HINT 13A: Any variant that is shared by a set of individuals, but is not present in the outgroup X implies that this set of individuals forms a clade.
HINT 13B: Think about the average difference between X and a random member of the studied species.
HINT 13C: + and – just denote presence or absence of a site where a restriction enzyme cuts. F and S denote different amino acids at the polymorphic sites and can be treated in the same way. There is no information on which are ancestral and which are derived, and so the tree cannot be rooted.
HINT 13D: Find the two sequences most closely related to l and to m.
HINT 13E: Focus on a single evolving lineage. In the absence of selection, the rate of mutation in a single lineage is the same as the rate of change of the whole population—a basic feature of the neutral theory; see p. 425.
HINT 13F: The overall probability of identity is the product of the probabilities that a site does not change on each individual branch.
HINT 13G: If we examine the genetic code as laid out in Fig. 2.26, we see that a change to the first position corresponds to a change in the row. Thus, the amino acid can only remain unchanged if the same amino acid appears in different rows.
HINT 13H: What is the chance of a random change giving the same amino acid sequence if amino acids were assigned at random for the 64 possible triplet codons?