An important step for protecting Endangered species is the identification of critical habitat. This can be especially challenging for deep ocean species. Northern bottlenose whales (Hyperoodon ampullatus) are deep-diving beaked whales of the North Atlantic. A population of this species occurs along the edge of the Scotian Shelf primarily in three submarine canyons that have been identified as critical habitat for the population: the Gully (the largest submarine canyon off eastern North America), Shortland Canyon and Haldimand Canyon. The Scotian Shelf population is considered Endangered mainly due to its small numbers and the anthropogenic threats it faces. The primary objective of my research was to further identify critical habitat of the population using passive acoustic monitoring, increasing knowledge of how the whales use the canyons and adjacent areas throughout the year. A review of the literature on cetacean associations with submarine canyons indicates that various mechanisms may act to attract cetaceans to these features. While many different species occur in canyons globally, they appear to be particularly important habitat for beaked whales. I developed an automated click detection algorithm customized for detecting northern bottlenose whale echolocation clicks, and long-term acoustic recordings were analyzed to examine the presence and relative abundance of northern bottlenose whales on the Scotian Slope over various spatial and temporal scales. The whales occurred in the area consistently throughout the year and all three canyons, as well as the area between canyons, appeared to be important foraging grounds for the population. The whales displayed diurnal foraging patterns. I also investigated niche separation between northern bottlenose whales and sperm whales (Physeter macrocephalus), another deep diving species. The presence of the two species was positively correlated over all spatial and temporal scales examined. These results indicate that areas within and adjacent to the Gully are important foraging grounds for northern bottlenose whales throughout the year. Furthermore, in addition to the canyons themselves, the shelf-edge areas between the Gully, Shortland and Haldimand canyons may constitute critical habitat for the whales. This research will be used to inform management measures relevant to the protection and recovery of this Endangered population.

This thesis develops and demonstrates an approach for estimating the three-dimensional (3D) location of a vocalizing underwater marine mammal using acoustic arrival time measurements at three spatially separated receivers while providing rigorous location uncertainties. To properly account for uncertainty in the measurements of receiver parameters (e.g., 3D receiver locations and synchronization times) and environmental parameters (water depth and sound speed correction), these quantities are treated as unknowns constrained with prior estimates and prior uncertainties. While previous localization algorithms have solved for an unknown scaling factor on the prior uncertainties as part of the inversion, in this work unknown scaling factors on both the prior and arrival time uncertainties are estimated. Maximum a posteriori estimates for sound source locations and times, receiver parameters, and environmental parameters are calculated simultaneously. Posterior uncertainties for all unknowns are calculated and incorporate both arrival time and prior uncertainties. Simulation results demonstrated that, for the case considered here, linearization errors are generally small and that the lack of an accurate sound speed profile does not necessarily cause large uncertainties or biases in the estimated positions. The primary motivation for this work was to develop an algorithm for locating underwater Pacific walruses in the coastal waters around Alaska. In 2009, an array of approximately 40 underwater acoustic receivers was deployed in the northeastern Chukchi Sea (northwest of Alaska) from August to October to record the vocalizations of marine mammals including Pacific walruses and bowhead whales. Three of these receivers were placed in a triangular arrangement approximately 400 m apart near the Hanna Shoal (northwest of Wainwright, Alaska). A sequence of walrus knock vocalizations from this data set was processed using the localization algorithm developed in this thesis, yielding a track whose estimated swim speed is consistent with current knowledge of normal walrus swim speed. An examination of absolute and relative walrus location uncertainties demonstrated the usefulness of considering relative uncertainties for applications where the precise location of the mammal is not important (e.g., estimating swim speed). / Graduate

High intensity focused ultrasound (HIFU) provides a wide range of noninvasive therapies ranging from drug delivery to the destruction of kidney stones. In particular, thermal ablation by HIFU presents an effective noninvasive method for the treatment of deep seated solid tumours. HIFU’s further uptake is limited by a need for improved treatment planning and monitoring. Two nonlinear acoustic phenomena that play key roles in HIFU treatment: finite amplitude effects that lead to the generation of harmonics and steepening of wavefronts, and acoustic cavitation. The former must be taken into careful consideration for treatment planning purposes, while the latter has the potential to provide fast, real-time, cost effective treatment monitoring. The first half of this thesis provides new measurements for the nonlinear acoustic properties of tissue, assesses the validity of two common modelling techniques for simulating HIFU fields. The second half develops a new method for combining passive acoustic mapping- an ultrasound monitoring technique- with MR thermometry, to assess estimates of cavitation enhanced heating derived from passive acoustic maps. In the first results chapter B/A was measured in ex-vivo bovine liver, over a heating/ cooling cycle replicating temperatures reached during HIFU ablation, adapting a finite amplitude insertion technique (FAIS), which also allowed for measurement of sound-speed and attenuation. The method measures the nonlinear progression of a plane-wave through liver and B/A was chosen so that numerical simulations matched measured waveforms. Results showed that attenuation initially decreased with heating then increased after denaturation, sound-speed initially increased with temperature and then decreased, and B/A showed an increase with temperature but no significant post-heating change. These data disagree with other reports that show a significant change and suggest that any nonlinear enhancement in the received ultrasound signal post-treatment is likely due to acoustic cavitation rather than changes in tissue nonlinearity. In the second results chapter two common methods of modelling HIFU fields were compared with hydrophone measurements of nonlinear HIFU fields at a range of frequencies and pressures. The two methods usedwere the KZK equation and the commercial package PZFlex. The KZK equation has become the standard method for modelling focused fields, while the validity of PZFlex for modelling these types of transducers is unclear. The results show that the KZK equation is able to match hydrophone measurements, but that PZFlex underestimates the magnitude of the harmonics. Higher order harmonics in PZFlex are not the correct shape, and do not peak around the focus. PZFlex performs worse at higher pressures and frequencies, and should be used with caution. In the final two chapters a system for estimating cavitation-enhanced heating from acoustic maps is developed and benchmarked against magnetic resonance thermometry methods. The first chapter shows that the ultrasound and MR monitoring systems are compatible, and registers the two imaging systems. The HIFUfocus is clearly visible in passive maps acquired in the absence of cavitation and these coincide with the centre of heating in MR temperature images. When cavitation occurs, it coincides spatially and temporally with the appearance of a clear spike in temperature, especially when the passive maps are processed using the Robust Capon Beamformer algorithm. The final chapter shows how passive maps can be converted into thermal heating inputs, and used to estimate cavitation-enhanced temperature increases. These estimates have the potential to closely match maximum temperature rise, and estimated thermal dose after the estimated temperature rise is spatially averaged. However, themethod is not always successful. This is partly due to uncertainties in MR thermometry estimates, partly due to uncertainties in the acoustic properties of tissue.

京都大学 / 新制・課程博士 / 博士(情報学) / 甲第24936号 / 情博第847号 / 新制||情||142(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 大手 信人, 准教授 小山 里奈, 教授 三田村 啓理, 准教授 市川 光太郎 / 学位規則第4条第1項該当 / Doctor of Informatics / Kyoto University / DFAM

Nightjars are a group of nocturnal and aerial insectivorous birds that have experienced long-term decline likely driven primarily by habitat loss and declines in prey populations. Eastern Whip-poor-will (Antrostomus vociferus) and Chuck-will’s-widow (Antrostomus carolinensis), two nightjar species native to Illinois, declined 69% and 58% since 1966, respectively. Although previous survey efforts have documented presence of Chuck-will’s-widow and Whip-poor-will, their current distribution in the state is not well known. Using Autonomous Recording Units (ARUs) deployed in a uniform, systematic grid, I surveyed 142 locations from May – July 2022 on public and private lands across the southern eleven counties of Illinois to assess Whip-poor-will and Chuck-will’s-widow distribution and estimate species occupancy. I estimated species relationships with proportion of landcover types, forest patch configuration, and proximity to other landcover types. Additionally, I quantified disturbances from the past 15 years to estimate species relationships to the severity and duration of disturbances. I deployed ARUs for 710 survey days collecting 170,400 minutes or 3,000 hours of recordings. Acoustic bird call identification software, BirdNet, was highly accurate at detecting focal species and greatly reduced the time spent manually reviewing acoustic data. BirdNet identified 43,922 calls of Whip-poor-will and 31,447 calls of Chuck-will’s-widow. I detected Whip-poor-will on 78 surveys with 100% accuracy and Chuck-will’s-widow on 75 surveys with 76% accuracy. Whip-poor-will were positively associated with forest patches with large core areas that neighbored pastures. Additionally, Whip-poor-will were likely to occupy landscapes that had experienced low to moderate disturbance within the previous 15 years. Covariates used to model Chuck-will’s-widow occupancy explained little variation in detection or occupancy and there were no significant relationships with any covariate. However, examining non-significant trends suggest similar relationships as Whip-poor-will in the area. Results highlight the efficiency of passive acoustic monitoring for these birds and the need for further investigation into Chuck-will’s-widow species-environmental relationships. In southern Illinois, Chuck-will’s-widow populations appears to be consistent with previous estimates from the 1990s while Whip-poor-will follow the broader trend of decline.

Passive acoustic monitoring has been used to investigate many aspects of marine mammal ecology, although methods to estimate absolute abundance and density using acoustic data have only been developed in recent years. The instrument configuration in an acoustic survey determines which abundance estimation methods can be used. Sparsely distributed arrays of instruments are useful because wide geographic areas can be covered. However, instrument spacing in sparse arrays is such that the same vocalisation will not be detected on multiple instruments, excluding the use of some abundance estimation methods. The aim of this thesis was to explore cetacean abundance and density estimation using novel sparse array datasets, applying existing methods where possible, or developing new approaches. The wealth of data collected by sparse arrays was demonstrated by analysing a 10-year dataset collected by the U.S. Navy's Sound Surveillance System in the north-east Atlantic. Spatial and temporal patterns of blue (Balaenoptera musculus) and fin whale (Balaenoptera physalus) vocal activity were investigated using generalised additive models. Distance sampling-based methods were applied to fin whale calls recorded by an array of Ocean Bottom Seismometers in the north-east Atlantic. Estimated call density was 993 calls/1000 km².hr⁻¹ (CV: 0.39). Animal density could not be estimated because the call rate was unknown. Further development of the call localisation method is required so the current density estimate may be biased. Furthermore, analysing a single day of data resulted in a high variance estimate. Finally, a new simulation-based method developed to estimate density from single hydrophones was applied to blue whale calls recorded in the northern Indian Ocean. Estimated call density was 3 calls/1000 km².hr⁻¹ (CV: 0.17). Again, density of whales could not be estimated as the vocalisation rate was unknown. Lack of biological knowledge poses the greatest limitation to abundance and density estimation using acoustic data.

Despite the extensive Brazilian coast areas, little is known on underwater acoustic environments in Brazil. Acoustic environments (or soundscape) are composed by biological, geological and man-made sound sources. Soundscapes are strongly linked to ecosystems dynamics, and follow temporal patters that can vary at daily and seasonal scales. Thus, for soundscape characterization, it is necessary to undertake sound recordings for long periods, which demands innovative analyzing methods. Accordingly, the present research focuses in two principal objectives: (1) to develop methods for analyzing long-term acoustic recordings and, (2) to characterize marine soundscapes of selected points in São Paulo State. Four deployment sites were selected for the underwater acoustic monitoring: a point located at the channel entrance of the Santos Harbor, and three marine Protected Areas (PAs) in Sao Paulo state. As a result, the largest underwater acoustic database from Brazilian seas was acquired. The present work used Power Spectral Density (PSD), Sound Pressure Level (SPL) and Spectrograms to develop an innovative methodology for analyzing long-term acoustic data. In addition, a new visualization tool and a method for automatic detection of dawn and dusk choruses are presented. The achieved results validated the proposed methodology as an effective tool for analyzing long-term acoustic data. The area close to the first site, the vicinity of Santos Harbor, was dominated by ship noise, which values reach levels that can affect some species of fish and marine mammals. The soundscapes of the other three remaining measurement sites were dominated by fish and crustacean choruses, with daily and seasonal patterns (related to sunrise and sunset). For the monitored regions, the present work signifies the first contribution for cataloguing fish choruses, and establishes a baseline for the study of their underwater acoustic environment. Although the proposed methodology has used long-term undersea acoustic datasets as case-study, it can also be extended for monitoring other aquatic or terrestrial ecosystems. Finally, the research indicates to Brazilian environmental agencies and to the related scientific community that passive acoustic monitoring is a noninvasive and cost-effective tool that can be used for the management of PAs and points of economic relevance. / Apesar da ampla área dos mares brasileiros, pouco se conhece sobre paisagens acústicas submarinas no Brasil. Estas paisagens são compostas por sons de origens biológicas, geológicas e as produzidas pelo homem. As paisagens acústicas estão fortemente ligadas à dinâmica dos ecossistemas, mostrando padrões temporais diários e sazonais. Para caracterizar paisagens acústicas é necessário realizar gravações de sons por períodos de tempos prolongados, o que demanda métodos de análise inovadores. Neste sentido, a presente pesquisa visa dois objetivos principais: (1) desenvolver métodos para a análise de gravações acústicas de longa duração, (2) caracterizar a paisagem acústica do litoral do estado de São Paulo. Quatro pontos de coleta foram selecionados para monitoramento acústico passivo: um ponto situado no canal de entrada do Porto de Santos e os outros três em áreas de proteção marinhas (APM) do estado de São Paulo. Como resultado foi obtida a base de dados de sons submarinhos mais extensa dos mares brasileiros. Do ponto de vista da análise destes dados, o presente trabalho baseia-se no cálculo da Densidade Espectral de Potência, Níveis de Pressão Sonora e Espectrogramas, obtendo métodos de análise novedosos a partir técnicas tradicionais. Neste contexto a tese apresenta uma ferramenta para a visualização de dados acústicos e um método para a detecção automática de coros biológicos matutinos e vespertinos. Os resultados obtidos permitiram validar a efetividade dos métodos propostos na descrição e análise de dados acústicos de longa duração. O ambiente acústico nas proximidades do Porto de Santos foi dominado por ruído de embarcações, alcançando valores de níveis sonoros capazes de afetar algumas espécies de peixes e mamíferos marinhos. As paisagens acústicas dos três pontos restantes foram dominadas por coros de peixes e crustáceos, com padrões diários e sazonais (relacionados ao nascer e pôr do sol). O presente trabalho constitui a primeira pesquisa que cataloga coro de peixes e que estabelece uma referência para o estudo do ambiente acústico das regiões monitoradas. Embora os métodos apresentados usaram como estudo de caso dados de sons submarinos, a sua aplicação pode ser estendida para o monitoramento de outros ambientes aquáticos ou terrestres. Por último, a pesquisa mostra aos órgãos ambientais brasileiros que o monitoramento acústico passivo é uma ferramenta eficaz para o manejo e monitoramento de áreas protegidas e pontos de relevância econômica.

ABSTRACT The zebra shark Stegostoma fasciatum is an oviparous, demersal carpet shark that forms temporary aggregations and is distributed within shallow, coastal, subtropical and tropical waters of the Indo-West Pacific (IWP) region. The IWP region encompasses various densities of human habitation leading to differences in the levels of exploitation of chondrichthyan fishes, which are targeted for local consumption and export. This is reflected in the two current regional IUCN Red List classifications for zebra sharks of ‘Least Concern’ and ‘Vulnerable’. Despite the conservation concerns for zebra sharks in the vulnerable parts of their range, as well as importance within the ecotourism industry and collection for aquarium trade, little is known about this species in the wild. The aim of this thesis was to conduct the first intensive examination of population ecology in the zebra shark by: (i) investigating the population structure and environmental parameters associated with a relatively unexploited aggregation of zebra sharks in south-east Queensland, Australia; and (ii) investigating the genetic continuity between zebra shark populations in areas with differing levels of exploitation. To investigate the size and structure of the aggregation at the site The Group in south-east Queensland, photo-identification and mark-recapture methods were employed over a three year period (2003 - 2006). In total 327 individual zebra sharks were identified from 570 photographs. Numbered dart tags on 15 zebra sharks were used to confirm pigmentation patterns were unique and persistent in wild zebra sharks for up to 810 days. Pollock’s robust design resulted in an annual population estimate of 458 individuals (95% CI = 298 – 618). The mean number of zebra sharks observed on a single day was 8 (± 8 SE) and the maximum number of zebra sharks seen on a single day was 34. In total, 27% of the sharks were sighted in more than one summer aggregation period and males had greater re-capture probabilities than females. The aggregation consisted exclusively of large (>1800 mm total length) adults with an overall female sex bias of 3.8:1, though sex-ratios varied temporally. Passive acoustic telemetry techniques were employed to investigate the seasonality and residency of the sharks and the environmental parameters associated with their presence at the study site. Five VR2 acoustic receivers were deployed for a period of 21 months (December 2004 – August 2006) and recorded ten acoustically-tagged zebra sharks (seven females and three males). The sharks showed clear seasonality in their visitation patterns with greatest presence during the austral summer months of November through to February and no presence at all during the winter months from June through to October. However their presence did not coincide with peak water temperatures. Rather there appeared to be a critical minimum water temperature of approximately 22 ºC, above which zebra sharks would be present. The tagged zebra sharks displayed greater visitation during the calmest sea conditions. The sharks further displayed diel periodicity with greater during daylight hours, and may be using The Group as a resting site during the inactive diurnal period of the day. Complementing the ecological study on the aggregation, the population genetic structure of 180 zebra sharks from 13 locations throughout the IWP was investigated to test the concordance of IUCN zones with demographic units that have conservation value. A zebra shark specific microsatellite library was developed consisting of 14 polymorphic loci of which 13 were employed for the population genetic analysis along with mitochondrial ND4 sequence data. Mitochondrial and microsatellite data-sets from samples collected throughout northern Australia and south-east Asia concord with the regional IUCN classifications. However, evidence of genetic subdivision was found within these regions, including subdivision between locations connected by habitat suitable for migration. Further, parametric FST analyses and Bayesian clustering analyses indicated the primary genetic break within the IWP is not represented by the IUCN classifications but rather is congruent with the Indonesian throughflow current. This study has demonstrated that zebra sharks form a large, predictable, shallow coastal aggregation comprised entirely of mature adults as well as display high genetic subdivision in the Indo-West Pacific region with little to no recruitment into over-exploited populations from healthy populations. These findings indicate that, if zebra sharks form similar aggregations as that which occurs at The Group in regions of high fishing pressure then, without sufficient protection and management localised depletion and extirpation will eventuate for zebra shark populations in heavily-fished areas.

Despite the extensive Brazilian coast areas, little is known on underwater acoustic environments in Brazil. Acoustic environments (or soundscape) are composed by biological, geological and man-made sound sources. Soundscapes are strongly linked to ecosystems dynamics, and follow temporal patters that can vary at daily and seasonal scales. Thus, for soundscape characterization, it is necessary to undertake sound recordings for long periods, which demands innovative analyzing methods. Accordingly, the present research focuses in two principal objectives: (1) to develop methods for analyzing long-term acoustic recordings and, (2) to characterize marine soundscapes of selected points in São Paulo State. Four deployment sites were selected for the underwater acoustic monitoring: a point located at the channel entrance of the Santos Harbor, and three marine Protected Areas (PAs) in Sao Paulo state. As a result, the largest underwater acoustic database from Brazilian seas was acquired. The present work used Power Spectral Density (PSD), Sound Pressure Level (SPL) and Spectrograms to develop an innovative methodology for analyzing long-term acoustic data. In addition, a new visualization tool and a method for automatic detection of dawn and dusk choruses are presented. The achieved results validated the proposed methodology as an effective tool for analyzing long-term acoustic data. The area close to the first site, the vicinity of Santos Harbor, was dominated by ship noise, which values reach levels that can affect some species of fish and marine mammals. The soundscapes of the other three remaining measurement sites were dominated by fish and crustacean choruses, with daily and seasonal patterns (related to sunrise and sunset). For the monitored regions, the present work signifies the first contribution for cataloguing fish choruses, and establishes a baseline for the study of their underwater acoustic environment. Although the proposed methodology has used long-term undersea acoustic datasets as case-study, it can also be extended for monitoring other aquatic or terrestrial ecosystems. Finally, the research indicates to Brazilian environmental agencies and to the related scientific community that passive acoustic monitoring is a noninvasive and cost-effective tool that can be used for the management of PAs and points of economic relevance. / Apesar da ampla área dos mares brasileiros, pouco se conhece sobre paisagens acústicas submarinas no Brasil. Estas paisagens são compostas por sons de origens biológicas, geológicas e as produzidas pelo homem. As paisagens acústicas estão fortemente ligadas à dinâmica dos ecossistemas, mostrando padrões temporais diários e sazonais. Para caracterizar paisagens acústicas é necessário realizar gravações de sons por períodos de tempos prolongados, o que demanda métodos de análise inovadores. Neste sentido, a presente pesquisa visa dois objetivos principais: (1) desenvolver métodos para a análise de gravações acústicas de longa duração, (2) caracterizar a paisagem acústica do litoral do estado de São Paulo. Quatro pontos de coleta foram selecionados para monitoramento acústico passivo: um ponto situado no canal de entrada do Porto de Santos e os outros três em áreas de proteção marinhas (APM) do estado de São Paulo. Como resultado foi obtida a base de dados de sons submarinhos mais extensa dos mares brasileiros. Do ponto de vista da análise destes dados, o presente trabalho baseia-se no cálculo da Densidade Espectral de Potência, Níveis de Pressão Sonora e Espectrogramas, obtendo métodos de análise novedosos a partir técnicas tradicionais. Neste contexto a tese apresenta uma ferramenta para a visualização de dados acústicos e um método para a detecção automática de coros biológicos matutinos e vespertinos. Os resultados obtidos permitiram validar a efetividade dos métodos propostos na descrição e análise de dados acústicos de longa duração. O ambiente acústico nas proximidades do Porto de Santos foi dominado por ruído de embarcações, alcançando valores de níveis sonoros capazes de afetar algumas espécies de peixes e mamíferos marinhos. As paisagens acústicas dos três pontos restantes foram dominadas por coros de peixes e crustáceos, com padrões diários e sazonais (relacionados ao nascer e pôr do sol). O presente trabalho constitui a primeira pesquisa que cataloga coro de peixes e que estabelece uma referência para o estudo do ambiente acústico das regiões monitoradas. Embora os métodos apresentados usaram como estudo de caso dados de sons submarinos, a sua aplicação pode ser estendida para o monitoramento de outros ambientes aquáticos ou terrestres. Por último, a pesquisa mostra aos órgãos ambientais brasileiros que o monitoramento acústico passivo é uma ferramenta eficaz para o manejo e monitoramento de áreas protegidas e pontos de relevância econômica.

This thesis investigates the development of a low-cost passive acoustic system for localizing moving vessels to monitor areas where human activities such as fishing, snorkeling and poaching are restricted. The system uses several off-the-shelf sensors with unsynchronized clocks where the Time Difference of Arrival (TDOA) or time delay is extracted by cross-correlation of the signal between paired sensors. The cross-correlation function uses phase correlation or Phase Transform (PHAT) which whitens the cross-spectrum in order to de-emphasize dominant frequency components. Using the locations of pairs of sensors as foci, hyperbolic equations can be defined using the time delay between them. With three or more sensors, multiple hyperbolic functions can be calculated which intersect at a unique point: the boat's location. It is also found that increasing separation distances between sensors decreased the correlation between the signals. However larger separation distances have better localization capability than with small distances. Experimental results from the Columbia and Willamette Rivers are presented to demonstrate performance.