Bone structure changes over time in the same way any other part of an organism does–by responding to selective pressures. A lot of these differences are brought about by changes in behavior that lead species to start to follow different evolutionary pathways. These pathways are often characterized by different ways of living off the environment, and that selects for different traits, while relaxing selection on others. They also may move into different environments, which can cause certain traits to be favored over others. Over time, the groups will stop mating with one another, which closes off new genes from entering their gene pool, and causes others to become more or less prevalent.
Just these seemingly tiny changes in behavior and environment can add up to big changes in bone structure–just look at chimpanzees and humans!