One reason I posted about how to run ADMIXTURE was so that the more readers themselves could become familiar with the biases of the program. That way they would get cautious about over-reading one particular set of results (the same goes for using PCA to visualize genetic relationships). Dienekes elaborates in detail on this point, A note of caution on admixture estimates:
Much more can be said on this issue, but let's summarize a couple of lessons: - The full extent of an admixture cline can be captured only if unadmixed populations on either side of the cline exist. Use as many populations as possible to capture the full extent of an admixture cline. - Use of an admixed population in lieu of an unadmixed native one inflates the inferred native component. Use native populations if possible instead of admixed ones . - Even in the absence of unadmixed native ...
