A best case scenario for unsupervised ADMIXTURE?

One of the great things about ADMIXTURE is that the population elements shake out of the data through the logic of the program. The worst thing is that it is then left up to you to make sense of the elements. A useful way to use ADMIXTURE and avoid excessive interpretive fogginess is to figure out individual proportions of contribution from X ancestral groups when you have a pretty good idea that an admixture event did occur between very distinct and distantly related population groups. To some extent the whole New World is a good laboratory for this process. Consider, for example, someone from the Dominican Republic or Puerto Rico. There is a good chance that their ancestry will fractionate into three elements: - An African one - An Amerindian one - A European one These three elements are sampled from very different locations geographically. The ancestral populations have been ...