Skip to main content

Advertisement

SpringerLink
Log in

Population genetic structure and phylogeography of cyprinid fish, Labeo dero (Hamilton, 1822) inferred from allozyme and microsatellite DNA marker analysis

  • Published:
Molecular Biology Reports Aims and scope Submit manuscript

Abstract

We examined population structure of Labeo dero (Hamilton, 1822) from different riverine locations in India using 10 polymorphic allozyme and eight microsatellite loci. For analysis, 591 different tissue samples were obtained from commercial catches covering a wide geographic range. Allozyme variability (An = 1.28–1.43, Ho = 0.029–0.071) was much lower than for microsatellites (An = 4.625–6.125, Ho = 0.538–0.633). Existence of rare alleles was found at three allozyme (MDH-2*, GPI* and PGDH*) and at two microsatellite loci (R-3* and MFW-15*). Deviation from Hardy–Weinberg equilibrium (P < 0.05, after the critical probability levels were adjusted for sequential Bonferroni adjustment) could be detected at three loci (EST-1*, -2* and XDH*) whereas, after correction for null alleles, two microsatellite loci (MFW-1*,-15*) deviated from HWE in the river Yamuna. Fst for all the samples combined over all allozyme loci was found to be 0.059 suggesting that 5.9% of the total variation was due to genetic differentiation while microsatellite analysis yielded 0.019 which was concordant to mean Rst (0.02). Hierarchical partition of genetic diversity (AMOVA) showed that greater variability (approx. 95%) was due to within population component than between geographical regions. Based on distribution of genetic differentiation detected by both markers, at least five different genetic stocks of L. dero across its natural distribution could be identified. These results are useful for the evaluation and conservation of L. dero in natural water bodies.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Log in via an institution

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Fig. 1
Fig. 2

Similar content being viewed by others

References

  1. Chonder SL (1999) Biology of finfish and shellfish, 1st edn. SCSC Publishers India, Howrah, pp 166–169

    Google Scholar 

  2. Sehgal KL (1988) The ecology and fisheries of mountain streams of N.W. Himalayas. Thesis for the award of D.Sc. Degree, Meerut University

  3. Sugunan VV (1997) Fisheries management of small water bodies in seven countries in Africa, Asia and Latin America. FAO fisheries circular no. 933. Rome, FAO, p 149

  4. HPFD (2005) Himachal Pradesh Fisheries Department, Uttaranchal India. http://himachal.nic.in/fisheries/reservior.htm

  5. Mahanta PC, Kapoor D, Dayal R, Ponniah AG (1994) Prioritization of the Indian fish species for conservation. In: Dehadrai PV, Das P, Verma SR (eds) Threatened fishes of India, Proceedings of the national seminar on endangered fishes of India, Nature Conservators, Muzaffarnagar, pp 377–386

  6. Ferguson A, Taggart JB, Prodohl PA, McMeel O, Thompson C, Stone C, McGinnity P, Hynes RA (1995) The application of molecular markers to the study and conservation of fish populations with special reference to Salmo. J Fish Biol 47(1):103–126

    Article  CAS  Google Scholar 

  7. Khuda-Bukhsh AR, Chanda T (1989) Somatic chromosomes of three species of hillstream fishes from Assam In: Das P, Jhingran AG (eds) Fish genetics in India, Proceedings of symposium on conservation and management of fish genetic resources of India, held on 11–13 April, 1986, pp 69–73

  8. Nielsen EE, Hansen MM, Loeschcke V (1999) Genetic variation in time and space: microsatellite analysis of extinct and extant populations of Atlantic salmon. Evolution 53:261–268

    Article  Google Scholar 

  9. Salini JP, Milton DA, Rahaman MJ, Hussein MG (2004) Allozyme and morphological variation throughout the geographic range of the tropical shad, hilsa Tenualosa ilisha. Fish Res 66:53–69

    Article  Google Scholar 

  10. DeWoody JA, Avise JC (2000) Microsatellite variation in marine, freshwater and anadromous fishes compared with other animals. J Fish Biol 56:461–473

    Article  CAS  Google Scholar 

  11. Neff BD, Gross MR (2001) Microsatellite evolution in vertebrates: inference from AC dinucleotide repeats. Evolution 55(9):1717–1733

    PubMed  CAS  Google Scholar 

  12. Liu ZJ, Cordes JF (2004) DNA marker technologies and their applications in aquaculture genetics. Aquaculture 238:1–37

    Article  CAS  Google Scholar 

  13. Mohindra V, Anshumala, Singh Rajeev K, Punia P, Kapoor D. Lal Kuldeep K (2005) Allozyme markers for population structure analysis in Labeo dero (Hamilton Buchanan, 1822). Asian Fish Sci 18(1–2):71–76

  14. Mohindra V, Anshumala, Punia P, Narain L, Kapoor D, Lal KK (2005) Microsatellite loci to determine population structure of Labeo dero (cyprinidae). Aquat Living Resour 18:83–85

    Article  CAS  Google Scholar 

  15. ECAFE (1966) A compendium of major international rivers in the ECAFE region. Water resources series, United Nation publication, no. 29

  16. Whitmore DH (1990) Electrophoretic and isoelectric focusing techniques in fisheries management. CRC Press, Inc., Florida, p 350

    Google Scholar 

  17. Ruzzante DE, Taggart C, Cook D, Goddard S (1996) Genetic differentiation between inshore and offshore Atlantic cod (Gadus morhua) of Newfoundland: microsatellite DNA variation and antifreeze level. Can J Fish Aquat Sci 53:634–645

    Article  Google Scholar 

  18. Wang D, Shi J, Carlson SR, Cregan PB, Ward RW, Diers BW (2003) A low-cast, high-throughput polyacrylamide gel electrophoresis system for genotyping with microsatellite DNA markers. Crop Sci 43:1828–1832

    Article  CAS  Google Scholar 

  19. Bovo D, Rugge M, Shiao Y-H (1999) Origin of spurious multiple bands in the amplification of microsatellite sequences. J Clin Pathol Mol Pathol 52:50–51

    Article  CAS  Google Scholar 

  20. Harlt DL, Clark AG (1997) Population substructure. In: Principles of population genetics, 3rd edn. Sinauer Associates, Inc., Sunderlands, Massachutetts, pp 111–159

  21. Belkhir K, Borsa P, Goudet J, Chikhi L, Bonhomme F (1997) Genetics logicielsous windows pour Ia ge’ ne’ Tique des populations. http://www.Univ-montz.fr/(gentix/genetix/html), version 4.05.2

  22. Chapuis MP, Estoup A (2006) FreeNA: microsatellite null alleles and estimation of population differentiation. Mol Biol Evol (submitted). chapuimp@ensam.inra.fr

  23. Raymond M, Rouseet F (1995) An exact test for population differentiation. Evolution 49:1280–1283

    Article  Google Scholar 

  24. Goudet J, Raymond M, de Meeus T, Rousset F (1996) Testing differentiation in diploid populations. Genetics 144:933–1940

    Google Scholar 

  25. Raymond M, Rousset F (1995) An exact test for population differentiation. Evolution 48:1280–1283

    Article  Google Scholar 

  26. Wright S (1951) The genetical structure of populations. Ann Eugen 15:323–354

    Article  Google Scholar 

  27. Weir BS, Cockerham CC (1984) Estimating F-statistics for the analysis of population structure. Evolution 38:1358–1370

    Article  Google Scholar 

  28. Excoffier LG, Laval G, Schneider S (2005) Arlequin ver. 3.0: an integrated software package for population genetics data analysis. Evol Bioinform Online 1:47–50

    PubMed  CAS  Google Scholar 

  29. Lessios HA (1992) Testing electrophoretic data for agreement with Hardy–Weinberg expectations. Mar Biol 112:517–523

    Article  Google Scholar 

  30. Cornuet JM, Luikart G, Piry S (1998) Bottleneck: description and power analysis of two tests for detecting recent population bottlenecks from allele frequency data. http://www.ensam.inra.fr/URLB

  31. Spencer CC, Neigel EJ, Leberg LP (2000) Experimental evaluation of the usefulness of microsatellite DNA for detecting demographic bottlenecks. Mol Ecol 9:1517–1528

    Article  PubMed  CAS  Google Scholar 

  32. Sainudiin R, Durrett RT, Aquadro CF, Nielsen R (2004) Microsatellite mutation models: insight from a comparison of Humans and Chimpanzees. Genetics 168:383–395

    Article  PubMed  CAS  Google Scholar 

  33. Gyllensten U (1985) The genetic structure of fish: differences in the distribution of biochemical genetic variation between marine, anadromous and freshwater species. J Fish Biol 26:691–699

    Article  Google Scholar 

  34. Ward RD, Woodwark M, Skinbinski DOF (1994) A comparison of genetic diversity levels in marine, freshwater and anadromous fishes. J Fish Biol 44:213–232

    Article  Google Scholar 

  35. Nevo E (1978) Genetic variation in natural populations: patterns and theory. Theor Popul Biol 13:121–177

    Article  PubMed  CAS  Google Scholar 

  36. Nevo E, Beiles A, Ben-Shlomo R (1984) The evolutionary significance of genetic diversity: ecological, demographic and life history correlates. In: Mani GS (ed) Evolutionary dynamics of genetic diversity. Springer-Verlag, Berlin, Germany, pp 13–213

    Google Scholar 

  37. Frankham R (1996) Relationship of genetic variation to population size in wildlife. Conserv Biol 10:1500–1508

    Article  Google Scholar 

  38. Bouvet Y, Soewardi K, Pattee E (1991) The discrimination of Roach Rutilus rutilus (Linnaeus 1758) population in different parts of a river system: an investigation using Biochemical markers. Hydrobiologia 209:161–167

    Article  Google Scholar 

  39. Coelho MC (1992) Genetic differentiation of the Iberian cyprinids Chondrostoma polylepis steind, 1865 and Ch-willkommi steind, 1866. Arch Hydrobiol 125:487–498

    Google Scholar 

  40. Alves MJ, Coehlo MM (1994) Genetic variation and population subdivision of the endangered Iberian cyprinid Chondrostoma lusitanicum. J Fish Biol 44:627–637

    Article  Google Scholar 

  41. Coelho MM, Brito RM, Oanbeco TR, Figueiredo D, Peris AM (1995) Genetic variation and divergence of Leuciscuspyrenaious and L. caroliterttii (Pisces, Cyprinidae). J Fish Biol 47(Suppl A):243–258

    Article  Google Scholar 

  42. Wright S (1965) The interpretation of population structure by F-statistics with special regard to systems of mating. Evolution 19:395–420

    Article  Google Scholar 

  43. Baranski M, Rourke M, Loughnan S, Austin C, Robinson N (2006) Isolation and characterization of 125 microsatellite DNA markers in the blacklip abalone, Haliotis rubra. Mol Ecol Notes 6:740–746

    Article  CAS  Google Scholar 

  44. Chauhan T, Lal KK, Mohindra V, Singh RK, Punia P, Gopalakrishnan A, Sharma PC, Lakra WS (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 

  45. Daniel RJR (2001) Endemic fishes of the Western Ghats and the Satpura hypothesis. Curr Sci 81:240–244

    Google Scholar 

  46. Lal BB (2002) The Saraswati flows on: the continuity of Indian culture. Aryan Books International, New Delhi, p 148

    Google Scholar 

  47. Hora SL (1949) Symposium on Satpura hypothesis of the distribution of Malayan fauna and flora to peninsular India. Proc Natl Inst Sci India 15:309–422

    Google Scholar 

  48. Karl SA, Avise JC (5053) Balancing selection at allozyme loci in oysters: implications from nuclear RFLPs. Science 256(5053):100–102

    Article  Google Scholar 

  49. Pogson GH, Mesa KA, Boutilier RG (1995) Genetic population structure and gene flow in the Atlantic cod, Gadus morhua: a comparison of allozyme and nuclear RFLP loci. Genetics 139:375–385

    PubMed  CAS  Google Scholar 

  50. Latta RG, Mitton JB (1997) A comparison of population differentiation across four classes of gene marker in limber pine (Pinus flexilis James). Genetics 146:1153–1163

    PubMed  CAS  Google Scholar 

  51. Allendorf FW, Seeb LW (2000) Concordance of genetic divergence among Sockeye salmon populations at allozyme, nuclear DNA, and mitochondrial DNA markers. Evolution 54(2):640–651

    PubMed  CAS  Google Scholar 

  52. Nauta MJ, Weissing FJ (1996) Constraints on allele size at microsatellite loci: implications for genetic differentiation. Genetics 143:1021–1032

    PubMed  CAS  Google Scholar 

  53. Ellegren H (2000) Heterogeneous mutation processes in human microsatellite DNA sequences. Nat Genet 24:400–402

    Article  PubMed  CAS  Google Scholar 

Download references

Acknowledgments

The authors thank Sh. R. S. Sah, Sh. A K. Mishra, Sh. Rajesh Kumar and Sh Shree Ram for their excellent assistance provided by during sampling and experimentations. The work was carried out under projects NATP-ICAR (sub project MM18) and NBFGR-DNA25A.

Author information

Authors and Affiliations

  1. National Bureau of Fish Genetic Resources (ICAR), Canal Ring Road, P.O. Dilkusha, Lucknow, 226 002, UP, India

    Anshumala Chaturvedi, Vindhya Mohindra, Rajeev K. Singh, Kuldeep K. Lal, Peyush Punia, Ranjana Bhaskar, Anup Mandal, Lalit Narain & W. S. Lakra

Authors
  1. Anshumala Chaturvedi
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Vindhya Mohindra
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Rajeev K. Singh
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Kuldeep K. Lal
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Peyush Punia
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. Ranjana Bhaskar
    View author publications

    You can also search for this author in PubMed Google Scholar

  7. Anup Mandal
    View author publications

    You can also search for this author in PubMed Google Scholar

  8. Lalit Narain
    View author publications

    You can also search for this author in PubMed Google Scholar

  9. W. S. Lakra
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Vindhya Mohindra.

Rights and permissions

Reprints and permissions

About this article

Cite this article

Chaturvedi, A., Mohindra, V., Singh, R.K. et al. Population genetic structure and phylogeography of cyprinid fish, Labeo dero (Hamilton, 1822) inferred from allozyme and microsatellite DNA marker analysis. Mol Biol Rep 38, 3513–3529 (2011). https://doi.org/10.1007/s11033-010-0462-y

Download citation

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s11033-010-0462-y

Keywords

Search

Navigation