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Panmictic stock structure of milkfish (Chanos chanos, Forsskål 1775) from Indian waters determined using mtDNA marker

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Abstract

Milkfish (Chanos chanos) belongs to the family Chanidae and it is a potential candidate species for aquaculture with the best biological characteristics. This study investigates the genetic diversity and population structure of C. chanos along the Indian coast using cytochrome b (cyt b) sequences of mitochondrial DNA (mtDNA). A total of 90 samples collected from five different locations across the Indian coast were sequenced for analysis using cyt b. The sequencing of a 1100-bp cyt b mtDNA fragment revealed the presence of 38 haplotypes with a haplotype diversity value of 0.835 and a nucleotide diversity value of 0.00400. The variation within and among populations accounted for about 97.33% and 2.67%, respectively. The fixation index analysis indicated that there is no significant genetic divergence among the populations from different geographical areas. Neighbour-joining tree analysis of the haplotype data showed no distinct patterns of phylogeographic structure. Results from this study indicated that there is a lack of genetic divergence between the populations of C. chanos along the Indian coast. The haplotype network showed star-like geneology which indicated the demographic expansion of the C. chanos population in these locations. The recent demographic expansion of the C. chanos population was also supported by the results of Tajima’s D statistics. Results from this study can be used for planning effective strategies for the conservation and management of the C. chanos population in the wild.

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References

  • Adiputra Y. T., Hsu T. H. and Gwo J. C. 2011 Genetic relationship of milkfish (Chanos chanos) from Indonesia, the Philippines and Taiwan using mitochondrial cytochrome b sequences: Genetic relationship of milkfish (Chanos chanos). J. Appl. Ichthyol. 27, 1100–1103.

    Article  Google Scholar 

  • Adiputra Y. T., Chuang J. L. and Gwo J. C. 2012 Genetic diversity of Indonesia milkfish (Chanos chanos) using amplified fragment length polymorphism (AFLP) analysis. Afr. J. Biotechnol. 11, 3055–3060.

    CAS  Google Scholar 

  • Ahmad W. and Naeem M. 2022 Genetic diversity in natural population of Notopterus notopterus evaluated through mitochondrial DNA marker ATPase 6/8 regions and cytochrome b gene. Mol. Biol. Rep. 49, 3903–3910.

    Article  PubMed  CAS  Google Scholar 

  • Akib N. A. M., Tam B., Phumee P., Muchlisin Z., Tamadoni S., Mather P. et al. 2015 High connectivity in Rastrelliger kanagurta: influence of historical signatures and migratory behaviour inferred from mtDNA Cytochrome b. PLoS One 10, e0119749.

    Article  PubMed  PubMed Central  Google Scholar 

  • Avise J. C. 2000 Phylogeography: The history and formation of species (https://doi.org/10.1668/0003-1569(2001)041[0134:BR]2.0.CO;2).

  • Avise J. C. 2004 Molecular markers, natural history, and evolution, 2nd edition. Sinauer Associates, Sunderland.

  • Bagarinao T. 1994 Systematics, distribution, genetics and life history of milkfish, Chanos chanos. Environ. Biol. Fishes 39, 23–41.

    Article  Google Scholar 

  • Begg G. A., Friedland K. D. and Pearce J. B. 1999 Stock identification and its role in stock assessment and fisheries management: an overview. Fish Res. 43, 1–8.

    Article  Google Scholar 

  • Billington N. and Hebert P. 1991 Mitochondrial DNA diversity in fishes and its implications for introductions. Can. J. Fish. Aquat. Sci. 48, 80–94.

    Article  Google Scholar 

  • Chang C.-H., Wang Y.-C. and Lee T.-H. 2021 Hypothermal stress-induced salinity-dependent oxidative stress and apoptosis in the livers of euryhaline milkfish, Chanos Chanos. Aquaculture 534, 736280.

    Article  CAS  Google Scholar 

  • Chauhan T. and Rajiv K. 2010 Molecular markers and their applications in fisheries and aquaculture. Adv. Biosci. Biotechnol. 01, 281–291.

    Article  CAS  Google Scholar 

  • Chauhan T., Lal K. K., Mohindra V., Singh R. K., Punia P., Gopalakrishnan A. et al. 2007 Evaluating genetic differentiation in wild populations of the Indian major carp, Cirrhinus mrigala (Hamilton–Buchanan, 1882): Evidence from allozyme and microsatellite markers. Aquaculture 269, 135–149.

    Article  CAS  Google Scholar 

  • Chenoweth S. F., Hughes J. M. and Connolly R. C. 2002 Phylogeography of the pipefish, Urocampus carinirostris, suggests secondary intergradation of ancient lineages. Mol. Biol. 141, 541–547.

    Google Scholar 

  • De Luca D., Catanese G., Procaccini G. and Fiorito G. 2014 An integration of historical records and genetic data to the assessment of global distribution and population structure in Octopus vulgaris. Front. Ecol. Evol. 2, 55.

    Google Scholar 

  • Excoffier L. and Lischer H. E. L. 2010 Arlequin suite ver 3.5: a new series of programs to perform population genetics analyses under Linux and Windows. Mol. Ecol. Res. 10, 564–567.

    Article  Google Scholar 

  • Excoffier L., Smouse P. E. and 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.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Farias I., Ortí G., Sampaio I., Schneider H. and Meyer A. 2001 The cytochrome b gene as a phylogenetic marker: The limits of resolution for analyzing relationships among cichlid fishes. J. Mol. Evol. 53, 89–103.

    Article  PubMed  CAS  Google Scholar 

  • Felsenstein J. 1985 Confidence limits on phylogenies: an approach using the bootstrap. Evolution 39, 783–791.

    Article  PubMed  Google Scholar 

  • Fernández M. V., Heras S., Maltagliati F., Turco A. and Ronald M. I. 2011 Genetic structure in the blue and red shrimp Aristeus antennatus and the role played by hydrographical and oceanographical barriers. Mar. Ecol. Prog. Ser. 421, 163–171.

    Article  Google Scholar 

  • Forster P., Torroni A., Renfrew C. and Röhl A. 2001 Phylogenetic star contraction applied to asian and papuan mtdna evolution. Mol. Biol. Evol. 18, 1864–1881.

    Article  PubMed  CAS  Google Scholar 

  • Grant W. S. and Bowen B. W. 1998 Shallow population histories in deep evolutionary lineages of marine fishes: Insights from sardines and anchovies and lessons for conservation. J. Hered. 89, 415–426.

    Article  Google Scholar 

  • Ha T. T. T., Nga T. T., Hang T. N. A. and Alam M. S. 2020 Genetic diversity in Pangasius spp. collected in Bangladesh based on mitochondrial cytochrome b gene sequence analysis. Aquac. Rep. 17, 100351.

    Article  Google Scholar 

  • Habib M., Lakra W. S., Mohindra V., Khare P., Barman A. S., Singh A. et al. 2011 Evaluation of cytochrome b mtDNA sequences in genetic diversity studies of Channa marulius (Channidae: Perciformes). Mol. Biol. Rep. 38, 841–846.

    Article  PubMed  CAS  Google Scholar 

  • Hackett S. J., Griffiths C. S., Bates J. M. and Klein N. K. 1995 Re: A commentary on the use of sequence data for phylogeny reconstruction. Mol. Phylogenet. Evol. 4, 350–356.

    Article  PubMed  CAS  Google Scholar 

  • Hall T. 1999 Bioedit: a user-friendly biological sequence alignment editor and analysis program for windows 95/98/ NT [WWW Document]. https://www.semanticscholar.org/paper/BIOEDIT%3A-A-USER-FRIENDLY-BIOLOGICAL-SEQUENCE-EDITOR-Hall/0ae262d9cf78536754bc064e07113ab5e978f208 (accessed 8.5.21).

  • Harpending H. C. 1994 Signature of ancient population growth in a low-resolution mitochondrial DNA mismatch distribution. Hum. Biol. 66, 591–600.

    PubMed  CAS  Google Scholar 

  • Harpending H. C., Sherry S. T., Rogers A. R. and Stoneking M. 1993 The genetic structure of ancient human populations. Curr. Anthropol. 34, 483–496.

    Article  Google Scholar 

  • Hartl D. L. and Clark A. G. 1997 Principles of population genetics, vol. 116. Sinauer Associates, Sunderland.

  • Kumar S., Stecher G. and Tamura K. 2016 MEGA7: molecular evolutionary genetics analysis version 7.0 for bigger datasets. Mol. Biol. Evol. 33, 1870–1874.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Kumar R., Pandey B. K., Sarkar U. K., Nagpure N. S., Baisva V. S., Agnihotri P. et al. 2017 Population genetic structure and geographic differentiation in butter catfish, Ompok bimaculatus, from Indian waters inferred by cytochrome b mitochondrial gene. Mitochondrial DNA Part DNA Mapp. Seq. Anal. 28, 442–450.

    CAS  Google Scholar 

  • Ladoukakis E. D. and Zouros E. 2017 Evolution and inheritance of animal mitochondrial DNA: rules and exceptions. J. Biol. Res.-Thessalon. 24, 2.

    Article  PubMed  PubMed Central  Google Scholar 

  • Lalitha R. and Chandavar V. R. 2018 Analysis of genetic diversity in cyt b and control region sequences of Melanochelys trijuga (Schweigger, 1812) from Karnataka. J. Asia-Pac. Biodivers. 11, 346–352.

    Article  Google Scholar 

  • Librado P. and Rozas J. 2009 DnaSP v5: a software for comprehensive analysis of DNA polymorphism data. Bioinforma. Oxf. Engl. 25, 1451–1452.

    Article  CAS  Google Scholar 

  • Lin L. S., Ying Y. P., Han Z. Q., Xiao Y. S. and Gao T. X. 2009 AFLP analysis on genetic diversity and population structure of small yellow croaker Larimichthys polyactis. Afr. J. Biotechnol. 8, 2700–2706.

    CAS  Google Scholar 

  • Liu S. V., Huang I.-H., Liu M.-Y., Lin H.-D., Wang F.-Y. and Liao T.-Y. 2015 Genetic Stock Structure of Terapon jarbua in Taiwanese Waters. Mar. Coast. Fish. 7, 464–473.

    Article  Google Scholar 

  • Lowe A, Harris S, Ashton P. 2004 Genetic diversity and differentiation – Ecological genetics: design, analysis, and application. pp. 50–105. Blackwell Publishing, Oxford.

  • Luhariya R. K., Lal K. K., Singh R. K., Mohindra V., Punia P., Chauhan U. K. et al. 2012 Genetic divergence in wild population of Labeo rohita (Hamilton, 1822) from nine Indian rivers, analyzed through MtDNA cytochrome b region. Mol. Biol. Rep. 39, 3659–3665.

    Article  PubMed  CAS  Google Scholar 

  • Mandal A., Mohindra V., Singh R. K., Punia P., Singh A. K. and Lal K. K. 2012 Mitochondrial DNA variation in natural populations of endangered Indian feather-back fish, Chitala chitala. Mol. Biol. Rep. 39, 1765–1775.

    Article  PubMed  CAS  Google Scholar 

  • Martinez F. S., Tseng M.-C. and Yeh S.-P. 2006 Milkfish (Chanos chanos) culture: situations and trends. J. Fish. Soc. Taiwan 33, 229–244.

    Google Scholar 

  • McGlashan D. J. and Hughes J. M. 2000 Reconciling patterns of genetic variation with stream structure, earth history and biology in the Australian freshwater fish Craterocephalus stercusmuscarum (Atherinidae). Mol. Ecol. 9, 1737–1752.

    Article  PubMed  CAS  Google Scholar 

  • Megarani D. V., Nugroho H. A., Andarini Z. P., Surbakti Y. D. R. B. R. and Widayanti R. 2020 Genetic characterization and phylogenetic study of Indonesian indigenous catfish based on mitochondrial cytochrome b gene. Vet. World 13, 96–103.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Miller S. A., Dykes D. D. and Polesky H. F. 1988 A simple salting out procedure for extracting DNA from human nucleated cells. Nucl. Acids Res. 16, 1215.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Nei S. and Kumar M. 2000 Molecular phylogenetics. Oxford University Press, New York.

  • Parmaksız A. 2021 Determination of genetic variations by using mitochondrial DNA cyt b sequences in populations of Carasobarbus luteus (Cyprinidae). Aqua Res. 4, 313–320.

    Article  Google Scholar 

  • Parson W., Pegoraro K., Niederstätter H., Föger M. and Steinlechner M. 2000 Species identification by means of cytochrome b gene. Int. J. Legal Med. 114, 23–28.

    Article  PubMed  CAS  Google Scholar 

  • Ramos-Onsins S. E. and Rozas J. 2002 Statistical properties of new neutrality tests against population growth. Mol. Biol. Evol. 19, 2092–2100.

    Article  PubMed  CAS  Google Scholar 

  • Rogers A. R. and Harpending H. 1992 Population growth makes waves in the distribution of pairwise genetic differences. Mol. Biol. Evol. 9, 552–569.

    PubMed  CAS  Google Scholar 

  • Ryman N. 1991 Conservation genetics considerations in fishery management. J. Fish Biol. 39, 211–224.

    Article  Google Scholar 

  • Saitou N. and Nei M. 1987 The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol. Biol. Evol. 4, 406–425.

    PubMed  CAS  Google Scholar 

  • Salzburger W., Ewing G. and von Haeseler A. 2011 The performance of phylogenetic algorithms in estimating haplotype genealogies with migration. Mol. Ecol. 20, 1952–1963.

    Article  PubMed  Google Scholar 

  • Santos B. S., Basiao Z. U. and Quilang J. P. 2019 Genetic diversity and patterns of demographic expansion in natural populations of milkfish, Chanos chanos (Forsskål, 1775), in the Philippines. Mitochondrial DNA Part A 30, 312–324.

    Article  CAS  Google Scholar 

  • Saraswat D., Lakra W. S., Nautiyal P., Goswami M., Shyamakant K. and Malakar A. 2014 Genetic characterization of Clupisoma garua (Hamilton 1822) from six Indian populations using mtDNA cytochrome b gene. Mitochondrial DNA 25, 70–77.

    Article  PubMed  CAS  Google Scholar 

  • Shaklee J. and Bentzen P. 1998 Genetic identification of stocks of marine fish and shellfish. Bull. Mar. Sci. 62, 589–621.

    Google Scholar 

  • Simonsen K. L., Churchill G. A. and Aquadro C. F. 1995 Properties of statistical tests of neutrality for DNA polymorphism data. Genetics 141, 413–429.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • SriHari M., Abidi Z. J. and Ayyathurai K. 2019 Lack of genetic differentiation in milkfish, Chanos chanos (Forsskål, 1775), revealed by mitochondrial ATPase 6/8 genes. Mitochondrial DNA Part A 30, 511–516.

    Article  CAS  Google Scholar 

  • Tajima F. 1989 Statistical method for testing the neutral mutation hypothesis by DNA polymorphism. Genetics 123, 585–595.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Timm J. and Kochzius M. 2008 Geological history and oceanography ofthe Indo-Malay Archipelago shape the genetic population structure in the False Clown Anemonefish (Amphiprion ocellar-is). Mol. Ecol. 17, 3999–4014.

    Article  PubMed  Google Scholar 

  • Tsaparis D., Lecocq T., Kyriakis D., Oikonomaki K., Fontaine P. and Tsigenopoulos C. S. 2022 Assessing genetic variation in wild and domesticated pikeperch populations: implications for conservation and fish farming. Animals 12, 1178.

    Article  PubMed  PubMed Central  Google Scholar 

  • Winans G. A. 1980 Geographic variation in milkfish Chanos chanos. I. Biochemical evidence. Evol. Int. J. Org. Evol. 34, 558–574.

    CAS  Google Scholar 

  • Yusuf M., Malik I., Subachri W., Ahyani N. and Yusuf C. 2014 Better management practices small scale fisheries guide series 776 “Milkfish Cultivation (Chanos chanos) on Environmentally Friendly Ponds”, pp. 38. WWF-Indonesia.

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Acknowledgements

The authors thank Dr Kuldeep K. Lal, Director, National Bureau of Fish Genetics Resources, Lucknow, for providing facilities and support. We are also grateful to Dr S. Suresh Kumar, Dean, Faculty of Ocean Science and Technology, Kochi, for his guidance and support. We express our gratitude to Dr SriHari, Associate Professor, Centurion University of Technology and Management, Odisha, for helping us to collect samples from various sites across India. We would also wish to show our gratitude to Dr Purushothaman P., Research scholar, PMFGR Centre, NBFGR, Kochi, for his technical and laboratory assistance.

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Authors and Affiliations

  1. Department of Ocean Science and Technology, Kerala University of Fisheries and Ocean Studies, Cochin, 682 018, India

    Divya Merin Jose

  2. Peninsular and Marine Fish Genetic Resources Centre, ICAR-NBFGR, CMFRI Campus, Cochin, 682 018, India

    Divya Merin Jose & P. R. Divya

  3. ICAR-National Bureau of Fish Genetic Resources, Canal Ring Road, P.O. Dilkusha, Lucknow, 226 002, India

    Kuldeep K. Lal

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  1. Divya Merin Jose
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Correspondence to Divya Merin Jose or P. R. Divya.

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Corresponding editor: Durgadas P. Kasbekar

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Jose, D.M., Divya, P.R. & Lal, K.K. Panmictic stock structure of milkfish (Chanos chanos, Forsskål 1775) from Indian waters determined using mtDNA marker. J Genet 102, 3 (2023). https://doi.org/10.1007/s12041-022-01395-6

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