Gophers and Lice: Jungle
Notes:
The jungle is much more complicated for this case, but it was still possible to solve the problem instance by hand!
Parts of the solution had to be in any optimal reconstruction: these are in white.
The green bits were common to both Page’s and Ronquist’s solutions.
The solution in light blue is that of Rod Page, which I found to be optimal with the costing scheme given. His optimality criterion was to maximize the number of cospeciations and minimise other events, which fits in well with the general scheme outlined previously (c Š 0; d, s, w > 0).
Ronquist’s solution is in purple. We find that his scheme cannot be optimal under the model outlined previously since he counts duplications with cost 0 - to have his reconstruction optimal would require c > d which is rather implausible and which would lead to huge numbers of solutions anyway.