Fig. 3: Demographic histories affect patterns of genetic variation in Mexico.

a, Small ROH prevalence is correlated with ancestry proxies inferred from ADMIXTURE reflecting an ancient bottleneck or relatively small population size in the past (n = 5,833 individuals). b, Sum of ROH per individual as a function of birth year (n = 5,833 individuals). Solid lines show ROH overall, and dashed lines indicate ROH overlapping ancestries from the Americas (AMR). ROH are divided into small, medium and large ROH, as in a. Smoothed conditional mean lines are shown using the locally estimated scatterplot smoothing method. Error bands represent 95% confidence intervals. c, Mutation burden in different ancestries shows the effects of bottleneck events in causing loss of rare variants (n = 5,818 individuals). Rare variants are correlated with levels of ancestries from the Americas, Western Europe or West Africa for rare variants (derived allele frequency ≤ 5%). Smoothed conditional mean lines are shown using a linear model. Error bands represent 95% confidence intervals. Spearman correlation values are shown (R and two-sided P values) for all ancestries. Analysis of whole-genome sequences from 1000 Genomes MXL samples shows that the rare mutation burden result is robust to ascertainment bias of Illumina’s Multi-Ethnic Global Array (Supplementary Figs. 39 and 40). Variants were annotated using the Variant Effect Predictor tool, and nonsynonymous (deleterious) variants are a combined set of missense variants predicted to be damaging by polyphen2 along with splice, stop lost and stop gained variants.