, Volume 123, Issue 1–2, pp 15–24 | Cite as

Testing hypotheses regarding the genetics of adaptation

  • Patrick C. PhillipsEmail author


Many of the hypotheses regarding the genetics of adaptation require that one know specific details about the genetic basis of complex traits, such as the number and effects of the loci involved. Developments in molecular biology have made it possible to create relatively dense maps of markers that can potentially be used to map genes underlying specific traits. However, there are a number of reasons to doubt that such mapping will provide the level of resolution necessary to specifically address many evolutionary questions. Moreover, evolutionary change is built upon the substitution of individual mutations, many of which may now be cosegregating in the same allele. In order for this developing area not to become a mirage that traps the efforts of an entire field, the genetic dissection of adaptive traits should be conducted within a strict hypothesis-testing framework and within systems that promise a reasonable chance of identifying the specific genetic changes of interest. Continuing advances in molecular technology may lead the way here, but some form of genetic testing is likely to be forever required.


association mapping evolution genomics microarrays QTL mapping quantitative genetics statistical genetics 


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  1. Barton, N.H., Turelli, M. 1989Evolutionary quantitative genetics: How little do we knowAnnu. Rev. Genet.23337370PubMedGoogle Scholar
  2. Beavis, W.D., 1994. The power and deceit of QTL experiments: lessons from comparative QTL studies, pp. 252–268 in 49th Annual Corn and Sorghum Research Conference, edited by American Seed Trade Association, Washington, DC.Google Scholar
  3. Beavis, W.D. 1998QTL analyses: power, precision, and accuracyPaterson, A.H. eds. Molecular Dissection of Complex TraitsCRC Press Boca Raton, FL145162Google Scholar
  4. Bost, B., Vienne, D. de, Hospital, F., Moreau, L., Dillmann, C. 2001Genetic and nongenetic bases for the L-shaped distribution of quantitative trait loci effectsGenetics15717731787PubMedGoogle Scholar
  5. Botstein, D., Risch, N. 2003Discovering genotypes underlying human phenotypes: past successes for mendelian disease, future approaches for complex diseaseNat. Genet.33S228237Google Scholar
  6. Castle, W.E. 1921An improved method of estimating the number of genetic factors concerned in cases of blending inheritanceScience54223PubMedGoogle Scholar
  7. Charlesworth, B. 1990Optimization models, quantitative genetics, and mutationEvolution44520538Google Scholar
  8. Cheverud, J.M., Routman, E.J., Irschick, D.J. 1997Plieotropic effects of individual gene loci on mandibular morphologyEvolution5120062016Google Scholar
  9. Coyne, J.A. 1983Genetic basis of difference in genital morphology among three sibling species of DrosophilaEvolution3711011118Google Scholar
  10. Crow, J.F. 1957Genetics of insect resistance to chemicalsAnn. Rev. Entomol.2227246Google Scholar
  11. Davidson, E.H. 2001Genomic Regulatory Systems: Development and EvolutionAcademic PressNew YorkGoogle Scholar
  12. Doebly, J., Stec, A., Gustus, C. 1995Teosinte branched1 and the origin of mazie: evidence for epistasis and the evolution of dominanceGenetics141333346Google Scholar
  13. Felsenstein, J., 1977. Multivariate normal genetic models with a finite number of loci, in proceedings of the Second International Conference on Quantitative Genetics, edited by Iowa State University Press, Ames, IA.Google Scholar
  14. Fisher, R.A. 1918The correlations between relatives on the supposition of Mendelian inheritanceTrans. Roy. Soc. Edinb.52399433Google Scholar
  15. Gibson, G. 2002Microarrays in ecology and evolution: a previewMol. Ecol.111724PubMedGoogle Scholar
  16. Glazier, A.M., Nadeau, J.H., Aitman, T.J. 2002Finding genes that underlie complex traitsScience29823452349CrossRefPubMedGoogle Scholar
  17. Greenberg, A.J., Moran, J.R., Coyne, J.A., Wu, C.I. 2003Ecological adaptation during incipient speciation revealed by precise gene replacementScience30217541757PubMedGoogle Scholar
  18. Jovelin, R., Ajie, B.C., Phillips, P.C. 2003Molecular evolution and quantitative variation for chemosensory behaviour in the nematode genus CaenorhabditisMol. Ecol.1213251337PubMedGoogle Scholar
  19. Juenger, T., Purugganan, M., Mackay, T.F. 2000Quantitative trait loci for floral morphology in Arabidopsis thalianaGenetics15613791392PubMedGoogle Scholar
  20. Kao, C.H., Zeng, Z.B. 2002Modeling epistasis of quantitative trait loci using Cockerham’s modelGenetics16012431261PubMedGoogle Scholar
  21. Khoury, M., Beaty, T.H., Cohen, B.H. 1993Fundamentals of Genetic EpidemiologyOxford University PressNew YorkGoogle Scholar
  22. Lande, R. 1976Natural selection and random genetic drift in phenotypic evolutionEvolution30314334Google Scholar
  23. Lande, R. 1981The minimum number of genes contributing to quantitative variation between and within populationsGenetics99544553Google Scholar
  24. Lande, R., 1988. Quantitative genetics and evolutionary theory, pp. 71–84 in Proceeding of the Second International Conference on Quantitative Genetics, edited by Sinauer, Sunderland, Mass.Google Scholar
  25. Lander, E.S., Schork, N.J. 1994Genetic dissection of complex traitsScience26520372048PubMedGoogle Scholar
  26. Laurie, C.C., True, J.R., Liu, J., Mercer, J.M. 1997An introgression analysis of quantitative trait loci that contribute to a morphological difference between Drosophila simulans and D. mauritianaGenetics145339348PubMedGoogle Scholar
  27. Lebreton, C.M., Visscher, P.M., Haley, C.S., Semikhodskii, A., Quarrie, S.A. 1998A nonparametric bootstrap method for testing close linkage vs. pleiotropy of coincident quantitative trait lociGenetics150931943PubMedGoogle Scholar
  28. Leips, J., Mackay, T.F. 2000Quantitative trait loci for life span in Drosophila melanogaster: interactions with genetic background and larval densityGenetics15517731788PubMedGoogle Scholar
  29. Lewontin, R.C. 1974The Genetic Basis of Evolutionary ChangeColumbia University PressNew YorkGoogle Scholar
  30. Lewontin, R.C. 1991Twenty-five years ago in Genetics: electrophoresis in the development of evolutionary genetics: milestone or millstoneGenetics128657662PubMedGoogle Scholar
  31. Long, A.D., Mullaney, S.L., Mackay, T.F., Langley, C.H. 1996Genetic interactions between naturally occurring alleles at quantitative trait loci and mutant alleles at candidate loci affecting bristle number in Drosophila melanogasterGenetics14414971510PubMedGoogle Scholar
  32. Long, A.D., Lyman, R.F., Langley, C.H., Mackay, T.F. 1998Two sites in the Delta gene region contribute to naturally occurring variation in bristle number in Drosophila melanogasterGenetics1499991017PubMedGoogle Scholar
  33. Long, A.D., Lyman, R.F., Morgan, A.H., Langley, C.H., Mackay, T.F. 2000Both naturally occurring insertions of transposable elements and intermediate frequency polymorphisms at the achaete-scute complex are associated with variation in bristle number in Drosophila melanogasterGenetics15412551269PubMedGoogle Scholar
  34. Lyman, R.F., Mackay, T.F. 1998Candidate quantitative trait loci and naturally occurring phenotypic variation for bristle number in Drosophila melanogaster: the Delta-Hairless gene regionGenetics149983998PubMedGoogle Scholar
  35. Mackay, T.F.C., Langley, C.H. 1990Molecular and phenotypic variation in the achaete-scute region of Drosophila melanogasterNature3486466PubMedGoogle Scholar
  36. Mackay, T.F.C. 2001aQuantitative trait loci in DrosophilaNat. Rev. Genet.21120Google Scholar
  37. Mackay, T.F.C. 2001bThe genetic architecture of quantitative traitsAnnu. Rev. Genet.35303339Google Scholar
  38. Nachman, M.W., Hoekstra, H.E., D’Agostino, S.L. 2003The genetic basis of adaptive melanism in pocket miceProc. Natl. Acad. Sci. USA10052685273PubMedGoogle Scholar
  39. Noor, M.A., Cunningham, A.L., Larkin, J.C. 2001Consequences of recombination rate variation on quantitative trait locus mapping studies Simulations based on the Drosophila melanogaster genomeGenetics159581588PubMedGoogle Scholar
  40. Oleksiak, M.F., Churchill, G.A., Crawford, D.L. 2002Variation in gene expression within and among natural populationsNat. Genet.32261266PubMedGoogle Scholar
  41. Orr, H.A. 1998The population genetics of adaptation: the distribution of factors fixed during adaptive evolutionEvolution52935949Google Scholar
  42. Orr, H.A. 2002The population genetics of adaptation: the adaptation of DNA sequencesEvolution5613171330PubMedGoogle Scholar
  43. Otto, S.P., Jones, C.D. 2000Detecting the undetected: estimating the total number of loci underlying a quantitative traitGenetics15620932107PubMedGoogle Scholar
  44. Pasyukova, E.G., Vieira, C., Mackay, T.F. 2000Deficiency mapping of quantitative trait loci affecting longevity in Drosophila melanogasterGenetics15611291146PubMedGoogle Scholar
  45. Peichel, C.L., Nereng, K.S., Ohgi, K.A., Cole, B.L., Colosimo, P.F., Buerkle, C.A., Schluter, D., Kingsley, D.M. 2001The genetic architecture of divergence between threespine stickleback speciesNature414901905PubMedGoogle Scholar
  46. Phillips, P.C. 1998The language of gene interactionGenetics14911671171PubMedGoogle Scholar
  47. Phillips, P.C. 1999From complex traits to complex allelesTrends Genet.1568PubMedGoogle Scholar
  48. Provine, W.B. 1971The Origins of Theoretical Population GeneticsThe University of Chicago PressChicagoGoogle Scholar
  49. Remington, D.L., Ungerer, M.C., Purugganan, M.D. 2001Map-based cloning of quantitative trait loci: progress and prospectsGenet. Res.78213218CrossRefPubMedGoogle Scholar
  50. Siegal, M.L., Hartl, D.L. 1998An experimental test for lineage-specific position effects on alcohol dehydrogenase (Adh) genes in DrosophilaProc. Natl. Acad. Sci. USA951551315518PubMedGoogle Scholar
  51. Slatkin, M. 1970Selection and polygenic charactersProc. Natl. Acad. Sci. USA668793PubMedGoogle Scholar
  52. Stam, L.F., Laurie, C.C. 1996Molecular dissection of a major gene effect on a quantitative trait: the level of alcohol dehydrogenase expression in Drosophila melanogasterGenetics14415591564PubMedGoogle Scholar
  53. Steinmetz, L.M., Sinha, H., Richards, D.R., Spiegelman, J.I., Oefner, P.J., McCusker, J.H., Davis, R.W. 2002Dissecting the architecture of a quantitative trait locus in yeastNature416326330CrossRefPubMedGoogle Scholar
  54. Stern, D.L. 2000Evolutionary developmental biology and the problem of variationEvolution5410791091PubMedGoogle Scholar
  55. The C. elegans Sequencing Consortium, 1998. Genome sequence of the nematode C. elegans: a platform for investigating biology. Science 282: 2012–2018.Google Scholar
  56. Vaughn, T.T., Pletscher, L.S., Peripato, A., King-Ellison, K., Adams, E., Erikson, C., Cheverud, J.M. 1999Mapping quantitative trait loci for murine growth: a closer look at genetic architectureGenet. Res.7431322PubMedGoogle Scholar
  57. Wayne, M.L., McIntyre, L.M. 2002Combining mapping and arraying: an approach to candidate gene identification.Proc. Natl. Acad. Sci. USA991490314906PubMedGoogle Scholar
  58. Weinig, C, Ungerer,  M.C., Dorn, L.A., Kane,  N.C., Toyonaga, Y., Halldorsdottir, S.S., Mackay, T.F., Purugganan, M.D., Schmitt, J. 2002Novel loci control variation in reproductive timing in Arabidopsis thaliana in natural environments.Genetics16218751884PubMedGoogle Scholar
  59. Wright, S. 1968Evolution and the Genetics of Populations Vol. 1. Genetic and Biometric Foundations. University of Chicago PressChicagoGoogle Scholar
  60. Zeng, Z.B., Houle, D., Cockerham, C.C. 1990How Informative is Wright’s estimator of the number of genes affecting a quantitative characterGenetics126235247PubMedGoogle Scholar
  61. Zeng, Z.B. 1992Correcting the bias of Wright’s estimates of the number of genes affecting a quantitative character: a further improved methodGenetics1319871001PubMedGoogle Scholar
  62. Zeng, Z.B., Liu, J., Stam, L.F., Kao, C.H., Mercer, J.M., Laurie, C.C. 2000Genetic architecture of a morphological shape difference between two Drosophila speciesGenetics154299310PubMedGoogle Scholar

Copyright information

© Springer 2005

Authors and Affiliations

  1. 1.Center for Ecology and Evolutionary BiologyUniversity of OregonEugeneUSA

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