<p> Culverts are ubiquitous in urban and natural environments, installed to provide road access and erosion control, but often impact fish movements in freshwater habitats. Effects of culverts on marine and estuarine fish are not well-studied. This study aimed to understand the potential impacts of a culvert, which connects a large tidal bay and a coastal lagoon, on the movements of several species of fish. Habitat characteristics of both sites were analyzed to better understand these movements, including water parameters, sediment characteristics, and zooplankton, benthic macroinvertebrate, and small fish communities. The two habitats differed in terms of temperature, salinity, dissolved oxygen, zooplankton abundance, and community composition of zooplankton, benthic macroinvertebrates, and small fish. The culvert and associated grate limited large fish from moving between the two habitats likely due to body size and other morphological characteristics. Removing this barrier and replacing it with an open channel would increase connectivity between these two habitats which could improve trophic quality in the lagoon habitat and increase functionality overall.</p><p>

Global biodiversity is being lost at an unprecedented rate, such that we have entered the sixth mass extinction in the history of the earth with emerging infectious diseases (EID) recognised as an important contributor to this loss. Amphibian chytridiomycosis is an EID that has driven very rapid declines in, or even extinctions of, hundreds of amphibian species. Infectious diseases such as chytridiomycosis, caused by the fungal pathogen Batrachochytrium dendrobatidis (Bd), often persist in biological and non-biological reservoirs making them difficult to eradicate. In turn, this makes reintroductions of target species challenging due to the risk of infection. This thesis investigates the critically endangered mountain chicken (Leptodactylus fallax) as a case study of the population impacts of a chytridiomycosis epidemic and to test the effectiveness of strategies to mitigate the effects of the disease. Specifically, this research (1) charts the decline of the mountain chicken on the only two islands on which it exists, and determines the impact on genetic diversity; (2) tests whether anti-fungal treatment can improve the survival of mountain chickens with Bd infection in the wild; (3) examines the role of Bd reservoir species in causing Bd infections of reintroduced mountain chickens; and (4) determines habitat features that are predictors of infection at release sites. Chytridiomycosis drove the mountain chicken to near extinction on Dominica in 2002 and Montserrat in 2009, in one of the fastest recorded vertebrate species declines, leading to a significant loss of genetic diversity. On Montserrat, treating mountain chickens with an anti-fungal drug (itraconazole) during the chytridiomycosis epidemic improved survival rates and reduced Bd infection rates in the short term, but did not provide long-term protection. Although mountain chickens have been driven to near-extinction by Bd infection on Montserrat, the pathogen persists in two sympatric reservoir species which are not impacted by Bd infection, the most prolific of which (Eleutherodactylus johnstonei) displays strong seasonality in Bd infection prevalence and load. Timing mountain chicken reintroduction to occur during the period when tree frog Bd infection was at its lowest was tested to determine the impact on reintroduction success. Multi-state mark-recapture modelling applied post-release showed that optimising the timing of release reduced Bd infection rates and increased survival. Radio-tracking was utilised with geographic profiling to determine that release site water bodies were likely sources of Bd infection in reintroduced mountain chickens. This could inform targeted mitigation of the pathogen and improve future reintroduction success. Where species have been extirpated in the wild, and an irreversible threat such as an EID persists, novel reintroduction strategies are required. These include optimising the timing and conditions of release in order to minimise the impact of the threat along with targeted mitigation measures such as individual level treatments.

<p> Rivers in semi-arid regions are highly sensitive and pressured yet can support diverse assemblages of species. In central New Mexico, the Rio Grande (River) is the lifeblood of the Middle Rio Grande Valley (MRGV), a semi-arid region which maintains large urban and agricultural centers and is also the principal wintering area for the Rocky Mountain Population of greater sandhill cranes (<i>Antigone canadensis tabida</i>). Human-induced environmental change has transformed the MRGV and habitat availability prompting concerns for the population. To address these concerns, I investigated dietary and behavioral responses of sandhill cranes to the collection of features that function as winter habitat. In Chapter 1, I demonstrated a novel application of stable isotopes to evaluate dietary reliance of sandhill cranes on corn subsidies provisioned by natural resource agencies, estimated rates of carbon isotope incorporation in tissues of sandhill cranes, and estimated tissue-derived winter arrival dates of sandhill cranes. I found subsidized corn was the primary dietary component of sandhill cranes, rates of carbon isotope incorporation in sandhill crane tissues differed predictably by metabolic activity, and estimated tissue-derived arrival dates on wintering grounds approximated actual arrival dates. In Chapter 2, I advanced a hierarchical Bayesian framework for overcoming challenges and improving analysis of behavioral data frequently generated in animal behavior studies and used behavioral observations of sandhill cranes as a case study. In Chapter 3, I estimated energetic and temporal availability of corn subsidies and seasonal energy requirements of sandhill cranes. I found seasonal energetic requirements of the population are likely satisfied by corn subsides but not without strategic planning. In Chapter 4, I examined how current landscape and riverine configuration influenced patterns of diel habitat selection by sandhill cranes. Sandhill cranes avoided sources of anthropogenic disturbance, relied heavily on managed public land resources, and selected roosting locations in the Rio Grande with a wider channel, interspersion of sandbars and shallow water, and low channel bank vegetation. My research suggests sandhill cranes have coped with alterations that have led to current conditions in the MRGV, however, habitat-related resources will need to be managed adaptively as drivers of environmental change will undoubtedly influence future circumstances. </p><p>

<p> Several state, federal and non-profit agencies have developed collaborative goals for restoring habitat in New England and New York for a declining rabbit species, the New England cottontail (<i>Sylvilagus transitionalis</i>, NEC). My goal was to evaluate habitat restorations at both the local, or site, scale, and the landscape scale. In order to objectively quantify the suitability of the sites being managed, I developed a Habitat Suitability Index, based on the HSI models designed the U.S. Fish and Wildlife Service. I identified candidate habitat variables for NEC, including types of cover and refuges, and food, and then asked a panel of NEC experts to rank the importance of the candidate variables. I collected data on the most important habitat variables at 60 sites managed for NEC across New England and eastern New York. The NEC experts also ranked the same 60 sites from 1 (unsuitable) to 5 (optimal). The model was optimized to improve agreement with expert opinions for the 60 sites. Specific applications may include determining when a site is suitable for releasing translocated or captive breed rabbits, and identifying habitat features that need modification as forest succession progresses. To evaluate habitat restoration efforts at a larger landscape scale, I created metapopulation models for two management focus areas (Cape Elizabeth and Kittery-Berwick) in Maine for population viability analyses. I ran simulations to compare the relative effects of the two focus areas as well as five management scenarios. I conducted a sensitivity analysis to determine the importance of various model parameters on extinction risk. The Cape Elizabeth focus area, which has more habitat patches that are closer together, had lower extinction risks than Kittery-Berwick. Reintroductions and creating additional habitat appeared especially important in the Kittery-Berwick focus area. The simulation results were sensitive to changes in the standard deviations of the survival and recruitment rates, and the probability of catastrophic mortality, indicating that variation is detrimental to NEC metapopulation growth. Variation in weather caused by climate change may need to be mitigated by monitoring and managing NEC habitat and populations.</p><p>

<p> The United States Fish and Wildlife service declared an unusual mortality event (UME) in 2006 when a high number of northern sea otters in Alaska were found dead beginning in 2002. Necropsies revealed the cause of death in 30% of cases to be septicemia with meningoencephalitis and/or vegetative valvular endocarditis (VVE) colonized by gram positive cocci, later determined to be primarily <i>Streptococcus infantarius</i> ss <i>coli</i> and <i>Streptococcus phocae</i>. While much work has been done to uncover the pathogenic agents responsible for these deaths in northern sea otters, the ecology of <i>S. infantarius</i> ss <i>coli</i> and <i>S. phocae</i> in the environment remains poorly understood. This study investigated the presence of <i>S. infantarius</i> ss <i> coli</i> and <i>S. phocae</i> in the marine environment by 1) developing a molecular method to detect <i>S. infantarius</i> ss <i>coli</i> 2) examining potential microbe-habitat associations in Kachemak Bay and Resurrection Bay, Alaska, and 3) determining the competency of otter prey species to act as reservoirs for these pathogens. A PCR assay was developed to detect the <i>sodA</i> gene of <i> S. infantarius</i> ss <i>coli</i> in both environmental and clinical samples. Water and bay mussels were collected from sites in Kachemak and Resurrection Bays and pathogen presence was determined using PCR. Habitat attributes were recorded onsite and determined using ShoreZone. Prey competency was determined via a dosing experiment in the lab. Our primer set for the <i> S. infantarius</i> ss <i>coli</i> <i>sodA</i> gene, as well as a previously published primer set for the <i>S. phocae</i> <i> sodA</i> gene, successfully identified our targets in clinical and environmental samples using conventional PCR. Primer sets we designed successfully quantified the <i>sodA</i> gene of <i>S. infantarius</i> ss <i> coli</i> and/or <i>S. phocae</i> in environmental samples and in dosed prey samples using qPCR. <i>S. infantarius</i> ss <i> coli</i> and/or <i>S. phocae</i> were present in water or mussels at 61 of 162 sites. Statistical analyses to determine bacterial correlations with habitat attributes revealed some correlations between habitat parameters selected and presence of our target bacteria in the environment. Prey competency experiments showed that bivalves were the most competent pathogen reservoirs. Results of this study will inform microbial ecologists and wildlife managers of the potential environmental risk factors for <i>S. infantarius</i> ss <i>coli</i> and <i>S. phocae</i> infection as well as provide information about pathogenic bacterial presence in the marine environment. </p><p>

<p> Apple snails are in the Family Ampullariidae, a family of freshwater gastropods. Some species in the genus <i>Pomacea</i> have gained considerable notoriety as very destructive invasive species. Ampullariids have a gill and breathe water; in some species, the mantle cavity is modified into an air sack that may function as a lung or flotation device. Apple snails definitively identified as <i>Pomacea maculata</i> have successfully invaded numerous localities in Louisiana, and studies of the physiology of these animals may enhance our understanding of the biology of highly invasive species and suggest effective approaches to controlling the invasive populations. This study investigated respiration of <i>P. maculata</i> in water and in air and the ability of the animals to survive long-term emersion in a state of aestivation. The ability of the animals to disperse over dry ground was studied. Finally, the anatomy of the gill and lung were examined. The results of the study indicate that the gill and the lung in <i>P. maculata</i> are vascularized, capable of gas exchange, and fully functional, which permits survival and respiration in water and during long- and short-term exposure to air. Both the capacity to sustain travel over dry land and the ability to survive long term aerial exposure in an aestivated state were demonstrated by <i>P. maculata</i>. The major physiological changes observed during aestivation include a decrease in heart rate, a reduction in VO2, and the use of discontinuous respiration. A review of published literature suggests that extensive physiological variation exists among populations of native and invasive <i>P. maculata</i>. In conclusion, <i>P. maculata </i> in Louisiana is well-adapted to life in both water and air, can move overland, and can survive emersion for over a year. These physiological adaptations suggest that controlling the further spread of <i>P. maculata </i> will be very difficult.</p><p>

<p> Information about population dynamics, life history variation, and connectivity patterns of threatened cutthroat trout (<i>O. clarkii</i> spp.) is critical for effective management and restoration. The Lahontan cutthroat trout (<i>O. c. henshawi;</i> LCT) is classified as threatened under the Endangered Species Act due to widespread extirpations across its range, and is at increased risk due to drought, habitat fragmentation, and climate change. This study was conducted in the Summit Lake Basin, NV (USA), which has a population of LCT that resides in Summit Lake and its tributary stream network. The objectives of this research were to (1) examine the population dynamics of stream- and lake-dwelling LCT in the context of drought, (2) quantify the amount of stream-resident versus adfluvial life histories in an adfluvial spawning tributary, and (3) identify the level of population connectivity between stream-resident and adfluvial components of the population. Chapter 1 shows that stream-dwelling trout were more resilient to drought disturbance and that drought refugia in the stream contribute to their resilience. Chapter 2 provides evidence for stream-residency in addition to high population connectivity across the lake and stream environments that is likely to increase in high flow years. While LCT and other cutthroat species have innate characteristics that allow them to persist in dynamic and harsh environments, this research highlights the importance of drought refugia and landscape connectivity to the long-term persistence and viability of co-occurring adfluvial and stream-resident fish.</p><p>

<p> Infectious disease can play a vital role in species conservation, as some diseases can cause massive population die-offs. In North American tortoises, population declines have been attributed to an upper respiratory tract disease, but the importance of this disease within and among tortoise hosts is controversial. In this dissertation, I use samples from the upper respiratory tract of wild tortoises representing multiple species in the genus <i>Gopherus</i> to answer questions regarding pathogen prevalence and co-infection, pathogen genetic diversity, and the ecology of pathogens within the upper respiratory tracts of tortoises. Using genetic methods including polymerase chain reaction (PCR), quantitative PCR, Sanger sequencing, and 454-pyrosequencing, the data presented herein supports hypotheses that pathogens in this disease system interact with each other and with other microbes in the respiratory tract differently in different tortoise host species. </p><p> In this system, both transmission and disease progression are found to be extremely slow in these long-lived hosts. Though pathogens were widespread among the sampled tortoises, few individuals were found with clinical signs of disease. Few individuals capable of transmitting disease (requiring nasal mucus and pathogen), along with few opportunities for pathogen transmission (requiring long periods of direct contact), indicate that it is unlikely for tortoises to fully clear themselves of these microbes without risk of the pathogen&rsquo;s extinction. If this is the case, then it is likely that more tortoises than we can detect have these microbes in their upper respiratory tracts. With this in mind, and considering the abundance of visibly healthy tortoises over ill tortoises, my collaborators and I suspect that pathogens in this system likely form commensal relationships with their hosts much of the time, until a stressor alters the system and leads to a parasitic interaction. </p><p> The results of this dissertation indicate that this disease is context dependent, depending on the host and likely other microbes in the community. Our understanding of the ecology of this disease system would greatly benefit from experimental inoculation and long-term resampling studies.</p><p>

<p> Due in part to its geographic isolation and unique climate, Hawai&lsquo;i has a high number of endemic species and is considered a biodiversity hotspot. At the same time, these characteristics make Hawai&lsquo;i vulnerable to species loss. To protect endangered species, conservationists focus on preserving Hawai&lsquo;i&rsquo;s native ecosystems through invasive species control and habitat restoration. Native forests are central to Hawai&lsquo;i&rsquo;s watershed, provide habitat for endemic pollinators, and foster bioculture. Pollinators are integral for ecosystem health as well as for human spaces, and worldwide pollinators have been on the decline. Since pollinators and their flowering counterparts are embedded in human lives, this research challenges traditional conservation approaches by contextualizing more-than-human entanglements within social, political, and cultural milieu. The purpose of this work is to draw from posthumanism, new materialism, and indigenous discourse to examine the biopolitical issues in which Hawaii&rsquo;s endemic pollinators situate to re-envision questions and ethics of conservation. The researcher followed endemic pollinators through native forests to explore the entangled relationship between humans, pollinators, and forests examining the question, what is the biopolitical culture of endemic pollinators in Hawai&rsquo;i? This multi-sited, multi-method research used a mix of autoethnography, participant observations and interviews, visual data, and archival and biocultural accounts to articulate emergent findings. The findings of this dissertation discuss the nuances of multispecies entanglements and mattering, politics of biological conservation and extinction, and material-discursive understandings of place. This study suggests human/more-than-human encounters are grounded in reciprocity and responsibility and co-create place.</p><p>

Protected areas have been identified as one of the most effective strategies for reducing biodiversity loss in a world where the negative effects of global change are increasing. However for species which migrate or which range beyond the borders of protected areas, these protected areas may only offer partial protection against the threats in the surrounding landscape. Understanding the role and limitations that protected areas can play in conserving threatened species can contribute to better conservation measures for species that may otherwise not benefit from more conventional conservation approaches. The Martial Eagle is a low-density apex predator currently declining across its African range. Changes in reporting rates from bird atlas surveys suggest declines of up to 60 % over the last 20 years (1987-1982 vs. 2007-2013) across South Africa. Worryingly, large protected areas were not immune to these declines. For instance reporting rates in Kruger National Park (KNP; ca. 20,000 km²), an area often considered a stronghold for Martial Eagles, recorded a 54 % decline in reporting rates. It is not clear what the major drivers of declines have been in South Africa, nor what is contributing to the declines in these large protected areas. In this thesis I study the ecology of Martial Eagles in KNP to improve our understanding of the threats they face and how these threats at various stages in their life cycle may be driving declines within protected areas where one would expect that the species should be well conserved. I hypothesised that the main driver of declines in protected areas is that juvenile Martial Eagles disperse beyond the borders of protected areas where they are at increased risk of unnatural mortality, thus leading to recruitment failure back into even the largest protected areas. To test this hypothesis, I fitted GPS tags to 9 juvenile eagles to understand their dispersal behaviour, an aspect of their life cycle for which no previous information existed, and to explore their survival rates. During a lengthy post fledging dependency phase (7 - 9 months) birds began making exploration trips that reached up to ca. 150 km from the nest site and beyond the borders of KNP. After dispersal onset, birds ranged widely up to 390 km from their nests covering areas that averaged ca. 6,500 km²; protected areas covered only 55 % of this area. In contrast to my hypothesis survival rates did not appear particularly low; from monitoring successfully dispersed juveniles over 36 months in total, only one immature bird was confirmed to have died presumably due to natural causes. To understand adult habitat preference and ranging behaviour, which can inform habitat requirements for the species conservation, I fitted GPS tags to eight adult birds. Models of their habitat preference indicated that the species preferred to utilise areas within their home ranges that were in areas with greater tree cover, with areas of dense bush rather than open bush or grassland, amongst other important features. These results were important to identify potential threats, such as the loss of trees in Savannah's, which is currently occurring due to elephant damage and fire influences. The species held large territories (ca. 108 km²) constraining the maximum number of pairs that the Park is able to support (max. 185 possible pairs), however models of distribution suggest the available habitat in KNP likely supports ca. 60 - 70 breeding pairs. Two adult individuals never held territories and another two abandoned their territories during the course of the study. These individuals ranged widely (ca. 44,000 km²) suggesting a floater population exists in the region. The death of three of these four floater individuals (two persecutions and an electrocution) indicates that adults are particularly at risk of mortality during these wide-ranging movements beyond protected area boundaries. Two natural mortalities of territorial birds within the park were also recorded. Overall therefore, despite our relatively small sample size, adult birds do appear to have worryingly low survival rates. Because my sample size of both adults and juveniles/immatures was relatively small (adults = 8, juveniles = 9), their movements may not be fully representative of the entire population. Therefore, I additionally modelled the distribution of Martial Eagles using independent sightings data to describe suitable areas for the species both within the KNP and adjacent areas (within ca. 400 km of the park). Identifying these areas provides conservation managers with more information to ensure adequate conservation measures are in place for this species in these areas. At least 29 % of KNP was predicted to be suitable for Martial Eagles, while neighbouring regions in Mozambique and Swaziland were also predicted to be highly suitable for the species. Given the adult mortalities and general scarcity of Martial Eagles in Mozambique the area may act as a population sink for KNP birds. Lastly, I compared current reproductive parameters to those reported in a considerable number of other studies on the species both within KNP and elsewhere. Productivity recorded during this study was lower than any previously recorded estimate. Using a population model, I show that current productivity within KNP is sufficiently low to have been solely responsible for the known levels of decline there, without the need to invoke any other contributory factors. A high hatching failure rate was mostly responsible for the low productivity. However, it is important to note that at least two of the three years of data collection occurred during low (drought) rainfall years, which may have constrained breeding, and thus may not be reflective of productivity levels more generally over the recent longer term. My research helps identify the most likely drivers of population declines in KNP, suggesting that elevated adult mortality and lower productivity may be the key factors. Drivers of low productivity require further investigation, however it is likely that changes in habitat quality or climate may be impacting on the species within KNP. The study also highlighted the difficulty of conserving wideranging and threatened species in protected areas, which may be prone to high mortality in the surrounding landscape. This research is therefore applicable to a number of species that range widely from KNP e.g. vultures, or migratory eagles. The research indicates that protected areas alone are unlikely to conserve these species and that additional conservation measures, such as education programmes, or trans boundary policy should be put in place to realise successful conservation for these species.