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Insafitri, Nursalim N, Kholilah N, Kurniasih EM, Cahyani NKD, Nugraha WA, Ambariyanto A. 2023. DNA barcode of seven species coral from Sepulu, Madura Island, Indonesia. Biodiversitas 24: 317-323. Diversity of coral species is needed because it affects the disruption of coral reef ecosystems, nutrient recycling, coral reef growth and the habitat of biota that live in these ecosystems. The main constituents of coral reef ecosystems are coral animals that belong to the Anthozoa class. Sepulu waters (Madura Island), Bangkalan District, East Java Province, Indonesia, has a percentage of coral cover that is in the bad category, management of coral reefs in this area has not been the main focus and it is feared that the situation will get worse so efforts are needed to maintain coral reefs to be sustainable and better. This management effort requires an analysis of species identification. DNA barcoding of corals has never been done on corals of Sepulu waters. The purpose of this study is to find out the DNA of barcoding coral species on Sepulu waters. Genetic marker Cytochrome Oxidase I of the mitochondrial genome DNA (mtDNA) was used to analyze genetic diversity. Reconstruction of phylogenetic tree and genetic diversity were done by using software MEGA X. Research results showed that sample DBP011101 closely related to Dipsatraea maxima 99.55%, DBP011102 closely related to Porites rus 99.4%, DBP011103 closely related to Acropora hyacinthus 99.11%, DBP011104 closely related to Porites cf lichen 98.66%, DBP011106 closely related to Dipsastraea rotumana 95.37%, DBP011107 closely related to Porites horrisoni 98.81%, and DBP011108 closely related to Acropora valida 98.38%. The results of the study are the first coral barcode DNA on Sepulu waters that can help in determining coral species that are useful in managing the sustainability of coral resources, especially on Sepulu waters.

DNA metabarcoding is an increasingly popular technique to investigate biodiversity; however, many methodological unknowns remain, especially concerning the biases resulting from marker choice. Regions of the cytochrome c oxidase subunit I (COI) and 18S rDNA (18S) genes are commonly employed “universal” markers for eukaryotes, but the extent of taxonomic biases introduced by these markers and how such biases may impact metabarcoding performance is not well quantified. Here, focusing on macroeukaryotes, we use standardized sampling from autonomous reef monitoring structures (ARMS) deployed in the world's most biodiverse marine ecosystem, the Coral Triangle, to compare the performance of COI and 18S markers. We then compared metabarcoding data to image‐based annotations of ARMS plates. Although both markers provided similar estimates of taxonomic richness and total sequence reads, marker choice skewed estimates of eukaryotic diversity. The COI marker recovered relative abundances of the dominant sessile phyla consistent with image annotations. Both COI and the image annotations provided higher relative abundance estimates of Bryozoa and Porifera and lower estimates of Chordata as compared to 18S, but 18S recovered 25% more phyla than COI. Thus, while COI more reliably reflects the occurrence of dominant sessile phyla, 18S provides a more holistic representation of overall taxonomic diversity. Ideal marker choice is, therefore, contingent on study system and research question, especially in relation to desired taxonomic resolution, and a multimarker approach provides the greatest application across a broad range of research objectives. As metabarcoding becomes an essential tool to monitor biodiversity in our changing world, it is critical to evaluate biases associated with marker choice.

Environmental DNA (eDNA) metabarcoding is an evolving tool that can provide broader assessments of marine biodiversity than conventional visual census methods. The outputs of this approach are, therefore, crucial to provide data for conservation priorities and to support fisheries management. We conducted a study using eDNA metabarcoding to understand the distribution of marine biodiversity across Indonesia and to investigate the abundance of three major phyla that comprise a majority of marine biodiversity. In this study, a total of 13,819,634 reads corresponding to 23,252 unique sequences belonging to the phyla Chordata, Mollusca, and Echinodermata were generated from COI amplicons obtained from 92 seawater eDNA samples collected from nine locations and 17 sites. Beta diversity differed significantly across locations (PERMANOVA: p

Cryptic organisms that live within the interstices of reef habitats contribute significantly to coral reef biodiversity. One example of this cryptic biodiversity is the high abundance of decapods in dead coral heads that associated with various biota. However, this diversity poorly studied especially species identification and species richness. This study aims to estimate the decapods diversity in Raja Ampat, Papua, using Pocillopora dead coral head method as semi-quantitative sampling approach. Raja Ampat in Papua is chosen because it situated in the center of Coral Triangle marine hotspot. Data were collected from 10 dead coral heads of genus Pocillopora from 10-meter depth near the islands of Kri and Misool. This study observed a total of 205 individuals Decapoda from Kri Island and 672 Individual from Misool Islands. Species richness observation (Chao1 and ACE) of the total samples reports only 11 families of decapoda detected in this study. Rarefaction curve reach an asymptote after all after all ten dead coral were analyzed; indicating that additional sample collection would not change estimates of diversity found in this study. The Shannon-Wiener index diversity on the Kri Island showed lower diversity value (2.09) compared to Misool Island (2.18). In the future, this research can be used as a basis for understanding the diversity of coral reefs as well as for management and conservation of coral reef ecosystems.

Astarini IA, Ningsih EY, Simanungkalit D, Ardiana SA, Al Malik MD, Yusmalinda NLA, Sembiring A, Pertiwi NPD, Cahyani NKD, Collins A. 2021. Genetic variation of longtail tuna Thunnus tonggol landed in four fish markets in Indonesia based on mitochondrial DNA. Biodiversitas 22: 1644-1651. Longtail tuna (Thunnus tonggol, Family: Scombridae) is an economically valuable neritic species found in tropical and subtropical waters in the Indo-Pacific region. High catch numbers, which have been decreasing, could negatively impact this tuna’s population level. Little research has been conducted on the longtail tuna population in Indonesia. This study aims to determine the genetic diversity and potential population structure of longtail tuna landed in four fish markets in Indonesia (representing three sampling locations because two markets are relatively close to each other) based on sequences of a region of mitochondrial control region (d-loop). A total of 101 samples, out of 110, were identified and confirmed as T. tonggol species by amplifying and sequencing a fragment of d-loop (amplicons ranging from 482 - 523 bp). Neighbor-joining analysis resulted in a topology with all samples grouped into one clade with an average genetic distance of 0.020. Meanwhile, haplotype diversity (Hd) and nucleotide diversity (?) values of the longtail tuna samples were 0.9939 and 0.0192, respectively. The fixation index (Fst) value was -0.00507, with p> 0.05, which indicates that there is no significant population structure among the longtail tuna collected from four fish markets representing three sampling locations. The results of this analysis can be used as basic data in planning sustainable fisheries management efforts.

Pertiwi NPD, Suhendro MD, Yusmalinda NLA, Putra ING, Putri IGRM, Artinigsih EY, Al Malik MD, Cahyani NKD, Sembiring A. 2020. Forensic genetic case study: Species identification and traceability of sea turtle caught in illegal trade in Bali, Indonesia. Biodiversitas 21: 4276-4283. Although known as protected endangered species, sea turtle trade is still occurring, especially in Indonesia. Understanding the species and population origin of sea turtle being sold in the illegal market is crucial for its conservation, where it will reveal the traceability of sea turtle trade to its population origin in the management unit areas. Thus, genetic forensic has been used as a key investigating tool to help with this problem. In this research, we aim to identify the species and population origin of the sea turtle caught and traded in the illegal market in Bali. Of the 20 samples collected from confiscated sea turtle during illegal trade, by-catch, and a traditional restaurant serving sea turtle meat, 17 samples were successfully analyzed and identified using PCR (polymerase chain reaction) methods. The result identified 15 samples as a green sea turtle (Chelonia mydas), while two samples were olive ridley sea turtle (Lepidochelys olivacea). Mixed Stock Analysis (MSA) with Bayesian indicated that the green sea turtle caught in illegal trade in Bali is originated mostly from the rookeries populations in Berau (29.98%), Terengganu (17.84%), Sarawak (14.84%), and Ashmore Reef (11.85%). Meanwhile, 18 other locations only showed the MSA value below 2%, including the locations of Penang and Perak, Vietnam, Perhentian, Redang, Pahang, Mersing, Sabah Turtle Island Park (TIP), Sipadan, Coral Sea, western New Caledonia, Commonwealth of the Northern Mariana Island and Guam, northern New Guinea, Gulf of Carpenteria, Scott Reef, West Java, North West Self, Cobourg Peninsula, Cocos Keeling Island. Therefore, the exploitation of sea turtle in Bali will impact the decline in the genetic diversity of sea turtles population Indonesia and adjacent locations. Monitoring and protection of sea turtle species in Bali have to be a high priority because Bali is known as the hub for sea turtle illegal trade, and the exploitation of sea turtle in Bali will have an impact on the sea turtle population in other locations.

Kasus Cetacea atau Paus dan Lumba-lumba terdampar di Indonesia sejak berapa tahun terakhir ini semakin sering terungkap dan ditangani oleh banyak pihak. Data dari Whale Stranding Indonesia (WSI) mencatat 40 kasus Cetacea terdampar di berbagai tempat di Indonesia selama tahun 2016 hingga bulan Februari 2017. Salah satu kendala bagi para penyelamat di lapangan adalah sulitnya mengidentifikasi jenis secara morfologi karena pada beberapa kasus, individu yang terdampar tidak dalam kondisi utuh. WSI mencatat lebih dari 21% jenis pada kejadian Cetacea terdampar di Indonesia, tidak teridentifikasi. Penelitian ini bertujuan memperkenalkan pendekatan genetika molekuler dalam mengidentifikasi jenis pada Cetacea terdampar. Gen Control Region dari DNA mitokondria diamplifikasi dengan menggunakan metode Polymerase Chain Reaction (PCR). Data sekuen dibandingkan dengan data di genebank dan dilihat persentase kesamaannya. Penelitian ini menggunakan 36 sampel individu dan 26 diantaranya teramplifikasi dengan panjang basa berkisar antara 445-490 bp (base pair). Metode molekuler berhasil mengidentifikasi 15 spesies dan 13 genus Cetacea yang diambil dari beberapa tempat di Indonesia. Studi ini menunjukkan bahwa teknik genetika molekuler dapat dijadikan metode untuk mengidentifikasi jenis dari Cetacea, terutama mamalia terdampar yang sulit untuk diidentifikasi secara morfologi. Data molekuler yang dihasilkan dapat melengkapi database yang ada di Indonesia serta menjadi penunjang bagi penelitian tentang keragaman genetik dan hubungan antar populasi mamalia akuatik di Indonesia.

Stranding cases of cetaceans in Indonesia including whales, dolphins, and porpoises have recently increasingly become unfold and handled by many people. According to data from Whale Stranding Indonesia (WSI), there have been 40 stranding cases in different parts of Indonesia from early 2016 until February 2017. One of the major obstacles for the people who are handling strandings is to identify the species based on morphology alone when the body is in an advanced stadium of decomposition. WSI recorded that 21% of the species are unidentifiable. For that reason, this research aims to introduce a molecular genetics approach for identifying stranded cetaceans. Mitochondrial DNA of the gene control region was amplified using a Polymerase Chain Reaction (PCR) method. Sequence data were compared with data from the genebank (https://www.ncbi. nlm.nih.gov) through percentage overlap. From the 36 individuals, which have been used in this research, 26 amplified sampels had base lengths varying between 445-490 base pairs. Molecular methods successfully identified 15 species and 13 genus of Cetacea from different localities in Indonesia. This study shows that molecular genetic techniques can be used as a method to identify species of cetaceans, in particular of stranded individual, which are hard to identify morphologically. The molecular data may complete the genetic database and become a reference for research on genetic diversity among marine mammal populations in Indonesia. Keywords: stranded Cetaceans, Indonesia, species identification, molecular technique

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.

One specimen (300 mm in standard length) of Saloptia powelli, belonging to the family Serranidae, was newly collected in a local fish market in Manado, North Sulawesi, constituting a new record for the species in the Indonesian archipelago. This species was diagnosed by the following morphological traits: dorsal rays VIII—11, anal rays III—8, well-defined opercular spines, pelvic fins below pectoral fins, caudal fin emarginate, mouth moderate in size, supplemental maxillary present, fine teeth in irregular rows on vomer and palatines. Head, body, and fins yellow in color. We suggest “kerapu emas”, a translation of its existing common name “golden grouper”, for the Indonesian species names.

High proportion of dead coral in coral reefs ecosystem are inhabited by a wide variety of associated organisms such as crustacean as a place to live. However, lack of study on the functional of dead corals in high diversity such Indonesian coral reefs. This study aimed to investigate the diversity and density of inhabitant decapod species from two different dead corals with different life form and complexity (Pocillopora verrucosa and Seriatopora histrix). A total of 235 individuals consisting of 7 families, 11 genera and 35 species was observed in P. verrucosa. While in S. histrix, a total of 74 individuals consisting of 5 families, 6 genera and 11 species were recorded. Index of diversity (H’) on dead coral P. verrucosa for decapods was higher than on S. histrix. Evenness index (E) in both types of dead coral was relatively steady. The domination index (D) for S. histrix was significantly higher than on P. verrucosa. The species density on P. verucosa was significantly higher (25 ± 11.34 ind/L) than on S. histrix (8 ±1.9 ind/L). This study is explaining the complexity of life form on the dead coral seems potentially inhabited by more and diverse decapods.

The research used 51 tissue samples taken from 51 individual Green Turtles in Pulau Panjang, EastKalimantan. The isolation of mtDNA was achieved by adding Proteinase K into the samples prior to the utilization ofthe PCR (Polimerase Chain Reaction) technique. The MEGA 3.1 computer program was employed to read the DNAsequences obtained through the PCR technique.Seven different haplotypes were identified from the analyzed samples. The haplotypes are: A3 (N=7; 13.73%),A4 (N=1; 1.96%), A6 (N=2; 3.92%), C3 (N=5; 9.80%), C5 (N=6; 11.76%), C14 (N=5; 9.80%) dan D2 (N=25;49.02%). Tag findings clearly demonstrated that the Green Turtles, which feed on the seagrass beds of Pulau Panjang,originated in different nesting sites, including Sabah and Trengganu in Malaysia, Sangalaki and Derawan inIndonesia, and Phillipine. The MSA (Mixed Stock Analysis) showed that the Green Turtles population in PulauPanjang was composed of several management units (nesting sites), which were Berau (47%), Sulu Sea (34%) andMicronesia (6%).

Kepulauan Indonesiamemiliki sejumlahArea Perlindungan Laut dan Taman Nasional yang merupakan tempat tinggal bagi organisme laut dengan tingkat keanekaragaman yang tinggi. Karimunjawa sebagai salah satu Taman Nasional, dikenal mempunyai keanekaragaman terumbu karang yang tinggi dan merupakan salah satu kawasan yang digunakan sebagai area studi keanekaragaman laut. Penelitian ini bertujuan untuk mengestimasi keanekaragaman organisme pada habitat terumbu karang yang terdapat di kawasan pesisir Karimunjawa. Metode sampling semi-kuantitatif digunakan untuk mengestimasi keanekaragaman terumbu karang, dengan menggunakan anggota kelompok dekapoda sebagai perwakilan. Enam belas terumbu karang mati (dead coral head) dari anggota Pocillopora, di koleksi dengan ukuran yang sama pada kedalaman 10 meter di kawasan Pulau Menjangan Besar, Karimunjawa. Seluruh dekapoda yang dikumpulkan, diidentifikasi sampai tingkat famili dan menunjukkan terdapat 11 famili dari total 203 individu. Nilai statistik dari kekayaan spesies ( Chao1 and ACE ) menunjukkan hanya 11 famili dekapoda yang dapat ditemukan di kawasan tersebut. Hasil kurva rarefaksi menunjukkan nilai yang mencapai titik kesetimbangan setelah karang mati ke-empat belas, yang mengindikasikan bahwa penambahan koleksi sampel tidak akan mengubah estimasi keanekaragaman yang ditemukan. Index keanekaragaman Shanon- Wiener juga menunjukkan nilai keanekaragaman yang rendah dengan nilai 1.9. Hasil penelitian ini dapat digunakan sebagai dasar pemahaman bagi keseluruhan keanekaragaman terumbu karang yang terdapat pada suatu kawasan dan sebagai dasar pengetahuan untuk tujuan pengamatan ekosistem terumbu karang bagi perlindungan dan konservasi. Kata kunci: keanekaragaman, terumbu karang, dekapoda, Indonesia, Karimunjawa. The Indonesian archipelago, with its higher number of Marine Protected Areas (MPA) and National Parks, is a home to a high diversity of marine organisms. Karimunjawa is an Indonesian National Park that is well known for its diverse coral reefs and therefore is an important place to study marine biodiversity. In the present study, the biodiversity of reef organisms was estimated in the coastal marine habitat of Karimunjawa. A semi-quantitative sampling method was used to estimate reef biodiversity using decapod group as a representative. Sixteen similar sized dead coral heads of Pocillopora were sampled from 10 m depth at Menjangan Besar Island, Karimunjawa. All decapods were sorted and identified to the family level, yielding 11 families from total 203-collected individuals. Species richness statistics (Chao1 and ACE) suggest that only 11 families of decapods can be found in this area. Rarefaction curves approached an asymptote after sampling fourteen heads, indicated that sample addition will not alter the estimate diversity found in this location with Shanon- Wiener diversity index of 1.9 indicated low diversity. Our findings may provide a basic understanding of the overall biodiversity of a reef area and a basic knowledge in monitoring coral reefs ecosystems for protection and conservation. Keywords: biodiversity, coral reefs, decapod, Indonesia, Karimunjawa