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

Freshwater mussels have played an important role in the history of human culture and also in ecosystem functioning. But during the past several decades, the abundance and diversity of mussel species has declined all over the world. To address the urgent need to maintain and restore populations of endangered freshwater mussels, quantitative population dynamics modeling is needed to evaluate population status and guide the management of endangered freshwater mussels. One endangered mussel species, the oyster mussel (Epioblasma capsaeformis), was selected to study its population dynamics for my research. The analysis was based on two datasets, length frequency data from annual surveys conducted at three sites in Clinch River: Wallen Bend (Clinch River Mile 192) from 2004-2010, Frost Ford (CRM 182) from 2005 to 2010 and Swan Island (CRM 172) from 2005 to 2010, and age-length data based on shell thin-sections. Three hypothetical scenarios were assumed in model estimations: (1) constant natural mortality; (2) one constant natural mortality rate for young mussels and another one for adult mussels; (3) age-specific natural mortality. A Bayesian approach was used to analyze the age-structured models and a Bayesian model averaging approach was applied to average the results by weighting each model using the deviance information criterion (DIC). A risk assessment was conducted to evaluate alternative restoration strategies for E. capsaeformis. The results indicated that releasing adult mussels was the quickest way to increase mussel population size and increasing survival and fertility of young mussels was a suitable way to restore mussel populations in the long term. The population of E. capsaeformis at Frost Ford had a lower risk of decline compared with the populations at Wallen Bend and Swan Island. Passive integrated transponder (PIT) tags were applied in my fieldwork to monitor the translocation efficiency of E. capsaeformis and Actinonaias pectorosa at Cleveland Islands (CRM 270.8). Hierarchical Bayesian models were developed to address the individual variability and sex-related differences in growth. In model selection, the model considering individual variability and sex-related differences (if a species has sexual dimorphism) yielded the lowest DIC value. The results from the best model showed that the mean asymptotic length and mean growth rate of female E. capsaeformis were 45.34 mm and 0.279, which were higher than values estimated for males (42.09 mm and 0.216). The mean asymptotic length and mean growth rate for A. pectorosa were 104.2 mm and 0.063, respectively. To test for the existence of individual and sex-related variability in survival and recapture rates, Bayesian models were developed to address the variability in the analysis of the mark-recapture data of E. capsaeformis and A. pectorosa. DIC was used to compare different models. The median survival rates of male E. capsaeformis, female E. capsaeformis and A. pectorosa were high (>87%, >74% and >91%), indicating that the habitat at Cleveland Islands was suitable for these two mussel species within this survey duration. In addition, the median recapture rates for E. capsaeformis and A. pectorosa were >93% and >96%, indicating that the PIT tag technique provided an efficient monitoring approach. According to model comparison results, the non-hierarchical model or the model with sex--related differences (if a species is sexually dimorphic) in survival rate was suggested for analyzing mark-recapture data when sample sizes are small. / Master of Science

We study game theoretic ecological models with cyclic competition in the case where the strategies can be mixed or pure. For both projects, reported in [49] and [50], we employ Monte Carlo simulations to study finite systems. In chapter 3 the results of a previously published paper [49] are presented and expanded upon, where we study the extinction time of four cyclically competing species on different lattice structures using Lotka-Volterra dynamics. We find that the extinction time of a well mixed system goes linearly with respect to the system size and that the probability distribution approximately takes the shape of a shifted exponential. However, this is not true for when spatial structure is added to the model. In that case we find that instead the probability distribution takes on a non-trivial shape with two characteristic slopes and that the mean goes as a power law with an exponent greater than one. This is attributed to neutral species pairs, species who do not interact, forming domains and coarsening. In chapter 4 the results of [50] are reported and expanded, where we allow agents to choose cyclically competing strategies out of a distribution. We first study the case of three strategies and find through both simulation and mean field equations that the probability distributions of the agents synchronize and oscillate with time in the limit where the agents probability distributions can be approximated as continuous. However, when we simulate the system on a one-dimensional lattice and the probability distributions are small and discretized, it is found that there is a drastic transition in stability, where the average extinction time of a strategy goes from being a power law with respect to system size to an exponential. This transition can also be observed in space time images with the emergence of tile patterns. We also look into the case of four cyclically competing strategies and find results similar to that of [49], such as the coarsening of neutral domains. However, the transition from power law to exponential for the average extinction time seen for three strategies is not observed, but we do find a transition from one power law to another with a different slope. This work was supported by the United States National Science Foundation through grants DMR-0904999 and DMR-1205309. / Ph. D.

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

Blueline Tilefish is a deepwater species that is found along the United States Atlantic coast and in the Gulf of Mexico. Fisheries for the species have developed in the past five decades, and large increases in landings from the mid-2000s to 2010s have raised management interest. During the most recent stock assessment, age reading difficulties found in the past persisted, and preferred age-structured models were not used. Additionally, maturity was estimated from a meta-analysis of other species with similar life histories. Research recommendations from independent peer reviewers thus included improving age determination as well as collection of small fish. We collaborated with charter fishermen to target small (< 400 mm total length [TL]) blueline tilefish. We also collaborated with scientists at South Carolina Department of Natural Resources (SCNDR) on histological reproductive phase coding and ageing of Blueline Tilefish otoliths. We optimized the information incorporated into sex ratio, reproduction, and growth analyses by merging datasets with SCDNR and Old Dominion University (ODU), and assessed first maturity to the increase immature sample size. Overall sex ratios exhibited a female bias, displaying statistically significant deviations from the expected 1:1 ratio in both the Southeast United States Atlantic (SEUS) and United States Mid-Atlantic (USMA) regions. All immature individuals collected measured below 400 mm. Our findings aligned with previously documented spawning seasons, which extend from April to October in the SEUS and from May to November in the USMA, and may extend to November in the SEUS. The spawning peak identified for the SEUS concurred with previous studies, and suggested October as a spawning peak in the USMA—later than previously described. Sex-specific gonadosomatic index analyses indicated no significant differences between regions. Age determination remained challenging, but the level of agreement in age estimates between the VT consensus and SCDNR readings resembled the highest value from previous studies. Evaluation based on AIC and BIC scores of weight-length relationships indicated potential regional differences and sexual dimorphism within both the SEUS and USMA regions. This sexual dimorphism was further supported by von Bertalanffy growth estimates, revealing L_∞ values of 574.7 and 630.1 mm TL and values of 0.22 and 0.24 for females and males, respectively. Analysis of AIC and BIC indicated sexual dimorphic growth. Length and age at 50% maturity estimates ranged from 283 to 357 mm TL and a few months to 3.7 years, respectively. Length at maturity models also indicated that most fish are mature around 400 to 500 mm, highlighting the importance of targeting smaller individuals to increase the sample size of immature fish. Differences in AIC and BIC scores for length and age at maturity models of three maturity scenarios were low (AIC and BIC < 2). We recommend continued investigation into blueline tilefish age determination, as well as targeted efforts to collect more immature blueline tilefish. Additionally, we propose the use of first maturity and data weighting for maturity estimation of this species. / Master of Science / Blueline tilefish, a deepwater species found in the US Atlantic and Gulf of Mexico, has become an increasing concern for fisheries managers due to rising catches in the mid-2000s to early 2010s. In our study, we aimed to better understand this species to support sustainable management as there are uncertainties in some biological characteristics, like early growth and maturity. To this end, we teamed up with charter fishermen and scientists at South Carolina Department of Natural Resources and Old Dominion University to collect small blueline tilefish and learn more about their reproduction and growth. We discovered that the species' sex ratios favor females, deviating significantly from the expected 1:1 ratio in both the Southeast United States Atlantic (SEUS) and United States Mid-Atlantic (USMA) regions. Our research agreed with spawning seasons found in previous studies, which occur from April to October in the SEUS and from May to November in the USMA. It also may suggest that SEUS Blueline Tilefish still spawn in November. We also delved into age determination, a challenging aspect of fisheries science. While it remains a complex task, our agreement rates in age estimates were similar to the highest documented values. Our studies also suggested potential regional differences and sex differences in blueline tilefish growth. Additionally, we estimated that blueline tilefish mature at around 283 to 357 mm in total length and a few months to 3.6 years. We recommend further research into age determination and the collection of more young, small blueline tilefish. Overall, our studies shed light on the unique characteristics of blueline tilefish and highlights the need for continued research to better manage this species.

学位プログラム名: 京都大学大学院思修館 / 京都大学 / 新制・課程博士 / 博士(総合学術) / 甲第25458号 / 総総博第34号 / 新制||総総||6(附属図書館) / 京都大学大学院総合生存学館総合生存学専攻 / (主査)准教授 趙 亮, 教授 山敷 庸亮, 准教授 SCHMOECKERJan-Dirk / 学位規則第4条第1項該当 / Doctor of Philosophy / Kyoto University / DFAM

<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.