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We establish that the natural permutation representation of highly transitive groups cannot be realized as the full group of automorphisms of an idempotent finite-dimensional evolution algebra acting on the set of lines spanned by natural elements. For instance, for any sufficiently large integer $n$, and $k\geq 4$, there exists no idempotent evolution algebra $X$ such that $\dim X=n$, and $\operatorname{Aut}(X)$ is isomorphic to a proper $k$-transitive subgroup of $S_n$. However, we demonstrate that for any (not necessarily faithful) permutation representation $\xi\colon G \to S_n$ and any field $\Bbbk$, there exists an idempotent finite-dimensional evolution $\Bbbk$-algebra $X$ such that $\operatorname{Aut}(X)\cong G$ and the induced representation given by the $\operatorname{Aut}(X)$-action on the natural idempotents of $X$ is equivalent to $\xi$., Comment: 14 pages, no figures