Chibchan (e.g., Colombian), and Andean (e.g., Quechua) populations. The closest relationship is clearly observed between Mexicans from Guadalajara and Nahua indigenous individuals.
We used the STRUCTURE ancestry estimates on the autosomes and X chromosome to estimate Native American, European, and African ancestry proportions of each Hispanic/Latino individual. We then compared the estimates of ancestry for each population on the autosomes vs. on the X chromosome [Fig. 8.5 and Figs. S3 and S4 (available online at www.pnas.org/cgi/content/full/0914618107/DCSupplemental)]. Whereas the Native American ancestry was significantly higher on the X chromosome than on the autosomes (including those populations with reduced Native American ancestry, i.e., Puerto Ricans and Dominicans), the autosomal vs. X-chromosome difference was more attenuated with regard to African ancestry. This reduced deviation is present even in those Hispanic/Latino populations analyzed whose non-European ancestry was principally