(A) Geographic distribution of African (green), (B) European (blue), (C) Amerindian (orange) ancestry based on individual estimates.

<p>To facilitate comparison, color intensity transitions occur at 10% ancestry intervals for all maps. Maps were obtained using Kriging interpolation (see <a href="http://www.plosntds.org/article/info:doi/10.1371/journal.pntd.0004045#sec002" target="_blank">Materials and Methods</a>).</p

Comparison of medians of ancestral components according to the geographical origin of the population, Andean vs. Atlantic regions (Mann-Whitney U-test).

<p>Comparison of medians of ancestral components according to the geographical origin of the population, Andean vs. Atlantic regions (Mann-Whitney U-test).</p

Dirichlet distributions of the ancestral components of the study population.

<p>The European component had a normal distribution and consisted of 40–60% of the study population. The African component had a non-normal distribution and consisted of less than 30% of the study population. The Native American (Amerindian) component had a non-normal distribution and consisted of 20% of the study population.</p

Additional file 1: Table S1. of Examining for an association between candidate gene polymorphisms in the metabolic syndrome components on excess weight and adiposity measures in youth: a cross-sectional study

Sequence of primer used to PCR. Table S2. Ancestral informative Markers (AIMs), allelic frequencies and delta (δ) of frequencies in the three ancestral populations (European, African and Amerindian). Table S3. Characteristics of the study population, stratified according to gender. Table S4. Association with anthropometric measures at 10 selected genetic variants on the subset of the samples with available ancestry information. Table S5. Interaction between SNP and socioeconomic and perinatal factors in determining body mass index. Figure S1. The histogram of body mass index, body fat percentage and waist circumference by gender. (DOCX 123 kb

Distribution of (A) Native American ancestry and (B) socioeconomic status (bands 1 to 6) in Antioquian T2D cases and controls.

<p>Distribution of (A) Native American ancestry and (B) socioeconomic status (bands 1 to 6) in Antioquian T2D cases and controls.</p

Box plots of (A) Native American ancestry and (B) BMI for socioeconomic status bands 1 to 6 in the Antioquian study sample.

<p>Box plots of (A) Native American ancestry and (B) BMI for socioeconomic status bands 1 to 6 in the Antioquian study sample.</p

Distribution of LOD-scores for disease association along the genome in the Antioquian T2D admixture mapping scan.

<p>Distribution of LOD-scores for disease association along the genome in the Antioquian T2D admixture mapping scan.</p

Illustration of the negative ascertainment scheme, with simulation.

<p>(a) A basic three population model, showing the joint site-frequency spectrum for populations 1 and 2 as a heat map. (b) Conditioning on variants not being observed in the out-population results in a SFS skewed towards rare variants. (c) A quantitatively similar effect can be obtained by introducing a drastic bottleneck at the root of the tree and considering only two populations.</p

Parameter estimates for the model displayed on Figure 6, assuming a bottleneck at the foundation of the Americas 16,000 years ago.

<p>Parameter estimates for the model displayed on <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1004023#pgen-1004023-g006" target="_blank">Figure 6</a>, assuming a bottleneck at the foundation of the Americas 16,000 years ago.</p

Subtypes of Native American ancestry and leading causes of death: Mapuche ancestry-specific associations with gallbladder cancer risk in Chile

<div><p>Latin Americans are highly heterogeneous regarding the type of Native American ancestry. Consideration of specific associations with common diseases may lead to substantial advances in unraveling of disease etiology and disease prevention.</p><p>Here we investigate possible associations between the type of Native American ancestry and leading causes of death. After an aggregate-data study based on genome-wide genotype data from 1805 admixed Chileans and 639,789 deaths, we validate an identified association with gallbladder cancer relying on individual data from 64 gallbladder cancer patients, with and without a family history, and 170 healthy controls. Native American proportions were markedly underestimated when the two main types of Native American ancestry in Chile, originated from the Mapuche and Aymara indigenous peoples, were combined together. Consideration of the type of Native American ancestry was crucial to identify disease associations. Native American ancestry showed no association with gallbladder cancer mortality (P = 0.26). By contrast, each 1% increase in the Mapuche proportion represented a 3.7% increased mortality risk by gallbladder cancer (95%CI 3.1–4.3%, P = 6×10⁻²⁷). Individual-data results and extensive sensitivity analyses confirmed the association between Mapuche ancestry and gallbladder cancer. Increasing Mapuche proportions were also associated with an increased mortality due to asthma and, interestingly, with a decreased mortality by diabetes. The mortality due to skin, bladder, larynx, bronchus and lung cancers increased with increasing Aymara proportions. Described methods should be considered in future studies on human population genetics and human health. Complementary individual-based studies are needed to apportion the genetic and non-genetic components of associations identified relying on aggregate-data.</p></div