SYLLABUS Short course in EVOLUTIONARY QUANTITATIVE GENETICS 30 Jan 10 Feb, 2012, University of Uppsala INSTRUCTOR: Bruce Walsh, Department of Ecology & Evolutionary Biology, University of Arizona jbwalsh@u.arizona.edu COURSE READINGS: Material will be posted via email to our goggle group. LN = Lecture notes LW = Lynch & Walsh: Genetics and Analysis of Quantitative Traits WL = Walsh & Lynch: Evolution and Selection of Quantitative Traits http://nitro.biosci.arizona.edu/zbook/newvolume_2/newvol2.html Background reading is included in the printed notes. Additional reading is further material that expands on the topic. LECTURE SCHEDULE Monday, 30 Jan. Background: Basic stats, population genetics 9:00 10:00 am General introduction, basic stat machinery LN 1; LW 2 & 3 10:30 12:00 Basic Linear Algebra LN 2; LW 8 Additional reading: LW A3; WL A4, A5 1:30 3:00 pm Basic Linear Models LN 2; LW 8 Additional reading: LW A3; WL A2, A3 3:30 5:00 pm Basic concepts in Mendelian & Pop Genetics LN 3, pp 1-14 Tuesday, 31 Jan Introduction to Basic Quantitative Genetics 8:30 10:00 am Introduction to Quantitative Genetics LN 3, pp 15 -end 10:30 12:00 Covariance between relatives
LN 4 1:30 3:00 pm Estimation of basic genetic parameters: basics LN 5 3:30 5:00 pm Review, general questions, in-class problems Wednesday, 1 Feb Mixed Models and their extensions 8:30 10:00 am Estimation of basic genetic parameters: mixed models 10:30 12:00 Random effects and mixed models 1:30 3:00 pm Bayesian Statistics: The basics 3:30 5:00 pm Bayesian Statistics: MCMC Thursday, 2 Feb Mapping genes 8:30 10:00 am QTL mapping in controlled crosses LN 9 10:30 12:00 QTL mapping in outbred pops LN 9 1:30 3:00 pm Association mapping 3:30 5:00 pm Pathways and gene networks Friday, 3 Feb Evolutionary response in quantitative traits 8:30 10:00 am Inbreeding and heterosis LN 6 10:30 12:00 Genetic drift
1:30 3:00 pm Tests of selection on traits 3:30 5:00 pm Short term selection response LN 10 Additional reading: WL Chapters 12, 13, 15 Monday, 6 Feb Detecting selection using molecular markers 8:30 10:00 am Selective sweeps and background selection Chapter 9 10:30 12:00 Detecting selection using molecular markers I Additional reading: WL Chapters 10, 11 1:30 3:00 pm Detecting selection using molecular markers II Additional reading: WL Chapters 10, 11 3:30 5:00 pm Status of the neutral theory LN 10 Tuesday, 7 Feb Multivariate selection response 8:30 10:00 am Multivariate response 1: Changes in the mean Chapter 30 10:30 12:00 Multivariate response 2: Changes in the covariance Chapter 31 Additional reading: WL Chapter 29 1:30 3:00 pm Multivariate response 3: Stability of G 3:30 5:00 pm Multivariate response 4: The dimensionality of G Background reading Wed, 8 Feb Estimating the fitness of traits 8:30 10:00 am Fitness estimation I: Univariate Chapter 28 10:30 12:00 Fitness estimation II: Multivariate Chapter 26 1:30 3:00 pm Fitness estimation III: Latent Variables, Aster models
Chapter 28 3:30 5:00 pm Responses in natural populations Chapter 28 Thur, 9 Feb Advanced topics in selection 8:30 10:00 am Index selection theory Chapter 33 Additional reading: WL Chapter 34 Chapter 26 10:30 12:00 Family Selection, maternal effects Additional reading: WL Chapters 10, 11 1:30 3:00 pm Associate effects models, kin/group selection, inclusive fitness I 3:30 5:00 pm Associate effects models, kin/group selection, inclusive fitness II Friday, 3 June G x E 8:30 10:00 am Basic concepts 10:30 12:00 Complex analysis of G x E 1:30 3:00 pm Random Regressions 3:30 5:00 pm Recap (we may potential end earlier to facilitate traveling)
Website for draft chapters from Volume 2 : Walsh & Lynch: Evolution and Selection on Quantitative traits http://nitro.biosci.arizona.edu/zbook/newvolume_2/newvol2.html ADDITIONAL BOOKS ON QUANTITATIVE GENETICS General Falconer, D. S. and T. F. C. Mackay. Introduction to Quantitative Genetics, 4th Edition Lynch, M. and B. Walsh. 1998. Genetics and Analysis of Quantitative Traits. Sinauer. Roff, D. A. 1997. Evolutionary Quantitative Genetics. Chapman and Hall. Mather, K., and J. L. Jinks. 1982. Biometrical Genetics. (3rd Ed.) Chapman & Hall. Animal Breeding Cameron, N. D. 1997. Selection Indices and Prediction of Genetic Merit in Animal Breeding. CAB International. Mrode, R. A. 1996. Linear Models for the Prediction of Animal Breeding Values. CAB International. Simm, G. 1998. Genetic Improvement of Cattle and Sheep. Farming Press. Turner, H. N., and S. S. Y. Young. 1969. Quantitative Genetics in Sheep Breeding. Cornell University Press. Weller, J. I. 2001. Quantitative Trait Loci Analysis in Animals. CABI Publishing. Plant Breeding Acquaah, G. 2007. Principles of Plant Genetics and Breeding. Blackwell. Bernardo, R. 2002. Breeding for Quantitative Traits in Plants. Stemma Press. Hallauer, A. R., and J. B. Miranda. 1986. Quantitative Genetics in Maize Breeding. Iowa State Press. Mayo, O. 1987. The Theory of Plant Breeding. Oxford. Sleper, D. A., and J. M. Poehlman. 2006. Breeding Field Crops. 5th Edition. Blackwell Wricke, G., and W. E. Weber. 1986. Quantitative Genetics and Selection in Plant Breeding. De Gruyter. Humans Khoury, M. J., T. H. Beaty, and B. H. Cohen. 1993. Fundamentals of Genetic Epidemiology. Oxford. Plomin, R., J. C. DeFries, G. E. McLearn, and P. McGuffin. 2002. Behavioral Genetics (4th Ed) Worth Publishers. Sham, P. 1998. Statistics in Human Genetics. Arnold.
Thomas, D. C. 2004. Statistical Methods in Genetic Epidemiology. Oxford. Weiss, K. M. 1993. Genetic Variation and Human Disease. Cambridge. Ziegler, A., and I. R. Konig. 2006. A Statistical Approach to Genetic Epidemiology. Wiley. Statistical and Technical Issues Bulmer, M. 1980. The Mathematical Theory of Quantitative Genetics. Clarendon Press. Kempthorne, O. 1969. An Introduction to Genetic Statistics. Iowa State University Press. Saxton, A. M. (Ed). 2004. Genetic Analysis of Complex Traits Using SAS. SAS Press. Sorensen, D., and D. Gianola. 2002. Likelihood, Bayesian, and MCMC Methods in Quantitative Genetics. Springer.