DNA barcoding of Mugilogobius mertoni and M. rambaiae from Siberut and Enggano Islands, the small outermost islands of Sumatra, Indonesia

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DEWI IMELDA ROESMA
DJONG HON TJONG
SYAIFULLAH
DYTA RABBANI AIDIL

Abstract

Abstract. Roesma DI, Tjong DH, Syaifullah, Aidil DR. 2025. DNA barcoding of Mugilogobius mertoni and M. rambaiae from Siberut and Enggano Islands, the small outermost islands of Sumatra, Indonesia. Biodiversitas 26: 386-395. Siberut and Enggano Islands are the small and outermost islands of Sumatra, Indonesia. These two islands' unique geological history allows evolutionary processes to produce high levels of endemicity. One of the interesting fish genera from the Siberut and Enggano Islands is Mugilogobius. Based on morphological identification, it was estimated there are two Mugilogobius species in the Siberut and Enggano Islands. Molecular identification of Mugilogobius using the Cytochrome Oxidase I gene (known as DNA barcoding) needs to be done to prove it. The liver tissue was used for molecular analysis. The BLAST analysis showed that Mugilogobius from Siberut and Enggano Islands have a similarity range of 97.49%-96.06% with Mugilogobius GenBank. Based on the 558 bp sequence analyzed, Mugilogobius mertoni and Mugilogobius rambaiae from Siberut and Enggano Islands have a low sequence of divergences at 0.0%-0.4%, respectively. M. rambaiae from Siberut and Enggano Islands share the same haplotype. The ability of the species to maintain their genetics and the similarity of conditions between the two islands share their high genetic similarities. M. mertoni and M. rambaiae from Siberut and Enggano Islands have a high sequence of divergences at 3.0-4.6% with M. mertoni and M. rambaiae GenBank, respectively. The long-distance location, the presence of the ocean as a barrier, and differences in habitat conditions contribute to the high variations between Mugilogobius from two islands and other populations. Mugilogobius from Siberut and Enggano Islands has a sequence of divergence at 12.4%-17.3% compared to other Mugilogobius species, supporting their differences at the species level in the same genera. This study contributed to presenting the first molecular data of Mugiologius that can be used as a sequence reference for identification and the sequences became the genetic richness data of fish in the small and outermost islands of Sumatra, Indonesia (Siberut and Enggano Islands).

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References
Abbas EM, Soliman T, El-Magd MA, Farrag MMS, Ismail RF, Kato M. 2017. Phylogeny and DNA barcoding of the family Sparidae inferred from mitochondrial DNA of the Egyptian waters. J Fish Aquat Sci 12 (2): 73-81. DOI: 10.3923/jfas.2017.73.81.
Abdel-Gaber R, Al Quraishy S, Alghamdi M, Aljawdah HM, Maodaa SN, Al-Shaebi EM. 2023. DNA barcoding of Argyrops filamentosus (Perciformes: Sparidae) based on mitochondrial COI gene and histopathological evaluation of gills infected by monogeneans. Indian J Anim Res BF-1626: 1-6. DOI: 10.18805/IJAR.BF-1626.
Abdulmalik-Labe OP, Quilang JP. 2024. DNA barcoding of common freshwater eleotrids (Gobiiformes: Eleotridae) in the Philippines, with a global comparison and notes on their conservation and management. Glob Ecol Conserv 53: e03014. DOI: 10.1016/j.gecco. 2024.e03014.
Afifi MA, Sarhan M, Khalaf-Allah HM, Alabssawy AN, Abbas MM, Abdel-Hamid F, El-Tabakh MA. 2023. DNA barcoding supports life stages of wrasse fish, Novaculichthys taeniourus (Family Labridae) in the Hurghada Red Sea, Egypt. Zool Anz 304: 84-93. DOI: 10.1016/j.jcz.2023.03.005.
Afrand M, Sourinejad I. 2023. Morphological identification and DNA barcoding confirm the discovery of Ambassis dussumieri (Ambassidae) in the Persian Gulf. J Ichthyol 63 (6): 1072-1079. DOI: 10.1134/S0032945223060012.
Ajayi VO. 2023. A review on primary sources of data and secondary sources of data. Eur J Educ Pedagogy 2: 1-7. DOI: 10.21091/ejedu.
Alshehri E, Alqahtani J, Al-Shaebi EM, Al-Quraishy S, Abdel-Gaber R. 2022. Identification of gnathiid isopods as ectoparasites of the brown-spotted grouper Epinephelus chlorostigma from the Red Sea of Saudi Arabia. Indian J Anim Res 57 (6): 754-761. DOI: 10.18805/IJAR.BF-1598.
Aninta SG, Noerfahmy S, Wiantoro S, Iskandar DT. 2022. Natural history collections reveal species richness on a small isolated tropical island: The bats of Siberut. Oryx 56 (6): 904-907. DOI: 10.1017/s0030605321001022.
Barber AJ, Crow MJ, Milsom JS. 2005. Sumatra: Geology, resources and tectonic evolution. In: Barber AJ, Crow MJ, Milsom JS (eds). Geological Society Memoirs No. 31. Geological Society, London. DOI: 10.1017/S0016756806212974.
Baylan M, Mazi G, Ozcan BD, Gundogdu S, Tekdal D. 2023. DNA barcoding and phylogenetic analysis of two species populations of Diplodus from the eastern Mediterranean coasts of Turkey. OKU J Institut Sci Technol 6 (1): 806-817. DOI: 10.47495/okufbed.1201878.
Burland TG. 2000. DNASTAR's lasergene sequence analysis software. In: Misener S, Krawetz SA (eds). Bioinformatics Methods and Protocols. Methods in Molecular Biology. Humana Press, New Jersey.
Ceruso M, Venuti I, Osca D, Caputi L, Anastasio A, Crocetta F, Sordino P, Pepe T. 2020. The complete mitochondrial genome of the sharpsnout seabream Diplodus puntazzo (Perciformes: Sparidae). Mitochondrial DNA B Resour 5 (3): 2379-2381. DOI: 10.1080/23802359. 2020.1775509.
Chan WW, Chang JJ, Tan CZ, Ng JX, Ng MH, Jaafar Z, Huang D. 2024. Eyeing DNA barcoding for species identification of fish larvae. J Fish Biol 105: 1784-1799. DOI: 10.1111/jfb.15920.
Dwifajri S, Tapilatu RF, Pranata B, Kusuma AB. 2022. Molecular phylogeny of grouper of Epinephelus genus in Jayapura, Papua, Indonesia inferred from Cytochrome Oxidase I (COI) gene. Biodiversitas 23 (3): 1449-1456. DOI: 10.13057/biodiv/d230332.
Eriegha OJ, Ekelemu JK, Nwachi OF. 2024. DNA barcoding of Caranx senegallus from three water bodies adjoining the gulf of Guinea, Nigeria. Fudma J Sci 8 (1): 293-298 DOI: 10.33003/fjs-2024-0801-2242.
Eschmeyer's Catalog of Fishes. 2024. Catalogue of Fishes. https://www.calacademy.org/scientists/projects/eschmeyers-catalog-of-fishes
Garcia-Cisneros A, Palacín C, Ventura CRR, Feital B, Paiva PC, Perez-Portela R. 2018. Intraspecific genetic structure, divergence and high rates of clonality in an amphi-atlantic starfish. Mol Ecol 27 (3): 752-772. DOI: 10.1111/mec.14454.
Ghouri MZ, Ismail M, Javed MA, Khan SH, Munawar N, Umar AB, Nisa MU, Afrab SO, Amin S, Khan Z, Ahmad A. 2020. Identification of edible fish species of Pakistan through DNA barcoding. Front Mar Sci 7: 554183. DOI: 10.3389/fmars.2020.554183.
Goistepan. 2016. Jenis-jenis ikan yang tertangkap di sungai siluitung desa sirilogui kecamatan siberut utara kabupaten kepulauan Mentawai [Thesis]. STKIP PGRI Sumatera Barat, Padang. [Indonesian]
Hadiaty RK, Sauri S. 2017. Iktiofauna air tawar Pulau Enggano, Indonesia. Jurnal Ikhtiologi Indonesia 17 (3): 273-287. DOI: 10.32491/jii.v1 7i3.365. [Indonesian]
Hall TA. 2011. BioEdit: An important software for molecular biology. GERF Bull Biosci 2 (1): 60-61.
Hasim, Lamadi A, Tuiyo R. 2023. DNA barcoding, phylogenetic tree and genetic distances of manggabai (Glossogobius aureus) from Limboto Lake, Indonesia. AACL Bioflux 16 (3): 1401-1409.
Haslawati B, Amatul-Samahah MA, Rizman-Idid M, Muniandy S. 2023. DNA barcoding and phylogenetics relationship of pangasiid cat fishes in Peninsular Malaysia revealed the impacts of aquaculture on the native species conservation. Hydrobiology 2 (2): 431-445. DOI: 10.3390/hydrobiology2020028.
Huang SP, Chen IS, Jang-Liaw N, Shao K, Mana M, Yung N. 2016b. Complete mitochondrial reveals a new phylogenetic perspective on the brackish water goby Mugilogobius group (Teleostei: Gobiidae: Gobionellinae). Zool Sci 33 (5): 566-574. DOI: 10.2108/ zs150154.
Huang SP, Chen IS, Yung MMN, Shao K. 2016. The recognition and Molecular phylogeny of Mugilogobius mertoni complex (Teleostei: Gobiidae), with description of a new cryptic species of M. flavomaculatus from Taiwan. Zool Studi 55: 39. DOI: 10.6620/ZS.2016.55-39
Hubert N, Hanner R, Holm E, Mandrak N, Taylor E. 2008. Identifying Canadian freshwater fishes through DNA barcodes. PLoS One 3 (e2490): 554183. DOI: 10.1371/journal.pone.0002490.
Huckstorf V, Larson, H. 2021. Mugilogobius mertoni. The IUCN Red List of Threatened Species 2021: e.T181000A58325572. DOI: 10.2305/IUCN.UK.2021-1.RLTS.T181000A58325572.en.
Kainama J, Louraine T, Wijayanti DP, Sabdono A, Dirgantara D. 2023. DNA barcoding and morphological characters of two trevally fish species (Caranx spp.) collected from Youtefa Bay, Papua, Indonesia. ILMU KELAUTAN: Indon J Mar Sci 28 (1): 97-104. DOI: 10.14710/ik.ijms.28.1.97-104.
Kartavtsev YP, Rozhkovan KV, Masalkova NA. 2016. Phylogeny based on two mtDNA genes (Co-1, Cyt-B) among Sculpins (Scorpaeniformes, Cottidae) and some other scorpionfish in the Russian Far East. Mitochondrial DNA A: DNA Mapp Seq Anal 27 (3): 2225-2240. DOI: 10.3109/19401736.2014.984164.
Kartavtsev YP. 2018. Barcode index number, taxonomic rank and modes of speciation: Examples from fish. Mitochondrial DNA A: DNA Mapp Seq Anal 29: 535-542. DOI: 10.1080/24701394.2017.1315570.
Khedkar GD, Jamdade R, Naik S, David L, Haymer D. 2014. DNA barcodes for the fishes of the Narmada, one of India's longest rivers. PLoS One 9: e101460. DOI: 10.1371/journal.pone.0101460.
Kodoatie RJ. 2012. Groundwater Spatial. Andi Publisher, Yogyakarta.
Kottelat M, Whitten AJ, Kartikasari SR, Wirjoatmodjo S. 1993. Freshwater Fishes of Western Indonesia and Sulawesi. Periplus, Hongkong.
Lamadi A, Paricahya AF, Iranawati F, Widodo MS, Wiadnya DGR. 2023. Genetic and morphological analysis of complex Giuris group species from Limboto Lake, Gorontalo Province, Indonesia. Biodiversitas 24 (10): 5223-5232. DOI: 10.13057/biodiv/ d241002.
Larson HK, Geiger MF, Hadiaty RK, Herder F. 2014. Mugilogobius hitam, a new species of freshwater goby (Teleostei: Gobioidei: Gobiidae) from Lake Towuti, Central Sulawesi, Indonesia. Raffles B Zool 62: 718-725.
Limbu JH, Rajbanshi D, Khanal L, Hui W, Adhikari RC, Thapa S, Yang JQ, Li C. 2024. DNA barcoding of catfishes (Order: Siluriformes) with new records of two species from Eastern Nepal. J Appl Ichthyol 2024 (1): 4907672. DOI: 10.1155/2024/4907672.
Lostrom S, Evans JP, Grierson PF, Collin SP, Davies PM, Kelley JL. 2015. Linking stream ecology with morphological variability in a native freshwater fish from semi-arid Australia. Ecol Evol 5: 3272-3287. DOI: 10.1002/ece3.1590.
Marnis H, Syahputra K, Darmawan J, Febrianti D, Tahapari E, Larashati S, Iswanto B, Primanita EP, Syaifudin M, Subangkit AT. 2024. DNA barcoding of fish diversity from Batanghari River, Jambi, Indonesia. Fish Aquat Sci 27 (2): 87-99. DOI: 10.47853/FAS.2024.e10.
Maryanto I, Hamidy A, Keim AP, Sihotang VBL, Lupiyaningdyah P, Irham M, Ardiyani M. 2017. Ekspedisi Pulau Enggano. LIPI Press, Jakarta.
Modeel S, Negi RK, Sharma M, Dolkar P, Yadav S, Siwach S, Yadav P, Negi T. 2024. A comprehensive DNA barcoding of Indian freshwater fishes of the Indus River system, Beas. Sci Rep 14 (1): 2763. DOI: 10.1038/s41598-024-52519-0.
Ndobe S, Nurdin MS, Hasanah N, Putra AE, Mansyur K, Nasir M, Rabuna Ml, Moore AM. 2023. DNA Barcoding detects resurrected taxon Giuris laglaizei (Sauvage 1880) in Sulawesi, Indonesia: Bolano Sau Lake payangka phylogeny, phenotypic characters and implications for Giuris spp. conservation. F1000Res 11: 295. DOI: 10.12688/F1000research.108970.2.
Nelson JS, Grande TC, Wilson MVH. 2016. Fishes of the World. John Wiley and Sons, New Jersey. DOI: 10.1002/9781119174844.
Nguyen LT, Schmidt HA, von Haeseler A, Minh BQ. 2015. IQ-TREE: A fast and effective stochastic algorithm for estimating maximum-likelihood phylogenies. Mol Biol Evol 32 (1): 268-274. DOI: 10.1093/molbev/msu300.
Pandey PK, Singh YS, Tripathy PS, Kumar R, Abujam SK, Parhi J. 2020. DNA barcoding and phylogenetics of freshwater fish fauna of Ranganadi River, Arunachal Pradesh. Gene 754: 144860. DOI: 10.1016/j.gene.2020.144860.
Panprommin D, Soontornprasit K, Tuncharoen S. 2019. DNA barcodes for the identification of species diversity in fish from Kwan Phayao, Thailand. J Asia-Pac Biodiversitas 12 (3): 382-389. DOI: 10.1016/j.japb.2019.05.003.
Perugia A. 1893. Sopra aleuni Pesci di Engano raccolti dal Dott. Elio Modigliani. Annali del Museo Civico di Storia Naturale at Genova 13 (2): 251-255. [Italiano]
Quinten M, Stirling F, Schwarze S, Dinata Y, Hodges K. 2014. Knowledge, attitudes and practices of local people on Siberut Island (West-Sumatra, Indonesia) towards primate hunting and conservation. J Threat Taxa 6: 6389-6398. DOI: 10.11609/JoTT. o3963.6389-98.
Rajkumar G, Bhavan PS, Udayasuriyan R, Vadivalagan C. 2015. Molecular identification of shrimp species, Penaeus semisulcatus, Metapenaeus dobsoni, Metapenaeus brevicornis, Fenneropenaeus indicus, Parapenaeopsis stylifera and Solenocera crassicornis inhabiting in the Coromandel coast (Tamil Nadu, India) using MT-COI gene. Intl J Fish Aquat Stud 2 (4): 96-106.
Regen R. 2011. Profil Kawasan Konservasi Enggano. Balai Konservasi Sumber Daya Alam (BKSDA) Provinsi Bengkulu, Bengkulu. [Indonesian]
Reguant R, Antipin Y, Sheridan R, Dallago C, Diamantoukos D, Luna A, Sander C, Gauthier NP. 2020. Alignment viewer: Sequence analysis of large protein families. F1000Res 15: 9. DOI: 10.12688/f1000 research.22242.2.
Renxie W, Haoran Z, Jing L, Sufang N, Yao X, Yongxia C. 2018. DNA barcoding of the family Sparidae along the coast of China and revelation of potential cryptic diversity in the Indo-West Pacific oceans based on COI and 16S rRNA genes. J Oceanol Limn 36 (5): 1753-1770. DOI: 10.1007/s00343-018-7214-6.
Roesma DI, Chornelia A, Mursyid A. 2019. Phenotype analysis of endemic mahseer fish (Neolissochilus sumatranus) from Batang Toru tributaries, North Sumatra, Indonesia. J Phys: Conf Ser 1317: 012099. DOI: 10.1088/1742-6596/1317/1/012099.
Roesma DI, Djong HT, Munir W, Aidil DR. 2018. New record species of Puntius (Pisces: Cyprinidae) from West Sumatra based on cytochrome oxidase1 gene. Intl J Adv Sci Eng Inform Technol 8 (1): 250-256. DOI: 10.18517/IJASEIT.8.1.4170.
Roesma DI, Tjong DH, Aidil DR, Prawira FDL, Saputra A. 2024. Freshwater fish diversity from Siberut Island, a small island in the western part of Sumatra, Indonesia. Biodiversitas 25 (2): 836-845. DOI: 10.13057/biodiv/d250244.
Roesma DI, Tjong DH, Aidil DR. 2020. Phylogenetic analysis of transparent gobies in three Sumatran lakes, inferred from mitochondrial Cytochrome Oxidase I (COI) gene. Biodiversitas 21 (1): 43-48. DOI: 10.13057/biodiv/d210107.
Roesma DI, Tjong DH, Janra MN, Aidil DR. 2022. DNA barcoding of freshwater fish in Siberut Island, Mentawai Archipelago, Indonesia. Biodiversitas 23 (4): 1795-1806. DOI: 10.13057/biodiv/d230411.
Rozas J, Ferrer-Mata A, Anchez-DelBarrio JCS, Guirao-Rico S, Librado P. 2017. DnaSP 6: DNA sequence polymorphism analysis of large data sets. Mol Biol Evol 34: 3299-3302. DOI: 10.1093/molbev/msx248.
Senoaji G. 2006. Laporan kegiatan: Studi daya dukung Pemanfaatan dan pengembangan Kepulauan Enggano [Activity report: Carrying capacity study for utilization and development of the Enggano Islands]. Pusat Penelitian Lingkungan, Lembaga Penelitian Universitas Bengkulu. Bengkulu.
Sreeraj CR, Hussna N, Sen A, Mol VPL. 2024. First report of Mugilogobius rambaiae (Smith, 1945) (Family: Gobiidae) from India along with geographical expansion of two goby fishes from Kerala. Discover Oceans 1 (12): 1-11. DOI: 10.1007/s44289-024-00016-7.
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.
Tapilatu RF, Tururaja TS, Sipriyadi S, Kusuma AB. 2021. Molecular phylogeny reconstruction of grouper (Serranidae: Epinephelinae) at the northern part of Bird's Head Seascape-Papua inferred from COI Gene. Fish Aquat Sci 24 (5): 181-190. DOI: 10.47853/FAS.2021.e18.
Thomas PO, Frances MDG, Reeves RR, Kreb D, Ding W, Smith B, Malik MI, Ryan GE, Phay S. 2019. Electrofishing as a potential threat to freshwater cetaceans. Endanger Species Res 39: 207-220. DOI: 10.3354/esr00962.
Tumonggor MK, Karafet TM, Hallmark B, Lansing JS, Sudoyo H, Hammer MF, Cox MP. 2013. The Indonesian archipelago: An ancient genetic highway linking Asia and the Pacific. J Hum Genet 58: 165-173. DOI: 10.1038/jhg.2012.154.
Utama IV, Mandagi IF, Lawelle SA, Masengi KWA, Watanabe K, Sawada N, Nagano AJ, Kusumi J, Yamahira K. 2022. Deeply divergent freshwater fish species within a single river system in Central Sulawesi. Mol Phyl Evol 173: 107519. DOI: 10.1016/J.Ympev.2022.107519.
van der Laan R. 2018. Freshwater Fish List. 24th edition. Almere, The Netherlands.
van Steenis CGGJ. 1950. Flora Malesiana: Spermatophyta. Noordhoff-Kolff, Jakarta.
von Rintelen K, Arida E, Hauser C. 2017. A review of biodiversity-related issues and challenges in megadiverse Indonesia and other Southeast Asian countries. Res Ideas Outcomes J 3: e20860. DOI: 10.3897/Rio.3.E20860.
Voris HK. 2000. Maps of Pleistocene Sea levels in Southeast Asia: Shorelines, river systems and time durations. J Biogeogr 27 (5): 1153-1167. DOI: 10.1046/j.1365-2699.2000.00489.x.
Ward RD, Zemlak ST, Innes BH, Last PR, Hebert PDN. 2005. DNA barcoding Australia's fish species. Philos T Roy Soc B 360 (1462): 1847-1857. DOI: 10.1098/rstb.2005.1716.
Yulianto D, Indra I, Batubara AS, Fadli N, Nur FM, Rizal S, Siti-Azizah MN, Muchlisi ZA. 2020. Morphometrics and genetics variations of Mullets (Pisces: Mugilidae) from Aceh Waters, Indonesia. Biodiversitas 21 (8): 3422-3430. DOI: 10.13057/biodiv/ d210802.
Ziyadi MSF. 2024. DNA barcoding of seven cyprinid fish species in the Iraqi inland waters using mitochondrial COI gene sequence. Baghdad Sci J 21: 4067-4072. DOI: 10.21123/bsj.2024.9802.

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