Conservation of coral reef associated sharks in Australia and Indonesia

In the past few decades, as a direct result of overfishing, shark numbers have declined dramatically across the world’s oceans, which in some cases has resulted in trophic cascades affecting entire ecosystems. Genetic data, particularly when interpreted in conjunction with direct observations of animal movements and behaviour, can be applied to identify management units, an essential step in the establishment of effective management strategies. This thesis is structured into two main themes: first, I summarize the challenges and successes of shark conservation and management, both globally (chapter 2) and specifically for Australia and Indonesia (chapter 3), and second, I apply genetic methods to obtain conservation relevant information for coral reef associated sharks (chapters 4 to 10). In the first part of my thesis I analyse trends in shark conservation research by evaluating 20 years of scientific output, with a focus on Australia and Indonesia. While scientific effort in shark conservation science has increased in the past two decades, it has done so with a strong geographic bias. Australia and the United States have made an overwhelming contribution to the research output, while countries like Indonesia, which is home to the largest shark fishery in the world, have historically contributed much less. This bias has important consequences in terms of shark conservation: countries which invested in shark research successfully established effective management policies, while nations which devoted less resources to shark conservation science failed to do so. Consequently, I suggest that poor management of shark fisheries might be remedied by increasing local research capacity, which has recently been driven by the establishment of international collaborations. In the second part of my PhD I investigate how habitat and local selection influence patterns of genetic variation in the grey reef shark (Carcharhinus amblyrhynchos), an abundant coral reef predator which has undergone dramatic declines in recent years. I discover that genetic connectivity is affected by the spatial distribution of coral reef habitats, which act as stepping stones through which genetic connectivity can be maintained across large distance (>5000 km) by male dispersal. Furthermore, I identify signatures of local selection, suggesting that grey reef sharks in different regions of Australia and Indonesia may be locally adapted. I discuss the conservation implications of these discoveries in conjunction with recent studies on the movement ecology of grey reef sharks. I also describe the potential applications of integrating information from neutral genetic markers and markers under selection to identify conservation units and for monitoring the international shark fin trade.