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Ecological and social processes of the Spermonde Archipelago, South Sulawesi, Indonesia, have been intensively studied during the Science for the Protection of Indonesian Coastal Ecosystems (SPICE) program. The archipelago is of specific interest to better understand how intensive exploitation of marine resources results in the degradation of reef systems. The projects specifically targeted (1) ecological processes in coral reefs, (2) genetic structure of populations, and (3) socialeecological dynamics relating to resource use, social networks, and governance structures. A modeling compo- nent emphasized (4) the integration of different ecological, social, and environmental components. Results indicated that reef resources in the Spermonde Archipelago are intensively exploited and further stressed by pollution effluents from hinterland processes. The lack of alternative livelihoods perpetuates dependencies within the patroneclient system of the artisanal fisheries and supports high exploitation and also destructive resource uses. Greater inclusion of local stakeholders in the governance may result in better conservation practices, sustainable resource use, and improved livelihoods for the people.

Information on the genetic population structure of endangered giant clams is important for conservation programmes and the understanding of ecological and evolutionary processes. In this study, the genetic population structures of three codistributed and ecologically similar giant clam species (Tridacna crocea, T. maxima and T. squamosa) are compared. A fragment of the cytochrome c oxidase I gene was sequenced as a genetic marker in three giant clam species sampled throughout the Indo-West Pacific, from the Western Indian Ocean (WIO) and Red Sea (RS) to the Eastern Indian Ocean (EIO), across the centre of marine biodiversity in the Indo-Malay Archipelago (IMA) to the Western Pacific (WP) and the Society Islands in the Central Pacific (CP). All three species showed limited gene flow and a highly significant genetic population structure. The Φst-values (P < 0.001) are 0.46, 0.81 and 0.68 for T. crocea, T. maxima and T. squamosa, respectively. Based on a hierarchical AMOVA they could be divided into three to six groups from West to East: (1) WIO (T. maxima and T. squamosa), (2) RS (T. maxima and T. squamosa), (3) EIO (including Java Sea in T. maxima), (4) central IMA, (5) WP and (6) CP (T. maxima). The distribution of the haplotype clades in the populations and the pairwise Φst-values between populations indicated a high level of gene flow in the central IMA for the three species. The concordant patterns suggest that geological history, sea-level changes during glacial periods of the Pliocene and Pleistocene, and oceanography are important factors shaping the genetic population structure of giant clams. The observed deep evolutionary lineages in the peripheral areas of the IMA might include cryptic species.

The fungiid Heliofungia actiniformis is one of the most popular scleractinian coral species in the growing live aquarium trade, with the majority of specimens ori- ginating in Indonesia. Details on population connectivity may potentially provide important information with regards to harvest management efforts. Genetic structure was examined, using ribosomal ITS1, 5.8S and partial ITS2 sequences on a small scale among populations in the Spermonde Archipelago, South Sulawesi (up to 65 km distance, Ust = 0.09), and on a large scale throughout the Indo-Malay Archipelago (up to 2,900 km distance, Ust = 0.26). Significant genetic structuring was found at both scales. Within the Spermonde Archipelago isolation by distance as well as local oceanographic features shaped patterns of genetic connectivity. On the large scale, the data revealed genetically distinct populations in Tomini Bay, New Guinea and the Thousand Islands near Jakarta, and a lack of genetic differentiation among populations lying close to or directlyin the path of the Indonesian throughflow: from the central Visayas to the Flores Sea (Uct = 0.32). Whilst the influence of both historical and present day processes on genetic structuring of H. actini- formis populations was revealed, large scale results further emphasised the importance of oceanographic dynamics on larval dispersal patterns in this species. Potential for larval input from surrounding populations, and the increased vulnerability of upstream as well as isolated populations should be taken into consideration when setting future harvest quotas.