I encourage you to have "conversations" with your daughter when you are both relaxed and enjoying each other's company. Deliberately and seriously ask:
You can probably come up with more and better topics than I have suggested for your talks. Above all, don't lecture. The idea is to get her to think about what you ask even if she doesn't respond. Plant the seeds of questioning. Continue to point out all her positive qualities and those of her nonpopular friends.
This is a very difficult developmental period for girls as they struggle to understand who they are and where they fit in the social structure. Because your attitude is so positive, my guess is that your daughter will reach an understanding similar to yours after struggling with this issue for a while. It's not easy for moms, but I gather you have the patience to stand beside her while she learns.