I was just watching a Richard Dawkins lecture at Randolph-Macon Women's College on YouTube. He was asked a question about the basis of atheistic morality. Dawkins proposed that our moral sense comes from the fact that our pre-historic ancestors lived mostly with next-of-kins hence 1) altruism will benefit the preservation of similar genes 2) there's a high probability of being in long-term contact with these individuals who can then reciprocate the good will.
I would propose that altruism serves to improve upon another evolutionary survival objective, the preservation of the species. When pre-historic human beings lived in tribes, there was a high risk of destruction from other animals, diseases, and natural elements. Hence at some point, competition to extinguish a rival member of the same species is out-weighed by the risk that the size of the species might fall below a critical threshold and threaten extinction. For example, you don't want to kill Adam for stealing your girlfriend because he and you can work together when the tigers attack tomorrow night.
If we think about tribes and animal social organizations as entire units, then that unit would be evolving to maximize its survival as a whole. If a society randomly generated a moral sense that does not include any altruism in an "attempt" to maximize individual benefits, that group as a whole (and consequently the individual) might have a lower probability of survival because the survival benefits that are derived from the group would be lost (i.e. strength in numbers). In another words, when the survival of the individual is linked to a certain critical mass and critical health of his immediate social organization unit, this species would likely evolve some moral sense due to the pressure of natural selection even though this moral sense, on the surface, appears to be anti-beneficial to the individual upon a first-order examination.