A critical examination of Popper’s falsificationism as a methodological criterion of demarcation led to the development o f a supplementary means of distinguishing science from pseudo- science The discipline is made the unit of appraisal and its pattern o f historical development b used as the indicator of demarcation. Results of a test of this indicator against astrology and physical optics accord with our basic judgm ents of these disciplines. The indicator effectively reveals that scientific creationism is pseudo-science, and that evolutionary biology is genuine science. Three fundam ental approaches to scientific investigation, viz. v erificationism , falsificationism and m ulti-cornered testing (M CT) are contrasted. MCT is distinguished by competition between hypotheses, which makes it more informative than at least the naive versions of the other two approaches. While competition does not produce immediate victors, it does make demands on theories, which can be augmented by prescribing a series of independent tests. The comparative method implies the existence of two types of evidence. Common evidence is that which io predicted or explained by two or more rival hypotheses. Discriminatory evidence favours one rival over the others. It is argued that in both the fields of species biology and speciation there have been instances o f over-relying on common evidence, o f indistinctly defining alternative hypotheses, of ro t following their logical consequences and of not using exisiing discriminatory evidence to adjudicate between these hypotheses. Species concepts and definitions of modes o f speciation are evaluated. Normative principles are suggested for defining species and other important terms in evolutionary biology, and for testing species concepts and modes of speciation. The advantages and limitations o f a historical indicator of demarcation and the merits and principles of the comparative approach to method are discussed and illustrated using the analoev of a mathematical game. Scientific crcanomsni is shown to have a coating of scientific method, but to have systematically violated fundamental methodological principles. D arn in ’* method in contrast, had a comparative structure, and distinguished between common *nd discriminatory evidence. While there are methodological problems sn evolutionary biology, these are shown to be minor in comparison to that four*! in to c n o fk ciratxxiiun.

The first of five chapters describe the study area and study species, including a short description about the impetus for this research. The second chapter describes a unique hydrologic model for application in tidal ecosystems. The second chapter represents new information on the effects of various abiotic and biotic factors on foraging wading birds in this highly dynamic environment. The third chapter identifies important factors affecting the abundance of foraging wading birds in intertidal environments. The fourth chapter presents a study of the foraging habitat preferences of two wading bird species in intertidal environments. The fifth chapter describes a conceptual model of wading bird foraging ecology and a predictive model of foraging habitat in intertidal zones. The conceptual model captures the major drivers and linkages between the abiotic and biotic variables thought to affect wading bird foraging abundance in intertidal habitats. The conceptual model also identifies major knowledge gaps in our understanding of foraging ecology of wading birds in coastal intertidal areas. The predictive model of foraging habitat is meant to be used by resource managers, but its framework may be useful for ecological studies in general. The final and sixth chapter provides a summary of all the major findings. Each chapter has been written so as to be independent of the other chapters. As such, a full background, along with a discussion of the relevance of the chapter's findings is provided for each chapter. / Includes bibliography. / Thesis (M.S.)--Florida Atlantic University, 2014. / FAU Electronic Theses and Dissertations Collection

Nesta tese investigamos modelos irreversíveis dentro do contexto da mecânica estatística de não-equilíbrio motivados por alguns problemas de dinâmicas de populações biológicas. Procuramos identificar a existência de transições de fase e as classes de universalidade às quais os modelos pertencem. Além disso, buscamos modelos que capturem as principais características dos sistemas biológicos que procuramos descrever. Encontramos a solução analítica exata para o modelo suscetível-infectado-recuperado (SIR) em uma rede unidimensional. Investigamos o modelo suscetível-infectado-recuperado com infecção recorrente. Mostramos que o modelo pertence à classe de universalidade da percolação isotrópica, salvo pelos parâmetros em que se torna o processo de contato. Obtivemos também a linha de transição entre as fases em que há e não há propagação da epidemia, através de aproximações de campo médio e por simulações de Monte Carlo do modelo na rede quadrada. Investigamos uma dinâmica para duas espécies biológicas e dois nichos ecológicos; para tanto introduzimos um modelo estocástico irreversível de quatro estados. Concluímos que o modelo oferece uma descrição para as oscilações temporais das populações das espécies e para a alternância de dominância entre estas. Para chegar a esta conclusão, utilizamos simulações de Monte Carlo do modelo na rede quadrada, aproximações de campo médio e a abordagem da equação mestra de nascimento e morte, a qual, para grandes populações, pode ser aproximada por uma equação de Fokker-Planck que é associada a um conjunto de equações de Langevin. Por fim, usando simulações de Monte Carlo, analisamos a dinâmica de duas espécies biológicas e dois nichos ecológicos incluindo difusão. Novamente verificamos que o modelo gera cenários com oscilações temporais das populações das espécies e alternância de dominância entre estas. Ademais, concluímos que modelo pertence à classe de universalidade da percolação direcionada e obtivemos o diagrama de fase. / In this thesis we investigate irreversible models within the context of nonequilibrium statistical mechanics motivated by some problems of biological population dynamics. We look for dentifying the existence of phase transition and the universality classes to which the models belong. In addition to that, we look for models that capture the main characteristics of the biological systems which we are interested in describing. We found the exact analytic solution of the susceptible-infected-recovered (SIR) model on one-dimensional lattice. We investigated the susceptible-infected-recovered model with recurrent infection. We showed that the model belongs to the isotropic percolation universality class, except for the parameters that make the model become a contact process. We obtained the transition line between the phases in which there is propagation of the epidemic and in which there is not, by means of mean-field approximations and Monte Carlo simulations on a square lattice. Furthermore, we investigated a dynamic for two biological species and ecological niches; for this purpose we introduced an irreversible stochastic model with four states. We conclude that the modoffers a description of time oscillations of the species populations and of the alternating dominance between them. To achieve this conclusion we used Monte Carlo simulations of this model on a square lattice, mean-field approximation, and the birth and death master equation approach, which for large populations can be approximated by a Fokker-Planck equation that is associated to a set of Langevin equations. Finally, using Monte Carlo simulations, we analyzed a dynamic for two biological species and ecological niches including diffusion. Again, we verified that the model generates scenarios with time oscillations of the species populations and with alternating dominance between them. Also, we conclude that the model belongs to the directed percolation universality class and we found the phase diagram.

Made available in DSpace on 2015-03-04T18:57:50Z (GMT). No. of bitstreams: 1 TESE_PORTUGUES_PEDRO_UFF.pdf: 2590907 bytes, checksum: 3b3623c02d38f036f56c8496b6542010 (MD5) Previous issue date: 2011-10-13 / Embora a compreensão dos fenômenos em nível molecular avance rapidamente, pouco se sabe ainda sobre os mecanismos que regulam a estabilidade e resiliência de ecossistemas tais quais, corais, florestas, lagos e oceanos. Modelos de dinâmica populacional são um possível meio para aperfeiçoar o entendimento dos mecanismos subjacentes a esses fenômenos. Estes modelos podem apresentar múltiplos estados de equilíbrio em virtude de características intrínsecas às espécies, bem como em decorrência de perturbações exógenas, como captura, remoção, aporte alóctone de nutrientes, dentre outros. A possibilidade de reversão entre esses estados de equilíbrio é geralmente ditada pela ocorrência da histerese em função da magnitude das perturbações exógenas. Neste trabalho analisam-se a estabilidade, resiliência e histerese em um conjunto de modelos populacionais sob o enfoque de manejo de ecossistemas.

Lyme borreliosis (LB) is the most frequent vectorborne disease in the Northern Hemisphere. It is a complex bacterial zoonosis involving vertebrate hosts and hard ticks of the genus Ixodes. The causative agents, bacteria of the LB group of spirochaetes, form a species complex comprising 17 named species. As is the case for most microbial pathogens, epidemiological and ecological studies require appropriate genotyping. Although the use of single loci may provide rapid results, there are serious disadvantages, in particular when inferring evolutionary relationships or geographic population structure. A novel multilocus sequence analysis (MLSA) system of the LB group spirochaetes has been developed based on housekeeping genes to overcome these problems. Here, the system is optimized and tested using extracted spirochaetal DNA directly from ticks and then utilized to obtain insights into the migration and spread of individual species as well as to investigate the evolutionary origins of the species complex. Species belonging to the LB group of spirochetes display different patterns and levels of host specialisation which makes this an ideal system to study the impact of host associations on spread of zoonotic tickborne diseases. For example, Borrelia valaisiana and B. garinii are transmitted exclusively by birds while B. afzelii is transmitted by rodents. I demonstrate that the migration of the LB species is dependent on, and limited by, the migration of their respective hosts. I also show the presence of B. afzelii strains in England and, through the use of the MLSA scheme, demonstrate that the strains are highly structured. A close evolutionary relationship between B. afzelii and its rodent host species is shown. Furthermore, through phylogenetic analyses, some evidence of a coevolutionary relationship between the LB group species and their major group of vector species, the Ixodes persulcatus species complex, is presented and a Eurasian origin for the species group is suggested.

The upland (Pseudacris feriarum) and midland (P. triseriata) chorus frogs are closely related cryptic species that are best distinguished genetically. The distribution of these species within the Commonwealth of Kentucky has previously been defined by only a handful of genetic samples, making delineation of range limits for each species difficult. Accurate understanding of species distributions, and the genetic structure within them, are vitally important for conservation management of amphibian species. In this study, I have collected genetic samples from across the putative ranges of P. triseriata and P. feriarum in Kentucky and used next-generation sequencing technology to generate more fine-scale estimates of species ranges. The genetic data generated in this study support the delineation of two species in Kentucky, and the species assignments of all individuals and populations are in general concordance with the previously hypothesized species distributions. However, I have identified two previously unrecognized contact zones for these species and revealed areas of hybridization. By delineating species distributions and identifying potentially important regions of genetic admixture, this study will be informative to future conservation management and conservation genetic research of chorus frogs in Kentucky.

Investigating how and why individuals interact is an important component to understanding species ecology. The type and patterning of relationships (social structure) provides pertinent insight into how ecological factors such as spatial heterogeneity of resources and predation influence associations between individuals. Many taxa exhibit temporally fluid association patterns, where individuals associate with a variety of others at different rates. Ungulate species exhibit prime examples of highly fluid grouping patterns and individuals form both temporary and long-term associations. The effects of human disturbance on ungulate behavior are well documented and these changes are further exacerbated during the hunting season. Species such as elk (Cervus canadensis) are highly managed having subsistence, recreational, and economic value. The demographic effects of selective take or harvest regimes on population dynamics are known, but how human disturbance, including hunting, influences ungulate social structure on a fine-scale has not been explored. I aimed to investigate the relationship between human disturbance and social structure in a population of elk residing in southeastern, Kentucky, USA. I choose to focus on female elk given the importance of adult female survival to population dynamics and previous knowledge of some social affinity between females. I begin by discussing factors that influence ungulate sociality, how human disturbance can influence sociality and how a better understanding of association patterns could aid in management decisions. I then present two distinct yet vital studies to understanding this relationship: (1) investigation of survival of elk in Kentucky and (2) investigation of association patterns in a human dominated landscape. Hunter harvest is the primary cause of elk mortality in both eastern and western populations in North America and 85.2% of all elk mortalities in Kentucky were hunter harvest related. Older (> 5) males and younger (< 2) females had significantly higher hazards of dying relative to other age classes. Moreover, the establishment of a limited entry hunting area to prevent local overharvest of males had no effect on male survival, but instead may have resulted in local overharvest of females at one site residing on publicly accessible land. Female elk exhibit both weak and strong association patterns. I found that relatedness was significantly greater within sites, similar to patterns found in other cervid species. Association patterns within sites were not explained by age class; and relatedness was only positively correlated at one site. The sites investigated differed in the type and frequency of human disturbance, specifically hunting, suggesting that the disparity in association patterns were driven by these differences. I conclude with two smaller studies, suggesting an indirect consequence of coal surface mining disturbance on ungulate foraging behavior and the potential for interstate transfer of ecto-parasites during reintroduction efforts. This research reinforces previous findings and further refines our understanding of ungulate social structure. Consideration of temporal variation in association patterns of ungulates and other species is important to quantify the effect of disturbance on population and social processes, but also to increase our understanding of dynamic structures. Quantifying the resiliency of structure to disturbance is a priority to further our understanding of the ecology and conservation of these species.

Phenotypic plasticity is favored in heterogeneous environments in which alternative phenotypes can exploit alternative resources. However, it’s not clear whether phenotypic plasticity is useful in environments that become more homogenous over an organism’s life cycle. I studied a population of grasshopper Melanoplus differentialis that experiences high resource diversity as nymphs but low resource diversity as adults to determine if individuals can undergo diet-induced morphological plasticity in head shape to increase biting ability and ingestion of hard diets. Insects on a soft diet were larger and had greater bite force than those on a hard diet. Head structures related to chewing ability changed shape with mass, heads became taller and narrower. Scaling relationships among body parts suggested that there wasn’t evidence for tradeoff in allocation to chewing vs. locomotor performance. Results are consistent with the idea that essential adult feeding morphology constrains the advantage of plasticity in feeding structures among nymphs.

Rhinichthys osculus, the Speckled Dace, is one of the most ubiquitous fish in western North America. Within the Southern California region, the local taxon is known as the Santa Ana Speckled Dace. The purpose of this study was to characterize and identify polymorphic microsatellite markers for R. osculus in which twenty-three were identified through Illumina pair-end sequencing. Seven of these loci were then used to examine the patterns of genetic variation and population structure that occurred within and among the watersheds in the Southern California. The study also examined the regional relationships among Southern California, Central California and Owen’s River Valley. Analysis of the microsatellite data revealed highly significant moderate levels of population structure exist within the Southern California region (RST=0.160, p=0.001). This structure is best explained by watershed as well as isolation by distance (R2=.2286, p=0.010). Highly significant geographic structure also exists among the geographic regions of Southern California, Central Coast, and Owen’s River Valley regions (RST= 0.600, p-value=0.001) that are congruent with the regional differentiation elucidated by mtDNA sequence data. In both cases, the degree of population differentiation was correlated with isolation by distance. Utilizing this information we were able gain a better understanding of the evolutionary relationships among the Southern California populations of Santa Ana Speckled Dace. Within the Santa Ana Speckled Dace populations we examined four models to explain the geographic structure: watershed, mountain range, tributary, and isolation by distance. While all were significant, the tributary model exhibited the higher level of population structure (RST= 0.160, p-value=0.001) and a significant correlation was exhibited between geographic distance and population structure, suggesting isolation by distance may be playing a role. The results of the microsatellite analysis are congruent with an earlier broad scale analysis of mtDNA sequence data that suggests the Central California and the Owens Valley populations diverged from each other prior to the divergence of the Santa Ana Speckled Dace populations from the Colorado Basin populations, and that the Central Coast populations were not established as a result of a migration event from the Southern California populations, as was previously hypothesized. Primarily due to human activity, Santa Ana Speckled Dace habitat has become highly fragmented resulting in some populations becoming extirpated. We hope this study will guide the strategies for the conservation of the remaining populations of Santa Ana Speckled Dace and watershed management in Southern California.

Rhinichthys osculus (Cyprinidae), the speckled dace, is the most widely distributed freshwater fish in the western United States. The southern California populations of R. osculus are identified as the Santa Ana speckled dace (SASD), though the SASD has not yet been formally recognized as a distinct taxon. Current mtDNA analysis performed in the Metcalf Lab has shown a reciprocally monophyletic relationship among three California regions; southern, central coast, and Owens Valley. Similarly, microsatellite genotyping has shown significant levels of geographic population structure. The purpose of this study was to provide nuclear DNA sequence data to determine the taxonomic status of the SASD to elucidate their evolutionary history and the relationships among the three regions, and to further define their evolutionary trajectory by comparing SASD sequence data to that of speckled dace from the Colorado River of Arizona. To examine this, three EPIC intron markers were sequenced on 54 samples representing all four regions. Based on the mtDNA and microsatellite data alone, there is strong support that the southern California populations of R. osculus are a reproductively isolated taxon at the species level. My study confirms this by showing the SASD to be reciprocally monophyletic for nuclear DNA markers, in conjunction with the mitochondrial DNA marker analyses. Because they are evolutionarily independent and face increased incidence of drought, fire, and flood, endangered species status should be considered.