Why do we need to integrate population genetics into South African marine protected area planning?

South Africa is home to a wide variety of marine flora and fauna distributed over at least three biogeographic provinces. Currently, 9% of the coastline is protected by ‘no-take’ marine protected areas (MPAs), but the distribution of MPAs is uneven between regions. This paper argues that in order for an MPA network to be effective, single MPAs need to be connected to function as part of a larger ecosystem. Methods such as larval surveys, biodiversity assessments and fish tagging are not always successful at elucidating connectivity between areas. Molecular tools addressing population genetics can additionally be successfully employed to assess genetic structuring, gene flow and connectivity between areas of a coastline. Data for southern African rocky shore and estuarine species show several patterns, such as genetic breaks across Cape Point, Cape Agulhas, east of Port Elizabeth and on the northern KwaZulu-Natal coast. Several areas of genetic interest, those including high genetic diversity of commercially exploited species, are highlighted for future conservation efforts.Keywords: connectivity; gene flow; marine protected areas; oceanography; population genetic structuring; South AfricaAfrican Journal of Marine Science 2009, 31(2): 263–26