DNA BARCODING IN THE VALIDATION OF SCAD SPECIES IDENTIFICATION (GENUS: DECAPTERUS) IN AMBON
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Abstract
Limitations on the morphology-based identification system and the decreasing number of taxonomists have become a problem that requires a molecular approach toward the recognition and identification of species. DNA barcoding has been considered an efficient solution to solve a few of taxonomy’s problems. This research intended to identify several scads species which have been found in the waters surrounding Ambon morphologically and molecularly through DNA barcoding. Fish samples were collected from January to June 2018 at the Mardika fish market Ambon, and then brought to the Laboratory of the Maritime and Marine Science Centre of Excellence Pattimura University for further analysis. Based on morphological identification, six species of scad were discovered, being Decapterus macarellus, D. macarellus (suspected), D. macrosoma, D. macrosoma (suspected), D. russelli (suspected)and D. kurroides. Using DNA barcoding, only four species of scad were found, being D. macarellus, D. macrosoma, D. russelli and D. kurroides with identification percentage ranging from 99-100%. After validation, the species of scad which can be found in Ambon’s waters are D. macarellus, D. macrosoma, D. russelli and D. kurroides. DNA barcoding is a complementary alternative that can reinforce morphology-based identification quickly and accurately.
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References
Abdussamad, E. M., Prathibha, R., Koya, K. P., Koya, S., Mohamed, H., Jeyabalan, K. 2013. Carangids (Family: Carangidae) in seas around Indian subcontinent with description of macro-taxonomic character for the field identification of genera and species. Kerala-India: Central Marine Fisheries Research Institude.
Astarloa, J.M.D., Mabragaña, E., Hanner, R. 2008. Morphological and molecular evidence for a new species of longnose skate (Rajiformes: Rajidae: Dipturus) from Argentinean waters based on DNA barcoding. Zootaxa 1921, 35–46.Ausubel, F. M., Brent R., Kingston R.E., Moore D.D., Seidman J.G., Smith J.A., Struhl K. 2003. Current Protocols in Molecular Biology. Volume I. John Wiley and Sons, Inc., New York.
Barry, J., Newton, M., Dodd, J.A., Hooker, O.E., Boylan, P., Lucas, M.C., Adams, C.E. 2016. Foraging specialisms influence space use and movement patterns of the European eel Anguilla anguilla. Hydrobiologia 766:333–348
Blaxter, M., 2006. Will DNA barcoding advance efforts to conserve biodiversity more effeciently than traditional taxonomix methods? Reply. Frontiers in Ecology and the Environmental, 4(5), 272-272
Bohlke, J. E., Chaplin, C.C.G. 1993. Fishes of the bahamas and adjacent tropical waters. 2 ed. University of texas press, Austin.
Carpenter, K. E, Volker, H. N. 1999. The Living Marine Resources Of The Western Central Pacific. Volume 4. Bony fishes part 2 (Mugilidae to Carangidae). Department of Biological Sciences Old Dominion UniversityNorfolk, Virginia, USA dan Marine Resources Service Species Identification dan Data Programme FAO Fisheries Department. Rome: Food dan Agriculture Organisztion Of The United Nations.
Cayetano, B.J., Honebrink, R.R. 2000. A review of biology of the family Carangidae, with emphasis on species found in Hawaiian waters. DAR Technical Report 20-01. Department of Land and Natural Resources, Hawaii, 37 p.
Ciardo, D.E., Scha¨r, G., Bo¨ttger, E.C., Altwegg, M., Bosshard, P.P. 2006. Internal transcribed spacer sequencing versus biochemical profiling for identification of medically important yeasts. J Clin Microbiol 44, 77–84.
Costa, F.O., Carvalho, G. R. 2007. The Barcode of Life Initiative: synopsis and prospective societal impacts of DNA barcoding of Fish. Genomics Society and Policy, 3(2), 29–40.
Dahlan, M.A., Nur, M., Nessa, M., Omar, B.A.S., Tresnati, J., Burhanuddin, A.I. 2014. Morphometric and Meristic Comparison of Decapterus macrosoma Bleeker, 1851 From Makassar Strait and Bone Bay, South Sulawesi, Indonesia. International Journal of Plant, Animal and Environmental Science (IJAPES).
DeSalle, R. 2006. What’s in a character? J Biomed Inform 39:6-17
Felsenstein, J. 1985. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 39, 783-791.
Genisa A.S. 1998. Beberapa catatan tentang biologi ikan layang marga Decapterus. Jurnal Genisa. 23: 27-36.
Golani, D. 2006. “The Indian scad (Decapterus russelli), (Osteichthyes: Carangidae), a new Indo-Pacific fish invader of the eastern Mediterranean,” Scientia Marina, vol. 70, no. 4, pp. 603-605.
Hebert, P.D.N., Cywinska, A., Ball, S.L., deWaard, J.R. 2003a. Biological identifications through DNA barcodes. Proc. R. Soc. B 270, 313–321.
Hebert, P. D. N., Ratnasingham, S., de Ward, J. R. 2003b. Barcoding animal life: cytochrome c oxidase subunit 1 divergence among closely related spesies. Proc. R. Soc. B 270, S96-S99.
Hubert N, Meyer C.P., Bruggemann, H.J., Guerin, F., Komeno, R.J., Espiau, B., Causse, R., Williams, J.T., Planes, S. 2012. Cryptic diverity in Indo Pacific coraal-reef fishes revealed by DNA-barcoding provides new support to the centre-of-overlap hypothesis. PloS One 7 (3): e289287. DOI: 10.1371/journal.pone.0028987
Heemstra, P.C., Randall, J.E. 1993. Vol.16. Groupers of the world (Family Serranidae, Subfamily Epinephelinae). FAO Spcies Catalogue
Ivanova, N.V., Zemlak, T.S., Hanner, R.H., Hebert, P.D.N. 2007. Universal primer cocktails for fish DNA barcoding. Mol. Ecol. Notes 7, 544–548.
Kimura, M. 1980. A simple method for estimating evolutionary rates of base subtitutions through comparative studies of nucleotide sequence.J. Mol. Evol. 16, 111-120
Kumar, S., Stecher, G., Peterson, D., Filipski, A., Tamura, K. 2018. MEGA X: molecular evolutionary genetics analysis across computing platforms. Molecular Biology and Evolution. 35: 1547-1549.
Lagler, K.F., Bardach, J.E., Miller, R.R., Passino, D.R.M. 1977. Ichthyology. Wiley, New York.
Lahaye, R, Van der Bank, M., Bogarin, D., Warner, J., Pupulin, F., Gigot, G., Maurin, O., Duthoit, S., Barraclough, T.G., Savolainen, V. 2008. DNA barcoding the floras of biodiversity hotspots. Proc. Nat. Acad. Sci., 105(8): 2923-2928
Lakra, W.S., Goswami, M., Gopalakrishnan, A. 2009. Molecular identification and phylogenetic relationships of seven Indian Sciaenids (Pisces: perciformes, Sciaenidae) based on 16S rRNA and cytochrome oxidase subunit I mitochondrial genes. Molecular Biology Reports, 36, 831–839.
Limmon, G.V., Khouw, A.S., Loupatty, S.V., Rijoly, F., Pattikawa, J.A. 2017a. Species richness of reef food fishes in Ambon Island waters, Maluku Province, Indonesia. AACL Bioflux 10(3):507-511.
Limmon, G.V., Rijoly, F., Ongkers, O.T.S., Loupatty, S.R., Pattikawa, J.A. 2017b. Reef fish in the southern coastal waters of Ambon Island, Maluku Province, Indonesia. AACL Bioflux 10(2):234-240.
Muschick, M., Barluenga, M., Salzburger, W., Meyer, A. 2011. Adaptive phenotypic plasticity in the Midas cichlid fish pharyngeal jaw and its relevance in adaptive radiation. BMC Evol Biol 11:116
Norman, J.R. 1935. The -carangid fishes of the genus Decapterus Bleeker. Ann. Mag. nat. Hist., Ser. 10. 16: 252--264
Pe£nikar, Ž.F., Buzan, E.V. 2014. 20 year since the introduction of DNA barcoding: from theory to application. J. Appl. Genet. 55, 43-52
Packer, L., Gibbs, J., Sheffield, C., Hanner, R. 2009. DNA Barcoding dan The Mediocrity of Morphology. Molecular Ecology Resources (2009) 9 (Suppl. 1), 42–50
Radulovici, A.E., Archambault, P. Dufresne, F. 2010. DNA Barcodes for Marine Biodiversity: Moving Fast Forward? Diversity 2:450-472.
Ran, K., Li, Q., Qi, L., Li, W., Kong, L. 2020. DNA barcoding for identification of marine gastropod species from Hainan island, China. Fisheries Research 225 (2020)105504
Rijoly, F. 1987. “Analisa sistematika dan ekologi ikan tangkapan sampingan trawl di perairan Pantai Timur Kepulauan Aru”. Ambon: Fakultas Perikanan dan Ilmu Kelautan-Universitas Pattimura.
Rijoly, F., Natan, Y., Pattikawa, J.A., Ongkers, O.T.S., Uneputty, P.A. 2016 Community structure of fish in inner Ambon bay, Maluku, Indonesia. International Journal of Fisheries and Aquatic Studies 4(5):264-269.
Saitou, N., Nei, M. 1987. The neighbor-joining method: A new method for reconstructing phylogenetic trees. Molecular Biology and Evolution 4:406-425.
Sakinan, S, Orek, Y.A. 2011. First record of Indo-Pacific Indian scad fish, Decapterus russelli, on the north-eastern Mediterranean coast of Turkey. Marine Biodiversity Records 4, (14) 1-3.
Savolainen, V., Cowan, R.S., Vogler, A.P., Roderick, G.K, Lane, R. 2005. Towards writing the encyclopedia of life: an introduction to DNA barcoding. Philosophical Transactions of the Royal Society. 360: 1805–1811.
Sen, S., Shrinivas J., Jaiswar, A.K., Chakraborty, S.K., Sajina, A.M., Dash, G. R. 2011. Stock structure analysis of Decapterus russelli (Ruppell, 1830) from east and west coast of India using truss network analysis. Elsevier.
Song, H., Buhay, J.E., Whiting, M.F., Crandall, K.A. 2008. Many species in one: DNA barcoding overestimates the number of species when nuclear mitochondrial pseudo genes are coamplified. Proceedings of the National Academy of Sciences of the United states of America, 105, 13486-13491.
Steinke D., Prosser, S.W.J., Hebert, P.D.N. 2016. DNA Barcoding of Marine Metazoans. In: Bourlat S (ed), Marine Genomics. Methods in Molecular Biology, vol 1452. Humana Press, New York, NY.
Steinke, D., Zemlak, T.S., Hebert, P.D.N. 2009. Barcoding Nemo: DNA-Based identifications for the ornamental fish Trade. PLos ONE 4, e6300.