Bayesian approaches in evolutionary quantitative genetics
Article first published online: 29 MAR 2008
© 2008 The Authors. Journal Compilation © 2008 European Society For Evolutionary Biology
Journal of Evolutionary Biology
Volume 21, Issue 4, pages 949–957, July 2008
How to Cite
O’HARA, R. B., CANO, J. M., OVASKAINEN, O., TEPLITSKY, C. and ALHO, J. S. (2008), Bayesian approaches in evolutionary quantitative genetics. Journal of Evolutionary Biology, 21: 949–957. doi: 10.1111/j.1420-9101.2008.01529.x
- Issue published online: 14 APR 2008
- Article first published online: 29 MAR 2008
- Received 4 December 2007; revised 26 February 2008; accepted 28 February 2008
- 2004. The Bayesian revolution in genetics. Nat. Rev. Genet. 5: 251–261. &
- 2007. Variance component and breeding value estimation for reproductive traits in laying hens using a Bayesian threshold model. Poultry Sci. 86: 823–828. , , , &
- 2007. Mapping quantitative trait loci underlying fitness-related traits in a free-living sheep population. Evolution 61: 1403–1416. , , , , &
- 2001. The Bayesian controversy in animal breeding. J. Anim. Sci. 79: 2023–2046.
- 2004. Population differentiation in G matrix structure due to natural selection in Rana temporaria. Evolution 58: 2013–2020. , , &
- 2005. Environmental quality and evolutionary potential: lessons from wild populations. Proc. R. Soc. Lond. B 272: 1415–1425. &
- 2003. Estimating selection on neonatal traits in red deer using elasticity path analysis. Evolution 57: 2879–2892. , , , &
- 2006. Performance of marker-based relatedness estimators in natural populations of outbred vertebrates. Genetics, 173: 2091–2101. , , , , , , &
- 2007. How to use Winbugs to draw inferences in animal models. J. Anim. Sci. 85: 1363–1368.
- 2006. Evolutionary aspects of population structure for molecular and quantitative traits in the freshwater snail Radix balthica. J. Evol. Biol. 19: 1071–1082. , &
- 1996. Introduction to Quantitative Genetics, 4th edn. Longman, Essex, UK. &
- 1918. The correlation between relatives on the supposition of Mendelian inheritance. Trans. R. Soc. Edinburgh 52: 399–433.
- 2007. Estimating genealogies from unlinked marker data: a Bayesian approach. Theor. Popul. Biol. 72: 305–322. , , , &
- 2006. Prior distributions for variance parameters in hierarchical models. Bayesian Anal. 1: 515–534.
- 2004. Bayesian Data Analysis, 2nd edn. Chapman & Hall/CRC, Boca Raton, FL. , , &
- 1986. Bayesian methods in animal breeding theory. J. Anim. Sci. 63: 217–244. &
- 1983. Sire evaluation for ordered categorical data with a threshold model. Genet. Sel. Evol. 15: 201–223. &
- 2003. On marker-assisted prediction of genetic value: beyond the ridge. Genetics 163: 347–365. , &
- 1995. Markov Chain Monte Carlo in Practice. Chapman & Hall/CRC, London, UK. , &
- 2004. Measurement Error and Misclassification in Statistics and Epidemiology: Impacts and Bayesian Adjustments. Chapman & Hall/CRC, London, UK.
- 2008. Estimating evolutionary parameters when viability selection is operating. Proc. R. Soc. Lond. B 275: 723–734.
- 2006. Towards unbiased parentage assignment: combining genetic, behavioural and spatial data in a Bayesian framework. Mol. Ecol. 15: 3715–3730. , &
- 2006. Molecular-level variation affects population growth in a butterfly metapopulation. PLoS Biol. 4: 719–726. &
- 1975. Best linear unbiased estimation and prediction under a selection model. Biometrics 31: 423–447.
- 2003. Phylogeny estimation: traditional and Bayesian approaches. Nat. Rev. Genet. 43: 275–284. &
- 2000. Genetic basis of climatic adaptation in Scots Pine by Bayesian quantitative trait locus analysis. Genetics 156: 1309–1322. , , , &
- 1994. Bayesian-inference on variance and covariance components for traits influenced by maternal and direct genetic-effects, using the Gibbs sampler. Acta Agric. Scand. Anim. Sci 44: 193–201. , , &
- 2005. Estimating heritabilities and genetic correlations with marker-based methods: an experimental test in Mimulus guttatus. J. Hered. 96: 368–375. &
- 2007. Contrasting levels of variation in neutral and quantitative genetic loci on Island populations of moor frogs (Rana arvalis). Conserv. Genet. 8: 45–56. , , &
- 1995. Maximum likelihood estimation of genetic parameters in life-history studies using the ‘Animal Model’. Funct. Ecol. 9: 122–126. , , &
- 2003. VCE-5 user’s guide and reference manual version 5.1. Department of Animal Sciences, University of Ljubljana, Slovenia. &
- 2004. Estimating genetic parameters in natural populations using the ‘animal model’. Philos. Trans. R. Soc. Lond. B 359: 873–890.
- 2000. Heritability of fitness in a wild mammal population. Proc. Natl Acad. Sci. 97: 698–703. , , , , &
- 1988. Local computations with probabilities on graphical structures and their application to expert systems. J. R. Stat. Soc. B 50: 157–224. &
- 2006. Double hierarchical generalized linear models (with discussion). J. R. Stat. Soc. A 55: 139–185. &
- 1937. Animal Breeding Plans. Iowa State University Press, Ames, IA.
- 1998. Genetics and Analysis of Quantitative Traits. Sinauer, Sunderland, MA. &
- 1995. Fluctuating asymmetry and measurement error. Syst. Biol. 44: 97–101. &
- 2001. Comparison of marker gene and quantitative genetic differentiation among populations. J. Evol. Biol. 14: 892–903. &
- 2001. Cryptic evolution in a wild bird population. Nature 412: 76–79. , &
- 2004. Local adaptation and genetics of acid-stress tolerance in the moor frog. Conserv. Genet. 5: 513–522. , , , &
- 1999. Repeated selection of morphometric traits in the Soay sheep on St Kilda. J. Anim. Ecol. 68: 472–488. , , , &
- 2002. BLUPF90 and related programs (BGF90). Proc. 7th World Congr. Genet. Appl. Livest. Prod., Montpellier, France. Communication No. 28-07. , , , , &
- 2005. Comparing the effects of genetic drift and fluctuating selection on genotype frequency changes in the scarlet tiger moth. Proc. R. Soc. Lond. B 272: 211–217.
- 2005. Bias and precision in QST estimates: problems and some solutions. Genetics 171: 1331–1339. &
- 2006. Estimating relatedness between individuals in general populations with a focus on their use in conservation programs. Genetics 173: 483–496. , , &
- 2008. A Bayesian framework for comparative quantitative genetics. Proc. R. Soc. Lond. B 275: 669–678. , &
- 2003. Genetic and maternal effect influences on viability of common frog tadpoles under different environmental conditions. Heredity 91: 117–124. , &
- 2003. Latitudinal divergence of common frog (Rana temporaria) life history traits by natural selection: evidence from a comparison of molecular and quantitative genetic data. Mol. Ecol. 12: 1963–1978. , , , , &
- 1971. Recovery of inter-block information when block sizes are unequal. Biometrika 58: 545–554. &
- 2006. Implications of the difference between true and predicted breeding values for the study of natural selection and micro-evolution. J. Evol. Biol. 19: 309–320.
- 1996. Marker-based method for inferences about quantitative inheritance in natural populations. Evolution 50: 1062–1073.
- 2004. Evidence for genetic control of adult weight plasticity in the snail Helix aspersa. Genetics 168: 2089–2097. , , , , , &
- 1987. Maximum-likelihood approaches applied to quantitative genetics of natural-populations. Evolution 41: 812–826.
- 2006. Association mapping of complex trait loci with context-dependent effects and unknown context variable. Genetics 174: 1597–1611. &
- 2002. A genome scan for quantitative trait loci in a wild population of red deer (Cervus elaphus). Genetics 162: 1863–1873. , , , , &
- 2002. Likelihood, Bayesian, and MCMC Methods in Quantitative Genetics. Springer-Verlag, New York. &
- 1994. Bayesian-analysis of genetic change due to selection using Gibbs sampling. Genet. Sel. Evol. 26: 333–360. , , &
- 2004. Bayesian Approaches to Clinical Trials and Health Care Evaluation. John Wiley & Sons, Chichester, UK. , &
- 1993. Population-structure in Daphnia obtusa– quantitative genetic and allozymic variation. Genetics 135: 367–374.
- 2005. Making Inference from Bayesian Animal Models Utilising Gaussian Markov Random Field Properties. Preprint, Statistics No. 10/2005, Norwegian University of Science and Technology, Trondheim, Norway. Available at: http://www.math.ntnu.no/preprint/statistics/2005/S10-2005.pdf. &
- 2006. Making BUGS Open. R News 6: 12–17. , , &
- 2008. Estimation of quantitative genetic parameters. Proc. R. Soc. Lond. B 275: 679–686.
- 2000. Elasticities and the link between demographic and evolutionary dynamics. Ecology 81: 666–679.
- 2001. Modelling developmental instability in relation to individual fitness: a fully Bayesian latent variable model approach. J. Evol. Biol. 14: 552–563.
- 2006a. Prior specification in Bayesian statistics: three cautionary tales. J. Theor. Biol. 242: 90–100.
- 2006b. Fluctuating asymmetry and developmental instability in evolutionary biology: past, present and future. J. Evol. Biol. 19: 552–563.
- 2007. What do we know about the heritability of developmental instability? Answers from a Bayesian model. Evolution 61: 1033–1042.
- 2007. Phenotypic and genetic variations and correlations in multitrait developmental instability : a multivariate Bayesian model applied to Speckled Wood butterfly (Pararge aegeria) wing measurements. Genet. Res. 89: 155–163. &
- 1996. Multiple-trait Gibbs sampler for animal models: flexible programs for Bayesian and likelihood-based (co)variance component inference. J. Anim. Sci. 74: 2586–2597. &
- 2004. A quantitative genetic method for estimating developmental instability. Evolution 58: 238–244.
- 2005. Comparing Bayesian estimates of genetic differentiation of molecular markers and quantitative traits: an application to Pinus sylvestris. Heredity 94: 623–629. , &
- 1993. Marginal inferences about variance components in a mixed linear model using Gibbs sampling. Genet. Sel. Evol. 25: 41–62. , &
- 1994. Bayesian-analysis of mixed linear-models via Gibbs sampling with an application to litter size in Iberian pigs. Genet. Sel. Evol. 26: 91–115. , &
- 1998. The repeatability of fluctuating asymmetry: a revision and extension. Proc. R. Soc. Lond. B 265: 1429–1431.
- 2006. Environmental coupling of selection and heritability limits evolution. PLoS Biol. 4: e216. , , , , , &
- 1921a. Systems of mating. I. The biometric relations between parents and offspring. Genetics 6: 111–123.
- 1921b. Systems of mating. II. The effects of inbreeding on the genetic composition of a population. Genetics 6: 124–143.
- 1921c. Systems of mating. III. Assortative mating based on somatic resemblance. Genetics 6: 144–161.
- 2000. Bayesian mapping of quantitative trait loci under the identity-by-descent-based variance component model. Genetics 156: 411–422. &
- 2005. A unified mixed-model method for association mapping that accounts for multiple levels of relatedness. Nat. Genet. 38: 203–208. , , , , , , , , , , &