Meaning of "native bottoms" in Thoreau's Walden

Solution 1:

It's definition 4b(a) in the full OED...

A ship, boat, or other vessel. (Now chiefly historical.)

...but that's behind a paywall for most, so here's dictionary.com's definition 8...

(in literary or commercial contexts) a boat or ship.

I imagine the usage arose by extension from earlier bottom = the keel or lower part of a ship's hull (OED definition 4a). That's the part of a ship most often used for carrying bulky cargo, so in contexts where the primary purpose of the ship is to carry that cargo, it would be natural to use the name of the cargo-carrying part to represent the whole ship.

Solution 2:

I did find this archaic meaning for bottom

1.9 archaic A ship, especially a cargo carrier.

Oxford Dictionaries