Organisms Diversity & Evolution

, Volume 13, Issue 4, pp 531–543 | Cite as

Fine-scale population genetic structure in Artemia urmiana (Günther, 1890) based on mtDNA sequences and ISSR genomic fingerprinting

  • Amin EimanifarEmail author
  • Michael Wink
Original Article


We investigated the genetic variability and population structure of the halophilic zooplankter Artemia urmiana from 15 different geographical locations of Lake Urmia using nucleotide sequences of COI (mtDNA cytochrome c oxidase subunit I) and genomic fingerprinting by ISSR-PCR (inter-simple sequence repeats). According to sequence data, A. urmiana exhibits a high level of haplotype diversity with a low level of nucleotide diversity. The haplotype spanning network recognized 36 closely related unique haplotypes. ISSR profiles confirmed a substantial amount of genomic diversity with a low level of population structure. No apparent genetic structure was recognized in Lake Urmia but rather a random geographic distribution of genotypes indicating a high degree of panmixia. The population genetic data indicate the possibility of an individual’s relationship, implying that differentiation of individuals is not affected by ecological factors. Therefore, the A. urmiana population from Lake Urmia should be considered as a single management unit for conservation.


Genetic variability Population structure Artemia urmiana Lake Urmia 



A.E. is grateful to the Deutscher Akademischer Austauschdienst (DAAD) for a PhD fellowship. We would like to express our appreciation to Alireza Asem, who provided samples of A. urmiana from the entire Lake Urmia. Thanks go to Theodor C.H. Cole for proofreading and for valuable suggestions regarding the manuscript.

Supplementary material

13127_2013_135_Fig5_ESM.jpg (378 kb)
Fig. S1

Bar plot of A. urmiana specimens showing admixture proportion of individuals for each locality calculated by STRUCTURE (K = 6). Sampling sites are shown below bar plot. In bar plot, each individual corresponds to a thin vertical line and the proportion of each locality is represented by its corresponding colours. (JPEG 377 kb)

13127_2013_135_MOESM1_ESM.eps (531 kb)
High Resolution Image (EPS 530 kb)


  1. Abatzopoulos, T. J., Zhang, B., & Sorgeloos, P. (1998). Artemia tibetiana: preliminary characterization of a new Artemia species found in Tibet (People’s Republic of China). International study on Artemia LIX. International Journal of Salt Lake Research, 7, 41–44.CrossRefGoogle Scholar
  2. Abatzopoulos, T. J., Amat, F., Baxevanis, A. D., Belmonte, G., Hontoria, F., Maniatsi, S., et al. (2009). Updating geographic distribution of Artemia urmiana Günther, 1890 (Branchiopoda: Anostraca) in Europe: an integrated and interdisciplinary approach. International Review of Hydrobiology, 94, 560–579.CrossRefGoogle Scholar
  3. Agh, N. (2007). Characterization of Artemia populations from Iran. PhD Thesis, Ghent University, Belgium.Google Scholar
  4. Akaike, H. (1974). A new look at the statistical model identification. IEEE Transactions on Automatic Control, 19, 716–723.CrossRefGoogle Scholar
  5. Alves, M. J., Coelho, H., Collares-Pereira, M. J., & Coelho, M. M. (2001). Mitochondrial DNA variation in the highly endangered cyprinid fish Anaecypris hispanica: importance for conservation. Heredity, 87, 463–473.PubMedCrossRefGoogle Scholar
  6. Arafeh, R. M. H., Sapir, Y., Shmida, A., Iraki, N., Fragman, O., & Comes, H. P. (2002). Patterns of genetic and phenotypic variation in Iris haynei and I. atrofusca (Iris sect. Oncocyclus the royal irises) along an ecogeographical gradient in Israel and the West Bank. Molecular Ecology, 11, 39–54.PubMedCrossRefGoogle Scholar
  7. Asem, A., Rastegar-Pouyani, N., & Agh, N. (2007). Biometrical study of Artemia urmiana (Anostraca: Artemiidae) cysts harvested from Lake Urmia (West Azerbaijan, Iran). Turkish Journal of Zoology, 31, 171–180.Google Scholar
  8. Asem, A., Rastegar-Pouyani, N., De Los Rios, P., Manaffar, R., & Mohebbi, F. (2010). Biometrical comparison of Artemia urmiana Günther, 1899 (Crustacea: Anostraca) cysts between rainy and drought years (1994–2003/4) from Urmia Lake, Iran. International Journal of Biological and Life Sciences, 6, 100–106.Google Scholar
  9. Asem, A., Mohebbi, F., & Ahmadi, R. (2012). Drought in Urmia Lake, the largest natural habitat of brine shrimp Artemia. World Aquaculture, 43, 36–38.Google Scholar
  10. Bandelt, H. J., Forster, P., & Röhl, A. (1999). Median-joining networks for inferring intraspecific phylogenies. Molecular Biology and Evolution, 16, 37–48.PubMedCrossRefGoogle Scholar
  11. Brendonck, L., & Riddoch, B. J. (1999). Wind-borne short-range egg dispersal in anostraceans (Crustacea: Branchiopoda). Biological Journal of the Linnean Society, 67, 87–95.CrossRefGoogle Scholar
  12. Cai, Y. (1989). A redescription of the brine shrimp (Artemia sinica). The Wasmann Journal of Biology, 47, 105–110.Google Scholar
  13. Chenoweth, S. F., & Hughes, J. M. (2003). Oceanic interchange and nonequilibrium population structure in the estuarine dependent Indo-Pacific tasselfish, Polynemus sheridani. Molecular Ecology, 12, 2387–2397.PubMedCrossRefGoogle Scholar
  14. Chiang, H. C., Hsu, C. C., Lin, H. D., Ma, G. C., Chiang, T. Y., & Yang, H. Y. (2006). Population structure of bigeye tuna (Thunnus obesus) in the South China Sea, Philippine Sea and western Pacific Ocean inferred from mitochondrial DNA. Fisheries Research, 79, 219–225.CrossRefGoogle Scholar
  15. Cowen, R. K., Lwiza, K. M. M., Sponaugle, S., Paris, C. B., & Olson, D. B. (2000). Connectivity of marine populations: open or closed? Science, 287, 857–859.PubMedCrossRefGoogle Scholar
  16. Dasmahapatra, K. K., Lacy, R. C., & Amos, W. (2008). Estimating levels of inbreeding using AFLP markers. Heredity, 100, 286–295.PubMedCrossRefGoogle Scholar
  17. Delju, A. H., Ceylan, A., Piguet, E., & Rebetez, M. (2013). Observed climate variability and change in Urmia Lake Basin, Iran. Theoretical and Applied Climatology, 111, 285–296. doi: 10.1007/s00704-012-0651-9.CrossRefGoogle Scholar
  18. Djamali, M., Kürschner, H., Akhani, H., De Beaulieu, J. L., Amini, A., Andrieu-Ponel, V., et al. (2008). Palaeoecological significance of the spores of the liverwort Riella (Riellaceae) in a late Pleistocene long pollen record from the hypersaline Lake Urmia, NW Iran. Review of Palaeobotany and Palynology, 152, 66–73.CrossRefGoogle Scholar
  19. Eimanifar, A., & Mohebbi, F. (2007). Urmia Lake (Northwest Iran): a brief review. Saline Systems, 3, 1–8.CrossRefGoogle Scholar
  20. Eimanifar, A., Rezvani, S., & Carapetian, J. (2006). Genetic differentiation of Artemia urmiana from various ecological populations of Urmia Lake assessed by PCR amplified RFLP analysis. Journal of Experimental Marine Biology and Ecology, 333, 275–285.CrossRefGoogle Scholar
  21. Erixon, P., Svennblad, B., Britton, T., & Oxelman, B. (2003). Reliability of Bayesian posterior probabilities and bootstrap frequencies in phylogenetics. Systematic Biology, 52, 665–673.PubMedCrossRefGoogle Scholar
  22. Evanno, G., Regnaut, S., & Goudet, J. (2005). Detecting the number of clusters of individuals using the software STRUCTURE: a simulation study. Molecular Ecology, 14, 2611–2620.PubMedCrossRefGoogle Scholar
  23. Excoffier, L., & Lischer, H. E. L. (2010). Arlequin suite ver 3.5: a new series of programs to perform population genetics analyses under Linux and Windows. Molecular Ecology Resources, 10, 564–567.PubMedCrossRefGoogle Scholar
  24. Falush, D., Stephens, M., & Pritchard, J. K. (2007). Inference of population structure using multilocus genotype data: dominant markers and null alleles. Molecular Ecology Notes, 7, 574–578.PubMedCrossRefGoogle Scholar
  25. Fu, Y. X. (1997). Statistical tests of neutrality of mutations against population growth, hitchhiking and background selection. Genetics, 147, 915–925.PubMedGoogle Scholar
  26. Gonzalez, J., & Wink, M. (2010). Genetic differentiation of the Thorn-tailed Rayadito Aphrastura spinicauda revealed by ISSR profiles suggest multiple paleorefugia and high recurrent gene flow. IBIS, 152, 761–774.CrossRefGoogle Scholar
  27. Green, A. J., Sánchez, M. I., Amat, F., Figuerola, J., Hontoria, F., Ruiz, O., et al. (2005). Dispersal of invasive and native brine shrimps Artemia (Anostraca) via waterbirds. Limnology and Oceanography, 50, 737–742.CrossRefGoogle Scholar
  28. Guindon, S., Dufayard, J. F., Lefort, V., Anisimova, M., Hordijk, W., & Gascuel, O. (2010). New algorithms and methods to estimate maximum-likelihood phylogenies: assessing the performance of PhyML 3.0. Systematic Biology, 59, 307–321.PubMedCrossRefGoogle Scholar
  29. Gunther, R. T. (1890). Crustacea: contribution to the natural history of lake Urmia, N. W. Persia and its neighborhood. In: Gunther, R.T. (Ed.), Journal of Linnaeus Society (Zoology), 27, 394–398.Google Scholar
  30. Hall, T. A. (1999). BioEdit: a user-friendly biological sequence alignment editor and analysis program for windows 95/98/NT. Nucleic Acids Symposium Series, 41, 95–98.Google Scholar
  31. Hamrick, J. L., & Godt, M. J. W. (1989). Allozyme diversity in plant species. In A. H. D. Brown, M. T. Clegg, A. T. Kahler, & B. S. Weir (Eds.), Plant population genetics, breeding, and genetic resources (pp. 43–63). Sunderland: Sinauer.Google Scholar
  32. Hassanzadeh, E., Zarghami, M., & Hassanzadeh, Y. (2012). Determining the main factors in declining the Urmia Lake level by using system dynamics modeling. Water Resources Management, 26, 129–145.CrossRefGoogle Scholar
  33. Havel, J. E., Colbourne, J. K., & Hebert, P. D. N. (2000). Reconstructing the history of intercontinental dispersal in Daphnia lumholtzi by the use of genetic markers. Limnology and Oceanography, 45, 1414–1419.CrossRefGoogle Scholar
  34. Hebert, P. D. N., Ratnasingham, S., & Waard, J. R. (2003). Barcoding animal life: cytochrome c oxidase subunit 1 divergences among closely related species. Proceedings of the Royal Society of London, Series B: Biological Sciences, 270, 96–99.CrossRefGoogle Scholar
  35. Hontoria, F., & Amat, F. (1992). Morphological characterization of adult Artemia (Crustacea, Branchiopoda) from different geographical origins. American populations. Journal of Plankton Research, 14, 1461–1471.CrossRefGoogle Scholar
  36. Hoseinpour, M., Fakheri Fard, A., Naghili, R. (2010). Death of Urmia Lake, a silent disaster investigating of causes, results and solutions of Urmia Lake drying. The 1st International Applied Geological Congress, Department of Geology, Islamic Azad University, Mashad Branch, Iran, 26–28.Google Scholar
  37. Hou, L., Li, H., Zou, X., Yao, F., Bi, X., & He, C. (2006). Population genetic structure and genetic differentiation of Artemia parthenogenetica in China. Journal of Shellfish Research, 25, 999–1005.Google Scholar
  38. Huelsenbeck, J. P., & Ronquist, F. (2001). MRBAYES: Bayesian inference of phylogenetic trees. Bioinformatics, 17, 754–755.PubMedCrossRefGoogle Scholar
  39. Hundsdörfer, A., Kitching, I. J., & Wink, M. (2005). The phylogeny of the Hyles euphorbiae complex (Lepidoptera: Sphingidae): molecular evidence from sequence data and ISSR-PCR fingerprints. Organisms, Diversity and Evolution, 5, 173–198.CrossRefGoogle Scholar
  40. Jaccard, P. (1908). Nouvelles recherches sur la distribution florale. Société Vaudoise des Sciences Naturelles, 44, 223–270.Google Scholar
  41. Jensen, J. L., Bohonak, A. J., & Kelley, S. T. (2005). Isolation by distance, web service. BMC Genetics, 6, 1–6.CrossRefGoogle Scholar
  42. Jonathan, K. P., Matthew, S., & Peter, D. (2000). Inference of population structure using multilocus genotype data. Genetics, 155, 945–959.Google Scholar
  43. Karbassi, A. R., Bidhendi, G. N., Pejman, A., & Bidhendi, M. E. (2010). Environmental impacts of desalination on the ecology of Lake Urmia. Journal of Great Lakes Research, 36, 419–424.CrossRefGoogle Scholar
  44. Kellogg, V. A. (1906). A new Artemia and its life conditions. Science, 24, 594–596.PubMedCrossRefGoogle Scholar
  45. Kelts, K., & Shahrabi, M. (1986). Holocene sedimentalogy of hypersaline Lake Urmia, northwestern Iran. Paleogeography, Paleoclimatology & Paleoecology, 54, 105–130.CrossRefGoogle Scholar
  46. Kimura, M. (1980). A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. Journal of Molecular Evolution, 16, 111–120.PubMedCrossRefGoogle Scholar
  47. Larkin, M. A., Blackshields, G., Brown, N. P., Chenna, R., McGettigan, P. A., McWilliam, H., et al. (2007). Clustal W and Clustal X version 2.0. Bioinformatics, 23, 2947–2948.PubMedCrossRefGoogle Scholar
  48. Librado, P., & Rozas, J. (2009). DnaSP v5: a software for comprehensive analysis of DNA polymorphism data. Bioinformatics, 25, 1451–1452.PubMedCrossRefGoogle Scholar
  49. Lynch, M., & Milligan, B. G. (1994). Analysis of population genetic structure with RAPD markers. Molecular Ecology, 3, 91–99.PubMedCrossRefGoogle Scholar
  50. Maggio, T., Brutto, S. L., Cannas, R., Deiana, A. M., & Arculeo, M. (2009). Environmental features of deep-sea habitats linked to the genetic population structure of a crustacean species in the Mediterranean Sea. Marine Ecology, 30, 354–365.CrossRefGoogle Scholar
  51. Manaffar, R., Zare, S., Agh, N., Siyabgodsi, A., Soltanian, S., Mees, F., et al. (2011). Sediment cores from Lake Urmia (Iran) suggest the inhabitation by parthenogenetic Artemia around 5000 years ago. Hydrobiologia, 671, 65–74.CrossRefGoogle Scholar
  52. Maniatsi, S., Kappas, I., Baxevanis, A. D., Farmaki, T., & Abatzopoulos, T. J. (2009). Sharp phylogeographic breaks and patterns of genealogical concordance in the brine shrimp Artemia franciscana. International Journal of Molecular Sciences, 10, 5455–5470.PubMedCrossRefGoogle Scholar
  53. Mantel, N. A. (1967). The detection of disease clustering and a generalized regression approach. Cancer Research, 27, 209–220.PubMedGoogle Scholar
  54. Montero-Pau, J., Gómez, A., & Muñoz, J. (2008). Application of an inexpensive and high-throughput genomic DNA extraction method for the molecular ecology of zooplanktonic diapausing eggs. Limnol. Oceanogr. Methods, 6, 218–222.CrossRefGoogle Scholar
  55. Muñoz, J., Gómez, A., Green, A. J., Figuerola, J., Amat, F., & Rico, C. (2008). Phylogeography and local endemism of the native Mediterranean brine shrimp Artemia salina (Branchiopoda: Anostraca). Molecular Ecology, 17, 3160–3177.PubMedCrossRefGoogle Scholar
  56. Muñoz, J., Gómez, A., Green, A. J., Figuerola, J., Amat, F., & Rico, C. (2010). Evolutionary origin and phylogeography of the diploid obligate parthenogen Artemia parthenogenetica (Branchiopoda: Anostraca). PLoS One, 5(8), e11932. doi: 10.1371/journal.pone.0011932.PubMedCrossRefGoogle Scholar
  57. Pengra, B. (2012). The drying of Iran’s Lake Urmia and its environmental consequences. UNEP-GRID, Sioux Falls, UNEP Global Environmental Alert Service (GEAS), February 2012.Google Scholar
  58. Piccinelli, M., & Prosdocimi, T. (1968). Descrizione tassonomica delle due species Artemia salina L. e Artemia persimilis n. sp. Rendiconti Istituto Lombardo Scienze e Lettere, B, 102, 170–179.Google Scholar
  59. Pilla, E. J. S., & Beardmore, J. A. (1994). Genetic and morphometric differentiation in Old word bisexual species of the brine shrimp Artemia. Heredity, 72, 47–56.CrossRefGoogle Scholar
  60. Posada, D. (2008). jModelTest: phylogenetic model averaging. Molecular Biology and Evolution, 25, 1253–1256.PubMedCrossRefGoogle Scholar
  61. Pritchard, J. K., Stephens, M., & Donnelly, P. (2000). Inference of population structure using multilocus genotype data. Genetics, 155, 945–959.PubMedGoogle Scholar
  62. Rohlf, F. J. (1998). NTSYSpc: Numerical taxonomy and multivariate analysis system, version 2.02. Setauket: Exeter Software.Google Scholar
  63. Ruiz, J. C., Roa Gamboa, O., & Arguello, I. M. (2011). Molecular ecology of genetic diversity of cacao cultivated in the south-east region of Nicaragua. International Research Journal of Agricultural Science and Soil Science, 1, 6–13.Google Scholar
  64. Sarwat, M. (2012). ISSR: A reliable and cost-effective technique for detection of DNA polymorphism. In N. J. Sucher (Ed.), Plant DNA fingerprinting and barcoding: Methods and protocols, methods in molecular biology (Vol. 862, pp. 103–121). Heidelberg: Springer.CrossRefGoogle Scholar
  65. Sokal, R., & Michener, C. (1958). A statistical method for evaluating systematic relationships. University of Kansas Science Bulletin, 38, 1409–1438.Google Scholar
  66. Tajima, F. (1989). Statistical methods to test for nucleotide mutation hypothesis by DNA polymorphism. Genetics, 123, 585–595.PubMedGoogle Scholar
  67. Tamura, K., Peterson, D., Peterson, N., Stecher, G., Nei, M., & Kumar, S. (2011). MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Molecular Biology and Evolution, 28, 2731–2739.PubMedCrossRefGoogle Scholar
  68. Tanabe, Y., & Watanabe, M. M. (2011). Local expansion of a panmictic lineage of water bloom-forming cyanobacterium Microcystis aeruginosa. PLoS One, 6, 1–7. doi: 10.1371/journal.pone.0017085. e17085.Google Scholar
  69. Tavaré, S. (1986). Some probabilistic and statistical problems in the analysis of DNA sequences. Lectures on Mathematics in the Life Sciences (American Mathematical Society), 17, 57–86.Google Scholar
  70. Triantaphyllidis, G. V., Criel, G. R., Abatzopoulos, T. J., & Sorgeloos, P. (1997). International study on Artemia: morphological study of Artemia with emphasis to Old World strains: bisexual populations. Hydrobiologia, 357, 139–153.CrossRefGoogle Scholar
  71. Van der Heijden, K., Petersen, J. M., Dubilier, N., & Borowski, C. (2012). Genetic connectivity between North and South mid-atlantic ridge chemosynthetic bivalves and their symbionts. PLoS One, 7(7), e39994. doi: 10.1371/journal.pone.0039994.PubMedCrossRefGoogle Scholar
  72. Van Stappen, G. (2002). Zoogeography. In T. H. Abatzopoulos, J. Beardmore, J. S. Clegg, & P. Sorgeloos (Eds.), Artemia: Basic and applied biology (pp. 171–224). Dordrecht: Kluwer.CrossRefGoogle Scholar
  73. Van Stappen, G., Yu, H., Wang, X., Hoffman, S., Cooreman, K., Bossier, P., et al. (2007). Occurrence of allochthonous Artemia species in the Bohai Bay area, PR China, as confirmed by RFLP analysis and laboratory culture tests. Fundamental and Applied Limnology, 170, 21–28.CrossRefGoogle Scholar
  74. Vekemans, X. (2002). AFLP-SURV vers. 1.0. Brussels, Belgium: Laboratoire de Génétique et Ecologie Végétale, Univ. Libre de Bruxelles. Available at

Copyright information

© Gesellschaft für Biologische Systematik 2013

Authors and Affiliations

  1. 1.Institute of Pharmacy and Molecular BiotechnologyHeidelberg UniversityHeidelbergGermany

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