Madduppa HH, Subhan B, Suparyani E, Siregar AM, Arafat D, Tarigan SA, Alimuddin, Khairudi D, Rahmawati F, Bramandito A. 2013. Dynamics of fish diversity across an environmental gradient in the Seribu Islands reefs off . The reefs of Seribu Islands have been affected by multitude of anthropogenic pressures. However, the biodiversity of reef fishes across the archipelago linked to environmental condition is poorly known. This study aimed to investigate the biodiversity and the trophic level of fish communities across the archipelago. The study on reef fish communities was conducted on 33 reef sites associated with islands or shoal randomly chosen from each zone along environmental gradients from the inshore water nearest of Jakarta Bay to the offshore water of the outer islands. The study sites represented each sub-districts within the archipelago, namely Pari, Tidung, Panggang, Kelapa, and Harapan. A total of 46,263 individual fishes were counted, belonging to 216 species and 29 families. The multivariate analysis of fish abundance using the Bray Curtis similarity index and non-metric multidimensional scaling (MDS) clearly showed the clustering of sub-districts, near and far from Jakarta Bay. The results showed that the sub-districts can be clustered into three groups. Group one consists of one sub-district (Pari) located in the southern part of the Seribu Islands near Jakarta Bay. Group two consists of three subdistricts (Tidung, Panggang, Kelapa) located in mid of the archipelago. The third group consists of one sub-district (Harapan) located in the northern part of the Seribu Islands. Based on species richness and fish diversity indices, the sub-districts can be clustered into two groups (1 = Pari and Tidung, 2 = Panggang Kelapa, Harapan). However, levels of similarities among sub-districts varied. The fish community in sub-district of Pari was dominated by carnivorous, omnivorous and herbivorous fishes, while those in the rest of subdistricts were dominated by omnivorous and carnivorous fishes. The present study results showed that the biodiversity of reef fishes across the Seribu Islands seemed to be linked to the environmental conditions.

Abstract. Jefri E, Zamani EP, Subhan B, Madduppa HH. 2015. Molecular phylogeny inferred from mitochondrial DNA of the grouper Epinephelus spp. in Indonesia collected from local fish market. . Groupers are widely distributed in the tropical and subtropical coastal waters, and are globally one of the most commercially important groups of marine fish, commanding high market price and are being heavily targeted in fisheries. Over fishing in Indonesia becomes a pivotal factor, which is seriously threatening the grouper biodiversity, as separate catch statistics are not reported for most species, and landings are often summarized as 'serranids' or 'groupers'. This lack of species-specific catch data is due to the difficulty of identifying many of the species. The focus of this study was the tracking of molecular phylogeny of Epinephelus spp. of the family Serranidae. DNA amplification using mitochondrial cytochrome oxidase I resulted in 526-base pairs long sequences all samples. A total of seven species were characterized that are (Epinephelus areolatus, E. merra, E. fasciatus, E. longispinis, E. coioides, E. ongus and E. coeruleopunctatus). All of which were found to belong to 7 different clades in the constructed phylogenetic tree. E. ongus is genetically closest to E. coeruleopunctatus with genetic distance 0.091 (9%), whereas the farthest genetic distance was successfully identified between E. ongus and E. merra with genetic distance 0.178 (18%). Migration activity on spawning and movement of larvae that are affected by Indonesian Through flow suspected as the cause of the closeness between species grouper Epinephelus spp. in the phylogeny tree from several Indonesian seas, although information about the location and time of Epinephelus spp. spawning activity sometimes difficult to obtain certainty. Fish identification using molecular phylogenetic approach has been successfully applied in this study. It seems need further application on this method to avoid misidentification and due to high variety of species landing at local fish market. Nevertheless, this study would be an important data in the genetic management for the sustainable conservation and trade of grouper (Epinephelus spp.) in Indonesia.

Abstract. Prehadi, Sembiring A, Kurniasih EM, Arafat D, Subhan B, Madduppa HH. 2015. DNA barcoding and phylogenetic reconstruction of shark species landed in Muncar fisheries landing site in comparison with Southern Java fishing port. . Sharks are one of main fisheries commodity that are currently exploited on a large scale because of their high economic value. The identification of sharks has been a difficult one due to the specimen's similarity in morphology and mostly have had key diagnostic features removed. This study aimed to identify and to review the status of sharks, and also to reconstruct the shark species that were landed at South Java fishing port using molecular approaches. The DNA amplification was using cytochrome oxidase I mitochondrial of locus and 600-700 basepairs. A total of seven species from 59 individuals was identified including Alopias pelagicus, Carcharhinus falciformis, C. sorrah, C. amblyrhynchos, Galeocerdo cuvier, Atelomycterus marmoratus, and Spyrna lewini. The diversity of shark species landed in Muncar during the last 2 years has been decreased. The identified sharks species in this study sites were about 18% of all Indonesian sharks. The result of this study is expected help the Government to manage shark fisheries in Indonesia.

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

RINGKASANTransplantasi karang merupakan teknik perbanyakan koloni karang dengan memanfaatkan reproduksi aseksual karang secara fagmentasi. Berbagai kalangan dapat terlibat dalam mengusahakan dan melakukan rehabilitasi karang dengan metode ini. Namun saat ini metode yang digunakan masih ada yang mengadopsi metode untuk perdagangan karang hias bukan untuk rehabilitasi. Metode dengan beton dan pengontrolan terhadap alga salah satu kunci keberhasilan dalam transplantasi karang. Pencarian bibit-bibit karang yang unggul yang kuat terhadap alga dan penyakit menjadi solusi penting dalam peningkatan keberhasilan transplantasi karang.Kata kunci: transplantasi karang, metode beton, penyakit karang, alga PERNYATAAN KUNCI Transplantasi karang merupakan teknik perbanyakan koloni karang deng an memanfaatkan reproduksi aseksual karang secara fagmentasi. Beberapa ahli sering juga menggunakan istilah propagasi sebagai kata lain untuk transplantasi karang. Metode transplantasi merupakan cara sederhana untuk perbaiki terumbu karang. Berbagai kalangan dapat terlibat dalam mengusahakan dan melakukan rehabilitasi karang dengan metode ini. Namun saat ini metode yang digunakan masih ada yang mengadopsi metode untuk perdagangan karang hias bukan untuk rehabilitasi. Setiap lokasi terumbu karang yang mengalami kerusakan memiliki keunikan tersendiri. Pada umunya pertimbangan pemilihan lokasi hanya berdasarkan kondisi fisik dan kimia perairan. Setiap tahap dalam pelaksanaan transplantasi karang merupakan faktor kunci dalam keberhasilan transplantasi karang. Tahaptahap transplantasi pemilihan lokasi, pembuatan substrat, pemilihan bibit, penanaman karang dan monitoring. REKOMENDASI KEBIJAKAN Transplantasi karang merupakan kegiatan jangka panjang sehingga tidak bisa berbasis proyek. Sistem program merupakan salah satu solusi untuk meningkatkan keberhasilan 159

Madduppa HH, Agus SB, Farhan AR, Suhendra D, Subhan B. 2012. Fish biodiversity in coral reefs and lagoon at the Maratua Island, East Kalimantan. Biodiversitas 13: 145-150. Fishes are one of the most important biotic components in the aquatic environment. They are filling different habitats, including coral reef and lagoon. This study aims to (i) assess biodiversity in coral reef and lagoon in Maratua Island, East Kalimantan, and (ii) compare the fish community indices (Shannon-Wiener diversity, Evenness, and Dominance) between the coral reef and lagoon. A total of 159 fish species of belonging to 30 families were observed during five visual census of the study period. The number of species on coral reefs is higher (121 species) than in the lagoons (47 species). Relative abundance (%) of each species also varied and did not form a specific pattern. However, a clear cluster between the coral reef and lagoon habitats from fish relative abundance based on multivariate analysis and dendogram Bray-Curtis Similarity was revealed. The Evenness index value (E) ranged from 0.814 to 0.874, the dominance index (C) ranged from 0.023 to 0.184, and the Shannon-Wiener diversity index (ln base, H') ranged from 1.890 to 4.133. Fish biodiversity in coral reefs was higher (H'= 3.290±0.301) than in the lagoon (H' = 2.495±0.578).

DNA Barcoding is a tool in the molecular taxonomy which allows a rapid and precise identification. This tool is needed to mitigate difficulties in identifying species of sea cucumbers in Indonesia. This study was conducted to reveal species diversity in sea cucumbers (Holothuridae and Stichopodidae), commonly harvested in the Kepulauan Seribu reefs, northern Jakarta, Indonesia, by using mitochondrial DNA. Neighbor-joining phylogenetic trees were reconstructed using the Kimura-2 parameter with 1000 of bootstrap values. The genetic distance within and between species was investigated. Conservation and trade status of the species were determined using IUCN and CITES, respectively. DNA barcoding using mitochondrial Cytochrome oxidase 1 (COI) revealed 7 species from 96 samples, of which 4 species belonged to the Stichopodidae (Stichopus herrmanni, Stichopus ocellatus, Stichopus horrens, Stichopus monotuberculatus), and 3 species to the Holothuridae (Bohadschia bivittata, Actinopyga lecanora and Holothuria leucospilota). Phylogenetic analysis showed that the two families were separated with a high bootstrap value. The neighbor-joining tree supported the result of identification of the sea cucumber species. The ingroup haplotypes were clustered into four main clades. Stichopus herrmanni and S. ocellatus were identified as closely related, which matches their morphological characteristics. Bohadschia bivittata is the most distinct species from other species due to the formation of a separate clade in the phylogenetic tree. Stichopus. horrens and S. monotuberculatus were also identified as very closely related, which might explain the frequent morphological misidentification of both types. The conservation status determined one of the investigated species was categorized as vulnerable, one as least concern, one as not evaluated, and four species in data deficient. The population trend of S.s herrmanni was recorded to be decreasing, whereas it remained unknown for the other 6 species. Surprisingly, all identified species in this study were not evaluated yet by CITES. This study suggests that a proper field monitoring and the establishment of a valid list of commercial and scientific names for the sea cucumbers harvested in Kepulauan Seribu is necessary. This would be valuable for keeping trade records and managing and conserving the targeted sea cucumber species in the region.

marine protected area reef zones (utility zone, open access zone, core zone) around Lombok Island using eDNA metabarcoding. Biological community composition, richness, and diversity were evaluated based on reads from mid-column water and sediment samples. A total of 58 species were identified from the eDNA samples using the Multiplex Barcode Research And Visualization Environment (mBRAVE) pipeline. The Shannon-Wiener index (H') showed significantly higher species diversity in the core zone than the utility and open access zones. There was no significant between-zone difference in community structure (ANOSIM, R = 0.11 < 0.25). NMDS analysis using the Bray-Curtis test showed significant betweenzone differences in species diversity and abundance (PERMANOVA Adonis Pr (> F) = 0.001, p < 0.05). Based on the high number of fish species detected in this study, eDNA can be recommended as an alternative tool or as a complement to visual survey methods for biological monitoring and diversity assessment of remote reefs, with less stringent requirements in terms of field conditions (e.g. visibility) and taxonomic expertise.