General methods for evolutionary quantitative genetic inference from generalized mixed models

Genetics

Volumn 204, Issue 3, 2016, Pages 1281-1294

  de Villemereuil, Pierre ^a   Schielzeth, Holger ^b,c   Nakagawa, Shinichi ^d   Morrissey, Michael ^e  

^a UNIVERSITÉ JOSEPH FOURIER   (France)

^b BIELEFELD UNIVERSITY   (Germany)

^c FRIEDRICH SCHILLER UNIVERSITY JENA   (Germany)

^d UNIVERSITY OF NEW SOUTH WALES   (Australia)

^e UNIVERSITY OF ST ANDREWS   (United Kingdom)

Author keywords

Additive genetic variance; Evolution; G matrix; Generalized linear model; Quantitative genetics; Statistics; Theory

Indexed keywords

ACCURACY; ARTICLE; COVARIANCE; GENETIC MODEL; GENETIC PARAMETERS; HERITABILITY; MOLECULAR EVOLUTION; NONHUMAN; PEDIGREE; PHENOTYPIC VARIATION; POISSON DISTRIBUTION; PRIORITY JOURNAL; QUANTITATIVE GENETICS; SIMULATION; VERTEBRATE; BIOLOGICAL MODEL; POPULATION GENETICS; PROCEDURES; QUANTITATIVE TRAIT; SOFTWARE;

EVOLUTION, MOLECULAR; GENETICS, POPULATION; MODELS, GENETIC; QUANTITATIVE TRAIT, HERITABLE; SOFTWARE;

EID: 84994820157     PISSN: 00166731     EISSN: 19432631     Source Type: Journal    
DOI: 10.1534/genetics.115.186536     Document Type: Article

References (46)

1. Ayers, D. R., R. J. Pereira, A. A. Boligon, F. F. Silva, F. S. Schenkel et al., 2013 Linear and Poisson models for genetic evaluation of tick resistance in cross-bred Hereford x Nellor cattle. J. Anim. Breed. Genet. 130: 417–424.
2. Browne, W. J., S. V. Subramanian, K. Jones, and H. Goldstein, 2005 Variance partitioning in multilevel logistic models that exhibit overdispersion. J. R. Stat. Soc. Ser. A Stat. Soc. 168: 599–613.
3. Bulmer, M. G., 1971 The effect of selection on genetic variability. Am. Nat. 105: 201–211.
4. Bérénos, C., P. A. Ellis, J. G. Pilkington, and J. M. Pemberton, 2014 Estimating quantitative genetic parameters in wild populations: a comparison of pedigree and genomic approaches. Mol. Ecol. 23: 3434–3451.
5. Dempster, E. R., and I. M. Lerner, 1950 Heritability of threshold characters. Genetics 35: 212–236.
6. de Villemereuil, P., O. Gimenez, and B. Doligez, 2013 Comparing parent–offspring regression with frequentist and Bayesian animal models to estimate heritability in wild populations: a simulation study for Gaussian and binary traits. Methods Ecol. Evol. 4(3): 260–275.
7. Falconer, D. S., 1960 Introduction to Quantitative Genetics. Oliver and Boyd, Edinburgh.
8. Fisher, R. A., 1918 The correlation between relatives on the supposition of Mendelian inheritance. Trans. R. Soc. Edinb. 52: 399–433.
9. Fisher, R. A., 1924 The biometrical study of heredity. Eugen. Rev. 16: 189–210.
10. Fisher, R. A., 1930 The Genetical Theory of Natural Selection. Clarendon Press, Oxford.
11. Foulley, J. L., and S. Im, 1993 A marginal quasi-likelihood approach to the analysis of Poisson variables with generalized linear mixed models. Genet. Sel. Evol. 25(1): 101.
12. Hadfield, J., 2010 MCMC methods for multi-response generalized linear mixed models: the MCMCglmm R package. J. Stat. Softw. 33(2): 1–22.
13. Henderson, C. R., 1950 Estimation of genetic parameters. Ann. Math. Stat. 21: 309–310.
14. Henderson, C. R., 1973 Sire evaluation and genetic trends, in Proceedings of the Animal Breeding and Genetics Symposium in Honour of Dr. Jay L. Lush, pp. 10–41. American Society of Animal Science and the American Dairy Science Association, Champaign, IL.
15. Hill, W. G., and M. Kirkpatrick, 2010 What animal breeding has taught us about evolution. Annu. Rev. Ecol. Evol. Syst. 41: 1–19.
16. Houle, D., 1992 Comparing evolvability and variability of quantitative traits. Genetics 130: 195–204.
17. Kruuk, L. E. B., 2004 Estimating genetic parameters in natural populations using the ‘animal model’. Philos. Trans. R. Soc. Lond. B Biol. Sci. 359: 873–890.
18. Lande, R., 1979 Quantitative genetic analysis of multivariate evolution, applied to brain:body size allometry. Evolution 33: 402–416.
19. Lande, R., and S. J. Arnold, 1983 The measurement of selection on correlated characters. Evolution 37: 1210–1226.
20. Lush, J. L., 1937 Animal Breeding Plans. Iowa State College Press, Ames, IA.
21. Lynch, M., and B. Walsh, 1998 Genetics and Analysis of Quantitative Traits. Sinauer Associates, Sunderland, MA.
22. Milot, E., F. M. Mayer, D. H. Nussey, M. Boisvert, F. Pelletier et al., 2011 Evidence for evolution in response to natural selection in a contemporary human population. Proc. Natl. Acad. Sci. USA 108(41): 17040–17045.
23. Morrissey, M. B., 2014 In search of the best methods for multivariate selection analysis. Methods Ecol. Evol. 5: 1095–1109.
24. Morrissey, M. B., 2015 Evolutionary quantitative genetics of nonlinear developmental systems. Evolution 69: 2050–2066.
25. Morrissey, M. B., C. A. Walling, A. J. Wilson, J. M. Pemberton, T. H. Clutton-Brock et al., 2012 Genetic analysis of life-history constraint and evolution in a wild ungulate population. Am. Nat. 179(4): E97–E114.
26. Morrissey, M. B., P. de Villemereuil, B. Doligez, and O. Gimenez, 2014 Bayesian approaches to the quantitative genetic analysis of natural populations, pp. 228–253 in Quantitative Genetics in the Wild, edited by A. Charmantier, D. Garant, and L. E. Kruuk. Oxford University Press, Oxford.
27. Nakagawa, S., and H. Schielzeth, 2010 Repeatability for Gaussian and non Gaussian data: a practical guide for biologists. Biol. Rev. Camb. Philos. Soc. 85(4): 935–956.
28. Price, G. R., 1970 Selection and covariance. Nature 227: 520–521.
29. R Core Team, 2015 R: A Language and Environment for Statistical Computing. R Foundation for Statistical Computing, Vienna.
30. Robertson, A., 1950 Heritability of threshold characters. Genetics 35: 212–236.
31. Robertson, A., 1966 A mathematical model of the culling process in dairy cattle. Anim. Prod. 8: 95–108.
32. Robertson, A., 1968 The spectrum of genetic variation, pp. 5–16 in Population Biology and Evolution, edited by R. C. Lewontin. Syracuse University Press, New York.
33. Roff, D. A., 1997 Evolutionary Quantitative Genetics. Chapman & Hall, New York.
34. Schielzeth, H., 2010 Simple means to improve the interpretability of regression coefficients. Methods Ecol. Evol. 1(2): 103–113.
35. Sillanpää, M. J., 2011 On statistical methods for estimating heritability in wild populations. Mol. Ecol. 20(7): 1324–1332.
36. Stein, C. M., 1973 Estimation of the mean of a multivariate normal distribution. Proc. Prague Symp. Asymptotic Stat. 1: 345–381.
37. Thompson, R., 2008 Estimation of quantitative genetic parameters. Proc. Biol. Sci. 275(1635): 679–686.
38. Walsh, B., and M. Lynch, 2008 Evolution and Selection of Quantitative Traits. Sinauer Associates, Sunderland, MA.
39. Wilson, A. J., 2008 Why h2 does not always equal VA/VP? J. Evol. Biol. 21(3): 647–650.
40. Wilson, A. J., D. Reale, M. N. Clements, M. B. Morrissey, C. A. W. E. Postma et al., 2010 An ecologist’s guide to the animal model. J. Anim. Ecol. 79: 13–26.
41. Wilson, A. J., M. B. Morrissey, M. J. Adams, C. A. Walling, F. E. Guinness et al., 2011 Indirect genetics effects and evolutionary constraint: an analysis of social dominance in red deer, Cervus elaphus. J. Evol. Biol. 24(4): 772–783.
42. Wright, S., 1934 An analysis of variability in number of digits in an inbred strain of Guinea pigs. Genetics 19: 506–536.
43. Dempster, E. R. and Lerner, I. M. (1950). Heritability of Threshold Characters. Genetics, 35(2):212-236.
44. Nakagawa, S. and Schielzeth, H. (2010). Repeatability for Gaussian and non Gaussian data: a practical guide for biologists. Biological Reviews, 85(4):935-956.
45. Price, G. R. (1970). Selection and covariance. Nature, 227:520-521.
46. Robertson, A. (1966). A mathematical model of the culling process in dairy cattle. Animal Production, 8:95-108.