1. Describe the interplay between gene flow, genetic drift, and selection. Under what
circumstances does one overwhelm the others? Selection can affect allele frequencies at
loci affecting fitness, but can selection also limit gene flow at unlinked neutral loci?
2. Kimura’s equation (k = µ) provides a powerful prediction for neutral genetic variation.
However, this prediction may not hold for neutral regions linked to regions that are
subjected to selection. How might background selection and rates of recombination affect
the substitution rates for neutral alleles?
3. How can expectations from coalescence theory allow us to detect the effects of selection?
Describe neutrality tests including the Ewens-Watterson and Tajima’s D tests. How can
these tests be confounded by violations of the assumption of constant population size?
How might we distinguish the effects of historical bottlenecks from the effects of
selection?
4. What can variation in levels of genomic differentiation (i.e. speciation islands, FST
outliers) tell us about the effects of selection during divergence among lineages? What
else besides selection can cause FST outliers? What would be a good way to confirm that
these genomic regions were responsible for adaptation to different habitats?
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