Jeffrey's pine vs pine tree

Jeffrey's pine and pine tree both are nouns.

Word	Noun	Adjective	Verb	Adverb
Jeffrey's pine	Yes	No	No	No
pine tree	Yes	No	No	No

As nouns, pine tree is a hypernym of Jeffrey's pine; that is, pine tree is a word with a broader meaning than Jeffrey's pine:

Jeffrey's pine: tall symmetrical pine of western North America having long blue-green needles in bunches of 3 and elongated cones on spreading somewhat pendulous branches; sometimes classified as a variety of ponderosa pine
pine tree: a coniferous tree

Other hypernyms of Jeffrey's pine include pine, true pine.

Jeffrey's pine (noun)	pine tree (noun)
tall symmetrical pine of western North America having long blue-green needles in bunches of 3 and elongated cones on spreading somewhat pendulous branches; sometimes classified as a variety of ponderosa pine	a coniferous tree