UNCOVERING GENETIC PATTERNS OF THE BARRED MUDSKIPPER ALONG THE WEST COAST OF BENGKULU USING THE COI GENE
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ARTICLE HIGLIGHTS
- First genetic baseline for mudskipper in western Sumatra
- One shared lineage links Bengkulu to southern Java
- High connectivity along an open, shallow coastline
- Coastal tides and currents shape genetic patterns
- Findings support regional scale conservation planning
ABSTRACT
The barred mudskipper, Periophthalmus argentilineatus, is an amphibious gobiid fish that exhibits fully terrestrial behavior during low tides. Previous research has suggested the presence of cryptic species within this taxon, complicating species identification due to highly similar morphological traits. Despite its ecological importance in intertidal ecosystems, information on the genetic variation and population structure of P. argentilineatus in Sumatra remains limited, and no such data have been reported from the West Coast of Bengkulu. Therefore, this study aimed to assess the genetic diversity and population structure of P. argentilineatus along this coastline using the mitochondrial COI gene. A total of 30 individuals were collected from three locations, i.e., Air Hitam Coast, Baai Mangrove Forest, and Teluk Sepang Coast. The COI gene was amplified (approximately 660 bp), and a final aligned fragment of 630 bp was used for genetic analyses. Phylogenetic reconstruction placed all Bengkulu samples within a single lineage corresponding to Clade C previously reported from southern Java. Clades A and B were not detected in the study area. Genetic distances among individuals ranged from 0.00 – 0.80%, indicating close relatedness within this lineage. Sequence analysis identified nine variable sites, including two parsimony-informative positions, resulting in nine haplotypes. Haplotype diversity was moderate (Hd = 0.708), whereas nucleotide diversity was low (π = 0.00182). Negative Tajima’s D values suggest recent demographic expansion or ongoing connectivity among populations. AMOVA and Fst analyses indicated low or undetectable genetic differentiation among sampling sites, consistent with substantial gene flow along the coastline. These findings establish a baseline genetic reference for P. argentilineatus in Bengkulu and contribute to understanding regional population connectivity along the western Indonesian coastline.
Abiaobo NO, Asuquo IE, Ejogu IN, James EJ. 2021. Ecology and evolutionary biology aspect of the biology of Periophthalamus barbarous (Mudskipper) from Jaja Creek, Niger Delta, Nigeria. Ecol Evol Biol 6(1):15–22. DOI: 10.11648/j.eeb.20210601.14
Aji KW, Arisuryanti T. 2021. Molecular identification of mudskipper fish (Periophthalmus spp.) from Baros Beach, Bantul, Yogyakarta. J Trop Biodivers Biotechnol 6(3):1–13. DOI: 10.22146/jtbb.66391
Arisuryanti T, Aji KW, Herawati H, Sari IP, Rha’ifa FA, Febriyanti D, Priyono DS. 2024. Cryptic diversity of barred mudskippers, Periophthalmus argentilineatus (Valenciennes, 1837), from the Southern Coast of Java and East Lombok, Indonesia inferred by COI mitochondrial gene. J Trop Biodivers Biotechnol 9(3):jtbb84328. DOI: 10.22146/jtbb.84328
Arisuryanti T, Firdaus NUN, Hakim L. 2020. Genetic characterization of striped snakehead (Channa striata Bloch, 1793) from Arut River, Central Kalimantan inferred from COI mitochondrial gene. AIP Conf Proc 2260(1):020001. Yogyakarta (ID): AIP Publishing LLC. DOI: 10.1063/5.0015905
Chanthran SSD, Lim PE, Li Y, Liao TY, Poong SW, Du J, …, Loh K-H. 2020. Genetic diversity and population structure of Terapon jarbua (Forskål, 1775) (Teleostei, Terapontidae) in Malaysian Waters. ZooKeys 911:139–160. DOI: 10.3897/zookeys.911.39222
Chen IS, Hong WS, Jang-Liaw NH, Shao KT. 2015. Population genetic structure of Boleophthalmus boddarti (Oxudercinae, Gobiidae) in the northwestern Pacific and the South China Sea. Hydrobiologia 762(1):85–98. DOI: 10.1007/s10750-015-2321-0
Corush JB, Lin C-H, Lee H-J, Chen C-A, Shiao J-C, Chou W-H. 2022.
Amphibious mudskipper populations are genetically connected along coastlines but differentiated across water gaps. J Biogeogr 49(3):655–669. DOI: 10.1111/jbi.14345
Darrib D, Taboada GL, Doallo R, Posada D. 2012. jModelTest 2: more models, new heuristics and parallel computing. Nat Methods 9(8):772. DOI: 10.1038/nmeth.2109
Febriyanti D, Aji KW, Priyono DS, Arisuryanti T. 2023. Genetic identification of two mudskipper species (Oxudercidae: Periophthalmus) from Kulon Progo, Special Region of Yogyakarta, Indonesia. J Trop Biodivers Biotechnol 8(2):78161. DOI: 10.22146/jtbb.78161
Gaffar S. 2020. Analisis sekuen mtDNA COI pari totol biru yang didaratkan di tempat pendaratan ikan Kota Tarakan. [Analysis of mtDNA COI sequences of the blue-spotted stingray landed at the fish landing site in Tarakan City]. J Harpodon Borneo 13(2):80–89. DOI: 10.35334/harpodon.v13i2.1835
Grant W, Bowen BW. 1998. Shallow population histories in deep evolutionary lineages of marine fishes: Insights from sardines and anchovies and lessons for conservation. J Hered 89:415–426. DOI: 10.1093/jhered/89.5.415
Hebert PD, Cywinska A, Ball SL, deWaard JR. 2003. Biological identifications through DNA barcodes. Biol Sci 270(1512):313–321. DOI: 10.1098/rspb.2002.2218
Kasim NS, Mat Jaafar TNA, Mat Piah R, Arshaad WM, Mohd Nor SA, Habib A, …, Tan MP. 2020. Recent population expansion of longtail tuna Thunnus tonggol (Bleeker, 1851) inferred from the mitochondrial DNA markers. PeerJ 8:e9679. DOI: 10.7717/peerj.9679
Kutschera U, Elliott JM. 2013. Do mudskippers and lungfishes elucidate the early evolution of four-limbed vertebrates?. Evol Educ Outreach 6:1-8. DOI: 10.1186/1936-6434-6-8
Liu Y, Zhang H, Zhang Y, Wang Z. 2025. Dynamics and drivers of tidal flat morphology in China. Nat Commun 16:2153. DOI: 10.1038/s41467-025-57525-4
Luo Y, Zhang Y, Cheng R, Li Q, Zhang Y, Li Y, Shen Y. 2023. Genetic diversity of Jinshaia sinensis (Cypriniformes, Balitoridae) distributed upstream of the Yangtze River. Fishes 8(2):75. DOI: 10.3390/fishes8020075
Lv J, Wu S, Zhang Y, Chen Y, Feng C, Yuan X, …, Lin X. 2014. Assessment of four DNA fragments (COI, 16S rDNA, ITS2, 12S rDNA) for species identification of the Ixodida (Acari: Ixodida). Parasit Vectors 7:1–11. DOI: 10.1186/1756-3305-7-93
Maddison WP, Maddison DR. 2019. Mesquite: A Modular System for Evolutionary Analysis. Version 3.6.1. [Internet]. Available from: http://www.mesquiteproject.org
Massimo G, Mario LM, Vincenzo C. 2009. Life style and genetic variation in teleosts: The case of pelagic (Aphia minuta) and benthic (Gobius niger) gobies (perciformes: gobiidae). Mar Biol 156:239–252. DOI: 10.1007/s00227-008-1078-9
Muhala V, Guimarães-Costa A, Bessa-Silva AR, Rabelo LP, Carneiro J, Macate IE, …, Sampaio I. 2024. Comparative mitochondrial genome brings insights to slight variation in gene proportion and large intergenic spacer and phylogenetic relationship of mudskipper species. Sci Rep 14(1):3358. DOI: 10.1038/s41598-024-52979-4
Murdy EO. 1989. A taxonomic revision and cladistic analysis of the oxudercine gobies (Gobiidae: Oxudercinae). Rec Aust Mus Suppl 11:1–93. DOI: 10.3853/j.0812-7387.11.1989.93
Peakall R, Smouse PE. 2012. GenAlEx 6.5: Genetic analysis in Excel. Population genetic software for teaching and research – An update. Bioinformatics 28(19):2537–2539. DOI: 10.1093/bioinformatics/bts460
Polgar G, Sacchetti A, Galli P. 2014. Phylogeography and demographic history of two widespread Indo-Pacific mudskippers (Gobiidae: Periophthalmus). Mar Biol 161:1325–1342. DOI: 10.1007/s00227-014-2414-0
Rambaut A. 2019. FigTree v 1.4.4. [Internet]. Available from: http://tree.bio.ed.ac. uk/software/figtree/
Restrepo-Arias MA, Zerpa-Catanho D, Martínez-Méndez N, Pérez-Pérez JE. 2025. Patterns of genetic diversity in five species across genus: A comparative analysis using conserved genes. J King Saud Univ Sci 37:102482. DOI: 10.1016/j.avrs.2025.100279
Rhaifa FA, Audrea DJ, Hakim L, Arisuryanti T. 2021. DNA barcode of barred mudskipper (Periophthalmus argentilineatus Valenciennes, 1837) from Tekolok Estuary (West Nusa Tenggara, Indonesia) and their phylogenetic relationship with other indonesian barred mudskippers. J Trop Biodivers Biotechnol 6(2):jtbb59702. DOI: 10.22146/jtbb.59702
Rozas J, Rerrer-Matta A, Sanchez-DelBarrio JC, Guirao-Rico S, Librado P, Ramos Onsins SE, Sanchez-Garcia A. 2017. DNA SP 6: DNA sequence polymorphism analysis of large data sets. Mol Biol Evol 13(12):3299–3302. DOI: 10.1093/molbev/msx248
Rumisha C, Ulotu ET, Mlay RM. 2024. Unveiling genetic diversity and connectivity of mudskippers in MPAs and NPAs along the Tanzanian Coastline. Reg Stud Mar Sci 77:103538. DOI: 10.1016/j.rsma.2023.103538
Satoh TP, Miya M, Mabuchi K, Nishida M. 2016. Structure and variation of mitochondrial genome of fishes. BMC Genomics 17:719. DOI: 10.186/s12864-016-3054-y
Shabrina FN, Wibowo K, Arisuryanti T. 2024. Cryptic diversity of mudskipper genus Boleophthalmus (Gobiiformes: Oxudercidae) from the north coast of East Java, Indonesia. Biodiversitas 25(1):412–420. DOI: 10.13057/biodiv/d250148
Soeprobowati TR, Aini N, Fitri M, Suwondo S. 2022. Species composition and distribution in the mangrove ecosystem in the City of Bengkulu. Water 14(22):3516. DOI: 10.3390/w14223516
Suchard MA, Lemey P, Baele G, Ayres DL, Drummond AJ, Rambaut A. 2018. Bayesian phylogenetic and phylodynamic data integration using BEAST 1.10. Virus Evol. 4:1–5. DOI: 10.1093/ve/vey016
Sunarni S, Maturbongs MR. 2016. Biodiversitas dan kelimpahan ikan gelodok (mudskipper) di daerah intertidal Pantai Payumb, Merauke [Biodiversity and abundance of mudskipper fish in the intertidal zone of Payumb Beach, Merauke]. Proceedings: National Seminar on Maritime Affairs and Small Islands Resources 1(1):125–131. Ternate (ID): Universitas Khairun.
Tamura K, Stecher G, Kumar S. 2021. MEGA11: Molecular Evolutionary Genetic Analysis Version 11. Mol Biol Evol 38(7):3022–3027. DOI: 10.1093/molbev/msab120
Tan MP, Gan HM, Nabilsyafiq MH, Mazlan AG, Mat Jaafar TNA, SitiAzizah MN, …, Sung YY. 2020. Genetic diversity of the Pearse’s mudskipper Periophthalmus novemradiatus (Perciformes: Gobiidae) and characterization of its complete mitochondrial genome. Thalassas Int J Mar Sci 36:103–113. DOI: 10.1007/s41208-019-00189-5
Tan MP, Sammogam R, Mohd Nur NF, Mohd Yusoff NIS, Mat Jaafar TNA, Mohd Nor SA, …, Megarajan S. 2022. Genetic polymorphism and phylogenetic relationships of the brushtooth lizardfish (Saurida undosquamis) based on mitochondrial DNA markers. Mar Biodivers 52:13. DOI: 10.1007/s12526-021-01250-4
Thacker CE. 2003. Molecular phylogeny of the gobioid fishes (Teleostei: Perciformes: Gobioidei). Mol Phylogenet Evol 26(3):354–368. DOI: 10.1016/S1055-7903(02)00361-5
Ward RD, Zemlak TS, Innes BH, Last PR, Hebert PDN. 2005. DNA barcoding Australia’s fish species. Philos Trans R Soc B Biol Sci 360(1462):1847–1857. DOI: 10.1098/rstb.2005.1716
Zhang Q, Hong W, Dai Q, Zhang J, Cai Y, Huang J. 1989. Studies on induced ovulation, embryonic development and larval rearing of the mudskipper (Boleophthalmus pectinirostris). Aquaculture 83:375–385. DOI: 10.1016/0044-8486(89)90048-3
Zou Z, Zhang J. 2020. Are synonymous mutations selectively neutral? Mol Biol Evol 37(1):1–8. DOI: 10.1093/molbev/msaa200
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