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Gave a better reference
Timothy Chow
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Corollary 2.7 of Norman Biggs's book Algebraic Graph Theory says that if $d$ is the diameter of the graph, then it has at least $d+1$ distinct eigenvalues. (This bound is tight, and is achieved for example by distance-regular graphs.) So in particular, having a lot of repeated eigenvalues does not necessarily indicate a lot of automorphisms; it might just mean that the diameter is small. For example, a strongly regular graph has only three distinct eigenvalues but often has trivial automorphism group.

Timothy Chow
  • 82.7k
  • 26
  • 363
  • 587