Population ecology of Indo-Pacific bottlenose dolphins along the south-east coast of South Africa

Abstract

In this study, the genetic population structure of the Indo-Pacific bottlenose dolphin (Tursiops aduncus) was assessed across the Agulhas and Natal Bioregions of South Africa. At the same time, the abundance, distribution and habitat use of T. aduncus was investigated using boat-based surveys along 145 km of coastline from Goukamma Marine Protected Area (MPA) to Tsitsikamma MPA along the south-east coast of South Africa (Agulhas Bioregion). Tursiops aduncus habitat preferences were assessed based on locations of sightings and recorded behaviour, and compared with those of the sympatric Indian Ocean humpback dolphins (Sousa plumbea). Strong patterns of differentiation between two sub-populations of T. aduncus were identified using double digest Restriction Site Associated DNA sequencing (ddRADseq). Pairwise FST were significant (p < 0.05) between individuals from the Agulhas and Natal Bioregions and yielded values of 0.033 for all the loci. Resource requirements, specialization and differences in habitat use possibly provided sufficient isolation allowing differentiation between sub-populations of the two ecologically distinct bioregions, despite the lack of any prominent boundary to gene flow. The two identified sub-populations should each be managed as a distinct conservation unit. The abundance estimate of T. aduncus for the study area according to an open population model (POPAN) was 2,295 individuals (95% CI: 1,157 - 4,553). Although closed models were considered inappropriate, such a model was applied for the Plettenberg Bay part of the study area in isolation, to allow for comparison with a previous estimate. The comparison showed a 72.3% decrease in abundance between the two periods: from 6,997 (95% CI: 5,230 - 9,492) in 2002 - 2003 to 1,940 (95% CI: 1,448 - 2,600) in 2014 - 2016. The mean group size also declined from 120 (range: 1 - 500) to 26 (range: 1 - 100). The results highlight the importance of assessing abundance changes at other sites to inform the revision of T. aduncus conservation status in South Africa. Tursiops aduncus were encountered throughout the area. The lowest encounter rate was along rocky and exposed shorelines. These areas were, however, associated with relatively larger group sizes and greater likelihood of travelling behaviour, whereas sandy bottomed areas, where encounter rates were highest (e.g. parts of Plettenberg Bay and the Goukamma MPA), were more likely to be associated with other behaviours (e.g. foraging, socialising). There was a relatively low association of encounters with MPAs, possibly due to the fact that two of the three MPAs in the area (Tsitsikamma and Robberg) were characterised by non-preferred habitat, namely rocky shorelines. Comparison with Sousa plumbea showed similarity in habitat preferences between the species, though S. plumbea also showed an affinity for estuarine habitats. Two areas that were highly utilised by both species were located along Goukamma MPA and the north-east section in Plettenberg Bay including the Keurbooms Estuary. The latter is unprotected and a management measure could be to create a controlled-use zone to reduce disturbance to dolphins there