The study you point to seem to have flaws like comparing a very narrow set of group, driving to conclusions about colour tones etc. They try to punch hole in David Reich paper by saying the size per group was not significant, but this is flawed as the number of group was diversely large i.e 30 compared to 2 in this study. They do not try to point flaws in previous works as well. Read this article for the original set of studies that led to the discrediting of AIT http://www.newslaundry.com/2014/08/11/indiana-jones-and-the-...
