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[Leonidas]

I'm trying a 2x2 embark for the first time, in an Untamed Wilds biome. The speed is amazing, but one of the drawbacks involves wildlife.  At first, it seemed like the many giant birds and insects ignored me. But now with a population around 50, I'm getting panic and job cancellation spam almost as soon as they appear.

With non-evil wildlife, what determines whether a creature will cause my civilians to flee? Is it inherent to the creature, or does it involve stress and proximity?

[anewaname]

So, I'm saying this from observation, and not from any source in the wiki...

It is probably not the population increase to 50 that is causing the panics and job cancellations, but the effects of the previous conflicts which increased the conflict level from Encounter to Non-Lethal between specific units, which means your dwarfs now respond to the nearness of the birds, instead of ignoring them. Usually this happens when your dogs are close to the creature and attack. Once that encounter level increases, your dwarfs will no longer ignore the creature and will immediately go into fight-or-flight mode. I am fairly sure that the encounter level remains between those specific units even if the creature leaves the map and returns, and that the encounter level is applied to all birds and all dwarfs that were within visual range of the combat.

One solution could be to get a squad of 4 or more dwarfs armed with two weapons, a melee weapon and a crossbow with metal bolts. Use 'm'ove orders to move near where the birds are so the dwarfs will start shooting, and if you really need to, built a shooting platform over your fort entrance so the dwarfs can shoot from a higher location.

[PatrikLundell]

You definitely don't need your animals on the surface to get bird interruption and vengeful thoughts.

Also, I don't think the animals that leave the embark can return, as they're not hist figs, and thus any new group of the same species entering would consist of newly created individuals. However, I haven't tested it with any rigor, but I'd try to use DFHack to name every critter entering the map and see if any of them return, but even if they do, it might be an effect of naming them... A more rigorous method would be to log the unit id of every critter that doesn't have a hist fig id and check if they return (invading non hist figs that kill a hist fig become histfigs and have been observed to return).

Once some dorf gets into conflict with a critter they have a tendency to drag everyone nearby into the conflict, which is why a group of keas can be devastating: even if they'd only result in a vengeful though once per dorf and animal (and I'm not sure it's limited to once), a group of 7 more or less immediately dumps 7 bad thoughts onto a large number of dorfs.

[Leonidas]

Increased population would fit the data as a source of the aggression. Another theory would be that the Giant tag makes a creature more prone to cause panic.

[Sarmatian123]

[...]the Giant tag makes a creature more prone to cause panic.

I think so too.
Usually the panic is caused back as well, so problem flies away.
In some cases, you need to send your xbow guards squad outside to station in some clearing or on a top of your surface bunker. Vultures are a pain.

For animals sneaking inside, you need to set an entrance up, as a 3 tiles (for wagons) wide entrance, with roof on top. Then you can station there inside a non-xbow normal squad. Chaining few dogs does help, but they do not stop Keas. Keas will easily pass by chained dogs. To fish up speedy Keas just add a solitary room on a side in this corridor for Trade Depot and end the corridor leading into your fortress with 3 rows of 3 cage traps. Except freaked up merchants sometimes (and if they do not leave, you need to deconstruct depot to force them to), this setup works like a beauty.