Geographic patterns of genome admixture in Latin American Mestizos

Abstract

The large and diverse population of Latin America is potentially a powerful resource for elucidating the genetic basis of complex traits through admixture mapping. However, no genome-wide characterization of admixture across Latin America has yet been attempted. Here, we report an analysis of admixture in thirteen Mestizo populations (i.e. in regions of mainly European and Native settlement) from seven countries in Latin America based on data for 678 autosomal and 29 X-chromosome microsatellites. We found extensive variation in Native American and European ancestry (and generally low levels of African ancestry) among populations and individuals, and evidence that admixture across Latin America has often involved predominantly European men and both Native and African women. An admixture analysis allowing for Native American population subdivision revealed a differentiation of the Native American ancestry amongst Mestizos. This observation is consistent with the genetic structure of pre-Columbian populations and with admixture having involved Natives from the area where the Mestizo examined are located. Our findings agree with available information on the demographic history of Latin America and have a number of implications for the design of association studies in population from the region.

Figure 1. Approximate Geographic Location of the Mestizo Populations Examined and of the Native American Populations Considered in the Analyses.

Mestizo populations are indicated as red triangles with names in bold italic font. The Native populations have been color coded based on their affiliation to one of the main Amerindian linguistic stocks according to the classification of Ruhlen. RGS = Rio Grande do Sul; CVCR = Central Valley of Costa Rica.

Figure 2. Ancestry Proportions in 13 Mestizo Populations.

For each population, proportions estimated with autosomal [-A] and X-chromosome [-X] markers are color-coded on separate bars. The populations have been ordered left to right based on decreasing autosomal European ancestry. The values of these ancestry estimates and their associated standard errors are shown in Table S2. Ancestry was estimated by grouping data for populations sampled in Europe, Africa and Native Americans into three continental population samples. Data for these populations was obtained from the HGDP-CEPH human genome diversity panel database (v 1.0) (http://www.cephb.fr/hgdp-cephdb/) and from Wang et al. (2007).

Figure 3. Heterozygosity vs. Proportion of European Ancestry in Mestizo Populations.

The heterozygosity predicted from the estimated ancestry of a population was calculated as described in Methods.

Figure 4. Distribution of Admixture Estimates for Individuals from Mexico City and Quetalmahue.

The position of each blue dot on the triangle plot indicates the proportion of European, Native American and African ancestry estimated for each individual in the population. The triangle plots for the other 11 Mestizo populations examined are shown in the Supporting Information (Figure S1).

Figure 5. Regional Native American Ancestry of 13 Mestizo Populations Considering the Major Native American Linguistic Stocks.

The relative partitioning of the Native American component is shown as the proportion of the colored bar (the European and African components are not shown). Ge-Pano-Carib is not included as it is represented here only by one population, the Kaingang.

Figure 6. Regional Native American Ancestry of 13 Mestizo Populations Considering each Individual Native Population.

The relative partitioning of the Native American component is shown as the proportion of the colored bar (the European and African components are not shown). These are coded in shades of a color corresponding to the main linguistic stocks shown in panel Figure 1 and Figure 5.

Figure 7. Correlation between Geographic Distance and Estimated Ancestry Components.

For each Mestizo population, the Pearson correlation coefficients were calculated between the logarithm of the geographic distance (Euclidean and effective, see methods) separating the Mestizo and Native populations, and the estimated ancestry components (from Figure 6). Correlation coefficients with associated P-values <0.05 are shown as filled symbols.