The sentence that contains a dependent clause is the first option provided.
"Although he and Alexander Hamilton worked together on the Federalist Papers, Madison opposed many of Hamilton’s ideas."
The structure considered a dependent clause in this sentence is the first one beginning with the word ALTHOUGH: "Although he and Alexander Hamilton worked together on the Federalist Papers."
This structure constitutes a dependente clause since it has a subject and a verb but it cannot stand alone because it does not provide a complete thought; it requieres another structure a clause to makes a complete sense.