NOTE 13B: Any number of other scenarios could be imagined, involving more recombination events and/or more mutations. Which scenario is most likely depends on the relative plausibility of recombination or mutation. If we know the relative rates of mutation and recombination, then we can weight them appropriately. Under the hypothesis shown here, some mutations occur twice (e.g., position 12 changes between a and c, and also between j and m). That is not implausible for a mutation caused by loss or gain of a restriction site, as shown here, but would be unlikely for (say) insertion of a transposable element at a particular site. Again, if we knew the relative plausibility of different kinds of mutation, we could better estimate the genealogy.
(See Table P13.3 and Figure P13.4.)