Spline smoothing is a popular technique for creating maps of a spatial phenomenon. Most smoothers use the Euclidean metric to measure the distance between data. This approach is flawed since the distances between points in the domain as experienced by the objects within the domain are rarely Euclidean. For example, the movements of animals and people are subject to both physical and political boundaries (respectively) which must be navigated. Measuring distances between the objects using the incorrect (Euclidean) metric leads to incorrect inference. The first part of this thesis develops a finite area smoother which does not su↵er from this problem when the shape of the area is complex. It begins by rejecting the use of the Schwarz-Christo↵el transform as a method for morphing complex domains due to its squashing of space. From there a method based on preserving within-area distances using multidimensional scaling is developed. High dimensional projections of the data are necessary to avoid a loss of ordering in the points. To smooth reliably in high dimensions Duchon splines are used. The model developed rivals the current best finite area method in prediction error terms and fits easily into larger models. Finally, the utility of projection methods to smooth general distances is explored. The second part of the thesis concerns distance sampling, a widely used set of methods for estimating the abundance of biological populations. The work presented here introduces mixture formulation for the detection function used to model the probability of detection. The use of mixture models leads to flexible but monotonic detection functions, avoiding the unrealistic shapes which conventional methods are prone to. These new models are then applied to several existing, problematic data sets.

Habitat loss is one of the leading causes of species decline across all taxa and conservation practices require information on population trends. The Mescalero Sands ecosystem, New Mexico, USA, is experiencing landscape changes associated with oil and gas development. The dune-dwelling lizard community contains a habitat specialist, Sceloporus arenicolus, that is of particular interest because it has a very limited geographic distribution that is entirely subject to oil and gas development. Distance sampling is widely used to estimate population densities of many vertebrate taxa however assumptions can be difficult to satisfy with certain species or in certain habitats. Researchers must investigate the likelihood that assumptions can be satisfied before implementing any population sampling method. I had two objectives. First to investigate the precision of population densities of dune-dwelling lizards estimated via distance sampling that was coupled with double-observer surveys. Second to compare abundances of dune-dwelling lizards among sites that varied in oil and gas development. I conducted distance line transects and compared those density estimates to densities obtained from total removal plots. I quantified the amount of oil and gas development, habitat quantity and quality and correlated those to lizard abundances to investigate the effects of oil and gas development on lizard populations. I found large differences in density estimates from distance sampling and total removal plots that resulted from violation of distance sampling assumptions. Although distance sampling is a low cost method, it does not produce reliable density estimates for dune-dwelling lizards and is not an appropriate sampling method in this system. I did not find oil and gas development effects on the habitat quantity, quality or on the abundances of lizards. Lizard abundances were most strongly correlated to habitat quantity. Lizard abundances may be influenced by complex interactions between oil and gas development and habitat quantity and quality but controlling for those interactions was beyond the scope of my study. Before and after experiments and long-term studies at multiple sites would be required to more fully address the effects of oil and gas development on lizard populations in the Mescalero Sands.

Habitat loss is one of the leading causes of species decline across all taxa and conservation practices require information on population trends. The Mescalero Sands ecosystem, New Mexico, USA, is experiencing landscape changes associated with oil and gas development. The dune-dwelling lizard community contains a habitat specialist, Sceloporus arenicolus, that is of particular interest because it has a very limited geographic distribution that is entirely subject to oil and gas development. Distance sampling is widely used to estimate population densities of many vertebrate taxa however assumptions can be difficult to satisfy with certain species or in certain habitats. Researchers must investigate the likelihood that assumptions can be satisfied before implementing any population sampling method. I had two objectives. First to investigate the precision of population densities of dune-dwelling lizards estimated via distance sampling that was coupled with double-observer surveys. Second to compare abundances of dune-dwelling lizards among sites that varied in oil and gas development. I conducted distance line transects and compared those density estimates to densities obtained from total removal plots. I quantified the amount of oil and gas development, habitat quantity and quality and correlated those to lizard abundances to investigate the effects of oil and gas development on lizard populations. I found large differences in density estimates from distance sampling and total removal plots that resulted from violation of distance sampling assumptions. Although distance sampling is a low cost method, it does not produce reliable density estimates for dune-dwelling lizards and is not an appropriate sampling method in this system. I did not find oil and gas development effects on the habitat quantity, quality or on the abundances of lizards. Lizard abundances were most strongly correlated to habitat quantity. Lizard abundances may be influenced by complex interactions between oil and gas development and habitat quantity and quality but controlling for those interactions was beyond the scope of my study. Before and after experiments and long-term studies at multiple sites would be required to more fully address the effects of oil and gas development on lizard populations in the Mescalero Sands.

No description available.

This study examined population density and habitat use of a species of greater galago, genus Otolemur, around Mt. Kasigau, Kenya. Mt. Kasigau has a unique regional microclimate, a cloud forest, which provides many different flora and fauna a home. To examine population density, two different methods were used. The first method was using line transects and analyzing results using Distance 6.0. These surveys were conducted during both dry and wet season and results were compared after the study. The second method was to trap individuals and use mark-recapture to determine population density. When caught in a trap, individuals were also weighed and measurements were taken. Accurate weight was taken for 17 individuals; ear height, tail length, and hind foot length were recorded for 21 individuals. Mark-recapture data were analyzed using Krebs/WIN 3.0. Population density estimates using both methods were compared and provided similar results; Distance 6.0 estimated 0.62 individuals per hectare and Krebs/WIN 3.0 estimated 0.51 individuals per hectare. Morphological measurements were not consistent with published data of known species of Otolemur garnettii, which is the most common greater galago in East Africa. It is possible the Mt. Kasigau population is reproductively isolated and DNA analysis should be conducted in the future. Habitat usage of greater and lesser galagos and diurnal primates was examined to determine which tree species are commonly used by these individuals.

Many natural resource agencies are managing white-tailed deer (Odocoileus virginianus) populations in suburban areas and require information about deer populations, deer impacts on vegetation, and human preferences toward deer and deer management to support decision making. My study based in the Chicago Metropolitan Area during 2007-2011, utilized a multi-faceted approach to investigate common obstacles in suburban deer management. In my findings, I discuss the need for managers to examine suburban deer populations and management issues at a broader scale (i.e., countywide versus single community) and the promotion of proactive deer management in lieu of the conventional paradigm of beginning management only when deer populations have become overabundant. Discussion topics include practicality and costs of deer density estimation and herbivory monitoring techniques over multiple plant communities and numerous study sites. In addition, I illustrate how a comprehensive human dimensions survey can identify determinants that contribute to the public's perceptions of deer density and assess the acceptability, conflict, and beliefs regarding deer management methods. Lastly, I describe the relationship between landscape characteristics and deer density; this information can be utilized to determine suburban lands that may be prone to high deer densities and inform land management practices. My work provides suburban natural resource managers with techniques to identify management practices supported by their public constituents and information useful for managing deer populations.

Current research is necessary to focus management of white-tailed deer (Odocoileus virginianus) in the agricultural Midwest, especially given the novel presence of chronic wasting disease in the region. My objectives were to: 1) examine the potential effects of weather and row-crop harvest on daily harvest of white-tailed deer by archery, and individual hunter variables (e.g., age, weapon preference, preference of hunting method) on individual hunter efficiency and success in 2 regions of Illinois (i.e., east-central and southern Illinois); 2) estimate white-tailed deer densities using direct (i.e., spotlighting deer from road transects) and indirect (i.e., counting pellet groups on randomly-placed transects) techniques across 3 study areas in the midwestern U.S.; 3) quantify sex, age, and season-specific survival and dispersal rates of white-tailed deer in east-central Illinois; and 4) assess habitat selection of white-tailed deer during the summer months in east-central Illinois. Knowledge of factors affecting hunter efficiency and success is vital given current trends in hunter attitudes and behaviors that are leading to a reduction in the efficacy of white-tailed deer hunting as a population management tool nationwide. Numerous techniques of density estimation for white-tailed deer have been developed, including aerial surveys, mark-recapture or resight methods, pellet counts, and thermal infrared imaging surveys. Distance sampling has shown great potential for estimating white-tailed deer density at a reduced cost relative to traditional survey techniques and may be useful within the agriculturally-dominated Midwest. Survival and dispersal rates are pertinent model parameters when examining chronic wasting disease (CWD) geographic spread. Structural changes in agricultural landscapes are frequent (i.e., temporally) and ecologically abrupt (i.e., spatially) due to crop harvest and rotation and human development. Providing sex-specific data on site selection would benefit agencies and private land owners by allowing compartmental focus for selective management strategies for either male or female white-tailed deer. Following the 2006 hunting season, I queried white-tailed deer hunters regarding factors potentially affecting hunter efficiency and success in east-central and southern Illinois using a mail-in survey (n = 2,000). I also examined the influence of weather and row-crop harvest progress on daily harvest of white-tailed deer by archery hunting. Hunter efficiency ( ¡À SE= 0.12 ¡À 0.01 deer/day) and hunter success (range = 1.25-1.39 deer/hunter) were similar between study areas. No relationship (r2 <0.01) was detected between respondent age and hunter efficiency, but had a weak influence (r2 = 0.006) on hunter success. Respondents that preferred shotguns, used 1 weapon, and those that preferred still hunting had 62%, 58%, and 52%, respectively, greater (P ¡Ü 0.001) mean hunter efficiency than those in the lowest group within their particular categories. There was no apparent difference (P ¡Ý 0.087) in hunter efficiency across categories of area familiarity, number of hunting methods used, and scouting hours, or categories related to access and use of reconnaissance tools. Respondents that had ¡Ý11 years of area familiarity, preferred archery hunting, used ¡Ý 3 weapons, used ¡Ý3 hunting methods, scouted ¡Ý30 hours, and preferred tree stands had 51%, 45%, 62%, 35%, 61% and 41%, respectively, greater (P ¡Ü 0.001) mean hunter success than those in the lowest group within their particular categories. Access and use of GIS did not appear to affect (P = 0.376) hunter success. Respondents that had access and used topographic maps, aerial or satellite photographs, or GPS had 35%, 34%, and 29% greater (P ¡Ü 0.049), respectively, hunter success than those in the lowest group within their particular categories. Crop harvest progress did not (P = 0.780) appear to affect daily harvest of white-tailed deer by archery hunting. Three models of weather impacts on daily harvest of white-tailed deer by archery hunting had AICc <2. The most parsimonious models¡¯ covariates were MaxWSP, MSLP, and WDSP1, with MaxWSP (¦Â = -0.005) having a negative influence and MSLP (¦Â = 0.00007) and WDSP1 (¦Â = 0.006) having a positive influence on daily harvest of white-tailed deer by archery. I compared direct- and indirect distance sampling techniques for estimating white-tailed deer densities on study areas in east-central Illinois (ECI), southern Illinois (SI, 2007 only), and northern lower peninsula of Michigan (MI) during winter 2007-08. Density estimates obtained via indirect distance sampling for MI, ECI, and SI were 6.1-12.7, 11.2-15.8, and 15.4 deer/km2, respectively. Density estimates obtained via direct distance sampling for MI, ECI, and SI were 18.3-25.2, 14.4-18.1, and 19.0 deer/km2, respectively. Upon examining confidence interval (CI) overlap between direct- and indirect distance sampling techniques by year and study area, only the MI study had non-overlapping CI values. An examination of sites used by deer in summer and quantification of their survival and dispersal rates were conducted in east-central Illinois. From December 2005 to September 2009, I monitored 105 white-tailed deer for 35,478 radiodays for survival and dispersal analysis. I used Program MARK to estimate rates of annual survival, seasonal survival, and dispersal for fawns, yearlings, and adults. I measured habitat variables at sites used by white-tailed deer in summer and random locations in east-central Illinois, examining potential differences in site selection by sex and at multiple scales. Male and female full-season (winter/spring [16 Dec¨C14 May], summer [15 May-30 Sep], fall/winter [1 Oct¨C15 Dec]) survival rate ranged from 0.56 to 0.95 and 0.84 to 0.95, respectively. Male survival was lower than that of females during the fall/winter season for a model not accounting for overdispersion. Averaging across parsimonious models, the dispersal rate for yearling and fawn males and yearling and fawn females were 0.44 ¡À 0.07 and 0.41 ¡À 0.07, respectively. Adult male dispersal rate was 0.46 ¡À 0.15 and no adult females dispersed. Slight differences were observed in habitat variables at sites used by male and female white-tailed deer, but hypotheses of sexual segregation between the sexes were not supported. Males were never observed in developed landcover. Sex differences in the use of developed landcover approached significance with females using sites with that landcover 131% more than males; they also used sites with 87% higher patch density of wetland landcover than males. Based on the best-fit AIC model, overall (i.e., both males and females) site selection of white-tailed deer was influenced by patch density of agriculture landcover, percentage of fallow field landcover, disjunct core area of the landscape, upper visual obstruction, and percentage of shrubs. Increases in upper visual obstruction and percent of shrub increased the likelihood of a site being selected. Decreases in patch density of agriculture landcover, percentage of fallow field landcover, and disjunct core area of the landscape increased the likelihood of a site being selected. This study provides updated information regarding white-tailed deer demographics, habitat use, survey methods, and hunter behavior to white-tailed deer managers in the Midwest. The data produced from mail-in surveys may provide knowledge of influences on hunter efficiency and success that may be used to manipulate deer harvest under a declining number of hunters in the U.S. Consistent estimates of density between indirect- and direct distance sampling shows utility for use of direct distance sampling within agriculturally-dominated regions of the Midwest. Fine-scale management by private landowners may benefit from my data by demonstrating a preference for a particular landscape signature by deer during the summer.

Wildlife management and conservation frequently rely on understanding mechanisms that influence distribution and abundance of animals. I quantified space use for a population of inland riverine adult male alligators in Mississippi. Results indicated habitat selection is a scale-dependent process and aquatic vegetation, water depth, and water temperature may be important factors influencing alligator foraging and thermoregulation. Apparent habitat suitability and low alligator density did not manifest in an observed body size-based dominance hierarchy. I also analyzed long-term Mississippi alligator spotlight survey data for trends and effects of environmental covariates on counts. Model results indicated alligator counts have increased over time. This response likely reflects benefits accrued from decades of protection and wetland conservation. Distance sampling does not appear to be a feasible monitoring technique for riverine alligator populations. Nevertheless, it is important that survey protocols and monitoring programs account for imperfect detection and model important covariates.

Made available in DSpace on 2017-07-10T14:38:18Z (GMT). No. of bitstreams: 1 LACERDA.pdf: 2108583 bytes, checksum: abf7b4231c66cc12a04083c0090487bb (MD5) Previous issue date: 2013-07-18 / The almost complete replacement of the native vegetation of the Atlantic Forest by agriculture and livestock generated an altered matrix in which are embedded fragments of different sizes and historical use and degradation. In this study, the population density of Sapajus nigritus was estimated in two forest fragments surrounded by agricultural crops in southern Brazil. We use the method of linear transect between September 2011 and January 2013, covering 344.08 km in area and 216 km in another. We recorded 119 sightings and 35, respectively. In the first area the population density of Sapajus nigritus was 92.15 individuals / km2, and 32.10 individuals / km2 for the second area. While the lowest value is within the limits found for the species throughout its geographical distribution, the value of 92.15 individuals / km2 is among the highest ever recorded. In addition to offering food crops by anthropogenic factors such as low hunting pressure and predation, as well as composition and forest structure may be related to the densities found / A quase completa substituição da vegetação nativa da Floresta Atlântica pela agricultura e pecuária gerou uma matriz alterada onde estão inseridos fragmentos de diferentes tamanhos e históricos de uso e degradação. Neste estudo, a densidade populacional de Sapajus nigritus foi estimada em dois remanescentes florestais cercados por cultivos agrícolas no sul do Brasil. Nós utilizamos o método de transecções lineares entre setembro de 2011 e janeiro de 2013, percorrendo 344,08 km em uma área e 216 km em outra. Foram registrados 119 e 35 avistamentos, respectivamente. Na primeira área a densidade populacional de Sapajus nigritus foi de 92,15 indivíduos/km2, e 32,10 indivíduos/km2 para a segunda área. Enquanto o valor mais baixo está dentro dos limites encontrados para a espécie ao longo de sua distribuição geográfica, o valor de 92,15 indivíduos/km2 está entre os mais elevados já registrados. Além da oferta de alimento de origem antrópica pelos cultivos, fatores como baixa pressão de caça e predação, além da composição e estrutura da floresta podem estar relacionados às densidades encontradas

Le déclin du thon rouge de l'Atlantique nord-est et de Méditerranée (ABFT, Thunnus thynnus) qui faisait suite à une forte surexploitation a été largement médiatisé au cours de la dernière décennie. Pour contrer cette tendance et reconstituer ce stock, d’importantes mesures de gestion ont été mises en place à partir de 2007. En dehors des difficultés liées à leur mise en œuvre et à leur contrôle, la gestion des pêcheries thonières est aussi limitée dans les capacités à suivre précisément les variations d’abondance de ces espèces dont les observations reposent principalement sur les données de pêche. Le manque d’indice d’abondance fiable fait que l’évaluation du thon rouge, comme celle des autres espèces de poissons grands pélagiques, est entachée d’importantes incertitudes. Cependant, les suivis aériens pourraient permettre de fournir un indice d’abondance du thon rouge. Ils sont en effet fréquemment utilisés pour l'évaluation de l'abondance des mammifères marins et aussi par les pêcheurs pour détecter les poissons épipélagiques, comme les thons. Dans ce contexte général, cette thèse a pour objectifs : (i) d'évaluer des facteurs qui affectent potentiellement la détectabilité des thons pendant les suivis aériens, (ii) d’analyser leur comportement horizontal et vertical et les facteurs environnementaux qui l’influencent, et (iii) d’intégrer les connaissances acquises pour développer un indice abondance robuste du thon rouge en Méditerranée Nord Occidentale. Les analyses reposent sur des suivis aériens conduits depuis 2000 dans le golfe du Lion, une zone de nourricerie importante pour le thon rouge. Une modélisation des données basée sur le « distance sampling » montre des effets significatifs des observateurs, de la taille des bancs de thons et de l'état de la mer sur l’estimation d’abondance. Cette étude confirme par ailleurs une augmentation importance des abondances entre 2003 et 2009, probablement en réponse aux mesures de gestion mises en œuvre depuis 2007 (notamment la taille minimale de débarquement de 30 kg). Pour évaluer les effets du comportement sur les estimations d'abondance, une étude a porté sur les trajectoires de thons issues du marquage électronique. Ces analyses montrent une disponibilité des thons rouge ainsi qu’une présence en surface dans la zone et la période (Août-Octobre) des suivis aériens ; résultat confortant la fiabilité de l’indice d’abondance. On note également des changements saisonniers du comportement, avec un approfondissement des thons à partir de mi-Novembre correspondant à la dé-stratification de la colonne d’eau. Le comportement de plongée profonde était particulièrement fréquent pendant les mois de forte productivité biologique (février-Mai), mais des plongées profondes ont également été observées à la fin de l'été en relation avec des fronts thermiques. La variabilité des schémas migratoires sur l’horizontale et du comportement sur la verticale indique une forte composante opportuniste, probablement liée à la disponibilité des ressources alimentaires. Les résultats obtenus durant cette thèse démontrent la faisabilité d’obtenir un indice d’abondance de thon rouge robuste à partir des suivis aériens (donc indépendants des données de pêche) et fournissent un cadre théorique et méthodologique pour une extension de ce type de suivi afin de diminuer les incertitudes autour de l’évaluation de ce stock. Outre le thon rouge, les suivis aériens ont également permis un suivi du rorqual commun (Balaenoptera physalus) et des dauphins rayés (Stenella coeruleoalba). La présence des mammifères marins semble également être liée à la productivité élevée et l'activité méso-échelle de la zone d'étude. Si les dauphins présentent une distribution spatiale en partie corrélée à celle du thon rouge, les rorquals ne présentent pas de forte co-occurrence avec le thon rouge, résultat qui confirmerait une certaine proximité des régimes alimentaires des thons et des dauphins. / Declines in Atlantic bluefin tuna stocks (ABFT, Thunnus thynnus), due to extensive over-fishing, have been widely publicized in recent decades. To counteract this trend, regulatory measures have been introduced by the fisheries managers, aiming at the rebuilding of ABFT stocks. However, apart from difficulties in controlling the implementation of these measures, fisheries management is limited in its capabilities to track their efficiency due to major uncertainties in the stock assessment. Indeed, there is a general need of reliable indicators of ABFT abundance. Aerial surveys may provide a helpful tool for the abundance monitoring of this highly exploited fish species. They are frequently used for the abundance assessment of marine mammals and also by fishermen to detect epipelagic fish, such as tunas. The aim of this thesis was to address these issues and to create a robust fishery-independent abundance index for ABFT through aerial surveys. To achieve this goal, the focus was set on (i) the assessment of factors that potentially affect the detectability of ABFT during the aerial surveys, (ii) the habitat use of ABFT, i.e. their horizontal and vertical behaviour as well as the factors driving it, and (iii) the integration of the knowledge gained through these analyses in the development of a robust index of ABFT abundance. Surveys were conducted from 2000 onwards in the Gulf of Lions, an important nursery ground for ABFT in the Northwestern Mediterranean Sea. Line transect modelling of the sighting data revealed significant effects of detectability changes on abundance estimates, related to the observer teams employed, the size of detected ABFT schools and the sea state during the aerial surveys. Derived estimates of ABFT abundance confirmed a significant increase from 2003 to 2009, likely reflecting the success of recently implemented management measures (e.g. minimum landing size of 30 kg since 2007). To assess behavioural effects on abundance estimates, auxiliary archival tagging experiments, conducted since 2007, focused on the presence and surface availability of ABFT during the aerial surveys, and aimed to identify factors influencing these variables. The data gained from these experiments demonstrated seasonal changes in the migratory behaviour of ABFT, but also a high area and surface presence of ABFT in the study zone during the survey period (August–October), supporting the reliability of the abundance index. Surface presence of ABFT decreased with the breakdown of the thermal stratification of the water column (mid-November), when the fish left the survey zone and moved South. By contrast, deep diving behaviour was particularly frequent during months of high biological productivity (February--May), although deep and unusual long spike dives were also observed during late summer in relation to thermal fronts. However, the variability in the migration patterns indicates a strong opportunistic component in both, the horizontal and vertical behaviour of ABFT, probably related to the availability of food resources. Apart from ABFT, the aerial surveys also allowed an abundance monitoring of fin whales (Balaenoptera physalus) and striped dolphins (Stenella coeruleoalba) as well as an analysis of their co-occurrence with ABFT. In fact, similar to ABFT, the presence of these species appeared to be related to the high productivity and mesoscale activity of the study zone, improving our understanding of their habitat use, essential for the conservation of these much less abundant and endangered species. Regarding the stock assessment of ABFT, the results gained through this thesis prove the feasibility to derive robust fishery independent abundance indicators for ABFT through aerial surveys, providing the theoretical and methodological background for an extension of these efforts for a more sustainable management of the stocks of this species.