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. Biodiversitas 16: 254-263. Groupers are widely distributed in thetropical and subtropical coastal waters, and are globally one of the most commercially important groups of marine fish, commandinghigh market price and are being heavily targeted in fisheries. Over fishing in Indonesia becomes a pivotal factor, which is seriouslythreatening 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 ofthis study was the tracking of molecular phylogeny of Epinephelus spp. of the family Serranidae. DNA amplification usingmitochondrial cytochrome oxidase I resulted in 526-base pairs long sequences all samples. A total of seven species were characterizedthat are (Epinephelus areolatus, E. merra, E. fasciatus, E. longispinis, E. coioides, E. ongus and E. coeruleopunctatus). All of whichwere found to belong to 7 different clades in the constructed phylogenetic tree. E. ongus is genetically closest to E. coeruleopunctatuswith genetic distance 0.091 (9%), whereas the farthest genetic distance was successfully identified between E. ongus and E. merra withgenetic distance 0.178 (18%). Migration activity on spawning and movement of larvae that are affected by Indonesian Through flowsuspected 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. Fishidentification using molecular phylogenetic approach has been successfully applied in this study. It seems need further application onthis method to avoid misidentification and due to high variety of species landing at local fish market. Nevertheless, this study would bean important data in the genetic management for the sustainable conservation and trade of grouper (Epinephelus spp.) in Indonesia.

Madduppa H, Taurusman AA, Subhan B, Anggraini NP, Fadillah R, Tarman K. 2017. DNA barcoding reveals vulnerable and not evaluated species of sea cucumbers (Holothuroidea and Stichopodidae) from Kepulauan Seribu reefs, Indonesia. Biodiversitas 18: 893-898. 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.

Objective: Despite advanced treatment options available, drug resistance develops in breast cancer (BC) patientsrequiring novel effective drugs. Stylissa carteri, a marine sponge predominantly living in Indonesia territories, hasnot been extensively studied as anti-cancer. Therefore, this study targeted to assess the anti-tumor activity of theethanol extract of S. carteri in BC cells. Methods: S. carteri was collected from Pramuka Island, at Kepulauan SeribuNational Park, Jakarta, Indonesia and extracted using ethanol. Different BC cells including MDA MB 231, MDAMB 468, SKBR3, HCC-1954 and MCF-7 cells were treated with this extract for cytotoxic analysis using MTT assay.Spheroid growth assay and apoptosis assay were conducted in HCC-1954 cells. In addition, cell migration analysis andsynergistic activity with doxorubicin or paclitaxel were conducted in MDA MB 231 cells. This extract was subjectedalso for GC-MS analysis. Results: The results show that ethanol extract of S. carteri demonstrated a cytotoxic activityin BC cells. The IC50 of this extract was lower 15 μg/ml in MDA MB 231, MDA MB 468, SKBR3, and HCC-1954cells. Moreover, this extract inhibited spheroids growth and induced apoptosis in HCC-1954 cells. It inhibited cellmigration and demonstrated a synergistic activity with doxorubicin or paclitaxel on triggering cell death in MDA MB231 cells. Furthermore, GC-MS analysis indicated that this extract contained 1,2-Benzenediol, Dibutyl phthalate and9,12-Octadecadienoic acid, ethyl ester. Conclusion: Our preliminary data indicate a potential anti-tumor activity ofethanol extract of S. carteri in breast cancer cells.

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

Hazeri G, Rahayu DL, Subhan B, Sembiring A, Anggoro AW, Ghozali AT, Madduppa HH. 2019. Latitudinal species diversity and density of cryptic crustacean (Brachyura and Anomura) in micro-habitat Autonomous Reef Monitoring Structures across Kepulauan Seribu, Indonesia. Biodiversitas 20: 1466-1474. Kepulauan Seribu is located in the north of Jakarta and has historically been affected by anthropogenic activities. Based on its anthropogenic pressure, the archipelago is divided latitudinally into three main parts; the southern part, is a collection of islands located closest to Jakarta Bay and characterized by poor water quality, large sediment and pollutant inputs from nearby rivers, the central and north part that possesses a better water quality. Brachyura and Anomura are dominant crustacean groups in the ocean, which inhabited areas from littoral zone to the deep sea. However, its diversity and abundance are relatively understudied especially in the area where anthropogenic pressure is severe like Kepulauan Seribu. The ARMS (Autonomous Reef Monitoring Structure) is a standardized monitoring method systematically designed for observing indications of organism’s biodiversity in units of time. This research was conducted by employing ARMS as a standardize monitoring procedure to catalog and provide census of Crustaceans (Brachyuran and Anomuran) distributed across the archipelago. All crustacean inhabiting each unit of ARMS were collected and identified. Species diversity was then evaluated to see whether gradient in anthropogenic pressure has a direct impact on species composition and abundance. A total of 24 ARMS units were deployed from 2013 to 2016, located in three zones: south (9), central (9) and north (6) of Kepulauan Seribu. This study identified 17 species from 8 different families of Brachyura and 11 Anomura species from 4 different families from all sites. However, low available identification references for Indonesian crustacean made some specimen were identified only up to family level. The highest species diversity of Brachyura was recorded from family Xanthidae, followed by Portunidae and Pilumnidae, while in Anomura was in Porcellanidae, followed by Paguridae, Galatheidae, and Diogenidae. The high species diversity and density of brachyurans and anomurans were recorded in the central zone. This research infers that the species diversity of Crustaceans (Brachyura dan Anomura) seems dependent on the environmental quality, but most likely all crustacean species depend on the availability of habitat structure.