Population Genetic of Kawakawa (Euthynnus affinis) in Sumatera Island

https://doi.org/10.22146/jfs.87578

Raymon Rahmanov Zedta(1*), Hawis H Maduppa(2), Neviaty Putri Zamani(3), Beginer Subhan(4), Lalu Mukhsin Iqbal Sani(5)

(1) Research Center for Conservation of Marine and Inland Water Resources, National Research and Innovation Agency (BRIN), Cibinong, West Java
(2) Faculty of Fisheries and Marine Science, IPB University, Bogor, West Java
(3) Faculty of Fisheries and Marine Science, IPB University, Bogor, West Java
(4) Faculty of Fisheries and Marine Science, IPB University, Bogor, West Java
(5) Faculty of Fisheries and Marine Science, IPB University, Bogor, West Java
(*) Corresponding Author

Abstract


Over the past five decades, there has been a growing trend in the capture of kawakawa (Euthynnus affinis), which, alongside its potential to support small-scale commercial fisheries, highlights its significance.However, there is inadequate data on this species for suitable management and conservation status. This study aimed to investigate the genetic diversity, population structure, and connectivity of the kawakawa in the three major fishing port in Sumatra, namely Belawan , Padang, and Lampung by using DNA mitochondria control region (d-loop) Sequence. In total, 78 sequences of kawakawa with an average size of 303 bp, we found 36 polymorphic sites and 56 haplotypes from all population were identified with DNA compatibility values of 97-100%. We found the genetic diversity values in Sumatera Island were high (h = 0.950; π = 0.034), with the highest genetic diversities value in Padang (h = 0.990; π = 0.082) and the lowest in Belawan (h = 0.929; π = 0.082). AMOVA and Fst analyses revealed no differentiation in each population (Fst = 0.005). The haplotype distribution and connectivity analyses showed genetic mixing among the three populations. This study showed a single stock at the study sites and suggests management measures at a regional level to maintain the population.

Keywords


Population structure; D-loop; artisanal

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References

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P., & Menezes, M. R. (2012). Low genetic variation suggest single stock of kawakawa Euthynnus affinis (Cantor, 1849) along the indian coast. Turkish Journal of Fisheries and Aquatic Sciences, 12(3), 555–564. https://doi.org/10.4194/1303-2712-V12_3_02 Kumar, G., Kunal, S. P., Menezes, M. R., & Meena, R. M. (2012). Single genetic stock of kawakawa Euthynnus affinis (Cantor, 1849) along the Indian coast inferred from sequence analyses of mitochondrial DNA D-loop region. Conservation Genetics, 13(4), 1119–1131. https://doi.org/10.1007/s10592-012-0359-5 Madduppa, H., Martaulina, R., Zairion, Z., Renjani, R. M., Kawaroe, M., Anggraini, N. P., Subhan, B., Verawati, I., & Sani, L. M. I. (2021). Genetic population subdivision of the blue swimming crab (Portunus pelagicus) across Indonesia inferred from mitochondrial DNA: Implication to sustainable fishery. PLOS ONE, 16(2), e0240951. https://doi.org/10.1371/JOURNAL.PONE.0240951 Marwayana O. N. (2015). Ekstraksi Asam Dioksiribonukleat (DNA) dari Sampel Jaringan Otot. Ocena, X(2), 1–9. Menezes, M. R., Ikeda, M., & Taniguchi, N. (2006). Genetic variation in skipjack tuna Katsuwonus pelamis (L.) using PCR-RFLP analysis of the mitochondrial DNA D-loop region. Journal of Fish Biology. https://doi.org/10.1111/j.0022-1112.2006.00993.x Nei, M. (1973). Analysis of gene diversity in subdivided populations. Proceedings of the National Academy of Sciences of the United States of America. https://doi.org/10.1073/pnas.70.12.3321 Nei, Masatoshi. (1987). Molecular Evolutionary Genetics. In Molecular Evolutionary Genetics. Columbia University Press. https://doi.org/10.7312/nei-92038 Ollé, J., Vilà-Valls, L., Alvarado-Bremer, J., Cerdenares, G., Duong, T. Y., Hajjej, G., Lino, P. G., Muñoz-Lechuga, R., Sow, F. N., Diaha, N. C., Araguas, R. M., Sanz, N., & Viñas, J. (2021). Population genetics meets phylogenetics: new insights into the relationships among members of the genus Euthynnus (family Scombridae): Euthynnus population genetics and phylogeny. Hydrobiologia, 849(1), 47–62. https://doi.org/10.1007/S10750-021-04707-6/FIGURES/4 Polzin, T., & Vahdati Daneshmand, S. (2003). On Steiner trees and minimum spanning trees in hypergraphs. Operations Research Letters, 31(1), 12–20. https://doi.org/10.1016/S0167-6377(02)00185-2 Rozas, J., Ferrer-Mata, A., Sanchez-DelBarrio, J. C., Guirao-Rico, S., Librado, P., Ramos-Onsins, S. E., & Sanchez-Gracia, A. (2017). DnaSP 6: DNA sequence polymorphism analysis of large data sets. Molecular Biology and Evolution, 34(12), 3299–3302. https://doi.org/10.1093/molbev/msx248 Sanger, F., Nicklen, S., & Coulson, A. R. (1977). DNA sequencing with chain-terminating inhibitors. Proceedings of the National Academy of Sciences of the United States of America, 74(12), 5463–5467. https://doi.org/10.1073/pnas.74.12.5463 Santos, M. D., Lopez, G. V., & Barut, N. C. (2010). A pilot study on the genetic variation of eastern little tuna (Euthynnus affinis) in Southeast Asia. Philippine Journal of Science, 139(1), 43–50. Tamura, K., Peterson, D., Peterson, N., Stecher, G., Nei, M., & Kumar, S. (2011). MEGA5: Molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Molecular Biology and Evolution, 28(10), 2731–2739. https://doi.org/10.1093/molbev/msr121 Tamura, K., Stecher, G., & Kumar, S. (2021). MEGA11: Molecular Evolutionary Genetics Analysis version 11. Molecular Biology and Evolution. https://doi.org/10.1093/molbev/msab120 Walsh, P. S., Metzger, D. A., & Higushi, R. (2013). Chelex 100 as a medium for simple extraction of DNA for PCR-based typing from forensic material. BioTechniques 10(4): 506-13 (April 1991). BioTechniques, 54(3), 134–139. https://doi.org/10.2144/000114018 Wernberg, T., Coleman, M. A., Bennett, S., Thomsen, M. S., Tuya, F., & Kelaher, B. P. (2018). Genetic diversity and kelp forest vulnerability to climatic stress. Scientific Reports 2018 8:1, 8(1), 1–8. https://doi.org/10.1038/s41598-018-20009-9 Zhang, Q., Sun, C., Zhu, Y., Xu, N., & Liu, H. (2020). Genetic diversity and structure of the round-tailed paradise fish (Macropodus ocellatus): Implications for population management. Global Ecology and Conservation, 21, e00876. https://doi.org/10.1016/J.GECCO.2019.E00876 Adams, N. L., Heyland, A., Rice, L. L., & Foltz, K. R. (2019). Procuring animals and culturing of eggs and embryos. Methods in Cell Biology, 150, 3–46. https://doi.org/10.1016/BS.MCB.2018.11.006 Amri, K., Nora, F. A., Ernaningsih, D., & Hidayat, T. (2018). Reproduction and Spawning Season of Kawakawa (Euthynnus Affinis) Based on Monsoon and SST Distribution in Indian Ocean South off Java-Nusa Tenggara. Bawal Widya Riset Perikanan Tangkap, 10(2), 155–167. Bandelt, H. J., Forster, P., & Röhl, A. (1999). Median-joining networks for inferring intraspecific phylogenies. Molecular Biology and Evolution, 16(1), 37–48. https://doi.org/10.1093/OXFORDJOURNALS.MOLBEV.A026036 Chen, W., Hong, W., Chen, S., Wang, Q., & Zhang, Q. (2014). Population genetic structure and demographic history of the mudskipper Boleophthalmus pectinirostris on the northwestern pacific coast. Environmental Biology of Fishes 2014 98:3, 98(3), 845–856. https://doi.org/10.1007/S10641-014-0320-1 Chiou, W. D., & Lee, L. K. (2004). Migration of kawakawa Euthynnus affinis in the waters near Taiwan. Fisheries Science, 70(5), 746–757. https://doi.org/10.1111/j.1444-2906.2004.00867.x Collette, B. B. (2001). Tunas (also, albacore, bonitos, mackerels, seerfishes, and wahoo). FAO Species Identification Guide for Fishery Purposes The Living Marine Resources of the Western Central Pacific. Collette, B. B., & Nauen, C. E. (1983). FAO Species Catalogue Vol . 2 Scombrids of the world an annotated and illustrated catalogue of Tunas, Mackerels, Bonitos and related species know to date. In FAO Fisheries Synopsis. https://doi.org/FAO Fish. Synop. 125(2) Delrieu-Trottin, E., Mona, S., Maynard, J., Neglia, V., Veuille, M., & Planes, S. (2017). Population expansions dominate demographic histories of endemic and widespread Pacific reef fishes. Scientific Reports 2017 7:1, 7(1), 1–13. https://doi.org/10.1038/srep40519 Excoffier, L., Smouse, P. E., & Quattro, J. M. (1992). Analysis of molecular variance inferred from metric distances among DNA haplotypes: Application to human mitochondrial DNA restriction data. Genetics, 131(2), 479–491. https://doi.org/10.5962/bhl.title.86657 Excoffier, Laurent, & 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(3), 564–567. https://doi.org/10.1111/j.1755-0998.2010.02847.x Fakhri, F., Narayani, I., & Mahardika, I. G. N. K. (2015). Genetic Diversity of Skipjack Tuna (Katsuwonus pelamis) From Jembrana and Karangasem Regencies, Bali. Jurnal Biologi, 19(1). http://garuda.ristekdikti.go.id/journal/article/366597 Forster, P., Torroni, A., Renfrew, C., & Röhl, A. (2001). Phylogenetic star contraction applied to Asian and Papuan mtDNA evolution. Molecular Biology and Evolution, 18(10), 1864–1881. https://doi.org/10.1093/OXFORDJOURNALS.MOLBEV.A003728 Frankham, R. (2005). Genetics and extinction. Biological Conservation, 126(2), 131–140. https://doi.org/10.1016/J.BIOCON.2005.05.002 Hidayat, T., Nugroho, T., & Chodrijah, U. (2018). Biologi Ikan Tongkol Komo (Euthynnus affinis) Di Laut Jawa. Journal of Tropical Fisheries Management, 2(1), 30–36. https://doi.org/10.29244/jppt.v2i1.25315 Hoban, S., Campbell, C. D., da Silva, J. M., Ekblom, R., Funk, W. C., Garner, B. A., Godoy, J. A., Kershaw, F., MacDonald, A. J., Mergeay, J., Minter, M., O’Brien, D., Vinas, I. P., Pearson, S. K., Pérez-Espona, S., Potter, K. M., Russo, I. R. M., Segelbacher, G., Vernesi, C., & Hunter, M. E. (2021). Genetic diversity is considered important but interpreted narrowly in country reports to the Convention on Biological Diversity: Current actions and indicators are insufficient. Biological Conservation, 261, 109233. https://doi.org/10.1016/J.BIOCON.2021.109233 Hosein, F. N., Austin, N., Maharaj, S., Johnson, W., Rostant, L., Ramdass, A. C., & Rampersad, S. N. (2017). Utility of DNA barcoding to identify rare endemic vascular plant species in Trinidad. Ecology and Evolution, 7(18), 7311–7333. https://doi.org/10.1002/ECE3.3220 IOTC. (2020). Report of the 10th Session of the IOTC Working Party on Neritic Tunas | IOTC. 10th Session of the IOTC Working Party on Neritic Tunas. https://iotc.org/documents/WPNT/10/RE Kasim, N. S., Jaafar, T. N. A. M., Piah, R. M., Mohd Arshaad, W., Mohd Nor, S. A., Habib, A., Abd. Ghaffar, M., Sung, Y. Y., Danish-Daniel, M., & Tan, M. P. (2020). Recent population expansion of longtail tuna Thunnus tonggol (Bleeker, 1851) inferred from the mitochondrial DNA markers. PeerJ, 8, e9679. https://doi.org/10.7717/PEERJ.9679/SUPP-1 Kumar, G., Kocour, M., & Kunal, S. P. (2016). Mitochondrial DNA variation and phylogenetic relationships among five tuna species based on sequencing of D-loop region. Mitochondrial DNA. Part A, DNA Mapping, Sequencing, and Analysis. https://doi.org/10.3109/19401736.2014.971313 Kumar, G., Kunal, S. P., & Menezes, M. R. (2012). Low genetic variation suggest single stock of kawakawa Euthynnus affinis (Cantor, 1849) along the indian coast. Turkish Journal of Fisheries and Aquatic Sciences, 12(3), 555–564. https://doi.org/10.4194/1303-2712-V12_3_02 Kumar, G., Kunal, S. P., Menezes, M. R., & Meena, R. M. (2012). Single genetic stock of kawakawa Euthynnus affinis (Cantor, 1849) along the Indian coast inferred from sequence analyses of mitochondrial DNA D-loop region. Conservation Genetics, 13(4), 1119–1131. https://doi.org/10.1007/s10592-012-0359-5 Madduppa, H., Martaulina, R., Zairion, Z., Renjani, R. M., Kawaroe, M., Anggraini, N. P., Subhan, B., Verawati, I., & Sani, L. M. I. (2021). Genetic population subdivision of the blue swimming crab (Portunus pelagicus) across Indonesia inferred from mitochondrial DNA: Implication to sustainable fishery. PLOS ONE, 16(2), e0240951. https://doi.org/10.1371/JOURNAL.PONE.0240951 Marwayana O. N. (2015). Ekstraksi Asam Dioksiribonukleat (DNA) dari Sampel Jaringan Otot. Ocena, X(2), 1–9. Menezes, M. R., Ikeda, M., & Taniguchi, N. (2006). Genetic variation in skipjack tuna Katsuwonus pelamis (L.) using PCR-RFLP analysis of the mitochondrial DNA D-loop region. Journal of Fish Biology. https://doi.org/10.1111/j.0022-1112.2006.00993.x Nei, M. (1973). Analysis of gene diversity in subdivided populations. Proceedings of the National Academy of Sciences of the United States of America. https://doi.org/10.1073/pnas.70.12.3321 Nei, Masatoshi. (1987). Molecular Evolutionary Genetics. In Molecular Evolutionary Genetics. Columbia University Press. https://doi.org/10.7312/nei-92038 Ollé, J., Vilà-Valls, L., Alvarado-Bremer, J., Cerdenares, G., Duong, T. Y., Hajjej, G., Lino, P. G., Muñoz-Lechuga, R., Sow, F. N., Diaha, N. C., Araguas, R. M., Sanz, N., & Viñas, J. (2021). Population genetics meets phylogenetics: new insights into the relationships among members of the genus Euthynnus (family Scombridae): Euthynnus population genetics and phylogeny. Hydrobiologia, 849(1), 47–62. https://doi.org/10.1007/S10750-021-04707-6/FIGURES/4 Polzin, T., & Vahdati Daneshmand, S. (2003). On Steiner trees and minimum spanning trees in hypergraphs. Operations Research Letters, 31(1), 12–20. https://doi.org/10.1016/S0167-6377(02)00185-2 Rozas, J., Ferrer-Mata, A., Sanchez-DelBarrio, J. C., Guirao-Rico, S., Librado, P., Ramos-Onsins, S. E., & Sanchez-Gracia, A. (2017). DnaSP 6: DNA sequence polymorphism analysis of large data sets. Molecular Biology and Evolution, 34(12), 3299–3302. https://doi.org/10.1093/molbev/msx248 Sanger, F., Nicklen, S., & Coulson, A. R. (1977). DNA sequencing with chain-terminating inhibitors. Proceedings of the National Academy of Sciences of the United States of America, 74(12), 5463–5467. https://doi.org/10.1073/pnas.74.12.5463 Santos, M. D., Lopez, G. V., & Barut, N. C. (2010). A pilot study on the genetic variation of eastern little tuna (Euthynnus affinis) in Southeast Asia. Philippine Journal of Science, 139(1), 43–50. Tamura, K., Peterson, D., Peterson, N., Stecher, G., Nei, M., & Kumar, S. (2011). MEGA5: Molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Molecular Biology and Evolution, 28(10), 2731–2739. https://doi.org/10.1093/molbev/msr121 Tamura, K., Stecher, G., & Kumar, S. (2021). MEGA11: Molecular Evolutionary Genetics Analysis version 11. Molecular Biology and Evolution. https://doi.org/10.1093/molbev/msab120 Walsh, P. S., Metzger, D. A., & Higushi, R. (2013). Chelex 100 as a medium for simple extraction of DNA for PCR-based typing from forensic material. BioTechniques 10(4): 506-13 (April 1991). BioTechniques, 54(3), 134–139. https://doi.org/10.2144/000114018 Wernberg, T., Coleman, M. A., Bennett, S., Thomsen, M. S., Tuya, F., & Kelaher, B. P. (2018). Genetic diversity and kelp forest vulnerability to climatic stress. Scientific Reports 2018 8:1, 8(1), 1–8. https://doi.org/10.1038/s41598-018-20009-9 Zhang, Q., Sun, C., Zhu, Y., Xu, N., & Liu, H. (2020). Genetic diversity and structure of the round-tailed paradise fish (Macropodus ocellatus): Implications for population management. Global Ecology and Conservation, 21, e00876. https://doi.org/10.1016/J.GECCO.2019.E00876



DOI: https://doi.org/10.22146/jfs.87578

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