Probability of Donatello being from a different clutch of eggs.

[Refractive Reflections]

Originally Posted by victory_angel

Donnie is the only one with dark colored eyes while his brothers all have light colored eyes. He also has Diastema (the Gap in his teeth).

Spoiler:

His face has more of an oval shape to it while his brothers have a slightly rounded and more squashed look to them.

There are other possible explanations for these these traits such as:

• All of the above mentioned could be a recessive trait.
  
• The gap in Donnie's teeth may actually be the result of Raphael or someone knocking one of Donnie's teeth out when they were kids.
  
• Or it may be some genetic traits from whoever pulled him out of the tank at the pet store.

The reason I suggest this probability is because it is something that could happen quite easily. As everyone knows Turtles hatch from eggs, and when they hatch they are put together in an aquarium tank until sold.

For humans it's not easy to tell one turtle from another so there could be one clutch or several different clutches in the same tank. For animals however they can tell who is family who isn't through sense of smell, patterning, or some cases vocal tones.

As I stated before just because one could be from another clutch doesn't make them any less brothers. However in someway it feels (to me at least) the other Turtles unconsciously don't recognize Donnie as one of them.

Yeah there are the teasing and poking fun like siblings do. But there are other times where Leo, Raph, and Mikey go off into their own world and Donnie is left standing on the sidelines as though he doesn't exist.

...That's... so much more detail than I think any of the writers, animators, or creators even considered probably.
...And here I thought Don's gap teeth, egg head, and scrawny body were used to fit the visual, physique stereotype of a nerd. As for him "standing on the sidelines", he's the only one interested in science. I don't think his teen brothers could grasp the complexity of the scientific concepts he thinks of. Naturally there's going to be some distance between two levels of highly contrasting intellect.