After they encountered a colony of the prairie dogs, Lewis and Clark managed to lure them out by pouring water into their burrows. They killed one and caught another alive. Records show that among the things sent back to the President was a caged prairie dog. It is likely that they sent the first one they caught alive. More prairie dogs were shot and their skin preserved. Lewis and his team also fed on some of the rodents and discovered that they were a palatable delicacy.
The expedition was commissioned by President Jefferson in attempts to explore the West. The idea was to create maps of the rivers, discover a route to the Northwest, make contact and build trade relationships with the native tribes, and discover the different aspects of the environment, including the weather that existed on the uncharted side of the region.
The expedition was largely successful given the detailed maps they were able to develop, and the relatively peaceful contact they made with the native communities.
https://lewisandclarkjournals.unl.edu/item/lc.jrn.1804-09-07
https://lewisandclarkjournals.unl.edu/item/lc.sup.johnsgard.01.03
https://www.monticello.org/thomas-jefferson/louisiana-lewis-clark/the-journey-west/
According to the journal kept by William Clark, the expedition encountered its first prairie dog on September 7, 1804. They commenced trying to catch the animals, and in the process killed one and caught another one alive. Throughout their expedition, they were tasked by President Thomas Jefferson with taking specimens of the flora and fauna of the region. The prairie dogs were fascinating to Lewis and Clark because they were so adept at burrowing. Clark relates that the men dug nearly six feet into the hard clay ground without breaching their tunnels. In some tunnels, Clark says, they dumped "5 barrels of water without driving [sic] them out." Once they captured the little animal, Clark describes its appearance as a sort of combination of a rabbit, dog, and ground squirrel. It had a mouth like a rabbit, eyes reminiscent of a dog, and a tail like a squirrel, which they would "Shake and make chattering noise." While investigating (or, more accurately, laying waste to) the prairie dog village, they killed a rattlesnake with one of the creatures in its stomach.
https://lewisandclarkjournals.unl.edu/item/lc.jrn.1804-09-07
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