Determination of genetic diversity between natural and cultured populations of Common Dentex (Dentex dentex) fish in the East Aegean Sea

• Autorzy: Kayaci Ali , Can Mehmet Fatih , Güner Yusuf , Güleç Fartih

Identyfikatory

DOI

10.26881/oahs-2023.1.04

• Języki publikacji: EN

Abstrakty

EN

Common dentex (Dentex dentex) is a commercial species of fish that is a highly valuable food source living naturally near Mediterranean and Atlantic Coasts. Therefore, monitoring and maintaining common dentex habitats are of high importance. A total of 53 specimens were collected from 6 natural habitats (from the Eastern Aegean and from the Antalya coast, which is the closest coast to the Western Mediterranean), and one aquaculture facility in the Eastern Aegean Sea. The mitochondrial Cytochrome Oxidase I (COI) gene was used to detect a total of 26 haplotypes. Along with the COI gene sequence, real-time PCR and high-resolution melting analyses were performed as rapid and inexpensive alternatives. Sequence analysis showed that the highest haplotype diversity was obtained from the aquaculture facility in Karaburun and Antalya Locations, Turkey. Analysis of Molecular Variance (AMOVA)based on the haplotype frequencies resulted in 92.54% genetic variation within localities and 7.46% genetic variation between/among localities. The mean fixation index (Fst) was calculated as 0.0746 (p < 0.001). Genetic distances were primarily in collaboration with geographical distances and were efficiently confirmed by high resolution melting (HRM) analysis. The results will be valuable in monitoring and maintaining natural habitats as well as aquaculture facilities where common dentex are grown.

Słowa kluczowe

EN

mtDNA; common dentex; genetic diversity; Aegean Sea

• Wydawca: Institute of Oceanography University of Gdańsk
• Czasopismo: Oceanological and Hydrobiological Studies
• Rocznik: 2023
• Tom: Vol. 52, No. 1
• Strony: 52--67
• Opis fizyczny: Bibliogr. 50 poz., fot., map., rys., tab. wykr.

Twórcy

autor

Kayaci Ali

• Faculty of Marine Science and Technology, Iskenderun Technical University, İskenderun, Hatay, Türkiye

autor

Can Mehmet Fatih

• Faculty of Marine Science and Technology, Iskenderun Technical University, İskenderun, Hatay, Türkiye

autor

Güner Yusuf

• Aquaculture Department, Faculty of Fisheries, Ege University, İzmir, Türkiye

autor

Güleç Fartih

• Aquaculture Department, Faculty of Fisheries, Ege University, İzmir, Türkiye

Bibliografia

• [1]. Amir, S. A., Zhang, B., Masroor, R., Li, Y., Xue, D. X., Rashid, S., Ahmad, N., Mushtaq, S., Durand, J.-D., & Liu, J. (2022). Deeper in the blues: DNA barcoding of fishes from Pakistani coast of the Arabian Sea reveals overlooked genetic diversity. Marine Biodiversity, 52(4), 37. https://doi.org/10.1007/s12526-022-01272-6
• [2]. Bargelloni, L., Alarcon, J. A., Alvarez, M. C., Penzo, E., Magoulas, A., Reis, C., & Patarnello, T. (2003). Discord in the family Sparidae (Teleostei): Divergent phylogeographical patterns across the Atlantic-Mediterranean divide. Journal of Evolutionary Biology, 16(6), 1149-1158. https://doi.org/10.1046/j.1420-9101.2003.00620.x PMID:14640406
• [3]. Behrens-Chapuis, S., Malewski, T., Suchecka, E., Geiger, M. F., Herder, F., & Bogdanowicz, W. (2018). Discriminating European cyprinid specimens by barcode high-resolution melting analysis (Bar-HRM)-A cost efficient and faster way for specimen assignment? Fisheries Research, 204, 61-73. https://doi.org/10.1016/j.fishres.2018.02.007
• [4]. Bilecenoğlu, M., Kaya, M., Cihangir, B., & Çiçek, E. (2014). An updated checklist of the marine fishes of Turkey. Turkish Journal of Zoology, 38(6), 901-929. https://doi.org/10.3906/zoo-1405-60
• [5]. Bramandito, A., Subhan, B., Prartono, T. R. I., Anggraini, N. P., Januar, H. I., & Madduppa, H. H. (2018). Genetic diversity and population structure of Siganus fuscescens across urban reefs of Seribu Islands, Northern of Jakarta, Indonesia. Biodiversitas (Surakarta), 19(6), 1993-2002. https://doi.org/10.13057/biodiv/d190603
• [6]. Candan, A., Karatas, S., Kucuktas, H., & Okumus, I. (2007). Marine aquaculture in Turkey. Turkish Marine Research Foundation.
• [7]. Ceruso, M., Mascolo, C., De Luca, P., Venuti, I., Biffali, E., Ambrosio, R. L., Smaldone, G., Sordino, P., & Pepe, T. (2021). Dentex dentex Frauds: Establishment of a New DNA Barcoding Marker. Foods, 10(3), 580. https://doi.org/10.3390/foods10030580 PMID:33802000
• [8]. Ergüden, D. (2002). Investigation of the Genetic and Morphological Structure of Sea Bass (Dicentrarchus labrax L., 1758) in the Seas of Turkey, Mustafa Kemal University, Institute of Science and Technology, Department of Fishing and Processing Technology, Master Thesis, 2002. (In Turkish).
• [9]. Ergüden, D. (2006). Molecular Systematics of shad (Alosa spp.) seas. PhD Thesis, Çukurova University, Institute of Science and Technology, Department of Fisheries, Adana, 94 p. (In Turkish).
• [10]. Eroğlu, O., Çiftçi, Y., & Firidin, S. (2008). Identification of Sturgeon Species Distributed in the Turkish Coasts of the Black Sea by Mitochondrial DNA Sequence Analysis Method, Sturgeon Conservation Strategy and Production Workshop, 30-31 October 2008, Samsun. (In Turkish).
• [11]. Excoffier, L., & Lischer, H. E. L. (2010). Arlequin suite ver 3.5: A new series of programs to perform population genetics analyses under Linux and Windows. Molecular Ecology Resources, 10, 564-567. https://doi.org/10.1111/j.1755-0998.2010.02847.x PMID:21565059
• [12]. FAO. (2020). The state of Mediterranean and Black Sea fisheries 2020. General Fisheries Commission for the Mediterranean., https://doi.org/10.4060/cb2429en
• [13]. Fayazi, J., Rahimi, G., Moradi, M., Ashtyani, R., & Galledari, H. (2006). Genetic differentiation and phylogenetic relationships among Barbus xanthopterus (Cyprinidae) populations in southwest of Iran using mitochondrial DNA markers.
• [14]. Fernandes, T. J. R., Costa, J., Oliveira, M. B. P. P., & Mafra, I. (2017). DNA barcoding coupled to HRM analysis as a new and simple tool for the authentication of Gadidae fish species. Food Chemistry, 230, 49- 57. https://doi.org/10.1016/j.foodchem.2017.03.015
• [15]. FGM. (2018). Federation of greek maricultures: greek aquaculture outlook 2016. Annu Rep.
• [16]. Folmer, O., Black, M., Hoeh, W., Lutz, R., & Vrijenhoek, R. (1994). DNA primers for amplification of mitochondrial cytochrome c oxidase subunit I from diverse metazoan invertebrates. Molecular Marine Biology and Biotechnology, 3, 294-299. PMID:7881515.
• [17]. Freeland, J. (2005). Molecular Ecology. John Wiley & Sons, Ltd.
• [18]. Frimodt, C. (1995). Multilingual Illustrated Guide to the World’s Commercial Warmwater Fish. Fishing News Books, Osney Mead.
• [19]. GFCM. (2021) GFCM capture production (1970-2018). http://www.fao.org/gfcm/data/capture-production/en/
• [20]. Grant, W. S. (2005). A second look at mitochondrial DNA variability in European anchovy (Engraulis encrasicolus): Assessing models of population structure and the Black Sea isolation hypothesis. Genetica, 125, 293-309. https://doi.org/10.1007/s10709-005-0717-z
• [21]. Guerriero, G., Rabbito, D., Alwany, M. A., Madonna, A., Temraz, T. A., Sulaiman, O. O., Bassem, S. M., Trocchia, S., Abdel-Gawad, F. K., & Ciarcia, G. (2017). Fisheries and biodiversity along Mediterranean Sea: Italian and Egyptian coast overview. Euro-Mediterranean Journal for Environmental Integration, 2(1), 1-14. https://doi.org/10.1007/s41207-017-0027-8
• [22]. Hall, T. A. (1999). BioEdit: A User-Friendly Biological Sequence Alignment Editor and Analysis Program for Windows 95/98/NT. Nucleic Acids Symposium Series, 41, 95-98.
• [23]. Hanel, R., & Tsigenopoulos, C. S. Phylogeny, evolution and taxonomy of sparids with some notes on their ecology and biology. In: Pavlidis MA, Mylonas CC, editors. Sparidae. Wiley-Blackwell; 2011. p. 51-73. https://doi.org/10.1002/9781444392210.ch2
• [24]. Hanel, R., & Sturmbauer, C. (2000). Multiple recurrent evolution of trophic types in northeastern Atlantic and Mediterranean seabreams (Sparidae, Percoidei). Journal of Molecular Evolution, 50(3), 276-283. https://doi.org/10.1007/s002399910032 PMID:10754071
• [25]. Hebert, P. D. N., Ratnasingham, S., & deWaard, J. R. (2003). Barcoding animal life: Cytochrome c oxidase subunit 1 divergences among closely related species. Proceedings. Biological Sciences, 270(Suppl 1), S96-S99. PMID:12952648
• [26]. Hedrick, P. W. (2005). Genetics of Population. Jones & Bartlett Publishers London UK.
• [27]. Jobling, M. A., Hurles, M., & Tyler-Smith, C. (2004). Human Evolutionary Genetics: Origins. Peoples and Disease Garland Science Publishing.
• [28]. Keskın, E., & Atar, H. H. (2013). DNA barcoding commercially important fish species of Turkey. Molecular Ecology Resources, 13(5), 788-797. https://doi.org/10.1111/1755-0998.12120
• [29]. Kimura, M. (1980). A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. Journal of Molecular Evolution, 16(2), 111-120. https://doi.org/10.1007/BF01731581
• [30]. Lakra, W. S., Verma, M. S., Goswami, M., Lal, K. K., Mohindra, V., Punia, P., Gopalakrishnan, A., Singh, K. V., Ward, R. D., & Hebert, P. (2011). DNA barcoding Indian marine fishes. Molecular Ecology Resources, 11, 60-71. https://doi.org/10.1111/j.1755-0998.2010.02894.x
• [31]. Lakra, W. S., Singh, M., Goswami, M., Gopalakrishnan, A., Lal, K. K., Mohindra, V., Sarkar, U. K., Punia, P. P., Singh, K. V., Bhatt, J. P., & Ayyappan, S. (2016). DNA barcoding Indian freshwater fishes. Mitochondrial DNA. Part A, DNA Mapping, Sequencing, and Analysis, 27(6), 4510-4517. https://doi.org/10.3109/19401736.2015.1101540
• [32]. Lee, B. B., Schott, E. J., Behringer, D. C., Bojko, J., Kough, A., & Plough, L. V. (2020). Rapid genetic identification of the blue crab Callinectes sapidus and other Callinectes spp. using restriction enzyme digestion and High Resolution Melt (HRM) assays. Frontiers in Marine Science, 7, 633. https://doi.org/10.3389/fmars.2020.00633
• [33]. Marengo, M., Culioli, J.-M., Santoni, M.-C., Marchand, B., & Durieux, E. D. H. (2015). Comparative analysis of artisanal and recreational fisheries for Dentex dentex in a Marine Protected Area. Fisheries Management and Ecology, 22(3), 249-260. https://doi.org/10.1111/fme.12110
• [34]. Marengo, M., Durieux, E. D. H., Marchand, B., & Francour, P. (2014). A review of biology, fisheries and population structure of Dentex dentex (Sparidae). Reviews in Fish Biology and Fisheries, 24(4), 1065-1088. https://doi.org/10.1007/s11160-014-9363-9
• [35]. Mascolo, C., Ceruso, M., Palma, G., Anastasio, A., Pepe, T., & Sordino, P. (2018). The complete mitochondrial genome of the Pink dentex Dentex gibbosus (Perciformes: Sparidae). Mitochondrial DNA. Part B, Resources, 3(2), 525-526. https://doi.org/10.1080/23802359.2018.1467230
• [36]. Mytilineou, Ch., Akel, E. H. Kh., Babali, N., Balistreri, P., Bariche, M., Boyaci, Y. Ö., Cilenti, L., Constantinou, C., Crocetta, F., Çelik, M., Dereli, H., Dounas, C., Durucan, F., Garrido, A., Gerovasileiou, V., Kapiris, K., Kebapcioglu, T., Kleitou, P., Krystalas, A., Zenetos, A. (2016). New Mediterranean biodiversity records (November, 2016). Mediterranean Marine Science, 17, 794-821. https://doi.org/10.12681/mms.1976
• [37]. Nei, M. (1987). Molecular Evolutionary Genetics. Columbia University Press. https://doi.org/10.7312/nei-92038
• [38]. Nei, M., & Kumar, S. (2000). Molecular evolution and phylogenetics. Oxford University Press.
• [39]. Papaconstantinou, C. (2014). Fauna Graeciae: An updated checklist of the fishes in the Hellenic Seas. Hellenic Center for Marine Research (HCMR). Publishing.
• [40]. Parmaksız, A., & Eksi, E. (2017). Genetic diversity of the cyprinid fish Capoeta trutta (Heckel, 1843) populations from Euphrates and Tigris rivers in Turkey based on mtDNA COI sequences. Indian Journal of Fisheries, 64(1), 18-22. https://doi.org/10.21077/ijf.2017.64.1.62396-03
• [41]. Phillips, J. D., Gillis, D. J., & Hanner, R. H. (2019). Incomplete estimates of genetic diversity within species: Implications for DNA barcoding. Ecology and Evolution, 9(5), 2996-3010. https://doi.org/10.1002/ece3.4757
• [42]. Planes, S., & Fauvelot, C. (2002). Isolation by distance and vicariance drive genetic structure of a coral reef fish in the Pacific Ocean. Evolution; International Journal of Organic Evolution,56(2), 378-399.
• [43]. Rozas, J., Sánchez-DelBarrio, J. C., Messeguer, X., & Rozas, R. (2003). DnaSP, DNA polymorphism analyses by the coalescent and other methods. Bioinformatics (Oxford, England), 19(18), 2496-2497. https://doi.org/10.1093/bioinformatics/btg359
• [44]. Singer-Sam, J., Tanguay, R. L., & Riggs, A. (1989). Use of Chelex to improve the PCR signal from a small number of cells. Amplifications, 3, 11.
• [45]. Untergasser, A., Cutcutache, I., Koressaar, T., Ye, J., Faircloth, B. C., Remm, M., & Rozen, S. G. (2012, August). Primer3—New capabilities and interfaces. Nucleic Acids Research, 40(15), e115. https://doi.org/10.1093/nar/gks596
• [46]. Valente, L. M., Moutou, K. A., Conceicao, L. E., Engrola, S., Fernandes, J. M., & Johnston, I. A. (2013). What determines growth potential and juvenile quality of farmed fish species? Reviews in Aquaculture, 5, S168-S193. https://doi.org/10.1111/raq.12020
• [47]. Viret, A., Tsaparis, D., Tsigenopoulos, C. S., Berrebi, P., Sabatini, A., Arculeo, M., Fassatoui, C., Magoulas, A., Marengo, M., Morales-Nin, B., Caill-Milly, N., & Durieux, E. D. H. (2018). Absence of spatial genetic structure in common dentex (Dentex dentex Linnaeus, 1758) in the Mediterranean Sea as evidenced by nuclear and mitochondrial molecular markers. PLoS One, 13(9), e0203866. https://doi.org/10.1371/journal.pone.0203866
• [48]. Walsh, S., Blake, E., & Higuchi, R. (1989). PCR inhibition and bloodstains (abstract). Proceedings of the International Symposium on the Forensic Aspects of DNA Analysis. United States Government, Printing Office, Washington, DC.
• [49]. Ward, R. D., Zemlak, T. S., Innes, B. H., Last, P. R., & Hebert, P. D. N. (2005). DNA barcoding Australia’s fish species. Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences, 360, 1847-1857. https://doi.org/10.1098/rstb.2005.1716
• [50]. Zink, R. M., & Barrowclough, G. F. (2008). Mitochondrial DNA under siege in avian phylogeography. Molecular Ecology, 17, 2107-2121. https://doi.org/10.1111/j.1365-294X.2008.03737.x

Uwagi

Opracowanie rekordu ze środków MEiN, umowa nr SONP/SP/546092/2022 w ramach programu "Społeczna odpowiedzialność nauki" - moduł: Popularyzacja nauki i promocja sportu (2022-2023).