The most significant threats to seagrass in the BHS are deforestation and coastal development causing increased turbidity and sedimentation from runoff, as well as reclamation of shallow coastal habitats that smothers seagrass beds. The BHS boasts the highest diversity of corals, reef fishes and stomatopods in the world (Veron et al., 2009, Huffard et al., 2009, Allen and Erdmann, 2009 and Allen and Erdmann, 2012). Surveys have recorded over 577 described species of scleractinian corals (75% of the world’s total), with individual reefs hosting up to 280 species per hectare click here (Veron et al., 2009 and Wallace et al., 2011). An additional 25–40 undescribed coral species have

also been collected, such that the total scleractinian diversity in the BHS is expected to exceed 600 species once taxonomic work is completed on these

collections (L. DeVantier and E. Turak, personal communication). Within the BHS the highest diversity of corals Sunitinib has been recorded in Raja Ampat, with 553 known species (Veron et al., 2009). Two rapid ecological assessments conducted in 2001 and 2002 in Raja Ampat also recorded 41 of the 90 Alcyonacean (soft coral) genera and 699 mollusc species (McKenna et al., 2002 and Donnelly et al., 2003), while more recent studies have documented 57 reef-associated stomatopod species in the BHS, four of which are considered endemic to the region (Huffard et al., 2009). Corals have been found to 160m depth in Raja Ampat, though those beyond the reaches of SCUBA remain uncharacterized (B. Robison, unpublished data). Similarly, intensive survey work around the BHS over the last decade has recorded 1638 species of coral reef fishes comprising 476 genera and 117 families (Allen and Erdmann, 2009 and Allen and Erdmann, 2012). Within the BHS, the highest diversities have been recorded in Raja Ampat (1437 spp.), the Fakfak-Kaimana coast (1005 spp.) and Cendrawasih Bay (965 spp.). Allen and Erdmann (2009) reported a total of 26 endemic reef fish species (from 14 families) in the BHS, though

more recent surveys have now increased this total to 41 (Dimara et al., 2010 and Allen and Erdmann, 2012). The factors that contribute to local endemism are Farnesyltransferase thought to be in part associated with the geological history of the region. For example, there is evidence that Cendrawasih Bay was isolated for a substantial period over the past 5 million years, resulting in high local endemism (11 endemic reef fishes and 18 endemic reef-building corals currently recognized), and significant genetic divergence of many marine invertebrate populations in the Bay (DeBoer et al., 2008, Crandall et al., 2008, Wallace et al., 2011 and Allen and Erdmann, 2012). The main reef types found in the region are fringing and patch reefs, and to a lesser extent seamounts, atolls and barrier reefs (Fig. 6; McKenna et al., 2002, WWF, 2003 and Donnelly et al.