You collect several thousand Drosophila melanogaster individualsfrom the UC Davis experimental orchard in Winters. Youuse1000 ofthese flies to establish a laboratory population, which youmaintain at a census population size of 1000 each generation. Youthen establish from the remaining field-collected flies a series ofreplicated populations of size 10, 100, 200, and 500and maintaineach at the starting size (10, 100, 200, 500) for severalgenerations. After some time, you sequence each lab population.
a. If one plotted for each lab population, the frequency of eachnucleotide variant vs. its true frequency in the UCD population,how would the correlations differ across lab populations?
b. Which lab populations do you think would provide the bestestimate of the true UCD frequencies? Why?
c. Now imagine that one carried out the same type of correlationanalysis of allele frequencies ,but instead of comparing eachpopulation to the true UCD frequencies you compare the allelefrequency of the replicated populations to each other (e.g., thepopulations of size 10 are compared to one another, the populationsof size 100 are compared to one another, etc.). How would thepairwise correlations of frequency vary from one population size toanother?
d. What two aspects of the sampling of flies in this entireexperiment would lead to allele frequency deviations from the trueUCD frequencies for sites free of natural selection?
e. You measure sequence divergence between each lab populationand the sibling species, Drosophila simulans. How will the expecteddivergence vary across replicated populations of different size?Why?
