Environmental DNA (eDNA) has the potential to provide more comprehensive biodiversity assessments, particularly for vertebrates in species-rich regions. However, this method requires the completeness of a reference database (i.e. a list of DNA sequences attached to each species), which is not currently achieved for many taxa and ecosystems. As an alternative, a range of operational taxonomic units (OTUs) can be extracted from eDNA metabarcoding. However, the extent to which the diversity of OTUs provided by a limited eDNA sampling effort can predict regional species diversity is unknown. Here, by modelling OTU accumulation curves of eDNA seawater samples across the Coral Triangle, we obtained an asymptote reaching 1531 fish OTUs, while 1611 fish species are recorded in the region. We also accurately predict ( R ² = 0.92) the distribution of species richness among fish families from OTU-based asymptotes. Thus, the multi-model framework of OTU accumulation curves extends the use of eDNA metabarcoding in ecology, biogeography and conservation.

Environmental DNA (eDNA) has the potential to provide more comprehensive biodiversity assessments particularly for vertebrates in species-rich regions. Yet, this method requires the completeness of a reference database, i.e. a list of DNA sequences attached to each species, which is never met. As an alternative, a diversity of Operational Taxonomic Units (OTUs) can be extracted from eDNA metabarcoding. However, the extent to which the diversity of OTUs provided by a limited eDNA sampling effort can predict regional species diversity is unknown. Here, by modelling OTU accumulation curves of eDNA seawater samples across the Coral Triangle, we obtained an asymptote reaching 1,531 fish OTUs while 1,611 fish species are recorded in the region. Besides, we also accurately predict (R² = 0.92) the distribution of species richness among fish families from OTUbased asymptotes. Thus, the multi-model framework of OTU accumulation curves extends the use of eDNA metabarcoding in ecology, biogeography and conservation.

Ikan terumbu karang memiliki peranan penting baik secara ekonomi maupun ekologi, namun kondisi terumbu karang termasuk di perairan Indonesia yang menjadi habitat utama ikan karang mengalami degradasi. Penelitian ikan karang sudah banyak dilakukan, namun di Indonesia kondisi habitat ikan karang memiliki karakter yang berbeda-beda. Tujuan penelitian ini adalah untuk mengetahui hubungan antara komposisi ikan karang target dan tutupan karang hidup. Penelitian ini dilakukan pada bulan Oktober 2019 di Kepulauan Kei Kecil, Maluku. Metode yang digunakan adalah UVC (Underwater Visual Census) untuk data ikan karang dan UPT (Underwater Photo Transect) untuk mengkaji tutupan karang hidup. Hasil pengamatan menunjukkan bahwa terdapat 130 spesies ikan karang target yang mewakili 19 famili, dengan variasi jenis ikan target antar lokasi pengamatan berkisar antara 25-66 spesies. Kepadatan rata-rata ikan karang target sebesar 8.811 ± 4.107 Ind/ha, dan biomassa rata-rata 1.335 ± 899 Kg/ha. Komposisi ikan karang target yang memiliki kedekatan dengan tutupan karang hidup yaitu famili Siganidae, Serranidae, Lutjanidae, Holocentridae, dan Pomacentridae. Akan tetapi hubungan tersebut rendah, dan kemungkinan besar ada faktor lain yang mempengaruhi. Reef fishes have an important economic and ecological values. However, the coral reef of the globe including in the most of the Indonesian waters which is the vital habitat for reef fishes is degraded. Study on the reef fishes is an abundance, while the habitat characteristic of reef fishes in Indonesian waters has a differences. The aim of this study is to determine the relationship between the target reef fishes compositions and the percentage live coral covers. This study was carried out in October 2019 at the Kei Kecil islands, Maluku. The method used in this study is UVC (Underwater Visual Census) for collecting the reef fishes data, and the UPT (Underwater Photo Transect) for assessing the live coral coverage. The result shows that there are about 130 fishes, which representing 19 families, with species variation ranges from 25 to 66 species among the observation sites. The average density of target fishes was about 8.811 ± 4.107 Ind/ha, whereas the average biomass of target fishes was 1,335 ± 899 Kg/ha. The target reef fishes compositions that has relation with live coral covers is family Siganidae, Serranidae, Lutjanidae, Holocentridae, and Pomacentridae. However, this relationship is weak, and may influenced by other factors.

<strong>Reef Fish Community in the Adjacent Waters of Ternate Island</strong>. Considering that the development of coastal region in the North of Moluccas may affect the population of reef fishes, a research on coral reef community structure is performed using underwater visual cencus on a permanent belt transect. The selected indicator monitoring used were eight families of reef fishes. A total of 108 species of reef fishes were identified, consisted of 31 species of corallivorous, 45 species of herbivorous fishes and 32 species carnivorous fishes (based on punctuation group). Density means of a corallivorous group is 1.598 ± 283 individual/ha, a herbivorous group is 4.751 ± 1.034 individual/ha, and a carnivorous group is 890 ± 622 ekor/ha. The average of reef fish stocks is 420 ± 162 kg/ha that consist of 320 ± 130 kg/ha for herbivorous fishes and 100 ± 64 kg/ha for carnivorous fishes. Indicator fish dominance were attained by Chaetodon baronessa, C. kleinii, C. lunulatus, C. melannotus, C. octofasciatus, C. trifascialis, and Heniochus varius. Herbivorous fishes (84%) more dominat than carnivorous (16%) in terms of individual composition. Dominant species of herbivorous fishes included Acanthurus pyroferus, Chlorurus bleekeri, C. Sordidus, Ctenochaetus binotatus, C. striatus, Scarus dimidiatus, S. ghobban, Siganus vulpinus, and Zebrasoma scopas. The one of carnivorous fishes dominated was only Lutjanus biguttatus. Increasing trend of species numbers and density for corallivorous, herbivorous and carnivorous fishes occured from 2015 until 2017 in majority of study sites. In contrast, the biomass values not increased in majority of the sampling sites.

Species inventories are the building blocks of our assessment of biodiversity patterns and human impact. Yet, historical inventories based on visual observations are often incomplete, impairing subsequent analyses of ecological mechanisms, extinction risk and management success. Environmental DNA (eDNA) metabarcoding is an emerging tool that can provide wider biodiversity assessments than classical visual-based surveys. However, eDNA-based inventories remain limited by sampling effort and reference database incompleteness. In this study, we propose a new framework coupling eDNA surveys and sampling-theory methods to estimate species richness in under-sampled and hyper-diverse regions where some species remain absent from the checklist or undetected by visual surveys. We applied this framework to the coastal fish diversity in the heart of the coral triangle, the richest marine biodiversity hotspot worldwide. Combining data from 279 underwater visual censuses, 92 eDNA samples and an extensive custom genetic reference database, we show that eDNA metabarcoding recorded 196 putative species not detected by underwater visual census including 37 species absent from the regional checklist. We provide an updated checklist of marine fishes in the 'Raja Ampat Bird's Head Peninsula' ecoregion with 2534 species including 1761 confirmed and 773 highly probable presences. The Chao lower-bound diversity estimator, based on the incidence of rare species, shows that the region potentially hosts an additional 123 fish species, including pelagic, cryptobenthic and vulnerable species. The extended and hidden biodiversity along with their asymptotic estimates highlight the ability of eDNA to expand regional inventories and species distributions to better guide conservation strategies.