Thesis (Ph. D.)--University of Wisconsin--Madison, 1984. / Typescript. Vita. Includes bibliographical references (leaves 222-225).

Thesis (M.Sc.(Wildlife Management ))--University of Pretoria, 2000. / Includes bibliographical references.

Thesis (Ph. D.)--University of Louisville, 2009. / Department of Teaching and Learning. Vita. "August 2009." Includes bibliographical references (leaves 304-320).

Thesis (Ph.D.)--Murdoch University, 2008. / Thesis submitted to the Faculty of Health Sciences. Includes two articles published in the Journal of Zoo and Wildlife Medicine, 2007 v. 34 (4) p. 567-573 and March 17, 2008. Includes bibliographical references (leaves 273-312)

Thesis (M. Sc.)--University of Hong Kong, 2006.

<p> Coexistence with people is one of the greatest challenges to survival for the African savannah elephant (<i>Loxodonta africana</i>), listed as Vulnerable in the IUCN Species Red List (Blanc 2008), in areas where human cultivation borders fragmented habitats (Hoare and Du Toit 1999; Osborn and Parker 2002), and crop-raiding occur. Electric fences are used more frequently. While they are effective at deterring the more risk-averse general population, they do not solve the problem of older, dominant bull elephants known as habitual (crop) raiders (HRs) that have learned to break through the most sophisticated fence designs without getting shocked (Kioko et al. 2008; Mutinda et al. 2014). There is no single solution to stop crop-raiding conflicts with HRs because they habituate to farm-based deterrents (Bell 1984; Tchamba 1995; Taylor 1999) and current novel approaches using chili-based repellents and beehive fences have had limited success but are labor-intensive and impractical for large-scale general crop protection. Further, important migration corridors have been closed off to mitigate conflicts, compromising the viability of local populations. HRs are responsible for causing 80-100% of crop-damage (Jackson et al. 2008; Alhering et al. 2011; Chiyo et al. 2011; Fernando 2011). They are not only singled out for lethal management or translocation by local authorities, they are targeted and killed by affected communities. However, HRs are keystone individuals and their constant removal has profound ecological and population implications. Focus needs to be shifted from constructing evermore elaborate fences to preventing the formation of &ldquo;problem&rdquo; elephants. Current management practices that increase aggression, increase crop-raiding conflicts, increase the risk of local extinctions, and has the potential to degrade the environment should be eliminated. In this thesis, I take an interdisciplinary approach to: (1) further understanding of HR behavioral ecology, the development of crop-raiding behavior and the potentially negative impacts of current management practices; (2) conduct a thorough analysis of HR fence-breaking/crop-raiding behavior in the Laikipia Plateau, Kenya, and suggest alternate methods to stop the conflicts; (3) introduce a behavior modification technique I designed that uses signal and solution learning to discourage HRs from raiding crops. It is my belief that any management approach, to be effective, must be developed with a clear understanding of the animal&rsquo;s capacity to learn, and the causation, development, evolution and adaptive value of the behavior to be modified.</p><p>

<p> Climate change is ostensibly one of the greatest modern selective pressures, and species with sensitive life histories or physiologies must adapt, migrate, or buffer its effects to persist. Some 15&ndash;37% of species are expected to be endangered or extinct by 2050. The most vulnerable include habitat specialists, local endemics, and species with low intrinsic growth rates. Yosemite toads (<i>Anaxyrus canorus</i>) are one such alpine endemic, having been extirpated from up to 69% of their historical range. Several features of their natural history make them vulnerable: small population sizes, high larval mortality, infrequent breeding, and specialized, patch-limited habitat prone to premature desiccation. In addition to their role as ecosystem flagships, Yosemite toads provide a model system for the many other specialists with similar life histories that are challenged by environmental change. The goal of this dissertation is to understand how historical evolutionary processes such as lineage divergence and secondary admixture, along with current levels of genetic connectivity, are expected to shape the future of Yosemite toad persistence in the face of climate change. The first chapter reconstructs phylogeographic patterns of lineage formation and fusion during repeated bouts of Pleistocene glaciation, and showcases a role for refugia in ecological divergence. The second chapter examines three contact zones as replicate tests of the hypothesis that loci associated with incipient speciation are distinct from those that readily cross ancient lineage boundaries. The third chapter models modern genetic connectivity as a network of environmental and climatic interactions, using a novel approach that incorporates phylogeographic structure. The fourth chapter forecasts the future selective pressure of climate change, and predicts where connectivity may be a mitigating force to restore genetic diversity. My dissertation provides an example of how conservation strategies can incorporate the many temporal processes (ancient, recent, and current) that have shaped current genetic diversity patterns, and use a &ldquo;total evidence&rdquo; approach to predict future adaptive potential.</p><p>

<p> Thirty-four percent of Earth&rsquo;s arable land has been converted to agricultural uses, and increased agricultural intensification has been correlated with contemporary decreases in avian abundance and functional diversity. Farm-scale biodiversity enhancement features such as native woody plant hedgerows have been planted in crop margins with the expectations of attracting beneficial predators and pollinators, and of improved pest control and pollination services in adjacent crops. Despite ongoing investment and perceived benefits of these types of enhancements for biodiversity, few evaluations have tested their effectiveness at increasing avian diversity. A growing body of research has quantified crop pest reduction by birds with indirect benefits for yield, yet few studies have evaluated whether farm-scale conservation activities improve effect sizes of these services. Further, whether or not crop margin habitats confer fitness benefits necessary for avian population viability (i.e., survival and reproduction) remains almost entirely unstudied. On each of these fronts, landscape effects can counteract or interact synergistically with the effects of local activities, and assessment of farmland habitat enhancement must be done with explicit reference to landscape context. I conducted field research in a system of extant woody hedgerows and semi-natural riparian habitat patches among farmlands of the Sacramento Valley of California&rsquo;s Central Valley, USA to investigate three questions. Does farm-scale biodiversity enhancement and retention of semi-natural landscape habitat 1) influence patterns in avian abundance and diversity, 2) increase the rate of pest reduction by birds in adjacent crops, and 3) provide quality habitat and confer fitness benefits for avian occupants? In Chapter 1, and with collaborators, I sampled birds and habitat characteristics in 111 crop margins and landscape buffers during two winter and breeding seasons. We found that margins with hedgerows, treelines, or remnant riparian habitat harbored 2&ndash;3 times as many bird species and 3&ndash;6 times greater abundance than bare or weedy margins. Margin habitat type interacted with distance from semi-natural woodlands; hedgerow or riparian margins further from woodlands harbored more bird species. In Chapter 2, I performed a sentinel prey exclosure experiment in walnuts to compare pest cocoon predation rates by birds in 10 orchards with and 10 orchards without woody vegetation patches in their margins, and I characterized semi-natural cover within landscape buffers. Avian predator richness and abundance was greater in habitat orchard margins than in bare margins, and birds were confirmed predators of 23&plusmn;29% pest cocoons per orchard (range 0 &ndash; 80%). Pest predation rates did not increase with the presence of woody margin habitat. Instead, predation rates increased with the increasing size of orchard trees, avian predator abundance, and percentage of semi-natural cover in the landscape. In Chapter 3, I used a suite of environmental, body condition, and population measures in long-distance migratory <i>Zonotrichia</i> sparrows to quantify habitat quality at hedgerows and natural reserves along a gradient of connectivity and landscape habitat amount. Abundance and within-winter apparent survival was highest in connected hedgerows and natural reserves with the most woodland landscape cover. Isolated hedgerows were of poor quality for first year Gambel&rsquo;s white-crowned sparrows <i>(Z. leucophrys gambelii)</i> and the differences in within-winter apparent survival between first year and adult birds decreased significantly with increasing woodland landscape cover. The combined results suggest that farm scale habitat enhancement can be beneficial for birds in terms of local abundance and diversity, and within-winter apparent survival if connected to and among a sufficient percentage of other similar habitats. Farm scale enhancements can also be beneficial to growers by increasing the number of avian predators of crop pests. Yet, growers appear to benefit most by having crops located in landscapes with greater percentages of semi-natural landscape cover, where avian predation rates of crop pests were highest.</p><p>

<p> Reservoirs throughout the country exhibit degraded shorelines and simplified littoral habitats because of aging. This study evaluated the establishment of agricultural plantings on reservoir mudflats and the effectiveness of supplemental brush pile structures in providing recruitment habitat for juvenile fish. The mudflats of Enid Reservoir, Mississippi were seeded during the winter drawdown in October of 2016 and 2017 with agricultural plantings. Monitoring of plantings found grasses performed best in terms of establishment and providing potential fish habitat. During Summer 2017 brush piles and control sites, without brush, were sampled in Enid Reservoir using rotenone to evaluate juvenile fish use. Juvenile fish exhibited greater abundances and larger sizes, on average, in brush pile sites. Larger brush piles placed in shallower water provided the greatest benefit to juvenile fish.</p><p>

Small, isolated populations can be at risk from genetic threats. In particular, inbreeding depression can threaten population viability, however the contribution of large-effect alleles to inbreeding depression in natural populations is largely unknown. Quantification of genetic threats requires estimation of the effective population size (Ne), which can be challenging given age-structure. Further, identification of large-effect alleles and estimation of Ne requires knowledge of a population's genetic mating system, which can itself be difficult to determine in populations with low genetic diversity. In this study, I quantified genetic threats to the small, isolated Scottish population of red-billed choughs (Pyrrhocorax pyrrhocorax), which is of high conservation concern, heightened by the recent occurrence of lethal blindness in nestlings. I first estimated extra-pair parentage rates to be low in Scottish choughs (~5% extra-pair offspring). I quantified inheritance patterns of blindness and found that the pattern of occurrence matched that expected for a single-locus recessive allele. Heterozygous carriers of the blindness allele are likely to be widely distributed in the population, limiting management options. Further, affected families had relatively larger broods than unaffected families, suggesting the blindness allele could persist in the population. Using a candidate gene approach, no consistent polymorphisms were found between blind and non-blind individuals in candidate gene amplicons and therefore a diagnostic marker for blindness could not be developed. I used demographic and genetic data to estimate Ne for Scottish choughs. Both demographic and genetic estimators suggested Ne is critically small (Ne≈30), such that future rates of loss of genetic variation will be high. The small Ne was largely due to high demographic variance, with high contributions to demographic variance from younger females and older males. Overall, this study adds to our understanding of genetic threats to small, wild populations and can thus inform management of threatened populations.