The Subtree Isomorphism problem asks whether a given tree is contained in another given tree. The problem is of fundamental importance and has been studied since the 1960s. For some variants, e.g., ordered trees, near-linear time algorithms are known, but for the general case truly subquadratic algorithms remain elusive. Our first result is a reduction from the Orthogonal Vectors problem to Subtree Isomorphism, showing that a truly subquadratic algorithm for the latter refutes the Strong Exponential Time Hypothesis (SETH). In light of this conditional lower bound, we focus on natural special cases for which no truly subquadratic algorithms are known. We classify these cases against the quadratic barrier, showing in particular that: (1) Even for binary, rooted trees, a truly subquadratic algorithm refutes SETH. (2) Even for rooted trees of depth O(log log n), where n is the total number of vertices, a truly subquadratic algorithm refutes SETH. (3) For every constant d, there is a constant ε_d > 0 and a randomized, truly subquadratic algorithm for degreed rooted trees of depth at most (1 + ε_d) log_dn. In particular, there is an O(min{2.85~h, n~2}) algorithm for binary trees of depth h. Our reductions utilize new "tree gadgets" that are likely useful for future SETH-based lower bounds for problems on trees. Our upper bounds apply a folklore result from randomized decision tree complexity.
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