Pinus jeffreyi vs pine tree

Pinus jeffreyi and pine tree both are nouns.

Word	Noun	Adjective	Verb	Adverb
Pinus jeffreyi	Yes	No	No	No
pine tree	Yes	No	No	No

As nouns, pine tree is a hypernym of Pinus jeffreyi; that is, pine tree is a word with a broader meaning than Pinus jeffreyi:

Pinus jeffreyi: 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 Pinus jeffreyi include pine, true pine.

Pinus jeffreyi (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