The whales Gracie and George were stated to have wandered into San Francisco as calves. Outside of feeding events which can include the famous bubble nets, humpback whale pods usually consist of a lone mother and calf (or calves) pairing with a trailing "escort" male. Humpbacks are one of the few mammals that can be nursing and still get pregnant. So anyway, the implication seems to be that if they were both calves and coming in the same time as a pod, they must have been orphaned from their mother and part of the same family group. Therefore, when its later revealed that Gracie is pregnant this one question comes to mind:
"Was the pregnancy a product of incest?"
No wonder they were originally going to be called Adam and Evie.
In beta canon it’s explained that, eventually, the humpback whale population of the 23rd Century is restored with the help of George and Gracie’s offspring together with cloned humpbacks from DNA stores, which establishes enough numbers for a breeding population.
(And to answer the inevitable follow-up question of "if they had whale DNA why did they have to go back in time?":
Cloning whales wouldn’t have helped because quite apart from not being able to grow clones in time, those whales would have no knowledge of whale songs - as Spock noted, they couldn’t just reproduce the sounds; they needed the meaning as well.
So the fact they didn’t clone whales doesn’t necessarily mean they didn’t have the genetic material. It just wasn’t a viable solution. One assumes George and Gracie would teach the newly cloned humpbacks about whalesong.)