I read this book 2-3 years ago. It involved two identical ships that each carried half of all the surviving humans. They were heading to another planet that was supposed to be colonized as the new Earth. One ship was supposed to be way ahead of the other as it had been sent out first, but slowed down to meet up with the other ship.
The two main characters were a girl and a boy who were in their late teens and the oldest kids on the ship; I think they were the first two to be born on board. I can't remember their names, but they were a couple and were expected to marry in the future. The boy was one of the few religious people on that ship while the girl was atheist. The ship that these two were on was mostly atheists and the other ship was mostly religious.
The religious ship slowed down so that they could board the other ship and kidnapped all of the females. The younger girls were separated from the adults. The people on the religious ship couldn't reproduce because the atheist ship had sabotaged them with a fake formula for some hormone that was supposed to increase fertility in the women, but did the opposite. The oldest of the kidnapped girls had a bunch of their ovum surgically removed without their consent and the "harvested" ovum was used to impregnate the women of the ship.
Meanwhile the atheist ship was really damaged from the attack and all of the adults died after fixing something that had to do with radiation, leaving behind the young boys. The main character boy was originally in charge, but was overthrown by the second oldest boy who I think was named Seth. I remember "Seth" had really blue eyes.
One thing I specifically remember is that the person in charge of the religious ship was the pastor who was named Anne Mather.
I remember a few other details, but I'm afraid this might get too long. I have tried a lot of different searches on google, but I don't remember the right details like main character names or anything about the author. It's been bothering me that I can remember all these details but can't find the book itself.