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The short story collection "Year's Best Sci-Fi 5" edited by David G. Hartwell (I believe it covered 1999) contains the story "Evolution Never Sleeps" by Elisabeth Malartre; it's basically killer chipmunks, though in a very hard sci-fi manner. It's more about how they would effect the eco-system (look away, owl fans) than people running from ground squirrels.

(The collection also contained Robert Reed's sorta-furry "Game of the Century," about genetically manipulated football players.)

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