With overfishing reducing the abundance of marine predators in multiple marine ecosystems, knowledge of genetic structure and local adaptation may provide valuable information to assist sustainable management. Despite recent technological advances, most studies on sharks have used small sets of neutral markers to describe their genetic structure. We used 5517 nuclear single-nucleotide polymorphisms (SNPs) and a mitochondrial DNA (mtDNA) gene to characterize patterns of genetic structure and detect signatures of selection in grey reef sharks (Carcharhinus amblyrhynchos). Using samples from Australia, Indonesia and oceanic reefs in the Indian Ocean, we established that large oceanic distances represent barriers to gene flow, whereas genetic differentiation on continental shelves follows an isolation by distance model. In Australia and Indonesia differentiation at nuclear SNPs was weak, with coral reefs acting as stepping stones maintaining connectivity across large distances. Differentiation of mtDNA was stronger, and more pronounced in females, suggesting sex-biased dispersal. Four independent tests identified a set of loci putatively under selection, indicating that grey reef sharks in eastern Australia are likely under different selective pressures to those in western Australia and Indonesia. Genetic distances averaged across all loci were uncorrelated with genetic distances calculated from outlier loci, supporting the conclusion that different processes underpin genetic divergence in these two data sets. This pattern of heterogeneous genomic differentiation, suggestive of local adaptation, has implications for the conservation of grey reef sharks; furthermore, it highlights that marine species showing little genetic differentiation at neutral loci may exhibit patterns of cryptic genetic structure driven by local selection.

For several decades, fishing sharks for their fins has provided important livelihoods for eastern Indonesian coastal communities that fish the Halmahera, Arafura and Timor Seas. Fishery and interview data collected in 2012-13 from three case studies on the islands of Seram, Aru and Rote were used to examine changes in shark fishers' livelihoods over the preceding 20 years. While recent declines in catches and shark fin prices have had a substantial impact on fishers' livelihoods, the fishery's low visibility in some areas of its geographic range and its political complexity in general have meant that government and international development agencies have largely been unaware of this impact. Many respondents remembered the Asian Financial Crisis in 1997-98 and the turn of the millennium as a time when sharks were still abundant and shark fin prices high, but were concerned about the ongoing fall of shark fin prices since March 2012. High-value species, particularly guitarfish, hammerhead and sandbar sharks were most affected, losing up to 40% of their pre-2012 value. These changes, combined with the loss of fishing grounds, few attractive options for alternative income and restrictive debt relationships with shark fin bosses, have led some fishers to resort to highrisk activities such as blast fishing, illegal transboundary fishing, and people smuggling. This paper examines the multi-layered causes and consequences of fishers' decision-making in response to adverse changes in their fishery, and explores options and obstacles to pursuing livelihoods that carry lower environmental, financial and personal risks.

For over two decades, Indonesia has reported higher average shark landings than any other nation, but very little local information exists on the fishery and life histories of targeted species. This poses severe challenges to shark sustainability and conservation in this vast archipelago. We draw on diverse sources of data to evaluate the sustainability of the shark fishery in eastern Indonesia, a particularly data-poor region where sharks are primarily targeted for their fins. Shark fishers from three coastal communities were interviewed on their perceptions of catch trends over the past twenty years and asked to collect fishing data during fishing trips in the Seram, Arafura and Timor Seas. For the most frequently harvested species, we estimated maximum intrinsic rates of increase (rmax) to predict their resilience to fishing pressure. Our results indicate that shark fishing practices in the region are likely to be unsustainable. The catches of several species largely comprised of immature individuals and most fishers attributed observed declines in shark numbers, size and species diversity to overfishing. Hammerhead sharks have relatively high intrinsic resilience but are nevertheless at risk of local extinction due to their availability to the fishery and the value of their fins. Sandbar, dusky and grey reef sharks have lower resilience and are frequently caught but not managed. We recommend a composite management approach, including consistent implementation of existing trade restrictions, fisheries research and opportunities for fishers’ livelihood diversification, to stem shark harvests in eastern Indonesia.

Fisheries are complex social-ecological systems, where managers struggle to balance the socioeconomic interests of fishing communities with the biology and ecology of fisheries species. Spatial closures are a popular measure to address conservation and fisheries management goals, including the protection of shark populations. However, very little research has been published on the effectiveness of shark-specific closures to protect sharks, or their impacts on fisher behavior. Situated within the global center of tropical marine biodiversity, Indonesia's shark fishery contributes more to the international shark fin trade than any other nation. Here we evaluate the effect of shark-specific closures on sharks and other species of interest, as well as shark fishers' responses to losing access to their former fishing grounds. We assessed shark diversity and abundance in an open access zone (OAZ) and two No-Take Zones (NTZs) of a Marine Protected Area within the recently established shark sanctuary in Raja Ampat, Indonesia, where sharks have high monetary value as a tourism attraction. Shark abundance was significantly higher in the privately managed NTZs than in the OAZ. Across all management zones, neither zone size, depth nor reef complexity explained variations in shark abundance, suggesting that governance is the main driver of successful shark conservation areas. These trends were also reflected in species targeted by small-scale reef fisheries, including snappers, emperor, groupers, tunas, mackerels, and large-bodied wrasse and parrotfish. Interviews with shark fishers who lost access to their primary fishing grounds when the shark sanctuary was established showed that while most fishers (88%) knew that sharks were protected in Raja Ampat, many were unsure about the purpose of the sanctuary. Few fishers felt that the agencies implementing fishing bans understood their livelihood needs. We found that shark fishers adapted to the loss of former fishing grounds by shifting fishing effort to other locations or diversifying their livelihoods, including illegal petrol transport. While conserving sharks for tourism can be effective, it may inadvertently result in displacing fishing effort to unprotected regions. Jaiteh et al. Shark Protection in Eastern Indonesia We propose that effective shark conservation in Indonesia will need to combine strategic spatial protection with efforts to support livelihood security and diversification.

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