Jonas has lighter eyes than others in his community.
Almost everyone in the community looks alike. Although we are not sure exactly how, it is clear that there is some kind of genetic modification going on.
Almost every citizen in the community had dark eyes. His parents did, and Lily did, and so did all of his group members and friends. But there were a few exceptions: Jonas himself, and a female Five who he had noticed had the different, lighter eyes. (Ch. 3)
Jonas notices that Gabriel, the baby that his father brings home because he doesn’t sleep well at night, has light eyes like him, and feels disturbed because he sees the "depth" in them that others see in his eyes.
The assumption is that the baby and Jonas have the same birthmother. This means that although there is genetic manipulation in the community, clearly, there are still people related to other people, and there are still birthmothers. Everyone is not created in a test tube.
By theory at least, Jonas is related to Gabriel and Katharine (the “female Five”), and this is why they all have the special gift that makes them able to receive the memories. Their birthmother must have had it too. It also makes them related to The Giver, and Rosemary.
The man was wrinkled, and his eyes, though piercing in their unusual lightness, seemed tired. The flesh around them was darkened into shadowed circles. (Ch. 10)
What does it mean that everyone who has the Capacity to See Beyond is related? For one thing, it seems like it would be pretty easy to predict who has the gift and who does not. The elders would be watching everyone from that genetic background early on. Also, in addition to seeing, or hearing, beyond, they have wisdom and intelligence beyond the other members of their community and an increased sense of justice, especially once they understand what is really happening in the community.
There is evidence that everyone in the community looks alike other than in the fact that Jonas is self-conscious about his eyes. The Giver mentions Fiona’s hair specifically.
"We've never completely mastered Sameness. I suppose the genetic scientists are still hard at work trying to work the kinks out. Hair like Fiona's must drive them crazy." (Ch. 12)
Everyone in the community has the same hair color, and everyone wears the same “neatly trimmed” haircut (Ch. 2). Sameness is very detailed in the community, and it is not just about everyone dressing alike and having the same manners. People are supposed to look alike too.
Jonas is different in another way. After adolescents have their first sexual dream, called a Stirring, they are forced to take pills for the Stirrings. These will prevent the feelings and possibly some elements of puberty. However, after Jonas begins his training, he stops taking the pills. He does not want his feelings controlled.
In just about every way, Jonas is different from his community. He is physically unique, but his personality is unique too. He says his eyes give him a look of having depth, but he does have depth. Jonas is someone who is not willing to take things as they are and accept them. He fights for change.