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Chibchan (e.g., Colombian), and Andean (e.g., Quechua) populations. The closest relationship is clearly observed between Mexicans from Guadalajara and Nahua indigenous individuals.

Sex Bias in Ancestry Contributions

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

FIGURE 8.5 Boxplots comparing autosomal vs. X-chromosome ancestry proportions by population, shown for European ancestry (Left), Native American ancestry (Center), and African ancestry (Right). Filled boxes correspond to autosomal ancestry estimates; open boxes show X-chromosome ancestry estimates. Median (solid line), first and third quartiles (box) and the minimum/maximum values, or to the smallest value within 1.5 times the IQR from the first quartile (whiskers). For each paired comparison of X chromosomes and autosomes, median Native American ancestries are consistently higher on the X chromosome in all Hispanic/Latino populations sampled, and European ancestries are lower across all populations.

FIGURE 8.5 Boxplots comparing autosomal vs. X-chromosome ancestry proportions by population, shown for European ancestry (Left), Native American ancestry (Center), and African ancestry (Right). Filled boxes correspond to autosomal ancestry estimates; open boxes show X-chromosome ancestry estimates. Median (solid line), first and third quartiles (box) and the minimum/maximum values, or to the smallest value within 1.5 times the IQR from the first quartile (whiskers). For each paired comparison of X chromosomes and autosomes, median Native American ancestries are consistently higher on the X chromosome in all Hispanic/Latino populations sampled, and European ancestries are lower across all populations.



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