What animal did the explorers discover that they first described as a barking squirrel?

The correct answer is a black-tailed prairie dog.

Explanation:

Lewis and Clark made their first reports of the flora and fauna they discovered along the Missouri River between 1804 and 1806. They also documented their observations of the Rocky Mountains and the Pacific Northwest. Lewis and Clark gave descriptions of at least 178 plants and 122 animals. Among these was the black-tailed prairie dog which the explorers described as a "barking squirrel." The explorers sent this specimen to President Jefferson to show some concrete evidence of their discoveries.