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Madduppa H, Putri ASP, Wicaksono RZ, Subhan B, Akbar N, Ismail F, Arafat D, Prabuning D, Sani LMI, Srimariana ES, Baksir A, Bengen DG. 2020. Morphometric and DNA Barcoding of endemic Halmaheran walking shark (Hemiscyllium halmahera, Allen, 2013) in North Maluku, Indonesia. Biodiversitas 21: 3331-3343. The walking shark (Hemiscyllium halmahera) commonly referred to as bamboo shark, is a shark species that belongs to the Hemiscyllidae family which is endemic in North Maluku, and Indonesian waters. These Hemiscyllium species are generally confined to the Australian-New Guinea region, save a specie which originates from Halmahera, an Indonesian island. Ever since its discovery, sufficient information on its existence has been largely unavailable. Hence, the purpose of this study is (1) to assess the morphology, using meristic measurements and length-weight relationship, and (2) to determine the molecular characteristics through DNA barcoding, phylogenetic reconstruction, and genetic diversity. The samples used in this research were obtained from Halmahera Archipelago, North Maluku, including Halmahera, Tidore, Ternate, Maitara, and Guraici in several expeditions between March 2017 and January 2018. 36 individuals in total were measured for morphometric parameters including Total Length (TL), Standard Length (SL), Head Length (HL), Body Circumference (BC), and Body Weight (BW). Out of a total of 36 sharks, tissue samples were obtained from 32 individuals for molecular identification. After the required measurements were obtained, all individuals sharks were released back to their habitat safely. Equations of linear regression were used to analyze the relationship between length and weight. Morphometric measurements indicated that the average total length of the walking shark samples obtained, were not more than 75± cm for both male and female specimens. The length-weight analysis revealed a positive allometric growth pattern in H. halmahera species, where weight was gained faster than an increase in length. The results of the DNA fragment length analysis from all samples were 793-bp. All 32 tissue samples identified as H. halmahera consisted of 3 samples from Ternate Island, 14 samples from Maitara Island, 9 samples from Guraici Island (South Halmahera), 10 samples from Central Halmahera, and 2 samples from Tidore Island. These results confirmed that DNA subsequence analysis indicates that H. halmahera is different from those sequences extracted from Genbank in the Australia-New Guinea region. This study successfully identified H. halmahera based on their morphological and molecular characters, and has therefore contributed to international genetic database (Barcoding Of Life Database-BOLD) for further studies.

Authors. 2018. Morphometric characteristics of two seagrass species (Enhalus acoroides and Cymodocea rotundata) in four small islands in North Maluku, Indonesia. Biodiversitas 19: 2035-2043. Seagrass has an important ecological role as a protector of coastlines and small islands. It is known to be capable of forming phenotypic plasticity through morphometric variation as a response to its environmental conditions. This study aimed to determine the distribution and morphological differences between populations of two important seagrass species (Enhalus acoroides and Cymodocea rotundata) in the waters around four small islands in North Maluku. The study was conducted at two stations in each of Ternate Island and Maitara Islands, three stations at Tidore Island and one station at Hiri Island. A line transect method was used to collect seagrass samples. Morphometric characteristics included leaf sheath length, leaf length, leaf width, rhizome diameter, root length, root diameter, and internode length were measured. Discriminant analysis was performed to describe morphometric characteristics distinctive of the four islands. Leaf sheath length, leaf length, rhizome diameter, and root length of E. Acoroides differed significantly among the populations from the various islands except for leaf width. Meanwhile, leaf sheath length, leaf width, rhizome diameter, root length, and internode length differed significantly in C. rotundata among the populations from different islands except for leaf length.

Utami RT, Zamani NP, Madduppa HH. 2018. Molecular identification, abundance and distribution of the coral-killing sponge Terpios hoshinota in Bengkulu and Seribu Islands, Indonesia. Biodiversitas 19: 2238-2246. Coral killing sponge Terpios hoshinota is one of threats to coral reefs. The outbreaks of T. hoshinota has been reported in the Indo-Pacific region. However, the current distribution of this species in Western of Sumatera Island is unknown, compared to Seribu Islands. This study aimed to identify coral-killing sponge molecularly and to compare the distribution and abundance of T. hoshinota in Bengkulu (Western of Sumatera) and in Seribu Islands (Northern of Java Island) and to record the preferences of coral substrate of T. hoshinota. Coral reefs and T. hoshinota data were collected using underwater photo transect method with 0.5x0.5m2 quadrate transect. Coral reefs covered by T. hoshinota was analyzed by using Correspondence Analysis, while the determination of biophysical and chemical environment was analyzed by Principal Component Analysis. The identity of the sponge was T. hoshinota. T. hoshinota has been expanding in many reefs across Indonesia especially in Tikus Island and Belanda Island. The most prevalent coral genera in the Seribu Islands infected by T. hoshinota was Acropora while those in Bengkulu were Porites and Pocillopora. Pearson correlation between the live coral cover and T. hoshinota cover was revealed not significant, while T. hoshinota cover and orthophosphate was significant. This study suggests that orthophosphate may play a role invasion of T. hoshinota outbreaks.

Ramadhaniaty M, Setyobudiandi I, Madduppa HH. 2018. Morphogenetic and population structure of two species marine bivalve (Ostreidae: Saccostrea cucullata and Crassostrea iredalei) in Aceh, Indonesia. Biodiversitas 19: 978-988. Oysters (Family Ostreidae) are mollusks, with high levels of phenotypic plasticity and wide geographic distribution. Oysters are a challenging group for morphological identification and genetic populations study. Saccostrea cucullata and Crassostrea iredalei are oysters from bivalve class that lives in the intertidal area and mangrove ecosystem. To clarify the morphology, genetic diversity and population structure of the two forms of S. cucullata and C. iredalei, we collected and studied oysters from three locations along the coastal region of Aceh by using morphometric method and 16 S mtDNA sequences analysis. We also added more oysters sequences from China, Japan, and Thailand to determine the connectivity between all populations. Morphometric characteristics of the oyster showed a negative allometric growth pattern, which means the rate of length gain is faster than that of the weight gain. The genetic distance from S. cucullata was 0.003-0.004 (Fst = 0.708) and C. iredalei was 0.000 (Fst = 0.971). The long genetic distance and high fixation index (Fst) in the oysters population are caused by the close geographical distance of the species in the three populations. The haplotype diversity value from S. cucullata and C. iredalei were 20 and 3, respectively. The haplotype showed the connectivity among the oyster populations which indicated by the gene flow pattern. The gene flow was affected by geographical distance and environmental complexity.

Pertiwi NPD, Nugraha B, Kartika R, Sulistyaningsih RK, Jatmiko I, Sembiring A, Mahardini A, Cahyani NKD, Anggoro AW, Madduppa HH, Ambariyanto A, Barber PH, Mahardika GN. 2017. Short Communication: Lack of differentiation within the bigeye tuna population of Indonesia. Biodiversitas 18: 1406-1413. All highly migratory tuna and tuna-like species have vast feeding grounds and spawning grounds. Indonesia’s tuna catch is the largest in the world. However, genetic diversity in the population structure within particular tuna species in Indonesia is very limited. Here we provide genetic data for bigeye tuna (Thunnus obesus) covering fishing grounds and local fish markets throughout Indonesia. A fragment of mitochondrial DNA in the D-loop control region was amplified from samples collected across Indonesia in the biennium 2012-2013. The results showed high haplotype diversity and low nucleotide diversity in our samples. Little differentiation occured between the eleven diverse sampling locations, nor was any separation detected between general regions of Indonesia, nor between samples from fishing grounds and samples from fish markets.

Madduppa H, Margaretha MK, Bramandito A, Prartono T, Subhan B, Arafat D, Anggraini NP. 2019. Short Communication: Intraspecific genetic diversity and population subdivision of rabbitfish (Siganidae: Siganus canaliculatus) in urbanized reefs of Jakarta Bay, Indonesia. Biodiversitas 20: xxxx. Indonesian coral reefs and seagrass are heavily influenced by human activities through pollution and habitat loss, and sea-level rise or the increase of ocean temperature due to the global change. In the Jakarta Bay and Seribu Islands, marine communities have been impacted by an increase in eutrophication and sedimentation levels. As a result, these habitats became degraded and could affect their associated organisms such as rabbitfish. Genetic diversity and population structure can provide information about a long-term condition in an aquatic organism. The study was conducted to assess genetic diversity and population structure of rabbitfish (Siganus canaliculatus) across an environmental gradient in Jakarta Bay and Seribu Islands. A total of 31 individuals were collected using gillnet in study sites. A molecular marker mitochondrial Cytochrome oxidase 1 (CO1) was used to amplify DNA. The result of the phylogenetic tree formed two major clades, which generally separate northern and southern region of Seribu Islands populations. AMOVA analysis showed significant genetic differentiation between the population of Siganus canaliculatus in the north zone (National Park) and south zone Seribu Island (FST = 0.38, p

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.

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 Jakarta. Biodiversitas 14: 17-24. 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.

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.