PAUL SMITHS, N.Y.—Here in the heart of New York’s Adirondack Park, scientists and a canister of ancient mud are challenging a fish story that has been part of the culture of this trout-fishing mecca for more than a half-century.

Since the early 1950s, state conservation agencies have been trying to purge yellow perch from lakes in the 6-million-acre park in the belief that the fish are an invasive species that has crowded out the native and highly prized brook trout.

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