1
|
Nugraha A, Zen F, Madduppa H, Lihtorng Chen R. Revisiting Indonesia's governance and conservation of cetaceans. iScience 2024; 27:108585. [PMID: 38161413 PMCID: PMC10757265 DOI: 10.1016/j.isci.2023.108585] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2024] Open
Abstract
Over the past few decades, Indonesia's marine conservation governance has been criticized. This article analyzes the overlaps and gaps in domestic law and policy regimes for cetaceans or marine mammal management and examines issues of institutional arrangements and legal frameworks related to cetacean conservation in Indonesia. The legal framework's progress on cetacean governance shows three distinct phases: 1975-1985 (species-focused governance approach), 1990-2009 (area-based approach), and 2010-present (broader marine governance approach). This study reveals that the main shortcoming of the legal framework is unclear mandates and overlapping jurisdictions. This study suggests several urgent policies that should be accommodated in the current legal regime to strengthen cetacean conservation. In addition, this research also recommends creating a collaboration mechanism between institutions and encouraging Indonesia to join as a full member of the International Whaling Commission and the Conservation of Migratory Species of Wild Animals Convention to strengthen cetacean governance and conservation.
Collapse
Affiliation(s)
- Adrian Nugraha
- Faculty of Law, Sriwijaya University, Palembang 30121, South Sumatra, Indonesia
| | - Febrian Zen
- Faculty of Law, Sriwijaya University, Palembang 30121, South Sumatra, Indonesia
| | - Hawis Madduppa
- Department of Marine Science and Technology, Faculty of Fisheries and Marine Science, Bogor Agricultural University, Bogor 16680, Indonesia
| | - Robert Lihtorng Chen
- Institute of the Law of the Sea, College of Ocean Law and Policy, National Taiwan Ocean University, Keelung 20224, Taiwan
| |
Collapse
|
2
|
Borbee EM, Ayu IP, Carvalho P, Restiana E, Setiawan F, Subhan B, Humphries AT, Madduppa H, Lane CE. Rubble fields shape planktonic protist communities in Indonesia at a local scale. J Eukaryot Microbiol 2023; 70:e12954. [PMID: 36401815 DOI: 10.1111/jeu.12954] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2022] [Revised: 11/04/2022] [Accepted: 11/10/2022] [Indexed: 11/21/2022]
Abstract
The Coral Triangle encompasses nearly 30% of the world's coral reefs and is widely considered the epicenter of marine biodiversity. Destructive fishing practices and natural disturbances common to this region damage reefs leaving behind fields of coral rubble. While the impacts of disturbances in these ecosystems are well documented on metazoans, we have a poor understanding of their impact on microbial communities at the base of the food web. We use metabarcoding to characterize protist community composition in sites of varying fisheries management schemes and benthic profiles across the island of Lombok, Indonesia. Our study shows that rubble coverage and net primary productivity are the strongest explainers of variation in protist communities across Lombok. More specifically, rubble fields are characterized by increases in small heterotrophic protists, including ciliates and cercozoans. In addition to shifts in heterotrophic protist communities, we also observed increases in diatom relative abundance in rubble fields, which corresponded to sites with higher net primary productivity. These results are the first to characterize protist communities in tropical marine rubble fields and provide insight on environmental factors potentially driving these shifts on a local scale.
Collapse
Affiliation(s)
- Erin M Borbee
- Department of Biological Sciences, University of Rhode Island, Kingston, Rhode Island, USA
| | - Inna Puspa Ayu
- Department of Marine Science and Technology, Institut Pertainian Bogor, Bogor, Indonesia
| | - Paul Carvalho
- Department of Fisheries, Animal, and Veterinary Sciences, University of Rhode Island, Kingston, Rhode Island, USA
| | - Ester Restiana
- Department of Marine Science and Technology, Institut Pertainian Bogor, Bogor, Indonesia.,Department of Fisheries, University of Jambi, Jambi, Indonesia
| | - Fahkrizal Setiawan
- Department of Marine Science and Technology, Institut Pertainian Bogor, Bogor, Indonesia
| | - Beginer Subhan
- Department of Marine Science and Technology, Institut Pertainian Bogor, Bogor, Indonesia
| | - Austin T Humphries
- Department of Fisheries, Animal, and Veterinary Sciences, University of Rhode Island, Kingston, Rhode Island, USA
| | - Hawis Madduppa
- Department of Marine Science and Technology, Institut Pertainian Bogor, Bogor, Indonesia
| | - Christopher E Lane
- Department of Biological Sciences, University of Rhode Island, Kingston, Rhode Island, USA
| |
Collapse
|
3
|
Yuanawati D, Farizky HS, Santanumurti MB, Jamal MT, Iqbal Sani LM, Madduppa H, Sari PDW. The newest COI molecular detection of Asian redtail catfish Hemibagrus nemurus (Valenciennes, 1840) in Progo River, Magelang, Central Java, Indonesia. J Adv Vet Anim Res 2022; 9:591-600. [PMID: 36714512 PMCID: PMC9868792 DOI: 10.5455/javar.2022.i628] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Revised: 09/19/2022] [Accepted: 09/26/2022] [Indexed: 01/13/2023] Open
Abstract
Objective This study describes the newest deoxyribonucleic acid (DNA) barcoding Asian redtail catfish (Hemibagrus nemurus) in the Progo River, Magelang, Central Java, Indonesia. Materials and Methods Ten fish were caught in the Progo River, Magelang, Central Java, Indonesia. The polymerase chain reaction was the molecular diagnosis to detect the sequences of DNA of Cytochrome Oxidase I compared to National Center for Biotechnology Information data (GenBank). Results The results showed that the percent identity was not 100% with H. nemurus data from other locations (GenBank), including Indonesia. The closest percent identity was H. nemurus from Java Island (Accession ID: MK312566.1) with 97.6% similarity. The genetic mutation that happened might be due to environmental change (pollution) in the Progo River recently. Conclusions This study showed a genetic mutation in H. nemurus from Progo River may be caused by environmental change. Low pollution exposure levels may not be detrimental (lethal) to fish. However, it can affect fish fertility, which leads to population degradation (gene variation). Attention must be increased for fish survival in the future.
Collapse
Affiliation(s)
- Desyiamililia Yuanawati
- Program Study of Aquaculture, Faculty of Fisheries and Marine, Universitas Airlangga, Surabaya, Indonesia
| | - Hutama Satriana Farizky
- Program Study of Aquaculture, Faculty of Fisheries and Marine, Universitas Airlangga, Surabaya, Indonesia
| | - Muhammad Browijoyo Santanumurti
- Department of Aquaculture, Faculty of Fisheries and Marine, Universitas Airlangga, Surabaya, Indonesia,Department of Marine Biology, Faculty of Marine Sciences, King Abdulaziz University, Jeddah, Kingdom of Saudi Arabia
| | - Mamdoh T. Jamal
- Department of Marine Biology, Faculty of Marine Sciences, King Abdulaziz University, Jeddah, Kingdom of Saudi Arabia
| | - Lalu M. Iqbal Sani
- Oceanogen Environmental Biotechnology Laboklinikum, Cilendek Timur, Bogor, Indonesia
| | - Hawis Madduppa
- Oceanogen Environmental Biotechnology Laboklinikum, Cilendek Timur, Bogor, Indonesia
| | - Putri Desi Wulan Sari
- Department of Aquaculture, Faculty of Fisheries and Marine, Universitas Airlangga, Surabaya, Indonesia
| |
Collapse
|
4
|
Pratomo A, Bengen DG, Zamani NP, Lane C, Humphries AT, Borbee E, Subhan B, Madduppa H. Diversity and distribution of Symbiodiniaceae detected on coral reefs of Lombok, Indonesia using environmental DNA metabarcoding. PeerJ 2022; 10:e14006. [PMID: 36312748 PMCID: PMC9610659 DOI: 10.7717/peerj.14006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2021] [Accepted: 08/14/2022] [Indexed: 01/19/2023] Open
Abstract
Background Dinoflagellates of family Symbiodiniaceae are important to coral reef ecosystems because of their contribution to coral health and growth; however, only a few studies have investigated the function and distribution of Symbiodiniaceae in Indonesia. Understanding the distribution of different kinds of Symbiodiniaceae can improve forecasting of future responses of various coral reef systems to climate change. This study aimed to determine the diversity of Symbiodiniaceae around Lombok using environmental DNA (eDNA). Methods Seawater and sediment samples were collected from 18 locations and filtered to obtain fractions of 0.4-12 and >12 µm. After extraction, molecular barcoding polymerase chain reaction was conducted to amplify the primary V9-SSU 18S rRNA gene, followed by sequencing (Illumina MiSeq). BLAST, Naïve-fit-Bayes, and maximum likelihood routines were used for classification and phylogenetic reconstruction. We compared results across sampling sites, sample types (seawater/sediment), and filter pore sizes (fraction). Results Phylogenetic analyses resolved the amplicon sequence variants into 16 subclades comprising six Symbiodiniaceae genera (or genera-equivalent clades) as follows: Symbiodinium, Breviolum, Cladocopium, Durusdinium, Foraminifera Clade G, and Halluxium. Comparative analyses showed that the three distinct lineages within Cladocopium, Durusdinium, and Foraminifera Clade G were the most common. Most of the recovered sequences appeared to be distinctive of different sampling locations, supporting the possibility that eDNA may resolve regional and local differences among Symbiodiniaceae genera and species. Conclusions eDNA surveys offer a rapid proxy for evaluating Symbiodiniaceae species on coral reefs and are a potentially useful approach to revealing diversity and relative ecological dominance of certain Symbiodiniaceae organisms. Moreover, Symbiodiniaceae eDNA analysis shows potential in monitoring the local and regional stability of coral-algal mutualisms.
Collapse
Affiliation(s)
- Arief Pratomo
- Raja Ali Haji Maritime University, Tanjungpinang, Indonesia,Department of Marine Science and Technology, Institut Pertanian Bogor, Bogor, Indonesia
| | - Dietriech G. Bengen
- Department of Marine Science and Technology, Institut Pertanian Bogor, Bogor, Indonesia
| | - Neviaty P. Zamani
- Department of Marine Science and Technology, Institut Pertanian Bogor, Bogor, Indonesia
| | - Christopher Lane
- Department of Biological Sciences, University of Rhode Island, Rhode Island, United States of America
| | - Austin T. Humphries
- Department of Fisheries, Animal and Veterinary Sciences, University of Rhode Island, Rhode Island, United States of America
| | - Erin Borbee
- Department of Biological Sciences, University of Rhode Island, Rhode Island, United States of America
| | - Beginer Subhan
- Department of Marine Science and Technology, Institut Pertanian Bogor, Bogor, Indonesia
| | - Hawis Madduppa
- Department of Marine Science and Technology, Institut Pertanian Bogor, Bogor, Indonesia,Oceanogen Research Center, Bogor, Indonesia
| |
Collapse
|
5
|
Chow SW, Keshavmurthy S, Reimer JD, de Voogd N, Huang H, Wang JT, Tang SL, Schupp PJ, Tan CH, Liew HC, Soong K, Subhan B, Madduppa H, Chen CA. Population genetics and demography of the coral-killing cyanobacteriosponge, Terpios hoshinota, in the Indo-West Pacific. PeerJ 2022; 10:e13451. [PMID: 35669953 PMCID: PMC9165603 DOI: 10.7717/peerj.13451] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2021] [Accepted: 04/26/2022] [Indexed: 01/14/2023] Open
Abstract
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 F ST and Isolation-by-distance by Mantel test of ITS2 showed moderate gene flow existed among most populations in the marine ecoregions of West Pacific, Coral Triangle, and Eastern Indian Ocean, but with a restricted gene flow between these regions and Maldives in the Central Indian Ocean. Demographic analyses of most T. hoshinota populations were consistent with the mutation-drift equilibrium, except for the Sulawesi Sea and Maldives, which showed bottlenecks following recent expansion. Our results suggest that while long-range dispersal might explain the capability of T. hoshinota to spread in the IWP, stable population demography might account for the long-term persistence of T. hoshinota outbreaks on local reefs.
Collapse
Affiliation(s)
- Savanna Wenhua Chow
- Department of Life Sciences, National Taiwan Normal University, Taipei, Taiwan,Biodiversity Research Center, Academia Sinica, Taipei, Taiwan,Department of Oceanography, National Sun Yat-sen University, Kaohsiung, Taiwan,Biodiversity Program, Taiwan International Graduate Program, Academia Sinica, Taipei, Taiwan
| | | | - James Davis Reimer
- Department of Biology, Chemistry, and Marine Science, University of Ryukyus, Naha, Okinawa, Japan,Tropical Biosphere Research Center, University of the Ryukyus, Okinawa, Japan
| | - Nicole de Voogd
- Naturalis Biodiversity Center, Leiden, The Netherlands,Institute of Environmental Sciences, Environmental Biology Department, Leiden University, Leiden, Netherlands
| | - Hui Huang
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology and Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China
| | - Jih-Terng Wang
- Department of Oceanography, National Sun Yat-sen University, Kaohsiung, Taiwan
| | - Sen-Lin Tang
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
| | - Peter J. Schupp
- Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg, Oldenburg, Germany,Helmholtz Institute for Functional Marine Biodiversity at the, University of Oldenburg (HIFMB), Oldenburg, Germany
| | - Chun Hong Tan
- School of Marine and Environmental Sceinces, University of Malaysia Terengganu, Terengganu, Malaysia
| | - Hock-Chark Liew
- Sdn Bhd. Jalan Hiliran, Kuala Terengganu, Alchemy Laboratory & Services, Terengganu, Malaysia
| | - Keryea Soong
- Department of Oceanography, National Sun Yat-sen University, Kaohsiung, Taiwan
| | - Beginer Subhan
- Department of Marine Science & Technology, Faculty of Fisheries & Marine Sciences, IPB University, Bogor, Indonesia
| | - Hawis Madduppa
- Department of Marine Science & Technology, Faculty of Fisheries & Marine Sciences, IPB University, Bogor, Indonesia
| | - Chaolun Allen Chen
- Department of Life Sciences, National Taiwan Normal University, Taipei, Taiwan,Biodiversity Research Center, Academia Sinica, Taipei, Taiwan,Biodiversity Program, Taiwan International Graduate Program, Academia Sinica, Taipei, Taiwan,Department of Life Science, Tunghai University, Taichung, Taiwan
| |
Collapse
|
6
|
Liu SYV, Green J, Briggs D, Hastings R, Jondelius Y, Kensinger S, Leever H, Santos S, Throne T, Cheng C, Madduppa H, Toonen RJ, Gaither MR, Crandall ED. Dongsha Atoll is an important stepping-stone that promotes regional genetic connectivity in the South China Sea. PeerJ 2021; 9:e12063. [PMID: 34540369 PMCID: PMC8415289 DOI: 10.7717/peerj.12063] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2021] [Accepted: 08/04/2021] [Indexed: 11/22/2022] Open
Abstract
Background Understanding region-wide patterns of larval connectivity and gene flow is crucial for managing and conserving marine biodiversity. Dongsha Atoll National Park (DANP), located in the northern South China Sea (SCS), was established in 2007 to study and conserve this diverse and remote coral atoll. However, the role of Dongsha Atoll in connectivity throughout the SCS is seldom studied. In this study, we aim to evaluate the role of DANP in conserving regional marine biodiversity. Methods In total, 206 samples across nine marine species were collected and sequenced from Dongsha Atoll, and these data were combined with available sequence data from each of these nine species archived in the Genomic Observatories Metadatabase (GEOME). Together, these data provide the most extensive population genetic analysis of a single marine protected area. We evaluate metapopulation structure for each species by using a coalescent sampler, selecting among panmixia, stepping-stone, and island models of connectivity in a likelihood-based framework. We then completed a heuristic graph theoretical analysis based on maximum dispersal distance to get a sense of Dongsha’s centrality within the SCS. Results Our dataset yielded 111 unique haplotypes across all taxa at DANP, 58% of which were not sampled elsewhere. Analysis of metapopulation structure showed that five out of nine species have strong regional connectivity across the SCS such that their gene pools are effectively panmictic (mean pelagic larval duration (PLD) = 78 days, sd = 60 days); while four species have stepping-stone metapopulation structure, indicating that larvae are exchanged primarily between nearby populations (mean PLD = 37 days, sd = 15 days). For all but one species, Dongsha was ranked within the top 15 out of 115 large reefs in the South China Sea for betweenness centrality. Thus, for most species, Dongsha Atoll provides an essential link for maintaining stepping-stone gene flow across the SCS. Conclusions This multispecies study provides the most comprehensive examination of the role of Dongsha Atoll in marine connectivity in the South China Sea to date. Combining new and existing population genetic data for nine coral reef species in the region with a graph theoretical analysis, this study provides evidence that Dongsha Atoll is an important hub for sustaining connectivity for the majority of coral-reef species in the region.
Collapse
Affiliation(s)
- Shang Yin Vanson Liu
- Dongsha Atoll Research Station, College of Marine Sciences, National Sun Yat-sen University, Kaohsiung City, Taiwan.,Department of Marine Biotechnology and Resources, National Sun Yat-Sen University, Kaohsiung City, Taiwan
| | - Jacob Green
- School of Natural Sciences, California State University, Monterey Bay, California, United States.,Department of Biological and Environmental Science, University of Rhode Island, Kingston, Rhode Island, United States
| | - Dana Briggs
- School of Natural Sciences, California State University, Monterey Bay, California, United States
| | - Ruth Hastings
- School of Natural Sciences, California State University, Monterey Bay, California, United States
| | - Ylva Jondelius
- School of Natural Sciences, California State University, Monterey Bay, California, United States
| | - Skylar Kensinger
- School of Natural Sciences, California State University, Monterey Bay, California, United States.,Department of Molecular, Cellular and Developmental Biology, University of California, Santa Cruz, Santa Cruz, California, United States
| | - Hannah Leever
- School of Natural Sciences, California State University, Monterey Bay, California, United States
| | - Sophia Santos
- School of Natural Sciences, California State University, Monterey Bay, California, United States
| | - Trevor Throne
- School of Natural Sciences, California State University, Monterey Bay, California, United States
| | - Chi Cheng
- Department of Marine Biotechnology and Resources, National Sun Yat-Sen University, Kaohsiung City, Taiwan
| | - Hawis Madduppa
- Department of Marine Science and Technology, Institut Pertanian Bogor, Bogor, Indonesia
| | - Robert J Toonen
- Hawai'i Institute of Marine Biology, University of Hawai'i at Mānoa, Kane'ohe, Hawai'i, United States
| | - Michelle R Gaither
- Department of Biology, University of Central Florida, Orlando, Florida, United States
| | - Eric D Crandall
- School of Natural Sciences, California State University, Monterey Bay, California, United States.,Department of Biology, Pennsylvania State University, University Park, Pennsylvania, United States
| |
Collapse
|
7
|
Aini NK, Wardiatno Y, Effendi H, Mashar A, Madduppa H. High genetic diversity and mixing of coastal horseshoe crabs ( Tachypleus gigas) across major habitats in Sundaland, Indonesia. PeerJ 2021; 9:e11739. [PMID: 34414023 PMCID: PMC8340900 DOI: 10.7717/peerj.11739] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2020] [Accepted: 06/17/2021] [Indexed: 11/20/2022] Open
Abstract
Species with limited dispersal abilities are often composed of highly genetically structured populations across small geographic ranges. This study aimed to investigate the haplotype diversity and genetic connectivity of the coastal horseshoe crab (Tachypleus gigas) in Indonesia. To achieve this, we collected a total of 91 samples from six main T. gigas habitats: Bintan, Balikpapan, Demak, Madura, Subang, and Ujung Kulon. The samples were amplified using primers for mitochondrial (mt) AT-rich region DNA sequences. The results showed 34 haplotypes, including seven shared and 22 unique haplotypes, across all localities. The pairwise genetic differentiation (F ST) values were low (0 to 0.13) and not significantly different (p > 0.05), except among samples from Ujung Kulon-Madura and Kulon-Subang (p < 0.05). Additionally, the 34 analysis of molecular variance (AMOVA) showed the most variation within populations (95.23%) compared to less among populations (4.77%). The haplotype network showed evidence of shared haplotypes between populations. Tajima's D and Fu's F S test values indicated a population expansion. Our results showed a low level of differentiation, suggesting a single stock and high connectivity. Therefore, a regionally-based conservation strategy is recommended for the coastal horseshoe crab in Indonesia.
Collapse
Affiliation(s)
- Naila Khuril Aini
- Study Program of Aquatic Resources, Department of Aquatic Resources Management, Faculty of Fisheries and Marine Sciences, Graduate School, Institut Pertanian Bogor, Bogor, Jawa Barat, Indonesia
| | - Yusli Wardiatno
- Department of Aquatic Resources Management, Faculty of Fisheries and Marine Sciences, Institut Pertanian Bogor, Bogor, Jawa Barat, Indonesia.,Environmental Research Center, Institut Pertanian Bogor, Bogor, Indonesia
| | - Hefni Effendi
- Department of Aquatic Resources Management, Faculty of Fisheries and Marine Sciences, Institut Pertanian Bogor, Bogor, Jawa Barat, Indonesia.,Environmental Research Center, Institut Pertanian Bogor, Bogor, Indonesia
| | - Ali Mashar
- Department of Aquatic Resources Management, Faculty of Fisheries and Marine Sciences, Institut Pertanian Bogor, Bogor, Jawa Barat, Indonesia
| | - Hawis Madduppa
- Department of Marine Science and Technology, Faculty of Fisheries and Marine Sciences, Institut Pertanian Bogor, Bogor, Jawa Barat, Indonesia.,Oceanogen Environmental Biotechnology Laboklinikum, Bogor, Indonesia
| |
Collapse
|
8
|
Carvalho PG, Setiawan F, Fahlevy K, Subhan B, Madduppa H, Zhu G, Humphries AT. Fishing and habitat condition differentially affect size spectra slopes of coral reef fishes. Ecol Appl 2021; 31:e02345. [PMID: 33817898 DOI: 10.1002/eap.2345] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/11/2020] [Revised: 10/30/2020] [Accepted: 01/15/2021] [Indexed: 06/12/2023]
Abstract
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.
Collapse
Affiliation(s)
- Paul G Carvalho
- Department of Fisheries, Animal and Veterinary Sciences, University of Rhode Island, 9 East Alumni Avenue, Kingston, Rhode Island, 02881, USA
| | - Fakhrizal Setiawan
- Department of Marine Science and Technology, Faculty of Fisheries and Marine Science, Institut Pertanian Bogor (IPB), Jalan Rasamala, Bogor, Darmaga, 16680, Indonesia
| | - Karizma Fahlevy
- Department of Marine Science and Technology, Faculty of Fisheries and Marine Science, Institut Pertanian Bogor (IPB), Jalan Rasamala, Bogor, Darmaga, 16680, Indonesia
| | - Beginer Subhan
- Department of Marine Science and Technology, Faculty of Fisheries and Marine Science, Institut Pertanian Bogor (IPB), Jalan Rasamala, Bogor, Darmaga, 16680, Indonesia
| | - Hawis Madduppa
- Department of Marine Science and Technology, Faculty of Fisheries and Marine Science, Institut Pertanian Bogor (IPB), Jalan Rasamala, Bogor, Darmaga, 16680, Indonesia
| | - Guangyu Zhu
- Department of Computer Science and Statistics, University of Rhode Island, 9 Greenhouse Road, Kingston, Rhode Island, 02881, USA
| | - Austin T Humphries
- Department of Fisheries, Animal and Veterinary Sciences, University of Rhode Island, 9 East Alumni Avenue, Kingston, Rhode Island, 02881, USA
- Graduate School of Oceanography, University of Rhode Island, 215 South Ferry Road, Narragansett, Rhode Island, 02882, USA
| |
Collapse
|
9
|
Madduppa H, Martaulina R, Zairion Z, Renjani RM, Kawaroe M, Anggraini NP, Subhan B, Verawati I, Sani LMI. Genetic population subdivision of the blue swimming crab (Portunus pelagicus) across Indonesia inferred from mitochondrial DNA: Implication to sustainable fishery. PLoS One 2021; 16:e0240951. [PMID: 33539423 PMCID: PMC7861520 DOI: 10.1371/journal.pone.0240951] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2020] [Accepted: 12/30/2020] [Indexed: 11/18/2022] Open
Abstract
The blue swimming crab (BSC), Portunus pelagicus (Linnaeus 1758), inhabits coastal areas of Southeast and East Asia, and is one of high fisheries commodities with an export value for Indonesia and an increasing global market demand, annually. However, the data of genetic diversity and their spatial connectivity of populations in Indonesia are not yet known, even when it is important to inform stock unit management and sustainable use. This study aimed to determine the genetic diversity and differentiation of blue swimming crabs across Indonesian populations in different Fishery Management Area (FMA), and their spatial genetic connectivity, as well as to deliver implications for sustainable fishery. A total of 297 individuals were collected and amplified using cytochrome oxidase I mitochondrial DNA. This study has showed the highest values for haplotype and nucleotide diversity in the eastern part of Indonesia, where exploitation is relatively low. Significant genetic differentiation between populations (FST = 0.954; p < 0.001) and the fisheries management areas (FST = 0.964; p < 0.001) were revealed. Low spatial connectivity was observed between populations in a distance of at least more than 60 kilometers. This study suggests that BSC populations in Indonesia, likely have several stock units, and preferably different fisheries management plans and actions across the region thoroughly and simultaneously. This would be effective for management and their sustainable conservation.
Collapse
Affiliation(s)
- Hawis Madduppa
- Department of Marine Science and Technology, Faculty of Fisheries and Marine Sciences, Institut Pertanian Bogor (IPB University), Bogor, Indonesia
- Indonesian Blue Swimming Crab Association (Asosiasi Pengelolaan Rajungan Indonesia–APRI), Surabaya, Indonesia
- Center for Coastal and Marine Resources Studies, Institut Pertanian Bogor (IPB University), Bogor, Indonesia
- Oceanogen Environmental Biotechnology Laboklinikum, West Java, Indonesia
| | - Rina Martaulina
- Department of Marine Science and Technology, Faculty of Fisheries and Marine Sciences, Institut Pertanian Bogor (IPB University), Bogor, Indonesia
| | - Zairion Zairion
- Department of Aquatic Resources Management, Faculty of Fisheries and Marine Sciences, Institut Pertanian Bogor (IPB University), Bogor, Indonesia
| | - Resha Mukti Renjani
- Department of Marine Science and Technology, Faculty of Fisheries and Marine Sciences, Institut Pertanian Bogor (IPB University), Bogor, Indonesia
| | - Mujizat Kawaroe
- Department of Marine Science and Technology, Faculty of Fisheries and Marine Sciences, Institut Pertanian Bogor (IPB University), Bogor, Indonesia
| | - Nurlita Putri Anggraini
- Department of Marine Science and Technology, Faculty of Fisheries and Marine Sciences, Institut Pertanian Bogor (IPB University), Bogor, Indonesia
| | - Beginer Subhan
- Department of Marine Science and Technology, Faculty of Fisheries and Marine Sciences, Institut Pertanian Bogor (IPB University), Bogor, Indonesia
| | - Indri Verawati
- Department of Marine Science and Technology, Faculty of Fisheries and Marine Sciences, Institut Pertanian Bogor (IPB University), Bogor, Indonesia
| | - Lalu M. Iqbal Sani
- Oceanogen Environmental Biotechnology Laboklinikum, West Java, Indonesia
| |
Collapse
|
10
|
Hadi S, Andayani N, Muttaqin E, Simeon BM, Ichsan M, Subhan B, Madduppa H. Genetic connectivity of the scalloped hammerhead shark Sphyrna lewini across Indonesia and the Western Indian Ocean. PLoS One 2020; 15:e0230763. [PMID: 33002022 PMCID: PMC7529310 DOI: 10.1371/journal.pone.0230763] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2020] [Accepted: 09/14/2020] [Indexed: 11/21/2022] Open
Abstract
Scalloped Hammerhead shark (Sphyrna lewini) is an endangered species which its populations have been declining globally including in Indonesia, the world’s top shark fishing country. However, there is a lack of information on the recent population structure of this species to promote proper management and its conservation status. This study aimed to investigate the genetic diversity, population structure, and connectivity of the S. lewini population, in three major shark landing sites: Aceh (n = 41), Balikpapan (n = 30), and Lombok (n = 29). Meanwhile, additional sequences were retrieved from West Papua (n = 14) and the Western Indian Ocean (n = 65) populations. From the analyses of the mitochondrial CO1 gene, a total of 179 sequences of S. lewini, with an average size of 594 bp, and 40 polymorphic loci in four and eight haplotypes for the Indonesian population and the Western Indian Ocean population were identified. The overall values of genetic diversity were high (h = 0.717; π = 0.013), with the highest values recorded in Aceh (h = 0.668; π = 0.002) and the lowest in Papua (h = 0.143; π = 0.000). On the contrary, the overall value was fairly low in the Western Indian Ocean (h = 0.232; π = 0.001). Furthermore, AMOVA and FST showed three significant subdivisions in Indonesia (FST = 0.442; P < 0.001), with separated populations for Aceh and West Papua, and mixed between Balikpapan and Lombok (FST = 0.044; P = 0.091). In contrast, genetic homogeneity was observed within the population of the Western Indian Ocean (FST = –0.013; P = 0.612). The establishment of a haplotype network provided evidence of a significantly different population and a limited genetic distribution between the Indonesian and the Western Indian Ocean populations (FST = 0.740; P < 0.001). This study showed the presence of a complex population of S. lewini with limited connectivity only in Indonesia separated from the Western Indian Ocean and requiring specific management measures based on the population structure at the regional level.
Collapse
Affiliation(s)
- Sutanto Hadi
- Department of Marine Science and Technology, Faculty of Fisheries and Marine Sciences, IPB University, Bogor, Indonesia
| | - Noviar Andayani
- Department of Biology, Faculty of Mathematics and Natural Science, University of Indonesia, Depok, Indonesia
- Wildlife Conservation Society Indonesia Program, Bogor, Indonesia
| | - Efin Muttaqin
- Wildlife Conservation Society Indonesia Program, Bogor, Indonesia
| | - Benaya M. Simeon
- Wildlife Conservation Society Indonesia Program, Bogor, Indonesia
| | - Muhammad Ichsan
- Wildlife Conservation Society Indonesia Program, Bogor, Indonesia
| | - Beginer Subhan
- Department of Marine Science and Technology, Faculty of Fisheries and Marine Sciences, IPB University, Bogor, Indonesia
| | - Hawis Madduppa
- Department of Marine Science and Technology, Faculty of Fisheries and Marine Sciences, IPB University, Bogor, Indonesia
- * E-mail:
| |
Collapse
|
11
|
Aini NK, Erwyansyah E, Kurnia R, Butet NA, Mashar A, Zairion Z, Funch P, Madduppa H, Wardiatno Y. Two morphotypes of tri-spine horseshoe crab, Tachypleus tridentatus (Leach, 1819) (Xiphosura Limulidae) in Indonesia and implications for species identification. Biodiversity Journal 2020. [DOI: 10.31396/biodiv.jour.2020.11.2.535.540] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
|
12
|
Putra ING, Syamsuni YF, Subhan B, Pharmawati M, Madduppa H. Strong genetic differentiation in tropical seagrass Enhalus acoroides (Hydrocharitaceae) at the Indo-Malay Archipelago revealed by microsatellite DNA. PeerJ 2018; 6:e4315. [PMID: 29576933 PMCID: PMC5855881 DOI: 10.7717/peerj.4315] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2016] [Accepted: 01/11/2018] [Indexed: 11/20/2022] Open
Abstract
The Indo-Malay Archipelago is regarded as a barrier that separates organisms of the Indian and Pacific Oceans. Previous studies of marine biota from this region have found a variety of biogeographic barriers, seemingly dependent on taxon and methodology. Several hypotheses, such as emergence of the Sunda Shelf and recent physical oceanography, have been proposed to account for the genetic structuring of marine organisms in this region. Here, we used six microsatellite loci to infer genetic diversity, population differentiation and phylogeographic patterns of Enhalus acoroides across the Indo-Malay Archipelago. Heterozygosities were consistently high, and significant isolation-by-distance, consistent with restricted gene flow, was observed. Both a neighbour joining tree based on DA distance and Bayesian clustering revealed three major clusters of E. acoroides. Our results indicate that phylogeographic patterns of E. acoroides have possibly been influenced by glaciation and deglaciation during the Pleistocene. Recent physical oceanography such as the South Java Current and the Seasonally Reversing Current may also play a role in shaping the genetic patterns of E. acoroides.
Collapse
Affiliation(s)
- I Nyoman Giri Putra
- Department of Marine Science and Technology, Faculty Fisheries and Marine Sciences, Bogor Agricultural University (IPB), Bogor, Indonesia.,Department of Marine Science, Faculty of Marine Science and Fisheries, Udayana University, Bukit Jimbaran, Bali, Indonesia
| | | | - Beginer Subhan
- Department of Marine Science and Technology, Faculty Fisheries and Marine Sciences, Bogor Agricultural University (IPB), Bogor, Indonesia
| | - Made Pharmawati
- Biology Department, Faculty of Mathematics and Natural Sciences, Udayana University, Bukit Jimbaran, Bali, Indonesia
| | - Hawis Madduppa
- Department of Marine Science and Technology, Faculty Fisheries and Marine Sciences, Bogor Agricultural University (IPB), Bogor, Indonesia.,Center for Coastal and Marine Resources Studies, Bogor Agricultural University (IPB), Bogor, Indonesia
| |
Collapse
|
13
|
Fahlevy K, Khodijah S, Nasrullah IA, Fathihatunnisa R, Subhan B, Madduppa H. Site and depth influence on coral reef structure and composition in Seribu Islands, Jakarta. ACEH J ANIM SCI 2017. [DOI: 10.13170/ajas.2.1.8212] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
|
14
|
Kusuma AB, Bengen DG, Madduppa H, Subhan B, Arafat D, Negara BFS. Close genetic connectivity of soft coral Sarcophyton trocheliophorum in Indonesia and its implication for marine protected area. Aceh J Anim Sci 2016. [DOI: 10.13170/ajas.1.2.4867] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
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 slowly to spread them self far away. Tanakeke island (Sulawesi population) might be a center connectivity of S. trocheliophorum populations. This island connected with islands in west and east Indonesia, therefore that area need to protect
Collapse
|