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Linked determinantal loci and limit linear series

We study (a generalization of) the notion of linked determinantal loci recently introduced by the second author, showing that as with classical determinantal loci, they are Cohen-Macaulay whenever they have the expected codimension. We apply this to prove Cohen-Macaulayness and flatness for moduli spaces of limit linear series, and to prove a comparison result between the scheme structures of Eisenbud-Harris limit linear series and the spaces of limit linear series recently constructed by the second author. This comparison result is crucial in order to study the geometry of Brill-Noether loci via degenerations.