* Corresponding Author
Genetic Identification of Two Mudskipper Species (Oxudercidae: Periophthalmus) from Kulon Progo, Special Region of Yogyakarta, Indonesia
https://doi.org/10.22146/jtbb.78161 Diana Febriyanti(1), Katon Waskito Aji(2), Dwi Sendi Priyono(3), Tuty Arisuryanti(4*)
(1) Laboratory of Genetics and Breeding, Faculty of Biology, Universitas Gadjah Mada, Jl. Teknika Selatan, Sekip Utara, Yogyakarta 55281
(2) Laboratory of Genetics and Breeding, Faculty of Biology, Universitas Gadjah Mada, Jl. Teknika Selatan, Sekip Utara, Yogyakarta 55281
(3) Laboratory of Animal Systematics, Faculty of Biology, Universitas Gadjah Mada, Jl. Teknika Selatan, Sekip Utara, Yogyakarta 55281
(4) Laboratory of Genetics and Breeding, Faculty of Biology, Universitas Gadjah Mada, Jl. Teknika Selatan, Sekip Utara, Yogyakarta 55281
(*) Corresponding Author
Abstract
Mudskippers are commonly cryptic species, making identification based solely on morphological characteristics challenging. This study used the DNA barcoding method to identify mudskipper species based on the COI mitochondrial gene. The analysis revealed two distinct species, P. kalolo (20 samples) and P. argentilineatus (3 samples) with high GC contents ranging from 42.94-45.2%. The genetic divergence analysis of P. kalolo showed that they divided into two clades, while P. argentilineatus is divided into three clades with two of the clades (C and D) still conspecific groups, and those two clades with clade E exhibit a genetic distance greater than 3.5%, suggesting the presence of cryptic species. These findings provide valuable insights into the intraspecies genetic diversity of mudskippers in Indonesia, which could have essential implications for conservation efforts and highlight the potential of DNA barcoding as a powerful tool for the identification of cryptic species. Further research combining molecular and morphological identification could lead to a more comprehensive understanding of species identification and help address the challenges posed by cryptic species.
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Aji, K.W. & Arisuryanti, T. 2021. Molecular identification of mudskipper fish (Periophthalmus spp.) from Baros Beach, Bantul, Yogyakarta. Journal of Tropical Biodiversity and Biotechnology, 6(3), jtbb66391. doi:10.22146/jtbb.66391
Aprilyanto, V. & Sembiring, L. 2016. Filogenetika Molekuler: Teori dan Aplikasi. Innosain.
Arisuryanti, T., Hasan, R.L., & Koentjana, J.P., 2018. Genetic identification of two mudskipper species (Pisces: Gobiidae) from Bogowonto Lagoon (Yogyakarta, Indonesia) using COI mitochondrial gene as a DNA barcoding marker. AIP Conference Proceedings, 2002, 020068. doi: 10.1063/1.5050164
Arisuryanti, T., Firdaus, N.U.N., Hakim, L., 2020. Genetic characterization of striped snakehead (Channa striata Bloch, 1793) from Arut River, Central Kalimantan inferred from COI mitochondrial gene. AIP Conference Proceedings, 2260, 020001. doi: 10.1063/5.0015905
Baeck, G.W., Takita, T. & Yoon, Y.H., 2008. Lifestyle of Korean mudskipper Periophthalmus magnuspinnatus with reference to a congeneric species Periophthalmus modestus. Ichthyological Research, 55, pp.43–52. doi: 10.1007/s10228-007-0009-y
Bingpeng, X. et al., 2018. DNA barcoding for identification of fish species in the Taiwan Strait. PloS one, 13(6), e0198109. doi: 10.1371/journal.pone.0198109
Chen, H., et al., 2014. Cryptic species and evolutionary history of the Boleophthalmus pectinirostris complex, along the northwestern Pacific coast. Acta Hydrobiologica Sinica, 38(1), pp.75-86. doi: 10.7541/2014.10
Dahruddin, H. et al., 2017. Revisiting the ichthyodiversity of Java and Bali through DNA barcodes: taxonomic coverage, identification accuracy, cryptic diversity and identification of exotic species. Molecular Ecology Resources, 17(2), pp.288-299. doi: 10.1111/1755-0998.12528
Darriba, D. et al., 2012. jModelTest 2: more models, new heuristics and parallel computing. Nature methods, 9(8), pp.772-772. doi:10.1038/nmeth.2109
Duggal, R. et al., 2020. Study of Variation in Nutrient Content of Mudskipper Boleopthalmus dussumieri Collected from Gujarat And Maharashtra State, India. Uttar Pradesh Journal of Zoology, 41(22), pp.24-30.
Froese, R. & Pauly, D., 2022, ‘FishBase’ in World Wide Web electronic publication, viewed 13 February 2022, from http://www.fishbase.org, version (08/2022).
García-De León, F.J. et al., 2018. Role of oceanography in shaping the genetic structure in the North Pacific hake Merluccius productus. PLoS One, 13(3), e0194646. doi: 10.1371/journal.pone.0194646
Hebert, P.D. et al., 2003a. Biological identifications through DNA barcodes. Proceedings of the Royal Society of London. Series B: Biological Sciences, 270(1512), pp.313-321. doi: 10.1098/rspb.2002.2218
Hebert, P.D., Ratnasingham, S, & Ward, JR. 2003b. Barcoding Animal Life: Cytochrome C Oxidase Subunit 1 Divergences among Closely Related Species. Proceedings of The Royal Society, 270, pp.96-99. doi: 10.1098/rsbl.2003.0025
Hidayat, S. et al., 2022, March. The Morphologies of Mudskipper Pelvic Fins in Relation to Terrestrial and Climbing Behaviour. In Proceedings of the Zoological Society, 75(1), pp.83-93. Springer India. doi: 10.1007/s12595-021-00422-1
Imtiaz, A. et al., 2017. Progress and potential of DNA barcoding for species identification of fish species. BIODIVERSITAS, 18(4), pp.1394-1405. doi: 10.13057/biodiv/d180415
Jaafar, Z. & Larson, H.K., 2008. A new species of mudskipper, Periophthalmus takita (Teleostei: Gobiidae: Oxudercinae), from Australia, with a key to the genus. Zoological Science, 25(9), pp.946-952. doi: 10.2108/zsj.25.946
Jaafar, Z. & Murdy E.O., 2017. Fishes Out of Water: Biology and Ecology of Mudskippers. CRC Press.
Jaafar, Z., Lim, K.K. & Chou, L.M., 2006. Taxonomical and morphological notes on two species of mudskippers, Periophthalmus walailakae and Periophthalmodon schlosseri (Teleostei: Gobiidae) from Singapore. Zoological Science, 23(11), pp.1043-1047. doi: 10.2108/zsj.23.1043
Jaafar, Z., Perrig, M. & Chou, L.M., 2009. Periophthalmus variabilis (Teleostei: Gobiidae: Oxudercinae), a valid species of mudskipper, and a re-diagnosis of Periophthalmus novemradiatus. Zoological Science, 26(4), pp.309-314. doi: 10.2108/zsj.26.309
Kombong, C.B.S. & Arisuryanti, T., 2018. The 16S and COI Mitochondrial DNA Nucleotide Composition of Stripped Snakehead (Channa striata Bloch, 1793) from Lake Sentani, Jayapura, Papua. UGM Journal of Fish, 20(2), pp.57-62. doi: 10.22146/jfs.35551
Kuang, T. et al., 2018. Phylogenomic analysis on the exceptionally diverse fish clade Gobioidei (Actinopterygii: Gobiiformes) and data-filtering based on molecular clocklikeness. Molecular Phylogenetics and Evolution, 128, pp.192-202. doi: 10.1016/j.ympev.2018.07.018
Kumar, S. et al., 2018. MEGA X: Molecular Evolutionary Genetics Analysis across Computing Platforms. Molecular Biology and Evolution, 35(6), pp.1547–1549. doi: 10.1093/molbev/msy096
Larson, H. K. 2008. Weber’s mudskipper Periophthalmus weberi: new record for the Daly River. Northern Territory Naturalist, 20, pp.19–21. doi: 10.5962/p.295507
Linh, N.M. et al., 2018. DNA barcoding application of mitochondrial COI gene to identify some fish species of family Gobiidae in Vietnam. Vietnam Journal of Marine Science and Technology, 18(4), pp.443-451. doi: 10.15625/1859-3097/13662
Maddison, W.P. & Maddison, D.R., 2021. Mesquite: a Modular System for Evolutionary Analysis, viewed 13 February 2023, from https://mesquiteproject.org.
Mahadevan, G. et al., 2021. Nutritional evaluation of elongate mudskipper Pseudapocryptes elongatus (Cuvier, 1816) from Diamond Harbor, West Bengal, India. Natural Product Research, 35(16), pp.2715-2721. doi: 10.1080/14786419.2019.1666388
McCraney, W.T., Thacker, C.E. & Alfaro, M.E., 2020. Supermatrix phylogeny resolves goby lineages and reveals unstable root of Gobiaria. Molecular phylogenetics and evolution, 151, 106862. doi: 10.1016/j.ympev.2020.106862
Miller, K.G. et al., 2005. The Phanerozoic record of global sea-level change. science, 310(5752), pp.1293-1298. doi: 10.1126/science.11164
Murdy, E.O., 1989. A taxonomic revision and cladistic analysis of the oxudercine gobies (Gobiidae: Oxudercinae). Records of the Australian Museum, Supplement, 11(August 1989), pp.1–93.
Nelson, J.S., Grande, T.C. & Wilson, M.V., 2016. Fishes of the World. John Wiley & Sons.
Polgar, G. & Bartolino, V., 2010. Size variation of six species of oxudercine gobies along the intertidal zone in a Malayan coastal swamp. Marine Ecology Progress Series, 409, pp.199–212. doi: 10.3354/meps08597
Polgar, G. & Crosa, G., 2009. Multivariate characterization of the habitats of seven species of Malayan mudskippers (Gobiidae: Oxudercinae). Marine Biology, 156, pp.1475–1486. doi: 10.1007/s00227-009-1187-0
Polgar, G. et al., 2014. Phylogeography and demographic history of two widespread Indo-Pacific mudskippers (Gobiidae: Periophthalmus). Molecular Phylogenetics and Evolution, 73, pp.161–176. doi: 10.1016/j.ympev.2014.01.014
Polgar, G., Sacchetti, A. & Galli, P., 2010. Differentiation and adaptive radiation of amphibious gobies (Gobiidae: Oxudercinae) in semi-terrestrial habitats. Journal of Fish Biology, 77, pp.1645–1664. doi: 10.1111/j.1095-8649.2010.02807.x
Pormansyah et al., 2019. A review of recent status on Mudskippers (Oxudercine Gobies) in Indonesian Waters. Oceanography and Fisheries, 9(4), 555769. doi: 10.19080/OFOAJ.2019.09.555769
Rha'ifa, F.A. et al., 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. Journal of Tropical Biodiversity and Biotechnology, 6(2), 59702. doi: 10.22146/jtbb.59702
Roesma, D.I. et al., 2020. Phylogenetic analysis of transparent gobies in three Sumatran lakes, Inferred from mitochondria Cytochrome Oxidase I (COI) gene. BIODIVERSITAS, 21(1), pp.43-48. doi: 10.13057/biodiv/d210107
Sachithanandam, V. et al., 2022. DNA barcode and phylogenetic analysis of Serranidae Fish (subfamily: Epinephelinae) from a Tropical Island Ecosystem of the Indian Ocean. Thalassas: An International Journal of Marine Sciences, 38, pp.843-853. doi.org/10.1007/s41208-022-00427-3
Sangur, K. et al., 2021. Mudskipper as an indicator species for lead, cadmium and cuprum heavy metal pollution in the Mangrove, Ambon, Indonesia. Journal of Ecological Engineering, 22(4), pp.1-9. doi: 10.12911/22998993/134077
Suchard, M.A. et al., 2018. Bayesian phylogenetic and phylodynamic data integration using BEAST 1.10. Virus Evolution, 4(1), vey016. doi: 10.1093/ve/vey016
Takita, T., Larson, H. K. & Ishimatsu, A., 2011. The natural history of mudskippers in northern Australia, with field identification characters. The Beagle, Records of the Museums and Art Galleries of the Northern Territory, 27, pp.189–204. doi: 10.5962/p.287482
Thacker, C.E., 2003. Molecular phylogeny of the gobioid fishes (Teleostei: Perciformes: Gobioidei). Molecular phylogenetics and evolution, 26(3), pp.354-368. doi: 10.1016/S1055-7903(02)00361-5
Triandiza, T. & Maduppa, H., 2018. Aplikasi Analisa Morfologi dan DNA Barcoding pada Penentuan Jenis Kepiting Porecelain (Pisidia sp.) yang Berasal dari Pulau Tunda, Banten. Jurnal Sumberdaya Akuatik Indopasifik, 2(2), pp.81-90.
Ude, G.N. et al., 2020. DNA barcoding for identification of fish species from freshwater in Enugu and Anambra States of Nigeria. Conservation Genetics Resources, 12, pp.643-658. doi: 10.1007/s12686-020-01155-7
Wang, Y. et al., 2021. DNA barcoding for identification of fishes in Xiangjiaba reservoir area in the downstream section of the Jinsha river. Conservation Genetics Resources, 13, pp.201-208. doi.org/10.1007/s12686-021-01196-6
Ward, R.D. et al., 2005. DNA barcoding Australia fish species. Philosophical Transactions of The Royal Society B, 360, pp.1847-1857. doi: 10.1098/rstb.2005.1716
Wu, R. et al., 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. Journal of Oceanology and Limnology, 36(5), pp.1753-1770. doi: 10.1007/s00343-018-7214-6
You, X. et al., 2018. Mudskippers and their genetic adaptations to an amphibious lifestyle. Animals, 8(2), 24. doi: 10.3390/ani8020024
Zemlak, T.S. et al., 2009. DNA barcoding reveals overlooked marine fishes. Moleculer Ecology Resources, 9, pp.237-242. doi: 10.1111/j.1755-0998.2009.02649.x
DOI: https://doi.org/10.22146/jtbb.78161
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