Genetic Similarity of Commerson’s Anchovy across Segara Anakan Cilacap Assessed Using Randomly Amplified Polymorphic DNA (RAPD) Markers
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Abstract
Segara Anakan areas can be divided into three different regions according to their salinity. Salinity differences suggested that Commerson’s anchovy population in that area can be divided into three subpopulations due to genetic differences. Genetic differences among subpopulation can be assessed through a population genetic study using random amplified polymorphic DNA. This study aims to evaluate the genetic variation and differences of Commerson's anchovy (Stolephorus commersonnii) collected at three different water salinities in Segara Anakan estuary Cilacap Indonesia. Total genomic DNA was isolated using the Chelex method. Genetic diversity and differences were assessed using RAPD markers and were analyzed statistically using an analysis of molecular variance, as implemented in Arlequin software. The results showed that high genetic diversity was observed within the subpopulations. However, no significant genetic differences were observed among subpopulations which indicate genetic similarity. A high number of offspring are likely to cause high genetic variation within subpopulations. Adult and larvae migration is the cause of genetics similarity across Segara Anakan. Another impressive result is that water salinity did not affect the genetic characteristic of Commerson,s anchovy. Genetic similarity of Commerson’s anchovy indicates that Segara Anakan forms a single genetic conservation unit.
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Genetic Similarity of Commerson’s Anchovy across Segara Anakan Cilacap Assessed Using Randomly Amplified Polymorphic DNA (RAPD) Markers. (2021). Jurnal Biota, 7(1), 42-50. https://doi.org/10.19109/Biota.v7i1.7201
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How to Cite
Genetic Similarity of Commerson’s Anchovy across Segara Anakan Cilacap Assessed Using Randomly Amplified Polymorphic DNA (RAPD) Markers. (2021). Jurnal Biota, 7(1), 42-50. https://doi.org/10.19109/Biota.v7i1.7201
References
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Correa-Herrera, T., Barletta, M., Lima, A. R. A., Jimenez-Segura, L. F., & Arango-Sanchez, L. B. (2017). Spatial Distribution and Seasonality of Ichthyoplankton and Anthropogenic Debris in a River Delta in the Caribbean Sea. Journal of Fish Biology, 90(4), 1356-1387.
Damerau, M., Matschiner, M., Salzburger, W., & Hanel, R. (2012). Comparative Population Genetics of Seven Notothenioid Fish Species Reveals High Levels of Gene Flow Along Ocean Currents in the Southern Scotia Arc, Antarctica. Polar Biology, 35(7), 1073-1086.
Excoffier, L. & Lischer, H. E. (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), 564-67.
Froese, R. & Pauly, D., Editors. (2019). FishBase. World Wide Web electronic publication.www.fishbase.org, version (12/2019).
Gustiano, R., Oktaviani, T., Soelistiyowati, D. T., Kusmini, I. I., Wahyutomo, & Huwoyon, G. H. (2013). Analysis of Genotype Variation and Truss Morphometricof Three Populations of Snakehead Fish [Channa striata (Bloch, 1793]. Berita Biologi, 12(3), 325-333
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Hayuningtyas, E. P., & Kadarini, T. (2016). Keragaman Genotipe Tiga Generasi Ikan Rainbow Kurumoi (Melanotaenia parva) Hasil Domestikasi Berdasarkan RAPD. Jurnal Riset Akukultur, 11(2), 107-114.
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Kusmini, I. I., Gustiano, R., & Mulyasari. (2011). Genetic Characterization of Kelabau Fish (Osteochilus kelabau) from Several Locations in West Kalimantan Using RAPD (Random Amplified Polymorphism DNA) Method. Berita Biologi, 10(4), 449-454.
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Melian, C. J., Alonso, D., Allesina, S., Condit, R. S., & Etienne, R. S. (2012). Does Sex Speed Up Evolutionary Rate and Increase Biodiversity? PLoS Computational Biology, 8(3), e1002414.
Moore, C. S., Ruocchio, M. J., & Blakeslee, A. M. H. (2018). Distribution and Population Structure in the Naked Goby Gobiosoma Bosc (Perciformes: Gobiidae) Along a Salinity Gradient in Two Western Atlantic Estuaries. PeerJ, 6, e5380.
Muharam, E. G., Buwono, I. D., & Mulyani, Y. (2012). Analaisis Kekerabatan Ikan Mas Koi (Cyprinus carpio koi) dan Ikan Mas Majalaya (Cyprinus carpiocarpio) Menggunakan Metode RAPD. Jurnal Perikanan dan Kelautan, 3(3), 15-23.
Mulyadi, G. K., Buwono, I. D., & Subhan, U. (2017). Analisis Kekerabatan Genetik Hibrid Ikan Nilem (Osteochilus hasselti) dan Ikan Mas (Cyprinus carprio L) Mengunakan PCR-RAPD. Jurnal Perikanan dan Kelautan, 3(1), 42-47.
Nugroho, L. A., Piranti, A. S., & Sastranegara, M. H. (2020) Plankton Community and Water Quality During Maximum Tidal Range in Segara Anakan Cilacap. IOP Conf. Series: Earth and Environmental Science, 593, 012020.
Nuryanto, A., Dewi, R. E., & Pramono, H. (2019a). Genetic Homogeneity of Commerson's Anchovy (Stolephorus commersonnii) in Segara Anakan Cilacap Central Java Inferred from PCR-RFLP Marker. Biogenesis, 7(1), 14-23.
Nuryanto, A., Komalawati, N., & Sugiharto. (2019b). Genetic Diversity Assessment of Hemibagrus nemurus from Rivers in Java Island, Indonesia Using COI Gene. Biodiversitas, 20(9), 2707-2717.
Nuryanto, A., Pramono, H., & Sastranegara, Moh. H. (2017). Molecular Identification of Fish Larvae from East Plawangan of Segara Anakan, Cilacap, Central Java, Indonesia. Biosaintifika, 9(1), 33-40.
Nuryanto, A. & Sastranegara, M. H. (2013). Molecular Characterization of Polymesoda erosa (Solander, 1786) Inhabits Two Different Habitats. Bionatura-Jurnal Ilmu-ilmu Hayati dan Fisik, 15(3), 184-89.
Nuryanto, A. & Susanto, AH (2010). Genetic Variability of Polymesoda erosa Population in the Segara Anakan Cilacap. Biotropia, 17(1), 22-30.
Regmi, B., Douglas, M. R., Anthonysamy, W. J. B., Doglas, M. E., & Leberg, P. L. (2016). Salinity and Hydrological Barriers Have Little Influence on Genetic Structure of the Mosquitofish in a Coastal Landscape Shaped by Climate Change. Hidrobiologia, 777, 209-223.
Sari, A. K., Nuryanto, A. & Susanto, A. H. (2014). Karakterisasi Beberapa Strain Gurami (Osphronemus gouramy Lac.) menggunakan Marka RAPD. Scripta Biologica, 1(1), 113-16.
Sastragengara, M. H., Widyartini, D. S., Fitriana, I., & Rani,K. M. (2020). The Plankton Composition from the Lagoon to the Marine Entrance at the West Part of Segara Anakan Mangrove Ecosystem in Cilacap. IOP Conf. Series: Earth and Environmental Science, 550, 012021
Silva, G., Horne, J. B., & Castilho, R. (2014a). Anchovies Go North and West Without Losing Diversity: Post-Glacial Range Expansions in a Small Pelagic fish. Journal of Biogeography, 41(6), 1171-1182.
Silva, G., Lima F. P., Martel, P., & Castilho, R. (2014b). Thermal Adaptation and Clinal Mitochondrial DNA Variation of European Anchovy. Proceedings of the Royal Society B, 281, 20141093.
Sukumaran, S., Sebastian, W., Francis, K. X. & Gopalakrishnan, A. (2019). Contemporary and Historic Patterns of Intraspecific Diversity in Indian Anchovy, Stolephorus indicus, from Indian Peninsular waters. Genetica, 147(3-4), 259-67.
Suprastini, Ardli, E.R. & Nuryanto, A., 2014. Diversitas dan Distribusi Ikan di Segara Anakan Cilacap. Scripta Biologica, 1(2), 147-51.
Vinas, J., Sanz, N., Penarrubia, L., Araguas, R. M., Manin, J. L. G., Roldan, M. I., Pla, C. (2014). Genetic population structure of European anchovy in the Mediterranean Sea and the Northeast Atlantic Ocean using sequence analysis of the mitochondrial DNA control region. ICES Journal of Marine Science, 71(2), 391-97.
Walsh, P. S., Metzger, D. A. & Higuchi, R. (2013). Chelex 100 as a Medium for Simple Extraction of DNA for PCR-Based Typing from Forensic Material. Biotechniques, 54(3), 134-39.
Whitehead, A., Roach, J. L., Zhang, S., & Galvez, F. (2011). Genomic mechanisms of evolved physiological plasticity in killifish distributed along an environmental salinity gradient. PNAS, 108(15), 6193–6198.
Chandra, G., Saxena, A., & Barat, A. (2010). Genetic diversity of two riverine populations of Eutropiichthys vacha (Hamilton, 1822) using RAPD markers and implications for its conservation. Journal of Cell and Molecular Biology, 8(2), 77-85.
Correa-Herrera, T., Barletta, M., Lima, A. R. A., Jimenez-Segura, L. F., & Arango-Sanchez, L. B. (2017). Spatial Distribution and Seasonality of Ichthyoplankton and Anthropogenic Debris in a River Delta in the Caribbean Sea. Journal of Fish Biology, 90(4), 1356-1387.
Damerau, M., Matschiner, M., Salzburger, W., & Hanel, R. (2012). Comparative Population Genetics of Seven Notothenioid Fish Species Reveals High Levels of Gene Flow Along Ocean Currents in the Southern Scotia Arc, Antarctica. Polar Biology, 35(7), 1073-1086.
Excoffier, L. & Lischer, H. E. (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), 564-67.
Froese, R. & Pauly, D., Editors. (2019). FishBase. World Wide Web electronic publication.www.fishbase.org, version (12/2019).
Gustiano, R., Oktaviani, T., Soelistiyowati, D. T., Kusmini, I. I., Wahyutomo, & Huwoyon, G. H. (2013). Analysis of Genotype Variation and Truss Morphometricof Three Populations of Snakehead Fish [Channa striata (Bloch, 1793]. Berita Biologi, 12(3), 325-333
Hartl, D. L., & Clark, A. G. (1997). Principles of population genetics. 3rd ed. Sunderland: Sinauer Associates.
Hayuningtyas, E. P., & Kadarini, T. (2016). Keragaman Genotipe Tiga Generasi Ikan Rainbow Kurumoi (Melanotaenia parva) Hasil Domestikasi Berdasarkan RAPD. Jurnal Riset Akukultur, 11(2), 107-114.
Kristanto, A. H., Subagja, J., Cahyanti, W., & Arifin, O. Z. (2017). Evaluasi Variasi Fenotipe dan Genotipe Populasi Ikan Tambakan dari Kalimantan Tengah, Jawa Barat, dan Jambi dengan Truss Morfometrik dan Random Amplified Polymorphic DNA (RAPD). Jurnal Riset Akuakultur, 12(3), 203-211.
Kusmini, I. I., Gustiano, R., & Mulyasari. (2011). Genetic Characterization of Kelabau Fish (Osteochilus kelabau) from Several Locations in West Kalimantan Using RAPD (Random Amplified Polymorphism DNA) Method. Berita Biologi, 10(4), 449-454.
Kusmini,I. I., Gustiano, R., Radona, D., Prakoso, V. A., Putri, F. P., & Prihadi, T. H. (2016). Karakterisasi Fenotipe dan Genotipe Tiga Populasi Ikan Tengadak, Barbonymus schwanenfeldii. Jurnal Riset Akuakultur, 11(3), 2017-216.
Melian, C. J., Alonso, D., Allesina, S., Condit, R. S., & Etienne, R. S. (2012). Does Sex Speed Up Evolutionary Rate and Increase Biodiversity? PLoS Computational Biology, 8(3), e1002414.
Moore, C. S., Ruocchio, M. J., & Blakeslee, A. M. H. (2018). Distribution and Population Structure in the Naked Goby Gobiosoma Bosc (Perciformes: Gobiidae) Along a Salinity Gradient in Two Western Atlantic Estuaries. PeerJ, 6, e5380.
Muharam, E. G., Buwono, I. D., & Mulyani, Y. (2012). Analaisis Kekerabatan Ikan Mas Koi (Cyprinus carpio koi) dan Ikan Mas Majalaya (Cyprinus carpiocarpio) Menggunakan Metode RAPD. Jurnal Perikanan dan Kelautan, 3(3), 15-23.
Mulyadi, G. K., Buwono, I. D., & Subhan, U. (2017). Analisis Kekerabatan Genetik Hibrid Ikan Nilem (Osteochilus hasselti) dan Ikan Mas (Cyprinus carprio L) Mengunakan PCR-RAPD. Jurnal Perikanan dan Kelautan, 3(1), 42-47.
Nugroho, L. A., Piranti, A. S., & Sastranegara, M. H. (2020) Plankton Community and Water Quality During Maximum Tidal Range in Segara Anakan Cilacap. IOP Conf. Series: Earth and Environmental Science, 593, 012020.
Nuryanto, A., Dewi, R. E., & Pramono, H. (2019a). Genetic Homogeneity of Commerson's Anchovy (Stolephorus commersonnii) in Segara Anakan Cilacap Central Java Inferred from PCR-RFLP Marker. Biogenesis, 7(1), 14-23.
Nuryanto, A., Komalawati, N., & Sugiharto. (2019b). Genetic Diversity Assessment of Hemibagrus nemurus from Rivers in Java Island, Indonesia Using COI Gene. Biodiversitas, 20(9), 2707-2717.
Nuryanto, A., Pramono, H., & Sastranegara, Moh. H. (2017). Molecular Identification of Fish Larvae from East Plawangan of Segara Anakan, Cilacap, Central Java, Indonesia. Biosaintifika, 9(1), 33-40.
Nuryanto, A. & Sastranegara, M. H. (2013). Molecular Characterization of Polymesoda erosa (Solander, 1786) Inhabits Two Different Habitats. Bionatura-Jurnal Ilmu-ilmu Hayati dan Fisik, 15(3), 184-89.
Nuryanto, A. & Susanto, AH (2010). Genetic Variability of Polymesoda erosa Population in the Segara Anakan Cilacap. Biotropia, 17(1), 22-30.
Regmi, B., Douglas, M. R., Anthonysamy, W. J. B., Doglas, M. E., & Leberg, P. L. (2016). Salinity and Hydrological Barriers Have Little Influence on Genetic Structure of the Mosquitofish in a Coastal Landscape Shaped by Climate Change. Hidrobiologia, 777, 209-223.
Sari, A. K., Nuryanto, A. & Susanto, A. H. (2014). Karakterisasi Beberapa Strain Gurami (Osphronemus gouramy Lac.) menggunakan Marka RAPD. Scripta Biologica, 1(1), 113-16.
Sastragengara, M. H., Widyartini, D. S., Fitriana, I., & Rani,K. M. (2020). The Plankton Composition from the Lagoon to the Marine Entrance at the West Part of Segara Anakan Mangrove Ecosystem in Cilacap. IOP Conf. Series: Earth and Environmental Science, 550, 012021
Silva, G., Horne, J. B., & Castilho, R. (2014a). Anchovies Go North and West Without Losing Diversity: Post-Glacial Range Expansions in a Small Pelagic fish. Journal of Biogeography, 41(6), 1171-1182.
Silva, G., Lima F. P., Martel, P., & Castilho, R. (2014b). Thermal Adaptation and Clinal Mitochondrial DNA Variation of European Anchovy. Proceedings of the Royal Society B, 281, 20141093.
Sukumaran, S., Sebastian, W., Francis, K. X. & Gopalakrishnan, A. (2019). Contemporary and Historic Patterns of Intraspecific Diversity in Indian Anchovy, Stolephorus indicus, from Indian Peninsular waters. Genetica, 147(3-4), 259-67.
Suprastini, Ardli, E.R. & Nuryanto, A., 2014. Diversitas dan Distribusi Ikan di Segara Anakan Cilacap. Scripta Biologica, 1(2), 147-51.
Vinas, J., Sanz, N., Penarrubia, L., Araguas, R. M., Manin, J. L. G., Roldan, M. I., Pla, C. (2014). Genetic population structure of European anchovy in the Mediterranean Sea and the Northeast Atlantic Ocean using sequence analysis of the mitochondrial DNA control region. ICES Journal of Marine Science, 71(2), 391-97.
Walsh, P. S., Metzger, D. A. & Higuchi, R. (2013). Chelex 100 as a Medium for Simple Extraction of DNA for PCR-Based Typing from Forensic Material. Biotechniques, 54(3), 134-39.
Whitehead, A., Roach, J. L., Zhang, S., & Galvez, F. (2011). Genomic mechanisms of evolved physiological plasticity in killifish distributed along an environmental salinity gradient. PNAS, 108(15), 6193–6198.