Quantitative Genetics in Natural Populations

Encyclopedia of Evolutionary Biology

Volumn , Issue , 2016, Pages 361-371

  Wilson, A J ^a   Poissant, J ^b  

^a UNIVERSITY OF EXETER   (United Kingdom)

^b UNIVERSITY OF CALGARY   (Canada)

Author keywords

Adaptation; Additive genetic variance; Animal model; Constraint; G matrix; Genetic correlation; Genotype by environment interaction; Heritability; Life history; Natural selection; Parent offspring regression; Pedigree; Trade off

Indexed keywords

EID: 84991814156     PISSN: None     EISSN: None     Source Type: Book    
DOI: 10.1016/B978-0-12-800049-6.00046-9     Document Type: Chapter

References (129)

1. Agrawal A.F., Stinchcombe J.R. How much do genetic covariances alter the rate of adaptation?. Proceedings of the Royal Society B-Biological Sciences 2009, 276:1183-1191.
2. Barrett R.D.H., Schluter D. Adaptation from standing genetic variation. Trends in Ecology and Evolution 2008, 23:38-44.
3. Bérénos C., Ellis P.A., Pilkington J.G., Pemberton J.M. Estimating quantitative genetic parameters in wild populations: A Comparison of Pedigree and Genomic Approaches. Molecular Ecology 2014, 23:3434-3451.
4. Bijma P., Muir W.M., Van Arendonk J.A.M. Multilevel selection 1: Quantitative genetics of inheritance and response to selection. Genetics 2007, 175:277-288.
5. Bijma P., Wade M.J. The joint effects of kin, multilevel selection and indirect genetic effects on response to genetic selection. Journal of Evolutionary Biology 2008, 21:1175-1188.
6. Blows M.W. A tale of two matrices: Multivariate approaches in evolutionary biology. Journal of Evolutionary Biology 2006, 20:1-8.
7. Blows M., Walsh B. Spherical cows grazing in flatland: Constraints to selection and adaptation. Adaptation and Fitness in Animal Populations 2009, 83-101. Springer, Dordrecht. J. van der Werf, H.-U. Graser, R. Frankham, C. Gondro (Eds.).
8. Bretman A., Rodríguez-Muñoz R., Walling C.A., Slate J., Tregenza T. Fine-scale population structure, inbreeding risk and avoidance in a wild insect population. Molecular Ecology 2011, 20:3045-3055.
9. Brommer J., Gustafsson L., Wilson A.J. Genetic, environmental and age-related variance components of annual fitness in the wild. American Naturalist 2007, 170:643-650.
10. Brommer J., Rattiste K. "Hidden" reproductive conflict between mates in a wild bird population. Evolution 2008, 62:2326-2333.
11. Charmantier A., Buoro M., Gimenez O., Weimerskirch H. Heritability of short-scale natal dispersal in a large-scale foraging bird, the wandering albatross. Journal of Evolutionary Biology 2011, 24:1487-1496.
12. Quantitative Genetics in the Wild 2014, Oxford University Press, Oxford. A. Charmantier, D. Garant, L.E.B. Kruuk (Eds.).
13. Charmantier A., Keyser A.J., Promislow D.E.L. First evidence for heritable variation in cooperative breeding behaviour. Proceedings of the Royal Society of London B, Biological Sciences 2007, 274:1757-1762.
14. Charmantier A., Reale D. How do misassigned paternities affect the estimation of heritability in the wild?. Molecular Ecology 2005, 14:2839-2850.
15. Clutton-Brock T., Sheldon B.C. Individuals and populations: The role of long-term, individual-based studies of animals in ecology and evolutionary biology. Trends in Ecology & Evolution 2010, 25:562-573.
16. Coltman D.W., O'Donoghue P., Hogg J.T., Festa-Bianchet M. Selection and genetic (co)variance in bighorn sheep. Evolution 2005, 59:1372-1382.
17. Coltman D.W., O'Donoghue P., Jorgenson J.T., et al. Undesirable evolutionary consequences of trophy hunting. Nature 2003, 426:655-658.
18. Davey J.W., Hohenlohe P.A., Etter P.D., et al. Genome-wide genetic marker discovery and genotyping using next-generation sequencing. Nature Reviews Genetics 2011, 12:499-510.
19. Davies N.B., Krebs J.R., West S.A. An Introduction to Behavioural Ecology 2012, Wiley-Blackwell, Oxford. fourth ed.
20. Devlin B., Risch N. A comparison of linkage disequilibrium measures for fine-scale mapping. Genomics 1995, 29:311-322.
21. Dingemanse N.J., Barber I., Wright J., Brommer J.E. Quantitative genetics of behavioural reaction norms: Genetic correlations between personality and behavioural plasticity vary across stickleback populations. Journal of Evolutionary Biology 2012, 25:485-496.
22. Dingemanse N.J., van der Plas F., Wright J., et al. Individual experience and evolutionary history of predation affect expression of heritable variation in fish personality and morphology. Proceedings of the Royal Society B-Biological Sciences 2009, 276:1285-1293.
23. Diz A.P., Martínez-Fernández M., Rolán-Alvarez E. Proteomics in evolutionary ecology: Linking the genotype with the phenotype. Molecular Ecology 2012, 21:1060-1080.
24. Ellegren H., Sheldon B. Genetic basis of fitness differences in natural populations. Nature 2008, 452:169-175.
25. Endler J.A. Natural Selection in the Wild 1986, Princeton University Press, Princeton, NJ.
26. Falconer D.S., McKay T.F.C. Introduction to Quantitative Genetics 1996, Longman, Harlow.
27. Fisher R.A. The Genetical Theory of Natural Selection 1930, Clarendon, Oxford.
28. Flint J., Mackay T.F.C. Genetic architecture of quantitative traits in mice, flies, and humans. Genome Research 2009, 10:723-733.
29. Frentiu F.D., Clegg S.M., Chittock J., et al. Pedigree-free animal models: The relatedness matrix reloaded. Proceedings of the Royal Society B-Biological Sciences 2008, 275:639-647.
30. Garant D., Kruuk L.E.B. How to use molecular marker data to measure evolutionary parameters in wild populations. Molecular Ecology 2005, 14:1843-1859.
31. Garant D., Sheldon B.C., Gustafsson L. Climatic and temporal effects on the expression of secondary sexual characters: Genetic and environmental components. Evolution 2004, 58:634-644.
32. George A.W., Visscher P.M., Haley C.S. Mapping quantitative trait loci in complex pedigrees: A two-step variance component approach. Genetics 2000, 156:2081-2092.
33. Gienapp P., Teplitsky C., Alho J.S., Mills J.A., Merila J. Climate change and evolution: Disentangling environmental and genetic responses. Molecular Ecology 2008, 17:167-178.
34. Gilmour A.R., Gogel B.J., Cullis B.R., Thompson R. ASReml User Guide Release 2.0 2006, VSN International Ltd, Hemel Hempstead.
35. Graham A.L., Hayward A.D., Watt K.A., et al. Fitness correlates of heritable variation in antibody responsiveness in a wild mammal. Science 2010, 330:662-665.
36. Grant P.R., Grant B.R. Predicting microevolutionary responses to directional selection on heritable variation. Evolution 1995, 49:241-251.
37. Griffing B. Selection in reference to biological groups. I. Individual and group selection applied to populations of unordered groups. Australian Journal of Biological Sciences 1967, 10:127-139.
38. Griffing B. Selection in reference to biological groups.VI. Use of extreme forms of nonrandom groups to increase selection efficiency. Genetics 1976, 82:723-731.
39. Hadfield J.D. MCMC methods for multi-response generalized linear mixed models: The MCMCglmm R package. Journal of Statistical Software 2010, 33:1-22.
40. Hadfield J., Wilson A.J., Garant D., Sheldon B.C., Kruuk L.E.B. The misuse of BLUP in ecology and evolution. American Naturalist 2010, 175:116-125.
41. Hadfield J.D., Wilson A.J., Kruuk L.E.B. Cryptic evolution: Environmental change or environmental deterioration?. Genetics 2011, 187:1099-1113.
42. Hadfield J.D., Heap E.A., Bayer F., Mittell E.A., Crouch N.M.A. Disentangling genetic and prenatal sources of familial resemblance across ontogeny in a wild passerine. Evolution 2013, 67:2701-2713.
43. Hairston N.G., Ellner S.P., Geber M.A., Yoshida T., Fox J.A. Rapid evolution and the convergence of ecological and evolutionary time. Ecology Letters 2005, 8:1114-1127.
44. Hayes B., Goddard M.E. The distribution of the effects of genes affecting quantitative traits in livestock. Genetics Selection Evolution 2001, 33:209-229.
45. Hayes B.J., Pryce J., Chamberlain A.J., Bowman P.J., Goddard M.E. Genetic architecture of complex traits and accuracy of genomic prediction: Coat color, milk-fat percentage, and type in Holstein cattle as contrasting model traits. PLoS Genetics 2010, 6:e1001139.
46. Hunt J., Blows M., Zajitschek F., Jennions M.D., Brooks R. Reconciling strong stabilizing selection with the maintenance of genetic variation in a natural population of black field crickets (Teleogryllus commodus). Genetics 2007, 177:875-880.
47. Jensen H., Szulkin M., Slate J. Molecular quantitative genetics. Quantitative Genetics in the Wild 2014, 209-227. Oxford University Press, Oxford. A. Charmantier, D. Garant, L.E.B. Kruuk (Eds.).
48. de Jong G., van Noordwijk A. Acquisition and allocation of resources: Genetic (co)variances, selection, and life histories. American Naturalist 1992, 139:749-770.
49. Kingsolver J., Diamond S.E., Siepielski A.M., Carlson S.M. Synthetic analyses of phenotypic selection in natural populations: Lessons, limitations and future directions. Evolutionary Ecology 2012, 26:1101-1118.
50. Kingsolver J.G., Hoekstra H.E., Hoekstra J.M., et al. The strength of phenotypic selection in natural populations. American Naturalist 2001, 157:245-261.
51. Koch M., Hadfield J.D., Sefc K.M., Sturmbauer C. Pedigree reconstruction in wild Cichlid fish populations. Molecular Ecology 2008, 17:4500-4511.
52. Kruuk L.E.B. Estimating genetic parameters in natural populations using the 'animal model'. Philosphical Transactions of the Royal Society of London B, Biological Sciences 2004, 359:873-890.
53. Kruuk L.E.B., Hadfield J. How to separate genetic and environmental causes of similarity between relatives. Journal of Evolutionary Biology 2007, 20:1890-1903.
54. Kruuk L.E.B., Slate J., Pemberton J.M., et al. Antler size in red deer: Heritability and selection but no evolution. Evolution 2002, 56:1683-1695.
55. Kruuk L.E.B., Slate J., Wilson A.J. New answers for old questions: The quantitative genetics of wild animal populations. Annual Review of Ecology, Evolution and Systematics 2008, 39:524-548.
56. Lande R. A quantitative genetic theory of life history evolution. Ecology 1982, 63:607-615.
57. Lande R., Arnold S.J. The measurement of selection on correlated characters. Evolution 1983, 37:1210-1226.
58. Lynch M., Walsh B. Genetics and Analysis of Quantitative Traits 1998, Sinauer Associates, Sunderland.
59. MacColl A., Hatchwell B.J. Heritability of parental effort in a passerine bird. Evolution 2003, 57:2191-2195.
60. Mackay T.F.C. The genetic architecture of quantitatve traits. Annual Review of Genetics 2001, 35:303-339.
61. Manolio T.A., Collins F.S., Cox N.J., et al. Finding the missing heritability of complex diseases. Nature 2009, 461:747-753.
62. McAdam A.G., Boutin S., Réale D., Berteaux D. Maternal effects and the potential for evolution in a natural population of animals. Evolution 2002, 56:846-851.
63. McAdam A.G., Garant D., Wilson A.J. The effect of others' genes: Maternal and other indirect genetic effects. Quantitative Genetics in the Wild 2014, 84-103. Oxford University Press, Oxford. A. Charmantier, D. Garant, L.E.B. Kruuk (Eds.).
64. McCarthy M.I., Abecasis G.R., Cardon L.R., et al. Genome-wide association studies for complex traits: Consensus, uncertainty and challenges. Nature Reviews Genetics 2008, 9:356-369.
65. McCleery R.H., Pettifor R.A., Armbruster P., et al. Components of variance underlying fitness in a natural population of the great tit Parus major. American Naturalist 2004, 164:E62-E72.
66. Merilä J., Sheldon B.C. Lifetime reproductive success and heritability in nature. American Naturalist 2000, 155:301-310.
67. Merilä J., Sheldon B.C., Kruuk L.E. Explaining stasis: Microevolutionary studies in natural populations. Genetica 2001, 112-113:199-222.
68. Moore A.J., Brodie E.D., Wolf J.B. Interacting phenotypes and the evolutionary process.1. Direct and indirect genetic effects of social interactions. Evolution 1997, 51:1352-1362.
69. Morrissey M.B., Hadfield J.D. Direction selection in temporally replicated studies is remarkably consistent. Evolution 2012, 66:435-442.
70. Morrissey M.B., Kruuk L.E.B., Wilson A.J. The danger of applying the breeder's equation in observational studies of natural populations. Journal of Evolutionary Biology 2010, 23:2277-2288.
71. Morrissey M.B., Parker D.J., Korsten P., et al. The prediction of adaptive evolution: Empirical application of the secondary theorem of selection and comparison to the breeder's equation. Evolution 2012, 66:2399-2410.
72. Morrissey M.B., Walling C.A., Wilson A.J., et al. Genetic analysis of life-history constraint and evolution in a wild ungulate population. American Naturalist 2012, 179:E97-E114.
73. Morrissey M.B., Wilson A.J. Pedantics: An R package for pedigree-based genetic simulation and pedigree manipulation, characterization and viewing. Molecular Ecology Resources 2010, 10:711-719.
74. Morrissey M.B., Wilson A.J., Pemberton J.M., Ferguson M.M. A framework for power and sensitivity analyses for quantitative genetic studies of natural populations, and case studies in Soay sheep (Ovis aries). Journal of Evolutionary Biology 2007, 20:2309-2321.
75. Niemela P.T., Dingemanse N.J., Alioravainen N., Vainikka A., Kortet R. Personality pace-of-life hypothesis: Testing genetic associations among personality and life history. Behavioral Ecology 2013, 24:935-941.
76. Nussey D.H., Postma E., Gienapp P., Visser M.E. Selection on heritable phenotypic plasticity in a wild bird population. Science 2005, 310:304-306.
77. Ovaskainen O., Cano Arias J.M., Merilä J. A Bayesian framework for comparative quantitative genetics. Proceedings of the Royal Society of London B, Biological Sciences 2008, 275:669-678.
78. Ozgul A., Childs D.Z., Oli M.K., et al. Coupled dynamics of body mass and population growth in response to environmental change. Nature 2010, 466:482-U485.
79. Pemberton J.M. Wild pedigrees: The way forward. Proceedings of the Royal Society of London B, Biological Sciences 2008, 275:613-622.
80. Poissant J., Reale D., Martin J.G.A., Festa-Bianchet M., Coltman D.W. A quantitative trait locus analysis of personality in wild bighorn sheep. Ecology and Evolution 2013, 3:474-481.
81. Poissant J., Wilson A.J., Coltman D.W. Sex-specific genetic variance and the evolution of sexual-dimorphism: A systematic review of cross-sex genetic correlations. Evolution 2010, 64:97-107.
82. Poissant J., Wilson A.J., Festa-Bianchet M., Hogg J.T., Coltman D.W. Quantitative genetics and sex-specific selection on sexually dimorphic traits in bighorn sheep. Proceedings of the Royal Society B: Biological Sciences 2008, 275:623-628.
83. Postma E. Implications of the difference between true and predicted breeding values for the study of natural selection and micro-evolution. Journal of Evolutionary Biology 2006, 19:309-320.
84. Postma E., Charmantier A. What 'animal models' can and cannot tell ornithologists about the genetics of wild populations. Journal of Ornithology 2007, 148:633-642.
85. Pujol B., Marrot P., Pannell J.R. A quantitative genetic signature of senescence in a short-lived perennial plant. Current Biology 2014, 7:744-747.
86. Rajon E., Plotkin J.B. The evolution of genetic architectures underlying quantitative traits. Proceedings of the Royal Society B: Biological Sciences 2013, 280:20131552.
87. Réale D., Festa-Bianchet M. Quantitative genetics of life-history traits in a long-lived wild mammal. Heredity 2000, 85:593-603.
88. Réale D., Festa-Bianchet M., Jorgenson J.T. Heritability of body mass varies with age and season in wild bighorn sheep. Heredity 1999, 83:526-532.
89. Reid J., Arcese P., Keller L., Losdat S. Female and male genetic effects on offspring paternity: Additive genetic (co)variances in female extra-pair reproduction and male paternity success in song sparrows (Melospiza melodia). Evolution 2014, 68:2357-2370.
90. Risch N., Merikangas K. The future of genetic studies of complex human diseases. Science 1996, 273:1516-1517.
91. Ritland K. A marker-based method for inferences about quantitative inheritance in natural populations. Evolution 1996, 50:1062-1073.
92. Robinson M.R., Wilson A.J., Pilkington J.G., et al. The impact of environmental heterogeneity on genetic architecture in a wild population of Soay sheep. Genetics 2009, 18:1639-1648.
93. Robinson M.R., Santure A.W., DeCauwer I., Sheldon B.C., Slate J. Partitioning of genetic variation across the genome using multimarker methods in a wild bird population. Molecular Ecology 2013, 22:3963-3980.
94. Roche D.G., Lanfear R., Binning S.A., et al. Troubleshooting public data archiving: Suggestions to increase participation. PLoS Biology 2014, 12:e1001779.
95. Roff D.A. Evolutionary Quantitative Genetics 1997, Chapman & Hall, New York, NY.
96. Santure A.W., De Cauwer I., Robinson M.R., et al. Genomic dissection of variation in clutch size and egg mass in a wild great tit (Parus major) population. Molecular Ecology 2013, 22:3949-3962.
97. Schielzeth H., Husby A. Challenges and prospects in genome-wide quantitative trait loci mapping of standing genetic variation in natural populations. Annals of the New York Academy of Sciences 2014, 1320:35-57.
98. Schroderus E., Koivula M., Koskela E., et al. Can number and size of offspring increase simultaneously? - A central life-history trade-off reconsidered. BMC. Evolutionary Biology 2012, 12:24.
99. Sgrò C.M. Genetic correlations, tradeoffs and environmental variation. Heredity 2004, 93:241-248.
100. Siepielski A.M., Gotanda K.M., Morrissey M.B., et al. The spatial patterns of directional phenotypic selection. Ecology Letters 2013, 16:1382-1392.
101. Slate J. Quantitative trait locus mapping in natural populations: Progress, caveats and future directions. Molecular Ecology 2005, 14:363-380.
102. Slate J. From Beavis to beak colour: A simulation study to examine how much QTL mapping can reveal about the genetic architecture of quantitative traits. Evolution 2013, 67:1251-1262.
103. Slate J., Gratten J., Beraldi D., et al. Gene mapping in the wild with SNPs: Guidelines and future directions. Genetica 2009, 136:97-107.
104. Slate J., Santure A.W., Feulner P.G.D., et al. Genome mapping in intensively studied wild vertebrate populations. Trends in Genetics 2010, 26:275-284.
105. Speed D., Balding D.J. Relatedness in the post-genomic era: Is it still useful?. Nature Reviews Genetics 2015, 16:33-44.
106. Spor A., Koren O., Ley R. Unravelling the effects of the environment and host genotype on the gut microbiome. Nature Reviews Microbiology 2011, 9:279-290.
107. Stinchcombe J.R. Cross-pollination of plants and animals: Wild quantitative genetics and plant evolutionary genetics. Quantitative Genetics in the Wild 2014, 128-146. Oxford University Press, Oxford. A. Charmantier, D. Garant, L.E.B. Kruuk (Eds.).
108. Stopher K.V., Walling C.A., Morris A., et al. Shared spatial effects on quantitative genetic parameters: Accounting for spatial autocorrelation and home range overlap reduces estimates of heritability in wild red deer. Evolution 2012, 66:2411-2426.
109. Stranger B.E., Stahl E.A., Raj T. Progress and promise of genome-wide association studies for human complex trait genetics. Genetics 2011, 187:367-383.
110. Teplitsky C., Mills J.A., Yarrall J.W., Merila J. Heritability of fitness components in a wild bird population. Evolution 2009, 63:716-726.
111. Teplitsky C., Mills J.A., Yarrall J.W., Merila J. Indirect genetic effects in a sex-limited trait: The case of breeding time in red-billed gulls. Journal of Evolutionary Biology 2010, 23:935-944.
112. Teplitsky C., Tarka M., Moller A.P., et al. Assessing multivariate constraints to evolution across ten long-term avian studies. PLoS ONE 2014, 9:e90444.
113. Visscher P.M., Medland S.E., Ferreira M.A.R., et al. Assumption-free estimation of heritability from genome-wide identity-by-descent sharing between full siblings. PLoS Genetics 2006, 2:e41.
114. Walling C.A., Morrissey M.B., Foerster K., et al. A multivariate analysis of genetic constraints to life history evolution in a wild population of red deer. Genetics 2014, 198:1735-1749.
115. Walsh B., Blows M.W. Abundant genetic variation plus strong selection = multivariate genetic constraints: A geometric view of adaptation. Annual Review of Ecology Evolution and Systematics 2009, 40:41-59.
116. Wang J. Marker-based estimates of relatedness and inbreeding coefficients: An assessment of current methods. Journal of Evolutionary Biology 2014, 27(3):518-530.
117. Wilson A.J. Competition as a source of constraint on life history evolution in natural populations. Heredity 2014, 112:70-78.
118. Wilson A.J., Charmantier A., Hadfield J. Evolutionary genetics of ageing in the wild: Empirical patterns and future perspectives. Functional Ecology 2008, 22:431-442.
119. Wilson A.J., Coltman D.W., Pemberton J.M., et al. Maternal genetic effects set the potential for evolution in a free-living vertebrate population. Journal of Evolutionary Biology 2005, 18:405-414.
120. Wilson A.J., Ferguson M.M. Molecular pedigree analysis in natural populations of fishes: Approaches, applications, and practical considerations. Canadian Journal of Fisheries and Aquatic Sciences 2002, 59:1696-1707.
121. Wilson A.J., McDonald G., Moghadam H.K., Herbinger C.M., Ferguson M.M. Marker assisted estimation of quantitative genetic parameters in rainbow trout, Oncorhynchus mykiss. Genetical Research 2003, 81:145-156.
122. Wilson A.J., Morrissey M.B., Adams M., et al. Indirect genetics effects and evolutionary constraint: An analysis of social dominance in red deer, Cervus elaphus. Journal of Evolutionary Biology 2011, 24:772-783.
123. Wilson A.J., Nussey D.H. What is individual quality? An evolutionary perspective. Trends in Ecology and Evolution 2010, 25:207-214.
124. Wilson A.J., Nussey D.H., Pemberton J.M., et al. Evidence for a genetic basis of aging in two wild vertebrate populations. Current Biology 2007, 17:2136-2142.
125. Wilson A.J., Pemberton J.M., Pilkington J.G., et al. Quantitative genetics of growth and cryptic evolution of body weight in an island population. Evolutionary Ecology 2007, 21:337-356.
126. Wilson A.J., Reale D., Clements M.N., et al. An ecologist's guide to the animal model. Journal of Animal Ecology 2010, 79:13-26.
127. Wolf J.B. Genetic architecture and evolutionary constraint when the environment contains genes. Proceedings of the National Academy of Science 2003, 100:4655-4660.
128. Wolf J.B.W. Principles of transcriptome analysis and gene expression quantification: An RNA-seq tutorial. Molecular Ecology Resources 2013, 13:559-572.
129. Yang J., Manolio T.A., Pasquale L.R., et al. Genome partitioning of genetic variation for complex traits using common SNPs. Nature Genetics 2011, 43:519-525.