Commercial harvest of fish stocks and their appropriate management requires an understanding of their population dynamics and of their ability to sustain exploitation. Here, some ecological and evolutionary consequences of excessive exploitation are examined. In Chapter 2 I evaluate the knowledge base and status of commercially exploited marine populations that undergo formal stock assessment. Despite a bias towards industrialised countries and stocks of commercial importance, I show the pervasiveness of overexploitation and, by using reference points of stock status, identify important regional differences in the effectiveness of fisheries management. In Chapter 3 I develop a data format suitable for ecological analyses to best disseminate the valuable information contained in scientific trawl surveys. This data format is suitable for inclusion into the public Ocean Biogeographic Information System (OBIS) and provides detailed observations that are suitable to the reconstruction of important fisheries-independent stock indices. In Chapter 4 I examine the spatiotemporal dynamics of groundfish populations. A positive abundance-occupancy relationship was estimated for the majority of groundfish populations examined suggesting that this well-described terrestrial pattern is also pervasive in the marine environment. Spatial hysteresis was exhibited by numerous populations, indicating that the spatial distribution of individuals failed to recover despite recoveries in abundance. In Chapter 5 I estimate the demographic consequences of changes in growth and maturation characteristics. The ability of a population to sustain harvest, and its ability to recover from previous depletions can be overestimated because of trends towards earlier maturation and slower growth. In Chapter 6 I conclude the thesis by discussing the implications of my research to fisheries science and management. I argue that trends in the spatial distribution and the overall productivity of populations must be accounted for when determining sustainable fishing levels and when predicting recovery trajectories under various catch abatement scenarios. While successful management measures have been implemented in a number of marine ecosystems, this thesis highlights the importance of improving our capacity to understand the dynamics of exploited populations and to fully use the wealth of available monitoring and assessment data.

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Understanding whether groups of individuals represent a single panmictic gene pool, or multiple genetically structured populations across a species range should aid in predicting whether specific conservation strategies would be more or less effective for species preservation. Further, contrasting the population structures of multiple coexisting taxa could foster an even deeper understanding of evolutionary divergence among demes and potentially even suggest local adaptation in the form of tight coevolutionary relationships. Finally, the analysis of population dynamics within small and isolated populations could improve our understanding of the relative importance that different evolutionary mechanisms have in predicting population persistence in the wild. Using microsatellite markers I characterized the population genetic structure in the critically endangered Cyclura cychlura cychlura iguanas on Andros Island. I found significant differences between inferred and realized rates of gene flow. This finding demonstrates that evolutionarily independent populations can occur even with high rates of dispersal. In the second and third study I contrasted patterns of genetic variability in Cyclura cychlura cychlura iguanas, ticks in the genus Amblyomma parasitizing these iguanas, and Rickettsia spp., potential pathogens transmitted by these ticks. I determined that genetic differences among Rickettsia samples and Amblyomma samples are highly concordant with genetic divergence among iguana populations. This finding suggests largely vertical dispersal of ticks and their super-parasite, a high specificity of this reptile-tick interaction, and historically low rates of dispersal in iguanas. This finding also indicates that island populations of iguanas may be locally adapted due to tight coevolutionary relationships. Finally, I investigated the mechanisms that eliminate harmful mutations in small isolated and natural populations of the critically endangered Cyclura cychlura cychlura iguanas. Using molecular tools I found indirect evidence suggesting that small natural populations can maintain significant levels of genetic variation in spite of strong selection acting against harmful mutations. Under regimes of random mating, the buildup of harmful mutations in small populations may result in a large number of inviable young. However, harmful mutations may also be eliminated when exposed to natural selection through increased competition, as population density increases. However, quantification of the relative role of competition was not feasible in this study.

Multisystem length limits are a popular output control implemented to regulate harvest of many gamefishes. Evaluating the direct effects of length limits is crucial in selecting a regulation, but to my knowledge, no formal methodology exists to model length limits for multiple systems. Without a formalized process, complexities associated with multisystem scales of management can preclude effective communication and interpretation of information. I created a quantitative decision model as an approach for comparing length limits applied to multiple systems. This approach combined an extension of the Beverton-Holt yield-per-recruit function and an additive utility function to compare multisystem length limits. I also conducted a sensitivity analyses to clarify the effect of input parameters and uncertainty on the expected utility, and on performance metrics. This approach provides a consistent methodology for evaluating multisystem length limits, and as a decision support tool, can improve transparency of the length-limit-selection process.

The lower airways of patients with chronic airway diseases including cystic fibrosis (CF) are colonized by diverse communities of microorganisms. Over-time the airways of some 60% of CF patients become permanently colonized and dominated by Pseudomonas aeruginosa. Chronic infection of P. aeruginosa has been associated with a decline in pulmonary function, worse prognosis, and eventual patient mortality. Although P. aeruginosa evolves within the CF airways resulting in complex populations, the mechanism by which these complex populations contribute to disease progression is not well understood. Here we show diversity among isolates by observed changes in genome sequences of a strain of P. aeruginosa, known as Prairie Epidemic Strain (PES). Using whole genome sequencing and comparative genomics we identified a large core genome across 195 PES isolates from 57 CF patients of the Calgary Adult Cystic Fibrosis Clinic (CACFC) where 88% of the pangenome was categorized as core genes. Single nucleotide polymorphism (SNPs) mutations were shown to be the largest contributor of diversity at the nucleotide level compared to other polymorphism types consisting of 87% of the total polymorphisms present across the 195 PES isolates. CRISPR arrays and mobile elements such as prophage and plasmids demonstrate this strain of P. aeruginosa was stable over 30 years. In a second aim, I show variation in the populations of P. aeruginosa across an exacerbation event further highlighting the complexity of the lung bacterial community. Distinct populations of P. aeruginosa at the onset and resolution of an exacerbation within a single CF patient were identified by SNPs. These results a model where adaptive radiation as well as natural mutations contribute to the heterogeneity and diversification within populations of P. aeruginosa in CF patients. Understanding the evolution and population structure of PES through the identification of important genes and mutations through the clinical course of an exacerbation can aid in identifying new targets for patient treatment of P. aeruginosa in CF. / Thesis / Master of Science (MSc) / Cystic fibrosis is a life-threatening disease characterized by cycles of stability and respiratory illness. Bacterial species within the lungs of these patients are the main contributor to disease progression. I investigated a specific transmissible epidemic strain, Pseudomonas aeruginosa Prairie Epidemic Strain, using a unique collection of samples provided by collaborators at the adult cystic fibrosis clinic in Calgary. Using these samples, I first explored the differences between patients over a period of 34 years. I hypothesized that similar changes in genome sequences will be observed in multiple patients with a possible commonality in disease progression. Second, I explored the role this bacterial pathogen may play in cycles of respiratory illness. I hypothesize that a specific bacterial subpopulation could initiate these cycles and be identified by changes at the genome level. This research provides further knowledge of an epidemic strain of cystic fibrosis.

In the early 1990's, a series of habitat changes caused by storms and subsequent beach management by the U.S. Army Corps of Engineers (USACE, The Corps) provided a unique opportunity to study piping plover population dynamics in a changing environment. In this study, 1993-2004, we attempt to determine the factors that limit or influence the abundance and distribution of piping plovers in West Hampton Dunes (WHD), Long Island, NY, a renourished, highly developed, and high human disturbance area. The piping plover population on Westhampton Island increased after the hurricane of 1938, and declined thereafter. The decline co-occurred with beach development and vegetative succession. After storms in the winter of 1992-1993 breached the island at West Hampton Dunes, piping plovers re-colonized the area. The New York District USACE filled the breach in 1993, and renourished the beach in 1996 and 2000-2001. USACE renourished parts of the groinfield in Westhampton Beach in 1997. Each spring and summer, we monitored plovers intensively at WHD and part of the adjacent town of Westhampton Beach (The Reference Area) 1993-2004. We located nests and estimated reproductive and nest and chick survival rates. We monitored plover management efforts and determined causes of nest loss when possible. We monitored piping plover behaviors and obtained an index to plover food supply. We estimated area of plover habitats and defined areas unsuitable for piping plover nesting. We also obtained indices to human and predator presence on the beach. The WHD piping plover population increased from 0 pairs in 1992 to 39 in 2000 then decreased to 18 pairs in 2004. This decline was closely associated with changes in potential nesting habitat which increased from 22.4 ha in 1992 to 50.1 ha in 2000 then declined to 31.1 ha in 2004 The primary process regulating the WHD population appears to be density dependent immigration and emigration. No other vital rates (clutch size, renest rate, fertility, egg survival, nest survival, chick survival, brood survival, chicks fledged/pair) were correlated with density. The higher equilibrium density at WHD (~1 pair/ha) than at The Reference Area (~0.4 pair/ha) appeared to be a function of the large bay intertidal flats at WHD. The most common nest predators, cats (WHD = 13% of known predated nests), American Crows (17% of known predated nests) and foxes (37% of known predated nests), are newcomers to piping plover habitats. Thus, plovers may be especially vulnerable to them. Predator removal from the study area appeared to improve nest success and chick survival (R2 = 0.79). Predator exclosures at nests reduced nest loss (WHD = 34% exclosed nests lost vs. 43% of unexclosed nests lost, though in one year, one or more foxes learned to exploit plovers in exclosures (22% of all exclosed nests were predated by foxes in 1995). This study highlights the long suspected piping plover paradox: increasing beach width can temporarily raise the carrying capacity of an area, but preventing overwash can reduce or eliminate the natural formation of the bay side foraging flats that increase piping plover density, and sometimes, survival. Moreover, beach stabilization allows human development of the habitat which also reduces the carrying capacity of the environment for piping plovers, increases human/plover interactions, and attracts potential predators. / Ph. D.

In this work, we present our investigations into two different systems, both far from equilibrium. We first present the relaxation and ordering processes in magnetic skyrmion systems. This is followed by a study of the behavior of many species interacting on a spatially heterogeneous lattice. Magnetic skyrmions have been a subject of great interest in recent years. They have been proposed to be at the heart of next-generation computing and information storage devices. One interesting feature of magnetic skyrmions is the presence of the non-dissipative Magnus force. The Magnus force causes the skyrmions to be deflected from their direction of motion. In this work, we examine the effect the strength of this Magnus force has on the late-time ordering behavior of magnetic skyrmions. We show that the late-time ordering also shows enhanced relaxation with an increase in the Magnus force. We also studied the behavior of magnetic skyrmions when confined to a narrow channel. We show that, like before, the Magnus force helps the system order faster while experiencing a constant drive. Interestingly, when the drive was periodic, the Magnus force inhibited the relaxation in the system. Interacting populations have been a topic of scientific interest since the late eighteenth century. We studied the effect of spatial heterogeneity on a two-dimensional lattice. Using cyclic predator-prey interaction schemes, we numerically simulated the effect of asymmetric predation rates inside "habitats." We show that, due to the non-linearity of the system, the species that had a chance to escape predation did not see the largest benefit from this change. Instead, the predator of this prey saw the largest benefit from this change. The material on skyrmion systems is based upon work supported by the U.S. Department of Energy, Office of Science, Office of Basic Energy Sciences, Division of Materials Science and Engineering under Award Number DE-SC0002308. The population dynamics research was sponsored by the Army Research Office and was accomplished under Grant No. W911NF17-1-0156. / Doctor of Philosophy / In this work, we present our investigations into two different systems. Both of these systems are considered to be not in equilibrium. We first present is the behavior of magnetic skyrmions as the system settles into an arranged state. This is followed by a study of the behavior of multiple species interacting on a lattice where different parts of the lattice have different rules of interaction. Magnetic skyrmions are small defects that occur in specific types of magnetic materials. They have been proposed to be useful in next-generation computing devices. Similar to a curve-ball in baseball, but due to a different physical phenomenon, magnetic skyrmions follow curved paths when pushed. This effect, known as a Magnus force, causes the magnetic skyrmions to settle faster into a position relative to the other magnetic skyrmions in the system. We show that this effect also occurs when the magnetic skyrmions are being pushed through a narrow channel. If the push is periodically started and stopped, the Magnus force instead slows down the ability for magnetic skyrmions to settle into a position relative to the other magnetic skyrmions. Interacting populations have been a topic of scientific interest since the late eighteenth century. We studied the effect of changing the rules of species interaction based on where on a two-dimensional lattice the interaction occurred. Using cyclic predator-prey interaction schemes, we numerically simulated the effect of asymmetric predation rates inside "habitats." We showed that, due to the complex interaction scheme present in the system, the species that had a chance to escape predation did not see the largest benefit from this change. Instead, the predator of this prey saw the largest benefit from this change. The material on skyrmion systems is based upon work supported by the U.S. Department of Energy, Office of Science, Office of Basic Energy Sciences, Division of Materials Science and Engineering under Award Number DE-SC0002308. The population dynamics research was sponsored by the Army Research Office and was accomplished under Grant No. W911NF17-1-0156.

The mean field analysis of stochastic dynamical system allows us to gain insight into the qualitative features of their complex behavior, as well as quantitative estimates of certain aspects of their coarse-grained properties. As such, it usually furnishes a first front in approaching new dynamical systems and informs us about their stability landscape in the absence of fluctuations among other things. A knowledge of this landscape can be a valuable tool in model building for describing real world systems and provides a guiding principle for a justifiable choice of form and model parameters. In this work, we contribute to this analysis for two generic classes of high-dimensional models that possess a cyclic symmetry in the network that specifies their stochastic dynamics at the microscopic level. Our analysis is carried out in a manner that can be readily adapted for the mean field analysis of further generalized models that possess this symmetry. Moreover, in the second class of these models, we propose a new basic process that can change the stability landscape of an existing model and, as such, endow us with potential alternatives to model systems with robust biodiverse regimes. / Ph. D.

Loggerhead sea turtles (Caretta caretta) are listed as threatened under the Endangered Species Act and are protected both on nesting beaches and in United States waters. Loggerhead sea turtles are long-lived species and are most easily studied on the beaches during the nesting season. Bald Head Island, North Carolina has one of the highest density nesting beaches of loggerhead sea turtles in the turtle's northern range on the East Coast of the United States. Key life history parameters were estimated and applied to a population model using 16 years of data from a mark-recapture study on the loggerhead sea turtle nesting population on Bald Head Island, North Carolina. The beach survey conducted on the island only allowed for the capture of adult female sea turtles during the breeding state even though females may spend multiple years in the unobservable non-breeding state. The majority of females captured over the last 16 years have never been recaptured at the original capture site. These transients in the data coupled with unobservable states violate the assumption of equal catchability in the available single state mark-recapture models. Therefore, a multistate mark- recapture model originally developed for leatherback sea turtles was applied to the Bald Head Island loggerhead population. Multistate modeling provides a new technique to estimate sea turtle demographic parameters in which all model assumptions can be met. The multistate model outputs female survival rates, capture probability, and transition probabilities between breeding and non-breeding states. A correction factor for trap-dependence and transients was included given that both factors tested significant in the global model goodness-of-fit tests. The estimates of annual adult survival rate and breeding transitions were then used to project population size for the northern subpopulation. For the first time, estimation error around estimates of benthic juvenile and adult survival rates was included in a loggerhead sea turtle model. I explored the effects of estimation error, three levels of clutch frequency, and larger TED openings on population growth rate and on the probability of reaching a nesting recovery threshold. The nesting recovery threshold was based upon recovery criteria from the Federal Recovery Plan and set as the probability of reaching 12,800 nests/season in the states of North Carolina, South Carolina, and Georgia within a 50 year time period. The results of this study provide important information to guide future management and research. / Master of Science

In a stochastic Lotka-Volterra model on a two-dimensional square lattice with periodic boundary conditions and subject to occupation restrictions, there exists an extinction threshold for the predator population that separates a stable active two-species coexistence phase from an inactive state wherein only prey survive. When investigating the non-equilibrium relaxation of the predator density in the vicinity of the phase transition point, we observe critical slowing-down and algebraic decay of the predator density at the extinction critical point. The numerically determined critical exponents are in accord with the established values of the directed percolation universality class. Following a sudden predation rate change to its critical value, one finds critical aging for the predator density autocorrelation function that is also governed by universal scaling exponents. This aging scaling signature of the active-to-absorbing state phase transition emerges at significantly earlier times than the stationary critical power laws, and could thus serve as an advanced indicator of the (predator) population's proximity to its extinction threshold. In order to study boundary effects, we split the system into two patches: Upon setting the predation rates at two distinct values, one half of the system resides in an absorbing state where only the prey survives, while the other half attains a stable coexistence state wherein both species remain active. At the domain boundary, we observe a marked enhancement of the predator population density, the minimum value of the correlation length, and the maximum attenuation rate. Boundary effects become less prominent as the system is successively divided into subdomains in a checkerboard pattern, with two different reaction rates assigned to neighboring patches. We furthermore add another predator species into the system with the purpose of studying possible origins of biodiversity. Predators are characterized with individual predation efficiencies and death rates, to which "Darwinian" evolutionary adaptation is introduced. We find that direct competition between predator species and character displacement together play an important role in yielding stable communities. We develop another variant of the lattice predator-prey model to help understand the killer- prey relationship of two different types of E. coli in a biological experiment, wherein the prey colonies disperse all over the plate while the killer cell population resides at the center, and a "kill zone" of prey forms immediately surrounding the killer, beyond which the prey population gradually increases outward. / Ph. D. / We utilize Monte-Carlo simulations to study population dynamics of Lotka–Volterra model and its variants. Our research topics include the non-equilibrium phase transition from a predator-prey coexistence state to an absorbing state wherein only prey survive, boundary effects in a spatially inhomogeneous system, the stabilization of a three species system with direct competition and “Darwinian” evolutionary adaption introduced, and the formation of spatial patterns in a biological experiment of two killer and prey E. coli species.