Automatic Detection and Compression for Passive Acoustic Monitoring of the African Forest Elephant

In this work, we consider applying machine learning to the analysis and compression of audio signals in the context of monitoring elephants in sub-Saharan Africa. Earth's biodiversity is increasingly under threat by sources of anthropogenic change (e.g. resource extraction, land use change, and climate change) and surveying animal populations is critical for developing conservation strategies. However, manually monitoring tropical forests or deep oceans is intractable. For species that communicate acoustically, researchers have argued for placing audio recorders in the habitats as a cost-effective and non-invasive method, a strategy known as passive acoustic monitoring (PAM). In collaboration with conservation efforts, we construct a large labeled dataset of passive acoustic recordings of the African Forest Elephant via crowdsourcing, compromising thousands of hours of recordings in the wild. Using state-of-the-art techniques in artificial intelligence we improve upon previously proposed methods for passive acoustic monitoring for classification and segmentation. In real-time detection of elephant calls, network bandwidth quickly becomes a bottleneck and efficient ways to compress the data are needed. Most audio compression schemes are aimed at human listeners and are unsuitable for low-frequency elephant calls. To remedy this, we provide a novel end-to-end differentiable method for compression of audio signals that can be adapted to acoustic monitoring of any species and dramatically improves over naive coding strategies

Socioecology, Acoustic Communication and Demography of Asian Elephants in Sri Lanka

SOCIOECOLOGY, ACOUSTIC COMMUNICATION AND DEMOGRAPHY OF ASIAN ELEPHANTS IN SRI LANKA Shermin de Silva (Author) Dorothy L. Cheney (Supervisor) Comparison of behavior across species brings to light the underlying social and ecological factors that have shaped social organization and communication. Elephantids, the only living members of the Proboscidean clade are cognitively sophisticated, long-lived, putatively social mammals. I examine how vocal communication and social organization in Asian elephants (Elephas maximus) compare to African savannah elephants (Loxodonta africana), as well as basic demographic and conservation issues concerning Asian elephants. The first chapter defines fourteen distinct acoustic signals based on their acoustic features, and describes the contexts in which they occur. Most vocalizations are employed in contexts of movement, and some vocalizations are used primarily during movement or non-aggressive social interactions. This suggests that elephants actively seek out association with particular individuals. The second chapter tests the hypothesis that associations among adult female Asian elephants are governed by resourced availability, and describes the temporal structure and strength of bonds. This study population demonstrates fission-fusion social dynamics in which individuals change companions over short time scales, influenced by rainfall, but maintain stable relationships over long time scales. In the third chapter I test the hypothesis that associations are purely the consequence of the spatial distribution of resources, rather than social preference, using a modeling approach based on the spatio-temporal coordinates of individuals. In all seasons, individuals appear to move in a coordinated manner, supporting the interpretation that observed associations reflect true social preference. At the same time, resource distributions do influence the size of social units, and their movements. In the fourth chapter I review the most recent demographic studies of elephant populations in Asia as well as Africa, and highlight the lack of data for much of Asia. I outline methods based on individual identification that may be used to address this challenge to conservation and management. I apply these methods to offer demographic estimates for the study site, and examine what constitutes good practice, in the fifth chapter

Bai Use in Forest Elephants (Loxodonta africana cyclotis): Ecology, Sociality & Risk

Forest elephant (Loxodonta africana cyclotis) sociality is relatively little-studied due to the difficulties of making direct observations in rainforests. In Central Africa elephants aggregate at large natural forest clearings known as bais, which have been postulated to offer social benefits in addition to nutritional resources. This thesis explores the role of these clearings as social arenas by examining bai use within three main themes; ecology, sociality and risk factors. Seasonal changes in elephant use of the Maya Nord bai (Republic of Congo) are described, along with the demography of the visiting population. Elephant visit rate was highly variable; the number of elephants using Maya Nord in an observation day ranged from 0 to 117 animals. This variability was unrelated to local resource availability and productivity suggesting that bai use occurs year round. Elephants in Odzala-Kokoua do not show high fidelity to a single clearing; 454 elephants were individually identified and re-sighted an average of 1.76 times (range 1-10) during the twelve month study period. Previous bai studies have yet to quantify how elephants associate with one another within the bai area. This study examines socio-spatial organisation and associate choice using two measures of association within the 0.23 km2 bai area; aggregations (all elephants present in the clearing) and parties (elephants spatially co-ordinated in activity and movement) and distinguishes these from parties that range together (i.e. arrive and leave together). Social network analyses (SocProg) were used to describe inter- and intra-sexual multi-level organisation in the bai environment, and to illustrate the non-random nature of elephant aggregations and parties. Bais were shown to function as social arenas; female elephants showed active choice of certain associates and active avoidance of others when creating parties, whereas males were less discriminatory. Parties formed in the clearing (mean size= 3.93, SE= 0.186) were larger than ranging parties (mean size= 2.71, SE= 0.084) and elephants stayed for 50% longer in the clearing when they associated with individuals from outside their ranging party. Inter- and intra-sexual relationships were maintained within the clearing, and these are suggested to offer elephants essential opportunities for social learning. The patterning and nature of the relationships observed at the Maya Nord clearing indicates that forest elephants use a fission-fusion social structure similar to that of savannah elephants (Loxodonta africana africana); relationships are significantly structured by age- and sex- and underpinned by individual identity. Old experienced females hold key roles for forest elephants, and male relationships are superimposed on the network of female associations. Odzala-Kokoua elephants use bais to maintain their social relationships despite being highly sensitive to the anthropogenic risks involved in using these open areas. The results of this study suggest that forest and savannah elephants lie on the same social continuum, balancing social “pulls” to aggregate against the ecological “pushes” that force groups to fission. Previous models of savannah elephant sociality construct levels of association and social complexity upwards from the basic mother-calf unit (e.g. Wittemyer & Getz 2007). My results suggest that it may be more appropriate to consider elephant sociality and associations as in dynamic equilibrium between social and ecological influences acting at all levels of grouping, and to explicitly test how these underlie the opportunity costs that elephants are willing to pay in order to maintain social groupings

Anti-predator behaviour of Guereza colobus monkeys (Colobus guereza)

Black-and-white colobus monkeys are renowned for their impressive vocal behaviour, but up to date there have been only very few systematic efforts to study this. These monkeys are able to produce loud and low-pitched roars that transmit over long distances, which has lead to the assumption that these calls function in inter-group spacing and male-male competition. The fact that the monkeys sometimes produce the same calls to predators as well, has not received much attention so far. This thesis presents a detailed description of the form and function of the anti-predator behaviour of one species of black-and-white colobus monkeys, the Guereza (Colobus guereza), with a specific focus on their alarm calling behaviour. A second aim was to determine the effects of predator experience on their anti-predator behaviour, with a specific focus on call comprehension and production. Data were collected from two populations of Guereza monkeys in the Budongo Forest Reserve, Uganda, that differ in predation pressures experienced by their main predators: leopards, eagles and chimpanzees. Results showed that Guerezas use a basic form of zoo-syntax in order to compose predator-specific call sequences that vary in the number of roaring phrases and snorts. These sequences are meaningful to recipients, at least at the level of the predator class, but there were also indications for additional levels of encoded information: Guerezas appear to have evolved a second system, based on acoustic variants of individual phrases, which allows them to narrow down the information content of call sequences, generating the potential to communicate highly specific information by using a mix of syntactic and semantic cues. The monkeys’ vocal behaviour was influenced by predator experience, but not strongly so. Monkeys without prior experience with leopards lacked some of the behavioural nuances seen in leopard-experienced monkeys, but they nevertheless responded appropriately to visual and acoustic leopard models, suggesting they had retained the basic capacities to recognise this predator type as relevant and dangerous. Results are discussed in light of the comparative approach to the study of human language evolution. Although human language is unique in a number of ways, for example through its use of complex syntax and intentional semantics, some animal communication systems have revealed similar features, and Guerezas, the first member of the colobine family to be studied in this respect, are no exception. The Guerezas’ alarm calling behaviour is complex and flexible, and these monkeys have provided another piece of empirical evidence that is directly relevant for the comparative approach to human language evolution

Bai use in forest elephants (Loxodonta africana cyclotis) : ecology, sociality ;risk

Forest elephant (Loxodonta africana cyclotis) sociality is relatively little-studied due to the difficulties of making direct observations in rainforests. In Central Africa elephants aggregate at large natural forest clearings known as bais, which have been postulated to offer social benefits in addition to nutritional resources. This thesis explores the role of these clearings as social arenas by examining bai use within three main themes; ecology, sociality and risk factors. Seasonal changes in elephant use of the Maya Nord bai (Republic of Congo) are described, along with the demography of the visiting population. Elephant visit rate was highly variable; the number of elephants using Maya Nord in an observation day ranged from 0 to 117 animals. This variability was unrelated to local resource availability and productivity suggesting that bai use occurs year round. Elephants in Odzala-Kokoua do not show high fidelity to a single clearing; 454 elephants were individually identified and re-sighted an average of 1.76 times (range 1-10) during the twelve month study period. Previous bai studies have yet to quantify how elephants associate with one another within the bai area. This study examines socio-spatial organisation and associate choice using two measures of association within the 0.23 km2 bai area; aggregations (all elephants present in the clearing) and parties (elephants spatially co-ordinated in activity and movement) and distinguishes these from parties that range together (i.e. arrive and leave together). Social network analyses (SocProg) were used to describe inter- and intra-sexual multi-level organisation in the bai environment, and to illustrate the non-random nature of elephant aggregations and parties. Bais were shown to function as social arenas; female elephants showed active choice of certain associates and active avoidance of others when creating parties, whereas males were less discriminatory. Parties formed in the clearing (mean size= 3.93, SE= 0.186) were larger than ranging parties (mean size= 2.71, SE= 0.084) and elephants stayed for 50% longer in the clearing when they associated with individuals from outside their ranging party. Inter- and intra-sexual relationships were maintained within the clearing, and these are suggested to offer elephants essential opportunities for social learning. The patterning and nature of the relationships observed at the Maya Nord clearing indicates that forest elephants use a fission-fusion social structure similar to that of savannah elephants (Loxodonta africana africana); relationships are significantly structured by age- and sex- and underpinned by individual identity. Old experienced females hold key roles for forest elephants, and male relationships are superimposed on the network of female associations. Odzala-Kokoua elephants use bais to maintain their social relationships despite being highly sensitive to the anthropogenic risks involved in using these open areas. The results of this study suggest that forest and savannah elephants lie on the same social continuum, balancing social “pulls” to aggregate against the ecological “pushes” that force groups to fission. Previous models of savannah elephant sociality construct levels of association and social complexity upwards from the basic mother-calf unit (e.g. Wittemyer ;Getz 2007). My results suggest that it may be more appropriate to consider elephant sociality and associations as in dynamic equilibrium between social and ecological influences acting at all levels of grouping, and to explicitly test how these underlie the opportunity costs that elephants are willing to pay in order to maintain social groupings.EThOS - Electronic Theses Online ServiceGBUnited Kingdo

A study on elephant and human interactions in Kodagu, South India

Increasing human populations have resulted in the extensive conversion of natural forests and range lands into agricultural lands, resulting in an expansion of the interface between people and elephants across the elephant range countries of Asia and Africa. This interface describes the nature of two-way interactions between people and elephants, which can be positive and reverential or hostile and negative. Elephant crop-raiding, one of the most negative interactions for people at the interface, is not only the result of decreased food resources and space, but has also been attributed to a preference for cultivated crops and to damage caused during elephant movements between habitats. The aim of this thesis was an attempt to understand the use of coffee agroforestry areas by elephant populations in a South Indian district, Kodagu, and to assess the risks to elephants and people of coffee plantations. Geographically, located at a significant position in the Western Ghats, Kodagu district is a part of one of the largest wild Asian elephant ranges harbouring India’s largest elephant population. Kodagu has a unique topography and coffee agroforestry system in considered as the boon for conservation. This thesis is the first long term (one year) study on the elephant populations using coffee estates in Kodagu. Crop-raiding events across Kodagu and their intensity of occurrence were determined from the Forest Department compensation records. Virjapet taluk was one of the three administrative units of Kodagu with frequent incidences of crop-raiding, including elephant mortality and human deaths. High rates of crop-damage in Virajpet included both coffee and paddy rice produce as the land is conducive for the cultivation of both. To understand the use of coffee estates by elephants, coffee estates in Virjapet were directly and indirectly monitored for the presence of elephants using dung sampling (N=202), camera trapping, video and photo documentation, as well as sightings (N=408) and reports by local workers, in order to identify the individuals or groups of elephants frequenting these coffee estates. Lone male and all male groups used coffee estates most frequently and family herds ranging in group size from 2 to 10 were present mainly during the peak season of coffee ripening (post monsoon). Presence of large numbers of elephants, especially with large female groups, was associated with crop-damage during the months of December-January. As seasonal movements of elephants in Kodagu districts are still not known, it is unclear why the number of elephants in coffee estates post-monsoon increases when food availability should also be higher in forests. These large coffee estates were used as refuge areas by elephants during the day by all individuals and groups, and feeding on estates occurred during the night to early morning hours. Dung analysis and observations suggested that coffee estates were attractive for elephants due to the constant availability of water (for irrigation), green fodder, and cultivated fruit trees, especially jackfruit. Coffee plants were damaged both due to consumption (47% of dung samples in this study) and accidental damage during elephant movements within the estates. Although the dung sampling could not confirm whether coffee had become a novel food resource, the presence of large number of elephants during the coffee ripening season suggested that the potential for coffee berries to be added regularly to the diet in the future, with potential consequences for coffee invasion of native forests through dung seed dispersal. People working on large coffee estates were accustomed to the presence of elephants and were generally knowledgeable of the areas that elephants frequented, thus avoiding fatal encounters. However, safety of farmers and other people working on the estates remains a major concern, especially for large coffee estates owners. The constant interaction between elephants and people also led to more negative perceptions of elephants, and reduced the tolerance of elephants in the area. The unique topography of Kodagu as a mosaic of forests and farms challenges the number of possible mitigation methods to prevent negative encounters between people and elephant. The elephants of Kodagu may have adapted behaviourally to the presence of people, but long-term monitoring of the elephant population is important to understand their ecological and social adaptations to the various costs and benefits of using this agroforestry landscape. Suggestions for management of the elephant-human interface and mitigation of negative attitudes and actions were made, through a model that incorporates a multiple stakeholder (including elephants) action plan

Body States of Asian Elephants Within and Around Protected Areas in the Salakpra Wildlife Sanctuary, Kanchanaburi, Thailand

Researchers are becoming increasingly aware that studying a species’ landscape of fear or, more broadly, their emotional states, can better inform cognitive questions about how animals navigate their environments. Vigilance behaviors are one way to determine how certain species perceive and respond to risky situations. Due to rapid environmental change, large animals such as elephants are experiencing risky encounters with humans more often than ever before. This study aims to investigate Asian elephants’ expressions of body states and how they might regulate their behavior based on perceived environmental risk or change. Specifically, we investigated the behavioral responses of Asian elephants to different locations in Thailand’s Western Forest Complex. To do this, camera traps were set up at watering holes within protected areas in Salakpra Wildlife Sanctuary and crop fields outside the protected area. Video footage was coded using instantaneous scan sampling with an ethogram that defined alert and relaxed body states. We found that Asian elephants showed a higher rate of the alert body state outside of protected areas than within them. There was no significant difference between the rate of relaxed body states between the two locations. Asian elephants observed alone showed a higher rate of the alert body state than elephants that were among conspecifics. Furthermore, there was no significant difference in the rate of alertness displayed when the elephants were either far from or close to crop fields outside the sanctuary. Together, these results suggest that elephants may regulate their expression of body state or emotion depending on environmental risk or their proximity to humans, and that their fear of humans may be an important factor for understanding how best to mitigate human-elephant conflict in the future

Um contributo para a conservação da biodiversidade e para a gestão de recursos naturais

A área da Conservação em Biologia tem como principais objetivos cuidar e encontrar meios de supervisão constante dos componentes dos ecossistemas. A eterna vigilância exige ao biólogo um olhar cada vez mais abrangente e interdisciplinar, não só dos processos específicos que ocorrem no mundo natural, mas também da procura de respostas para a gestão (dentro daquilo que é possível) desse mesmo mundo natural. O presente estudo focou-se em pesquisar um conjunto de indicadores informativos sobre o status dos serviços dos ecossistemas e de elementos da diversidade biológica de uma área no norte de Moçambique, que compreendeu a “Messalo Wilderness Area” e as praias da Ilha de Vamizi. Aplicou-se, assim uma metodologia “bottom-up”, em que o exercício de diagnóstico implicou o envolvimento dos “stakeholders” locais, e.g. na auscultação de carências, benefícios vivenciados, e de soluções para conflitos com a vida selvagem. O diagnóstico confirmou uma área de riqueza biológica considerável, pressionada pelo número crescente de habitantes no local, e de habitantes temporários oriundos, por exemplo, da Tanzânia. Como resposta à necessidade de gerir os recursos locais de forma mais eficaz, com vista à sua preservação mas também ao alívio da pobreza local, foi elaborado um plano de gestão para a “Messalo Wilderness Area”. Conta-se entre as espécies emblemáticas ameaçadas na região, as tartarugas marinhas, Chelonia mydas e Eretmochelys imbricata, assim como os seus habitats de nidificação; e o elefante africano, Loxodonta africana, que compete com o Homem diretamente por recursos naturais (água em períodos de estação seca, e alimentos com invasão e destruição de propriedade /campos de cultivo). Como contributos para conservação da espécie emblemática em terra e por ser um problema grave identificado pelos locais desenvolveu-se e testou-se uma solução tecnológica de sinalização de elefantes. Os sensores mostraram resultados positivos para os objetivos estipulados: uma solução mais barata e não invasiva para a mitigação do conflito Homem-elefante. Como contributos para conservação das espécies emblemáticas na costa, nos seus habitats de nidificação, realizou-se um estudo da biologia reprodutiva das tartarugas marinhas nidificantes na ilha de Vamizi, tendo-se gerado os indicadores de nidificação para esta região de Moçambique, e que permitiram comparações com outras regiões do Índico e do Globo. Das análises efetuadas chegou-se à conclusão que seria fundamental melhorar a monitorização das tartarugas marinhas, tendo-se desenvolvido uma aplicação tecnológica para o campo, o “software Turtles”, que foi testada num estudo piloto com sucesso. Trata-se de um contributo com implicações a nível global, e que altera a metodologia de campo. Os dados recolhidos e analisados de Vamizi pré software mostram taxas de eclosão e de emergência de juvenis elevados (acima dos 80% para as green e para as hawksbill), conferindo à ilha um destaque/estatuto de boa incubadora de tartarugas marinhas. A análise de ADN mitocondrial revelou, também, um considerável número de haplótipos para a região (11 para as green e 14 para as hawksbill), pelo que o estudo aprofundado de outras amostras de outros habitats próximos (de nidificação e de desenvolvimento) revelarão interconectividades e padrões de dispersão geográfica com relevância para a definição de uma “Regional Management Unit” mais sólida. Os resultados demonstram a necessidade de alargar as medidas de conservação das tartarugas marinhas na região, com intensificação dos programas de monitorização nas praias nidificantes, de monitorização da atividade dos pescadores nos habitats de desenvolvimento dos juvenis, e na colheita de amostras para análises moleculares e cruzamento dessa informação com dados de outras partes do Índico Oeste. Dado que a redistribuição de espécies marinhas em consequência da interferência das atividades antropogénicas com os ciclos biogeoquímicos, é uma constatação anunciada por estudos científicos, criar uma “consciência ecológica”, ou uma cultura do “cuidar” torna-se uma meta a atingir em termos globais. Assim, o desenho de um plano curricular para o ensino das Ciências, que colmatem essa necessidade de uma forma inequívoca é, também apresentado à comunidade, como base para debate.Conservation biology has the main objective of caring and finding strategies for constant supervision of ecosystems components. This eternal vigilance mode demands an interdisciplinary and wider vision from biologists, not only concerning specific processes of the natural world, but also in searching for management answers (in what is possible) for that same natural world. This study focused in searching a group of indicators about ecosystems services status and about biological diversity elements from an area in the North of Mozambique, which comprised the “Messalo Wilderness Area” and the beaches of Vamizi Island. A “bottom-up” approach was applied, using a diagnose exercise involving local stakeholders, e.g., in documenting experienced needs and benefits, and inquiring for solutions to solve the human-wildlife conflicts. The results confirmed an area with considerable biological richness, pressured by the crescent number of local inhabitants, and of foreign people from, for example, Tanzania. As a response to the need of managing effectively local resources, aiming at preserving, but also alleviating local poverty, a management plan was designed for the “Messalo Wilderness Area”. As emblematic species at risk in the area we list the marine turtles, Chelonia mydas and Eretmochelys imbricata, as well as their nesting habitats; and the African elephant, Loxodonta africana, which competes directly with man for natural resources (water in dry season periods, and food with invasion and destruction of crops and property). As contributions for the conservation of emblematic species on land, and because it is a grave problem identified by local people, a technological solution to signal elephants was developed and tested. The sensors showed positive results for the stipulated objectives: an affordable and non-invasive solution to mitigate the human-elephant conflict. As contributions for the conservation of emblematic species on the coast, at the nesting habitats, a reproductive biology study of the nesting marine turtles from the Vamizi Island was carried, that generated nesting indicators for that Mozambican region, and that enabled comparing it with other Indian Ocean and Globe regions. The analysis concluded that the monitoring program needs to be improved, hence the development of a field technological application, the “Turtles” software, which was tested with success in a pilot study. This is a contribution with global implications, that changes field methodology. The data collected in Vamizi and analysed before the software development, showed high hatching and emergency successes (above 80% for the green turtles and for the hawksbill turtles), conferring to the Island the status of good incubation spot for marine turtle’s eggs. The mitochondrial DNA analysis revealed, also, a considerable number of haplotypes for the region (11 for the green’s, and 14 for the hawksbill’s), hence an in-depth study of more samples from nearby habitats (nesting and development) will reveal relevant interconnectivities and geographic dispersal patterns for the definition of a more solid Regional Management unit. The results show the need for extend the conservation strategies for the marine turtle’s conservation in the region, with the intensification of the nesting beach monitoring programs, of the fisherman practices monitoring in the development habitats, and in collecting samples for molecular analysis to crosscheck information with other nesting/foraging/development spots in the Indian Ocean. Because it is an announced scientific evidence that a redistribution of marine species is occurring due to the interference of Man on the biogeochemical cycles, to build up an “ecological conscience”, or a “caring culture” is a goal to achieve globally. Hence, the design of a curriculum to teach Science to fulfil this need in an unambiguous way, is also shown to the scientific community, to start a debate.Programa Doutoral em Biologi