I don't know if there is a specific article about how yields are modified with improvements and such. I think you can easily find in Civopedia what each terrain type yields, and yields on terrain are modified by the following: tile improvements, buildings, social policies (including ideology) and religion (pantheon beliefs). There is also the golden age bonus that makes each tile that originally yields at least one gold yield one more, but that is temporary.
All the modifiers only add yields to a tile, they don't remove yields. BUT you have to be careful when improving a jungle or forest tile because most improvements will remove the jungle or forest and you may lose bonuses specific to forest/jungle. Only trading posts, camps, lumber mills, forts and some unique improvements (like brazilwood camp) are the improvements that do not remove the forest/jungle. And of course roads + railroads.
In your case by improving the jungle tile you cleared the jungle from that tile, and you lost the +2 science bonus that you might get with universities, and also the +1 culture bonus that comes from the Sacred Path pantheon belief, because they only apply to jungle tiles. Sometimes is better to chop the jungle to get more food with a farm, or production with a mine, but sometimes it's better to put a trading post on it and get a tile that yields 2 food, 2 gold and 2 science (that can be further buffed with Sacred Path pantheon belief, and Free Though social policy, and commerce finisher to 2 food, 3 gold (4 during golden ages), 3 science and 1 culture.