Assessment of genetic diversity of an endangered tooth-carp, Aphanius farsicus (Teleostei: Cyprinodontiformes: Cyprinodontidae) using microsatellite markers

Document Type: Original article


1 Zoology Section, Department of Biology, College of Sciences, Shiraz University, Shiraz, Iran

2 Fishery Faculty, Gorgan University of Agriculture Science and Natural Resources, Gorgan, Iran


Genetic structure of an endemic tooth-carp fish, Aphanius farsicus from four different water bodies in the Maharlu Lake basin was investigated by applying five microsatellite markers. All of the five examined microsatellite loci showed polymor-phism pattern. A total of four alleles were detected at five microsatellite loci, with an average of 2.8 to 3.5 alleles per locus. Average values of observed and expected heterozygosity were 0.95±0.09 and 0.64±0.02 respectively. None of the tests of linkage disequilibrium were significant between each pair of loci and no deviation from Hardy-Weinberg equilibrium were detected to test for heterozygote deficiency within populations. The Nei's genetic distance values ranged between 0.03 – 0.13. Analysis of pairwise genetic differentiation between each pair of the populations revealed that fixation index (FST) values ranged from 0.013 to 0.039 and RST ranged from 0.005 to 0.065. High genetic diversity observed within the populations (99%) and low diversity (1%) among them indicating probably high level of gene flow among the studied populations of Fars tooth-carp at the present time or in the past. Regarding low genetic differentiation among the studied populations and results of population assignment test, two hypotheses are suggested and supporting evidence for each hypothesis are provided.


1.Gholami Z, Teimori A, Esmaeili HR, Schulz-Mirbach T, Reichenbacher B. Scale surface microstructure and scale size in the tooth-carp genus Aphanius (Teleostei, Cyprinodontidae) from endorheic basins in Southwest Iran. Zootaxa 2013;3619:467-490.

2. Eschmeyer WN, Fricke R. (eds.) Catalog of fishes. California Academy of Sciences, SanFrancisco.[Electronicversion;2015.]

3. Keyvani Y, Esmaeili HR. Threatened fishes of the world: Aphanius farsicus Teimori, Esmaeili and Reichenbacher, 2011 (Cyprinodontidae).Croat J Fish 2013;71:192-194.

4. Jarne P, Lagoda PJ. Microsatellite, from molecules to populations and back. Trends Ecol Evol 1996;11:424-429.

5. O'Connell M, Wright JM. Microsatellite DNA in fishes. Rev Fish Biol Fish1997;7: 331-363.

6. Beaument MA, Brufrod MW). Microsatellite in conversation genetics. In: Goldstein D, Schlӧtterer C. (Eds), Microsatellites: Evolution and Applications. Oxford University Press 1999; New York, PP:155-182.

7. Dewoody JA, Avise JC. Microsatellite variation in marine freshwater and anadromous fishes compared with other animals. J Fish Biol 2000;56:461-473.

8. Chen L, Li Q, Yang J. Microsatellite genetic variation in wild and hatchery populations of the sea cucumber (Apostichopus japonicus Selenka) from northern China. Aquac Res 2008;39:1541-1549.

9. Hoseini A, Shaabani A, Rezaei H. The comparison of genetic structure of Zagros tooth-carp (Aphanius vladykovi) in Gandoman and Shalamzar wetland in the Chaharmahall-O-Bakhtiari province by using microsatellite markers. J Anim Biol 2013;5:32-47.

10. Gholami Z, Esmaeili HR, Erpenbeck D, Riechenbacher B. Genetic connectivity and phenotypic plasticity in the Cyprinodont Aphanius farsicus from the Maharlu Basin, south-western Iran. J Fish Biol 2015;86:882-906.

11. Hillis DM, Mable BK, Larson A, Davis SK, Zimmer EA. Nucleic acids IV: sequencing and cloning. In: Molecular Systematics. Sinauer Associates 1996; Sunderland, USA, PP:342-343.

12. King TL, Kalinowski ST, Schill WB, Spide AP, Lubinski BA. Population structure of Atlantic Salmon (Salmo salar L.): arrange- wide perspective from microsatellite DNA variation. Mol Ecol 2001;10:807-821.

13. Babbucci M, Pappalardo A, Ferrito V, Barbisan F, Patarnello T, Tigano C. Isolation and characterization of eight polymorphic microsatellite markers in Aphanius fasciatus (Teleostei: Cyprinodontidae). Mol Ecol Notes 2007;7:293-295.

14. Bassam BJ, Caetano-Anolles G, Gressheff PM. Fast and silver staining of DNA in polyacrylamide gels. Anal Biochem 1991;196:80-83.

15. Oosterhout CV, Hutchinson WF, Wills DPM, Shipley P. MICRO-CHECKER: software for identifying and correcting genotyping errors in microsatellite data. Mol Eco Notes 2004;4:535-538.

16. Yeh F, Yang R, Boyle T. POPGENE Version 1.32; Microsoft Window-based Freeware for Population Genetic Analysis; Molecular Biology and Biotechnology Center, University of Alberta: Edmonton, AB, Canada,1999.

17. Peakall R, Smouse PE. GENALEX 6: genetic analysis in Excel. Population genetic software for teaching and research. Mol Eco Notes 2006;6:288-295.

18. DeWoody JA, Avise JC. Microsatellite variation in marine, freshwater and anadromous fishes compared with other animals. J Fish Biol 2000;56: 461-473.

19. Plomion CH, Bousquet J, kole CH. (eds) Genetics, genomics and breeding of Conifers. CRC Press and Edenbridge Science Publishers 2011, New York.

20. Ciftci Y, Okumus I. Fish population genetics and applications of molecular markers to fisheries and aquaculture: I-Basic principles of fish population genetics. Fish Aquat Sci 2002;2:145-155.

21. Castric V, Bernatchez L,  Belkhir K,  Bonhomme F. Heterozygote deficiencies in small lacustrine populations of brook charr Salvelinus Fontinalis Mitchill (Pisces, Salmonidae): a test of alternative hypotheses. Heredity 2002;89:27-35.

22. Grassi F, Imazio S, Gomarasca S, Citterio S, Aina R, Sgorbati S, Sala F, Patrignani G, Labra, M. Population structure and genetic variation within Valeriana wallrothii Kreyer in relation to different ecological locations. Plant Sci 2004;166:1437-1441.

23. Ballox F, Lugon-Moulin N. The estimate of population differentiation with microsatellite markers. Mol Ecol 2002;11:155-165.

24. Wright, S. (1978). Evolution and the Genetics of Populations, Vol. 4: Variability Within and Among Natural Populations. University of Chicago Press 1978; Chicago.

25. Wachirachaikarn A, Rungsin W, Srisapoome P, Na-Nakorn U. Crossing of African catfish, Clarias gariepinus (Burchell, 1822), strain based on strain selection using genetic diversity data. Aquaculture 2009;290:53-60.