Increasingly, baseline knowledge of habitat preferences and movement patterns of marine species is required to inform anthropogenic developments. The aim of this study was to determine baseline spatio-temporal distribution and habitat preference of cetaceans in the coastal waters of Algoa Bay. Areas of potential conflict with anthropogenic activities were also assessed. Monthly sea-based surveys were conducted between June 2008 and May 2011. A total of 500 cetacean sightings comprising six species were recorded in 106 surveys. Tursiops aduncus (Indo-Pacific bottlenose dolphin), Sousa plumbea (Indian Ocean humpback dolphin), Delphinus capensis (long-beaked common dolphin) and Balaenoptera brydei (Bryde's whale) were observed year-round, while Eubalaena australis (southern right whale) and Megaptera novaeangliae (humpback whale) were recorded from May to December. A large portion of sightings were associated with a Marine Protected Area and shipping zones. Eubalaena australis, T. aduncus and S. plumbea were found inshore (water depths < 12 m), while the other species were associated with deeper waters. Tursiops aduncus were most commonly seen (233 sightings). Megaptera novaeangliae were sighted often in austral winter, with 113 sightings. Only nine D. capensis sightings were recorded. Spatial distributions of species were corrected for search effort to identify habitat preferences. A number of key observations were made, including opportunistic foraging in M. novaeangliae, and the expansion of nursery grounds for E. australis, to include Algoa Bay. Four preferred habitat areas are proposed, providing important information for conservation and management of cetaceans in Algoa Bay. The spatial approach can be used to inform future relevant management decisions elsewhere.

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1. In South Africa, the humpback dolphin (Sousa plumbea) has been recognized as the most endangered marine mammal, with a low abundance, a discontinuous distribution, and numerous threats. This research was initiated in 2008 to estimate the number of individual humpback dolphins in Algoa Bay, as well as studying their residency patterns and distribution.2. The last boat-based study on humpback dolphins, conducted 24 years ago, formed an important reference against which to compare current findings. This study reveals that since the 1990s the number of identified animals decreased from 70 to 50 individuals, and the mean group size of humpback dolphins has also decreased, from seven to three animals.3. Humpback dolphin behaviour was predominantly that of foraging and travelling, although the overall frequency of foraging still seems to have decreased since early 1990s. 4. Although the species was seen almost all year round, the number of sightings per survey was lowest in January, March, and April. The number of sightings per kilometre surveyed substantially decreased from 0.018 sightings per kilometre in 2008 to 0.004 in 2011, and the number of animals per kilometre also decreased from 0.042 to 0.009. The re-sighting rates were low, ranging from one to eight times, with 52% of identified dolphins seen only once throughout the study period. Only 6% of the individuals were seen more than three times. 5. Reduced humpback dolphin numbers and sighting rates could be indicative of the rise in anthropogenic activities, such as shipping and recreational boating, as well as a rise in pollution from vessels and urban development.6. Conservation strategies, such as a Biodiversity Management Plan for the species, are urgently needed in Algoa Bay, especially in the south-west part of the bay, between Cape Recife and the Port Elizabeth Harbour, where the species occurs most frequently.

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