Ritmos biológicos e sua sincronização por ciclos ambientais geralmente são estudados em roedores, mantidos em laboratório. Nosso grupo vem estudando ritmos de atividade/repouso de roedores subterrâneos sul-americanos conhecidos como tuco-tucos (Ctenomys aff. knighti) em laboratório e campo. Na natureza, sabemos que os tuco-tucos emergem à superfície diariamente em episódios de até uma hora. Registros curtos da atividade de superfície dos tuco-tucos, anteriormente obtidos pelo grupo, haviam sugerido que o padrão diário das saídas variava sazonalmente, sendo crepusculares durante o verão e concentrados no meio do dia, durante o inverno. Esse mesmo padrão sazonal já foi observado em populações de outros roedores de deserto e foi atribuído a reações dos roedores às variações diárias de temperatura, no verão e inverno. Por outro lado, a sazonalidade dos padrões de atividade de várias espécies de mamíferos e aves também pode ser explicada pela sincronização diária do ritmo de atividade a diferentes fotoperíodos. O objetivo desse trabalho é caracterizar a variação sazonal dos ritmos diários de atividade dos tuco-tucos, com uso de bio-logging, e verificar a contribuição dos fatores ambientais para a sazonalidade desses padrões. Ao longo do ano, acelerômetros e luxímetros foram presos a 29 animais recentemente capturados (15 fêmeas e 14 machos). Cada animal foi mantido individualmente em arenas semi-naturais por um mês. Variáveis ambientais foram registradas simultaneamente. Outros 18 animais (9 fêmeas e 9 machos) foram mantidos em laboratório, expostos ao fotoperíodo natural e em ambiente com temperatura constante. Os resultados confirmaram a sazonalidade do padrão temporal de atividade de superfície dos tuco-tucos. Os acelerômetros se mostraram mais precisos e sensíveis a pequenos movimentos corporais do que os registros de telemetria encontrados na literatura. Esses sensores também revelaram padrões de atividade subterrânea e noturna, em ambiente semi-natural. Durante o verão, a atividade de superfície diária dos tuco-tucos foi melhor prevista pelo horário do dia (fator endógeno) do que pelas variações de temperatura ambiental (fator exógeno). Durante o inverno, entretanto, a temperatura ambiental teve maior contribuição no padrão de saídas dos tuco-tucos, indicando complexas contribuições dos fatores endógenos e exógenos no delineamento dos padrões de atividade / Biological rhythms and their synchronization by environmental cycles are generally studied in rodents, inside laboratory. Our group studies activity/rest rhythms of South American subterranean rodents known as tuco-tucos (Ctenomys aff. knighti), in laboratory and field. In nature, it is known that tuco-tucos emerge daily to the surface, in brief episodes. Short records of tuco-tucos\' individual surface activity, previously collected by our group, had suggested that daily temporal pattern of emergence varied seasonally, being crepuscular in summer and concentrated around midday in winter. The same seasonal pattern was observed in populations of other desert rodents and was attributed to daily variations of environmental temperature, in summer and winter. At the same time, seasonality of activity patterns of various species of mammals and birds can be explained by daily synchronization of the activity rhythm by different photoperiods. Our aim is to characterize seasonal variation of daily activity rhythms of tuco-tucos, using bio-logging, and to verify the contribution of environmental factors in the seasonality of these patterns. Throughout the year, accelerometers and luximeters were tied to 29 freshly caught animals (15 females and 14 males). Each animal was kept inside semi natural enclosures for one month. Environmental variables were recorded simultaneously. Other 18 animals (9 females and 9 males) were kept inside laboratory, exposed to natural photoperiod, in a room with constant temperature. We confirmed the seasonality of temporal pattern of surface activity of tuco-tucos. The accelerometers resulted to be more precise and sensitive to small body movements than telemetry records found in literature. They also revealed nocturnal and subterranean activity patterns inside the enclosures. During summer, daily surface activity of tuco-tucos was better predicted by time of day (endogenous factor) than by environmental temperature (exogenous factor). During winter season, however, environmental temperature has a stronger contribution on the emergence pattern in tuco-tucos, indicating complex contributions of endogenous and exogenous factors that outline activity patterns

De nombreux prédateurs marins se nourrissent directement des prises des pêcheurs. Ces interactions, définies comme de la déprédation, engendrent des conséquences socio-économiques considérables pour les pêcheurs ainsi que des implications de conservation pour la faune sauvage. D’un côté, la déprédation endommage le matériel et augmente l’effort de pêche pour atteindre les quotas. D’un autre côté, la déprédation augmente le risque de mortalité des prédateurs marins (prise accidentelle ou rétorsion létale par les pécheurs). La pêcherie à la palangre est la plus impactée par la déprédation, principalement par les odontocètes, ce qui incite à trouver des solutions. La majorité des études se concentrant sur la déprédation s’est principalement basée sur des observations en surface, de ce fait la manière dont les prédateurs retirent les poissons sur les lignes reste confuse. Par ailleurs, l’impact de la déprédation sur le comportement des pêcheurs ainsi que les facteurs expliquant leur détectabilité n’ont reçu que peu d’intérêt. L’objectif de cette thèse est donc d’étudier ces problématiques par un suivi acoustique, une utilisation de balises et une approche en écologie comportementale humaine, en se concentrant sur la pêcherie palangrière française ciblant la légine australe (Dissostichus eleginoides) impactée par la déprédation des orques (Orcinus orca) et des cachalots (Physeter macrocephalus). Les capitaines ont été décrits comme recherchant leur ressource selon la théorie de « l’optimal foraging », mais avec des perceptions de la compétition et du succès de pêche qui divergent. Certains capitaines seraient ainsi plus enclins à remonter les palangres au plus proche et à rester sur une zone, même en présence de compétition, augmentant alors le risque d’interaction. L’acoustique des navires a révélé que certaines manoeuvres (marche arrière par exemple) propagent différemment sous l’eau. La manière dont les capitaines manoeuvrent leur palangrier influencerait ainsi leur détectabilité et donc leur risque d’interaction avec les prédateurs. D’autre part, l’utilisation de capteurs sur les palangres et les animaux a révélé que les orques et les cachalots sont capables de déprédater sur les palangres posées sur le fond marin. Ces observations laissent à penser que les odontocètes sont en mesure de localiser l’activité de pêche bien avant la remontée de la ligne, ce qui pourrait être expliqué par une signature acoustique spécifique du déploiement de la ligne. L’ensemble des résultats de cette thèse suggère que la déprédation sur les palangres démersales est très probablement sous-estimée. Cette thèse apporte également des éléments importants pour la lutte contre la déprédation, en montrant la nécessité de protéger les palangres dans l’intégralité du processus de pêche. / Many marine predator species feed on fish caught by fishers directly from the fishing gear. Known as depredation this interaction issue has substantial socio-economic consequences for fishermen and conservation implications for the wildlife. Costs for fishers include damages to the fishing gear and increased fishing effort to complete quotas. For marine predators, depredation increases risks of mortality (lethal retaliation from fishers or bycatch on the gear). Longline fisheries are the most impacted worldwide, primarily by odontocetes (toothed whales) depredation, urging the need for mitigation solutions to be developed. Most of studies assessing depredation have primarily relied on surface observation data, thus the way odontocetes interact with longlines underwater remains unclear. Besides, the way fishermen respond to depredation during fishing operations, or can influence their detectability to odontocetes, have been poorly investigated. This thesis therefore aimed at investigating these aspects through a passive acoustic monitoring, bio-logging and human ecology approaches, focusing on the French Patagonian toothfish (Dissostichus eleginoides) longline fisheries impacted by killer whales (Orcinus orca) and sperm whales (Physeter macrocephalus). Firstly, this thesis reveals that captains behave as optimal foragers but with different personal perception of competition and fishing fulfilment. Some captains would thus be more likely to stay within a patch or to haul closest longline even in presence of competition, suggesting these captains would show higher interaction rates. Additionally, the propagation of vessels’ acoustics varied depending on the type of manoeuvre (e.g. going backward vs. forward). The way captains use their vessels to navigate may therefore influence their detectability and so their depredation level. Secondly, loggers deployed on both the longlines (accelerometers) and odontocetes (GPS-TDR) revealed that killer whales and sperm whales are able to depredate on longlines while soaking on the seafloor. These observations suggest, therefore, that odontocetes can localise fishing activity before the hauling, which could be partially explained by specific acoustic signatures recorded during the setting process. Altogether, the results of the thesis suggest that depredation rates on demersal longlines are most likely underestimated. The thesis also brings some important insights for mitigation measures, suggesting that countermeasures should start from setting to hauling.

Recent bio-logging technology and associated techniques have uncovered the distribution, behaviour, and phenology of marine predators at remote locations, providing us with insights of not only scientific merit, but also in terms of conservation and management. This thesis explores the at-sea behaviour of marine birds using field studies and ethoinformatic approaches by using multiple data loggers, focusing on four species of free-ranging seabirds breeding in the UK. Key findings and conclusions are: Extending travel distance in central place foragers in the wild is associated with higher prey quality as estimated by an indirect method based on dive profiles. This result is consistent with a prediction of optimal foraging theory, but my results show empirically that seabirds are able to increase reward with distance at the extended scale of the marine environment. Razorbills Alca torda are capable of adjusting their foraging behaviour in response to proximate environmental conditions. The potential mechanisms underlying this adaptive behaviour are independent of breeding stage, but the magnitude of flight orientation is scale-dependent. These results suggest that Razorbills are capable of optimising their foraging adaptively, possibly reading cues from the environment or conspecifics. Diving behaviour in sympatric Atlantic Puffins Fratercula arctica and Razorbills is very similar, in contrast to the predictions of the competitive exclusion principle. They are likely to be near carrying capacity for the location and this may explain why Skomer’s Razorbill population is declining while its puffin population is stable. Differences in foraging trip duration of chick-rearing Manx Shearwaters Puffinus puffinus reflect differences in resource allocation between provisioning offspring and self-feeding. I developed a model based on patch quality and travel time to show that birds should use bimodal foraging trip durations to optimise feeding rates for their offspring. Individual reproductive performance in Manx Shearwaters can be predicted from previous breeding phenology and is linked to differences in overwintering behaviour patterns. This carry-over effect reveals the existence of a trade-off between current parental investment and future reproductive performance.

Du fait de l’isolement géographique de l’océan austral et des conditions météorologiques qui y règnent, la collecte de données océanographiques par les moyens conventionnels est particulièrement couteuse dans cette région du globe. Pour pallier à ces difficultés, l’utilisation d’enregistreurs électroniques embarqués sur des prédateurs marins, et notamment sur les éléphants de mer austraux, s’est révélée être une approche intéressante. Les femelles éléphants de mer s’alimentent en grande partie de petits poissons méso-pélagiques bioluminescents, les myctophidés. Leur forte abondance et leur comportement de migration nycthémérale confèrent à ces organismes un rôle écologique de première importance dans l’océan austral. Cependant, la distribution spatiale des proies de l’éléphant de mer, et les processus physiques et biologiques qui influent sur la dynamique de cette distribution sont encore mal connus. Cette thèse se propose d’enquêter sur ces sujets à partir des données à haute fréquence d’échantillonnage collectées par des femelles éléphants de mer. L’analyse du comportement de plongée des femelles éléphants de mer, en relation avec les variations du taux de rencontre de proie dont les données d’accélération permettent d'avoir une estimation, est au cœur des différents travaux développés dans cette thèse. Les résultats obtenus suggèrent notamment, (1) une diminution de l’abondance des proies avec la profondeur ainsi qu’une homogénéisation de leur distribution, (2) une distribution en couches de cette ressource, (3) l’intervention de contraintes verticales délimitant l’étendue verticale de ces couches et ainsi capable de moduler leur densité, (4) au sein des couches, une dispersion relativement importante des proies en comparaison de la portée des capacités de perception du prédateur, et enfin (5) un rôle significatif des tourbillons méso-échelle et de leur bordure sur la structuration de la distribution des ressources alimentaires de l’éléphant de mer durant l’été austral. / Because of the remoteness and harsh meteorological conditions of the southern ocean, data sampling is more costly in this area. Use of electronic devices attached to marine predators (Bio-logging), such as southern elephant seals, has emerged as an interesting approach to cope with this problem. Female southern elephant seals primarily feed on small bioluminescent meso-pelagic fishes called myctophids. Because of their large abundance and of their diel vertical migration behaviour, these organisms have a major ecological importance in the southern ocean. However, the spatial distribution of the elephant seals prey, as well as the bio-physical processes affecting the dynamics of this distribution, are still poorly known. This thesis intends to investigate this issue using high sampling frequency bio-logging data collected by female southern elephant seals. This work is based on the analysis of elephant seals diving behaviour in relation to changes in the occurrence of prey encounter events detected from acceleration data. Our results suggest that (1) prey abundance decreases with depth and that their distribution tend to standardize, (2) prey are distributed into layers, (3) vertical constraints could modulate the prey density by acting on the vertical spread of these layers, (4) prey items are well dispersed in comparison to the perception range of elephant seals, and finally (5) that meso-scale eddies, notably their edges, play a structuring role in the prey distribution during the austral summer.

Le compromis d’allocation de l’énergie entre les fonctions concurrentielles de la reproduction et de la maintenance (et à long terme la survie) est largement tributaire de la capacité de l’organisme à acquérir des ressources dans son milieu. Les mécanismes physiologiques sousjacents aux décisions d’acquisition et d’allocation de l’énergie sont actuellement peu connus. Le but de cette thèse est d’étudier le rôle de deux hormones, la corticostérone et la prolactine, dans ces prises de décisions chez un oiseau marin longévif, le manchot Adélie (Pygoscelis adeliae), et ce, pendant une phase couteuse en énergie : la période d’élevage des poussins. Pour ce faire, nous avons conduit des approches expérimentales couplant d’une part la manipulation hormonale (augmentation des niveaux de corticostérone ou diminution des niveaux de prolactine) et la mesure du comportement en mer grâce à l’utilisation d’enregistreurs miniaturisés de l’effort de plongée. Par ailleurs, le budget temps, la condition corporelle, le régime alimentaire (analyses des isotopes stables du carbone et de l’azote) ainsi que le succès de reproduction des individus ont été considérés. A l’échelle de la plongée, nous avons observé des rôles positifs et négatifs de la corticostérone et de la prolactine, respectivement, sur le comportement de recherche alimentaire. De façon contradictoire, il semble que la corticostérone ait eu un effet négatif à plus large échelle (e.g. diminution de la durée des voyages alimentaires). La complexité de l’implication de ces deux hormones dans le compromis entre survie et reproduction est finalement discutée à la lumière de ces résultats. / The trade-off in the allocation of energy between the competitive functions of reproduction and maintenance (and survival in the long term basis) is largely dependent on the capacity of organisms to acquire resources in its environment. However, physiological mechanisms underlying decisions of energy acquisition and allocation are currently poorly known. Theaim of this PhD is to examine the role of two hormones, corticosterone and prolactin, in these decision processes in a long-lived seabird, the Adélie penguin (Pygoseclis adeliae) during an energetically costly period: the chick-rearing stage. To achieve this, we conducted experimental approaches coupling hormonal manipulation (increasing corticosterone levels ordecreasing prolactin levels) and the monitoring of at-sea behaviour by using miniaturised time-depth recorders. Moreover, time budget, body condition, diet (via stable isotopes analyses) and reproductive success of individuals were considered. At the dive scale, we observed positive and negative roles of corticosterone and prolactin on the foraging behaviour, respectively. However on the contrary, it seems that corticosterone had a negative effect at a larger scale (e.g. a decrease in at-sea trip duration). The complexity of the involvement of these hormones in the trade-off between survival and reproduction is discussed in the light of these results.

京都大学 / 新制・課程博士 / 博士(情報学) / 甲第23318号 / 情博第754号 / 新制||情||129(附属図書館) / 京都大学大学院情報学研究科社会情報学専攻 / (主査)教授 守屋 和幸, 教授 大手 信人, 教授 三田村 啓理 / 学位規則第4条第1項該当 / Doctor of Informatics / Kyoto University / DFAM

Large carnivores are among the most challenging species to conserve in our modern and crowded world. Having large spatial requirements and living in low density, they generally require wide and relatively undisturbed areas. In Europe, one of the most anthropized areas of the planet, these needs must be fulfilled in a complex human-dominated landscape. The reintroduced brown bear population living in the Central Alps represents one of the most emblematic examples of a constrained carnivore: despite a steady population increase in the first few years after reintroduction, the population did not substantially expand its range, nor has the Alpine-Dinaric metapopulation been reestablished as envisioned. Although humans have lived in the Alps for centuries, little is known about their impact on the bear population. In other environments humans are known to function as a “super-predator” by changing habitats, competing for space, consuming resources, and harvesting, which alters the ecological niche of animals, especially large carnivores. This dissertation aims to evaluate this phenomenon by assessing the effects of human disturbance on brown bears in the Alps. Anthropogenic disturbance is generally assessed by structural proxies, such as infrastructure and land use, which overlook the impact of human presence. In the first Chapter, we developed the Cumulative Outdoor activity Index (COI) to derive anthropogenic disturbance using crowdsourced data by Strava and validated it with ground truth observations derived from a local camera trapping survey. The intensity of COI provided an effective measure of functional anthropogenic disturbance, and it outperformed all commonly-used proxies of structural disturbance in predicting bear habitat use. When displacement is not an option because of habitat limitations and social mechanisms, bear mobility may clash with human activity. During the moments of lowest mobility, such as resting periods, animals have decreased ability to cope with risky situations, and therefore the selection of suitable resting areas is crucial for the long-term survival of individuals. In the second Chapter, we measured multi-scale response to risk perception (i.e., COI) and resource proximity using bedding sites by GPS radio-collared adult brown bears in the Alps. To map resources across the study area, we developed a GIS-database combining spatial and non-spatial ecological information to map fruit availability. We observed that bears apply a security-food trade-off strategy, avoiding functional anthropogenic disturbance while in proximity to resources. In the third Chapter, we explicitly tested the effect of an abrupt interruption of human mobility during COVID-19 lockdown on bears’ use of ecological corridors. Using bear occurrences reported to local authorities during the recent COVID-19 outbreak, we observed that bears used human-dominated areas more frequently, approached more intensively hot spots for road crossing network, and used areas further from the population core areas more often than previous years, suggesting that connectivity increased with reduced human mobility. In a comparatively human-free system, for the fourth Chapter we used longitudinal morphometric data to analyze drivers of changes in body mass as part of an international collaboration with biologists studying the grizzly bear in the Greater Yellowstone Ecosystem. Specifically, we analyzed changes in lean body mass and fat percentage during years of major ecosystem perturbations. We observed that individual lean body mass during the last two decades was primarily associated with population density, but not body fat percentage, showing density-dependent factors. Our combined findings (Chapters 1-3) showed that brown bears have to adapt their space use, movement, and resource proximity as a result of functional anthropogenic disturbance. In Chapter 4 we explored one effect of unconstrained bear space use on individuals, as manifested through density-dependent effects on body size. In the Alps, however, we found multiple instances of the human-super predator outcompeting bears so as to make density-dependent effects likely less significant as compared to human-caused mortality. These effects could occur in a variety of socio-ecological contexts across Europe, jeopardizing the long-term establishment of both newly reintroduced bear populations, as well as spatially limiting those naturally present in the environment. In response to disturbance, bears have had to reduce their ecological niche in human-dominated landscapes. Allowing humans and bears to coexist in the same landscape is a challenging task, but it is essential for the long-term survival of this newly reintroduced population that are otherwise at risk of extinction.