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Red foxes (Vulpes vulpes) have been identified as a key predator of the threatened piping plover (Charadrius melodus) along the U.S. Atlantic coast. However, little is known about coastal red fox ecology, making it difficult to create effective red fox management strategies in these settings. Here, we quantify aspects of red fox population, spatial, and dietary ecology and interactions with threatened piping plovers on Fire Island, New York. We conducted remote camera surveys, scat and sign surveys, den monitoring, and GPS tracking of red foxes on the island in 2015–2018. We used these data to estimate red fox occupancy, reproduction, survival, and population density. We used GPS data to investigate red fox space use, habitat selection, and responses to piping plover nest exclosure setup, pre-hatch pipping, and hatching. We used fecal dietary analyses and data from den prey item surveys to quantify the frequency of piping plover predation and to identify major prey items of red foxes on the island. Red fox occupancy remained high even after substantial decreases in abundance, population density, annual reproduction, and seasonal survival following 2 sarcoptic mange outbreaks. Within their home ranges, red foxes selected areas that were closer to vegetation during the daytime and twilight hours, but farther from vegetation at night. We did not find clear evidence that red foxes in our study area keyed in on piping plover nest exclosure setup, pipping, or hatching at the spatial scales considered in our comparisons, although fox penetration of and digging at exclosures was an issue in 2015 at Smith Point County Park. Items from Orders Rodentia (rodents, 43% of scats), Coleoptera (beetles, 38%), and Decapoda (crabs and other crustaceans, 29%) were most frequently found in 293 red fox scats examined. Skates (Family Rajidae, 89% of dens with food items) and Atlantic surf clams (Spisula solidissima, 67%) were found most frequently outside of dens. We did not find any identifiable piping plover remains in red fox scats or outside of dens. Our results suggest that direct interactions between red foxes and piping plovers during our study period and in our study area were less frequent than expected, but concurrent work by collaborators documented that the trap success of red foxes was negatively related to piping plover reproductive output during our study period. Lethal removal of red foxes is unlikely to eliminate them from shorebird nesting areas unless complete eradication of foxes from the island can be achieved. We recommend strategic vegetation management in and around piping plover nesting areas to reduce daytime resting areas and hunting cover for red foxes, and continued use of nest exclosures. We also recommend further investigation into indirect impacts of red foxes on piping plover populations, and into the possibility that anthropogenic food resources could be subsidizing the island's red fox population. / Doctor of Philosophy / Red foxes have been identified as a key predator of the piping plover, a small migratory shorebird that breeds along the U.S. Atlantic coast and is considered 'threatened' (at risk of becoming endangered and eventually disappearing) within the United States. The lack of information about red fox ecology in coastal settings has been a challenge for wildlife biologists tasked with reducing predation on piping plovers. We investigated red fox ecology, behavior, and interactions with piping plovers on Fire Island, New York. We used trail cameras, collected scat (feces), monitored dens, and tracked red foxes on the island with global positioning system (GPS) collars in 2015–2018. We used these data to estimate red fox distribution, litter sizes, survival rates, and population sizes. We used GPS data to estimate red fox territory sizes, describe habitat selection, and investigate responses to piping plover nest exclosure setup, pipping (a period before hatching during which chicks vocalize inside the eggs), and hatching. We dissected red fox scats and recorded prey items found outside of dens to determine what red foxes on the island were eating. The proportion of each study area used by red foxes remained high even after substantial decreases in abundance, population density, annual reproduction, and seasonal survival following 2 parasitic disease (sarcoptic mange) outbreaks. Within their territories, red foxes selected areas that were closer to vegetation during the daytime and twilight hours but farther from vegetation at night. We did not find clear evidence that red foxes in our study area keyed in on piping plover nest exclosure setup, pipping, or hatching, although fox penetration of and digging at exclosures was an issue in some years at a site not included in those comparisons. Rodents, beetles, and crustacean remains were found most frequently in red fox scats. Skates and surf clams were found most frequently outside of dens. We did not find any identifiable piping plover remains in red fox scats or outside of dens. Our results suggest that that direct interactions between red foxes and piping plovers may be less frequent than previously believed, but concurrent work by collaborators documented that the trap success of red foxes was negatively related to piping plover reproductive output during our study period. Lethal removal of red foxes is unlikely to eliminate red foxes from shorebird nesting areas unless all foxes on the island are removed. We recommend strategic vegetation removal in and around piping plover nesting areas to reduce daytime resting spots and hunting cover for red foxes, and continued use of nest exclosures. We also recommend further investigation into indirect impacts of red foxes on piping plover populations, and into the possibility that anthropogenic food resources could be subsidizing the island's red fox population.

I investigated ruffed grouse (Bonasa umbellus) population ecology in the southern and central Appalachians as part of the Appalachian Cooperative Grouse Research Project (ACGRP). Several hypotheses have been offered to explain the low abundance of ruffed grouse in the region including inadequate quantity of early-successional forests due to changes in land use, additive harvest mortality, low productivity and recruitment, and nutritional stress. Through the cooperative nature of the ACGRP, researchers tracked >3,000 ruffed grouse between October 1996 and September 2002 and gathered data on reproduction, recruitment, survival, and mortality factors. As part of the ACGRP My objectives were (1) estimate reproductive rates, (2) estimate survival and cause-specific mortality rates, (3) determine if ruffed grouse harvest in the Appalachian region is compensatory, and (4) estimate ruffed grouse finite population growth. Ruffed grouse population dynamics in the Appalachian region differed greatly from the core of ruffed grouse range. In general, ruffed grouse in the Appalachian region had lower productivity and recruitment, but higher survival than reported for populations in the Great Lakes and southern Canada. However, within the southern and central Appalachian region, ruffed grouse population dynamics differed between oak-hickory and mixed-mesophytic forest associations. Productivity and recruitment were lower in oak-hickory forests, but adult survival was higher than in mixed-mesophytic forests. Furthermore, ruffed grouse productivity and recruitment were more strongly related to hard mast (i.e., acorn) production in oak-hickory forests than in mixed-mesophytic forests. The leading cause of ruffed grouse mortality was avian predation (44% of known mortalities). Harvest mortality accounted for only 12% of all known mortalities and appeared to be compensatory. Population models indicate ruffed grouse populations in the Appalachian region are declining, but estimates vary greatly stressing the need for improved understanding of annual productivity and recruitment. We posit ruffed grouse in the Appalachian region exhibit a clinal population structure and changes in life-history strategies due to gradual changes in the quality of food resources, changes in snow fall and accumulation patterns, and predator communities. Recommendations are presented for habitat and harvest management and future research and management needs. / Ph. D.

<p>  </p> <p>Bats serve important ecological and economic roles in their communities. However, due to anthropogenic land use and human-introduced disease, bat populations in North America are facing unprecedented declines. To better inform conservation efforts for bat species in northeastern Indiana, I studied two aspects of bat ecology: (1) the effects of urbanization and agriculture on bat community composition in northeastern Indiana and (2) the roosting behavior of a population of state endangered/federally threatened northern long-eared bats (<em>Myotis septentrionalis</em>; hereafter northern myotis) in a restored mesic forest adjacent to a moderately sized city (Fort Wayne, IN). To study the first aspect, I deployed acoustic detectors in green spaces throughout Fort Wayne and the surrounding rural areas of Allen County. For each detector site, I compared species occupancy rates with site-specific characteristics at the plot scale (e.g., % canopy cover, midstory density) and at multiple landscape scales (e.g., % impervious cover within 1 km). Across 429 survey nights, acoustic detectors recorded calls from eight unique bat species, of which six species were abundant enough to conduct occupancy modeling. In four of the six species, measures of the amount of forest and forest edge in the landscape were included in one or more of the top models. The top models for the two other bat species, tricolored bats (<em>Perimyotis subflavus</em>) and silver-haired bats (<em>Lasionycteris noctivagans</em>), included measures of urban land cover and revealed a negative relationship between probability of occupancy and the proportion of high-density urban land in the area. The effect of habitat scale also differed between species. For example, models in the confidence set for eastern red bats (<em>Lasiurus borealis</em>) included variables associated with the plots surrounding detectors and with landscape features within 100 m of detectors. In contrast, the top models for hoary bats (<em>Lasiurus cinereus</em>) included landscape features at larger scales, within 500m and 1 km of detector sites. These findings suggest that both generalist and forest-obligate bat species in this study area selected spaces with greater levels of forested habitat. Furthermore, heavily urbanized areas were less likely to support the same levels of bat diversity as areas with forests and other green space.</p> <p>To accomplish the second aspect of my project, I captured bats in Fox Island County Park (Fort Wayne, IN) using mist-nets and affixed temperature-sensitive radio transmitters to four northern myotis individuals. I tracked these individuals back to day roosts, where I recorded roost characteristics (e.g., tree height, # of roost trees within 0.1 ha) and monitored bat skin temperatures (Tsk). I compared the characteristics of selected roosts to those of randomly assigned available trees in the same landscape to determine trends in roost selection preferences. Northern myotis in this study strongly preferred standing dead trees within a 31-ha patch of flooded forest on the northern border of Fox Island. These trees were highly exposed to solar radiation and were consistently warmer than ambient weather conditions, which suggests they may provide important thermoregulatory benefits to reproductive females and other members of the population.</p> <p>My research offers valuable information regarding resource use by bat communities in a landscape dominated by anthropogenic development. Urban areas containing large stretches of forests with trees in various stages of decay will be more likely to meet the needs of bats that would otherwise struggle in developed landscapes. The results of this study can be used to inform conservation efforts aimed at protecting populations of bats throughout Indiana and the Midwestern United States.</p>

Biologists have long used demographic approaches to answer questions in ecology and evolution. The utility of these approaches has meant a constant development and refinement of methods. A key milestone has been the development of phenotype structured population models that link ecology and evolution. Moreover, biostatistical research steadily improves methods to coax demographic information from scarce data. In this thesis, I build upon some of the recent advances in the field. My first three studies focus on the consequences of sex differences in life history for population dynamics. Firstly, I test whether males matter for the dynamics of African lion (Panthera leo) populations via a previously unquantified mechanism: the inheritance of phenotype from father to offspring. Secondly, I develop a method to estimate age-specific mortality rates for both sexes in species where one of the sexes disperses around the age of maturity. Thirdly, I apply this method to study variation in mortality between the sexes and between two populations of African lions. After these three chapters, which make contributions to the field of sex-structured population dynamics, I focus on the integration of phenotype structured modelling and quantitative genetics. I illustrate how heritability of a quantitative character that develops with age depends on (i) viability selection, (ii) fertility selection, (iii) the development of the phenotype with age, and (iv) phenotype inheritance from parents to offspring. Our results question the adequacy of quantitative genetics methods to obtain unbiased estimates of heritability for wild populations. This thesis advances our understanding of population development over ecological time scales. This knowledge has applications in conservation and population management, but also contributes to untangling evolutionary processes in wild animals.

<div>Inferring genetic population structure in endangered, highly migratory species such as sea turtles is a necessary but difficult task in order to design conservation and management plans. Genetically discrete populations are not obvious in highly migratory species, yet require unique conservation planning due to unique spatial and behavioral life-history characteristics. Population structure may be inferred using slowly evolving mitochondrial DNA (mtDNA), but some populations may have diverged recently and are difficult to detect using mtDNA. In these cases, rapidly evolving nuclear microsatellites may better elucidate population structuring. Bayesian inference and ordination may be useful for assigning individuals to inferred populations when populations are unknown. It is important to carefully examine population inference results to detect hierarchical population structuring, and to use multiple, mathematically diverse methods when inferring and describing population structure from genetic data. Here I use Bayesian inference, ordination, and multiple genetic analyses to investigate population structure in Olive ridley sea turtles (ORs; Lepidochelys olivacea) nesting in northwestern Costa Rica (NWCR) and across the entire Eastern Tropical Pacific (ETP). Mitochondrial DNA did not show structure within NWCR, and existing data from prior studies are not appropriately published to compare NWCR to Mexican ORs. In NWCR, Bayesian inference suggested one population, but ordination suggested four moderately structured populations with high internal relatedness, and moderate to high levels of connectivity. In the ETP, Bayesian inference suggested a Mexican and Central American population, but hierarchical analysis revealed a third subpopulation within Mexico. Ordination revealed nine cryptic clusters across the ETP that primarily corresponded to Mexican and Central American populations but contained individuals from both populations, some from other, distant nesting sites. The subpopulation within Mexico was well-defined after ordination, and all clusters displayed high 10 internal relatedness and moderate genetic differentiation. Bottlenecks were detected in both putative populations, at seven Mexican and two Central American nesting beaches, and in six out of nine inferred clusters, including three out of four Mexican clusters. Bottleneck events may have played some role in cluster differentiation. Migration was significant from Mexico to Central America at multiple levels, but did not necessarily agree with potential migrants elucidated by ordination. Migration was generally lower between ordination-inferred clusters than between nesting sites or Bayesian-inferred clusters. Phylogenetic trees generally supported structuring by ordination, rather than by Bayesian inference. Structuring in ordination not tied to bottleneck events could be due to mating behaviors or patterns of nesting beach colonization dictated by environmental features. In this study, ordination provided a more practical and nuanced framework for defining MUs and DIPs in ETP ORs than did STRUCTURE. This may be due to hierarchical structuring within ETP ORs that may be present in other sea turtle populations and species. In the case of ETP ORs, hierarchical structure may be an artefact of recent population bottlenecks and subsequent recolonization of nesting beaches, or due to mating at foraging grounds or along migratory routes. Bayesian inference may not be the best method for population inference in highly migratory species such as sea turtles, which have a high potential for broad scale genetic connectivity, and therefore may display hierarchical population structuring not easily related to nesting sites. Future studies, and perhaps published studies, should incorporate Bayesian inference and ordination, as well as other measures of population divergence and descriptive statistics, when searching for population structure in highly migratory species such as sea turtles.</div>

O presente projeto estudou aspectos da ecologia populacional de duas novas espécies troglomórficas de Siluriformes dos gêneros Rhamdia e Ancistrus, sintópicas em um riacho subterrâneo da área cárstica da Serra da Bodoquena, Mato Grosso do Sul. Foram investigados os tamanhos e as densidades populacionais com base em censo visual e marcação e recaptura, as taxas de sobrevivência, a taxa de crescimento individual, a frequência de comprimento-padrão, de peso e de fator de condição, e os deslocamentos. Adicionalmente, foi estudado o comportamento de Rhamdia sp. n., com foco na ritmicidade locomotora e na reação à luz. Foram realizados seis eventos de coleta entre 2010 e 2011 para tomada de dados populacionais, além de prospecções por novas localidades com ocorrência dessas espécies. O tamanho populacional estimado para Rhamdia sp. n. foi de 391 indivíduos na Gruta das Fadas e 104, na Gruta Cinco de Ouros. Com base nos resultados de densidade, a população de Ancistrus parece ser menor do que a de Rhamdia sp. n., com tamanho populacional na ordem de 100 indivíduos. A densidade populacional média estimada através do censo visual para Rhamdia sp. n. foi de 0,09 ind/ m² na Gruta das Fadas e 0,1 ind./ m² na Gruta Cinco de Ouros, valores inferiores ao calculado com base nos resultados de marcação e recaptura, 0,76 ind./ m² e 1,48 ind./m², respectivamente. Em Ancistrus sp. n., a densidade populacional média foi de 0,018 ind/ m². Foi observado que Rhamdia sp. n. se concentra mais em poções, enquanto que Ancistrus sp. n., em corredeira. A pequena variação ao longo do ano nas densidades, no peso, e no fator de condição de ambas as espécies na Gruta das Fadas, indica maior estabilidade ambiental nessa caverna em comparação com a Gruta Cinco de Ouros. Em Rhamdia sp. n., indivíduos sem olhos externamente visíveis (anoftálmicos) apresentaram maior taxa de sobrevivência quando comparados com aqueles com olhos assimétricos ou dois olhos normais. O crescimento individual de Rhamdia sp. n. foi heterogêneo, sem relação com o tamanho do indivíduos e apresentou, pelo modelo de von Bertalanffy, comprimento máximo médio de 170 mm CP e constante de crescimento (K) de 0,241 A longevidade máxima média foi de aproximadamente 15 anos. Com a maior parte das recapturas ocorridas no mesmo setor da captura anterior, indivíduos de Rhamdia sp. n. apresentam filopatria, enquanto que Ancistrus sp. n. se deslocou mais, com somente um registro de recaptura no mesmo setor da captura anterior. Quanto ao comportamento de Rhamdia sp n., os exemplares apresentaram ritmicidade circadiana significante, com diferenças intra-específicas nos valores de potência espectral. No estudo de reação à luz, observou-se variação intra-específica no grau de fotofobia relacionado com a morfologia dos olhos. Prospecções realizadas em 24 cavernas do Assentamento Campina revelam que Rhamdia sp. n. ocorre até o momento somente nas cavernas Fadas, Cinco de Ouros, Manoel Cardoso e Dona Benedita, enquanto que ncistrus sp. n. somente na Gruta das Fadas. O mosaico de variações morfológicas observado em Rhamdia sp. n. e em Ancistrus sp. n., a forte ritmicidade circadiana da atividade locomotora e o elevado grau de fotofobia observado em Rhamdia sp. n., sugere que estas espécies estão em estágio inicial de fixação de caracteres troglomórficos, indicando um isolamento recente no hábitat subterrâneo / This project studied aspects of the population ecology of two troglomorphic Siluriformes of genera Rhamdia and Ancistrus, which are syntopics in a subterranean stream of Serra da Bodoquena karst area, Mato Grosso do Sul. The research comprised the investigation of the population sizes and densities, survival rates, individual growth rate, frequency of standard length, weight and condition factor, and displacements. Adicionally, the behavior of Rhamdia sp. n. was investigated with focus on locomotor rhythmicity and reaction to light. Six collections were made between 2010 and 2011 to gather population data, based on visual census and mark-recapture, as well as search for other localities to investigate the distribution range of these species. The population size estimated to Rhamdia sp. n. was 391 individuals in Fadas Cave and 104 individuals in the Cinco de Ouros Cave. The population densities of Ancistrus sp. n. suggests a lower population size compared to Rhamdia sp. n., possibly with less than 100 individuals in the studied area. The average population density estimated through visual census to Rhamdia sp. n. was 0.09 ind / m² in the Fadas Cave and 0.1 ind. / m² in the Cinco de Ouros Cave, lower than the results estimated by mark-recapture, 0. 76 ind. / m² and 1.48 ind. / m², for each cave, respectively. To Ancistrus sp. n., the average population density was 0.018 ind / m². The low variability throughout the year in population densities, weight, and in condition factor for both species in Fadas Cave, indicate and higher environmental stability in this cave compared to Cinco de Ouros Cave. In Rhamdia sp. n., individuals without externally visible eyes (anophthalmics) showed higher survival rate compared to those with asymmetric or two normal eyes. The individual growth of Rhamdia sp. n. was heterogeneous with no relation to individuals\' size and through the von Bertalanffy model estimate the maximum length (L &infin;) of 170 mm and growth constant (K) of 0.241. The median maximum longevity was 15 years. With little movement between sectors, individuals of Rhamdia sp. n. exhibited philopatry, while Ancistrus sp. n. moved around, with only one individual recaptured in the same cave sector. In relation do behavior Rhamdia sp n. showed significant circadian rhythmicity, with intra-specific differences in the spectral power values. In the study of light reduction, the intra-specific variation was observed in the degree of photophobia related to eyes morphology. Surveys conducted in 24 caves in the Campina settlement revealed that Rhamdia sp. n. occurs in the Fadas, Cinco de Ouros, Manoel Cardoso and Dona Benedita caves, while Ancistrus sp. n. occurs only in the Fadas Cave. The mosaic of morphological variations observed in Rhamdia sp. n. and Ancistrus sp. n., the strong circadian locomotor activity and the high degree of photophobia observed in Rhamdia sp. n. suggests that these species are in early stages of setting troglomorphic characters, indicating a recent isolation in subterranean environment

We develop and adapt absolute stability results for nonnegative Lur'e systems, that is, systems made up of linear part and a nonlinear feedback in which the state remains nonnegative for all time. This is done in both continuous and discrete time with an aim of applying these results to population modeling. Further to this, we consider forced nonnegative Lur'e systems, that is, Lur'e systems with an additional disturbance, and provide results on input-to-state stability (ISS), again in both continuous and discrete time. We provide necessary and sufficient conditions for a forced Lur'e system to have the converging-input converging-state (CICS) property in a general setting before specializing these results to nonnegative, single-input, single-output systems. Finally we apply integral control to nonnegative systems in order to control the output of the system with the key focus being on applications to population management.

Orientador: Otavio Augusto Vuolo Marques / Banca: Ricardo Jannini Sawaya / Banca: Fausto Erritto Barbo / Resumo: Neste trabalho investigamos a existência de diferenças no tamanho corporal, disponibilidade de presas e pressão de predadores em duas populações de Bothrops jararaca de dois parques do Município de São Paulo sujeitos a diferentes graus de urbanização. As serpentes não apresentaram diferenças de comprimento e robustez entre as duas populações, entretanto houve uma tendência de uma maior proporção de fêmeas maiores no parque com maior influência urbana. A oferta de recursos e a pressão de predadores foram significativamente maiores no ambiente com menor influência da cidade. Os resultados sugerem que a menor oferta de presas no parque urbano não diminui significativamente o crescimento de B. jararaca, porém a menor incidência de predadores pode resultar em um maior tempo de vida das serpentes e consequentemente maior proporção de serpentes com tamanho corporal superior / Abstract: Maintenance of suitable habitat is essential for animal population persistence. Quantitative and qualitative alterations in the environment may generate serious ecological consequences. One of the most common causes of alterations in quality, habitable area decrease and isolation is the forest fragmentation carried by urbanization. Forest remnants can function as oceanic islands, and the resident animal species may show morphological variation like dwarfism or gigantism, caused generally by the modification of diet and/or predator incidence. Here, we investigate the body size, prey availability and predation pressure in populations of Bothrops jararaca in two parks subject to different urbanization degree. We found no differences in snakes length, neither stoutness between the two populations. However the prey availability and predator incidence was significantly higher in the park with less urban influence. The results suggest that smaller food availability offer in the isolated urban park did not decrease significantly B. jararaca growth rate, but the lesser predators incidence can result in longer lifetime and consequently higher proportion of snakes with superior body length / Mestre

The formal access of transnational actors (TNA) to international organizations (IO) has increased steadily over the past five decades, and a growing body of literature is at the moment concerned with the theoretical and normative implications of these developments. However, very little is known as of yet about who the TNAs in global governance are, where they come from, which issue areas they focus on, and when and where they choose to participate. Using analytical tools from interest group theory, in particular a subfield called population ecology, this study describes and explains the chronological development of two populations of TNAs in global governance, namely the observer communities of the United Nations Framework Convention on Climate Change and the United Nations Convention on Biological Diversity. TNAs’ financial resources and their geographical proximity to global governance venues emerge as important factors influencing their capacity to participate, causing these TNA populations to be stratified and volatile.