Neal's answer is really good - it implies that the birds are also alive and well.
Even simply "has/had" works well. Other possibilities are: held, showcased, housed... I'm sure there's more.
"Contained" is technically correct but sounds a bit cold, and doesn't indicate if the birds are alive or not (this may be important). You could equally say "the encyclopedia contained different species of birds", or "the freezer compartment contained different species of birds".