Conservation biologists require information on the distribution, ecology, behaviour and genetic diversity of endangered species in order to identify threatened populations, determine which mechanisms are driving populations closer to extinction, and design appropriate mitigating solutions. The hazel dormouse, Muscardinus avellanarius, is declining across much of its northern range. Dormice are detrimentally affected by habitat degradation, loss and fragmentation. Despite extensive studies and conservation work on hazel dormice, there remain many gaps in our understanding. This thesis aims to fill some of those gaps. Hazel dormice are elusive, and therefore difficult to monitor in the wild. I demonstrate the utility of novel monitoring techniques for the rapid determination of dormouse presence, and provide algorithms for the objective verification of species identity from small mammal footprints. I design and utilise genetic microsatellite markers to investigate molecular ecology in this species. In one of the first studies of hazel dormouse population genetics, I describe high levels of population differentiation and genetic isolation across the southwest UK range. I find a powerful signal of reduction in genetic diversity, and an increase in differentiation between core and peripheral populations. I consider rival hypotheses for the mechanisms driving this population genetic pattern, and place the results in the context of conservation strategies for UK dormice. Further, I use molecular data to investigate the prevalence of multiple paternity in wild dormouse populations. Results contradict a recent estimate of very high rates of polyandry, but remain high at 50%. I investigate the effect of food availability on the hibernation behaviour of dormice. My findings, which demonstrate dormice are variable and flexible in their response to winter diet, increases our understanding of the trade-offs dormice must make in order to survive winter periods. I hope that the research undertaken for this thesis will add to the understanding and conservation of an iconic British mammal, ultimately contributing to the persistence of this species.

京都大学 / 新制・課程博士 / 博士(農学) / 甲第24243号 / 農博第2522号 / 新制||農||1094(附属図書館) / 学位論文||R4||N5414(農学部図書室) / 京都大学大学院農学研究科応用生物科学専攻 / (主査)教授 松浦 健二, 教授 大門 高明, 教授 日本 典秀 / 学位規則第4条第1項該当 / Doctor of Agricultural Science / Kyoto University / DFAM

Le cachalot, Physeter macrocephalus le plus grand des odontocètes, a été longtemps exposé à la pêche pour extraire l'huile contenue dans sa tête (spermaceti), et est maintenant vulnérable. Les cachalots nagent dans divers endroits du globe et atteignent les plus grandes profondeurs, où ils chassent par écholocation. Ils émettent des sons, des clics à large bande, à structure multi-pulsée générée par des réflexions intra-tête. Ces clics contiennent de l'information sur la taille de l'animal et sur son orientation, reposant sur les délais entre les pulses qui le composent (intervalle inter-pulse 'IPI'). Ces mesures sont utiles dans la préservation et les efforts de suivi populationnel du cachalot, puisqu'il est impossible de filmer ces mammifères nageant en grandes profondeurs.Les avancées technologiques permettant un essor considérable du nombre d'enregistrements sous-marins. Des algorithmes d'analyse automatiques sont alors requis pour le suivi de cette population ou des études comportementales et mesures de protection. La littérature offre une variété de méthodes pour le calcul de l'IPI. Cependant, elles souffrent d'un mélange des différents délais entre pulses résultant en une estimation de l'IPI peu précise et, par conséquent, de la taille de l'animal. De plus, ce mélange des différents délais entre pulses ne permet pas l'extraction de données sur l'orientation de l'animal. Dans cette thèse, une nouvelle méthode pour une analyse fine de l'IPI est présentée. Elle ne mélange pas les différents délais entre pulses, mais sélectionne les pulses à travers une analyse combinatoire et statistique. Il en résulte une meilleure estimation de la taille du cachalot. De plus une information supplémentaire, sur son orientation, est extraite. Notre algorithme est comparé avec ceux de l'état de l'art. Nous en discutons ses forces et faiblesses.Les résultats expérimentaux sont donnés autant sur des exemples avec un ou plusieurs cachalots émettant en même temps, que sur des données obtenues en différentes zones géographiques (France, Italie, Etats-Unis) et à partir de différents systèmes d'enregistrement. Ceci démontre la robustesse de la méthode proposée, et donne des perspectives pour le suivi des cachalots à l'échelle du globe. / The sperm whale, Physeter macrocephalus, the largest odontocete has been exposed for years to whaling due to the presence of liquid wax located in its head (spermaceti). This species is now considered as vulnerable. Sperm whales are located in various oceans and seas around the world. These animals are able to reach the deepest depths, where they use an echolocation technique to hunt. They emit broadband clicks that are comprised of a multi-pulse structure resulting from intra-head reflexions(spermaceti). These clicks contain information about the length of the animal and on its orientation, which reside in the delays between the pulse structure within the clicks, known as the Inter-Pulse-Interval (IPI). Measurement of these IPIs are determinant in the in the global preservation and the monitoring of sperwhales population since it is highly difficult to obtain visual clues of these deep-diving mammals.Moreover, the increasing technological advances have enabled the obtention of larger amount of underwater recordings. Therefore, the use of computational methodologies to automatically analyze the sperm whales click sounds have become a necessity in order to carry out populations monitoring and marine ecosystems studies. The current literature offers a variety of methodologies to calculate the IPI. However, these methodologies suffer from a merging of the different pulse delays and thus leading to less accurate estimation of the IPI and, in turn, of the whale's size. Moreover, from this merging methods no additional information regarding the orientation of the sperm whale can be easily extracted. In this thesis work, a new methodology for accurate IPI estimation is presented without relying on the merging of the different pulse delays, but, instead, by selecting the unique candidate pulse through a combinatorial and statistical analysis resulting in a better precision in the final estimation of the sperm whale's size and providing additional information on the whale's orientation.Our methodologies are compared with the known state of the art algorithms and their strengths and weaknesses are discussed. Experimental results are showcased of single and multi-whale examples from a variety of data obtained in different locations such as France, Italy and Canada and diverse acquiring systems. This strategy permits to testify and evaluate the robustness of the proposed methods and give perspectives in sperm whale monitoring at a global scale.

O presente trabalho teve como objetivo conhecer os fatores que propiciam as grandes densidades ecológicas de capivaras, através da comparação das dinâmicas populacionais de dois agrupamentos, em diferentes localidades do município de Pirassununga, SP (Campus Administrativo da Universidade de São Paulo – USP/Pirassununga e o Centro de Pesquisa e Gestão de Recursos Pesqueiros e Continentais – CEPTA/Ibama), para que futuramente seja possível propor uma metodologia de manejo que promova o controle populacional dessa espécie no Estado de São Paulo. Para tanto, foi realizado o monitoramento populacional de ambos agrupamentos durante 15 meses, através da contagem direta dos animais, constituindo na principal fonte de informação para determinar as dinâmicas populacionais. Adicionalmente realizaram-se as capturas dos indivíduos de ambas populações pelo uso de bretes fixos, para que fossem feitas as pesagens, sexagens e marcações eletrônicas pelo uso de microchips e assim, conhecer a distribuição etária, bem como a proporção entre sexos. O uso de ceva no interior dos bretes, para a atração dos animais, possibilitou a realização das contagens diretas e das capturas e recapturas. Para a análise das dinâmicas populacionais foram realizadas as comparações descritivas e estatísticas das densidades ecológicas das populações e das respectivas classes etárias, além do cálculo da taxa de crescimento das mesmas. A alimentação em ceva apresentou-se influenciada pela hierarquia de dominância social, o que fez com que apenas as parcelas dominantes fossem capturadas. Percebeu-se, através das capturas, que o número de fêmeas apreendidas foi superior ao de machos nas parcelas dominantes das duas populações. Por meio das observações foram detectados indivíduos satélites e subagrupamentos, cuja ocorrência pode caracterizar um sistema biológico de metapopulação. A comparação descritiva e estatística das densidades ecológicas das populações, bem como a comparação das taxas de crescimento revelaram superioridade populacional do agrupamento do CEPTA/Ibama em relação ao Campus da USP/Pirassununga, provavelmente pelo maior número de picos de acasalamentos observados, os quais possivelmente são influenciados pelo tipo de habitat antropizado e abundante em recursos hídricos presente no CEPTA/Ibama. / The present research aimed the knowledge of the factors that allow the high ecological densities of capybaras through the population dynamics comparison of two capybara groups in the district of Pirassununga, SP (Campus Administrativo da Universidade de São Paulo – USP/Pirassununga and Centro de Pesquisa e Gestão de Recursos Pesqueiros e Continentais – CEPTA/Ibama), intending to propose forward a management methodology for capybara population control in the State of São Paulo. The populations monitoring was carried out through direct count of animals during 15 months, which played the main role to determine the population dynamics. Fixed traps were used to allow the weightings, sex definitions and identification through microchips, and also to know the age distribution and sex ratios. It was used bait inside the traps to attract animals and thus make direct counting and capture possible. To analyze population dynamics it was used the population ecological densities comparisons (statistically and descriptively) and also their rates of increase. It was detected social dominance hierarchy inside the traps, thus only the dominant part of population could be caught. Females represented the majority among captured animals. Satellites individuals and new groups were seen during observations and their existence might characterize a biological system of metapopulation. The descriptive and statistic comparisons of population ecological densities, as well as their rates of increase showed population superiority of CEPTA/Ibama’s group probably for its bigger reproduction effort detected, which possibly receives influence of anthropogenic and water abundant habitats of CEPTA/Ibama.

The Corn Bunting Emberiza calandra is one of the most severely declining farmland birds across Europe. In the UK, numbers fell by 86% between 1967 and 2008. Corn Buntings favour open landscapes, nest on or close to the ground, are often polygynous, double-brooded, and have a seed-based diet supplemented in summer by invertebrates. This study investigated the recent causes of decline in arable and mixed farmland in eastern Scotland, and sought to identify potential conservation solutions that could be delivered through agri-environment schemes (AES). Combining new data with analyses of existing long-term datasets, I investigated habitat associations during summer and winter, the timing and success of nesting attempts, and measured reproductive and population responses to AES. Corn Buntings declined almost to extinction in one study area where, over 20 years, the main recorded intensifications of farming were reduced weed abundance within crops and removal of boundaries to make bigger fields. Territory locations, late-summer occupancy and polygyny were all strongly associated with weedy fields. There were also positive associations with overhead wires and in early summer with winter barley and forage grasses. Late-summer occupancy was associated with spring-sown cereals, crops that are amongst the last to be harvested. Changes in habitat associations and to aspects of the mating system as the population declined and agriculture intensified are discussed. Intensive monitoring showed that Corn Buntings laid clutches from mid-May to mid-August, mostly in fields of forage grasses and autumn-sown cereals in early summer, and spring sown cereals in late summer. A preference for nesting in dense swards explained this seasonal variation. Breeding success in forage grasses was poor, due to high rates of nest loss during mowing. However, in experimental trials, nest success in fields with delayed mowing was fivefold that of control fields. With sufficient uptake through AES, delayed mowing could raise productivity to levels required to reverse population declines. In winter, cereal stubbles and AES unharvested crop patches were the main foraging habitats used. Unharvested crops with abundant cereal grain in their first winter of establishment were favoured. Population monitoring over seven years and 71 farms revealed increases on farms with AES targeted at Corn Buntings, no significant change on farms with general AES, and declines on control farms. In arable-dominated farmland, management that increased food availability reversed declines, but on mixed farmland where Corn Buntings nested in forage grasses, delayed mowing was essential for population increase. This study has already influenced the design of AES targeted at Corn Buntings in Scotland, and I make further recommendations for the species’ conservation and design of AES that are applicable to farmland throughout Britain and Europe.

Developing cost-effective tools for population monitoring and research is fundamental to wildlife management programs. This is a major challenge for solitary-nesting, secretive seabirds distributed throughout remote areas of Alaska: the marbled murrelet (Brachyramphus marmoratus) and Kittlitz’s murrelet (B. brevirostris). Both species have experienced major population declines in Alaska, which is the centre of the distribution of their global populations. In 2010-2012, I tested the reliability of two new remote-sensing approaches, marine radar surveys and autonomous acoustic monitoring, to assess population size, trends and distributions of Brachyramphus murrelets in the Kodiak Archipelago. The goals were to compare new and existing assessment tools, to identify differences in spatial and temporal patterns of activity by Brachyramphus murrelets at high latitudes, and to make recommendations for integrating remote-sensing methods into existing monitoring programs. Autonomous acoustic sensors provided a reliable index of marbled murrelet abundance at fine spatial scales (2-3 ha forest stands). Detections of marbled murrelet vocalizations by acoustic sensors and human observers were not statistically different across weekly means. Because high temporal replication could be achieved at no extra cost, automated acoustic sampling provided the best seasonal resolution in patterns of murrelet activity. Radar surveys identified a prolonged (150 min) duration of pre-sunrise inland flight activity relative to lower-latitude populations, reflecting the longer duration of twilight at high latitude. A clear trend in seasonal activity, increasing from June to late July, was identified by radar, audio-visual, and acoustic surveys. The strong seasonal increase in activity detected by radar surveys appears to be an important factor to consider in planning population monitoring programs. Radar surveys could not distinguish between Kittlitz’s and marbled murrelets, but identified potentially greater frequency of inland flight by Kittlitz’s murrelets during darkness based on comparisons between sites. Spatial patterns of abundance, estimated by radar counts, were best predicted by combinations of marine and terrestrial habitat variables within 5 km of nesting flyways, including area of steep slopes (45-90˚), area of old-growth forest, and at-sea densities < 200 m from shore in June. The largest murrelet populations occurred in both forested and unforested watersheds with steep topography; indicating that unforested steep slopes appear to be of greater importance to nesting marbled murrelets in Alaska than previously recognized, particularly in areas adjacent to marine productivity hotspots. I recommend that radar sampling protocols be modified for high latitude surveys to begin 2 h before sunrise to accommodate longer activity periods, and that surveys be repeated at similar dates across years to avoid confounding population change with seasonal changes in abundance. I propose integrating new remote-sensing tools into existing monitoring programs to increase power to detect population trends, reduce costs and risks associated with field personnel, and increase capacity for long-term monitoring of murrelet response to environmental change at multiple spatial scales. / Graduate / 0329 / 0472 / jenna.cragg@gmail.com

O presente trabalho teve como objetivo conhecer os fatores que propiciam as grandes densidades ecológicas de capivaras, através da comparação das dinâmicas populacionais de dois agrupamentos, em diferentes localidades do município de Pirassununga, SP (Campus Administrativo da Universidade de São Paulo – USP/Pirassununga e o Centro de Pesquisa e Gestão de Recursos Pesqueiros e Continentais – CEPTA/Ibama), para que futuramente seja possível propor uma metodologia de manejo que promova o controle populacional dessa espécie no Estado de São Paulo. Para tanto, foi realizado o monitoramento populacional de ambos agrupamentos durante 15 meses, através da contagem direta dos animais, constituindo na principal fonte de informação para determinar as dinâmicas populacionais. Adicionalmente realizaram-se as capturas dos indivíduos de ambas populações pelo uso de bretes fixos, para que fossem feitas as pesagens, sexagens e marcações eletrônicas pelo uso de microchips e assim, conhecer a distribuição etária, bem como a proporção entre sexos. O uso de ceva no interior dos bretes, para a atração dos animais, possibilitou a realização das contagens diretas e das capturas e recapturas. Para a análise das dinâmicas populacionais foram realizadas as comparações descritivas e estatísticas das densidades ecológicas das populações e das respectivas classes etárias, além do cálculo da taxa de crescimento das mesmas. A alimentação em ceva apresentou-se influenciada pela hierarquia de dominância social, o que fez com que apenas as parcelas dominantes fossem capturadas. Percebeu-se, através das capturas, que o número de fêmeas apreendidas foi superior ao de machos nas parcelas dominantes das duas populações. Por meio das observações foram detectados indivíduos satélites e subagrupamentos, cuja ocorrência pode caracterizar um sistema biológico de metapopulação. A comparação descritiva e estatística das densidades ecológicas das populações, bem como a comparação das taxas de crescimento revelaram superioridade populacional do agrupamento do CEPTA/Ibama em relação ao Campus da USP/Pirassununga, provavelmente pelo maior número de picos de acasalamentos observados, os quais possivelmente são influenciados pelo tipo de habitat antropizado e abundante em recursos hídricos presente no CEPTA/Ibama. / The present research aimed the knowledge of the factors that allow the high ecological densities of capybaras through the population dynamics comparison of two capybara groups in the district of Pirassununga, SP (Campus Administrativo da Universidade de São Paulo – USP/Pirassununga and Centro de Pesquisa e Gestão de Recursos Pesqueiros e Continentais – CEPTA/Ibama), intending to propose forward a management methodology for capybara population control in the State of São Paulo. The populations monitoring was carried out through direct count of animals during 15 months, which played the main role to determine the population dynamics. Fixed traps were used to allow the weightings, sex definitions and identification through microchips, and also to know the age distribution and sex ratios. It was used bait inside the traps to attract animals and thus make direct counting and capture possible. To analyze population dynamics it was used the population ecological densities comparisons (statistically and descriptively) and also their rates of increase. It was detected social dominance hierarchy inside the traps, thus only the dominant part of population could be caught. Females represented the majority among captured animals. Satellites individuals and new groups were seen during observations and their existence might characterize a biological system of metapopulation. The descriptive and statistic comparisons of population ecological densities, as well as their rates of increase showed population superiority of CEPTA/Ibama’s group probably for its bigger reproduction effort detected, which possibly receives influence of anthropogenic and water abundant habitats of CEPTA/Ibama.

Cougars (Puma concolor) are difficult to census due to their large home ranges, low densities, and cryptic nature. The conventional “gold-standard” method for estimating cougar abundance entails the capture and radio-tagging of individuals in a study area in an attempt to acquire a direct enumeration of animals in the population. While this method provides an accurate abundance estimate, it is logistically challenging and prohibitively expensive. Noninvasive survey techniques may offer the ability to both accurately and inexpensively monitor cougar populations. While noninvasive techniques have been used on cougar populations, there remain questions on their accuracy and comparative efficacy. We estimated the density of a cougar population in Northwest Wyoming using direct enumeration, and used this estimate as a reference with which to evaluate the accuracy and cost-effectiveness of three types of noninvasive surveys performed between 2010 and 2014. The noninvasive methods included two annual mark- recapture sessions of: 1) remote camera trapping, 2) winter hair-collection transects, and 3) scat detection dog surveys. We GPS tracked 13 adult cougars (males = 5, females = 8) over 3 annual periods (Sep 2010 – Sep 2013). We used proportional home range overlap to determine density in a 1,570 km2 area. The average density was 0.82 cougars/100 km2 (± 0.10 SD; n = 3 years). The remote camera surveys produced a mean density of 0.60 cougars/100 km2 (n = 2 years; relative SD = 56.5%). The scat detection dog surveys produced an average density of 2.41 cougars/100 km2 (n = 2 years; relative SD = 12.6%). The winter transects failed to produce a sample size large enough for an abundance estimate. Due to the inclusion of non-adults in the scat sampling, and the fact that the reference estimate was essentially a minimum count of adults, we believe that the scat-based estimate was more accurate than the lower estimate produced by remote cameras. Additional analysis indicated that individual identification of cougars in photographs may not be reliable, challenging the validity of photo-based abundance estimates of cougars. On a cost-per-detection basis, scat detection dogs were the most cost effective method (scat detection dogs = $341; remote cameras = $3,241; winter transects = $7,627).

Monitoring population trend and estimating vital demographic parameters are essential for effective management of a mule deer (Odocoileus hemionus) population. Because of financial constraints, many wildlife agencies use computer models to obtain indirect indices of population size and trend as an alternative to annual field-based estimates of population size. These models are based primarily on herd composition counts and harvest rates from hunter-harvest surveys, and are rarely field validated. I developed an alternative method for monitoring population dynamics of wintering populations of mule deer. I designed a hybrid monitoring program that combined annual vital rate monitoring to track changes in population growth rate with a field-based approach for estimating population abundance. The program allocated resources optimally towards the most critical components of mule deer population dynamics, and consisted of 4 field surveys: annual monitoring of age ratios, overwinter fawn survival, and annual doe survival, with field-based estimates of population size only once every 4 years. Surveys were conducted from 2006 to 2008 in Wildlife Management Unit (WMU) 2, Utah, and cost $29,298 per year, prorated over 4 years. Unfortunately, financial constraints prohibit the implementation of this monitoring program in every WMU in Utah. Instead, the program can be implemented in select WMUs throughout the state, with survival data collected in these core units, providing estimates for nearby satellite units. To establish core-satellite unit pairs, I developed a proxy method for determining correlation in survival rates between core and satellite units using model-simulated estimates. I demonstrated this core-satellite method using WMU 2 as a core and WMU 3, an adjacent unit, as a satellite. Finally, I compared a multiple data sources (MDS) model with a herd composition-based population model, POP-II. The MDS model better approximated observed data, and provided statistical rigor. Overall, the hybrid program was less costly and provided more precise estimates of population trend than could be achieved with a monitoring program focused on abundance alone, and was more defensible than herd composition monitoring. After establishing correlations in doe and fawn survival between core and satellite units, data collected in core units via the hybrid program could then be used to model the mule deer population dynamics of other units using MDS modeling procedures. This combined approach could be an effective statewide program for monitoring mule deer populations.

This research spans a variety of research topics with a common theme, providing decision support through the development and analysis of methods that assist decision making for natural resource and wildlife management. I used components of structured decision making and decision analysis to address natural resources management problems, specifically monitoring and estimating the status of harvested populations, as well as data collection decisions for landscape conservation. My results have implications for the way populations are monitored and their status is estimated. I find that the inclusion of error in data collection can have a substantial impact of the performance of abundance and growth rate estimates of harvested species and that the selection of estimation methods depends on what management objectives are most important. For example, the Sex-Age-Kill population estimation method best estimates the size of populations, while the Downing population reconstruction method better estimates trends in population growth rates. I provide a framework to support selection of the best estimation method while considering a monitoring program as a whole. Based on this framework the Vermont Fish and Wildlife Department will obtain the most benefits from a monitoring program including necropsy analysis that uses the Downing method to track population status. Finally, I demonstrated the use of value of information analysis as a tool to determine the relative expected benefits of addition spatial data collection for use in landscape mapping and conservation. This type of analysis can provide conservation agencies with a planning tool to direct budgets and mapping efforts.