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Türkiye denizlerindeki Pomatomus saltatrix (Linnaeus, 1766)'in mikrosatelit DNA tabanlı popülasyon genetiği

Year 2025, Volume: 42 Issue: 2, 138 - 147, 15.06.2025

İlyas Kutlu , Zehra Duygu Düzgüneş , Şirin Firidin , Melike Alemdağ , Ayşe Cebeci , İbrahim Turan

https://doi.org/10.12714/egejfas.42.2.06

Abstract

Lüfer (Pomatomus saltatrix (Linnaeus, 1766)), ticari açıdan oldukça önemli ve göç eden bir yırtıcı balık türü olup, Türkiye kıyılarında bulunmaktadır. Buna rağmen, Türkiye'deki Lüfer popülasyonlarının genetik yapısı hakkında detaylı bir çalışma yapılmamıştır. Ülkelerin biyolojik çeşitliliğini korumak için doğal kaynaklarda bulunan genetik çeşitliliğin belirlenmesi gerekmektedir. Bu çalışmada, Türkiye'nin kıyı bölgelerindeki Lüfer popülasyon yapısını inceledik; Türkiye kıyılarındaki 14 bölgeden toplanan Lüfer örneklerini mikrosatelit DNA analizi yaparak tanımlamayı amaçladık. Mikrosatelit analizi için sekiz lokus (ELF 17, ELF 37, ELF 49, ELF 19, ELF 39, ELF 46, ELF 44, ELF 50) analiz edildi. Toplam 14 popülasyondan 433 örnek incelendi. Toplamda tüm popülasyonlarda ve tüm lokuslarda 207 alel ve 61 spesifik alel tanımlanmıştır. Gözlemlenen en yüksek (Ho) heterozigot değerler ELF 50 (Ho: 0,991) iken en düşük değer ELF 19'dur (Ho: 0,716). Beklenen en yüksek (He) heterozigot değerler ELF 39 (He: 0,952) iken en düşük değer ELF 50'dir (He: 0,518). Hardy-Weinberg analiz sonuçlarına göre tüm popülasyonlarda önemli bir sapma olduğu belirlenmiştir. Lüfer popülasyonları filogenetik soylarına göre temel koordinat analizi (PCoA) uygulanarak kümelendirildiğinde ilk üç eksen toplam genetik varyasyonun %94'ünü göstermektedir. En yüksek varyasyon değerleri ve öz değerler 3. eksende bulunmuştur. Analiz sonuçları incelendiğinde Mersin lüfer popülasyonunun diğer popülasyonlardan farklı olarak kümelendiği açıkça görülmektedir. Mantel testine göre genetik ve coğrafi mesafe arasında düşük bir korelasyon (R2 = 0,3061, P = 0,01) tespit edilmiştir. Sonuç olarak Tüm popülasyonlarda karışık bireylerin olduğu ve düşük genetik farklılaşma gözlenmiştir.

Keywords

Lüfer lokus mikrosatelit allel Fst

Ethical Statement

All experiments were carried out considering the ethical rules of the authorities, with the approval coded as 325.04.02-12 by the Ethical Committee of Animal Experiments of Central Fisheries Research Institute.

Supporting Institution

su ürünleri merkez araştırma enstitüsü müdürlüğü

Project Number

TAGEM/ HAYSÜD /Ü/20/A6/P3/1814).

Thanks

The authors would like to thank Assoc. Prof. Dr. iBRAHİM TURAN for his valuable contributions in writing the article

References

  • Akşiray, F. (1987). Pomatomidae. Turkish Marine Fishes and Identification Key. (Pomatomidae. Türkiye Deniz Balıkları ve Tayin Anahtarı). İstanbul Üniversitesi Rektörlüğü Yayınları, 370-372. (Istanbul University Rectorate Publications)( in Turkish).
  • Bal, H., Yanık, T., & Türker, D. (2018). Growth and reproductive characteristics of the bluefish Pomatomus saltatrix (Linnaeus, 1766) in the Marmara Sea. Ege Journal of Fisheries and Aquatic Sciences, 35(1), 95-101. https://doi.org/10.12714/egejfas.2018.35.1.15
  • Bal, H. (2015). The populations of living bluefish in Turkey seas investigation of morphologically and investigation some properties biological of South Marmara Sea population. Doctoral dissertation, Atatürk University, Erzurum. (in Turkish with English abstract).
  • Benjamini, Y., & Hochberg, Y. (1995). Controlling the false discovery rate: A practical and powerful approach to multiple testing. Journal of the Royal Statistical Society. Series B (Methodological), 57(1), 289–300. https://doi.org/10.1111/j.2517-6161.1995.tb02031.x
  • Briggs, J.C. (1960). Fishes of world-wide (circumtropical) distribution. Copeia, 3, 171-180. https://doi.org/10.2307/1439652
  • Chapuis, M.P., & Estoup, A. (2007). Microsatellite null alleles and estimation of population differentiation, Molecular Biology and Evolution, 24, 621-631. https://doi.org/10.1093/molbev/msl191
  • Dos Santos, S.M., Klopper, A.W., Oosthuizen, C.J., & Bloomer, P. (2008). Isolation and characterization of polymorphic tetranucleotide microsatellite loci in the pelagic perciform fish Pomatomus saltatrix (Linnaeus, 1766) from South Africa. Molecular Ecology Resources, 8(5), 1065–1067. https://doi.org/10.1111/j.1755-0998.2008.02156.x
  • 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, 479-491. https://doi.org/10.1093/genetics/131.2.479
  • Falush, D., Stephens, M., & Pritchard, P.J. (2003). Inference of population structure using multilocus genotype data: Linked loci and correlated allele frequencies. Genetics, 164, 1567 1587. https://doi.org/10.1093/genetics/164.4.1567
  • Glaubitz, J.C. (2004). Convert: A user‐friendly program to re-format diploid genotypic data for commonly used population genetic software packages, Molecular Ecology Notes, 4, 2, 309-310. https://doi.org/10.1111/j.1471-8286.2004.00597.x
  • Goudet, J. (1995). FSTAT (Version 1.2): A Computer Program to Calculate F-Statistics, Journal of Heredity, 86 (6), 485–486. https://doi.org/10.1093/oxfordjournals.jhered.a111627
  • Juanes, F., Hare, J.A., & Miskiewicz, A. G. (1996). Comparing early life history strategies of Pomatomus saltatrix: A global approach. Marine Freshwater Research, 47, 365-379. https://doi.org/10.1071/MF9960365
  • Kalinowski, S.T., & Taper, M.L. (2006). Maximum likelihood estimation of the frequency of null alleles at microsatellite loci. Conservation Genetics. 7(6), 991-995. https://doi.org/10.1007/s10592-006-9134-9
  • Kalinowski, S.T., Taper, M.L., & Marshall, T.C. (2007). Revising how the computer program CERVUS accommodates genotyping error ıncreases success in paternity assignment. Molecular Ecology, 16, 1099-1106. https://doi.org/10.1111/j.1365-294X.2007.03089.x
  • Liu, K., & Muse, S.W. 2005. PowerMarker: An Integrated analysis environment for genetic marker analysis. Bioinformatics, 21, 2128–2129. https://doi.org/10.1093/bioinformatics/bti282
  • Miralles, L., Juanes, F. & Garcia-Vazquez, E. (2014a). Interoceanic sex-biased migration in bluefish. Transactions of the American Fisheries Society, 143(5), 1308–1315. https://doi.org/10.1080/00028487.2014.935480
  • Miralles, L., Juanes, F., Pardiñas, A.F., & Garcia-Vazquez, E. (2014b). Paleoclimate shaped bluefish structure in the Northern Hemisphere, Fisheries, 39(12), 578 586. https://doi.org/10.1080/03632415.2014.976701
  • Miralles, L., Mrugala, A., Sanchez-Jerez, P., Juanes, F., & Garcia-Vazquez, E. (2016). Potential impact of Mediterranean aquaculture on the wild predatory bluefish. Marine and Coastal Fisheries, 8, 1, 92-99, https://doi.org/10.1080/19425120.2015.1125977
  • Mantel, N. (1967). The detection of disease clustering and a generalized regression approach, Cancer Research, 27, 209–220.
  • Pardiñas, A.F., Campo, D., Pola, I.G., Miralles, L., Juanes, F. & Garcia-Vazquez, E. (2010). Climate change and oceanic barriers: genetic differentiation in Pomatomus saltatrix (Pisces: Pomatomidae) in the North Atlantic Ocean and the Mediterranean Sea. Journal of Fish Biology, 77(8), 1993–1998. https://doi.org/10.1111/j.1095-8649.2010.02774.x
  • Reid, K, Hoareau, T.B., Graves, J.E., Potts, W.M., Dos Santos, S. M., Klopper, A.W., & Bloomer, P. (2016). Secondary contact and asymmetrical gene flow in a cosmopolitan marine fish across the Benguela upwelling zone. Heredity (Edinb). 117(5), 307-315. https://doi.org/10.1038/hdy.2016.51
  • Raymond, M. & Rousset, F. (1995). GENEPOP (Version 1.2): Population genetics software for exact tests and ecumenicis. Journal of Heredity, 86(3), 248-249. https://doi.org/10.1093/oxford journals. jhered. a111573
  • Rousset, F. (2008). Genepop'007: A complete re-implementation of the genepop software for Windows and Linux. Molecular Ecology Resources, 8, 103-106. https://doi.org/10.1111/j.1471-8286.2007.01931.x
  • Taki, Y., Vincenot, C.E., Sato, Y., & Inoue-Murayama, M. (2021). Genetic diversity and population structure in the Ryukyu flying fox inferred from remote sampling in the Yaeyama archipelago. PLoS One, 16(3), e0248672. https://doi.org/10.1371/journal.pone.0248672
  • Türgan, G. (1959). About the biology of bluefish (Pomatomus saltatrix, L.). Hidrobiyoloji Mecmuası, İstanbul Üniversitesi Fen Fakültesi, Hidrobiyoloji Enstitüsü, 5(1-4), 144-184. (in Turkish)
  • Van der Elst, R. (1976). Gamefish of the east coast of southern Africa. 1. The biology of the elf, Pomatomus saltatrix (Linnaeus), in the coastal waters of Natal. Investigational Report Oceanographic Research Institute, South African Association of Marine Biological Research 44, 1-59.
  • Van Oosterhout, C., Hutchison, W.F., Wills, D.P.M. & Shipley, P. (2004). Micro-Checker: Software for identifying and correcting genotyping errors in microsatellite data. Molecular Ecology, 4(3), 535-538. https://doi.org/10.1111/j.1471-8286.2004.00684.x
  • Weir, B.S. & Cockerham, C. C. (1984). Estimating F-statistics for the analysis of population structure. Evolution, 38, 1358-1370. https://doi.org/10.2307/2408641
  • Wilk, S.J. (1977). Biological and fisheries data on bluefish, Pomatomus saltatrix. National Marine Fisheries Service, Sandy Hook Laboratory, Technical Series Report No. 11. USA.

Population genetics of Pomatomus saltatrix (Linnaeus, 1766) in the seas of Türkiye based on microsatellite DNA

Year 2025, Volume: 42 Issue: 2, 138 - 147, 15.06.2025

İlyas Kutlu , Zehra Duygu Düzgüneş , Şirin Firidin , Melike Alemdağ , Ayşe Cebeci , İbrahim Turan

https://doi.org/10.12714/egejfas.42.2.06

Abstract

Bluefish, (Pomatomus saltatrix (Linnaeus, 1766)) a commercially important and highly migratory predatory fish species, is found along the coasts of Türkiye. Despite it’s widespread presence along these coasts, there has been no detailed study on the genetic structure of bluefish populations in Türkiye. In order to protect the biological diversity of countries, the genetic diversity present in natural resources must be identified. In this study, we examined the population structure of bluefish in the coastal regions of Türkiye; We aimed to identify bluefish samples collected from 14 regions along Türkiye coast by analyzing microsatellit DNA. For the microsatellite analysis, eight loci (ELF 17, ELF 37, ELF 49, ELF 19, ELF 39, ELF 46, ELF 44, ELF 50) were analyzed. A total of 433 samples from 14 populations were studied. In total 207 alleles and 61 specific alleles were identified across all populations and all loci. The highest observed (Ho) heterozygous values are ELF 50 (Ho: 0,991) while the lowest value is ELF 19 (Ho: 0.716). The highest expected (He) heterozygous values are ELF 39 (He: 0.952) while the lowest value is ELF 50 (He: 0.518). According to the Hardy-Weinberg analysis results, it was determined that there was a significant deviation in all populations. When bluefish populations are clustered according to their phylogenetic lineages by applying principal coordinate analysis (PCoA), the first three axes show 94% of the total genetic variation. The highest variation values and eigenvalues were found on the 3rd axis. When the analysis results are examined, it is clearly seen that the Mersin bluefish population is clustered differently from other populations. According to the Mantel test, a low correlation (R2 = 0.3061, P = 0.01) was detected between genetic and geographical distance. Admixed individuals and low genetic differentiation were observed in all populations.

Keywords

Bluefish loci microsatellite allele Fst

Ethical Statement

All experiments were carried out considering the ethical rules of the authorities, with the approval coded as 325.04.02-12 by the Ethical Committee of Animal Experiments of Central Fisheries Research Institute.

Supporting Institution

The Republic of Türkiye Ministry of Agriculture and Forestry General Directorate of Agricultural Research and Policies Agricultural (Funding No: TAGEM/ HAYSÜD /Ü/20/A6/P3/1814).

Project Number

TAGEM/ HAYSÜD /Ü/20/A6/P3/1814).

References

  • Akşiray, F. (1987). Pomatomidae. Turkish Marine Fishes and Identification Key. (Pomatomidae. Türkiye Deniz Balıkları ve Tayin Anahtarı). İstanbul Üniversitesi Rektörlüğü Yayınları, 370-372. (Istanbul University Rectorate Publications)( in Turkish).
  • Bal, H., Yanık, T., & Türker, D. (2018). Growth and reproductive characteristics of the bluefish Pomatomus saltatrix (Linnaeus, 1766) in the Marmara Sea. Ege Journal of Fisheries and Aquatic Sciences, 35(1), 95-101. https://doi.org/10.12714/egejfas.2018.35.1.15
  • Bal, H. (2015). The populations of living bluefish in Turkey seas investigation of morphologically and investigation some properties biological of South Marmara Sea population. Doctoral dissertation, Atatürk University, Erzurum. (in Turkish with English abstract).
  • Benjamini, Y., & Hochberg, Y. (1995). Controlling the false discovery rate: A practical and powerful approach to multiple testing. Journal of the Royal Statistical Society. Series B (Methodological), 57(1), 289–300. https://doi.org/10.1111/j.2517-6161.1995.tb02031.x
  • Briggs, J.C. (1960). Fishes of world-wide (circumtropical) distribution. Copeia, 3, 171-180. https://doi.org/10.2307/1439652
  • Chapuis, M.P., & Estoup, A. (2007). Microsatellite null alleles and estimation of population differentiation, Molecular Biology and Evolution, 24, 621-631. https://doi.org/10.1093/molbev/msl191
  • Dos Santos, S.M., Klopper, A.W., Oosthuizen, C.J., & Bloomer, P. (2008). Isolation and characterization of polymorphic tetranucleotide microsatellite loci in the pelagic perciform fish Pomatomus saltatrix (Linnaeus, 1766) from South Africa. Molecular Ecology Resources, 8(5), 1065–1067. https://doi.org/10.1111/j.1755-0998.2008.02156.x
  • 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, 479-491. https://doi.org/10.1093/genetics/131.2.479
  • Falush, D., Stephens, M., & Pritchard, P.J. (2003). Inference of population structure using multilocus genotype data: Linked loci and correlated allele frequencies. Genetics, 164, 1567 1587. https://doi.org/10.1093/genetics/164.4.1567
  • Glaubitz, J.C. (2004). Convert: A user‐friendly program to re-format diploid genotypic data for commonly used population genetic software packages, Molecular Ecology Notes, 4, 2, 309-310. https://doi.org/10.1111/j.1471-8286.2004.00597.x
  • Goudet, J. (1995). FSTAT (Version 1.2): A Computer Program to Calculate F-Statistics, Journal of Heredity, 86 (6), 485–486. https://doi.org/10.1093/oxfordjournals.jhered.a111627
  • Juanes, F., Hare, J.A., & Miskiewicz, A. G. (1996). Comparing early life history strategies of Pomatomus saltatrix: A global approach. Marine Freshwater Research, 47, 365-379. https://doi.org/10.1071/MF9960365
  • Kalinowski, S.T., & Taper, M.L. (2006). Maximum likelihood estimation of the frequency of null alleles at microsatellite loci. Conservation Genetics. 7(6), 991-995. https://doi.org/10.1007/s10592-006-9134-9
  • Kalinowski, S.T., Taper, M.L., & Marshall, T.C. (2007). Revising how the computer program CERVUS accommodates genotyping error ıncreases success in paternity assignment. Molecular Ecology, 16, 1099-1106. https://doi.org/10.1111/j.1365-294X.2007.03089.x
  • Liu, K., & Muse, S.W. 2005. PowerMarker: An Integrated analysis environment for genetic marker analysis. Bioinformatics, 21, 2128–2129. https://doi.org/10.1093/bioinformatics/bti282
  • Miralles, L., Juanes, F. & Garcia-Vazquez, E. (2014a). Interoceanic sex-biased migration in bluefish. Transactions of the American Fisheries Society, 143(5), 1308–1315. https://doi.org/10.1080/00028487.2014.935480
  • Miralles, L., Juanes, F., Pardiñas, A.F., & Garcia-Vazquez, E. (2014b). Paleoclimate shaped bluefish structure in the Northern Hemisphere, Fisheries, 39(12), 578 586. https://doi.org/10.1080/03632415.2014.976701
  • Miralles, L., Mrugala, A., Sanchez-Jerez, P., Juanes, F., & Garcia-Vazquez, E. (2016). Potential impact of Mediterranean aquaculture on the wild predatory bluefish. Marine and Coastal Fisheries, 8, 1, 92-99, https://doi.org/10.1080/19425120.2015.1125977
  • Mantel, N. (1967). The detection of disease clustering and a generalized regression approach, Cancer Research, 27, 209–220.
  • Pardiñas, A.F., Campo, D., Pola, I.G., Miralles, L., Juanes, F. & Garcia-Vazquez, E. (2010). Climate change and oceanic barriers: genetic differentiation in Pomatomus saltatrix (Pisces: Pomatomidae) in the North Atlantic Ocean and the Mediterranean Sea. Journal of Fish Biology, 77(8), 1993–1998. https://doi.org/10.1111/j.1095-8649.2010.02774.x
  • Reid, K, Hoareau, T.B., Graves, J.E., Potts, W.M., Dos Santos, S. M., Klopper, A.W., & Bloomer, P. (2016). Secondary contact and asymmetrical gene flow in a cosmopolitan marine fish across the Benguela upwelling zone. Heredity (Edinb). 117(5), 307-315. https://doi.org/10.1038/hdy.2016.51
  • Raymond, M. & Rousset, F. (1995). GENEPOP (Version 1.2): Population genetics software for exact tests and ecumenicis. Journal of Heredity, 86(3), 248-249. https://doi.org/10.1093/oxford journals. jhered. a111573
  • Rousset, F. (2008). Genepop'007: A complete re-implementation of the genepop software for Windows and Linux. Molecular Ecology Resources, 8, 103-106. https://doi.org/10.1111/j.1471-8286.2007.01931.x
  • Taki, Y., Vincenot, C.E., Sato, Y., & Inoue-Murayama, M. (2021). Genetic diversity and population structure in the Ryukyu flying fox inferred from remote sampling in the Yaeyama archipelago. PLoS One, 16(3), e0248672. https://doi.org/10.1371/journal.pone.0248672
  • Türgan, G. (1959). About the biology of bluefish (Pomatomus saltatrix, L.). Hidrobiyoloji Mecmuası, İstanbul Üniversitesi Fen Fakültesi, Hidrobiyoloji Enstitüsü, 5(1-4), 144-184. (in Turkish)
  • Van der Elst, R. (1976). Gamefish of the east coast of southern Africa. 1. The biology of the elf, Pomatomus saltatrix (Linnaeus), in the coastal waters of Natal. Investigational Report Oceanographic Research Institute, South African Association of Marine Biological Research 44, 1-59.
  • Van Oosterhout, C., Hutchison, W.F., Wills, D.P.M. & Shipley, P. (2004). Micro-Checker: Software for identifying and correcting genotyping errors in microsatellite data. Molecular Ecology, 4(3), 535-538. https://doi.org/10.1111/j.1471-8286.2004.00684.x
  • Weir, B.S. & Cockerham, C. C. (1984). Estimating F-statistics for the analysis of population structure. Evolution, 38, 1358-1370. https://doi.org/10.2307/2408641
  • Wilk, S.J. (1977). Biological and fisheries data on bluefish, Pomatomus saltatrix. National Marine Fisheries Service, Sandy Hook Laboratory, Technical Series Report No. 11. USA.
There are 29 citations in total.

Details

Primary Language English
Subjects Fish Physiology and Genetics
Journal Section Articles
Authors

İlyas Kutlu 0000-0002-6679-8399

Zehra Duygu Düzgüneş 0000-0001-6243-4101

Şirin Firidin 0000-0002-2926-1576

Melike Alemdağ 0000-0001-7352-0574

Ayşe Cebeci 0000-0002-4288-8525

İbrahim Turan 0000-0003-3400-5494

Project Number TAGEM/ HAYSÜD /Ü/20/A6/P3/1814).
Early Pub Date June 14, 2025
Publication Date June 15, 2025
Submission Date December 25, 2024
Acceptance Date April 7, 2025
Published in Issue Year 2025 Volume: 42 Issue: 2

Cite

APA Kutlu, İ., Düzgüneş, Z. D., Firidin, Ş., … Alemdağ, M. (2025). Population genetics of Pomatomus saltatrix (Linnaeus, 1766) in the seas of Türkiye based on microsatellite DNA. Ege Journal of Fisheries and Aquatic Sciences, 42(2), 138-147. https://doi.org/10.12714/egejfas.42.2.06
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