The use of RAPD in ecotoxicology

Mutation Research - Reviews in Mutation Research

Volumn 566, Issue 3, 2004, Pages 249-262

  De Wolf, Hans ^a   Blust, Ronny ^a   Backeljau, Thierry ^a,b  

^a UNIVERSITY OF ANTWERP   (Belgium)

^b ROYAL BELGIAN INSTITUTE OF NATURAL SCIENCES   (Belgium)

Author keywords

Bottleneck; DNA damage; Genetic variability; Random amplified polymorphic DNA; Selection

Indexed keywords

TOXIC SUBSTANCE;

ECOTOXICOLOGY; GENE LOCUS; GENE PROBE; GENE SEQUENCE; GENETIC VARIABILITY; MATHEMATICAL COMPUTING; MOLECULAR CLONING; PRIORITY JOURNAL; RANDOM AMPLIFIED POLYMORPHIC DNA; REVIEW; SEQUENCE DATABASE; STATISTICAL ANALYSIS;

ANIMALS; ECOLOGY; ENVIRONMENTAL EXPOSURE; ENVIRONMENTAL POLLUTANTS; GENETIC MARKERS; GENETICS, POPULATION; HUMANS; MODELS, GENETIC; RANDOM AMPLIFIED POLYMORPHIC DNA TECHNIQUE; VARIATION (GENETICS);

EID: 1842781205     PISSN: 13835742     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.mrrev.2003.10.003     Document Type: Review

References (110)

1. Koh H.L., Hallam T.G., Lee H.L. Combined effects of environmental and chemical stressors on a model Daphnia population. Ecol. Model. 103:1997;19-32.
2. Stark J.D., Banken J.A.O. Importance of population structure at the time of toxicant exposure. Ecotoxicol. Environ. Safety. 42:1999;282-287.
3. Burger R., Lynch M. Evolution and extinction in a changing environment - a quantitative genetic analysis. Evolution. 49:1995;151-163.
4. Allmon W.D. Nutrients, temperature, disturbance, and evolution: a model for the late Cenozoic marine record of the western Atlantic. Palaeogeogr. Palaeoclimat. Palaeoecol. 166:2001;9-26.
5. Becerril C., Acevedo H., Ferrero M., Sanz F., Castaño A. DNA fingerprint comparison of rainbow trout and RTG-2 cell line using random amplified polymorphic DNA. Ecotoxicology. 10:2001;115-124.
6. Belfiore N.M., Anderson S.L. Effects of contaminants on genetic patterns in aquatic organisms: a review. Mutat. Res. 489:2001;97-122.
7. Bjerregaard P., Depledge M.H. Cadmium accumulation in Littorina littorea, Mytilus edulis and Carcinus maenas the influence of salinity and calcium ion concentrations. Mar. Biol. 119:1994;385-395.
8. Jackson B.P., Lasier P.J., Miller W.P., Winger P.W. Effects of calcium, magnesium and sodium on elevating cadmium toxicity to Hyalella azteca. Bull. Environ. Contam. Toxicol. 64:2000;279-286.
9. Theodorakis C.W. Integration of genotoxic and population genetic endpoints in biomonitoring and risk assessment. Ecotoxcicology. 10:2001;245-256.
10. Staton J.L., Schizas N.V., Chandler G.T., Coull B.C., Quattro J.M. Ecotoxicology and population genetics: the emergence of "phylogeographic and evolutionary ecotoxicology" Ecotoxicology. 10:2001;217-222.
11. Hebert P.D.N., Luiker M.M. Genetic effects of contaminant exposure - towards an assessment of impacts on animal populations. Sci. Total Environ. 191:1996;23-58.
12. Bickham J.W., Sandhu S., Hebert P.D.N., Chikhi L., Athwal R. Effects of chemical contaminants on genetic diversity in natural populations: implications for biomonitoring and ecotoxicology. Mutat. Res. 463:2000;33-51.
13. Becerril C., Ferrero M., Sanz F., Castaño A. Detection of mitomycin C-induced genetic damage in fish cells by use of RAPD. Mutagenesis. 14:1999;449-456.
14. Cronin M.A., Bickham J.W. A population genetic analysis of the potential for a crude oil spill to induce heritable mutations and impact natural populations. Ecotoxicology. 7:1998;259-278.
15. Farag A.M., Boese C.J., Woodward D.F., Bergman H.L. Physiological-changes and tissue metal accumulation in rainbow-trout exposed to foodborne and waterborne metals. Environ. Toxicol. Chem. 13:1994;2021-2029.
16. Depledge M.H., Billinghurst Z. Ecological significance of endocrine disruption in marine invertebrates. Mar. Pollut. Bull. 39:1999;32-38.
17. Troncoso L., Galleguillos R., Larrain A. Effects of copper on the fitness of the Chilean scallop Argopecten purpuratus (Mollusca: Bivalvia). Hydrobiologia. 420:2000;185-189.
18. Lande R. Anthropogenic, ecological and genetic factors in extinction and conservation. Res. Popul. Ecol. 40:1998;259-269.
19. Beasley G., Kneale P. Reviewing the impact of metals and PAH's on macro invertebrates in urban watercourses. Prog. Phys. Geogr. 26:2002;236-270.
20. Edwards C.A. Assessing the effects of environmental pollutants on soil organisms, communities, processes and ecosystems. Eur. J. Soil Biol. 38:2002;225-231.
21. D.L. Hartl, A.G. Clark, Principles of Population Genetics, second ed., Sinauer Associates, Inc., Suderland, USA, 1998.
22. Wright S. Evolution in Mendelian populations. Genetics. 16:1931;97-159.
23. Bernardes A.T. Mutation load and the extinction of large populations. Physica A. 230:1996;156-173.
24. R.B. Gillespie, S.I. Guttman, Chemical-induced changes in the genetic structure of populations: effects on allozymes, in: V.E. Forbes (Ed.), Genetics and Ecotoxicology, Taylor & Francis, Philadelphia, 1999, pp. 55-77.
25. A Atienzar F., Conradi M., Evenden A.J., Jha A.N., Depledge M.H. Qualitative assessment of genotoxicity using random amplified polymorphic DNA: comparison of genomic template stability with key fitness parameters in Daphnia magna exposed to benzo[a]pyrene. Environ. Toxicol. Chem. 18:1999;2275-2282.
26. Lavie B., Nevo E. Heavy metal selection of phosphoglucose isomerase allozymes in marine gastropods. Mar. Biol. 71:1982;17-22.
27. Lavie B., Nevo E. Genetic selection of homozygote allozyme genotypes in marine gastropods exposed to cadmium. Sci. Total Environ. 57:1986;91-98.
28. Nevo B., Ben-Shlomo R., Lavie B. Mercury selection of allozymes in marine organisms: predictions and verification in nature. Proc. Natl. Acad. Sci. U.S.A. 81:1984;1258-1259.
29. Nevo B., Noy R., Lavie B., Beiles A., Muchtar S. Genetic diversity and resistance to marine pollution. Biol. J. Linn. Soc. 29:1986;139-144.
30. Tranvik L., Sjörgen M., Bengtsson G. Allozyme polymorphism and protein profile in Orchesella bifasciata (Collembola): indicative of extended metal pollution? Biochem. Syst. Ecol. 22:1994;13-23.
31. Williams J.G.K., Kubelik A.R., Livak K.J., Rafalski J.A., Tingey S.V. DNA polymorphisms amplified by arbitrary primers are useful as genetic markers. Nucleic Acids Res. 18:1990;6531-6535.
32. Welsh J., McClelland M. Fingerprinting genomes using PCR with arbitrary primers. Nucleic Acids Res. 18:1990;7213-7218.
33. Caetano-Anolles G., Bassam B.J., Grensshoff P.M. DNA amplification fingerprinting using very short arbitrary oligonucleotide primers. Biotechnology. 9:1991;553-557.
34. B.A. Schaal, W.J. Leverich, S.H. Rogstad, A comparison of methods for assessing genetic variation in plant conservation biology, in: D.A. Falk, K.E. Holsinger (Eds.), Genetics and Conservation of Rare Plants, Oxford University Press, New York, 1991, pp. 123-134.
35. P. Fritsch, L.H. Rieseberg. The use of random amplified polymorphic DNA (RAPD) in conservation genetics, in: T.B. Smither, R.K. Wayne (Eds.), Molecular Genetic Approaches in Conservation, Oxford University Press, 1996, pp. 55-73.
36. S.A. Harris, RAPDs in systematics - a useful methodology? in: P.M. Hollingsworth, R.M. Bateman, R.J. Gornal (Eds.), Molecular Systematics and Plant Evolution, The Systematics Association Special Volume Series 57, Taylor & Francis, London, UK, 1999, pp. 211-228.
37. Benter T., Papadopoulos S., Pape M., Manns M., Poliwoda H. Optimization and reproducibility of random amplified polymorphic DNA in human. Anal. Biochem. 230:1995;92-100.
38. Gravesen A., Jacobsen T., Møller P.L., Hansen F., Larsen A.G., Knøchel S. Genotyping of Listeria monocytogenes: comparison of RAPD, ITS, and PFGE. Int. J. Food Microbiol. 57:2000;43-51.
39. Fraga J., Rojas L., Sariego I., Sarria C.A. Optimization of random amplified polymorphic DNA techniques for its use in genetic studies of Trichomonas vaginalis isolates, Infection. Genet. Evolut. 2:2002;73-75.
40. Blixt Y., Knutsson R., Borch E., Rådström P. Interlaboratory random amplified polymorphic DNA typing of Yersinia enterocolitica and Y. enterocolitica-like bacteria. Int. J. Food Microbiol. 83:2003;15-26.
41. Kump B., Javornik B. Evaluation of genetic variability among common buckwheat (Fagopyrum esculentum Moench) populations by RAPD markers. Plant Sci. 114:1996;149-158.
42. Aagaard J.E., Krutovskii K.V., Strauss S.H. RAPD markers of mitochondrial origin exhibit lower population diversity and higher differentiation than RAPDs of nuclear origin in Douglas fir. Mol. Ecol. 7:1998;801-812.
43. Bouzat J.L. The population genetic structure of the greater rhea (Rhea americana) in an agricultural landscape. Biol. Conserv. 99:2001;277-284.
44. Ge X.-J., Yu Y., Zhao N.-X., Chen H.-S., Qi W.-Q. Genetic variation in the endangered inner Mongolia endemic shrub Tetraena mongolica Maxim. (Zygophyllaceae). Biol. Conserv. 11:2003;427-434.
45. Maltagliati F., Domenici P., Fosh C.F., Cossu P., Casu M., Castelli A. Small-scale morphological and genetic differentiation in the Mediterranean killifish Aphanius fasciatus (Cyprinodontidae) from a coastal brackish-water pond and an adjacent pool in northern Sardinia. Oceanol. Acta. 26:2003;111-119.
46. M. Lynch, B.G. Milligan, Analysis of population genetic structure with RAPD markers, Mol. Ecol. 3 (1994) 91-99.
47. Backeljau T., De Bruyn L., De Wolf H., Jordaens K., Van Dongen S., Verhagen R., Winnepenninckx B. Random amplified polymorphic DNA (RAPD) and parsimony methods. Cladistics. 11:1995;119-130.
48. Nicese F.P., Hormaza J.I., McGranahan G.H. Molecular chracterisation and genetic ralatedness among walnut (Juglans regia L.) genotypes based on RAPD markers. Euphytica. 101:1998;199-206.
49. Lacerda D.R., Lemos J.P., Acedo M.D.P., Lovato M.B. Molecular differentiation of two vicariant neotropical tree species, Plathymenia foliolosa and P. reticulata (Mimosoidea), inferred using RAPD markers. Plant Syst. E. 235:2002;67-77.
50. Barman H.K., Barat A., Yadav B.M., Banerjee S., Meher P.K., Reddy P.V.G.K., Jana R.K. Genetic variation between four species of Indian major carps as revealed by random amplified polymorphic DNA assay. Aquaculture. 217:2003;115-123.
51. Atienzar F.A., Billinghurst Z., Depledge M.H. 4-n-Nonylphenol and 17-β estradiol may induce common DNA effects in developing barnacle larvae. Environ. Pollut. 120:2002;735-738.
52. Atienzar F.A., Evenden A.J., Jha A.N., Depledge M.H. Use of the random amplified polymorphic DNA (RAPD) assay for the detection of DNA damage and mutations: possible implications of confounding factors. Biomarkers. 7:2002;94-101.
53. Atienzar F.A., Venier P., Jha A.N., Depledge M.H. Evaluation of the random amplified polymorphic DNA (RAPD) assay for the detection of DNA damage and mutations. Mutat. Res. 521:2002;151-163.
54. Atienzar F.A., Cheung V.V., Jha A.N., Depledge M.H. Fitness parameters and DNA effects are sensitive indicators of copper induced toxicity in Daphnia magna. Toxicol. Sci. 59:2001;241-250.
55. Atienzar F.A., Cordi B., Donkin M.E., Evenden A.J., Jha A.N., Depledge M.H. Comparison of ultraviolet-induced genotoxicity detected by random amplified polymorphic DNA with chlorophyll fluorescence and growth in a marine macroalgae, Palmaria palmate. Aquat. Toxicol. 50:2000;1-12.
56. Jones C., Kortenkamp A. RAPD library fingerprinting of bacterial and human DNA: applications in mutation detection. Teratogen. Carcinogen. Mutagen. 20:2000;49-63.
57. Conte C., Mutti I., Puglisi P., Ferrarini A., Regina G., Maestri E., Marmiroli N. DNA fingerprinting analysis by a PCR based method for monitoring the genotoxic effects of heavy metals pollution. Chemosphere. 37:1998;2739-2749.
58. Ross K., Cooper N., Bidwell J.R., Elder J. Genetic diversity and metal tolerance of two marine species: a comparison between populations from contaminated and reference sites. Mar. Pollut. Bull. 44:2002;671-679.
59. Theodorakis C.W., Shugart L.R. Genetic ecotoxicology. II. Population genetic structure in mosquitofish exposed in situ to radionuclides. Ecotoxicology. 6:1997;335-354.
60. Theodorakis C.W., Bickham J.W., Elbl T., Shugart L.R., Chesser R.K. Genetics of radionuclide-contaminated mosquitofish populations and homology between Gambusia affinis and G. holbrooki. Environ. Toxicol. Chem. 17:1998;1992-1998.
61. Turuspekov Y., Adams R.P., Kearney C.M. Genetic diversity in three perennial grasses from Semipalatinsk nuclear testing region of Kazakhstan after long-term radiation exposure. Biochem. Syst. Ecol. 30:2002;809-817.
62. Lynch M. The similarity index and DNA fingerprinting. Mol. Biol. E. 7:1990;478-484.
63. James E.A., Ashburner G.R. Intraspecific variation in Astelia australiana (Liliaceae) and implications for the conservation of this Australian species. Biol. Conserv. 82:1997;253-261.
64. Maldonado San Martin A.P., Adamec L., Suda J., Mes T.H.M., Štorchová H. Genetic variation within the endangered species Aldrovanda vesiculosa (Droseraceae) as revealed by RAPD analysis. Aquat. Bot. 75:2003;159-172.
65. J. Czekanowski, Zarys method statystycznyck (Die grundzuge der statistisken methoden), Warsaw, 1913.
66. Dice L.R. Measures of the amount of ecological association between species. Ecology. 26:1945;297-302.
67. Sørensen T. A method for establishing groups of equal amplitude in plant sociology based on similarity of species content and its applications to analysis of the vegetation on Danish commons. Biol. Skr. 5:1948;1-34.
68. Nei M., Li W.H. Mathematical model for studying genetic variation in terms of restriction endonucleases. Proc. Natl. Acad. Sci. U.S.A. 74:1979;5267-5273.
69. Bertorelle G., Bucchini L., Pilastro A., Matessi C. DNA fingerprinting data and the analysis of population genetic structure by comparing band-sharing patterns. Mol. Ecol. 8:1999;1851-1866.
70. Danforth B.N., Freeman-Gallant C.R. DNA fingerprinting data and the problem of non-independence among pairwise comparisons. Mol. Ecol. 5:1996;221-227.
71. A.E. Magurran, Ecological Diversity and Its Measurement, Chapman and Hall, London, 1988.
72. N. Wiener, Cybernetics: or Control and Communication in the Animal and Machine, Wiley, New York, 1948.
73. C.E. Shannon, W. Weaver, The Mathematical Theory of Communication, University of Illinois Press, Urbana, IL, 1949.
74. Simpson E.H. Measurement of diversity. Nature. 163:1949;688.
75. Cardoso M.A., Provan J., Powell W., Ferreiras P.C.G., De Oliveira D.E. High genetic differentiation among remnant populations of the endangered Caesalpinia echinata Lam. (Leguminosae - Caesalpinioideae). Mol. Ecol. 7:1998;601-608.
76. Gabrielsen T.M., Brochmann C. Sex after all: high levels of diversity detected in the arctic clonal plant Saxifraga cernua using RAPD markers. Mol. Ecol. 7:1998;1701-1708.
77. Gaudeul M., Taberlet P., Till-Bottraud I. Genetic diversity in an endangered alpine plant, Eryngium alpinum L. (Apiaceae), inferred from amplified fragment length polymorphism markers. Mol. Ecol. 9:2000;1625-1637.
78. Nagendra H. Opposite trends in response for the Shannon and Simpson indices of landscape diversity. Appl. Geogr. 22:2002;175-186.
79. Hirschfeld H.O. A connection between correlation and contingency. Proc. Cambridge Philos. Soc. 31:1935;520-524.
80. Fisher R.A. The precision of discriminant functions. Anal. Eugen. 10:1940;422-429.
81. Shennan I., Long A.J., Rutherford M.M., Green F.M., Innes J.B., Lloyd J.M., Zong Y., Walker K.J. Tidal marsh stratigraphy, sea level change and large earthquakes, I: a 5000-year record in Washington, USA. Quat. Sci. Rev. 15:1996;1023-1059.
82. Thomas V., Treitz P., Jelinski D., Miller J., Lafleur P., McCaughey J.H. Image classification of a northern peatland complex using spectral and community data. Remote Sens. Environ. 84:2002;83-99.
83. Shaltout K.H., Sheded M.G., El-Kady H.F., Al-Sodany Y.M. Phytosociology and size structure of Nitraria retusa along the Egyptian Red Sea coast. J. Arid Environ. 53:2003;331-345.
84. Amsellem L., Noyer J.L., Le Bourgeois T., Hossaert-McKey M. Comparison of genetic diversity of the invasive weed Rubus alceifolius Poir (Rosaceae) in its native range and in areas of introduction, using amplified fragment length polymorphism (AFLP) markers. Mol. Ecol. 9:2000;443-455.
85. B.F.J. Manly, Multivariate Statistical Methods: A Primer, Chapman and Hall, London, 1994.
86. M.O. Hill, TWINSPAN - A FORTRAN Programme for Arranging Multivariate Data in an Ordered Two-Way Table by Classification of the Individuals and Attributes, Cornell University, Ithaca, NY, 1979.
87. Gauch H.G. Jr., Whittacker R.H. Hierarchical classification of community data. J. Ecol. 69:1981;537-557.
88. Mezquita F., Hernandez R., Rueda J. Ecology and distribution of ostracods in a polluted Mediterranean river. Palaeogeogr. Palaeoclim. Palaeoecol. 148:1999;87-103.
89. S. Wright, Variability Within and Among Natural Populations, vol. 4, The University of Chicago Press, Chicago, USA, 1978.
90. B. Black, RAPDFST 4.0.1 - A FORTRAN Program to Estimate F(ST) and Effective Migration Rates Among Subpopulations Using RAPD-PCR Files, Colorado State University, 1997.
91. Apostol B.L., Black W.C., Reiter P., Miller B.R. Population genetics with RAPD-PCR markers: the breeding structure of Aedes aegypti in Puerto Rico. Heredity. 76:1996;325-334.
92. De Wolf H., Backeljau T., Verhagen R. Congruence between allozyme and RAPD data in assessing macrogeographical genetic variation in the periwinkle Littorina striata (Mollusca, Gastropoda). Heredity. 81:1998;486-492.
93. Bártfai R., Egedi S., Yue G.H., Kovács B., Urbányi B., Tamás G., Horváth L., Orbán L. Genetic analysis of two common carp broodstocks by RAPD and microsatellite markers. Aquaculture. 219:2003;157-167.
94. Theodorakis C.W., Bickham J.W., Lamb T. Integration of genotoxicity and population genetic analyses in kangaroo rats (Dipodomys merriami) exposed to radionuclide contamination at the Nevada test site, USA. Environ. Toxicol. Chem. 20:2001;317-326.
95. Ma X.L., Cowles D.L., Carter R.L. Effect of pollution on genetic diversity in the bay mussel Mytilus galloprovincialis and the acorn barnacle Balanus glandula. Mar. Environ. Res. 50:2000;559-563.
96. Yan G.Y., Chadee D.D., Severson D.W. Evidence for genetic hitchhiking effect associated with insecticide resistance in Aedes aegypti. Genetics. 148:1998;793-800.
97. Borowsky R.L. Estimating nucleotide diversity from random amplified polymorphic DNA and amplified fragment length polymorphism data. Mol. Phylogen. Evol. 18:2001;143-148.
98. Excoffier L., Smouse P.E., Quatro J.M. Analysis of molecular variance inferred from metric distances among DNA haplotypes: application to human mitochondrial DNA restriction data. Genetics. 131:1992;479-491.
99. Porter J.S., Ryland J.S., Cravalho G.R. Micro- and macrogeographic genetic structure in bryozoans with different larval strategies. J. Exp. Mar. Biol. Ecol. 272:2002;119-130.
100. Todd C.D., Walker A.M., Wolff K., Northcott S.J., Walker A.F., Ritchie M.G., Hoskins R., Abbott R.J., Hazon N. Genetic differentiation of populations of the copepod sea louse Lepeophtheirus salmonis (Krøyer) ectoparasite on wild and farmed salmonids around the coasts of Scotland: evidence from RAPD markers. J. Exp. Mar. Biol. Ecol. 210:1997;251-274.
101. Huang B.X., Peakall R., Hanna P.J. Analysis of genetic structure of blacklip abalone (Haliotis rubra) populations using RAPD, minisatellite and microsatellite markers. Mar. Biol. 136:2000;207-216.
102. Jäggi C., Wirth T., Baur B. Genetic variability in subpopulations of the asp viper (Vipera aspis) in the Swiss Jura mountains: implications for a conservation strategy. Biol. Conserv. 94:2000;69-77.
103. Mengoni A., Gonnelli C., Galardi F., Gabbrielli R., Bazzicalupo M. Genetic diversity and heavy metal tolerance in populations of Silence paradoxa L. (Caryophyllaceae): a random amplified polymorphic DNA analysis. Mol. Ecol. 9:2000;1319-1324.
104. Michelmore R.W., Paran I., Kesseli R.V. Identification of markers linked to disease-resistance genes by bulked segregant analysis: a rapid method to detect markers in specific genomic regions by using segregating populations. Proc. Natl. Acad. Sci. U.S.A. 88:1991;9828-9832.
105. Chun S.J., Lee Y.H. Genetic analysis of a mutation on appressorium formation in Magnaporthe grisea. FEMS Microbiol. Lett. 173:1999;133-137.
106. Parsons Y.PaltiJ.E., Thorgaard G.H. Identification of candidate DNA markers associated with IHN virus resistance in backcrosses of rainbow (Oncorynchus mykiss) and cutthroat trout (O. clarki). Aquaculture. 173:1999;81-94.
107. Dehmer K.J., Friedt W. Development of molecular markers for high oleic acid content in sunflower (Helianthus annuus L.). Ind. Crops Prod. 7:1998;311-315.
108. Wirthensohn M.G., Collins G., Jones G.P., Sedgley M. Variability in waxiness of Eucalyptus gunnii foliage for floriculture. Sci. Hortic. 82:1999;279-288.
109. Ramirez L., Muez V., Alfonso M., Garcia Barrenechea A., Alfonso L., Pisabarro A.G. Use of molecular markers to differentiate between commercial strains of the button mushroom Agaricus bisporus. FEMS Microbiol. Lett. 198:2001;45-48.
110. Wu J.-Y., Wu H.-K., Chung M.-C. Co-dominant RAPD markers closely linked with two morphological genes in rice (Oryza sativa L.). Bot. Bull. Acad. Sin. 43:2002;171-180.