The self-sustaining status of Georgian Bay’s trophy muskellunge (Esox masquinongy) fishery is owed in part to the widespread distribution of high quality coastal wetlands used as nursery habitat. The specific wetland features that promote the recruitment of young-of-the-year (YOY) muskellunge in Georgian Bay have not been clearly defined, and without such information, it is unclear to what extent an unprecedented period of sustained low water-levels (c. 1999), and/or shoreline modifications, will continue to degrade the suitability of nursery habitats used by muskellunge throughout Georgian Bay. In this thesis, I use data from two years of intensive sampling in two embayments of northern Georgian Bay to statistically differentiate between wetlands that were found with and without YOY muskellunge. By doing so, I have provided the first quantifiable definition of suitable nursery habitat for muskellunge in Georgian Bay. Muskellunge nurseries have a structurally complex community of submersed aquatic vegetation (SAV; e.g. Potamogeton richardsonii) within the water column (≤ 1-m depth) and a fish community that had abundant suitable prey (e.g. Cypinid species) and a scarcity of early-life predators (e.g. Perca flavescens). Some key aspects of the SAV community were governed by wetland's bathymetry, and this relationship makes it possible to model the effect of changing water-level scenarios on habitat suitability. I translated these results into a management tool for fish management agencies by creating an Index of Nursery Habitat Suitability (INHS) that can be applied to other embayments in Georgian Bay to identify high quality early-life habitats for muskellunge. I developed two INHS models and applied them to an independent dataset from other regions of Georgian Bay, and found them to differentiate between sites that were known to be used by YOY muskellunge and those where YOY were absent. These were also able to track deterioration in habitat quality associated with the recent decade of low water levels. Both INHS models rely on variables based on robust ecological relationships known to favour YOY survivorship that can be readily collected by fish management agencies, and one INHS model does not require detailed information of the aquatic plant community. Both models were also designed to minimize the frequency of false negatives (suitable nursery sites misidentified as unsuitable) and false positives (unsuitable nursery sites misidentified as suitable). These INHS models should become an important tool that will complement harvest regulations to promote this economically and ecologically valuable, self-sustaining muskellunge population in Georgian Bay. / Thesis / Doctor of Philosophy (PhD) / The following Ph.D. describes how a period of sustained low water levels and shoreline modifications in Georgian Bay, Lake Huron, have impacted the coastal wetland habitat used by muskellunge during their early life. To counteract these adverse effects, the thesis provides a definition of the wetland features that promote the survival of young-of-the-year muskellunge in Georgian Bay. Included is a proposed management tool in the form of an Index of Nursery Habitat Suitability (INHS) for muskellunge that can be used to identify high-quality, early-life habitat of muskellunge. Furthermore, the INHS can be used to predict how the quality of this habitat responds to different water-level scenarios and to shoreline modification in Georgian Bay, and to guide rehabilitative efforts of degraded wetland habitat.

The streams of the southeastern United States are both hotspots for biodiversity and centers of imperilment. The specific spatiotemporal scales at which stressors impact biota are often unknown, partly due to inadequate knowledge about many species' life-histories. I conducted two complementary studies to investigate the habitat associations of an imperiled highland stream fish, the Candy Darter Etheostoma osburni. In Chapter 2, I asked (1) does micro-habitat suitability correlate with the "robustness" (i.e., viability) of four distinct populations? In Chapter 3, I expanded the extent of investigation, and asked (2) which environmental factors, expressed at what spatial scales, best explain in-stream conditions, and (3) do stream segments where Candy Darters persist have cooler temperatures and less fine-sediment than segments where the species is extirpated or historically went undetected? Chapter 2 revealed Candy Darters demonstrate ontogenetic habitat shifts, with age-0 individuals selecting slower water velocities than adults. Despite, clear habitat selection for multiple habitat variables, suitability attributed to fine-sediment avoidance most strongly correlated with population robustness across streams. Chapter 3 indicated Candy Darters are extirpated from most areas in Virginia and southern West Virginia. Land use and natural catchment features, including geology, elevation, and stream geomorphology, predominantly explained instream conditions. Populations persist in segments with cool stream temperatures and low embeddedness year-round. To recover Candy Darters, managers will need to remedy pervasive land-use threats and restore stream habitat, while operating within the impending context of warming air and water temperatures and the existential threat of the introduced Variegate Darter E. variatum. / M. S.

Efforts to reintroduce and maintain populations of pronghorn (Antilocapra americana) to the California Central Valley, specifically the Carrizo Plain National Monument (CPNM) and the Mojave Desert (Antelope Valley) portion of Tejon Ranch, have largely been unsuccessful due to dwindling numbers of translocated animals. The objective of this study was to improve upon previous models for the CPNM using aerial survey data and then apply the model to the Tejon Ranch. Aerial survey data collected from 2000-2010 on the CPNM was used to establish “use” and “non-use” areas in the model. Model variables included vegetation type (forest, shrub, grassland, semi-desert scrub, crops, and bare areas), slope, and road density. Vegetation and road density variables were treated categorically and slope as a continuous variable. Kernel density estimation (KDE) was used to estimate utilization distributions and home ranges (Fieberg 2007). An 80% isopleth was used to define “used” and “unused” habitat areas within the study site. Binary logistic regression was used to detect correlations between habitat variables and habitat use by pronghorn. Results of the regression analysis indicated overall significance with a p-value of < 0.0001 (testing that all slopes = 0). Each habitat variable comparison was made after adjusting for the other variables (e.g., slope effects were evaluated after adjusting for road density and vegetation type) and was found to be significant. Each variable coefficient was then included in a predictive equation and entered into GIS to generate a map to predict where pronghorn would likely be observed. Similar layers were created for the Tejon Ranch and the predictive equation was run with the CPNM statistical analysis. Limited conclusions about habitat suitability on the CPNM or the Tejon Ranch can be made based on the habitat data available for this model. While slope, road density, and vegetation type are all significant habitat variables influencing pronghorn habitat use, further study is needed to understand the mechanisms driving these relationships. With additional data expansion of the current habitat suitability model would help to further define pronghorn habitat use, specifically the creation of a focused model of a particular season, life history period, or individual animal use to identify more detailed habitat use patterns.

Rio Grande wild turkey (RGWT) abundance in portions of the Edwards Plateau has declined steadily since the late 1970s as compared to other areas of the Edwards Plateau where populations have exhibited no trend. The reasons for this decline remain unclear. Possible factors include changes in habitat, and increased human population. The overall objective of this study was to identify landscape changes and habitat characteristics that affect RGWT populations using spatial analysis and modeling at multiple spatial scales. Specific objectives for this study included the quantification of flood-induced landscape changes between 1972 and 1995 along the Medina River bottomlands and their impact on RGWT habitat, the quantification of landscape characteristics of stable and declining study sites in the Edwards Plateau, and the development and evaluation of a GIS-based habitat-suitability model for female RGWTs during the breeding season that will allow the assessment of the spatial distribution of adequate habitat in the Edwards Plateau.The analysis of the landscape characteristics along the North Prong Medina River due to flooding in 1978 had a negative impact on RGWT habitat. Changes in the spatial distribution of woody cover in the bottomlands and the removal of woody cover along riparian zones most likely limited habitat use and dispersal of RGWT along the North Prong Medina River. The analysis of landscape characteristics in sites with stable and declining of RGWTs populations showed that disturbance and a high proportion of woody cover were important factors influencing RGWT populations in areas where turkey numbers had declined. Landscape attributes were used as habitat variables to develop a habitat-suitability model for female RGWTs during the breeding season. The model performed well in characterizing high-suitability habitat for adult female RGWT during the breeding season in the study areas. The use of two scales relevant to RGWT provided important information about the high-suitability areas for female RGWT in stable and declining sites in the Edwards Plateau.

A phenomenon of large, upland breeding colonies of cattle egrets in residential areas of Central Texas has been observed since the early 1960s. These large concentrations of breeding birds can be a nuisance to nearby residents and their management has been difficult. To help understand why cattle egrets choose upland, residential breeding sites, and predict where these might occur, the geographic extent of the phenomenon was bounded within Texas, a habitat suitability model constructed, and reproductive success compared by breeding habitat type to evaluate if residential nesting confers an adaptive advantage.. Records of upland cattle egret colonies were found only in Central Texas, not other parts of the state. The habitat suitability model was constructed using total edge of three land use classes: water, forest, and developed classes. The model classified 78.6 % of upland colonies in very high or high suitability classes and 7.1% of colonies in low or very low suitability classes. This distribution was significantly different than expected considering the overall ratio of suitability scores in the entire raster model (p = 0.036). Nineteen active colonies were found in or bordering the Post Oak Savannah and Blackland Prairie ecoregions. Colonies were in residential, urban, island, and flooded tree and shrub habitat. Nests were found in 12 different tree and shrub species. Residential colonies had more breeding pairs, greater nest survival, and were less productive than non-residential colonies on average, but these differences were not statistically significant. Colonies where nest substrate was removed were not reused and no breeding was initiated nearby the next year. Propane cannons discouraged reuse of colony after prolonged application. Herons and egrets likely use residential sites when wetland habitats are limited. Their overall breeding distribution reflects state wide rainfall and wetland availability patterns with upland nesting in Central Texas, wetland nesting in eastern and coastal regions, and little large scale nesting in western Texas. Egrets and herons may use edges of development as breeding sites to limit predation by ground predators when flooded tree and shrub or island habitats are absent, but this hypothesis needs more testing.

Rio Grande wild turkey (RGWT) abundance in portions of the Edwards Plateau has declined steadily since the late 1970s as compared to other areas of the Edwards Plateau where populations have exhibited no trend. The reasons for this decline remain unclear. Possible factors include changes in habitat, and increased human population. The overall objective of this study was to identify landscape changes and habitat characteristics that affect RGWT populations using spatial analysis and modeling at multiple spatial scales. Specific objectives for this study included the quantification of flood-induced landscape changes between 1972 and 1995 along the Medina River bottomlands and their impact on RGWT habitat, the quantification of landscape characteristics of stable and declining study sites in the Edwards Plateau, and the development and evaluation of a GIS-based habitat-suitability model for female RGWTs during the breeding season that will allow the assessment of the spatial distribution of adequate habitat in the Edwards Plateau.The analysis of the landscape characteristics along the North Prong Medina River due to flooding in 1978 had a negative impact on RGWT habitat. Changes in the spatial distribution of woody cover in the bottomlands and the removal of woody cover along riparian zones most likely limited habitat use and dispersal of RGWT along the North Prong Medina River. The analysis of landscape characteristics in sites with stable and declining of RGWTs populations showed that disturbance and a high proportion of woody cover were important factors influencing RGWT populations in areas where turkey numbers had declined. Landscape attributes were used as habitat variables to develop a habitat-suitability model for female RGWTs during the breeding season. The model performed well in characterizing high-suitability habitat for adult female RGWT during the breeding season in the study areas. The use of two scales relevant to RGWT provided important information about the high-suitability areas for female RGWT in stable and declining sites in the Edwards Plateau.

Large carnivores in the United States are making a comeback following decades of systematic eradication. Black bears (Ursus americanus), cougars (Puma concolor), and gray wolves (Canis lupus) may recolonize the midwestern United States provided there is substantial suitable habitat. However, viability of large carnivore populations is as dependent on social acceptance as on biological factors. I developed individual and combined models of suitable habitat for black bears, cougars, and wolves in 18 midwestern states using geospatial data, expert-opinion surveys, and multi-criteria evaluation. I also assessed attitudes and perceptions of Illinois citizens about large carnivores via a mail-in survey. Experts indicated land cover was the most important variable for predicting potential habitat for black bears and cougars; human density was the most influential variable for wolves. Large, contiguous areas of suitable habitat comprised 35%, 21%, and 13% of the study region for wolves, bears, and cougars, respectively. About 12% of the region was considered suitable for all 3 species. Arkansas, Minnesota, Texas, and Wisconsin had the highest proportions (>40%) of suitable habitat for black bears; Arkansas, Michigan, Missouri, Texas, and Wisconsin had the most (≥20%) suitable cougar habitat; and only 4 states in the study region contained <29% suitable wolf habitat. Models were validated by comparing suitability values of independent sets of known carnivore locations to those of random locations, and models appeared accurate. More than 70% of survey respondents (n = 791) were male and their average age was 60; 55% were hunters. Approximately 40% were unsure about the population status of large carnivores in Illinois; of the remaining respondents, most (ranging from 20% for black bears to 41% for cougars) believed the presence of all 3 species had increased over the past decade. More residents supported protection (43%) and increasing numbers of large carnivores (39%) than opposed them (26%), although support for black bears was slightly higher than for cougars and wolves. Rural residents and livestock owners were the most likely to want carnivore numbers to decrease and least likely to support their protection; higher levels of education corresponded to positive attitudes toward large carnivores. My research provides the foundation for well-informed management plans, policy decisions, and educational initiatives for large carnivores in midwestern states where large carnivore populations have been absent for decades.

The Tropical Andes Biodiversity Hotspot holds a remarkable amount of species at risk of extinction due to climate change and human activities. One of these species, the Critically Endangered yellow-tailed woolly monkey (Lagothrix flavicauda), has experienced alterations in its known geographical range, along with a recent sighting in the region Junín, 206 kilometers south of previous observations, calling for a re-evaluation of potential suitable habitat. In this thesis, I fit, evaluate, and apply predictions of a habitat suitability model within the country of Peru. I used a generalized linear modeling approach across various range constraints, incorporating bioclimatic variables, forest cover, distance to cities and elevation as predictor variables. Precipitation features most strongly influencing observations of species presence in my model and evaluation measures showed the elevation-constrained model accuracy to be around 95%. Habitat suitability maps illustrate novel areas of potentially suitable habitat in central Huánuco, Pasco, and limited areas in Junín. The newly discovered population was found to be in an area of low suitability, calling for further investigation of the species in this area. Areas of suitable habitat should be surveyed to decrease bias in occurrence data, increasing the accuracy of habitat modeling for this species. Surveying these areas may also reveal corridors of gene flow between these populations, and could facilitate landscape genetics studies to characterize the viability of this taxon. Better characterization of the true distribution of the species will provide information to conservation stakeholders in priority areas, helping to protect this species and associated threatened wildlife.

Human activities have fundamentally shaped ecosystems across the globe. While this is often associated with degradation, cultures with alternative philosophies can leave a different kind of legacy. First Nations in the temperate rainforest of coastal British Columbia, like the Heiltsuk and Wuikinuxv, have inhabited the land for over 14,000 years, leaving behind tangible legacies in the plant communities we see today. From fine-scale effects of enriched plant leaves to landscape-level species distributions, this research investigates the ecological legacies of human land use and management—both past and present. In one chapter, I test if plants growing on ancient, human-modified soils are enriched in nutrients. I find that plants growing on these sites contain more phosphorus and sodium, which generally benefit fruit production and overall growth. This aligns with oral histories that describe fertilized shrubs as having berries that are bigger, healthier, tastier, and more productive. In the following chapter, I create models that predict the distribution of culturally important plants. With the Heiltsuk Integrated Resource Management Department, I develop a framework for habitat suitability modelling that can be used as a tool for aiding their resource management decisions. All models performed well (AUC = 0.9 overall), and offer insight into suitable habitat across a 3,600 km2 area. Out of five predictor variables, distance to shore, site series (a vegetation index), and human influence contributed the most to model performance. This research contributes a practical tool for resource management and adds to the growing body of interdisciplinary knowledge that uses scientific methods to answer questions of cultural significance. In a time of overlapping environmental crises—like climate change and biodiversity loss—it is important to be aware of the positive influence humans can have on the environment, and how this can offer a hopeful direction for resource management into the future. / Graduate

Indiana University-Purdue University Indianapolis (IUPUI) / The distribution of the Common Mudpuppy (Necturus maculosus maculosus) is widespread but greatly understood. It is assumed that mudpuppy populations are declining due to poor habitat quality. However, there is not enough data to support this claim. The distribution of the mudpuppy is throughout the entire state, but only 43 of the 92 counties in Indiana have records. This project utilized habitat suitability modeling, focused on Indiana, to gain a better understanding of their distribution within the state. Data from Ohio and the Salamander Mussel (Simpsonais ambigua) were included to bolster the dataset. Environmental DNA was included to validate the model. Variables used in this analysis were Strahler Stream Order, distance to forest, percent agriculture, and tree canopy cover. Results showed that stream orders 4 to 6, a shorter distance to forest, less agriculture, and 30 to 40% of tree canopy cover was what contributed to suitable habitat. Stream order was the variable that contributed to the model the most. The areas of suitable habitat found were the HUC08 sub-watersheds in the northeastern and southwestern corners of the state. These areas included 19 counties were there were no previous records of mudpuppies. Environmental DNA showed that the negative samples were not found in suitable habitat. Further supporting the predicted area of suitable habitat. It is recommended that conservation efforts focus on the northeastern and southwestern regions. Interpreting this data to align with the regions set by the Indiana State Wildlife Action Plan shows that conservation should focus in the Great Lakes, Interior Plateau, and Valley and Hills area. It is recommended that more environmental data be conducted and that proactive conservation measures are implemented.