Yes, he said.
( Yes ( , ( he ( said . ) ) ) )
(ROOT (S (INTJ (UH Yes)) (, ,) (NP (PRP he)) (VP (VBD said)) (. .)))
He said in the affirmative.
( He ( ( said ( in ( the affirmative ) ) ) . ) )
(ROOT (S (NP (PRP He)) (VP (VBD said) (PP (IN in) (NP (DT the) (JJ affirmative)))) (. .)))