Phylogenetics and Molecular Divergence of Tilapia Fish (Oreochromis Species) Using Mitochondrial D-Loop and Cytochrome b Regions — Oak Academic Publishing
Research ArticleOpen AccessGoogle Scholar indexed
Phylogenetics and Molecular Divergence of Tilapia Fish (Oreochromis Species) Using Mitochondrial D-Loop and Cytochrome b Regions
Department of Genetics and Biotechnology, University of Calabar, Calabar, Nigeria
,
Department of Genetics and Biotechnology, University of Calabar, Calabar, Nigeria
,
Department of Genetics and Biotechnology, University of Calabar, Calabar, Nigeria
,
Department of Animal Breeding and Genetics, Federal University of Agriculture, Abeokuta, Nigeria
,
Department of Genetics and Biotechnology, University of Calabar, Calabar, Nigeria
,
Department of Genetics and Biotechnology, University of Calabar, Calabar, Nigeria
,
Department of Animal Breeding and Genetics, Federal University of Agriculture, Abeokuta, Nigeria
,
Department of Animal Breeding and Genetics, Federal University of Agriculture, Abeokuta, Nigeria
1 Department of Genetics and Biotechnology, University of Calabar, Calabar, Nigeria
2 Department of Genetics and Biotechnology, University of Calabar, Calabar, Nigeria
3 Department of Genetics and Biotechnology, University of Calabar, Calabar, Nigeria
4 Department of Animal Breeding and Genetics, Federal University of Agriculture, Abeokuta, Nigeria
5 Department of Genetics and Biotechnology, University of Calabar, Calabar, Nigeria
6 Department of Genetics and Biotechnology, University of Calabar, Calabar, Nigeria
7 Department of Animal Breeding and Genetics, Federal University of Agriculture, Abeokuta, Nigeria
8 Department of Animal Breeding and Genetics, Federal University of Agriculture, Abeokuta, Nigeria
Understanding the level of genetic diversity in any population is an important requisite towards strategizing measures for conservation and improvement of stocks. This study focused on the assessment of phylogenetics and molecular divergence of tilapia fish species obtained from two populations (Domita in South-South and Odeda in South-West, Nigeria) using the displacement loop (D-loop) and cytochrome b region of the mitochondrial deoxyribonucleic acid (mtDNA). A total of 28 samples (15 from South-South and 13 from South- West) were used for the genetic analysis. DNA was extracted from the tissue of all the samples using Quik-gDNA TM miniPrep kit. The D-loop containing the hypervariable region was sequenced for all samples from the two populations, while cytochrome b (Cyt b) region of mtDNA was only sequenced for samples from South-South population. Chromatograms of the sequences were viewed and edited using Bioedit software. Multiple sequence alignment was carried out using molecular evolutionary genetic analysis (MEGA) software before subsequent genetic analyses. Phylogenetic analysis grouped the samples into two clusters based on population. Also, when the two mitochondrial regions were pooled together, they clustered into two major groups based on mitochondrial regions. Analysis of molecular variance (AMOVA) revealed 37.32% variation within population and 62.68% variation among population with a significant fixation index of 0.627 (p < 0.05). The genetic distance inferred between D-loop regions of South-South and South-West populations was 0.243. Maternal lineage analysis revealed that the origin of tilapia fish from both populations could be traced to Oreochromis spirilus and Oreochromis leucostictus based on mitochondrial D-loop region. The findings of this study revealed molecular divergence among the tilapia populations and may serve as pivot information for the genetic improvement of this important species .
KeywordsPhylogeneticsMolecular DivergenceMaternal LineageTilapia Fish
Food and Agriculture Organization (2012) Cultured Aquatic Species Information Programme on Oreochromis niloticus. FAO Fisheries and Aquaculture Department, Rome.
Picker, M.D. and Griffiths, C.L. (2011) Alien and Invasive Animals: A South African Perspective. Randomhouse/Struik, Cape Town.
Agricultural Research Service (ARS), United States Department of Agriculture (USDA) (2009) Nutrient Data Release 22. http://www.ars.usda.gov/ba/bhnrc/ndl
Sparkpeople (2013). Food vs. Food. http://www.sparkpeople.com/
Oyakhilomen, O. and Zibah, R.G. (2013) Fishery Production and Economic Growth: Pathway for Sustainable Development. Journal of Sustainable Development, 15, 2.
Agbo, D.I. (2015) Bridging the Fish Demand, Supply Gap in Nigeria. Daily Trust Newspaper, 14 May.
De-Silva, M.P.K.S.K. (2015) Genetic Diversity of Genetically Improved Farmed Tilapia (GIFT) Broodstocks in Sri Lanka. International Journal of Scientific Research and Innovative Technology, 2, 66-76.
Hockaday, S., Beddow, T.A., Stone, M., Hancock, P. and Ross, L.G. (2000) Using Truss Networks to Estimate the Biomass of Oreochromis niloticus and to Investigate Shape Characters. Journal of Fish Biology, 57, 981-1000.
Samaradivakara, S.P., Hirimuthugoda, N.Y., Gunawardana, R.H.A.N.M., Illeperuma, R.J., Fernandopulle, N.D., De-Silva, A.D. and Alexander, P.A.B.D. (2012) Morphological Variation of Four Tilapia Populations in Selected Reservoirs in Sri Lanka. Tropical Agricultural Research, 23, 105-116.
Thompson, J.D. (1991) Phenotypic Plasticity as a Component of Evolutionary Change. Trends in Ecology and Evolution, 6, 246-249.
Wimberger, P.H. (1992) Plasticity of Fish Body Shape, the Effects of Diet, Development, Family and Age in Two Species of Geophagus (Pisces: Cichlidae). Biology Journal of Linnean Society, 45, 197-218.
Ikpeme, E.V., Ekerette, E.E., Udensi, O.U. and Ozoje, M.O. (2017) Assessment of Morphological Variation in Wild and Cultured Populations of Tilapia Fish (Oreochromis niloticus). Journal of Advances in Biology & Biotechnology, 13, 1-10.
Na-Nakorn, U. (2001) Genetic Differentiation of Fishes in the Genera, Clarias and Prophagorus in Thailand, Using Protein Electrophoresis and RAPD-PCR. In: Baimai, V. and Kumhom, R., Eds., BRT Research Reports, Biodiversity Research Training Program, Jirawat Express, Bangkok.
Jesslin, G., Sabaridasan, A., Edwinthahgam, P., Palanikani, R. and Soranam, R. (2013) Electrophoretic Studies on the Muscle Proteins of Three Species of Genus Puntius (Osteichthyes-Cyprinidae). International Journal of Research in Fisheries and Aquaculture, 2, 16-20.
Adeleke, M.A., Peters, S.O., Ozoje, M.O., Ikeobi, C.O.N., Adebambo, A.O., Olowofeso, O., Bamgbose, A.M. and Adebambo, O.A. (2013) A Preliminary Screening of Genetic Lineage of Nigerian Local Chickens Based on Blood Protein Polymorphisms. Animal Genetic Resources, 48, 23-28.
Wilson, A.C., Cann, R.L., Carr, S.M., George, M., Gyllensten, U.B., Helm-Bychowski, K.M., Higuchi, R.G., Palumbi, S.R. and Prager, E.M. (1985) Mitochondrial DNA and Two Perspectives on Evolutionary Genetics. Biological Journal of Linnean Society, 26, 375-400. https://doi.org/10.1111/j.1095-8312.1985.tb02048.x
Abdul, H.A.A., Zakirah, T., Nabilah, M.A., Nur, A.A., Muhd, D.D.A., Wong, L.L., Seah, Y.G., Tun, N.A.M.J., Abol, M.A.B., Awang, A.A.K. and Shahreza, M.S. (2015) Mitochondrial DNA Diversity of Terubok (Tenualosa toli) from Daro and Mukah, Sarawak Inferred by Partial Cytochrome b (Cyt-b). Journal of Fisheries and Aquatic Science, 10, 92-101. https://doi.org/10.3923/jfas.2015.92.101
Brown, J.R., Bechenbach, A.T. and Smith, M.J. (1993) Intraspecific DNA Sequence Variation of the Mitochondrial Control Region of White Sturgeon (Acipenser transmontanus). Molecular Biology and Evolution, 10, 326-341.
Meyer, A. (1993) Evolution of Mitochondrial DNA in Fishes. In: Mochachka, P.W. and Mommsen, T.P., Eds., Biochemistry and Molecular Biology of Fishes, Elsevier Press, New York.
Fajen, A. and Breden, F. (1992) Mitochondrial DNA Sequence Variation among Natural Populations of the Trinidad Gtppy, Poecilia reticulata. Evolution, 46, 1457-1465. https://doi.org/10.1111/j.1558-5646.1992.tb01136.x
Abdel-Hamid, Z.G., Heba, A.M., El-Kader, A., Aboelhassan, D.M. and Mahrous, K.F. (2014) Genetic Diversity in Egyptian Tilapia Species using PCR-RFLP of D-Loop Mitochondrial DNA Gene. Research Journal of Pharmaceutical, Biological and Chemical Sciences, 5, 469-475.
Agbebi, O.T., Echefu, C.J., Adeosun, I.O., Ajibade, A.H., Adegbite, E.A., Adebambo, A.O., Ilori, M.B., Durosaro, S.O. and Ajibike, A.B. (2016) Mitochondrial Diversity and Time Divergence of Commonly Cultured Cichlids in Nigeria. British Biotechnology Journal, 13, 1-7. https://doi.org/10.9734/BBJ/2016/25470
Fontana, F., Conterio, F., Gandolfi, G., Tagliavini, J., Rosenthal, H., Bronzi, P. and McKenzie, D.J. (2007) Mitochondrial DNA Sequences of 6 Sturgeon Species and Phylogenetic Relationships within Acipenseridae. Journal of Applied Ichthyology, 15, 17-22.
Bouza, C., Vilas, R. and Castro, J. (2008) Mitochondrial Haplotype Variability of Brown Trout Populations from North-Western Iberian Peninsula: A Secondary Contact Area between Lineages. Conservative Genetics, 9, 917-920. https://doi.org/10.1007/s10592-007-9398-8
Norfatimah, M.Y., Abdulah, M.N.S., Othman, A.S., Patimah, I. and Jamsari, A.F.J. (2009) Genetic Variation of Lates Calcarifer in Peninsular Malaysia Based on the Cytochrome B Gene. Aquaculture Research, 40, 1742-1749. https://doi.org/10.1111/j.1365-2109.2009.02279.x
Pereyra, S., Garcia, G., Miller, P., Oviedo, S. and Domingo, A. (2010) Low Genetic Diversity and Population Structure of the Narrownose Shark (Mustelus schmitti). Fisheries Research, 106, 468-473. https://doi.org/10.1016/j.fishres.2010.09.022
Tseng, M.C., Shiao, J.C. and Hung, Y.H. (2011) Genetic Identification of Thunnus orientalis, Thunnus thynnus and Thunnus maccoyii by a Cytochrome b Gene Analysis. Environmental Biology of Fishes, 91, 103-115. https://doi.org/10.1007/s10641-010-9764-0
Ajibike, A.B. (2016) Genetic Diversity of Nigerian Indigenous Chicken using Microsatellite Markers and Mitochondrial D-loopDNA Sequences. M. Agric. Dissertation, Department of Animal Breeding and Genetics, Federal University of Agriculture, Abeokuta.
Hall, T.A. (1999) Bioedit: A User Friendly Biological Sequence Alignment Editor and Analysis Program for Windows 95/98/NT. Nucleic Acid Symposium Series, 41, 95-98.
Tamura, K., Stecher, G., Peterson, D., Filipski, A. and Kumar, S. (2013) MEGA6: Molecular Evolutionary Genetics Analysis Version 6.0. Molecular Biology and Evolution, 30, 2725-2729. https://doi.org/10.1093/molbev/mst197
Excoffier, L., Guillaume, L. and Stefan, S. (2005) Arlequin. Version 3.0, an Integrated Software Package for Population Genetics Data Analysis. Evolutionary Bioinformatics Online, 1, 4750. https://doi.org/10.1177/117693430500100003
Habib, M., Lakra, W.S., Vindhya, M., Praveen, K., Barman, A.S., Akanksha, S., Kuldeep, K.L., Peyush, P. and Asif, A.K. (2010) Evaluation of Cytochrome b mtDNA Sequences in Genetic Diversity Studies of Channa marulius (Channidae: Perciformes). Molecular Biology Reports, 6, 41-49.
Chambers, J.K., Macdonald, L.E., Sarau, H.M., Ames, R.S., Freeman, K., Foley, J.J., Zhu, Y., McLaughlin, M.M., Murdock, P., McMillan, L., Trill, J., Swift, A., Aiyar, N., Taylor, P., Vawter, L., Naheed, S., Szekeres, P., Hervieu, G., Scott, C., Watson, J.M., Murphy, A., Duzic, E., Klein, C., Bergsma, D.J., Wilson, S. and Livi, P. (2000) AG Protein-Coupled Receptor for UDP-Glucose. Journal of Biological Chemistry, 15, 10767-10771. https://doi.org/10.1074/jbc.275.15.10767
Michu, E. (2007) A Short Guide to Phylogeny Reconstruction. Plant Soil and Environment, 53, 442-446.
Singh, N.S., Bijay, K.B. and Anil, P.S. (2013) Population Structure of Puntius sophore Inferred from Variation in Mitochondrial. International Journal of Research in Fisheries and Aquaculture, 3, 112-115.
Brahmane, M.P., Kundu, S.N., Das, M.K. and Sharma, A.P. (2013) Low Genetic Diversity and Absence of Population Differentiation of Hilsa (Tenualosa ilisha) Revealed by Mitochondrial DNA Cytochrome b Region in Ganga and Hooghly Rivers. African Journal of Biotechnology, 12, 3383-3389.
Masel, J. (2011) Genetic Drift. Current Biology, 21, R837-R838. https://doi.org/10.1016/j.cub.2011.08.007
Holsinger, K.E. and Bruce, S.W. (2009) Genetics in Geographically Structured Populations: Defining, Estimating and Interpreting Fixation Index (FST). Nature Reviews Genetics, 10, 639-650. https://doi.org/10.1038/nrg2611
Nei, M. (1987) Molecular Evolutionary Genetics. Columbia University Press, New York.
Rieseberg, L.H., Widmer, A., Arntz, A.M. and Burke, J.M. (2002) Directional Selection Is the Primary Cause of Phenotypic Diversification. Proceedings of National Academy of Science, 99, 12242-12245. https://doi.org/10.1073/pnas.192360899