1. For a diploid species, assume one set of 100 demes, each with a constant size of 50 individuals, and another set of 100 demes, each with 100 individuals. (a) If in each deme the frequencies of neutral alleles A1 and A2 are 0.4 and 0.6 respectively, what fraction of demes in each set is likely to become fixed for allele A1 versus A2? (b) Assume that a neutral mutation arises in each deme. Calculate the probability that it will become fixed in a population of each size. In what number of demes (approximately) do you expect it to become fixed? (c) If a fixation occurs, how many generations do you expect it to take?
2. Assuming that the average rate of neutral mutation is 10–9 per base pair per gamete, how many generations would it take, on average, for 20 base pair substitutions to be fixed in a gene with 2000 base pairs? Suppose that the number of base pair differences in this gene between species A and B is 92, between A and C is 49, and between B and C is 91. Assuming that no repeated replacements have occurred at any site in any lineage, draw the phylogenetic tree, estimate the number of fixations that have occurred along each branch, and estimate the number of generations since each of the two speciation events.
3. Some evolutionary biologists have argued that the neutral theory should be taken as the null hypothesis to explain genetic variation within species or populations and genetic differences among them. In this view, adaptation and natural selection should be the preferred explanation only if genetic drift cannot explain the data. Others might argue that since there is so much evidence that natural selection has shaped species’ characteristics, selection should be the explanation of choice and that the burden of proof should fall on advocates of the neutral theory. Why might one of these points of view be more convincing than the other?
4. Some critics of Darwin’s theory of evolution by natural selection have claimed that the concept of natural selection is tautologous (i.e., it is a “vicious circle”). They say, “Natural selection is the principle of the survival of the fittest. But the fittest are defined as those that survive, so there is no way to prove or disprove the theory.” Argue against this statement, based on the contents of this chapter.
5. How can gene trees be used to estimate rates of gene flow among geographic populations of a species? What assumptions would have to be made? (See Slatkin and Maddison 1989.)
6. Suppose that several investigators want to use genetic markers such as allozymes or SNPs to estimate gene flow (the average number of migrants per generation) among populations of several species. One wants to study movement of howler monkeys among forest patches left by land clearing in Brazil; another plans to study movement among populations of mink frogs in lakes in Ontario, north of Lake Superior; a third intends to study the warbler finch on the 17 major islands of the Galápagos archipelago, near the Equator. For which of these species is this approach most likely, or least likely, to yield a valid estimate of gene flow? Why?
7. Could the principles of this chapter be used to estimate when an infectious disease organism first entered the human population? What conditions or characteristics of the organism would help to make this feasible? See, for example, “Timing the ancestor of the HIV-1 pandemic strains” by B. Korber et al. (Science 288:1789–1796, 2000).
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