I respectfully disagree with the others. You can absolutely see changes that early. Here are some duck eggs at Day 3 taken about 12 hours apart.
What you described as "darkening of the yolk" could absolutely be an early sign of fertility. Without being there myself it's difficult to give a definitive answer on someone else's eggs.
I'll also add a picture of a Cream Legbar egg at 72 hours (day 3). You can see the embryo and changes to the yolk. This is my current hatch. Are you in the April hatch a long? If not you should join.