Penumbra Overture dogs?

[Xanatos]

All the infected humanoids looked the same too.

I think the Archaic were conducting experiments on live animals and had the dogs brought in from the outside (note the containers that looked like cages in later parts of the mine in Overture) which might explain the mutations. Then, after the Tuurngait got released, things inevitably went chaotic and the dogs escaped, finding their own ways into the mine.