An interesting question.
First off, I'm not so sure conscience is solely human. Those who have dogs or cats for pets, know that they can sometimes look really guilty when they've done something they know they weren't supposed to (something they've been yelled at for doing before).
In humans, I'm not so sure conscience is the locked, metaphysical phenomenon some people seem to think it is. Even religious (maybe especially religious) people agree that our conscience is something that needs to be trained if it is to be effective. In other words, to have an "efficient" conscience, we need to learn what things are OK and what things are not. This to me indicates that 'conscience' is not some special part of our brain, or our 'soul', but is simply something learned through experience, and will work differently from human to human dependent on the ethical/moral values we have fed our brain.
Conscience is however not a process of using logic and thinking in order to reach a conclusion, but is more like a quick reflex, almost literally a gut feeling happening in an instant. But I think it is still learned, in that we have these notions stored in the back of our brains, and when we come to a situation that goes against what we've been taught, it triggers a response dependent on that.
As for how conscience evolved in the first place, I first of all don't think it necessarily did at all, but may simply be an automatic cause of intelligence and memory (we weigh a new situation up against what we've experienced before, or have been taught before, but do it subconsciously so that it seems like a reflex).
-If it is indeed a trait that evolved, it could be said that in a society, it may be an advantage because you'd be better liked if you showed others that you have a conscience and are a better person toward others because of it. OK - that's a little weak for an explanation; let's go a little further back:
What we now know as 'conscience' may have started out as a different emotion, which directly would be beneficial for survival. Kinda like how we learn that if we've been burnt once, we make sure not to make the same mistake again; at least try a little different approach. That notion may have evolved into a more ethically driven emotion; "I stole from Ugh, but now I remember how angry and sad I got when Ugh stole from me - I must have made him feel the same now as he made me feel then. I now wish I hadn't stolen from Ugh." - - or - - "My mother told me that lying was wrong because it may mislead other people to do things they otherwise wouldn't do - - and now I lied anyway, and said there were lots of prey just over that mountain, just so I could keep them away from the flock of prey I recently discovered close to here. Now they may die on that mountain without finding any prey, and I regret having lied because of it, and having done something my mother warned me against."
This notion, this emotion when applied to a small society, may have made them close knit compared to another small society that had no such notions, and so the society with a 'conscience' may have had an advantage because of it. They may have stood more united than the other society/tribe when faced with trouble.
Something along those lines.
Small children learn very fast. If they do something that results in an angry outburst from a parent, it will instill fear in them, and they will understand that doing what they were about to do or did, is 'bad'. Still - curiosity or desire to have/do something may be strong enough that they do it again later - and if they are then caught, they know they are doing something their parents do not approve of, and their conscience - or perhaps fear of retribution at this point - make them feel remorse.
Think of all the things you would have a bad conscience about doing while you were a JW, but you would now do with no bad feelings. 'Conscience' is not a 'thing' as such in my opinion, but a 'pliable' emotion driven by past experiences and what we are taught.
