Genetic of stranded Dugong dugon (Müller 1776) in the Java Sea, Indonesia, through COX1-based DNA barcoding
##plugins.themes.bootstrap3.article.sidebar##
Issue
Section
Articles
This work is licensed under a Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International License.
##plugins.themes.bootstrap3.article.main##
Abstract
Abstract. Dewi CSU, Wahyudi S, Tarno H, Wiadnya DGR, Iranawati F, Sukandar, Martinah A, Sani LMI, Subhan B, Herandarudewi SM, Faiqoh E, Ciptadi G. 2025. Genetic of stranded Dugong dugon (Müller 1776) in the Java Sea, Indonesia, through COX1-based DNA barcoding. Biodiversitas 26: 951-962. The dugong (Dugong dugon (Müller 1776)), an endangered herbivorous marine mammal, is listed as the Red List of the IUCN and CITES Appendix I. Considering its protected categorizing, its population is persistently decreasing globally, particularly in Indonesia, accordingly requiring significant conservation measures. This study aimed to assess the conservation status of the species, analyze the morphology, morphometry, and genetic profile of stranded dugongs, and evaluate surrounding seagrass meadows. Fieldwork undertaken in February, March, and September 2023 concentrated on stranded dugongs, gathering morphological, morphometric, and genetic data, in addition to surveying seagrass habitats using satellite photography. Morphological observations encompassed 14 criteria, whilst tissue samples from pectoral fins were utilized for genetic profiling by phylogenetic analysis. Geographic coordinates identified stranded dugongs, whereas seagrass regions were assessed with Sentinel-2 data and QGIS. The results indicated that genetic investigation verified the species' strong affinity with populations in the Java Sea and New Zealand, with more divergence from dugongs in Kerala, India. The seagrass beds adjacent to the dugongs' habitat ranged from 0.21 to 16.68 hectares within a larger network of 55.38 to 85.35 hectares, underscoring their potential as a protection zone. These findings underscore the essential link between dugong conservation and seagrass ecosystem conservation, making it clear that both aspects are interconnected and necessitate combined protection methods.
##plugins.themes.bootstrap3.article.details##
References
Adulyanukosol A, Cherdsukjai P, Boukaew P. 2011. Morphology and organ weight of dugongs (Dugong dugon) in Thai waters. Proceeding of the 6th International Symposium on SEASTAR2000 and Asian Bio-Logging Science (The 10th SEASTAR2000 Workshop). Graduate school of Informatics, Kyoto University, March 2011.
Andriansyah M. 2023. Marine conservation analysis of dugong life habitat ecosystem. J Oceanogr Aquat Sci 1 (2): 37-41. DOI: 10.56855/joane.v1i2.340.
Anwar MA, Nurjanah SN, Rahayu WP. 2022. Aplikasi Basic Local Alignment Search Tool (BLAST) NCBI pada penelitian molekuler Salmonella spp. Syntax Literate: Jurnal Ilmiah Indonesia 7 (11): 15446-15464. DOI: 10.36418/syntax-literate.v7i11.9037. [Indonesian]
Awadh A, Mwakumanya MA, Omar M. 2024. The viability of seagrass ecosystems for supporting dugong recovery in Kenya. West Indian Ocean J Mar Sci 23 (1): 19-26. DOI: 10.4314/wiojms.v23i1.3.
Blair D, McMahon A, McDonald B, Tikel D, Waycott M, Marsh H. 2014. Pleistocene sea level fluctuations and the phylogeography of the dugong in Australian Waters. Mar Mamm Sci 30 (1): 104-121. DOI: 10.1111/mms.12022.
Boonsri B, Nganvongpanit K, Buddhachat K, Punyapornwithaya V, Kongtueng P, Kaewmong P, Kittiwattanawong K. 2021. Morphometric analysis of cervical vertebrae in some marine and land mammals. Anat Histol Embryol 50 (5): 812-825. DOI: 10.1111/ahe.12725.
Budiarsa AA, De Iongh HH, Kustiawan W, van Bodegom PM. 2021. Dugong foraging behavior on tropical intertidal seagrass meadows: The influence of climatic drivers and anthropogenic disturbance. Hydrobiologia 848: 4153-4166. DOI: 10.1007/s10750-021-04583-0.
Burgess EA, Lanyon JM, Keeley T. 2012. Testosterone and tusks: Maturation and seasonal reproductive patterns of live, free-ranging male dugongs (Dugong dugon) in a subtropical population. Reproduction 143 (5): 683-697. DOI: 10.1530/REP-11-0434.
Chavez J, Payuse INAD, Kuntayuni, Campera M, Nijman V. 2024. Tourism, international wildlife trade and the (in)effectiveness of CITES. Environ Conserv 51: 64-70. DOI: 10.1017/S0376892923000292.
Cleguer C, Garrigue C, Fuentes MMPB, Hamann M, Payri C, Marsh H. 2024. Temporal changes in habitat use by dugongs in a spatially restricted coral reef environment. Pac Conserv Biol 30: PC23036. DOI: 10.1071/PC23036.
Cleguer C, Garrigue C, Marsh H. 2020. Dugong (Dugong dugon) movements and habitat use in a coral reef lagoonal ecosystem. Endanger Species Res 43: 167-81. DOI: 10.3354/esr01061.
Cleguer C, Marsh H. 2023. An Inventory of Dugong Aerial Surveys in Australia. Centre for Tropical Water and Aquatic Ecosystem Research (TropWATER). James Cook University, Townsville.
Collier CJ, Waycott M. 2014. Temperature extremes reduce seagrass growth and induce mortality. Mar Pollut Bull 83 (2): 483-490 DOI: 10.1016/j.marpolbul.2014.03.050.
De Iongh HH, Kiswara W, Kustiawan W, Loth PE. 2007. A review of research on the interactions between dugongs (Dugong dugon Müller 1776) and intertidal seagrass beds in Indonesia. Hydrobiologia 591: 73-83. DOI: 10.1007/s10750-007-0785-4.
Dewi CSU, Wahyudi S, Tarno H, Ciptadi G, Wiadnya DGR. 2024. Dugong dugon (Muller 1776) and its habitat in coastal areas and small islands of East Java Province, Indonesia. IOP Conf Ser: Earth Environ Sci 1328: 012003. DOI: 10.1088/1755-1315/1328/1/012003.
Domning DP, Beatty BL. 2007. Use of tusks in feeding by dugongid sirenians: Observations and tests of hypotheses. Anat Rec 290 (6): 523-538. DOI : 10.1002/ar.20540.
Domning DP. 2012. Sirenia (Dugongs and Manatees). Evolution and Diversity of Life. eLS. John Wiley & Sons, Ltd: Chichester. DOI: DOI: 10.1002/9780470015902.a0001576.pub3.
Folmer O, Black M, Hoeh W, Lutz R, Vrijenhoek R. 1994. DNA primers for amplification of mitochondrial cytochrome c oxidase subunit I from diverse metazoan invertebrates. Mol Mar Biol Biotechnol 3 (5): 294-299.
Furness LH, Kersten O, Boilard A, Keith-Diagne L, Brito C, Barrett JH, Kitchener A, Sabin R, Lavery S, Plön S, Star B. 2024. Population structure of dugong dugon across the Indo-Pacific revealed by historical mitogenomes. R Soc Open Sci 11 (8): 240599. DOI: 10.1098/rsos.240599.
Gaffar S, Sumarlin S. 2020. Analisis sekuen MtDNA COI pari totol biru yang didaratkan di tempat pendaratan ikan Kota Tarakan. J Harpodon Borneo 13: 80-89. DOI: 10.35334/harpodon.v13i2.1835. [Indonesian]
Gole S, Prajapati S, Prabakaran N, Johnson JA, Sivakumar K. 2023. Herd size dynamics and observations on the natural history of dugongs (Dugong dugon) in the Andaman Islands, India. Aquat Mamm 49 (1): 53-61. DOI: 10.1578/AM.49.1.2023.53.
Gredzens C, Marsh H, Fuentes MMPB, Limpus CJ, Shimada T, Hamann M. 2014. Satellite tracking of sympatric marine megafauna can inform the biological basis for species co-management. PLoS One 9 (6): e98944. DOI: 10.1371/journal.pone.0098944.
Hanif F. 2021. Upaya perlindungan satwa liar Indonesia melalui instrumen hukum dan perundang-undangan. Jurnal Hukum Lingkungan Indonesia 2 (2): 29-48. DOI: 10.38011/jhli.v2i2.24. [Indonesian]
Herandarudewi SMC. 2019. Panduan Survei dan Monitoring Duyung dan Lamun. ITB Press, Bandung. [Indonesian]
Heudier M, Mouillot D, Mannocci L. 2023. Assessing the effects of coral reef habitat and marine protected areas on threatened megafauna using aerial surveys. Aquat Conserv: Mar Freshw Ecosyst 33 (3): 286-297. DOI: 10.1002/aqc.3923.
Hunter ME, Meigs-Friend G, Ferrante JA, Kamla AT, Dorazio RM, Diagne LK, Luna F, Lanyon JM, Reid JP. 2018. Surveys of Environmental DNA (EDNA): A new approach to estimate occurrence in vulnerable manatee populations. Endanger Species Res 35: 101-111. DOI: 10.3354/esr00880.
Husna R, Kusumawati I. 2022. Teknik penanganan dan identifikasi mamalia laut terdampar di Pantai Ujung Seukee, Aceh Besar. J La’ot Ilmu Kelautan IV 4: 154-163. DOI: 10.35308/jlik.v4i2.5288. [Indonesian]
Jeunen G-J, von Ammon U, Cross H, Ferreira S, Lamare M, Day R, Treece J, Pochon X, Zaiko A, Gemmell NJ, Stanton J-AL. 2022. Moving Environmental DNA (EDNA) technologies from benchtop to the field using passive sampling and PDQeX extraction. Environ DNA 4 (6): 1420-1433. DOI: 10.1002/edn3.356.
Kayanne H, Hara T, Arai N, Yamano H, Matsuda H. 2021. Local extinction of an isolated dugong population near Okinawa Island, Japan. Res Sq 2021: 1-13. DOI: 10.21203/rs.3.rs-453039/v1.
Kayanne H, Hara T, Arai N, Yamano H, Matsuda H. 2022. Trajectory to local extinction of an isolated dugong population near Okinawa Island, Japan. Sci Rep 12: 6151. DOI: 10.1038/s41598-022-09992-2.
Khamis A, Abdulla A, D'Souza E, Kelkar N, Arthur R, Al Khalifa E, Bader H, Alcoverro T. 2023. Long-term persistence of large dugong groups in a conservation hotspot around Hawar Island, Kingdom of Bahrain. Aquat Coserv: Mar Freshw Ecosyst 33 (6): 592-605. DOI: 10.1002/aqc.3936.
Kurniawati A, Hidayat JW. 2018. The role of the coastal communities as first responders of stranded marine mammals in East Java. E3S Web Conf 73: 02006. DOI: 10.1051/e3sconf/20187302006.
Lanyon JM, Athousis C, Sneath HL, Burgess EA. 2021. Body scarring as an indicator of social function of Dugong (Dugong dugon) tusks. Mar Mamm Sci 37 (3): 962-981. DOI: 10.1111/mms.12788.
Lee PB, Nijman V. 2015. Trade in dugong parts in Southern Bali. J Mar Biol Assoc U K 95: 1717-1721. DOI: 10.1017/S0025315415001423.
Lin M, Turvey ST, Han C, Huang X, Mazaris AD, Liu M, Ma H, Yang Z, Tang X, Li S. 2022. Functional extinction of dugongs in China. R Soc Open Sci 9 (8): 211994. DOI: 10.6084/m9.figshare.c.6135564.
Marsh H, Sobtzick S. 2019. Dugong dugon (amended version of 2015 assessment). The IUCN Red List of Threatened Species 8235: eT6909A160756767. DOI: 10.2305/IUCN.UK.2015-4.RLTS.T6909A160756767.en.
Marshall CD, Maeda H, Iwata M, Furuta M, Asano S, Rosas F, Reep RL. 2003. Orofacial morphology and feeding behaviour of the dugong, Amazonian, West African and Antillean manatees (Mammalia: Sirenia): Functional morphology of the muscular-vibrissal complex. J Zool 259 (3): 245-260. DOI: 10.1017/S0952836902003205.
McGowan AM, Lanyon JM, Clark N, Blair D, Marsh H, Wolanski E, Seddon JM. 2023. Cryptic marine barriers to gene flow in a vulnerable coastal species, the dugong (Dugong dugon). Mar Mamm Sci 39 (3): 918-939. DOI: 10.1111/mms.13021.
Nakaoka M, Mukai H, Chunhabundit S. 2002. Impacts of dugong foraging on benthic animal communities in a Thailand seagrass bed. Ecol Res 17: 625-638. DOI: 10.1046/j.1440-1703.2002.00520.x.
Nganvongpanit K, Buddhachat K, Kaewmong P, Cherdsukjai P, Kittiwatanawong K. 2017. What the skull and scapular morphology of the dugong (Dugong dugon) can tell us: Sex, habitat and body length?. Sci Rep 7: 1964. DOI: 10.1038/s41598-017-01899-7.
Ooi V, McMichael L, Hunter ME, Kamla AT, Lanyon JM. 2022. Development of a new faecal dna extraction method (HV-CTAB-PCI) for amplification of mitochondrial and nuclear markers used in genetic analyses of dugongs (Dugong dugon). bioRxiv 2022: 1-55. DOI: 10.1101/2022.11.24.517804.
Panyawai J, Prathep A. 2022. A systematic review of the status, knowledge, and research gaps of dugong in Southeast Asia. Aquat Mamm 48 (3): 203-222. DOI: 10.1578/AM.48.3.2022.203.
Plön S, Thakur V, Parr L, Lavery SD. 2019. Phylogeography of the dugong (Dugong dugon) based on historical samples identifies vulnerable Indian Ocean populations. PLoS One 14 (9): e0219350. DOI: 10.1371/journal.pone.0219350.
Poommouang A, Kriangwanich W, Buddhachat K, Brown JL, Piboon P, Chomdej S, Kampuansai J, Mekchay S, Kaewmong P, Kittiwattanawong K, Nganvongpanit K. 2021. Genetic diversity in a unique population of dugong (Dugong dugon) along the sea coasts of Thailand. Sci Rep 11 (1): 11624. DOI: 10.1038/s41598-021-90947-4.
Poommouang A, Piboon P, Buddhachat K, Brown JL, Kriangwanich W, Chomdej S, Kampuansai J, Mekchay S, Kaewmong P, Kittiwattanawong K, Nganvongpanit K. 2022. Microsatellite polymorphism and the population structure of dugongs (Dugong dugon) in Thailand. Animals 12 (3): 235. DOI: 10.3390/ani12030235.
Rodrigues FR, da Silva VMF, Barcellos JFM. 2014. The mammary glands of the Amazonian manatee, Trichechus Inunguis (Mammalia: Sirenia): Morphological characteristics and microscopic anatomy. Anat Rec 297 (8): 1532-1535. DOI: 10.1002/ar.22956.
Rosalina D, Jamil K, Arafat Y, Amalia R, Leilani A. 2023. Mapping of seagrass ecosystem on Bontosua Island, Pangkep District, South Sulawesi, Indonesia. Biodiversitas 24 (4): 2023-2030. DOI: 10.13057/biodiv/d240411.
Satyaningtijas AS, Suprayogi A, Darusman HS, Nurdin A, Hanadhita D. 2020. Relative white blood cell counts, heterophil-to-lymphocyte ratio, and discovery of blood parasites in wild dugong (Dugong dugon) at Lingayan Island, Toli-Toli, Indonesia. Vet World 13 (9): 1849-1853. DOI: 10.14202/vetworld.2020.1849-1853.
Scott AL, York PH, Duncan C, Macreadie PI, Connolly RM, Ellis MT, Jarvis JC, Jinks KI, Marsh H, Rasheed MA. 2018. The role of herbivory in structuring tropical seagrass ecosystem service delivery. Front Plant Sci 9: 127. DOI: 10.3389/fpls.2018.00127.
Seal S, Bayyana S, Pande A et al. 2024. Spatial prioritization of dugong habitats in India can contribute towards achieving the 30 × 30 global biodiversity target. Sci Rep 14 (1): 13984. DOI: 10.1038/s41598-024-64760-8.
Srinivas Y, Pande A, Gole S et al. 2021. Mitochondrial phylogeography reveals high haplotype diversity and unique genetic lineage in Indian dugongs (Dugong Dugon). Aquat Conserv: Mar Freshw Ecosyst 31 (4): 818-829. DOI: 10.1002/aqc.3490.
Sun X, Zhang Z, Sun Y, Li J, Xu S, Yang G. 2017. Comparative genomics analyses of alpha-keratins reveal insights into evolutionary adaptation of marine mammals. Front Zool 14: 41. DOI: 10.1186/s12983-017-0225-x.
Tamura K, Stecher G, Kumar S. 2021. MEGA11: Molecular Evolutionary Genetics Analysis version 11. Mol Biol Evol 38 (7): 3022-3027. DOI: 10.1093/molbev/msab120.
Thibault M, Letoumeur Y, Cleguer C, Bonneville C, Briand MJ, Derville S, Bustamante P, Garrigue C. 2024. C and N stable isotopes enlighten the trophic behaviour of the dugong (Dugong dugon). Sci Rep 14 (1): 896. DOI: 10.1038/s41598-023-50578-3.
Toon A, Pérez?Losada M, Schweitzer CE, Feldmann RM, Carlson M, Crandall KA. 2010. Gondwanan radiation of the Southern Hemisphere crayfishes (Decapoda: Parastacidae): Evidence from fossils and molecules. J Biogeogr 37 (12): 2275-2290. DOI: 10.1111/j.1365-2699.2010.02374.x.
Yamato C, Ichikawa K, Arai N, Tanaka K, Nishiyama T, Kittiwattanawong K. 2021. Deep neural networks based automated extraction of dugong feeding trails from UAV images in the intertidal seagrass beds. PLoS One 16 (8): e0255586. DOI: 10.1371/journal.pone.0255586.
Most read articles by the same author(s)
- HAGUS TARNO, YOGO SETIAWAN, BAMBANG TRI RAHARDJO, JIANGUO WANG, Evaluation of the ambrosia beetles traps on Pterocarpus indicus in Indonesia , Biodiversitas Journal of Biological Diversity: Vol. 22 No. 3 (2021)
- FRANS TONY, SOEMARNO, DEWA GEDE RAKA WIADNYA, LUCHMAN HAKIM, Diversity of reef fish in Halang Melingkau Island, South Kalimantan, Indonesia , Biodiversitas Journal of Biological Diversity: Vol. 21 No. 10 (2020)
- YOGO SETIAWAN, FADEL MUHAMMAD HAMDOEN, FAIZ NASHIRUDDIN MUHAMMAD, KUNIHIKO HATA, HAGUS TARNO, JIANGUO WANG, Species composition of Bactrocera fruit flies (Diptera: Tephritidae) and their parasitoids on horticultural commodities in Batu City and Malang District, East Java, Indonesia , Biodiversitas Journal of Biological Diversity: Vol. 25 No. 1 (2024)
- GESTEN HAZERI, DWI LISTYO RAHAYU, BEGINER SUBHAN, ANDRIANUS SEMBIRING, AJI WAHYU ANGGORO, AHMAD TAUFIK GHOZALI, HAWIS H MADDUPPA, Latitudinal species diversity and density of cryptic crustacean (Brachyura and Anomura) in micro-habitat Autonomous Reef Monitoring Structures across Kepulauan Seribu, Indonesia , Biodiversitas Journal of Biological Diversity: Vol. 20 No. 5 (2019)
- PREHADI PREHADI, ANDRIANUS SEMBIRING, EKA MAYA KURNIASIH, RAHMAD RAHMAD, DONDY ARAFAT, BEGINER SUBHAN, HAWIS H. MADDUPPA, DNA barcoding and phylogenetic reconstruction of shark species landed in Muncar fisheries landing site in comparison with Southern Java fishing port , Biodiversitas Journal of Biological Diversity: Vol. 16 No. 1 (2015)
- ANDIKA NOVRIANSYAH, MAREIKE HUHN, HERDIAN WICAKSONO, BUDIONO SENEN, BEGINER SUBHAN, DOUGLAS FENNER, HAWIS MADDUPPA, P. JOANA DIAS, First observations of coral spawning at the Banda Islands, Maluku, Indonesia , Biodiversitas Journal of Biological Diversity: Vol. 24 No. 11 (2023)
- WASIS SENOAJI, Bambang Tri, Hagus Tarno, Proteomic approach: Identification of Nephotettix virescens vector protein transmitting the tungro virus in rice , Biodiversitas Journal of Biological Diversity: Vol. 22 No. 5 (2021)
- DEWA GEDE RAKA WIADNYA, NIA KURNIAWAN, ANIK MARTINAH HARIATI, SEPTIANA SRI ASTUTI, AKHSAN FIKRILLAH PARICAHYA, MUHAMMAD DAILAMI, WAHYU ENDRA KUSUMA, DNA barcoding of the most common marine ornamental fish species spilled over from a small-sized marine protected area, Bali Barat National Park, Indonesia , Biodiversitas Journal of Biological Diversity: Vol. 24 No. 1 (2023)
- SEPTIANA SRI ASTUTI, ANIK MARTINAH HARIATI, WAHYU ENDRA KUSUMA, ATING YUNIARTI, NIA KURNIAWAN, DEWA GEDE RAKA WIADNYA, Anthropogenic introduction of the Spotted Barb, Barbodes binotatus, across the Wallace Line in western Sulawesi, Indonesia , Biodiversitas Journal of Biological Diversity: Vol. 24 No. 3 (2023)
- ANDIK ISDIANTO, RIDHA AYU WIBOWO, AMELINDA VIVIAN KUDRATI, DIAN ALIVIYANTI, MUHAMMAD ARIF ASADI, CITRA SATRYA UTAMA DEWI, ARIEF SETYANTO, TRI DJOKO LELONO, AGUS TUMULYADI, LISA NUR HIDAYAH, AULIA LANUDIA FATHAH, BERLANIA MAHARDIKA PUTRI, NOVAR KURNIA WARDANA, SUPRIYADI, OKTIYAS MUZAKY LUTHFI, Assessing the relationship between coral cover and coral recruitment in the degraded ecosystems of Sempu Nature Reserve, East Java, Indonesia , Biodiversitas Journal of Biological Diversity: Vol. 25 No. 9 (2024)