Molecular Identification of Mudskipper Fish (Periophthalmus spp.) from Baros Beach, Bantul, Yogyakarta

https://doi.org/10.22146/jtbb.66391

Katon Waskito Aji(1), Tuty Arisuryanti(2*)

(1) Laboratory of Genetics and Breeding, Faculty of Biology, Universitas Gadjah Mada
(2) Laboratory of Genetics and Breeding, Faculty of Biology, Universitas Gadjah Mada
(*) Corresponding Author

Abstract


Mudskipper fish is amphibious fish belonging to the family Gobiidae. Coastal communities widely consume mudskipper to meet their animal protein needs. Mudskipper is primarily cryptic species that are morphologically difficult to identify and distinguish from other mudskipper fish species. Consequently, it can be confused with the naming of mudskipper fish species and can affect the conservation efforts of the fish in their habitat. One of the molecular approaches that can be used to identify the fish species quickly and accurately is DNA barcoding using the COI mitochondrial gene. However, the research on the identification of mudskipper fish in Indonesia is still very limited. Therefore, this study aimed to identify 26 mudskipper fish from Baros Beach, Bantul, Yogyakarta, using COI mitochondrial gene as a molecular marker for DNA barcoding. The method used in this study was a PCR method with universal primers, FishF2 and FishR2. The data obtained were then analyzed using GeneStudio, DNASTAR, BLAST, Identification Engine, Mesquite, MEGAX, and BEAST. The analysis was conducted to obtain similarity, genetic distance and reconstruct a phylogenetic tree. The result revealed that all 26 samples of mudskippers collected from Baros Beach were identified in one genus, namely Periophthalmus, and consisted of 3 species, namely P. kalolo (16 samples), P. argentilineatus (9 samples), and P. novemradiatus (1 sample). Furthermore, this study also discovered a suspected cryptic species in P. argentilineatus with a genetic distance of 5.46-5.96% between clade E, F compared with clade G. Further morphological studies are needed to confirm the species status of these three clades before solidly proclaim that they are cryptic species.

 


Keywords


COI; cryptic species; DNA barcoding; mudskipper

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References

Andem, A.B. & Ekpo, P.B., 2014. Proximate and mineral compositions of mudskipper fish (Periophthalmus barbarus) in the mangrove swamp of Calabar River, southern Nigeria. The International Journal of Science and Technoledge, 2(2), pp.72-76.

Arisuryanti, T. et al., 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.

Arisuryanti, T. et al., 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.

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.

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.

Darriba, D. et al., 2012. jModelTest 2: more models, new heuristics and parallel computing. Nature methods, 9(8), pp.772-772.

Froese, R. et al., 2019. FishBase. in World Wide Web electronic publication, viewed 28 May 2021, from http://www.fishbase.org, version (12/2019).

Hebert, P.D. et al., 2003. Barcoding animal life: cytochrome c oxidase subunit 1 divergences among closely related species. Proceedings of the Royal Society of London. Series B: Biological Sciences, 270(suppl_1), pp.S96-S99.

Hogg, I.D. & Hebert, P.D., 2004. Biological identification of springtails (Hexapoda: Collembola) from the Canadian Arctic, using mitochondrial DNA barcodes. Canadian Journal of Zoology, 82(5), pp.749-754.

Huang, S. P. et al., 2016. The recognition and molecular phylogeny of Mugilogobius mertoni complex (Teleostei: Gobiidae), with description of a new cryptic species of M. flavomaculatus from Taiwan. Zoological Studies, 55, e39.

Hutama, A. et al., 2017. Identifying spatially concordant evolutionary significant units across multiple species through DNA barcodes: Application to the conservation genetics of the freshwater fishes of Java and Bali. Global Ecology and Conservation, 12, pp.170-187.

Kanejiya, J. et al., 2017. Nutrient content of three species of Mudskipper (Gobiidae; Oxudercinae) in Bhavnagar coast, Gujarat, India. Liver, 2, pp.2-5.

Kumar, S. et al., 2018. MEGA X: Molecular evolutionary genetics analysis across computing platforms. Molecular Biology and Evolution 35, pp.1547-1549.

Maddison, W. P. & Maddison, D. R., 2018. Mesquite: a modular system for evolutionary analysis. Evolution, 62, pp.1103-1118.

Mahadevan, G. et al., 2021. Nutritional evaluation of elongate mudskipper Pseudapocryptes elongatus (Cuvier, 1816) from Diamond Harbor, West Bengal, India. Natural Product Research, 35, pp.2715-2721.

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.

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.

Pormansyah et al., 2019. A review of recent status on Mudskippers (Oxudercine Gobies) in Indonesian Waters. Oceanography and Fisheries, 9(4), 555769.

Rambaut, A. 2019, ‘FigTree v 1.4.4.’ viewed 31 March 2021, from http://tree.bio.ed.ac.uk/software/figtree/.

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), jtbb.59702.

Suchard, M.A. et al., 2018. Bayesian phylogenetic and phylodynamic data integration using BEAST 1.10. Virus evolution, 4(1), vey016.

Thacker, C.E., 2003. Molecular phylogeny of the gobioid fishes (Teleostei: Perciformes: Gobioidei). Molecular Phylogenetics and Evolution, 26(3), pp.354-368.

Tornabene, L. et al., 2015. Support for a ‘Center of Origin’in the Coral Triangle: Cryptic diversity, recent speciation, and local endemism in a diverse lineage of reef fishes (Gobiidae: Eviota). Molecular Phylogenetics and Evolution, 82, pp.200-210.

Van Der Laan, R. et al., 2014. Family-group names of recent fishes. Zootaxa, 3882(1).

Vasil'eva, E.D. et al., 2016. Cryptic species of Ponto-Caspian bighead goby of the genus Ponticola (Gobiidae). Journal of Ichthyology, 56(1), pp.3-21.

Victor, B.C., 2010. The Redcheek Paradox: the mismatch between genetic and phenotypic divergence among deeply-divided mtDNA lineages in a coral-reef goby, with the description of two new cryptic species from the Caribbean Sea. Journal of the Ocean Science Foundation, 3(1), pp.1-16.

Victor, B.C., 2014. Three new endemic cryptic species revealed by DNA barcoding of the gobies of the Cayman Islands (Teleostei: Gobiidae). Journal of the Ocean Science Foundation, 12, pp.25-60.

Winterbottom, R. et al., 2014. A cornucopia of cryptic species-a DNA barcode analysis of the gobiid fish genus Trimma (Percomorpha, Gobiiformes). ZooKeys, 381, pp.79-111.

You, X. et al., 2014. Mudskipper genomes provide insights into the terrestrial adaptation of amphibious fishes. Nature Communications, 5(1), 5594.

You, X. et al., 2018. Mudskippers and their genetic adaptations to an amphibious lifestyle. Animals, 8(2), 24.

Zemlak, T.S. et al., 2009. DNA barcoding reveals overlooked marine fishes. Molecular Ecology Resources, 9, pp.237-242.

 



DOI: https://doi.org/10.22146/jtbb.66391

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