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This list of resources is maintained as an electronic supplement to our forthcoming two volume textbook on Quantitative Genetics to be published by
Sinauer Associates. Links to web pages, particular programs, and notes/comments on all issues in quantitative genetics (i.e., animal breeding, plant breeding, evolutionary genetics, human genetics) can be found under the
appropriate chapters for each volume.
The authors are Mike Lynch
(in the Department of Biology at Indiana University at Bloomington) and myself (
Bruce Walsh in the Department of Ecology and Evolutionary Biology at the
University of Arizona).
Email the authors.
Published December 1997. Deals with
basic biology and estimation of quantitiative characters.
Current list of Typos and Other Still Errors (last updated 25 August 2003)
Details and Ordering information
Topics Covered (Complete list of chapters)
 Resemblance between relatives
 Genetic variance components
 Detecting major genes
 Polygenes and polygenetic mutation
 QTL mapping in inbred and outbred populations
 Line cross analysis, inbreeding and outbreeding depression
 Distribution theory, matrix methods, scaling and transformation
 Estimation: regression, ANOVA, BLUP, and REML
 Sibs, dialleles, correlated characters, GxE, maternal effects, sexlinked, threshold characters
For updates, programs, notes on new material, see the webpage for the appropriate chapter

 Comments to the publisher from original reviewers of the manuscript
(W. G. Hill, James Crow, Ruth Shaw)
 Reviews:
 Warren Ewens, American Journal of Human Biology 11: 798800. [ review
 Trudy MacKay, Evolution 53: 307309.
[ review ]
 Jim Cheverud, Am. J. Phys. Anthrop. 108: 375376.
[ review ]
 J. J. Colleau, Genetics, Selection, Evolution 30: 203204.
[ review ]

Nick Barton, Genetical Research 72: 73.
[ review ]
 Paul Siegel, Journal of Heredity 90: 256257. [ review ]
 Mary Marazita, Trends in Genetics 15: 120.
[ review ]
 Outi Savolainen, Forest Genetics 6: 88
[ review ]
 William A. Nelson and Elizabeth E. Crone, The Quarterly Review of Biology 74: 225. [review ]
 Christopher Basten, Theoretical Population Biology 57: 307 [review ]
 Suzanne Leal,
American Journal of Human Genetics 68: 548549. [ review ]

Courses using Volume 1 (partial list):
[ Please drop us an email so we can add your course to this list! ]
 BioStatistics 578,
Statistical Methods in Quantitative Genetics. Stephanie Monks, University of Washington (Winter Quarter, 2000).

Biometrical Genetics and Plant Breeding, Chris Cramer, New Mexico State University.
 Module 8: Quantitative Trait Gene Mapping I, NCSU Summer Institute in Statistical Genetics, ZB. Zeng, C. J. Basten, and R. Doerge.

Module 10: Quantitative Trait Gene Mapping II , NCSU Summer Institute in Statistical Genetics, ZB Zeng, C.J. Basten, B. Yandell and I. Hoeschele.

Short Course in QTL mapping, as part of the Quantitative Genetics and Genome Analysis MSc degree at the
University of Edinburgh.
S. Knott (and others).
This is about 70 percent finished) will follow, and deals with
natural and artificial selection on quantitative characters. Draft chapters
can be downloaded from the Vol. 2 webpage.
Topics Covered (Complete list of chapters)
 Genetic drift, including changes in nonadditive variances
 Selection theory: changes in means and variances, short and longterm response, effects of finite population size, index selection.
 Measuring selection in natural populations
 Phenotypic evolution models: applications to ecology, paleobiology, marcoevolution, sexual selection
 Maintenance of quantitative genetic variability
Guest log
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Notes on Program Links
 Most programs are listed under the appropriate chapters.
 There is a seperate list of
generalpurpose educational programs .
 Only programs that are available free to the general community will be listed!!
 To include your listing or report of errors, please
email me. Thanks!
Recent Books on Quantitative Genetics
Recent books not cited in our book.
 Gallais, A. 2003. Quantitative Genetics and Breeding Methods in Autopolyploid Plants INRA, Paris 513 pp.
 Sorensen, D., and D. Gianola. 2002 Likelihood, Bayesian, and MCMC Methods in Quantitative Genetics. Springer 739 pp.
ISBN 0387954406. $89.95
webpage
 Bernardo, Rex 2002
Breeding for Quantitative Traits in Plants. Stemma Press 369 pp. ISBN 0972072405. $65.
Webpage
 Knoury, Muin J., Terri H. Beaty, and Bernice H. Cohen. 1993.
Fundamentals of Genetic Epidemiology. Oxford. 383 pp.
ISBN 0195052889. $59.50
 Lange, K. 1997. Mathematical and statistical methods for genetic analysis. Springer.
288PP.
HARDCOVER $54.95
ISBN 0387949097 (Available at amazon.com)
 An excellent short text with a strong emphasis on probablistic and statistical issues, with a focus on human applications.
 Introduction:
During the past decade, geneticists have constructed detailed maps
of the human genome and cloned scores of Mendelian disease genes.
They now stand on the threshold of sequencing the genome in its entirety.
The unprecedented insights into human disease and evolution offered by mapping
and sequencing will transform medicine and agriculture. This revolution depends
vitally on the contributions of applied mathematicians, statisticians, and computer scientists.
Mathematical and Statistical Methods for Genetic Analysis is written to equip
graduate students in the mathematical sciences to understand and model the epidemiological
and experimental data encountered in genetics research. Mathematical, statistical, and
computational principles relevant to this task are developed hand in hand with applications
to gene mapping, risk prediction, and the testing of epidemiological hypotheses. The book
includes many topics currently accessible only in journal articles, including pedigree analysis
algorithms, Markov chain Monte Carlo methods, reconstruction of evolutionary trees, radiation
hybrid mapping, and models of recombination. Exercise sets are included.
 Contents:
1. Basic principles of population genetics;
2. Counting methods and the EM algorithm; 3. Newton's method and scoring;
4. Hypothesis testing and categorical data; 5; Genetic identity coefficients;
6. Applications of identity coefficients; 7. Computation of Mendelian likelihoods;
8. The polygenic model; 9. Markov chain Monte Carlo methods;
10. Reconstruction of evolutionary trees; 11. Radiation hybrid mapping;
12. Models of recombination; 13. Poisson approximation;
Appendix A: Molecular genetics in brief.
 Simm, G. 1998. Genetic Improvement of Cattle and Sheep. Farming Press. ISBN 0852363516. Softcover $49.95 (Available at amazon.com, search on title, not author)
 Haines, J. L. and M. A. PericakVance (eds). 1998 .Approaches to Gene Mapping in Complex Human Diseases . ISBN 0471171956. Softcover $79.95. 320 pages. (Available at amazon.com )
 Sham, Pak. 1998. Statistics in Human Genetics ISBN 0340662417 Softcover $44.95 (Available at amazon.com ). 304 pages. Topics covered include the estimation of allele frequencies; the testing for HardyWeinberg
equilibrium; classical and complex segregation analysis; linkage analysis for Mendelian and complex diseases and quantitative
traits; the detection of allelic associations; the estimation of heritability for multifactorial traits; and path analysis.
 Ott, Jurg. 1999. Analysis of Human Genetic Linkage (3rd ed). ISBN 0801861403. Johns Hopkins Univ Press. Softcover $55.00. 424 pages. (Available at amazon.com )
 Plomin, Robert, John C. DeFries, Gerlad E. McClearn, and Peter McGuffin. Behavioral Genetics (4th ed). ISBN 0716751593. Worth Publishers, New York. $89.50 449 pages. (Available at amazon.com )
 Thompson, Elizabeth A. 2000.
Statistical Inferences from Genetic Data on Pedigrees .
ISBN 0940600498 .
 This monograph is based on lectures presented at a 1999 CBMS Summer Research Conference. It develops the probability models for genetic data on
related individuals, from the meiosis level to data on extended pedigrees. The focus is on simple Mendelian traits, such as DNA markers, but on joint
models for data at multiple genetic loci, such as arise in modern genome scan studies. The statistical approach is that of likelihood, maximum likelihood
estimation, and methods for the analysis of latentvariable and hiddenMarkov models including the EM algorithm, the Baum algorithm, and Monte Carlo imputation methods.
The first half of the monograph develops the basic concepts and approaches, focusing on the ideas of gene identity by descent and the tracing of gene
descent in pedigrees using meiosis indicators or inheritance vectors. This material should be accessible to firstyear graduate students in statistics or
biostatistics. Only a basic understanding of discrete probability and mathematical statistics (likelihood inference) are assumed. No genetic knowledge is
presupposed, although some familiarity with basic terminology will be helpful.
Building on these foundations, the second half of the monograph develops Markov chain Monte Carlo (MCMC) and Monte Carlo likelihood methods
for the analysis of data on individuals in a known pedigree structure. This material is more specialized, but should be accessible to those who have
mastered the earlier chapters, or who have studied hidden Markov models and MCMC methods. The objective is Monte Carlo estimation of likelihood
surfaces and conditional probabilities, rather than Bayesian sampling of parameter spaces and posterior distributions. The penultimate chapter illustrates
the methods presented, through detailed analysis of two examples, using recently implemented MCMC samplers and likelihood estimation procedures.
The final chapter discusses related research areas and the potential for further development of methods.

Ordering information ($30.00)
 Quantitative Trait Loci Analysis in Animals , by Joel Weller. $50.00 (US) 304 pages. More details
Links to webpages on Quantitative Genetics
Class Notes (Some of these links appear to only be active when the class is taught)
 Statistical Genetics, with a focus on Animal and Plant Breeding . Wyman Nyquist, Purdue University. Very extensive notes (essentially an online textbook)
 Armidale Animal Breeding Summer Course 2003 . David Lindsay, Julius van der Werf, Mike Goddard, Ben Hayes, University of New England, Armidale NSW.
 Armidale Animal Breeding Summer Course 2004.
 2003 Nordic postgraduate course: Quantitative Genetics in Animal Breeding. Bruce Walsh and Bill Muir, Helsinki, Finland.
 Quantitative Genetics and Animal Models . L. R. Schaeffer, University of Guelph.
 Estimation of Genetic Parameters . L. R. Schaeffer, University of Guelph.
 EEB 348: Population Genetics . Kent Holsinger, Univ. Conn.
Genomes
 AnimalGenome Size Database ( Cvalues for
over 2,100 species and subspecies of vertebrates and 800 invertebrates)
 Human

Mouse

Fugu (Puffer fish)

Arabidopsis

Flybase (Drosophila)

Mosquito

Wormbase (C. elegans)

Dictyostelium

TIGR Microbial Database
Karen Ayres (University of Reading ) very extensive
Statistical Genetics webpage
Software
Meetings
 Upcoming
 Recent Past

Gordon Conference on Quantitative Genetics , February 9  14, 2003. Ventura, California.
 Conference on
Long term selection . June 17  19, 2002,
Urbana, Illinois.

Seventh World Congress on Genetics Applied to Livestock Production (7th WCGALP)
August 1923, 2002. Montpellier, France.

Population and Evolutionary Genetics of Forest Tree Species
Star‡ Lesn‡, Slovakia, August 2529, 2002

Gordon Conference on Quantitative Genetics , February 1823, 2001. Ventura, California.

Quantitative Genetics and Plant Breeding in the 21st Century. A Symposium held by the LSU Chapter of Sigma Xi
from March 26 thru March 28, 2001 in Baton Rouge, Louisiana.
 Summaries from Previous meetings
 Report and Recommendations from the NIH meeting on The Genetic Architecture of Complex Traits held at the (US) National Institutes of Health on December 1011, 1997.
 Reports from Sixth World Congress on Genetics Applied to Livestock Production, University of New England, Australia (January 1116th 1998).
Advanced Classes/Workshops
 Summer Institute in Statistical Genetics, from University of Washington
 The M.Sc./Diploma in
Quantitative Genetics and Genome Analysis at the
University of Edinburgh.
QuantitativeGenetics related listserves

ANGENMAP
(ANimal GENe MAPpers) is an internet discussion group for all gene
mappers and interested parties
Directories for Finding People

Evolution and population genetics

Animal Breeders and Geneticists

Animal Gene Mapping Community Directory
Animal Breeding and Genetics
Plant Breeding
Forest Breeding
Evolution
Human Genetics

Online Mendelian Inheritance in Man. This database is a catalog of human genes and genetic disorders authored and edited by
Dr. Victor A. McKusick and his colleagues at Johns Hopkins and elsewhere, and developed for the World Wide Web by NCBI, the National Center for
Biotechnology Information. The database contains textual information, pictures, and reference information. It also contains copious links to NCBI's
Entrez database of MEDLINE articles and sequence information.

Genetic Linkage Analysis server at Rockerfeller.

Statistical Genetics Group
at the University of Michigan

SAGE
Statistical Analysis for Genetic Epidemiology package
 USCF's big
Epidemiology page

American Society of Human Genetics
Departments and Programs
Journals
Searchable bibliographices
Home Pages:
[ Walsh] 
[ Volume One] 
[ Volume Two] 
[ What's new ]
Created 25 February 1995, last updated 31 Jan 2002
Bruce Walsh. jbwalsh@u.arizona.edu .
Comments welcome.
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