The development of effective management plans for animal populations relies on an understanding of how the population is utilizing the habitat as well as the identification of any critical habitat areas. The St. Johns River (SJR), an urban estuary with a high level of anthropogenic disturbance, is home to a resident population of bottlenose dolphins (Tursiops truncatus). In chapter one, SJR dolphin habitat use patterns, the factors that influenced these patterns, and the critical habitat areas were identified. Significant associations were found in most pair-wise comparisons between season, behavioral state, group size, water depth, and location, indicating that the overall habitat use patterns of SJR dolphins were influenced by complex interactions among these variables. Additionally, two critical habitat areas were identified. Both critical habitats had high levels of anthropogenic activity and the SJR will undergo further development during the Jacksonville Port expansion project. In conjunction with increasing levels of activity, anthropogenic sound can have numerous effects on cetaceans including the masking of signals, alterations in behavior, abandonment of critical habitats, and physiological stress. In chapter two, the soundscape of the SJR was characterized to evaluate the potential impacts of anthropogenic sound on SJR dolphins. Sound levels in the SJR were consistently high and anthropogenic sound was pervasive throughout the river. Therefore, the dolphins in the SJR are at risk of experiencing long-term behavioral and physiological stress due to anthropogenic sound. Together, this work provides valuable knowledge about dolphin habitat use and the soundscape ecology of an urbanized estuary that will enable more informed management decisions and hopefully lead to more effective conservation practices.

Dolphins use stereotyped, individually distinctive, frequency modulated whistles, referred to as signature whistles, in order to broadcast their identity. In this study, we trained six dolphins at Kolmården Zoo, Sweden, to be called over, either upon hearing their own signature whistle (SW) or upon hearing a biologically irrelevant ”trivial” sound (TS), with the aim to prove the Whistle caller concept. The Whistle caller concept is based on the fact that dolphins occasionally use other dolphins’ signature whistles in order to address specific group members and convene.  Our hypotheses were that (1) dolphins call-over trained using their SW would learn the behaviour faster than dolphins trained using TSs, and (2) dolphins trained with their SW would be able to discriminate between different SWs better than dolphins trained with a TS would be at discriminating between different TSs.  Three out of three dolphins were successfully call-over trained using their SW, and two out of three dolphins using their assigned TS. When discriminating between different sounds, two of the dolphins trained using their SW performed significantly better than one of the dolphins trained using a TS. However, there were large intra-group differences in the results, indicating that we cannot eliminate the possibility that these results stem from individual differences in these dolphins’ ability to learn new behaviours overall, rather than an understanding of the sounds they heard. We suggest that future studies focus on (1) male-female differences in discrimination success when applying the Whistle caller concept, (2) how the characteristics of the trivial sounds affect discrimination success, and (3) the option of calling more than one animal at a time by sending out several SWs in succession.

Bottlenose dolphins exhibit fission-fusion social systems in which group size and composition change fluidly throughout the day. Societies are typically sexually segregated, and the quality and patterning of individual relationships in this social species shape the social structure of a population. Female dolphins usually have a large network of associates with whom they form recurring moderate bonds, while male associations are highly variable due to their mating strategies. Males employ one of two strategies; males may be solitary, and encounter and herd females individually, while others may form strong bonds with one to two other males and cooperatively herd individual females in the shape of a first-order alliance. Second-order alliances are more uncommon and have only been observed in Shark Bay, Australia, and more recently within the St. Johns River (SJR), Jacksonville, Florida. Given the inter-population variation in male mating strategies, greater documentation of social structure in neighboring populations along the Atlantic coast is needed. Therefore, chapter one documents the social structure of the Indian River Lagoon (IRL) estuarine system where dolphins have experienced recurrent cetacean morbillivirus (CeMV) epizootics. Although environmental disturbances can affect both social and mating systems, IRL dolphin sociality does not seem to be affected by the 2008 CeMV mass mortality event. Additionally, males only form first-order alliances within this population. Because multi-level alliances are unique to the SJR in this region, chapter two analyzes the stability and function of SJR alliances. Both first- and second-order alliances exhibited variation in stability, while alliance association appears dependent on female presence. Thus, SJR alliances likely function within a reproductive context. Together, this work provides insight into the social and mating systems of bottlenose dolphins, as well as the function of multi-level alliances at a relatively new study site.

The south coast of South Africa represents the extreme western end of the range of the Indo-Pacific humpback (Sousa chinensis, plumbea type) and Indo-Pacific bottlenose dolphins (Tursiops aduncus), which are both confirmed to range as far west as False Bay (Jefferson & Karczmarski, 2001; Hammond et al., 2008). Individual ranging behaviour for both species however is not well resolved. Recent genetic analyses suggest that animals currently considered as plumbea type Sousa chinensis (Reeves et al., 2008) may be a separate species, Sousa plumbea (Mendez et al., 2013). In South African waters less than 1000 adult humpback dolphins (Sousa chinensis, plumbea type hereafter “humpback dolphin”) may comprise the entire population (Karczmarski, 1996), while all estimates suggest the bottlenose dolphin (Tursiops aduncus, hereafter “bottlenose dolphins”) population is relatively large, numbering thousands of animals (Cockcroft et al., 1992; Reisinger & Karczmarski, 2010). Both dolphin species are exposed to variable levels of anthropogenic impacts throughout their range including vessel traffic, chemical pollution and habitat degradation associated with coastal development. This thesis describes the results of a study investigating: 1) the environmental and anthropogenic factors which influence the habitat use of humpback and bottlenose dolphins in two adjacent bays on the southern Cape coast, South Africa – Mossel Bay and Vlees Bay; 2) the abundance of humpback dolphins using Mossel Bay and 3) the interaction of these two dolphin species with white sharks, and the influence this has on dolphin group sizes and habitat use in Mossel Bay. Both land-based and boat-based survey platforms were used in this study with land-based data collected during dedicated watch periods at sites in Mossel Bay (n = 6) and Vlees Bay (n = 4) between February 2011 and March 2013, with a focus on humpback and bottlenose dolphins. A surveyor’s theodolite was used at these sites to collect positional data on animals, while behavioural data were collected through direct observation. Boat-based photographic identification surveys were used to collect data on the presence of individual humpback dolphins in Mossel Bay between April 2011 and November 2013. White shark data from Mossel Bay between February 2011 and March 2013 were provided from boat-based chumming surveys for the collection of photo-ID data from the Master’s thesis of Rabi’a Ryklief, based at Oceans Research. Data were analysed using ANOVA’s, Tukey honest significance tests and generalised additive modelling (Wood, 2006) in programme R, while capture histories of humpback dolphins were analysed with RMark (Laake, 2013) using POPAN open population models (Schwarz & Arnason, 1996) and Huggins heterogeneity closed capture models (Huggins, 1989; Chao et al., 1992). Humpback dolphins socialised over sandy beach habitats in both bays, while feeding/foraging occurred over reef systems in Mossel Bay and off fine grained sandy beach habitats in Vlees Bay. Humpback dolphin resting behaviour was observed at a very low frequency and occurred in all of the primary habitat types in Mossel Bay, while in Vlees Bay resting was only observed over reefs. Bottlenose dolphins in both bays preferentially used wave cut rocky platform habitats for feeding/foraging and resting while socialising occurred in the vicinity of estuaries in Mossel Bay and fine grained sandy beach habitats in Vlees Bay. Higher sighting rates were recorded in the control site, Vlees Bay, than in Mossel Bay for both dolphin species. The largest reverse osmosis desalination plant commenced operations in the sheltered corner of Mossel Bay in October 2011 and discharged approximately five million litres (Ml) of effluent per day (between October 2011 and February 2012) and 18 Ml per day in March and April 2012. In Mossel Bay higher sighting rates of humpback dolphins occurred in the period before desalination began while bottlenose dolphin sighting rates were highest after active desalination decreased to once per month (May, 2012). During the period of peak brine discharge in Mossel Bay, sighting rates were highest for both species in Vlees Bay. Even after desalination operations decreased the sighting rate of humpback dolphins remained low. The operation of the desalination plant at full capacity in Mossel Bay may have led to reduced use of this area by both humpback and bottlenose dolphins. Key habitats in Mossel Bay for both dolphin species are shared with great white sharks (Carcharodon carcharias hereafter “white sharks”) and focus around the three estuaries and their associated near-shore reef systems. The presence of predatory white sharks may limit the time dolphins spend in a specific habitat and influence the number of animals within groups, with larger humpback dolphin groups at sites with high shark utilisation. Both dolphin species had lower individual sighting rates during periods when white shark abundance peaked. Large group sizes of humpback dolphins at Seal Island, and of bottlenose dolphins at Hartenbos and Tergniet, combined with increased rates of travelling and decreased resting and socializing suggest that these areas may pose the largest threat to dolphins due to the variety of shark size classes’ present, especially larger sharks. Closed capture models generated within year population estimates ranging from 48 to 97 individual humpback dolphins (2011: 97, 95% CI: 46 – 205; 2012: 48, 28 – 81; 2013: 68, 35 – 131) while open population modelling produced a ‘super-population’ estimate of 116 animals (95% CI: 54 – 247) using Mossel Bay. During the study 67 humpback dolphins were individually identified with 94.3 % of the individuals in good quality photographs distinctively marked. Fewer humpback dolphins may be present on the south-east and southern Cape coast, including between Algoa Bay and Mossel Bay, than initially thought (Karczmarski, 1996), as definite links exist between Algoa Bay and Plettenberg Bay (Smith-Goodwin, 1997), and Plettenberg Bay and Mossel Bay (this study). The Gouritz River mouth (21º 53' E; Ross, 1984) and De Hoop (20º 30' E; Findlay et al., 1992) were previous suggested as the western limit of this species, but within the last 20 years knowledge on the extent of their range has been greatly improved, and range extension of this species may be occurring to the west with animals present as far west as False Bay (18º 48' E; Jefferson & Karczmarski, 2001). Due to the vulnerability of this species and their wide ranging behaviour, conservation plans need to be implemented on a wide scale to ensure protection of these animals from human impacts throughout their range. A concerted effort is required to further establish the population links between the various locations on the southern Cape coast that these animals frequent. / Dissertation (MSc)--University of Pretoria, 2014. / Zoology and Entomology / MSc / Unrestricted

The goal of this long-term study was to better understand the reproductive biology of the female bottlenose dolphin (Tursiops truncatus) and provide a hypothesis for how dolphins may communicate reproductive readiness to one another. Utilizing conditioned dolphins in aquaria, this dissertation examined several previously unknown aspects of dolphin reproduction, including ovarian follicular dynamics during the luteinizing hormone surge, urinary prolactin levels, estrus behavior, vaginal fluid arboriform arrangement, in-situ vaginal and cervical anatomy during estrus, reversed-phase high-performance liquid chromatography (RP-HPLC) of urine samples to identify proteins and peptides that may be used in chemical communication, and a review and anatomical analysis of dolphin vibrassal crypts. The diffusely seasonal dolphin estrous cycle is not controlled by photoperiod and has a 10-day follicular and 20-day luteal phase. A brief ovulatory LH surge is followed by ovulation within 48 hours. An ethogram of 20 reproductive behaviors was developed, and all occurrences of reproductive behavior were analyzed during conceptive estrous cycles. A novel form of standing heat estrus, termed immobility, was observed, and estrus dolphins displayed genital nuzzling, active and passive mounting with other females, and an increase of standing heat intensity as LH levels rose. Prolactin plays a role in pregnancy maintenance, mammary development, allo-mothering behavior, lactation, and lactational anestrus. Dolphins are similar to sows where weaning causes a return to estrus, and in the boar effect, where days to ovulation are shortened in the presence of a mature male. Dolphin vaginal fluid showed crystallization arrangements with large open mesh patterns, conducive to sperm transport, during the estrogenic follicular phase, and closed mesh during the luteal phase. RP-HPLC analysis revealed that urine contained large amounts of peptides and proteins with peaks that change throughout the estrous cycle and with changes in social grouping. Remnant vibrissae from dolphin follicular crypts were sectioned, and it was hypothesized that trigeminal nerve endings could act similarly to those found in the nasal mucosa of terrestrial species and respond to chemical stimuli. This study provides new data to better understand the reproductive biology of a holaquatic mammal.