Title Details

Description of Revised Content of Population Genetics and Microevolutionary Theory

Chapter 1.  Fuse current chapters 1 and 2 into a single chapter entitled:  “Population Genetics: Scope, Premises, and The Hardy-Weinberg Model of Microevolution.”

I would delete the section on “Methodological approaches in population genetics” that appears in the current Chapter 1, and the example of Darwin’s finches would be deferred to the chapters dealing with natural selection.  This would allow me to expand the section on linkage disequilibrium that is currently in Chapter 2.  In particular, I would go into additional measures of linkage disequilibrium such as r² and DUO, a recent vector measure of disequilibrium.  I would also define haplotypes in this new fused chapter, and show how linkage disequilibrium arises in haplotype blocks and can also be used to detect them.  Also, the construction and meaning of extended haplotypes of indeterminate length will be introduced here.

Chapter 2 (Currently Chapter 3).  Systems of Mating.  Few changes are required in this chapter.  I will insert a brief discussion of the work of Keller et al (Genetics 189: 237-249, 2011) that shows that pedigree inbreeding due to distant ancestors can be estimated from runs of homozygosity using markers scattered across the entire genome.

Chapter 3 (Currently Chapter 4 and part of Chapter 5).  Genetic Drift.  A box will be inserted on the diffusion equation approximation to genetic drift.  I will add a new section on the use of effective sizes in conservation biology, focusing on effective sizes in African rhinos.  Finally, I will move the part about the neutral theory of evolution (Currently in Chapter 5) to the end of the revised Chapter 3, but I will delete the section on newly arisen mutations that is currently at the beginning of Chapter 5.

Chapter 4.  (Currently part of Chapter 5).  Coalescence.  I will update the examples used in the current book with more recent examples.  Such an update is particularly needed for the discussion of the infinite sites model and the role it plays in coalescent models.  The section on recombination and coalescence also needs updating.  A new section will be inserted on coalescence and effective population size in order to integrate this chapter more thoroughly with the previous chapter.

Chapter 5 (Currently Chapter 6).  Gene Flow and Population Subdivision.  Much of the material requires no updating, except for the substitution of more recent examples.  A new section on using extended haplotypes to trace gene flow will be inserted, and a  second new section on Bayesian Assignment models and parentage analysis will end the revised chapter.

Chapter 6 (Currently Chapter 7).  Gene Flow and Population History.  This chapter needs to be thoroughly rewritten.  The section on ancient DNA will be expanded and new examples given, focusing on archaic humans.  The section on multi-locus associations will be updated, particularly with respect to principal components, and a new section on landscape genetics will be inserted.  The section on population trees needs to be rewritten in light of new statistical developments in this area.  A new section on Approximate Bayesian Computation in phylogeography will be inserted, along with a comparison of ABC with multi-locus nested clade analysis showing their relative strengths and weaknesses.  There will also be a discussion of skyline plots and its relationship to coalescence.

Chapter 7 (Currently Chapters 8 and 9).  Classical Quantitative Genetics.  No major revisions are needed in terms of the material, but I intend to fuse the current chapters 8 and 9 into one, eliminating some redundancies and shortening the material currently found in Chapter 9. 

Chapter 8 (Currently Chapter 10).  Quantitative Genetics:  Measured Genotypes. 
This chapter will be extensively rewritten and reorganized.  It will deal with admixture mapping, linkage mapping, and genome-wide association studies, followed by an updated treatment of candidate loci.  The updated section on candidate loci will also include a discussion of gene expression arrays and their analysis.

Chapter 9 (Currently Chapter 11).  Natural Selection.  Very little revision is needed here, just a few updated references.

Chapter 10 (Currently Chapter 12).  Interactions of Natural Selection with Other Evolutionary Forces.   The first half of this chapter will be mostly the same.  A new discussion of coadapted gene complexes will be made, emphasizing new developments in their detection and usefulness.  The section on interactions with drift and mutation will be expanded, particularly with respect to genome-wide measures of detecting natural selection and the many new developments and applications in this area.

Chapter 11 (Currently Chapter 13).  Units and Targets of Selection.  The main revision will be to substitute newer examples for some of the ones currently in this chapter.

Chapter 12 (Currently Chapter 14).  Selection in Heterogeneous Environments.  A section on epigenetic adaptation to changing environments will be added.  The discussion about Darwin’s finches would be moved here as an example of selection in a temporally heterogeneous environment.  A new section will be inserted about using genome-wide markers to detect local selection and ecological genomics.

Chapter 13 (Currently Chapter 15).  Selection in Age-Structured Populations.  I will expand the section on life history evolution to discuss the concepts of elasticity and sensitivity and their interactions with pleiotropy.  A new section on effective size in age-structured populations will be added.

 Appendix 1.  Genetic Survey Techniques.  This appendix needs to be updated given the technological advances that have been made.

 Appendix 2.  Probability and Statistics.  I will expand the section on Bayesian inference to discuss the role of computer simulations in generating posterior probabilities.  This will be useful since the text will now discuss programs such as STRUCTURE and ABC