I don't believe for a moment that most of my students have mastered the concept. I know from a test that was given (using questions from old regents exams) that they are struggling to pull all the ideas together. This is not exactly unexpected. Evolution and natural selection take a while to sort out, the idea of change occurring over generations is difficult to grasp. A few students have latched onto Lamarckian explanations, and can't seem to get past the idea that adaptation happens to individuals, that it is somehow a matter of individuals "getting used to" environmental conditions.
I don't know where the Lamarckian ideas come from, it must be somehow intuitive, because I purposely didn't teach Lamarck's theory for fear of suggesting an idea that some of them might find attractive. I have now addressed the issue since it did come up in their analyses, but it will take some more work to get students past the idea.
I plan to weave evolution and natural selection into other topics whenever possible. I did take advantage of the discovery of Homo floresiensis to discuss human evolution briefly, although I hadn't planned on addressing human evolution until after we have done the heredity/genetics component. That way when we discuss DNA evidence of the chimp/human relationship, it will be more compelling. A full unit on modern synthesis, history of life on earth, and human evolution are scheduled for early next year, after we complete heredity & cell bio.