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Indonesia is an archipelagic country that provides important nesting and foraging habitats for the critically endangered hawksbill turtle (Eretmochelys imbricata). Although many studies have investigated this migratory species globally, there is a lack of information on the population structure and geographic boundary of this species in Indonesia. This study aims to investigate the genetic diversity and population structure of six nesting sites in the Java Sea region of Indonesia. The control region (d-loop) sequence (818 bp) was obtained from 152 individuals, resulting in 20 haplotypes. This study revealed 13 new haplotypes, 12 of which were rare and observed only in a single sampling location. Results showed that the Indonesian population shares haplotypes with rookeries from Peninsular Malaysia and Australia, as indicated by EiIP08 and EiIP49. The haplotype diversity (h) was highest at the more northern rookery sites (Segama Besar Island, Kimar Island, East Belitung, Penambun Island) (h: 0.6033 - 0.9167; 4 - 9 haplotypes) compared to the other two rookeries located in the Seribu Archipelago (Tidung Island and Harapan Island) (h: 0.3354 - 0.5965; 3 - 6 haplotypes). Furthermore, population structure analysis showed a pan-mixed population between Tidung Island and Harapan Island (FST: 0.003, P > 0.05) but significant population structure across all other rookery sites (FST: 0.083 - 0.486, P < 0.05), resulting in five newly identified Management Units (MUs) in this area. This study showed the presence of a complex population structure with local haplotypes and narrow population boundaries for rookeries in relatively close proximity within the Java Sea, prompting local management and highlighting the need for more research on hawksbill turtle populations in Indonesia.

Summary: Over the past few decades, Indonesia’s marine conservation governance has been criticized. This article analyzes the overlaps and gaps in domestic law and policy regimes for cetaceans or marine mammal management and examines issues of institutional arrangements and legal frameworks related to cetacean conservation in Indonesia. The legal framework’s progress on cetacean governance shows three distinct phases: 1975–1985 (species-focused governance approach), 1990–2009 (area-based approach), and 2010–present (broader marine governance approach). This study reveals that the main shortcoming of the legal framework is unclear mandates and overlapping jurisdictions. This study suggests several urgent policies that should be accommodated in the current legal regime to strengthen cetacean conservation. In addition, this research also recommends creating a collaboration mechanism between institutions and encouraging Indonesia to join as a full member of the International Whaling Commission and the Conservation of Migratory Species of Wild Animals Convention to strengthen cetacean governance and conservation.

Highlight Research • The very first attempt to investigated and revealing biodiversity of crustacean crab in coral reef ecosystem at Tidung Island, Indonesia • Conservation area (Tidung Kecil) has more abundant crab species than tourism area (Tidung Besar). • A microhabitat that suffers anthropogenic pressure may alter the composition of crustacean biodiversity, especially in crab group. • Different characteristics and complexity of coral habitat affect the dynamics of cryptic crustacean communities Abstract Recent studies have been widely carried out on the important role and ecological function of coral reefs. However, little attention has been given to small and cryptic crustaceans organisms living within different microhabitat in dead corals. This study aimed to reveal the diversity of crustaceans that inhabit dead corals in Tidung Islands, Indonesia. A total of 134 individuals from 41 species in 13 families were recorded within eight dead corals taken from two different sites. Furthermore, the species identified from Tidung Kecil were significantly different and more diverse than Tidung Besar. It was suggested that differences in anthropogenic pressure between Tidung Besar and Kecil might have an important role in the spread of crab crustaceans' organisms. Xanthidae from infraorder Brachyura were observed to be the most dominant family, while Galatheidae and Porcellanidae from infraorder Anomura spread almost equally in both sites. Additionally, Psaumis cavipes and Chlorodiella nigra were species with the largest contribution of crab crustaceans' communities in the death of coral's ecosystem in the Tidung Islands. This result indicated that dead corals might play a key role in supporting and providing a habitat for crustacean cryptic.

Objective: This study describes the newest deoxyribonucleic acid (DNA) barcoding Asian redtail catfish (Hemibagrus nemurus) in the Progo River, Magelang, Central Java, Indonesia. Materials and Methods: Ten fish were caught in the Progo River, Magelang, Central Java, Indonesia. The polymerase chain reaction was the molecular diagnosis to detect the sequences of DNA of Cytochrome Oxidase I compared to National Center for Biotechnology Information data (GenBank). Results: The results showed that the percent identity was not 100% with H. nemurus data from other locations (GenBank), including Indonesia. The closest percent identity was H. nemurus from Java Island (Accession ID: MK312566.1) with 97.6% similarity. The genetic mutation that hap¬pened might be due to environmental change (pollution) in the Progo River recently. Conclusions: This study showed a genetic mutation in H. nemurus from Progo River may be caused by environmental change. Low pollution exposure levels may not be detrimental (lethal) to fish. However, it can affect fish fertility, which leads to population degradation (gene variation). Attention must be increased for fish survival in the future. [J Adv Vet Anim Res 2022; 9(4.000): 591-600]

Biodiversity assessment surveys are necessary for establishing conservation areas. However, such surveys are typically expensive, primarily if they cover a large area and take a long time. The survey difficulty increases when applied to cryptic, sparse, and fast-moving organisms. In addition, it requires expertise in taxonomic-biota classification. The breakthrough environmental DNA (eDNA) metabarcoding technique promises to overcome all the hurdles of assessing the potential for marine biodiversity in a non-invasive, rapid, extensive, and more effective way. We evaluated the ability of the eDNA survey to reveal the potential diversity and character of marine eukaryotes in the Lombok Island Marine Protected Area. A sampling of seawater and sediment eDNA in pore size fractions of 0.4-12 ?m and >12 ?m was carried out in the Core Zone, Non-Core Zone, and Non-Conservation Area, in east, north, and west Lombok, respectively. The detection and classification of eukaryotes using bioinformatics analysis were accomplished following extraction, amplification, and DNA sequencing. We identified 20,478 unique sequences of potential species classified in five kingdoms to 654 marine eukaryotes families. The comparison results show differences in community structure between locations, as well as differences in diversity between media and factions. The eDNA survey can assess marine biodiversity at a macro level and has implications for management in conservation areas. Keywords: Biodiversity, Marine eukaryotes, environmental DNA, the Primary V9-SSU 18S rRNA gene

Ocean Census is a new Large-Scale Strategic Science Mission aimed at accelerating the discovery and description of marine species. This mission addresses the knowledge gap of the diversity and distribution of marine life whereby of an estimated 1 million to 2 million species of marine life between 75% to 90% remain undescribed to date. Without improved knowledge of marine biodiversity, tackling the decline and eventual extinction of many marine species will not be possible. The marine biota has evolved over 4 billion years and includes many branches of the tree of life that do not exist on land or in freshwater. Understanding what is in the ocean and where it lives is fundamental science, which is required to understand how the ocean works, the direct and indirect benefits it provides to society and how human impacts can be reduced and managed to ensure marine ecosystems remain healthy. We describe a strategy to accelerate the rate of ocean species discovery by: 1) employing consistent standards for digitisation of species data to broaden access to biodiversity knowledge and enabling cybertaxonomy; 2) establishing new working practices and adopting advanced technologies to accelerate taxonomy; 3) building the capacity of stakeholders to undertake taxonomic and biodiversity research and capacity development, especially targeted at low- and middle-income countries (LMICs) so they can better assess and manage life in their waters and contribute to global biodiversity knowledge; and 4) increasing observational coverage on dedicated expeditions. Ocean Census, is conceived as a global open network of scientists anchored by Biodiversity Centres in developed countries and LMICs. Through a collaborative approach, including co-production of science with LMICs, and by working with funding partners, Ocean Census will focus and grow current efforts to discover ocean life globally, and permanently transform our ability to document, describe and safeguard marine species.

Soft corals of the genus Clavularia (Blainville 1830) have complex and difficult to distinguish morphological characteristics, making them rather difficult to identify. A paucity of information exists for Indonesian coral reefs, a complex biogeographic region at the confluence of the Pacific and Indian Ocean that covers an extensive geographic area and several marine ecoregions, is subject to several ocean current systems, and includes a high diversity of habitats. Specimens of Clavularia inflata were collected from eleven study sites across the Indonesian archipelago, morphologically described based on their sclerite characteristics, and compared among sites. Sclerite observations were divided into four parts for each colony, namely pinnules, crowns, calyces, and stolons. The sclerites found in C. inflata comprised various forms such as rods, fingers, sticks, and brackets. Morphometric measurements of C. inflata showed specimens from Kepulauan Seribu had the largest pinnule, calyx, and stolon sclerites compared to other locations. The maximum mean size of crown sclerites was observed for specimens from Maluku Tenggara Barat. Similarities in the shape of sclerites resulted in specimens from Kangean, Morotai, Tanjung Lesung, Bontang, Lombok and Natuna forming a cluster, while those from Maluku Tenggara Barat and Arborek were dissimilar to other sites. Smaller sclerite sizes in specimens from Arborek are likely related to strong currents at that site. In conclusion, there were variations in the size of sclerites across the eleven study sites, with several sites forming a cluster of similar sclerite dimensions. Further studies using molecular markers are suggested to further explore the possibility of cryptic species.

Gaining extensive knowledge of prey sources is an essential approach for understanding trophic structure and relationships, especially in highly diverse coral reef ecosystems. Groupers are a major Asian reef fish commodity, making it important to study grouper prey and the trophic relations involved. The wide distribution of groupers across different environments could lead to distinctive predatory behaviour. Therefore, this study was conducted to investigate and compare the taxonomic classification and composition of prey in the diets of two common groupers (Epinephelus areolatus and E. malabaricus) based on DNA metabarcoding of stomach contents and potential prey detection using environmental DNA tools at sites in the coral reefs of Raja Ampat, Indonesia. DNA recovered from the water column comprised taxa from the Arthropoda, Chordata, Cnidaria and Mollusca, several of which were also found in grouper guts, with Cnidaria the most abundant class. Diversity was high for potential prey species in the environment and prey consumed by each grouper species. The high overlap in prey identified from gut contents indicates these two epinephelids have a similar feeding strategy. However, nMDS ordination showed segregation between the prey consumed by each species and potential prey available in the environment. The results indicate a low likelihood of competition between the two grouper species, related to the abundance and wide choice of potential prey in the highly biodiverse Raja Ampat coral reef ecosystem.

Coral reef fish are play key role in coral reef ecosystem. The presence of reef fish affected by antrophogenic and natural factors, such seasonal changes. This study aimed to asess the temporal variation of coral reef fish group in Tidung Kecil Island using eDNA metabarcoding and Undewater Visual Census. This research was conducted at December 2019 (West season) and August 2020 (East season). Target group are dominated in west season (64.1%) and east season (59.25%) using eDNA metabarcoding. While, major group fish are the highest relative abundance in both season by using Underwater Visual Census. Family Carangidae are the highest species richness (15 species) in wet season and Serranidae (3 species) in east season, respectively. Futhermore, famili Pomacentridae are the most richness species in west and east seasons 10 and 11 species respectively. Thus, it can be concluded these two methods are effective for monitoring structure or abundance of coral reef fish based on seasonal variation. Ikan karang menjadi indikator dalam menilai keanekaragaman hayati di ekosistem tersebut. Keberadaan ikan di ekosistem terumbu karang dapat dipengaruhi oleh faktor antropogenik dan faktor alam salah satunya perubahan musim. Penelitian ini bertujuan untuk menganalisis kelimpahan kelompok ikan terumbu karang di Pulau Tidung Kecil menggunakan eDNA metabarkoding dan Sensus Visual. Pengambilan data dilakukan pada bulan Desember 2019 (musim barat) dan Agustus 2020 (musim timur). Ikan target mendominasi pada musim barat dan timur dengan persentase sebesar 64.11% dan 59.25%. Sensus visual berhasil mendeteksi ikan mayor dengan persentase tertinggi 62.5% di musim barat dan 82.8% di musim timur. Famili Carangidae merupakan famili dengan jumlah spesies tertinggi di musim barat (15 species) dan Siganidae di musim timur menggunakan eDNA metabarkoding (3 species). Hasil UVC menunjukkan famili Pomcentridae memilki jumlah spesies tertinggi di kedua musim (11 dan 10 spesies) menggundakan sensus visual. Dapat disimpulkan bahwa kedua metode tersebut dapat menjadi pendekatan dalam monitoring struktur atau kelimpahan ikan terumbu karang berdasarkan musim.

Background Dinoflagellates of family Symbiodiniaceae are important to coral reef ecosystems because of their contribution to coral health and growth; however, only a few studies have investigated the function and distribution of Symbiodiniaceae in Indonesia. Understanding the distribution of different kinds of Symbiodiniaceae can improve forecasting of future responses of various coral reef systems to climate change. This study aimed to determine the diversity of Symbiodiniaceae around Lombok using environmental DNA (eDNA). Methods Seawater and sediment samples were collected from 18 locations and filtered to obtain fractions of 0.4–12 and >12 µm. After extraction, molecular barcoding polymerase chain reaction was conducted to amplify the primary V9-SSU 18S rRNA gene, followed by sequencing (Illumina MiSeq). BLAST, Naïve-fit-Bayes, and maximum likelihood routines were used for classification and phylogenetic reconstruction. We compared results across sampling sites, sample types (seawater/sediment), and filter pore sizes (fraction). Results Phylogenetic analyses resolved the amplicon sequence variants into 16 subclades comprising six Symbiodiniaceae genera (or genera-equivalent clades) as follows: Symbiodinium, Breviolum, Cladocopium, Durusdinium, Foraminifera Clade G, and Halluxium. Comparative analyses showed that the three distinct lineages within Cladocopium, Durusdinium, and Foraminifera Clade G were the most common. Most of the recovered sequences appeared to be distinctive of different sampling locations, supporting the possibility that eDNA may resolve regional and local differences among Symbiodiniaceae genera and species. Conclusions eDNA surveys offer a rapid proxy for evaluating Symbiodiniaceae species on coral reefs and are a potentially useful approach to revealing diversity and relative ecological dominance of certain Symbiodiniaceae organisms. Moreover, Symbiodiniaceae eDNA analysis shows potential in monitoring the local and regional stability of coral–algal mutualisms.

Environmental DNA (eDNA) methods are increasingly viewed as alternate or complementary approaches to conventional capture-based surveys for marine conservation and fisheries management purposes, especially at large spatial scales in mega-biodiversity regions such as Indonesia. Decapod crustacean distribution and diversity across Indonesia are still poorly known, even for economically important fisheries commodities. This study assessed coral reef associated decapod diversity and distribution by sampling 40 sites in three regions (West, Central, East), representing 17 provinces and 10 Fisheries Management Areas (FMAs) across Indonesia, with a special focus on the blue swimming crab Portunus pelagicus. DNA sequencing (Illumina iSeq100) data were analysed in mBRAVE (Multiplex Barcode Research And Visualization Environment) yielded 406 OTUs belonging to 32 families, with 47 genera and 51 species identified. The number of families identified was highest in the Central region (25), while the most genera (31) and species (36) were identified in the West region. Alpha diversity did not differ significantly between regions or provinces, while Beta diversity differed significantly between provinces but not between regions. Our results also showed 31 species are possibility native based on the distribution meanwhile 12 species do not appear to have been recorded based of SeaLifeBase or WorMS. While providing a reference for further exploration of Indonesian coastal and small island decapod biodiversity, the high proportion of unidentified taxa calls for concerted efforts to develop and maintain reference specimen and sequence repositories and expand species conservation status assessments. The economically important decapod crustaceans identified in this study included three crabs (Charybdis anisodon, Charybdis japonica, Portunus pelagicus), a freshwater prawn (Macrobrachium nipponense), a lobster (Panulirus stimpsoni) and two penaeid shrimps (Mierspenaeopsis hardwickii and Trachysalambria aspera). For most decapod taxa, observed patterns indicate management under existing provincial and/or FMA level management structures is appropriate. Furthermore, the data can inform science-based fisheries management strategies, in particular for P. pelagicus.

The first occurrence of the cyanobacteriosponge Terpios hoshinota was reported from coral reefs in Guam in 1973, but was only formally described in 1993. Since then, the invasive behavior of this encrusting, coral-killing sponge has been observed in many coral reefs in the West Pacific. From 2015, its occurrence has expanded westward to the Indian Ocean. Although many studies have investigated the morphology, ecology, and symbiotic cyanobacteria of this sponge, little is known of its population genetics and demography. In this study, a mitochondrial cytochrome oxidase I (COI) fragment and nuclear ribosomal internal transcribed spacer 2 (ITS2) were sequenced to reveal the genetic variation of T. hoshinota collected from 11 marine ecoregions throughout the Indo-West Pacific. Both of the statistical parsimony networks based on the COI and nuclear ITS2 were dominated by a common haplotype. Pairwise FST and Isolation-by-distance by Mantel test of ITS2 showed moderate gene flow existed among most populations in the marine ecoregions of West Pacific, Coral Triangle, and Eastern Indian Ocean, but with a restricted gene flow between these regions and Maldives in the Central Indian Ocean. Demographic analyses of most T. hoshinota populations were consistent with the mutation-drift equilibrium, except for the Sulawesi Sea and Maldives, which showed bottlenecks following recent expansion. Our results suggest that while long-range dispersal might explain the capability of T. hoshinota to spread in the IWP, stable population demography might account for the long-term persistence of T. hoshinota outbreaks on local reefs.

Species list of economical fish landed in Muara Baru Modern Fish Market, Jakarta needs to be examined. Fish species information needs to know the species of fish being traded. However, many species are difficult to identify morphologically. The aim of this research was to identify fish based on their morphological characters and DNA barcoding. The methods of this research were morphologic, morphometric, and molecular identification with DNA barcoding using PCR. Morphological analysis results showed that fish samples have unique characteristics in the presence of spots on their bodies and fading in the abdomen. Morphometric observations were made with 19 different characters and weight measurements. The 19 fish characters observed have a standard deviation of

Highlight • Identification and morphological analysis of Selaroides leptolepis fish. • Molecular analysis using the DNA Barcoding method with the COI gene (mitochondrial cytochrome oxidase subunit I). • The number of base pairs in S. leptolepis from the sequencing results was 675bp. • The morphological and molecular similarities of Selaroides leptolepis fish Abstract Yellowstripe scad is one of the commercially important fish from the Carangidae family, which is marketed at Muara Baru Modern Fish Market, North Jakarta. In- formation regarding the presence of Selaroides leptolepis fish in the waters allows for effective conservation, and management of marine resources. A morphological identification of fish species is still considered inaccurate, so the molecular anal- ysis is necessary. This study aims to identify commercially important fish species deriving from Muara Baru Modern Fish Market, North Jakarta, employing mor- phological, and molecular analysis. A total of 30 specimens were collected from the field. The morphological analysis utilized a visual identification method, and morphometric measurement, while molecular analysis with DNA barcoding em- ployed the mitochondrial cytochrome oxidase subunit I (COI) gene. The results of the morphological analysis indicated that the fish species were yellowstripe scad (S. leptolepis). It also followed the results of molecular analysis of DNA barcoding that the fish was a S. leptolepis species. Therefore, the combination of morphological and genetic analysis has succeeded in identifying the fish species of S. leptolepis.

Yellow-tailed fish (Caesio cuning) have morphologically similarities with Lutjanidae families, it causes ambiguity on species authentication process. The process of species identification using morphological characteristic does not provide a precise information related to the species.This study was aimed to identify the morphometric and molecular of Yellow-tailed fish (Caesio cuning) which landed on Muara Baru Fish Market, Jakarta using COI gene. A total 30 fishes were observed their nineteen morphometric characters, and 1 fish sample was taken from the fins for DNA extraction, amplification using PCR method, electrphoresis visualization, and sequensing. Sample was analyzed by MEGA 6 software. Based on morphological analysis showed that sampel are Yellow-tailed fish which part of Caesio genus and Caesionidae family. While, genetic analysis using COI gene showed has similarities with database of Genbank NCBI. It can be concluded that identification using morphological character and DNA barcoding methode showed the species belong to Yellow-tailed fish (Caesio cunning). Ikan Ekor Kuning (Caesio cuning) memiliki kemiripan morfologi dengan anggota famili Lutjanidae lainnya, hal tersebut menyebabkan kesulitan dalam proses autentikasinya. Proses identifikasi pada suatu spesies menggunakan karakteristik morfologinya belum mampu memberikan informasi yang akurat terkait spesies tersebut. Penelitian ini bertujuan untuk mengidentifikasi ikan ekor kuning (Caesio cuning) yang didaratkan di Pasar Muara Baru, Jakarta melalui kajian karakteristikmorfometrik dan DNA barcoding menggunakan marka gen COI. Total 30 ikan diamati karakter morfometriknya, dan 1 sampel ikan diambil bagian siripnya untuk dilakukan ekstraksi DNA, amplfikasi PCR, elektroforesis, sekuensing dan dianalisis menggunakan aplikasi MEGA 6. Hasil analisis morfologi menunjukkan sampel ikan berasal dari genus Caesio dan termasuk famili Caesionidae. Sedangkan berdasarkan analisis secara molekuler menggunakan marka gen COI, didapatkan hasil bahwa spesies yang diamati (Caesio cuning) memiliki kemiripan dengan database GenBank NCBI. Dapat simpulkan bahwa identifikasi secara morfologi dan DNA menunjukkan bahwa spesies yang di peroleh yaitu Ikan ekor kuning (Caesio cuning).

Ekosistem lamun dihuni oleh banyak jenis invertebrata bentik, organisme demersal serta pelagis yang menetap maupun yang tinggal sementara di ekosistem lamun. Penelitian ini bertujuan untuk menganalisis kepadatan makrozoobentos dalam dua fase bulan yang berbeda dan mengetahui kontribusi setiap spesies makrozoobentos di setiap stasiun penelitian di padang lamun. Pengambilan sampel organisme makrozoobentos diambil di Pulau Panggang pada tiga stasiun pengamatan (barat, timur, dan selatan) dengan menggunakan transek quadrat 1 x 1 m dan corer sedimen dengan diameter 10 cm. Analisis data secara statistik, analisis data dilakukan dengan mencari tahu persentase kesamaan kontribusi spesies menggunakan uji SIMPER. Hasil penelitian ini menunjukkan bahwa macrozoobentos yang ditemukan untuk dua fase bulan bervariasi di setiap stasiun. Total makrozoobentos yang ditemukan selama dua fase bulan adalah 28 dan 11 spesies di stasiun barat, 24 dan 20 spesies di stasiun timur, dan 18 dan 24 spesies di stasiun selatan, masing-masing. Di ketiga stasiun, dua jenis spesies makrozoobentos tertinggi dan terendah selama dua fase bulan yaitu Cerithium salebrosum (283 ind/m2) dan Cerithium punctatum (169 ind/m2); dan Geotrochus multicarinatum (7 ind/m2). Selain itu, spesies makrozoobentos yang paling banyak di habitat lamun di seluruh stasiun adalah Cerithium salebrosum.

Species with limited dispersal abilities are often composed of highly genetically structured populations across small geographic ranges. This study aimed to investigate the haplotype diversity and genetic connectivity of the coastal horseshoe crab (Tachypleus gigas) in Indonesia. To achieve this, we collected a total of 91 samples from six main T. gigas habitats: Bintan, Balikpapan, Demak, Madura, Subang, and Ujung Kulon. The samples were amplified using primers for mitochondrial (mt) AT-rich region DNA sequences. The results showed 34 haplotypes, including seven shared and 22 unique haplotypes, across all localities. The pairwise genetic differentiation (FST) values were low (0 to 0.13) and not significantly different (p > 0.05), except among samples from Ujung Kulon-Madura and Kulon-Subang (p

Background Understanding region-wide patterns of larval connectivity and gene flow is crucial for managing and conserving marine biodiversity. Dongsha Atoll National Park (DANP), located in the northern South China Sea (SCS), was established in 2007 to study and conserve this diverse and remote coral atoll. However, the role of Dongsha Atoll in connectivity throughout the SCS is seldom studied. In this study, we aim to evaluate the role of DANP in conserving regional marine biodiversity. Methods In total, 206 samples across nine marine species were collected and sequenced from Dongsha Atoll, and these data were combined with available sequence data from each of these nine species archived in the Genomic Observatories Metadatabase (GEOME). Together, these data provide the most extensive population genetic analysis of a single marine protected area. We evaluate metapopulation structure for each species by using a coalescent sampler, selecting among panmixia, stepping-stone, and island models of connectivity in a likelihood-based framework. We then completed a heuristic graph theoretical analysis based on maximum dispersal distance to get a sense of Dongsha’s centrality within the SCS. Results Our dataset yielded 111 unique haplotypes across all taxa at DANP, 58% of which were not sampled elsewhere. Analysis of metapopulation structure showed that five out of nine species have strong regional connectivity across the SCS such that their gene pools are effectively panmictic (mean pelagic larval duration (PLD) = 78 days, sd = 60 days); while four species have stepping-stone metapopulation structure, indicating that larvae are exchanged primarily between nearby populations (mean PLD = 37 days, sd = 15 days). For all but one species, Dongsha was ranked within the top 15 out of 115 large reefs in the South China Sea for betweenness centrality. Thus, for most species, Dongsha Atoll provides an essential link for maintaining stepping-stone gene flow across the SCS. Conclusions This multispecies study provides the most comprehensive examination of the role of Dongsha Atoll in marine connectivity in the South China Sea to date. Combining new and existing population genetic data for nine coral reef species in the region with a graph theoretical analysis, this study provides evidence that Dongsha Atoll is an important hub for sustaining connectivity for the majority of coral-reef species in the region.

The area of mangrove Segara Anakan has a high economic value so that there is a high interest to various land uses in this area. This condition leads to the change in ecological function of the mangrove which has impacts on the decreased production of mangrove crabs. This study was desighed to analyze the areas of catching crabs related to mangrove ecosystem. This study was conducted for six months in the 3 mudcrab catching areas (Western Area, Central Area, and Eastern Area). The analysis used in this study was a one way ANOVA statistic for the crabs catching in these 3 catching areas, and a simple linear regression to analyxe the correlation betwen annual crab production and mangrove area. The results showsed that mud crabs catchings in the 3 areas is 5861.7; 6072.87; dan 7689.4 kg were significantly different (P

The blue swimming crab (BSC), Portunus pelagicus (Linnaeus 1758), inhabits coastal areas of Southeast and East Asia, and is one of high fisheries commodities with an export value for Indonesia and an increasing global market demand, annually. However, the data of genetic diversity and their spatial connectivity of populations in Indonesia are not yet known, even when it is important to inform stock unit management and sustainable use. This study aimed to determine the genetic diversity and differentiation of blue swimming crabs across Indonesian populations in different Fishery Management Area (FMA), and their spatial genetic connectivity, as well as to deliver implications for sustainable fishery. A total of 297 individuals were collected and amplified using cytochrome oxidase I mitochondrial DNA. This study has showed the highest values for haplotype and nucleotide diversity in the eastern part of Indonesia, where exploitation is relatively low. Significant genetic differentiation between populations (FST = 0.954; p < 0.001) and the fisheries management areas (FST = 0.964; p < 0.001) were revealed. Low spatial connectivity was observed between populations in a distance of at least more than 60 kilometers. This study suggests that BSC populations in Indonesia, likely have several stock units, and preferably different fisheries management plans and actions across the region thoroughly and simultaneously. This would be effective for management and their sustainable conservation.

Scalloped Hammerhead shark (Sphyrna lewini) is an endangered species which its populations have been declining globally including in Indonesia, the world's top shark fishing country. However, there is a lack of information on the recent population structure of this species to promote proper management and its conservation status. This study aimed to investigate the genetic diversity, population structure, and connectivity of the S. lewini population, in three major shark landing sites: Aceh (n = 41), Balikpapan (n = 30), and Lombok (n = 29). Meanwhile, additional sequences were retrieved from West Papua (n = 14) and the Western Indian Ocean (n = 65) populations. From the analyses of the mitochondrial CO1 gene, a total of 179 sequences of S. lewini, with an average size of 594 bp, and 40 polymorphic loci in four and eight haplotypes for the Indonesian population and the Western Indian Ocean population were identified. The overall values of genetic diversity were high (h = 0.717; π = 0.013), with the highest values recorded in Aceh (h = 0.668; π = 0.002) and the lowest in Papua (h = 0.143; π = 0.000). On the contrary, the overall value was fairly low in the Western Indian Ocean (h = 0.232; π = 0.001). Furthermore, AMOVA and FST showed three significant subdivisions in Indonesia (FST = 0.442; P < 0.001), with separated populations for Aceh and West Papua, and mixed between Balikpapan and Lombok (FST = 0.044; P = 0.091). In contrast, genetic homogeneity was observed within the population of the Western Indian Ocean (FST = -0.013; P = 0.612). The establishment of a haplotype network provided evidence of a significantly different population and a limited genetic distribution between the Indonesian and the Western Indian Ocean populations (FST = 0.740; P < 0.001). This study showed the presence of a complex population of S. lewini with limited connectivity only in Indonesia separated from the Western Indian Ocean and requiring specific management measures based on the population structure at the regional level.

Metabolite profiles and antioxidant activity of Caulerpa racemosa extract with different handlings were investigated. Three different handlings during transportation were applied, namely samples chilled with ice, stored in liquid nitrogen and soaked in seawater. The different handling significantly affected the yield of ethanolic crude extracts and inorganic fractions but insignificantly to organic fractions. Different handlings resulted in differences of major fractions of C. racemosa extracts. Major fractions of the sample that was handled with chilling temperature contained low polar fractions (K10, K11, K12, and K13), while seawater handling extract contained very polar (K1, K2 and K3), polar (K6, K7, and K8) and low polar (K13) fractions. The extract of the sample handled in liquid nitrogen contained balanced fractions. Chilling temperature handling produced highest antioxidant activity (IC50 below 2,000 ppm) in ethanolic extract of C. racemosa. Keywords: antioxidant activity, Caulerpa racemosa, ethanolic extract,handlings, IC50

The coral reefs structure and composition are influenced by environmental condition and depth. Therefore, this study was conducted to find and examine the influence of depth against coral reef structures in Pramuka Island regions, Seribu Islands, located in the northern of Jakarta. The study was carried out from November to December 2016.The data was taken by using Line Intercept Transect Method which is laid 20 meters x 3 replication parallels with shoreline at the depth of 3 and 10 meters. There was a dominant of higher hard coral (HC) coverage recorded at the depth of 3 m and the lowest percentage located in West of Pramuka. Coral mortality index varied and ranged from 0.39 to 0.98. West of Pramuka Island dominant have the lowest value of average number of families, genera, and life form. Percentage of hard coral cover, coral mortality index, average number of family, genera, and life form differed significantly between sites. The different of depth only influencing the percentage of coral cover and average number of life form.

Penelitian yang dilakukan untuk mengetahui pengaruh cahaya terhadap pertumbuhan karang lunak Lobophytum strictum hasil transplantasi dilakukan dengan pemeliharaan karang lunak pada dua buah kolam, yaitu kolam terbuka (cahaya) dan kolam tertutup (tanpa cahaya). Pada masing-masing kolam ditempatkan 16 fragmen karang lunak yang sudah ditransplantasikan. Kelangsungan hidup dan pertumbuhan karang lunak berbeda signifikan antar perlakuan cahaya (P

The genetic connectivity of soft coral is influenced by current and distance between islands. The complexity of islands and geographical region in Indonesia might influence the distribution of soft corals. The information of genetic connectivity can be used to design marine protected areas and to avoid destruction and possible extinction. The objective of the present study was to analyze genetic connectivity of one species of soft coral, Sarcophyton trocheliophorum, in three populations spanning Java, Nusa Tenggara, and Sulawesi’s waters, and to describe its implication for marine protected area. The mitochondrial protein-coding gene (750 bp of ND2) was used to analyze genetic population structure and genetic connectivity. Genetic connectivity was found in all populations with Fst value of 0.227 to 0.558, indicating populations had the close genetic relationship. The local and Indonesian currents were expected to distribute the larva to islands as a stepping stone, they moved slowly to spread them self far away. Tanakeke island (Sulawesi population) might be a center connectivity of S. trocheliophorum populations. This island connected with islands in west and east Indonesia, therefore that area need to protect

Reliable and precise species identification is important to fisheries management and conservation. However, many rays and skates in Indonesia are currently being exploited and landed into traditional fish market without a proper identification. Therefore, this study was conducted to identify species of skates and stingrays that were landed and traded in three fish markets in Indonesia (Palabuhanratu, Muara Saban, and Lampung) using molecular techniques and to determine the conservation status of the identified species based on IUCN (International Union for Conservation of Nature and Natural Resources) as well as defined by CITES (Convention on International Trade in Endangered Species). The mitochondrial cytochrome oxidase I (COI) gene was amplified by polymerase chain reaction (PCR) using a pair of primer, fish-BCL and fish-BCH. Of 29 tissue samples collected from the study sites, a total of five species were successfully identified: Dipturus chilensis (4), Himantura walga (1), Neotrygon kuhlii (11), Taeniura lymma (9) and Rhinoptera javanica (4). The Neighbor Joining phylogeny of mitochondrial lineages, based on partial COI gene sequences, the ingroup haplotypes were clustered into five main clades representing each species. The identified stingrays were being listed as vulnerable (D. chilensis and R. javanica), near threatened (H. walga and T. lymma), and data deficient (N. kuhlii) by IUCN, with two species (D. chilensis and H. walga) population were indicated decreased. Unfortunately, all of identified species have not been evaluated by CITES regarding their trade status. As a consequences, a valuable effort should be placed to create a scientific network for monitoring programmes not only on a local scale, and to make pressure on governments for adopting molecular techniques as tools for controlling and avoiding misidentification. Keywords: Mitochondrial DNA, Phylogeny, Coral Triangle, Taxonomy, Fisheries

Genetik menjadi kunci konservasi karena berperan penting dalam mempertahankan dan memulihkan populasi dari kerusakan. Kerusakan pada ekosistem terumbu karang dapat menjadi pemicu kepunahan organisme laut. Salah satu organisme yang tidak terhindar dari kerusakan tersebut ialah Sarcophyton trocheliophorum. Kerusakan tersebut dapat menyebabkan menurunnya keragaman genetik S. trocheliophorum. Tujuan dari penelitian ini adalah menganalisis keanekaragaman genetik dari S. trocheliophorum yang terdapat pada tiga populasi di Perairan Jawa, Sulawesi dan Nusa Tenggara serta mendeskripsikan implikasinya terhadap kawasan konservasi di Indonesia. Penelitian ini menggunakan penanda genetik ND2 untuk menganalisis struktur populasi, konektivitas, dan keragaman genetik. Keragaman genetik S. trocheliophorum pada Perairan Jawa, Sulawesi, Nusa Tenggara masing-masing 0.600, 0.815, dan 0.972. Keragaman genetik pada populasi Perairan Jawa lebih kecil dibandingkan pada Populasi Perairan Sulawesi dan Nusa Tenggara. Hal ini dimungkinkan karena banyaknya aktivitas manusia pada pesisir utara Laut Jawa, sehingga berdampak pada menurunnya ukuran populasi S. trocheliophorum. Oleh karena itu perlu adanya perlindungan yang ketat pada populasi Jawa untuk menjaga kelestarian keanekaragaman hayati Indonesia.

The Indo-Malay Archipelago is regarded as a barrier that separates organisms of the Indian and Pacific Oceans. Previous studies of marine biota from this region have found a variety of biogeographic barriers, seemingly dependent on taxon and methodology. Several hypotheses, such as emergence of the Sunda Shelf and recent physical oceanography, have been proposed to account for the genetic structuring of marine organisms in this region. Here, we used six microsatellite loci to infer genetic diversity, population differentiation and phylogeographic patterns of Enhalus acoroides across the Indo-Malay Archipelago. Heterozygosities were consistently high, and significant isolation-by-distance, consistent with restricted gene flow, was observed. Both a neighbour joining tree based on DA distance and Bayesian clustering revealed three major clusters of E. acoroides. Our results indicate that phylogeographic patterns of E. acoroides have possibly been influenced by glaciation and deglaciation during the Pleistocene. Recent physical oceanography such as the South Java Current and the Seasonally Reversing Current may also play a role in shaping the genetic patterns of E. acoroides.

Penelitian teritip spons Indonesia jarang dilakukan sejak kelompok ini pertama kali dideskripsikan hingga saat ini. Tujuan dari penelitian ini adalah untuk mengkaji karakter morfologi teritip spons Indonesia dan untuk mengkaji hubungan spesies spesifik teritip terhadap spons. Pengambilan sampel pada penelitian ini dilaksanakan sejak Oktober sampai Desember 2012 di tiga lokasi yaitu Pulau Weh, Kepulauan Seribu, dan Kepulauan Karimunjawa. Metode penelitian menggunakan metode survei dan titik pengambilan sampel dipilih berdasarkan keberadaan spons. Sampel diamati menggunakan mikroskop stereo dan mikroskop elektron kemudian diidentifikasi berdasarkan deskripsi Darwin (1854), Pilsbry (1916), Martin dan Davis (2001), dan Kolbasov (1993). Hasil penelitian didapatkan empat spesies teritip spons yaitu Acasta cyathus, A. fenestrata, Euacasta dofleini, dan Membranobalanus longirostrum. Terdapat hubungan spesies spesifik antara teritip dan spons inang yaitu antara teritip E. dofleini dan spons Haliclona sp. dan antara teritip M. longirostrum dan spons Suberites sp.