Indonesian Biodiversity Research Center

Denpasar, Indonesia

Indonesian Biodiversity Research Center

Denpasar, Indonesia
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Ransome E.,Smithsonian Institution | Geller J.B.,Moss Landing Marine Laboratories | Timmers M.,University of Hawaii at Manoa | Timmers M.,National Oceanic and Atmospheric Administration | And 7 more authors.
PLoS ONE | Year: 2017

The advancement of metabarcoding techniques, declining costs of high-Throughput sequencing and development of systematic sampling devices, such as autonomous reef monitoring structures (ARMS), have provided the means to gather a vast amount of diversity data from cryptic marine communities. However, such increased capability could also lead to analytical challenges if the methods used to examine these communities across local and global scales are not standardized. Here we compare and assess the underlying biases of four ARMS field processing methods, preservation media, and current bioinformatic pipelines in evaluating diversity from cytochrome c oxidase I metabarcoding data. Illustrating the ability of ARMS-based metabarcoding to capture a wide spectrum of biodiversity, 3,372 OTUs and twenty-eight phyla, including 17 of 33 marine metazoan phyla, were detected from 3 ARMS (2.607 m2 area) collected on coral reefs in Mo'orea, French Polynesia. Significant differences were found between processing and preservation methods, demonstrating the need to standardize methods for biodiversity comparisons. We recommend the use of a standardized protocol (NOAA method) combined with DMSO preservation of tissues for sessile macroorganisms because it gave a more accurate representation of the underlying communities, is cost effective and removes chemical restrictions associated with sample transportation. We found that sequences identified at 97% similarity increased more than 7-fold (5.1% to 38.6%) using a geographically local barcode inventory, highlighting the importance of local species inventories. Phylogenetic approaches that assign higher taxonomic ranks accrued phylum identification errors (9.7%) due to sparse taxonomic coverage of the understudied cryptic coral reef community in public databases. However, a 85% sequence identity cut-off provided more accurate results (0.7% errors) and enabled phylum level identifications of 86.3% of the sequence reads. With over 1600 ARMS deployed, standardizing methods and improving databases are imperative to provide unprecedented global baseline assessments of understudied cryptic marine species in a rapidly changing world.


Burhanuddin A.I.,Hasanuddin University | Hardianty S.,Hasanuddin University | Tassakka A.C.M.,Hasanuddin University | Cahyani N.K.D.,Indonesian Biodiversity Research Center | Tucker S.J.,Indonesian Biodiversity Research Center
Journal of Ichthyology | Year: 2017

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. © 2017, Pleiades Publishing, Ltd.


Borsa P.,Institute Of Recherche Pour Le Of Veloppement Ird Ur 227 | Sembiring A.,Indonesian Biodiversity Research Center | Fauvelot C.,Institute Of Recherche Pour Le Of Veloppement Ird Ur 227 | Chen W.-J.,National Taiwan University
Comptes Rendus - Biologies | Year: 2014

Previous phylogeographic studies of the humbug damselfish, a widespread Indo-West Pacific coral reef fish, have revealed a split of two main mitochondrial lineages distributed on either side of the Indo-Pacific barrier. This has been interpreted as the result of vicariance. It has been hypothesized that reproductive barriers might currently limit gene flow between humbug damselfish populations from the Indian Ocean and the Pacific Ocean. In this study, we review the published phylogeographic information to update the distribution of the two main mitochondrial lineages of humbug damselfish. The Indian lineage was distributed from the Red Sea to the eastern extremity of the Sunda Shelf while the Pacific lineage, which diverged from the former by 0.6% net nucleotide divergence and diagnostic substitutions at three nucleotide sites at the cytochrome b locus, was distributed east and north of the Sunda Shelf. The two forms, which are also genetically distinct at nuclear loci, were also characterized by distinct pigmentation patterns. We argue that the two forms represent geminate species. Epithet aruanus Linnaeus is maintained for the Pacific Ocean humbug damselfish while epithet abudafur (Forsskål. ) is here resurrected for the Indian Ocean humbug damselfish. Future studies should focus on the population genetic structure of the transition zone between Dascyllus abudafur and D. . © 2014 Acade´mie des sciences.


Borsa P.,Institute Of Recherche Pour Le Developpement Ird Ur 227 | Sembiring A.,Indonesian Biodiversity Research Center | Fauvelot C.,Institute Of Recherche Pour Le Developpement Ird Ur 227 | Chen W.-J.,National Taiwan University
Comptes rendus biologies | Year: 2014

Previous phylogeographic studies of the humbug damselfish, a widespread Indo-West Pacific coral reef fish, have revealed a split of two main mitochondrial lineages distributed on either side of the Indo-Pacific barrier. This has been interpreted as the result of vicariance. It has been hypothesized that reproductive barriers might currently limit gene flow between humbug damselfish populations from the Indian Ocean and the Pacific Ocean. In this study, we review the published phylogeographic information to update the distribution of the two main mitochondrial lineages of humbug damselfish. The Indian lineage was distributed from the Red Sea to the eastern extremity of the Sunda Shelf while the Pacific lineage, which diverged from the former by 0.6% net nucleotide divergence and diagnostic substitutions at three nucleotide sites at the cytochrome b locus, was distributed east and north of the Sunda Shelf. The two forms, which are also genetically distinct at nuclear loci, were also characterized by distinct pigmentation patterns. We argue that the two forms represent geminate species. Epithet aruanus Linnaeus is maintained for the Pacific Ocean humbug damselfish while epithet abudafur (Forsskål) is here resurrected for the Indian Ocean humbug damselfish. Future studies should focus on the population genetic structure of the transition zone between Dascyllus abudafur and D. aruanus. Copyright © 2014 Académie des sciences. Published by Elsevier SAS. All rights reserved.


Pharmawati M.,Udayana University | Kurniasih E.M.,Indonesian Biodiversity Research Center
AIP Conference Proceedings | Year: 2016

Rice is a staple food for many Asian countries including Indonesia. High human population growth, reduction of the fertile field and water source resulted in a limitation of rice production. These conditions promote the development of rice that resistant to drought. Evaluation of characters that contribute to adaptation strategy of rice to drought is important in rice breeding. The adaptation process involves the expression of genes specific such as DREB (dehydration responsive element binding) and SOD (superoxide dismutase). This research aims to provide basic information on the sequence of DREB and SOD genes from Bali local rice cultivars for later study of rice drought resistance. Three cultivars of Bali local rice namely "Mansur A", "Merah Cendana" and "Putih Cempaka" were used in this study. Seedlings were grown hydroponically and leaves were harvested for DNA extraction at two weeks after transfer to a hydroponic system. PCR reactions were carried out using DREB and SOD specific primers. Agarose electrophoresis revealed a DREB fragment of 1020 bp. Sequence alignment showed identical DREB sequences between the three Bali rice cultivars. A neighbor-joining analysis of other DREB sequences showed that sequences from the Bali rice cultivars tested were very closely related to DREB1 of Oryza sativa Indica Group. PCR of SOD gene of the three Bali rice cultivars showed 970 bp fragments in agarose gel. Sequence relationships using Neighbor-Joining analysis showed that SOD gene sequence from the three Bali rice cultivars was closely related to Oryza sativa Japonica Group cytosolic cooper/zinc superoxide dismutase gene. © 2016 Author(s).


Sembiring A.,Indonesian Biodiversity Research Center | Kurniasih E.M.,Bogor Agricultural University | Kurniasih E.M.,Indonesian Biodiversity Research Center | Arafat D.,Bogor Agricultural University | And 2 more authors.
Biodiversitas | Year: 2015

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, Galeocardo 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. © 2015, Society for Indonesian Biodiversity. All rights reserved.

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