Learn French: Cette espèce est petite, pourtant elle mange le prédateur ! - This species is small, yet it eats the predator!

Both words express opposition, but pourtant strongly emphasizes an unexpected contradiction (being small usually means you are the prey, not the eater). Cependant is a bit more neutral and formal, much like the English however. That said, you could grammatically use cependant here without changing the core meaning.

Why do we use elle? Does this mean the animal doing the eating is female?

Not necessarily! The pronoun elle is used because it refers back to the noun espèce (species). In French, espèce is always a feminine noun, so any adjectives or pronouns referring to it must be feminine (cette, petite, elle), regardless of the actual biological sex of the animal.

Could I just use mais (but) instead of pourtant?

Yes, using mais works perfectly to connect the clauses. However, using pourtant (yet or even so) makes the contrast much stronger. It highlights the surprise of a tiny animal eating a predator. You will also sometimes see them combined as mais pourtant for extra emphasis.

Can I place pourtant somewhere else in the sentence?