Claytor Lake, Virginia), 2) to examine grass carp population dynamics and hydrilla growth dynamics in Claytor Lake to guide long-term management efforts, and 3) to describe the aquatic plant community in the New River upstream of Claytor Lake to assess the potential for alterations due to potential grass carp herbivory. Only 3% of radio-tagged grass migrated out of Claytor Lake during the 2-year study. Grass carp movement patterns were significantly correlated with temperature-, weather-, and habitat-related variables. Grass carp selected specific cove, shoal and tributary habitats colonized by hydrilla. First-year survival of grass carp was 44% in 2011, and 25% in 2012. Grass carp growth rates were rapid in 2011, but declined in 2012 concurrent with significant reductions in hydrilla abundance. Based on grass carp population dynamics observed in Claytor Lake, our stocking model predicted that hydrilla could be controlled through 2030 by a grass carp standing stock of 5-6 metric tons. We documented 12 plant species in the New River upstream of Claytor Lake, 9 of which are preferred plants for grass carp suggesting that the plant community could be altered if migration rates increase. Grass carp can be effective for managing hydrilla in riverine reservoirs; however, continued monitoring of grass carp population dynamics, migration rates, and vegetation abundance could facilitate greater precision in management efforts. / Master of Science

We present an investigation of two non-equilibrium systems: spatial many-species predator-prey games and systems of interacting magnetic skyrmions. We numerically study two predator-prey systems characterized by nested pattern formations. We first consider a six species game in which spiral patterns spontaneously form within coarsening domains. Through a systematic investigation of relevant correlation functions, the interface width, and other quantities, we show that the non-trivial in-domain dynamics affect the coarsening process and the interfacial properties. The exponents which govern domain growth, aging, and interface fluctuations differ from those expected from curvature driven coarsening. The response to perturbations of the reaction rates is also studied. Furthermore, we introduce a nine species model characterized by nested spiral pattern formations. Quantitative evidence of the existence of two length and time scales associated to the spiral levels is presented in the form of correlation lengths and a temporal Fourier analysis of the species densities. A generalized interaction scheme is proposed for dynamically generated hierarchies. Magnetic skyrmions are particle-like spin configurations found in certain chiral magnets. We study the effect of the Magnus force on the relaxation dynamics through Langevin molecular dynamics simulations. The Magnus force enhances the disorder of the system at high noise strengths while we observe a dynamic regime with slow decaying correlations at low noise strengths. The different regimes are characterized by changes in the aging exponent. In general, the Magnus force accelerates the approach to the steady state. In the presence of quenched disorder, we find that the relaxation dynamics are more robust in systems with a strong Magnus force. We also examine periodically driven skyrmion systems and show that a transition from reversible to irreversible flow exists in the presence of attractive defects. The Magnus force enhances the irreversible regime in this case. The work on predator-prey systems was supported by the U.S. National Science Foundation through Grant No. DMR-1606814 whereas the work on skyrmions was supported by the US Department of Energy, Office of Basic Energy Sciences (DOE-BES), under Grant No. DE-FG02-09ER46613. / Doctor of Philosophy / We present an investigation of two non-equilibrium systems: spatial many-species predator- prey games and systems of interacting magnetic skyrmions. We numerically study two predator-prey systems characterized by nested pattern formations. We first consider a six species game in which spiral patterns spontaneously form within coarsening domains. Through a systematic investigation of relevant correlation functions, the interface width, and other quantities, we show that the non-trivial in-domain dynamics affect the coarsening process and, to a greater extent, properties at the interface between competing groups of species. The exponents which govern domain growth, aging, and interface fluctuations are shown to differ from those expected in typical games of competition. We also study the change of the system due to a perturbation of the reaction rates, which could represent an abrupt change in the environment. Furthermore, we introduce a nine species model characterized by the emergence of nested spiral pattern formations. Quantitative evidence of the existence of two distinct spiral levels is presented. We also propose a generalized interaction scheme for dynamically generated spiral hierarchies. Magnetic skyrmions are particle-like spin configurations found in certain chiral magnets. We study the effect of the Magnus force on the dynamic properties of skyrmion systems through particle-based simulations. The Magnus force enhances the disorder of the system at high noise strengths while accelerating the formation of the triangular lattice at low noise strengths. We find that, in general, the Magnus force accelerates the approach to the steady state. In the presence of randomly placed attractive pinning sites, we find that a strong Magnus force can prevent caging effects and allow skyrmions to more easily move around pinning sites. We also examine periodically driven skyrmion systems and show that a transition from reversible to irreversible flow exists in the presence of attractive defects. The Magnus force is shown to enhance the irreversible regime in this case. The work on predator-prey systems was supported by the U.S. National Science Foundation through Grant No. DMR-1606814 whereas the work on skyrmions was supported by the US Department of Energy, Office of Basic Energy Sciences (DOE-BES), under Grant No. DE-FG02-09ER46613.

Quantitative population dynamics modeling is needed to evaluate the stock status and fisheries management plans to provide robust model and management strategies. Atlantic Weakfish (Cynoscion regalis), one important commercial and recreational fish species along the west coast of Atlantic Ocean that was found to be declining in recent years, was selected as an example species. My study aimed to explore the possible spatial heterogeneity of CPUE (catch per unit effort) year trend based on three fishery independent surveys and explore the influence of nonstationary natural mortality on the fisheries management through a MSE (Management Strategy Evaluation) algorithm based on the Weakfish stock assessment results. Five models for catch rate standardization were constructed based on the NEAMAP (NorthEast Area Monitoring and Assessment Program) survey data and the ‘best' two models were selected based on the ability to capture nonlinearity and spatial autocorrelation. The selected models were then used to fit the other two survey data to compare the CPUE year trend of Weakfish. Obvious differences in distribution pattern of Weakfish along latitude and longitude were detected from these three surveys as well as the CPUE year trend. To test the influence of the model selection on the MSE, five stock-recruitment models and two forms of statistical catch-at-age models were used to evaluate the fishery management strategies. The current biomass-based reference point tends to be high if the true population dynamics have nonstationary natural mortality. A flexible biomass based reference point to match the nonstationary process is recommended for future fisheries management. / Master of Science

The Piping Plover (Charadrius melodus) is an imperiled shorebird that inhabits sandy beaches along the North American Atlantic Coast. The species' decline has been attributed to habitat loss, disturbance, and predation throughout its range, although most conservation efforts have focused on increasing reproductive output during the breeding season. On the coast of North Carolina, Piping Plovers breed in areas with large amounts of recreational and tourism use. Beach recreation is known to reduce nest success, chick survival, and potentially fitness in other parts of the species' range. To reduce potential negative effects from human activities on breeding Piping Plovers, managers close areas to pedestrian and vehicle access using exclusion buffers delineated by symbolic fencing. However, the reproductive success and population size of Piping Plovers in parts of North Carolina has not appeared to increase as a result of these management strategies, despite the importance of the park and its protections to these birds on their southward migration in the fall. To understand how disturbance and attempts to mitigate it affected plover demography, we examined Piping Plover population dynamics, brood movement, and migration in North Carolina from 2015–2017. We monitored 46 nests and 19 broods, and we used a logistic exposure nest survival model and Cormack-Jolly-Seber model to estimate reproductive success. We uniquely banded 77 adults and 49 chicks to understand annual survival and fidelity rates using a live encounter mark-recapture model. During the pre-fledge period, we observed movements of Piping Plover broods, and we gathered information on their environment that may affect their behavior. We recorded 191 brood locations, collected 132 focal chick behavior samples, and 113 potential disturbance environmental samples. We used multiple linear regression to evaluate several hypotheses regarding daily and hourly brood movement rates. We also conducted 22 migratory surveys after the breeding season in 2016 at an area in Cape Hatteras National Seashore thought to be used by large numbers of south-bound migrating Piping Plovers. We used integrated Jolly-Seber and binomial count models on resighting and count data to estimate stopover superpopulation and stopover duration of migrating birds based on their breeding region of origin. Annual survival of adults from North Carolina (x ̅ = 0.69, SE = 0.07) was not different from another population on Fire Island, New York (x ̅ = 0.73, SE = 0.04), but the North Carolina population annually had low reproductive success, primarily due to low rates of chick survival. As a result, the North Carolina population was predicted to decline during the study period (λ<1 each year). Historically this population has not met the estimated rate of reproductive output needed for a stationary population (1.07 chicks per pair, SE = 0.69); therefore, it is likely the population is sustained by immigration from an unknown source. Daily (x ̅ = 71.5m/24hr) and hourly (x ̅ = 183.3m/hr) brood movements each had considerable variation (Daily: SD = 70.6, range = 0.0–327.2m; Hourly: SD = 262.3, range = 0.2–1450.9m). Chicks did not appear to move in response to the environmental factors we examined. The rate of brood movement suggests regular daylight monitoring is necessary to adequately protect unfledged broods from anthropogenic disturbance under current management methods. We found that 569 Piping Plovers (95% CI: 502–651), nearly 15% of the estimated Atlantic Coast population, stopped at a single area in Cape Hatteras National Seashore, North Carolina during fall migration. Birds stayed an average 4–7 weeks, depending on the breeding region from which they migrated, and they primarily used a relatively new protected area. These findings suggest that North Carolina is an important area for Piping Plover ecology during multiple stages of their annual cycle. / Master of Science / A federally threatened species, the Piping Plover (Charadrius melodus) lives on sandy beaches along the North American Atlantic Coast. On the coast of North Carolina, Piping Plovers breed in areas with large amounts of recreational and tourism use. To reduce potential negative effects on breeding Piping Plovers from human activities, land managers close areas to pedestrian and vehicle access. However, the plover population there has not appeared to grow as a result of these management strategies, but large numbers of migrant Piping Plovers have capitalized on this management. Recent work that hypothesized population dynamics in North Carolina may function differently than other Piping Plover populations, and this study was designed to test that hypothesis. To understand how disturbance, and attempts to mitigate it, affected plover demography, we studied Piping Plover population dynamics, chick movement, and migration in North Carolina from 2015–2017. We monitored breeding efforts of Piping Plovers and used banding techniques to understand survival of chicks and adults. We observed behavior and movements of Piping Plover chicks before they fledged and gathered information on habitat they selected and potential risks that may alter their behavior. We also conducted migratory surveys after the breeding season at an area thought to be used by large numbers of Piping Plovers. Survival of adult plovers from North Carolina was not substantially different from that of plovers from other areas, but the North Carolina population had low reproductive success caused by low chick survival, and we estimated the population was declining. However, historically this population has not had enough breeding success to maintain itself; therefore, it is likely the population relies on plovers that immigrate to North Carolina from elsewhere. Plover brood movement was variable, and did not move in response to several environmental factors. The rate of brood movements we observed suggest regular daylight monitoring is necessary to adequately protect unfledged broods from anthropogenic disturbance and mortality using current management methods. We found that nearly 15% of Atlantic Coast plovers stopped at a single area in Cape Hatteras National Seashore, North Carolina, during fall migration, staying an average 4–7 weeks. These findings suggest that North Carolina is a unique area to Piping Plover ecology during multiple stages of their annual cycle.

Pinus palustris Miller (longleaf pine), in Virginia, is at the northernmost extent of its range. During presettlement times, this species occurred throughout the Piedmont and Coastal Plain of Virginia in pure and mixed stands, covering 607,000 hectares. This forest type has since been reduced to 81 hectares or 0.01% of its former range. Around 5,000 individual Pinus palustris remain on six sites in the coastal plains. Seacock Swamp and Everwoods are both sites known to have naturally regenerated Pinus palustris native to Virginia occurring in mixed-species stands. At both sites, I measured height and diameter of all Pinus palustris and cored individuals greater than 10 cm in diameter at breast height. A total of 71 trees were cored; the cores were crossdated and measured and crossdating was verified with the COFECHA program. A strong competition signal within the tree ring records at both sites signified the importance of stand dynamics on Pinus palustris in second-growth loblolly pine stands. These results are probably due to the mix of species within these stands and competition from loblolly pine as both the dominant understory and overstory species. Using Black and Abrams (2003) boundary line method, we calculated release and suppression events from the tree-ring record over the last century and found a very dynamic system. During the 1950s and 1960s, Seacock Swamp experienced major and moderate releases (23% moderate release and 18% major release in the 1950s and 33% moderate release and 49% major release in the 1960s) in response to a diameter-limit cut in 1953. Other major and moderate releases varied at both sites and may be attributed to different forest management practices that were in place throughout the last century however locating historical land use records to validate this was not possible at the present. / Master of Science

<p>New and old mosquito-borne diseases have emerged and re-emerged in temperate regions over the recent past, but an understanding of mosquito population dynamics, a fundamental step toward disease control, remains elusive. In particular, we are still lacking reliable predictive models of mosquito abundance in temperate areas due to the subtle links between the fluctuation of mosquito population and highly heterogeneous environmental drivers. Hence, this doctoral dissertation presents an interdisciplinary approach towards an improved understanding and prediction of the fluctuations in mosquito abundance in temperate regions. In the first part of this dissertation a hierarchical Gompertz-based model is used to assess the relative importance of endogenous (density dependence) and exogenous (environmental forcings) controls and their interactions in regulating the dynamics of a West Nile Virus vector (Culex pipiens) in the Po River delta in Italy. The results clearly detect the effects of density-dependence in the observed population dynamics for the mosquito species analyzed and highlight the controls exerted by environmental forcings and habitat conditions. Subsequently, the characteristic scales of temporal variability in mosquito populations, and the representativeness of observations at different sampling resolutions, are investigated using a 10 year daily mosquito sample from Brunswick County, North Carolina. The species present in the sample (among which Aedes vexans and Culiseta melanura are addressed in greater detail, as vectors of East Equine Encephalitis and West Nile Virus) are investigated using a combination of time series analysis, individual based simulations, and density-dependent modeling approaches. Significant population fluctuations with characteristic periodicity between 2 days and several years are found in response to different regulation mechanisms. In particular, the observed fast fluctuations are importantly determined by a varying mosquito activity, rather than by reproduction/mortality processes, driven by rapid changes in meteorological conditions. Finally, in the third part of this study, a state space reconstruction (SSR) approach is used to understand how the predictability of mosquito abundance varies with aggregation time scale and with the prediction horizon, and how much can the prediction of mosquito abundance be improved by using daily observations compared to the commonly used once-per-week samples. The results show that the predictability of mosquito abundance decreases as the time scale of the models increases from one week to one month, while the predictability of per capita growth rate increases together with the modeling scale. It is also shown that the prediction of mosquito per capita growth rate can be improved using daily abundance observations. Furthermore, many mosquito models compare the observed and predicted abundance as a measure of model performance. However, my results suggest that short term forecasts of mosquito abundance may appear to have a significant capability due to the positive autocorrelation between abundance in subsequent time steps, even when the model's ability to predict the abundance change is low. Model capability should thus be evaluated comparing observed and modelled per capita rates of change.</p> / Dissertation

An Allee effect is a density-dependent process that can be responsible for the extinction of small populations. This thesis focuses on the detection of Allee effects, along with other density-dependent processes, and their influence on population synchrony. In chapter 2 I investigate the spatial variation in influential density-dependent processes and density-independent weather factors for the large skipper butterfly Ochlodes sylvanus across its British range. I find both qualitative and quantitative spatial variation in these processes and factors driving population dynamics. In chapter 3, I develop and test a Bayesian methodology, that I then use in chapter 4 to analyse local population level dynamics for 38 British butterfly species. For 35 of these species I found population level Allee effects and also found that phylogeny significant influenced a species’ susceptibility to Allee effects. Finally, in chapter 5 I examine the influence Allee effects have on network population synchrony in a theoretical framework.

Thesis (MSc)--Stellenbosch University, 2011. / ENGLISH ABSTRACT: Age and temperature are two factors that affect mortality in adult tsetse flies. Both are found to be very important, but the simultaneous effect of these factors on the mortality rate have not been studied. This study seeks to address this, with an application to a population of female tsetse, using a model based on partial differential equations. Adult mortality is agedependent and is modelled as the sum of two exponentials, with four parameters (coefficients of each exponential): numerical analysis of a population model with this mortality structure predicts exponential growth. Analysis of each of the parameters through parameter variation shows that two of these parameters control the mortality of the nulliparous (ages 0 − 10 days) flies only while the other two only take care of flies of mature ages. Measurement of the impact of these parameters on the mortality of tsetse of different ages by the normalized forward sensitivity index method is also carried out. This is followed by fitting the model based on the age-dependent mortality along with a constant tsetse birth rate to data representing the catches of female Glossina pallidipes at Rekomitjie Research station, Zimbabwe. Considering a three parameter adult tsetse mortality, parameter analysis shows the effect of one of the parameters to affect the mortality of flies of all ages while a second controls only the mature tsetse flies of reproductive ages. A further analysis resulted in the estimate of these parameters as functions of temperature, thereby leading to the establishment of an age and temperature-dependent adult tsetse mortality. Using data for the daily average temperature records obtained in 1981 on Antelope Island, Lake Kariba, Zimbabwe, daily changes in the pupal duration (adult tsetse birth rate) changes negatively with temperature change. Incorporating this (temperature-dependent ) birth rate into the model, together with the established age and temperature-dependent adult mortality, the adult tsetse population dynamics is explored numerically. The latter model is then fitted to population data of female Glossina morsitans morsitans obtained from the same Island and for the same period as used for the temperature data. The data suggests peak tsetse population to be in the month of July and lowest in the month of December. The first quarter of the year is predicted to be most favorable for breeding tsetse while the second, showed a period of stable growth rate and a time of tsetse abundance. In addition, the dynamics with both age and temperature showed a non-uniform daily population growth contrary to that with age effect only. This study has enhanced our understanding of tsetse population dynamics for age and temperature-dependent adult mortality with temperature-dependent pupal duration and suggests the period of tsetse abundance on Antelope Island. / AFRIKAANSE OPSOMMING: Geen opsomming in Afrikaans.

A new strategy to fight mosquito-borne disease is based on infections of the maternally-transmitted, intracellular bacterium Wolbachia pipientis. Estimates predict that Wolbachia infects nearly half of all insect species, as well as other arthropods and some nematodes. Wolbachia manipulates the reproduction of its host to promote infection, most commonly causing a form of conditional sterility known as cytoplasmic incompatibility. Generally, Wolbachia infections are benign and do not inflict significant costs upon its host. However, studies demonstrate that some infections are associated with substantial costs to its host. These same infections can also induce pathogen interference and decrease vector competency of important disease vectors. Theory predicts that organisms that incur costs relative to conspecifics are less competitive and their competitive exclusion is expected. In the case of Wolbachia, the bacterium can influence reproduction such that phenotypes with lower fitness may still reach fixation in natural populations. In this dissertation, I describe theoretical and empirical experiments that aim to understand the invasion and stability of Wolbachia infections that impose costs on their host. Particular attention is paid to immature insect lifestages, which have been previously marginalized. These results are discussed in relation to ongoing vector control strategies that would use Wolbachia to manipulate vector populations. Specifically, I discuss the cost of novel Wolbachia infections in Aedespolynesiensis, which decreases larval survival and overall fitness relative to wild-type mosquitoes. Then, a theoretical framework was developed to determine the significance of reductions in larval viability in relation to the population replacement disease control strategy. Further theoretical studies determined that Wolbachia infections, once established, resist re-invasion by uninfected individuals despite relatively high costs associated with infection so long as the infection produces reproductive manipulations. Additional studies determined that larvae hatched from old eggs experience reduced survival in mosquito strains with novel Wolbachia infections when compared to the wild-type. To validate the theoretical studies, model predictions were tested empirically to determine the importance of the larval viability. Finally, a COPAS PLUS machine was evaluated and its role in understanding early larval development in mosquitoes is discussed. The importance of integrated research in disease control is highlighted.

Perissodus microlepis is a species of cichlid fish endemic to Lake Tanganyika (Africa). Adult P. microlepis are lepidophages, feeding on the scales of other living fish. As an adaptation for this feeding behavior P. microlepis exhibit lateral asymmetry with respect to jaw morphology: the mouth either opens to the right or left side of the body. Field data illustrate a temporal phenotypic oscillation in the mouth-handedness, and this oscillation is maintained by frequency-dependent selection. To better understand the oscillation, Takahashi and Hori model frequency-dependent selection in P. microlepis using a population genetic model. Their results are intriguing, and the purpose of this dissertation is to improve and extend their model, which fails to account for important biological aspects.We model P. microlepis with a novel approach that fuses the disparate modeling traditions of population genetics and population dynamics; we account for both processes since, in the case of P. microlepis, they occur on the same time scale (a case of microevolution). We construct our models using systems of difference equations. We prove the existence and uniqueness of a positive equilibrium, which corresponds to a 1 : 1 phenotypic ratio. Using a local stability and bifurcation analysis, we show that the equilibrium becomes unstable when frequency-dependent selection is sufficiently strong. We determine necessary and sufficient conditions for onset of oscillation. Local bifurcation analysis indicates key features of the oscillation that may suggest critical experiments.We determine the role of stage structure and the role of strong and weak intraspecific competition. We show that stage-structure is not necessary for, but enhances, oscillatory behavior. Finally we demonstrate the complicated interplay between population dynamic and population genetic processes. Our findings indicate that classical population genetic models can fail to elucidate complex dynamics.