beginer subhan | Bogor Agricultural University, Indonesia (original) (raw)

Papers by beginer subhan

Depik

Soft corals of the genus Clavularia (Blainville 1830) have complex and difficult to distinguish m... more Soft corals of the genus Clavularia (Blainville 1830) have complex and difficult to distinguish morphological characteristics, making them rather difficult to identify. A paucity of information exists for Indonesian coral reefs, a complex biogeographic region at the confluence of the Pacific and Indian Ocean that covers an extensive geographic area and several marine ecoregions, is subject to several ocean current systems, and includes a high diversity of habitats. Specimens of Clavularia inflata were collected from eleven study sites across the Indonesian archipelago, morphologically described based on their sclerite characteristics, and compared among sites. Sclerite observations were divided into four parts for each colony, namely pinnules, crowns, calyces, and stolons. The sclerites found in C. inflata comprised various forms such as rods, fingers, sticks, and brackets. Morphometric measurements of C. inflata showed specimens from Kepulauan Seribu had the largest pinnule, calyx,...

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PeerJ

The first occurrence of the cyanobacteriosponge Terpios hoshinota was reported from coral reefs i... more The first occurrence of the cyanobacteriosponge Terpios hoshinota was reported from coral reefs in Guam in 1973, but was only formally described in 1993. Since then, the invasive behavior of this encrusting, coral-killing sponge has been observed in many coral reefs in the West Pacific. From 2015, its occurrence has expanded westward to the Indian Ocean. Although many studies have investigated the morphology, ecology, and symbiotic cyanobacteria of this sponge, little is known of its population genetics and demography. In this study, a mitochondrial cytochrome oxidase I (COI) fragment and nuclear ribosomal internal transcribed spacer 2 (ITS2) were sequenced to reveal the genetic variation of T. hoshinota collected from 11 marine ecoregions throughout the Indo-West Pacific. Both of the statistical parsimony networks based on the COI and nuclear ITS2 were dominated by a common haplotype. Pairwise FST and Isolation-by-distance by Mantel test of ITS2 showed moderate gene flow existed am...

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IOP Conference Series: Earth and Environmental Science

This research is located at Sop Island, Sorong, West Papua. The data was collected using the Belt... more This research is located at Sop Island, Sorong, West Papua. The data was collected using the Belt Transect method, stretching a line for 50 meters with a width of vision for 2.5 meters to the left and 2.5 meters to the right. The depth of the transect is 5 meters, recorded all genera from Family Fungiidae. Five genera were found on The Sop Island, namely Ctenactis, Fungia, Herpolitha, Polyphyllia, and Sandalolitha, but only Ctenactis, Fungia, and Sandalolitha were found on the three sites of observation. Fungia is the most abundant genera found at Sop Island. So, however, the study also found many unhealthy symptoms that infected Fungia. Of the three observation sites, six categories of unhealthy coral are found: Tissue Loss - non-predation - Coloured Band Disease, Tissue Discoloration - White, Tissue Discoloration non-white, Compromised Health Growth Anomalies, and Unknown. The most common categories infected with the Fungiidae at Sop Island are Tissue Loss - non-predation - Colour...

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Trends in Sciences

Characteristics of Waters During Transitional Season, Senimba Bay, Batam Indonesia. Senimba Bay i... more Characteristics of Waters During Transitional Season, Senimba Bay, Batam Indonesia. Senimba Bay is a water area in Batam City. It is necessary to develop the waters of Senimba Bay due to its location around the bay, which is still not arranged. Development such as changes in sea transportation lines and structuring the bay area requires Hidro-oceanography data, such as current data, waves, tides, and bathymetry. The research discusses the Gulf of Senimba waters' characteristics in the transition season, namely in April-May. The primary data taken is current data, bathymetry, waves, tides, and secondary data is wind data from ECMWF. Retrieval of current and wave data using ADCP (Acoustic Doppler Current Profiler) with several layers of depth. The method used for tides is Least-Square. Flow in the transition season in the Gulf of Senimba waters has a southwest direction during the high tide and northeast when low tides with mixed tides are double inclines, and the direction of the...

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IOP Conference Series: Earth and Environmental Science, 2021

Nudibranch has high species diversity with complex morphological characters and is challenging to... more Nudibranch has high species diversity with complex morphological characters and is challenging to identify at the species level. The lack of knowledge about nudibranchs makes it difficult to identify conventionally using morphological characters. This study aims to identify nudibranchs at the species level using the DNA barcoding method from the mitochondrial cytochrome oxidase 1 (CO1) gen. The results of DNA barcoding using the Cytochrome Oxidase I (COI) gene showed 18 species of 51 samples analyzed. The phylogenetic tree reconstruction revealed 11 main clades belonging to 11 genera. The genetic distance between and within species clearly shows the difference between individuals. Interspecific genetic distance shows the lowest value between species was found between Chromodoris annae and Chromodoris magnifica is 0.075, and the largest genetic distance observed between species Glossodoris rufomarginata and Tritonidae sp is 0.354. This study shows molecular analysis can be used to id...

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Indonesia, as a country having a unique sea lane known as the Indonesian Archipelagic Sea Lanes (... more Indonesia, as a country having a unique sea lane known as the Indonesian Archipelagic Sea Lanes (ASLs), has become one of the busiest countries in the world with varied shipping activities. These actions have the ability to facilitate the transmission of species (bio-invasion). Until recently, the number of global introduced species has increased, with negative consequences for environment and the economy. Environmental DNA (eDNA) approaches for detecting the presence of invasive species are currently receiving a lot of interest as a broad approach method in ecological research. As a result, the study used the eDNA technique to compare the quantity and variety of introduced species from the Cnidaria and Porifera Phyla, as well as to characterize their invasiveness status and possible presence in the waters of Jakarta Bay. Based on data from the inside Zone of National Park (ZI) and Outside Zone of National Park (ZO), the biological community composition, richness, and diversity were...

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Ecological Applications, 2021

Marine food webs are structured through a combination of top-down and bottom-up processes. In cor... more Marine food webs are structured through a combination of top-down and bottom-up processes. In coral reef ecosystems, fish size is related to life-history characteristics and size-based indicators can represent the distribution and flow of energy through the food web. Thus, size spectra can be a useful tool for investigating the impacts of both fishing and habitat condition on the health and productivity of coral reef fisheries. In addition, coral reef fisheries are often data-limited and size spectra analysis can be a relatively cost-effective and simple method for assessing fish populations. Abundance size spectra are widely used and quantify the relationship between organism size and relative abundance. Previous studies that have investigated the impacts of fishing and habitat condition together on the size distribution of coral reef fishes, however, have aggregated all fishes regardless of taxonomic identity. This leads to a poor understanding of how fishes with different feeding strategies, body size-abundance relationships, or catchability might be influenced by top-down and bottom-up drivers. To address this gap, we quantified size spectra slopes of carnivorous and herbivorous coral reef fishes across three regions of Indonesia representing a gradient in fishing pressure and habitat conditions. We show that fishing pressure was the dominant driver of size spectra slopes such that they became steeper as fishing pressure increased, which was due to the removal of large-bodied fishes. When considering fish functional groups separately, however, carnivore size spectra slopes were more heavily impacted by fishing than herbivores. Also, structural complexity, which can mediate predator-prey interactions and provisioning of resources, was a relatively important driver of herbivore size spectra slopes such that slopes were shallower in more complex habitats. Our results show that size spectra slopes can be used as indicators of fishing pressure on coral reef fishes, but aggregating fish regardless of trophic identity or functional role overlooks differential impacts of fishing pressure and habitat condition on carnivore and herbivore size distributions.

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. Yellowfin tuna (Thunnus albacares) is a large pelagic fish that have high economic value and in... more . Yellowfin tuna (Thunnus albacares) is a large pelagic fish that have high economic value and inhabits the Moluccas Sea , I ndonesia. Tuna catches in the Moluccas sea was very high and might decrease the yellowfin tuna population in this region . The research on population genetic of yellowfin tuna is fundamental to answer the problem. This information can be used as baseline data for future management, utilization, and basis of genetic conservation. The objective of this research was to infer the genetic population structure of two populations (North Maluku and Ambon) in the Moluccas Sea, Indonesia. In total, 41 tissue samples from pectoral fins of yellowfin tuna were collected in this study (North Maluku 33 samples and Ambon 8 samples) . T he results showed that genetic distances were low between the two populations. Additionally, the c omparison of genetic distance between the Moluccas population and Indian Ocean waters also showed no significant differences. The Fst analysis sh...

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PLOS ONE, 2020

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Biodiversity and Conservation, 2021

Environmental DNA (eDNA) metabarcoding is an evolving tool that can provide broader assessments o... more 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 < 0.05) based on Bray–Curtis and Jaccard indices. Taxa of interest were not distributed equally and there were no discernible patterns detected across the sampling area. This might be due to the highly variable percentage of sequenced species between families, preventing robust estimation of species richness. Overall, 45% of reads were identified to species level while 55% were classified as unidentified taxa. Interestingly, the percentage of unidentified taxa was similar between two locations with distinct characteristics representing eastern and western extremities of the sampling region. Despite a relatively poor rate of assignment to species level, our results highlight unprecedented levels of marine biodiversity and strong differences in species composition. This further supports the contention that the eDNA approach is a sensitive method that can provide useful data, in particular to detect changes in species composition. Importantly, this method is clearly advantageous to evaluate marine biodiversity on a large scale and can provide data to support region-wide coral reef management strategies. Knowing species diversity and the degree to which various taxa are distributed is a fundamental for advancing our knowledge of marine ecology and can play an important role in forecasting population dynamics and evolution as well as in refining conservation practices.

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Environmental Biology of Fishes, 2018

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Jurnal Ilmu dan Teknologi Kelautan Tropis, 2010

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Biodiversitas Journal of Biological Diversity, 2017

Madduppa H, Taurusman AA, Subhan B, Anggraini NP, Fadillah R, Tarman K. 2017. DNA barcoding revea... more 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 ...

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Jurnal Teknologi Perikanan dan Kelautan, 2017

Penelitian ini dilakukan pada 5 stasiun (yaitu Barat Daya Pramuka, Area Perlindungan Laut, Timur ... more Penelitian ini dilakukan pada 5 stasiun (yaitu Barat Daya Pramuka, Area Perlindungan Laut, Timur Laut Pramuka, Timur Pramuka, dan Dermaga 1) di Pulau Pramuka, Kepulauan Seribu, Jakarta. Pengambilan data menggunakan metode Belt Transect, yaitu membentangkan roll meter sepanjang 60 meter dengan lebar jarak pandang 2 meter pada kedalaman 5 meter. Karang yang didata adalah karang dari Suku Fungiidae. Marga dari karang Fungiidae yang ditemukan di Pulau Pramuka ada lima, yaitu Heliofungia, Herpolitha, Fungia, Ctenactis, dan Sandalolitha. Dari total 106 individu karang Fungiidae yang ditemukan di 5 stasiun pengamatan di Pulau Pramuka, sebanyak 38,68% (41 individu) dalam kondisi sehat dan 61,32% (65 individu) terserang penyakit karang. Fungia merupakan marga karang dari Fungiidae yang paling banyak terkena penyakit karang. 19 dari 61 individu karang Fungia (31,15%) masih dalam kondisi sehat dan 42 individu (68,85%) terkena penyakit karang. Pada 24 individu karang Ctenactis yang ditemukan di...

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Jurnal Teknologi Perikanan dan Kelautan, 2017

Ekosistem lamun merupakan salah satu penyusun pantai tropis yang memiliki peranan penting dalam s... more Ekosistem lamun merupakan salah satu penyusun pantai tropis yang memiliki peranan penting dalam struktur ekologi wilayah pesisir, selain itu lamun juga diketahui memiliki potensi dimanfaatkan sebagai bahan baku farmasi, sehingga keberadaan lamun di suatu wilayah sangat penting untuk diketahui dan dianalisis. Penelitian ini dilakukan dengan metode transek garis pada tiga stasiun, dan bertujuan untuk memberikan informasi keragaman, kerapatan, dan penutupan jenis lamun di Teluk Banten. Padang lamun di Teluk Banten terdiri dari lima jenis, yaitu: <em>Cymodocea rotundata, Cymodocea serrulata, Enhalus acoroides, Halophila ovalis</em>, dan <em>Thalassia hemprichii</em>. Kerapatan lamun tertinggi ditemukan di Pulau Tunda (193 individu/m²), dan terendah di Pulau Panjang (44 individu/m²). Penutupan lamun terendah ditemukan pada Pulau Panjang (62.5%), sedangkan tertinggi pada Pulau Kalih (90%), dan didominasi oleh jenis ...

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RISALAH KEBIJAKAN PERTANIAN DAN LINGKUNGAN: Rumusan Kajian Strategis Bidang Pertanian dan Lingkungan, 2017

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Aceh Journal of Animal Science, 2016

The genetic connectivity of soft coral is influenced by current and distance between islands. The... more The genetic connectivity of soft coral is influenced by current and distance between islands. The complexity of islands and geographical region in Indonesia might influence the distribution of soft corals. The information of genetic connectivity can be used to design marine protected areas and to avoid destruction and possible extinction. The objective of the present study was to analyze genetic connectivity of one species of soft coral, Sarcophyton trocheliophorum, in three populations spanning Java, Nusa Tenggara, and Sulawesi’s waters, and to describe its implication for marine protected area. The mitochondrial protein-coding gene (750 bp of ND2) was used to analyze genetic population structure and genetic connectivity. Genetic connectivity was found in all populations with Fst value of 0.227 to 0.558, indicating populations had the close genetic relationship. The local and Indonesian currents were expected to distribute the larva to islands as a stepping stone, they moved slowl...

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Aacl Bioflux, Mar 1, 2015

The study was conducted to identify sex and size range composition of whale shark individuals fro... more The study was conducted to identify sex and size range composition of whale shark individuals from sightings and their appearance behavior in Cenderawasih Bay National Park, Indonesia. A total of 74 fishermen lift-nets ‘bagans’ in Sowa, Kwatisore, and Yaur areas from March to June 2013 were visited to document date, time, location, sex, size range, and number of whale sharks seen each day. Photographic identification was used as a non-invasive means to describe the population throughout the study period. Shark sizes were estimated using a diver body as reference length. A total of 134 whale sharks sightings was recorded within study areas. The highest frequency appearance of whale shark was within Sowa region with 76 sightings, followed by 51 sightings in Kwatisore region, and 7 sightings in Yaur region. From 37 whale sharks identified individual observed in Cenderawasih Bay, there were 36 individuals were identified as male and one as female with a size range of 3-7 meter, dominated by individual with size under 4 meter. From all the observed whale sharks, 44.44% were found not having any scars on their body, but some were having scars on their fins and mouth. Whale sharks in Cenderawasih Bay National Park can be seen moving around in water surface near the lift-net as their feeding behaviour. The fishermen activities might also have an impact on this behaviour, as the fishermen catching activities might

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Depik

Soft corals of the genus Clavularia (Blainville 1830) have complex and difficult to distinguish m... more Soft corals of the genus Clavularia (Blainville 1830) have complex and difficult to distinguish morphological characteristics, making them rather difficult to identify. A paucity of information exists for Indonesian coral reefs, a complex biogeographic region at the confluence of the Pacific and Indian Ocean that covers an extensive geographic area and several marine ecoregions, is subject to several ocean current systems, and includes a high diversity of habitats. Specimens of Clavularia inflata were collected from eleven study sites across the Indonesian archipelago, morphologically described based on their sclerite characteristics, and compared among sites. Sclerite observations were divided into four parts for each colony, namely pinnules, crowns, calyces, and stolons. The sclerites found in C. inflata comprised various forms such as rods, fingers, sticks, and brackets. Morphometric measurements of C. inflata showed specimens from Kepulauan Seribu had the largest pinnule, calyx,...

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PeerJ

The first occurrence of the cyanobacteriosponge Terpios hoshinota was reported from coral reefs i... more The first occurrence of the cyanobacteriosponge Terpios hoshinota was reported from coral reefs in Guam in 1973, but was only formally described in 1993. Since then, the invasive behavior of this encrusting, coral-killing sponge has been observed in many coral reefs in the West Pacific. From 2015, its occurrence has expanded westward to the Indian Ocean. Although many studies have investigated the morphology, ecology, and symbiotic cyanobacteria of this sponge, little is known of its population genetics and demography. In this study, a mitochondrial cytochrome oxidase I (COI) fragment and nuclear ribosomal internal transcribed spacer 2 (ITS2) were sequenced to reveal the genetic variation of T. hoshinota collected from 11 marine ecoregions throughout the Indo-West Pacific. Both of the statistical parsimony networks based on the COI and nuclear ITS2 were dominated by a common haplotype. Pairwise FST and Isolation-by-distance by Mantel test of ITS2 showed moderate gene flow existed am...

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IOP Conference Series: Earth and Environmental Science

This research is located at Sop Island, Sorong, West Papua. The data was collected using the Belt... more This research is located at Sop Island, Sorong, West Papua. The data was collected using the Belt Transect method, stretching a line for 50 meters with a width of vision for 2.5 meters to the left and 2.5 meters to the right. The depth of the transect is 5 meters, recorded all genera from Family Fungiidae. Five genera were found on The Sop Island, namely Ctenactis, Fungia, Herpolitha, Polyphyllia, and Sandalolitha, but only Ctenactis, Fungia, and Sandalolitha were found on the three sites of observation. Fungia is the most abundant genera found at Sop Island. So, however, the study also found many unhealthy symptoms that infected Fungia. Of the three observation sites, six categories of unhealthy coral are found: Tissue Loss - non-predation - Coloured Band Disease, Tissue Discoloration - White, Tissue Discoloration non-white, Compromised Health Growth Anomalies, and Unknown. The most common categories infected with the Fungiidae at Sop Island are Tissue Loss - non-predation - Colour...

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Trends in Sciences

Characteristics of Waters During Transitional Season, Senimba Bay, Batam Indonesia. Senimba Bay i... more Characteristics of Waters During Transitional Season, Senimba Bay, Batam Indonesia. Senimba Bay is a water area in Batam City. It is necessary to develop the waters of Senimba Bay due to its location around the bay, which is still not arranged. Development such as changes in sea transportation lines and structuring the bay area requires Hidro-oceanography data, such as current data, waves, tides, and bathymetry. The research discusses the Gulf of Senimba waters' characteristics in the transition season, namely in April-May. The primary data taken is current data, bathymetry, waves, tides, and secondary data is wind data from ECMWF. Retrieval of current and wave data using ADCP (Acoustic Doppler Current Profiler) with several layers of depth. The method used for tides is Least-Square. Flow in the transition season in the Gulf of Senimba waters has a southwest direction during the high tide and northeast when low tides with mixed tides are double inclines, and the direction of the...

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IOP Conference Series: Earth and Environmental Science, 2021

Nudibranch has high species diversity with complex morphological characters and is challenging to... more Nudibranch has high species diversity with complex morphological characters and is challenging to identify at the species level. The lack of knowledge about nudibranchs makes it difficult to identify conventionally using morphological characters. This study aims to identify nudibranchs at the species level using the DNA barcoding method from the mitochondrial cytochrome oxidase 1 (CO1) gen. The results of DNA barcoding using the Cytochrome Oxidase I (COI) gene showed 18 species of 51 samples analyzed. The phylogenetic tree reconstruction revealed 11 main clades belonging to 11 genera. The genetic distance between and within species clearly shows the difference between individuals. Interspecific genetic distance shows the lowest value between species was found between Chromodoris annae and Chromodoris magnifica is 0.075, and the largest genetic distance observed between species Glossodoris rufomarginata and Tritonidae sp is 0.354. This study shows molecular analysis can be used to id...

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Indonesia, as a country having a unique sea lane known as the Indonesian Archipelagic Sea Lanes (... more Indonesia, as a country having a unique sea lane known as the Indonesian Archipelagic Sea Lanes (ASLs), has become one of the busiest countries in the world with varied shipping activities. These actions have the ability to facilitate the transmission of species (bio-invasion). Until recently, the number of global introduced species has increased, with negative consequences for environment and the economy. Environmental DNA (eDNA) approaches for detecting the presence of invasive species are currently receiving a lot of interest as a broad approach method in ecological research. As a result, the study used the eDNA technique to compare the quantity and variety of introduced species from the Cnidaria and Porifera Phyla, as well as to characterize their invasiveness status and possible presence in the waters of Jakarta Bay. Based on data from the inside Zone of National Park (ZI) and Outside Zone of National Park (ZO), the biological community composition, richness, and diversity were...

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Ecological Applications, 2021

Marine food webs are structured through a combination of top-down and bottom-up processes. In cor... more Marine food webs are structured through a combination of top-down and bottom-up processes. In coral reef ecosystems, fish size is related to life-history characteristics and size-based indicators can represent the distribution and flow of energy through the food web. Thus, size spectra can be a useful tool for investigating the impacts of both fishing and habitat condition on the health and productivity of coral reef fisheries. In addition, coral reef fisheries are often data-limited and size spectra analysis can be a relatively cost-effective and simple method for assessing fish populations. Abundance size spectra are widely used and quantify the relationship between organism size and relative abundance. Previous studies that have investigated the impacts of fishing and habitat condition together on the size distribution of coral reef fishes, however, have aggregated all fishes regardless of taxonomic identity. This leads to a poor understanding of how fishes with different feeding strategies, body size-abundance relationships, or catchability might be influenced by top-down and bottom-up drivers. To address this gap, we quantified size spectra slopes of carnivorous and herbivorous coral reef fishes across three regions of Indonesia representing a gradient in fishing pressure and habitat conditions. We show that fishing pressure was the dominant driver of size spectra slopes such that they became steeper as fishing pressure increased, which was due to the removal of large-bodied fishes. When considering fish functional groups separately, however, carnivore size spectra slopes were more heavily impacted by fishing than herbivores. Also, structural complexity, which can mediate predator-prey interactions and provisioning of resources, was a relatively important driver of herbivore size spectra slopes such that slopes were shallower in more complex habitats. Our results show that size spectra slopes can be used as indicators of fishing pressure on coral reef fishes, but aggregating fish regardless of trophic identity or functional role overlooks differential impacts of fishing pressure and habitat condition on carnivore and herbivore size distributions.

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. Yellowfin tuna (Thunnus albacares) is a large pelagic fish that have high economic value and in... more . Yellowfin tuna (Thunnus albacares) is a large pelagic fish that have high economic value and inhabits the Moluccas Sea , I ndonesia. Tuna catches in the Moluccas sea was very high and might decrease the yellowfin tuna population in this region . The research on population genetic of yellowfin tuna is fundamental to answer the problem. This information can be used as baseline data for future management, utilization, and basis of genetic conservation. The objective of this research was to infer the genetic population structure of two populations (North Maluku and Ambon) in the Moluccas Sea, Indonesia. In total, 41 tissue samples from pectoral fins of yellowfin tuna were collected in this study (North Maluku 33 samples and Ambon 8 samples) . T he results showed that genetic distances were low between the two populations. Additionally, the c omparison of genetic distance between the Moluccas population and Indian Ocean waters also showed no significant differences. The Fst analysis sh...

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PLOS ONE, 2020

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Biodiversity and Conservation, 2021

Environmental DNA (eDNA) metabarcoding is an evolving tool that can provide broader assessments o... more 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 < 0.05) based on Bray–Curtis and Jaccard indices. Taxa of interest were not distributed equally and there were no discernible patterns detected across the sampling area. This might be due to the highly variable percentage of sequenced species between families, preventing robust estimation of species richness. Overall, 45% of reads were identified to species level while 55% were classified as unidentified taxa. Interestingly, the percentage of unidentified taxa was similar between two locations with distinct characteristics representing eastern and western extremities of the sampling region. Despite a relatively poor rate of assignment to species level, our results highlight unprecedented levels of marine biodiversity and strong differences in species composition. This further supports the contention that the eDNA approach is a sensitive method that can provide useful data, in particular to detect changes in species composition. Importantly, this method is clearly advantageous to evaluate marine biodiversity on a large scale and can provide data to support region-wide coral reef management strategies. Knowing species diversity and the degree to which various taxa are distributed is a fundamental for advancing our knowledge of marine ecology and can play an important role in forecasting population dynamics and evolution as well as in refining conservation practices.

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Environmental Biology of Fishes, 2018

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Jurnal Ilmu dan Teknologi Kelautan Tropis, 2010

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Biodiversitas Journal of Biological Diversity, 2017

Madduppa H, Taurusman AA, Subhan B, Anggraini NP, Fadillah R, Tarman K. 2017. DNA barcoding revea... more 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 ...

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Jurnal Teknologi Perikanan dan Kelautan, 2017

Penelitian ini dilakukan pada 5 stasiun (yaitu Barat Daya Pramuka, Area Perlindungan Laut, Timur ... more Penelitian ini dilakukan pada 5 stasiun (yaitu Barat Daya Pramuka, Area Perlindungan Laut, Timur Laut Pramuka, Timur Pramuka, dan Dermaga 1) di Pulau Pramuka, Kepulauan Seribu, Jakarta. Pengambilan data menggunakan metode Belt Transect, yaitu membentangkan roll meter sepanjang 60 meter dengan lebar jarak pandang 2 meter pada kedalaman 5 meter. Karang yang didata adalah karang dari Suku Fungiidae. Marga dari karang Fungiidae yang ditemukan di Pulau Pramuka ada lima, yaitu Heliofungia, Herpolitha, Fungia, Ctenactis, dan Sandalolitha. Dari total 106 individu karang Fungiidae yang ditemukan di 5 stasiun pengamatan di Pulau Pramuka, sebanyak 38,68% (41 individu) dalam kondisi sehat dan 61,32% (65 individu) terserang penyakit karang. Fungia merupakan marga karang dari Fungiidae yang paling banyak terkena penyakit karang. 19 dari 61 individu karang Fungia (31,15%) masih dalam kondisi sehat dan 42 individu (68,85%) terkena penyakit karang. Pada 24 individu karang Ctenactis yang ditemukan di...

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Jurnal Teknologi Perikanan dan Kelautan, 2017

Ekosistem lamun merupakan salah satu penyusun pantai tropis yang memiliki peranan penting dalam s... more Ekosistem lamun merupakan salah satu penyusun pantai tropis yang memiliki peranan penting dalam struktur ekologi wilayah pesisir, selain itu lamun juga diketahui memiliki potensi dimanfaatkan sebagai bahan baku farmasi, sehingga keberadaan lamun di suatu wilayah sangat penting untuk diketahui dan dianalisis. Penelitian ini dilakukan dengan metode transek garis pada tiga stasiun, dan bertujuan untuk memberikan informasi keragaman, kerapatan, dan penutupan jenis lamun di Teluk Banten. Padang lamun di Teluk Banten terdiri dari lima jenis, yaitu: <em>Cymodocea rotundata, Cymodocea serrulata, Enhalus acoroides, Halophila ovalis</em>, dan <em>Thalassia hemprichii</em>. Kerapatan lamun tertinggi ditemukan di Pulau Tunda (193 individu/m²), dan terendah di Pulau Panjang (44 individu/m²). Penutupan lamun terendah ditemukan pada Pulau Panjang (62.5%), sedangkan tertinggi pada Pulau Kalih (90%), dan didominasi oleh jenis ...

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RISALAH KEBIJAKAN PERTANIAN DAN LINGKUNGAN: Rumusan Kajian Strategis Bidang Pertanian dan Lingkungan, 2017

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Aceh Journal of Animal Science, 2016

The genetic connectivity of soft coral is influenced by current and distance between islands. The... more The genetic connectivity of soft coral is influenced by current and distance between islands. The complexity of islands and geographical region in Indonesia might influence the distribution of soft corals. The information of genetic connectivity can be used to design marine protected areas and to avoid destruction and possible extinction. The objective of the present study was to analyze genetic connectivity of one species of soft coral, Sarcophyton trocheliophorum, in three populations spanning Java, Nusa Tenggara, and Sulawesi’s waters, and to describe its implication for marine protected area. The mitochondrial protein-coding gene (750 bp of ND2) was used to analyze genetic population structure and genetic connectivity. Genetic connectivity was found in all populations with Fst value of 0.227 to 0.558, indicating populations had the close genetic relationship. The local and Indonesian currents were expected to distribute the larva to islands as a stepping stone, they moved slowl...

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Aacl Bioflux, Mar 1, 2015

The study was conducted to identify sex and size range composition of whale shark individuals fro... more The study was conducted to identify sex and size range composition of whale shark individuals from sightings and their appearance behavior in Cenderawasih Bay National Park, Indonesia. A total of 74 fishermen lift-nets ‘bagans’ in Sowa, Kwatisore, and Yaur areas from March to June 2013 were visited to document date, time, location, sex, size range, and number of whale sharks seen each day. Photographic identification was used as a non-invasive means to describe the population throughout the study period. Shark sizes were estimated using a diver body as reference length. A total of 134 whale sharks sightings was recorded within study areas. The highest frequency appearance of whale shark was within Sowa region with 76 sightings, followed by 51 sightings in Kwatisore region, and 7 sightings in Yaur region. From 37 whale sharks identified individual observed in Cenderawasih Bay, there were 36 individuals were identified as male and one as female with a size range of 3-7 meter, dominated by individual with size under 4 meter. From all the observed whale sharks, 44.44% were found not having any scars on their body, but some were having scars on their fins and mouth. Whale sharks in Cenderawasih Bay National Park can be seen moving around in water surface near the lift-net as their feeding behaviour. The fishermen activities might also have an impact on this behaviour, as the fishermen catching activities might

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