Killer whales inhabiting coastal waters of the northeastern Pacific are listed under the Canadian Species at Risk Act, which requires the identification of critical habitats for the recovery of their populations. Little is known about their distribution during the winter and what areas are important for their survival during these months. Passive acoustic monitoring is a valuable complementary method to traditional visual and photographic surveys although it has seldom been used to study killer whales and there are limitations in practice. There is a need to develop tools and protocols to maximize the efficiency of such studies. In this thesis, long-term acoustic data collected with autonomous recorders were analyzed 1) to assess the performance of two types of analysis (Manual and Long Term Spectral Averages) for detecting and identifying killer whale calls and to compare the effects of using two different duty cycles (1/3 and 2/3); and 2) to investigate the seasonal occurrence of different killer whale populations at two sites off the west coasts of Vancouver Island and Washington: Swiftsure Bank and Cape Elizabeth. Both the use of Long Term Spectral Averages and a lower duty cycle resulted in a decrease in call detection and resolution of call identification, leading to underestimations of the amount of time the whales spent at the site. A compromise between a lower resolution data processing method and a higher duty cycle (and vice-versa) is therefore suggested for future passive acoustic monitoring studies of killer whales. Killer whale calls were detected on 186 days at Swiftsure Bank and on 39 days at Cape Elizabeth. The seasonal occurrence of killer whales at Swiftsure Bank highlights its importance as a killer whale hotspot, with year-round presence of Southern Residents and British Columbia Transients, Northern Residents in spring and fall, and California Transients on rare occasions. These results support the expansion of Southern Resident’s critical habitat to include Swiftsure Bank. Temporal habitat partitioning between Resident populations was observed at Cape Elizabeth, with Southern Residents detected from January through June and Northern Residents from July to September. These results show that Northern Residents use the southern parts of their range more frequently than previously thought. Both Transient populations were frequently detected throughout the year, suggesting habitat overlapping. / Graduate

Ndumo Game Reserve is the only officially protected area within the Phongolo Floodplain; an area in the northern parts of KwaZulu-­‐Natal known to boast a rich diversity of amphibians, thus becoming one of the focal areas for this study. The study’s aim was to monitor and record amphibian diversity, as well as associated blood parasite biodiversity. For the purpose of monitoring, a number of active and passive techniques were employed. Habitat preferences for the expected species were divided into five types, namely endorheic, lacustrine, palustrine, riverine and terrestrial. Endorheic habitats were found to harbour the highest diversity (70%) of frog species. A permanent song meter was used to passively record calling activity of frog species associated with endorheic systems. This call data indicated peak breeding season, preferred calling times and intensities of the different species. Historical records from the same area were used as a basis to which this study’s data were compared. In the case of the polychromatic Argus Reed Frog Hyperolius argus Peters, 1854, questions were raised concerning the major colour changes during development of the apparent sub-­‐adult to adult life stages, an observation which was has caused some confusion as to whether these forms represented a single species or multiple cryptic species. These issues were clarified using techniques such as DNA extraction and polymerase chain reaction (PCR). Furthermore, a blood parasite survey was conducted. Thin blood smears for morphometrics and whole blood for molecular work, were collected from 29 species and 436 individual frogs. For the majority of the recorded parasites, techniques such as light microscopy were utilized for the morphological description and classification of these parasites. Among the recorded frog blood parasites observed, 20% of the frog specimens were infected with at least one blood parasite group. Hepatozoon and Trypanosoma species accounted for most of the infections; the former demonstrated significant differences in intensity of infection across species, families and habitat types (P = 0.028; P = 0.006; P = 0.007 respectively). Methods, such as transmission electron microscopy, examining the ultrastructure, as well as parasite DNA extraction and 18S rDNA gene sequences for the molecular and phylogenetic characterization, were reserved for Hepatozoon species infecting common toad species (Amietophrynus). Parasite stages observed were measured and compared to each other, as well as to other described African bufonid haemogregarines. Resulting sequences were compared with each other and to comparative haemogregarine sequences selected from GenBank. In the current study a number of important aspects with regards to monitoring and assessment of amphibians in their natural environment were explored, including looking at and determining diversity and prevalence of blood parasites. Furthermore, important data on gaining a better understanding of amphibians and their behavioural activities were also gathered, which should be able to assist in conservation actions to effectively protect South African anurans and their required habitat types. / MSc (Environmental Sciences), North-West University, Potchefstroom Campus, 2015

Ndumo Game Reserve is the only officially protected area within the Phongolo Floodplain; an area in the northern parts of KwaZulu-­‐Natal known to boast a rich diversity of amphibians, thus becoming one of the focal areas for this study. The study’s aim was to monitor and record amphibian diversity, as well as associated blood parasite biodiversity. For the purpose of monitoring, a number of active and passive techniques were employed. Habitat preferences for the expected species were divided into five types, namely endorheic, lacustrine, palustrine, riverine and terrestrial. Endorheic habitats were found to harbour the highest diversity (70%) of frog species. A permanent song meter was used to passively record calling activity of frog species associated with endorheic systems. This call data indicated peak breeding season, preferred calling times and intensities of the different species. Historical records from the same area were used as a basis to which this study’s data were compared. In the case of the polychromatic Argus Reed Frog Hyperolius argus Peters, 1854, questions were raised concerning the major colour changes during development of the apparent sub-­‐adult to adult life stages, an observation which was has caused some confusion as to whether these forms represented a single species or multiple cryptic species. These issues were clarified using techniques such as DNA extraction and polymerase chain reaction (PCR). Furthermore, a blood parasite survey was conducted. Thin blood smears for morphometrics and whole blood for molecular work, were collected from 29 species and 436 individual frogs. For the majority of the recorded parasites, techniques such as light microscopy were utilized for the morphological description and classification of these parasites. Among the recorded frog blood parasites observed, 20% of the frog specimens were infected with at least one blood parasite group. Hepatozoon and Trypanosoma species accounted for most of the infections; the former demonstrated significant differences in intensity of infection across species, families and habitat types (P = 0.028; P = 0.006; P = 0.007 respectively). Methods, such as transmission electron microscopy, examining the ultrastructure, as well as parasite DNA extraction and 18S rDNA gene sequences for the molecular and phylogenetic characterization, were reserved for Hepatozoon species infecting common toad species (Amietophrynus). Parasite stages observed were measured and compared to each other, as well as to other described African bufonid haemogregarines. Resulting sequences were compared with each other and to comparative haemogregarine sequences selected from GenBank. In the current study a number of important aspects with regards to monitoring and assessment of amphibians in their natural environment were explored, including looking at and determining diversity and prevalence of blood parasites. Furthermore, important data on gaining a better understanding of amphibians and their behavioural activities were also gathered, which should be able to assist in conservation actions to effectively protect South African anurans and their required habitat types. / MSc (Environmental Sciences), North-West University, Potchefstroom Campus, 2015

<p>Passive acoustic monitoring is being used more frequently to examine the occurrence, distribution, and habitat use of cetaceans. Long-term recordings from passive acoustic recorders allow the examination of diel, seasonal, and inter-annual variation in the occurrence of vocalizing marine mammals. With the increased use of passive acoustics as a tool for studying marine mammals, the ability to classify calls to the species level is becoming more important. While studies have found distinctive vocalizations in some cetacean species, further work is required in order to differentiate the vocalizations of delphinid species. I sought to classify odontocete vocalizations to species and to describe temporal variation and depth-related differences in the occurrence of cetacean vocal events detected in archival passive acoustic recordings in Onslow Bay, North Carolina. To determine if odontocete species in offshore waters of North Carolina could be distinguished by their whistles and clicks, I used a towed hydrophone array to make acoustic recordings of species encountered during concurrent visual and acoustic surveys between 2007 and 2010. I recorded whistles from four species (Atlantic spotted dolphins, bottlenose dolphins, rough-toothed dolphins, and short-finned pilot whales) and clicks from five species (Risso's dolphins in addition to the four species listed above). After running a classification and regression tree (CART) analysis on 22 measured variables from the contours of four species' whistles, I generated an optimal classification tree that had a correct classification rate of 74.2%. My results indicate that species-specificity exists in the four species' whistles. My examination of the spectral structure of clicks showed that only Risso's dolphins produced clicks with distinctive spectral banding patterns, although I found that other click parameters, particularly peak and center frequency, might be useful in differentiating the other species. I then used the distinctive banding pattern that I observed in Risso's dolphin clicks to identify this species in recordings made by archival passive acoustic recorders that were deployed at various times and locations between 2007 and 2010. I used these recordings to determine how vocal events varied temporally and spatially in Onslow Bay. My analysis of vocal events observed in these recordings showed that Risso's dolphins, sperm whales, and other delphinids are present in Onslow Bay throughout the year; Kogia spp. occur sporadically; and fin and minke whales produce calls that can be detected only between late fall and early spring. I also detected low-frequency downsweeps and two types of low-frequency pulse trains produced by unknown species. After looking at the occurrence of fin whale 20-Hz pulses in relation to downsweeps, I suggest that the downsweeps are produced by sei whales due to the lack of overlap in occurrence. When I looked for diel patterns in the odontocete vocal events, I found a nocturnal increase in the occurrence of clicks from Risso's dolphins and sperm whales, but no diel variation in Kogia clicks. I also found that unidentified delphinids showed either an increase in click events at dawn or at night, depending on the time of year and recording location. Finally, my analysis of acoustic data from five recorders deployed in three different depth ranges revealed that there was greater unidentified delphinid and sperm whale vocal activity on recorders located in deep waters, suggesting a greater diversity and density of animals in deeper waters of Onslow Bay. Together, the results of my dissertation demonstrate the value of passive acoustic monitoring in understanding the distribution and temporal trends in cetacean occurrence, and highlight the importance of classifying sounds to the species level in order to better understand the temporal and spatial patterns found.</p> / Dissertation

Videotape and audio recordings of a patch reef in Ant Atoll, Pohnpei, Micronesia were analyzed for the presence of bioacoustic activity produced by species of the teleost family Pomacentridae. The acoustic parameters of fish calls were measured and then identified as belonging to either Amphiprion melanopus or Stegastes nigricans. Visual and statistical methods of analysis were combined to compare the calls of the two species and to test for measurable differences in the acoustic parameters of their calls. Soundscape data showed similar patterns to previously observed tropical reef environments. Fish produced single or multi-pulsed calls in the frequency range of 0-1000 Hz that were often accompanied by observable behaviors such as a chases and displays of dominance. Results indicated that the species on this atoll produce similar calls that cannot be distinguished using acoustic data alone. Visual confirmation was necessary for definitive identification of sound producers and in many cases was not possible beyond the family level. Implications for passive acoustic monitoring are that acoustic data collection alone may be able to capture fish abundance but may not be sufficient to fully capture species richness in regions where populations of closely related fish have similar signals.

京都大学 / 0048 / 新制・課程博士 / 博士(理学) / 甲第19547号 / 理博第4207号 / 新制||理||1603(附属図書館) / 32583 / 京都大学大学院理学研究科生物科学専攻 / (主査)教授 幸島 司郎, 教授 伊谷 原一, 教授 村山 美穂 / 学位規則第4条第1項該当 / Doctor of Science / Kyoto University / DFAM

Passive acoustic monitoring (PAM) has historically been used as a noninvasive technique to study biodiversity, activity patterns, distribution, and species dispersal. The use of acoustic data has expanded in ecological research; however, studies focusing on primates are underrepresented, especially for nocturnal species. This study seeks to increase the understanding of acoustic activity in the nocturnal Milne-Edwards' sportive lemur (Lepilemur edwardsi). This species is endangered and endemic to the lowland dry forests in northwest Madagascar. Specifically, this study aims to describe the daily and annual acoustic activity patterns of the L. edwardsi. The PAM survey was conducted using AudioMoth recorders in the Mariarano Forest at 20 sites, with a recording being taken one minute every hour for a year. L. edwardsi presence and absence data were obtained from the recordings by using semi-automated analysis tools from ARBIMON (Rainforest Connection®). The results show that the parametric coefficients, Month and Hour, have an effect on the vocal activity of L. edwardsi with the various locations of the sites being taken into account. The probability of recording a L. edwardsi presence increases as the year progresses. Conversely, the probability of a L. edwardsi presence being recorded increases as the night progresses until midnight and decreases until the early morning hours. These results suggest that acoustic communication is important in L. edwardsi offspring rearing and parental investment. In addition, this study demonstrates the great potential of PAM in monitoring endangered and elusive species.

Soundscape ecology is a rising field in recent years as the effects of anthropogenic sound pollution are widely discussed. Nowadays, scientists are trying to find the best way to describe environmental health using quantitative acoustic measurements. In search of the best acoustic index/indices that can be used for real-time and long-term underwater acoustic monitoring, we tested five different acoustic indices for their effectiveness and suitability for distinguishing and differentiating various types of sounds. One dataset with anthropogenic noises (boat, ship, and diver noises), natural ambient sounds (wind, water turbulence, and reef background noises), and biotic sounds (damselfish Dascyllus reticulatus and snapping shrimps sounds) was analyzed using Raven Pro and R. Our results suggest that acoustic richness (AR) and acoustic complex index (ACI) are capable of separating sound types with the consistency of subjective impression. We also find a strong positive linear correlation between sound exposure level (SEL) and average power spectral density (PSD). The AR exhibits a polynomial relationship with the increase of SEL. Acoustic entropy (H) does not have a significant difference between the three types of sounds. These results agree with the previous studies that AR can be used for differentiating random noises and pure tones, and ACI is capable of quantifying sound complexity. / 2024-09-30T00:00:00Z

Soundscape Ecology, the physical combination of sounds at a particular time and place, is a rapidly growing field. As acoustic technology advances, several possible future uses of passive acoustic monitoring (PAM), such as biodiversity counts and monitoring of habitat health, are being explored. This thesis is divided into two chapters; each is a stand-alone paper. The first chapter provides a review of soundscape ecology, ambient sound, current recording methods and data analysis used in PAM studies, and identifies several major future recommendations for the field. One of these recommendations is to standardize recording methods and indices used during analysis in long-term studies. The second chapter analyzes a 55-minute continuous recording on a coral reef in Tunicate Cove, Belize in 1996 by Professor P. Lobel. This recording was then subsampled with several intermittent recording schedules to explore the amount of acoustic information lost as periods of active and inactive recording vary. The continuous recording consisted of a high frequency band (3-4 kHz), which may correspond to abiotic sounds, and a low frequency band (0.1-0.5 kHz), which generally corresponds to biotic sounds. Two recording schedules, 30 seconds every 4 minutes and 2 minutes every 10 minutes, were significantly correlated with the continuous recording. The statistical significance of the other five recording schedules varied among the three parameters tested in this study (average power (dB), average entropy, and aggregate entropy).

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.