In class we proved that the conjugacy map preserves cycle structure, and I was wondering if this was the case for any automorphism of a permutation group.
I intuitively think that it should be the case, because automorphisms are isomorphisms from a group to itself and isomorphisms should not modify any fundamental structure of an element (i.e. generators must map to generators, an element of a certain power is mapped to one of the same power etc..). However, I don't have any actual reason to think that cycle structure is a fundamental property of an element of a permutation group, and I'm struggling to prove the assertion in the general case.
Anyone have any ideas or insights?
Considering joriki's comment, I'll interpret 'permutation group' as meaning 'symmetric group', because otherwise it is obvious that cycle structure isn't preserved; the permutation group $$V:=\{\operatorname{id}_{S_4},(1\ 2),(3\ 4),(1\ 2)(3\ 4)\}\subset S_4,$$ has many automorphisms that do not preserve cycle structure, for example.
First some terminology: An inner automorphism of a group $G$ is a $\varphi\in\operatorname{Aut}(G)$ for which $$\exists x\in G:\ \forall g\in G:\qquad \varphi(g)=xgx^{-1}.$$ That is, the automorphism $\varphi$ is given by conjugation by $x\in G$. Automorphisms that are not inner are called outer automorphisms. It is a nice and instructive exercise to check that the inner automorphisms form a normal subgroup $\operatorname{Inn}(G)\unlhd\operatorname{Aut}(G)$.
For symmetric groups conjugation preserves cycle structure, as you proved in class. Put briefly, conjugating a $g\in S_n$ by some permutation $x\in S_n$ simply permutes the numbers in any cycle representation of $g$ by the permutation $x$, so this preserves the cycle structure. That is to say, $$\text{ If }\qquad g(i)=j\qquad \text{ then }\qquad (xgx^{-1})(x(i))=x(j).$$ This means all inner automorphisms of $S_n$ preserve cycle structure.
It is a weird and nontrivial fact that all automorphisms of all symmetric groups are inner automorphisms, except for some automorphisms of $S_6$. These outer automorphisms do not preserve cycle structure. You can check this by looking at explicit outer automorphisms of $S_6$. User 2015's answer gives a construction for such automorphisms, and google will give you many more constructions, for example here and here.
I don't know of a simple proof of the fact that all automorphisms of $S_n$ are inner for $n\neq6$, but here is a nice and elegant proof by user anon using only basic group theory and combinatorics.