Pinus pungens vs pine tree

Pinus pungens and pine tree both are nouns.

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

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

Pinus pungens: a small two-needled upland pine of the eastern United States (Appalachians) having dark brown flaking bark and thorn-tipped cone scales
pine tree: a coniferous tree

Other hypernyms of Pinus pungens include pine, true pine.

Pinus pungens (noun)	pine tree (noun)
a small two-needled upland pine of the eastern United States (Appalachians) having dark brown flaking bark and thorn-tipped cone scales	a coniferous tree