The most obvious evidence who the father was (SPOILERS)
It's Matt.
He goes on and on the entire show publicly lamenting his daughter, he loves his daughter, etc etc, he gets his own search parties together, but then when he finally finds her, he goes alone (no witnesses), he's not happy to see Tui, he doesn't help Tui, he just takes the baby - the baby that could send him to jail.
He then points his gun at the baby and screams what do you want from me? As in how could you possibly expect me to accept your existence? What do you expect me to do? I can't have you around. He's ready to execute the baby to protect himself.
A number of times he whips himself at the grave - he has enormous guilt over what he did. He feels he's being watched.
He keeps Tui's room pristine, ready for things go back to they were before the pregnancy. Hoping he can make things as they were.
He got the bikers to search for Tui so he could get her first before the police.
There's no evidence Matt had any idea about the pedophile ring Al was running out of the coffee shop. Al had the big boat and the house because Matt was paying him off for his silence on the drug business.
All this talk about DNA test switches may have indeed happened, but Matt's actions prove he was the father.
I do have a question about Jamie - why did he have a bottle of roofies?