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I am looking for a book (or any good source of information) that offers an in-depth discussion and models about the evolution and analysis of complex traits and complex genetic architecture. Do you have any suggestions?

I'd define complex traits as those traits whose variance in the population is explained by quite a lot of various genetic loci and environmental factors.

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    $\begingroup$ You might like "The mathematical theory of selection, recombination, and mutation" by R Bürger $\endgroup$ – rg255 Apr 29 '14 at 15:27
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    $\begingroup$ Lynch and Walsh's Genetics and Analysis of Quantitative Traits (sinauer.com/genetics-and-analysis-of-quantitative-traits.html) is pretty comprehensive (if not necessarily comprehensible). $\endgroup$ – kmm Apr 29 '14 at 17:53
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Suggestions:

Evolutionary Genetics : Concepts and Case Studies: Concepts and Case Studies

Edited by Lexington Charles W. Fox Department of Entomology University of Kentucky, Faculty of Life Sciences University of Manchester Jason B. Wolf Lecturer

The mathematical theory of selection, recombination, and mutation

by R Bürger (as suggested by @rg255 in the comments)

Lynch and Walsh's Genetics and Analysis of Quantitative Traits

(as suggested by @kmm in the comments)

PS: Do tell us if you found a better one.

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