This thesis investigated the use of a static acoustic data logger known as a Cetacean and Porpoise Detection (C-POD) device for monitoring two species of dolphins that occur in Mossel Bay, South Africa: the Indo-Pacific bottlenose dolphin, Tursiops aduncus, and the Indian Ocean humpback dolphin, Sousa plumbea. These two species have a near shore distribution which brings them into frequent contact with human activities such as boating, fishing, desalination plants and the onshore component of gas extraction facilities which can potentially affect their behaviour and populations dynamics. Although both species are relatively well studied within South Africa in terms of biology and abundance, this has been limited to the KwaZulu-Natal coast and Algoa Bay with little information available for areas west of Algoa Bay, and almost no information available locally on their acoustic behaviour. This study aimed to: 1) calculate the detection range and effective detection radius (EDR) of C-PODs for T. aduncus and S. plumbea taking into account environmental and group parameters that may affect these and 2) distinguish T. aduncus from S. plumbea based on temporal variation in specific echolocation click parameters. Field work took place in Mossel Bay from a land-based platform during the period May 2013 to August 2014. A surveyor‟s theodolite was used to collect positional data on dolphins and behavioural information was collected through visual observations. A C-POD was deployed near the land based site and serviced and downloaded on a monthly basis for the same survey period. Visual detections were matched to acoustic detections (echolocation clicks) made within a 60 sec and 30 sec time window. Data were analysed using the software programme R. General Estimating Equations (GEE) were used to 1) model the detection probability and EDR of a C-POD for both species during both time windows; 2) model differences between the two species for seven click parameters produced by the C-POD. The impact of background noise on C-POD detections was also assessed. As cetaceans are not the only form of sound in a marine environment distinguishing dolphin clicks from all other noise sources can be a challenge. Sources of background noise include clicking shrimp, movement of sediment, boat traffic and chorusing by reef fish and crustaceans during reproductive or territorial displays and storms which can either mask the clicks produced by dolphins or fill up the memory card. Data collected from two different deployment locations at different depths were subsequently compared after significant ix interference from other noise source was detected at the first deployment location. Mean number of detected dolphin clicks after filtering increased from 6463.33 to 97820 clicks per deployment and mean number of minutes in which detections were recorded increased from 0.23 min to 2.79 min per deployment. Average detection probability for bottlenose dolphins was 0.357 (95% CI: 0.352 - 0.363) for the 60 sec window and 0.257 (95% CI: 0.253 - 0.262) for the 30 second window. For humpback dolphins the average detection probability was 0.084 (95% CI: 0.082 - 0.087) for the 60 sec window, and 0.043 (95% CI: 0.042 - 0.044) for the 30 sec window. EDR for bottlenose dolphins was 1161.38 mm (95% CI: 1150.14m – 1172.62 m) for the 60 sec window and 1035.761 m (95% CI: 1024.89 m – 1046. 64 m) for the 30 sec window. EDR for humpback dolphins was 765.25m (95% CI: 755.64 m – 774.85 m) for the 60 sec window and 751.00 m (95% CI: 741. 40 m – 760. 60 m) for the 30 sec window. Detection probability and EDR were higher for bottlenose dolphins than humpback dolphins over both time windows. For both species, during both windows, detection probability was significantly influenced by group size (p < 0.05). Four out of the seven parameters produced by the C-POD yielded significant pairwise differences (p < 0.05) between the species. Average inter-click interval was the only co-variable that was significant in the GEE model. The average ICI for bottlenose dolphins was 55.91 ms (95% CI: 51.23 – 60.60) whilst the average ICI for humpback dolphins was longer at 119.76 ms (95% CI: 119.76 – 174.00). The interaction between average ICI and modal frequency was also significant (p < 0.05) indicating that a combination of co-variables might be required in order to differentiate between the two species. Despite the small sample size and the challenges associated with acoustic studies in a noisy marine environment this study provided valuable information regarding the use of static acoustic data loggers such as C-POD in South Africa. As newer versions of C-POD are frequently introduced many of the challenges encountered in this study will be minimized. / Dissertation (MSc)--University of Pretoria, 2016. / Zoology and Entomology / Unrestricted

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior / Os delfinídeos possuem um variado repertório de emissões sonoras, que são produzidos em diferentes contextos comportamentais e são importantes para as relações entre os indivíduos. As emissões sonoras dos delfinídeos são predominantemente utilizadas para a comunicação e são divididas em duas categorias: os sons pulsantes e os assobios. O presente estudo apresenta comparações entre os repertórios de assobios de três espécies de delfinídeos encontrados na costa do Estado do Rio de Janeiro: Stenella frontalis, Steno bredanensis e Sotalia guianensis. Três sistemas de gravação foram utilizados. Estes foram compostos por hidrofones HTI-96-MIN e C54XRS, e gravadores PMD 671 Marantz, FOSTEX (taxa de amostragem de 96 kHz) e SONY TCD-T8 (taxa de amostragem de 48 kHz). As análises dos espectrogramas foram realizadas no software Raven 1.4. Os assobios foram classificados em categorias de formas de contorno e 15 parâmetros acústicos foram mensurados em cada um destes sinais. A estatística descritiva foi realizada para os assobios de cada espécie, e estes foram comparados a partir de testes de comparação de médias e análise discriminante. Um total de 838 assobios foi analisado. Assobios com forma de contorno ascendente de S. frontalis, S. bredanensis, S. guianensis da Baía de Guanabara, da Baía de Ilha Grande e da Baía de Sepetiba corresponderam a 48,1% (N=63), 40,8% (N=47), 49,8% (N=98), 63,9% (N=126) e 58,1% (N=115) do repertório de cada grupo, respectivamente. Diferenças foram encontradas em praticamente todos os parâmetros entre assobios de S. bredanensis e S. guianensis. O maior número de semelhanças ocorreu entre assobios das populações distintas de S. guianensis. A taxa de classificação correta geral foi de 52,4%. Assobios de S. bredanensis apresentaram a maior classificação correta (84,3%). Assobios de S. frontalis apresentaram taxa de classificação correta de 55,7% e os de S. guianensis da Baía de Guanabara, Baía de Ilha Grande e Baía de Sepetiba apresentaram taxas de 57,9%, 48,7% e 29,8%, respectivamente. A análise discriminante realizada entre assobios ascendentes resultou em uma taxa de classificação correta menor (49%). As variáveis consideradas mais importantes para a discriminação entre espécies foram: FF, 3Q, 1Q, MOD e FM. Por meio de parâmetros acústicos foi possível discriminar grande parte dos assobios de espécies simpátricas, apesar de haver ainda sobreposições entre variáveis acústicas dos assobios das espécies comparadas neste estudo. / Delphinids have a diverse acoustic repertoire, in which sounds are emitted in different behavioral contexts and are important for the relationships among individuals. The acoustic signals are predominantly used for communications and are divided in two categories: burst-pulses and whistles. The present study presents comparisons amog whistles of three different species of delphinids found in the Rio de Janeiro State Coast: Stenella frontalis, Steno bredanensis e Sotalia guianensis. Three sound recording systems were used. They were composed by hydrophones HTI-96-MIN and C54XRS, and recorders PMD 671 Marantz, FOSTEX (sample rate of 96 kHz) e SONY TCD-T8 (sample rate of 48 kHz). The spectrograms were analysed in the software Raven 1.4. The whistles were classified in countour form categories and 15 acoustic parameters were measured in each of the signals. Descriptive statistic was used for the whistles of each species and these whistles were compared by the use of mean comparison tests and discriminant analysis. A total of 838 whistles were analysed. Whistles with ascending contour form of S. frontalis, S. bredanensis, S. guianensis from Guanabara Bay, Ilha Grande Bay and Sepetiba Bay corresponded to 48.1% (N=63), 40.8% (N=47), 49.8% (N=98), 63.9% (N=126) and 58.1% (N=115) of the repertoire of each group, respectively. Differences were found between whistles of S. bredanensis and S. guianensis in pratically every parameter. The greater number of similarities occurred among the whistles of different populations of S. guianensis. The total correct classification percentage was 52.4%. Whistles of S. bredanensis presented the largest correct classification score (84.3%). Whistles of S. frontalis presented correct classification percentage of 55.7% and the whistles of S. guianensis from Guanabara Bay, Ilha Grande Bay and Sepetiba Bay presented correct classification scores of 57.9%, 48.7% and 29.8%, respectively. The discriminant analysis among ascending whistles resulted in a lower correct classification percentage (49%). The variables that were considered most important to discriminate among species were: FF, 3Q, 1Q, MOD e FM. Through the use of acoustic parameters it was possible to discriminate a great number of whistles of the simpatric species, despite the overlap that exists among the variable values of the whistles of the species compared in this study.

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior / Os delfinídeos possuem um variado repertório de emissões sonoras, que são produzidos em diferentes contextos comportamentais e são importantes para as relações entre os indivíduos. As emissões sonoras dos delfinídeos são predominantemente utilizadas para a comunicação e são divididas em duas categorias: os sons pulsantes e os assobios. O presente estudo apresenta comparações entre os repertórios de assobios de três espécies de delfinídeos encontrados na costa do Estado do Rio de Janeiro: Stenella frontalis, Steno bredanensis e Sotalia guianensis. Três sistemas de gravação foram utilizados. Estes foram compostos por hidrofones HTI-96-MIN e C54XRS, e gravadores PMD 671 Marantz, FOSTEX (taxa de amostragem de 96 kHz) e SONY TCD-T8 (taxa de amostragem de 48 kHz). As análises dos espectrogramas foram realizadas no software Raven 1.4. Os assobios foram classificados em categorias de formas de contorno e 15 parâmetros acústicos foram mensurados em cada um destes sinais. A estatística descritiva foi realizada para os assobios de cada espécie, e estes foram comparados a partir de testes de comparação de médias e análise discriminante. Um total de 838 assobios foi analisado. Assobios com forma de contorno ascendente de S. frontalis, S. bredanensis, S. guianensis da Baía de Guanabara, da Baía de Ilha Grande e da Baía de Sepetiba corresponderam a 48,1% (N=63), 40,8% (N=47), 49,8% (N=98), 63,9% (N=126) e 58,1% (N=115) do repertório de cada grupo, respectivamente. Diferenças foram encontradas em praticamente todos os parâmetros entre assobios de S. bredanensis e S. guianensis. O maior número de semelhanças ocorreu entre assobios das populações distintas de S. guianensis. A taxa de classificação correta geral foi de 52,4%. Assobios de S. bredanensis apresentaram a maior classificação correta (84,3%). Assobios de S. frontalis apresentaram taxa de classificação correta de 55,7% e os de S. guianensis da Baía de Guanabara, Baía de Ilha Grande e Baía de Sepetiba apresentaram taxas de 57,9%, 48,7% e 29,8%, respectivamente. A análise discriminante realizada entre assobios ascendentes resultou em uma taxa de classificação correta menor (49%). As variáveis consideradas mais importantes para a discriminação entre espécies foram: FF, 3Q, 1Q, MOD e FM. Por meio de parâmetros acústicos foi possível discriminar grande parte dos assobios de espécies simpátricas, apesar de haver ainda sobreposições entre variáveis acústicas dos assobios das espécies comparadas neste estudo. / Delphinids have a diverse acoustic repertoire, in which sounds are emitted in different behavioral contexts and are important for the relationships among individuals. The acoustic signals are predominantly used for communications and are divided in two categories: burst-pulses and whistles. The present study presents comparisons amog whistles of three different species of delphinids found in the Rio de Janeiro State Coast: Stenella frontalis, Steno bredanensis e Sotalia guianensis. Three sound recording systems were used. They were composed by hydrophones HTI-96-MIN and C54XRS, and recorders PMD 671 Marantz, FOSTEX (sample rate of 96 kHz) e SONY TCD-T8 (sample rate of 48 kHz). The spectrograms were analysed in the software Raven 1.4. The whistles were classified in countour form categories and 15 acoustic parameters were measured in each of the signals. Descriptive statistic was used for the whistles of each species and these whistles were compared by the use of mean comparison tests and discriminant analysis. A total of 838 whistles were analysed. Whistles with ascending contour form of S. frontalis, S. bredanensis, S. guianensis from Guanabara Bay, Ilha Grande Bay and Sepetiba Bay corresponded to 48.1% (N=63), 40.8% (N=47), 49.8% (N=98), 63.9% (N=126) and 58.1% (N=115) of the repertoire of each group, respectively. Differences were found between whistles of S. bredanensis and S. guianensis in pratically every parameter. The greater number of similarities occurred among the whistles of different populations of S. guianensis. The total correct classification percentage was 52.4%. Whistles of S. bredanensis presented the largest correct classification score (84.3%). Whistles of S. frontalis presented correct classification percentage of 55.7% and the whistles of S. guianensis from Guanabara Bay, Ilha Grande Bay and Sepetiba Bay presented correct classification scores of 57.9%, 48.7% and 29.8%, respectively. The discriminant analysis among ascending whistles resulted in a lower correct classification percentage (49%). The variables that were considered most important to discriminate among species were: FF, 3Q, 1Q, MOD e FM. Through the use of acoustic parameters it was possible to discriminate a great number of whistles of the simpatric species, despite the overlap that exists among the variable values of the whistles of the species compared in this study.

L’étude de l’écologie des communautés et de la ségrégation écologique revêt une importance particulière, notamment pour ses apports en biologie évolutive mais aussi pour ses applications dans le domaine de la conservation. La présente étude s’intéresse à la ségrégation écologique des delphinidés de l’île de Mayotte (Canal de Mozambique, sud-ouest de l’océan Indien) à deux échelles : la communauté d’espèces (approche interspécifique) et les communautés d’individus (approche intra-spécifique). Autour de cette île, une communauté diversifiée de delphinidés se partage l’espace et les ressources, et ce à de très faibles échelles spatiales. Sur treize espèces observées, au moins cinq sont observées régulièrement et ont donc été étudiées : le grand dauphin de l’Indo-Pacifique (Tursiops aduncus), le dauphin à long bec (Stenella longirostris), le dauphin tacheté pantropical (Stenella attenuata), le péponocéphale (Peponocephala electra) et le dauphin de Fraser (Lagenodelphis hosei). Chez les espèces vivant en sympatrie, des mécanismes de ségrégation devraient s’observer selon les trois dimensions principales de la niche écologique : l’espace, la ressource et le temps. A l’échelle interspécifique, les analyses de l’habitat défini par les caractères physiographiques associés à chaque observation, de l’utilisation des ressources exprimée par les isotopes stables du carbone et de l’azote et des budgets d’activités montrent que les delphinidés occupent des niches écologiques distinctes. Parallèlement, certaines espèces jumelles peuvent constituer des associations poly-spécifiques, les mettant apparemment en situation de compétition pour les ressources et les habitats. Il a été montré que ces associations, notamment chez les delphinidés du genre Stenella, n’avaient pas de signification trophique, mais constituaient plutôt une stratégie de vigilance contre les prédateurs. Le dernier volet de l’étude s’intéresse à la ségrégation intra-spécifique et à la structure de population à fine échelle, notamment chez le grand dauphin de l’Indo-Pacifique, la principale espèce de delphinidé à vivre dans les eaux intérieures du lagon. La combinaison d’approches dont les échelles sont emboitées : de l’échelle évolutive populationnelle (structure génétique) à l’échelle de la vie de l’individu (domaine vital), a permis de démontrer que l’unique groupe panmictique de Mayotte se segmentait en communautés (définies par des ensembles d’individus ayant un domaine vital commun). Au moins deux communautés ont été identifiées, utilisant des domaines distincts, formant des groupes sociaux stables mais non constitués d’individus apparentés. L’ensemble de l’étude montre que la ségrégation écologique s’observe aux échelles inter- et intra-spécifiques chez les delphinidés, et que celle-ci ne peut être mis en évidence que par des approches multi-échelles et transdisciplinaires. / The study of communities and ecological segregation is of primary importance, especially for its contribution to the field of evolutionary biology and its applications to conservation. The present study aims to assess ecological segregation of tropical delphinids of the island of Mayotte (Mozambique Channel, SW Indian Ocean) at two scales: interspecies and intra-species level. Around Mayotte, a diverse community of delphinids can be found within a restricted range. Thirteen species have been recorded, among which five species regularly occur: the Indo-Pacific bottlenose dolphin (Tursiops aduncus), the spinner dolphin (Stenella longirostris), the pantropical spotted dolphin (Stenella attenuata), the melon-headed whale (Peponocephala electra) and the Fraser’s dolphin (Lagenodelphis hosei). In species living in sympatry, segregation mechanisms should be observed along the three main dimensions of the ecological niche: habitat, resource and time. In inter-specific comparisons, analyses of habitat defined by physiographic variables at sighting locations, resource use expressed as carbon and nitrogen stable isotope signatures, and activity budgets revealed that each species occupies its own ecological niche. At the same time, sibling species form mixed-species associations that place them in situation of apparent competition for habitats. It has been shown that these mixed-species associations, especially among dolphins of the genus Stenella, do associate for anti-predator vigilance rather than for trophic benefits. Finally, the last approach of this study aims to investigate fine scale population structure and intra-species segregation in the Indo-Pacific bottlenose dolphin, the main delphinid occurring in the inner lagoon. The combination of approaches over temporal scales: from the genetic population structure to the community characteristics at individual life-scale (home range), showed that a single panmictic group of Indo-Pacific bottlenose dolphins was segmented into communities (defined by a common home range). At least two bottlenose dolphin communities were found, using a common home range and within which genetically unrelated individuals are preferentially associated. The whole study underlines that ecological segregation can be observed inter- and intra-specifically in delphinids, and this segregation can only be assessed by using multi-scale and multidisciplinary approaches.