How to detect polymorphisms undergoing selection in marine fishes? A review of methods and case studies, including flatfishes

Journal of Sea Research

Volumn 51, Issue 3-4, 2004, Pages 167-182

  Guinand, Bruno ^a   Lemaire, Christophe ^a   Bonhomme, François ^a  

^a UNIV MONTPELLIER   (France)

Author keywords

Adaptation; Molecular markers; Selection; Statistical tests

Indexed keywords

GENETIC MARKER; POLYMORPHISM; POPULATION DYNAMICS; SALINITY; SELECTION; TEMPERATURE;

PISCES; PLEURONECTIFORMES;

EID: 2342561231     PISSN: 13851101     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.seares.2003.10.002     Document Type: Article

References (99)

1. Akey J.M., Zhang G., Zhang K., Jin L., Shriver M.D. Interrogating a high-density SNP map for signature of natural selection. Genome Res. 12:2002;1805-1814
2. Arnaud-Haond S., Bonhomme F., Blanc F. Large discrepancies in differentiation of allozymes, nuclear and mitochondrial DNA loci in recently founded Pacific populations of the pearl oyster Pinctada margaritifera. J. Evol. Biol. 16:2003;388-396
3. st: fish, allozymes and the Lewontin-Krakauer test revisited. Genetics. 152:1999;653-659
4. Bailey K.M. Structural dynamics and ecology of flatfish populations. J. Sea Res. 37:1997;269-280
5. Bargelloni L., Marcato S., Patarnello T. Antarctic fish haemoglobins: evidence for adaptive evolution at subzero temperature. Proc. Natl. Acad. Sci. USA. 95:1998;8670-8675
6. Barton N.H. Genetic hitchhiking. Phil. Trans. R. Soc. Lond. 355:2000;1553-1562
7. Beaumont M.A., Nichols R.A. Evaluating loci for use in the genetic analysis of population structure. Proc. R. Soc. Lond. B263:1996;1619-1626
8. Begun D.J., Aquadro C.F. Levels of naturally occuring DNA polymorphism correlate with recombination rate in D. melanogaster. Nature. 356:1992;519-520
9. Bernardi G., Sordino P., Powers D.A. Concordant mitochondrial and nuclear DNA phylogenies for populations of the teleost fish, Fundulus heteroclitus. Proc. Natl. Acad. Sci. USA. 90:1993;9271-9274
10. Bernatchez L., Landry C. Mhc studies in non-model vertebrates: what have we learned about natural selection in the past 15 years? J. Evol. Biol. 16:2003;363-377
11. Blier P.U., Lemieux H. The impact of thermal sensitivity to cytochrome oxidase on the respiration rate of Arctic charr red muscle mitochondria. J. Comp. Physiol. Biol. 171:2001;247-253
12. Blier P.U., Dufresne F., Burton R. Natural selection and the evolution of mtDNA encoded peptides: insights from studies of protein function and cytonuclear coadaptation. Trends Genet. 17:2001;400-406
13. Bowcock A.M., Kidd J.R., Mountain J.L., Hebert J.M., Carotenuto L., Kidd K.K., Cavalli-Sforza L.L. Drift, admixture, and selection in human evolution: a study with DNA polymorphisms. Proc. Natl. Acad. Sci. USA. 88:1991;839-843
14. Brown B.L., Chapman R.W. Gene flow and mitochondrial DNA variation in the killifish, Fundulus heteroclitus. Evolution. 45:1991;1147-1161
15. Burton R.S., Rawson P.D., Edmands S. Genetic architecture of physiological phenotypes: empirical evidence for coadapted gene complexes. Am. Zool. 39:1999;451-462
16. Campana S.E. Chemistry and composition of fish otoliths: pathways, mechanisms and applications. Mar. Ecol. Prog. Ser. 188:1999;263-297
17. Carey M., Smale S.T. Transcriptional Regulation in Eukaryotes: Concepts, Strategies, and Techniques. 2000;Cold Spring Harbor Laboratory Press, Cold Spring Harbor
18. Cheung V.G., Spielman R.S. The genetics of variation in gene expression. Nat. Genet. 32:2002;S522-S525
19. Chikhi L. Différenciation génétique chez Sardinella aurita and S. maderensis: allozymes et ADN mitochondrial. 1995;ORSTOM Editions, Paris
20. Cohen S. Strong positive selection and habitat-specific amino-acid substitution patterns in Mhc from an estuarine fish under intense pollution stress. Mol. Biol. Evol. 19:2002;1870-1880
21. Conover D.O. Local adaptations in marine fishes: evidence and implications for stock enhancement. Bull. Mar. Sci. 62:1998;305-311
22. Conover D.O. Darwinian fishery science. Mar. Ecol. Prog. Ser. 208:2000;303-307
23. Conover D.O., Munch S.B. Sustaining fisheries yields over evolutionary time scales. Science. 297:2001;94-96
24. Conover D.O., Schultz E.T. Phenotypic similarity and the evolutionary significance of countergradient variation. Trends Ecol. Evol. 10:1995;248-252
25. Crawford D.L., Powers D.A. Evolutionary adaptation to different thermal environments via transcriptional regulation. Mol. Biol. Evol. 9:1992;806-813
26. Danzmann R.G., Ferguson M.M. Heterogeneity in the body size of cultured Ontario rainbow trout with different mitochondrial haplotypes. Aquaculture. 137:1995;231-244
27. Debenham P., Brzezinski M.A., Foltz K.R. Evaluation of sequence variation and selection in the bindin locus of the Red Sea urchin, Strongylocentrotus franciscanus. J. Mol. Evol. 51:2000;481-490
28. Depledge M.H. Genetic ecotoxicology: a review. J. Exp. Mar. Biol. Ecol. 200:1996;57-66
29. DiMichele L., Powers D.A. Physiological basis for swimming endurance differences between LDH-B genotypes of Fundulus heteroclitus. Science. 216:1982;1014-1016
30. DiMichele L., Powers D.A. Developmental heterochrony and differential mortality in the model teleost, Fundulus heteroclitus. Physiol. Zool. 64:1991;1426-1443
31. Doiron S., Bernatchez L., Blier P.U. A comparative mitogenomics analysis of potential adaptive value of Arctic charr mtDNA introgression in Brook charr populations (Salvelinus fontinalis Mitchill). Mol. Biol. Evol. 19:2002;1902-1909
32. Eanes W.F. Analysis of selection on enzyme polymorphisms. Ann. Rev. Ecol. Syst. 30:1999;301-326
33. Endo T., Ikeo K., Gojobori T. Large-scale search for genes on which positive selection may operate. Mol. Biol. Evol. 13:1996;685-690
34. Fauvelot C., Bernardi G., Planes S. Reductions in the mitochondrial DNA diversity of coral reef fish provide evidence of population bottlenecks resulting from Holocene sea-level change. Evolution. 57:2003;1571-1583
35. Ferguson M.M., Danzmann R.G. Inter-strain differences in the association between mitochondrial DNA haplotype and growth in cultured Ontario rainbow trout (Oncorhynchus mykiss). Aquaculture. 178:1999;245-252
36. Ford M.J. Applications of selective neutrality tests to molecular ecology. Mol. Ecol. 11:2002;1245-1262
37. Frank K.T., Leggett W.C. Fisheries ecology in the context of ecological and evolutionary theory. Ann. Rev. Ecol. Syst. 25:1994;401-422
38. Fu Y.-X. New statistical tests of neutrality for DNA samples. Genetics. 143:1996;557-570
39. Fu Y.-X. Statistical tests of neutrality of mutations against population growth, hitchhiking and background selection. Genetics. 146:1997;915-925
40. Gerber A.S., Loggins R., Kumar S., Dowling T. Does non neutral evolution shape observed patterns of DNA variation in animal mitochondrial genomes? Ann. Rev. Genet. 35:2001;539-566
41. Gillespie J.H. The Causes of Molecular Evolution. 1991;Oxford University Press, Oxford
42. Hauser L., Ward R.D. Population identification in pelagic fishes: the limits of molecular markers. Carvalho G.R. Advances in Molecular Ecology. 1998;191-224 IOS Press, Amsterdam
43. Hellberg M.E., Moy G.W., Vacquier V.D. Positive selection and propeptide repeats promote rapid interspecific divergence of a gastropod sperm protein. Mol. Biol. Evol. 17:2000;458-466
44. Hoarau G., Rijnsdorp A.D., Van der Veer H.W., Stam W.T., Olsen J.L. Population structure of plaice (Pleuronectes platessa L.) in Northern Europe: microsatellites revealed large-scale spatial and temporal homogeneity. Mol. Ecol. 11:2002;1165-1176
45. Huang C.S., Weng C.F., Lee S.C. Distinguishing two types of gray mullet, Mugil cephalus L. (Mugiliformes: Mugilidae), by using glucose-6-phosphate isomerase (GPI) allozymes with special reference to enzyme activities. J. Comp. Physiol. B171:2001;387-394
46. Hutchings J.A. Numerical assessment in the front seat, ecology and evolution in the back seat: time to change drivers in fisheries and aquatic sciences? Mar. Ecol. Prog. Ser. 208:2000;299-303
47. Kim T., Parker P., Hedrick P. Major histocompatibility complex differentiation in Sacramento River chinook salmon. Genetics. 151:1999;1115-1122
48. Kimura M. The Neutral Theory of Molecular Evolution. 1983;Cambridge University Press, Cambridge
49. Kreitman M. Methods to detect selection in populations with applications to the human. Ann. Rev. Genom. Hum. Genet. 1:2000;539-559
50. Laroche J., Quiniou L., Juhel G., Auffret M., Moraga D. Genetic and physiological responses of flounder (Platichthys flesus) populations to chemical contamination in estuaries. Environ. Toxicol. Chem. 21:2002;2705-2712
51. Law R. Fishing, selection, and phenotypic evolution. ICES J. Mar. Sci. 57:2000;659-668
52. Lemaire C., Allegrucci G., Naciri M., Bahri-Sfar L., Kara H., Bonhomme F. Do discrepancies between microsatellite and allozyme variation reveal differential selection between sea and lagoon in the sea bass (Dicentrarchus labrax)? Mol. Ecol. 9:2000;457-467
53. Lewontin R.C., Krakauer J. Distribution of gene frequency as a test of the theory of selective neutrality of polymorphisms. Genetics. 74:1973;175-195
54. Manzon L.A. The role of prolactin in fish osmoregulation: a review. Gen. Comp. Endocrin. 125:2002;291-310
55. Marchand J., Tanguy A., Laroche J., Quiniou L., Moraga D. Responses of European flounder Platichthys flesus populations to contamination in different estuaries along the Atlantic coast of France. Mar. Ecol. Prog. Ser. 260:2003;273-284
56. Maynard-Smith J., Haigh J. The hitchhiking effect of a favorable gene. Genet. Res. 23:1974;23-35
57. McCormick S.D. Endocrine regulation of osmoregulation in teleost fish. Am. Zool. 41:2001;781-794
58. Miller K., Withler R., Beacham T. Molecular evolution of the Mhc genes in two populations of chinook salmon Oncorrhynchus tshawytscha. Mol. Ecol. 6:1997;937-954
59. Mitton J. Selection in Natural Populations. 1997;Oxford University Press, Oxford
60. Mitton J.B., Koehn R.K. Genetic organization and adaptive response of allozymes to ecological variables in Fundulus heteroclitus. Genetics. 79:1975;97-111
61. Murray B., Michaud R., White B. Allelic and haplotype variation of major histocompatibility complex class II DRB1 and DQB loci in the St. Lawrence beluga (Delphinapterus leucas). Mol. Ecol. 8:1999;1127-1139
62. Nacci D., Coiro L., Champlin D., Jayaraman S., McKinney R., Gleason T.R., Munns W.R. Jr., Speker J.L., Cooper K.R. Adaptations of wild populations of the estuarine fish Fundulus heteroclitus to persistent environmental contaminants. Mar. Biol. 134:1999;9-17
63. Nei M., Maruyama T. Lewontin-Krakauer test for neutral genes. Genetics. 80:1975;395
64. Nevo E., Ben-Shlomo R., Lavie B. Mercury selection of allozymes in marine organisms: prediction and verification in nature. Proc. Natl. Acad. Sci. USA. 81:1984;1258-1259
65. Nielsen R. Statistical tests of selective neutrality in the age of genomics. Heredity. 86:2001;641-647
66. Oleksiak M.F., Churchill G.A., Crawford D.L. Variation in gene expression within and among natural populations. Nat. Genet. 32:2002;261-266
67. Palumbi S.R. All males are not created equal: fertility differences depends on gamete recognition polymorphisms in sea urchins. Proc. Natl. Acad. Sci. USA. 96:1999;12632-12637
68. Pogson G.H. Nucleotide polymorphism and natural selection at the pantophysin (Pan I) locus in the Atlantic cod, Gadus morhua (L.). Genetics. 157:2001;317-330
69. Pogson G.H., Fevolden S.E. DNA heterozygosity and growth rate in the Atlantic cod, Gadus morhua (L.). Evolution. 52:1998;915-920
70. Pogson G.H., Mesa K.A., Boutilier R.G. Genetic population structure and gene flow in the Atlantic cod Gadus morhua: a comparison of allozyme and nuclear RFLP loci. Genetics. 139:1995;375-385
71. Pogson G.H., Taggart C.T., Mesa K.A., Boutilier R.G. Isolation-by- distance in the Atlantic cod, Gadus morhua, a comparison of allozyme and nuclear RFLP. Evolution. 55:2001;131-146
72. Powers D.A., Schulte P.M. Evolutionary adaptations of gene structure and gene expression in natural populations in relation to a changing environment: a multidisciplinary approach to address the million-year saga of a small fish. J. Exp. Zool. 282:1998;71-94
73. Ramos-Onsins S.E., Rozas E. Statistical properties of new neutrality tests against population growth. Mol. Biol. Evol. 19:2002;2092-2100
74. Rawson P.D., Burton R.S. Functional coadaptation between cytochrome c and cytochrome c oxidase within allopatric populations of a marine copepod. Proc. Natl. Acad. Sci. USA. 99:2002;12955-12958
75. Rijnsdorp A.D. Fisheries as a large-scale experiment on life-history evolution: disentangling phenotypic and genetic effects in maturation and reproduction of North Sea plaice, Pleuronectes platessa L. Oecologia. 96:1993;391-401
76. Robertson A. Remarks on the Lewontin-Krakauer test. Genetics. 80:1975;396
77. Robertson A. Gene frequency distribution as a test of selective neutrality. Genetics. 81:1975;775-785
78. Roy N.K., Kreamer G.-L., Konkle B., Grunwald C., Wirgin I. Characterization and prevalence of a polymorphism in the 3′ untranslated region of cytochrome P4051A1 in cancer-prone Atlantic tomcod. Arch. Biochem. Biophys. 322:1995;204-213
79. Ruzzante D.E., Taggart C.T., Cook D. A review of the evidence for genetic structure of cod (Gadus morhua) populations in the NW Atlantic and population affinities of larval cod off Newfoundland and the gulf of St. Lawrence. Fish. Res. 43:1999;79-97
80. Schlötterer C. A microsatellite-based multilocus screen for the identification of local selective sweeps. Genetics. 160:2002;753-763
81. Schlötterer C. Towards a molecular characterization of adaptation in local populations. Curr. Opin. Genet. Dev. 12:2002;683-687
82. Schulte P.M. Environmental adaptations as windows for molecular evolution. Comp. Biochem. Physiol. B128:2000;597-611
83. Schulte P.M., Gomez-Chiarri M., Powers D.A. Structural and functional differences in the promoter and 5′ flanking region of the Ldh-B within and between populations of the teleost Fundulus heteroclitus. Genetics. 145:1997;759-769
84. Schulte P.M., Glemet H.C., Fiebig A.A., Powers D.A. Adaptive variation in the lactate dehydrogenase-B gene expression: role of a stress-responsive regulatory element. Proc. Natl. Acad. Sci. USA. 97:2000;6597-6602
85. Segal J.L., Schulte P.M., Powers D.A., Crawford D.L. Descriptive and functional characterization of variation in Fundulus heteroclitus proximal promoter. J. Exp. Zool. 275:1996;355-364
86. Skibinski D.O.F. DNA tests of neutral theory: applications in marine genetics. Hydrobiologia. 420:2000;137-152
87. Simonsen K.L., Churchill G.A., Aquadro C.F. Properties of statistical tests of neutrality for DNA polymorphism data. Genetics. 141:1995;413-429
88. Slatkin M. Hitchhiking and associative overdominance at a microsatellite locus. Mol. Biol. Evol. 12:1995;473-480
89. Slatkin M., Hudson R.R. Pairwise comparisons of mitochondrial DNA sequences in stable and exponentially growing populations. Genetics. 129:1991;555-562
90. Stergiou K.I. Overfishing, tropicalization of fish stocks, uncertainty and ecosystem management: resharpening Ockham' razor. Fish Res. 55:2002;1-9
91. Streelman J.T., Kocher T.D. Microsatellite variation associated with prolactin expression and growth of salt-challenged tilapia. Physiol. Genomics. 9:2002;1-4
92. Taylor M.S., Hellberg M.E. Genetic evidence for local retention of pelagic larvae in a Caribbean reef fish. Science. 299:2003;107-109
93. Tajima D. Statistical method for testing the neutral mutation hypothesis by DNA polymorphism. Genetics. 123:1989;585-595
94. Tsakas S., Krimbas C.B. Testing the heterogeneity of F values: a suggestion and a correction. Genetics. 84:1976;399-401
95. Vacquier V.D., Swanson W.J., Lee Y.H. Positive Darwinian selection on two homologous fertilization proteins: what is the selective pressure driving their divergence? J. Mol. Evol. 44:1997;S15-S22
96. Vitalis R., Dawson K.R., Boursot P. Interpretation of variation across marker loci as evidence of selection. Genetics. 158:2001;1811-1823
97. Waples R.S. Separating the wheat from the chaff: patterns of genetic differentiation in high gene flow species. J. Hered. 89:1998;438-450
98. Weir B.S., Cockerham C.C. Estimating F-statistics for the analysis of population structure. Evolution. 38:1984;1358-1370
99. Wright S.W. The genetical structure of populations. Ann. Eugen. 15:1951;323-354