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Genetic structure characterization of Chileans reflects historical immigration patterns.

Eyheramendy S, Martinez FI, Manevy F, Vial C, Repetto GM - Nat Commun (2015)

Bottom Line: Sex-chromosome analyses confirm imbalanced contribution of European men and Native-American women.Previously known genes under selection contain SNPs showing large difference in allele frequencies.Two observations, that African ancestry proportions systematically decrease from North to South, and that European ancestry proportions are highest in central regions, show that the genetic structure of Chileans is under the influence of a diffusion process leading to an ancestry gradient related to geography.

View Article: PubMed Central - PubMed

Affiliation: Department of Statistics, Facultad de Matemáticas, Pontificia Universidad Católica de Chile, Av. Vicuña Mackenna 4860, Macul, Santiago 6904411, Chile.

ABSTRACT
Identifying the ancestral components of genomes of admixed individuals helps uncovering the genetic basis of diseases and understanding the demographic history of populations. We estimate local ancestry on 313 Chileans and assess the contribution from three continental populations. The distribution of ancestry block-length suggests an average admixing time around 10 generations ago. Sex-chromosome analyses confirm imbalanced contribution of European men and Native-American women. Previously known genes under selection contain SNPs showing large difference in allele frequencies. Furthermore, we show that assessing ancestry is harder at SNPs with higher recombination rates and easier at SNPs with large difference in allele frequencies at the ancestral populations. Two observations, that African ancestry proportions systematically decrease from North to South, and that European ancestry proportions are highest in central regions, show that the genetic structure of Chileans is under the influence of a diffusion process leading to an ancestry gradient related to geography.

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Spatial ancestry analysis.(a) All populations, (b) Chilean and African populations, (c) Chilean and European populations and (d) Chilean and Native-American populations. Chileans appear in black with its global African, European and Native-American ancestry proportions in (b), (c) and (d), respectively, as estimated by local ancestry methods.
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f1: Spatial ancestry analysis.(a) All populations, (b) Chilean and African populations, (c) Chilean and European populations and (d) Chilean and Native-American populations. Chileans appear in black with its global African, European and Native-American ancestry proportions in (b), (c) and (d), respectively, as estimated by local ancestry methods.

Mentions: We perform an analysis of spatial ancestry28, results are shown in Fig. 1. Figure 1a shows that the spatial analysis clearly separates the three ancestral population and, as expected, the admixed Chileans are scattered between the European and the Native-Americans. We restrict our spatial analysis to the Chileans with each of its ancestral populations. Figure 1b shows the Chilean-admixed population clearly separated from the African populations. Within Africans, the Yoruba in Ibadan, Nigeria (YRI) and the Luhya in Webuye, Kenya (LWK) are close together, but the African Ancestry from Southwest United States (ASW) is spread along a line and is the closest to the Chileans. Figure 1c shows that the Europeans are separated into two groups, Britain (GBR) and North Europe (CEU) together and Spaniards and Italians together, closer to the Chileans. Figure 1d shows the Chileans together with the Native-Americans. Figure 1b–d shows the Chileans with their global proportion of African, European and Native-American ancestry, respectively, estimated by the LAI method. We observe consistency between the ancestral proportion estimates given by the LAI methods and the spatial ancestry analysis as individuals with higher/lower proportion in ancestry are closer/farther to the ancestral populations.


Genetic structure characterization of Chileans reflects historical immigration patterns.

Eyheramendy S, Martinez FI, Manevy F, Vial C, Repetto GM - Nat Commun (2015)

Spatial ancestry analysis.(a) All populations, (b) Chilean and African populations, (c) Chilean and European populations and (d) Chilean and Native-American populations. Chileans appear in black with its global African, European and Native-American ancestry proportions in (b), (c) and (d), respectively, as estimated by local ancestry methods.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4382693&req=5

f1: Spatial ancestry analysis.(a) All populations, (b) Chilean and African populations, (c) Chilean and European populations and (d) Chilean and Native-American populations. Chileans appear in black with its global African, European and Native-American ancestry proportions in (b), (c) and (d), respectively, as estimated by local ancestry methods.
Mentions: We perform an analysis of spatial ancestry28, results are shown in Fig. 1. Figure 1a shows that the spatial analysis clearly separates the three ancestral population and, as expected, the admixed Chileans are scattered between the European and the Native-Americans. We restrict our spatial analysis to the Chileans with each of its ancestral populations. Figure 1b shows the Chilean-admixed population clearly separated from the African populations. Within Africans, the Yoruba in Ibadan, Nigeria (YRI) and the Luhya in Webuye, Kenya (LWK) are close together, but the African Ancestry from Southwest United States (ASW) is spread along a line and is the closest to the Chileans. Figure 1c shows that the Europeans are separated into two groups, Britain (GBR) and North Europe (CEU) together and Spaniards and Italians together, closer to the Chileans. Figure 1d shows the Chileans together with the Native-Americans. Figure 1b–d shows the Chileans with their global proportion of African, European and Native-American ancestry, respectively, estimated by the LAI method. We observe consistency between the ancestral proportion estimates given by the LAI methods and the spatial ancestry analysis as individuals with higher/lower proportion in ancestry are closer/farther to the ancestral populations.

Bottom Line: Sex-chromosome analyses confirm imbalanced contribution of European men and Native-American women.Previously known genes under selection contain SNPs showing large difference in allele frequencies.Two observations, that African ancestry proportions systematically decrease from North to South, and that European ancestry proportions are highest in central regions, show that the genetic structure of Chileans is under the influence of a diffusion process leading to an ancestry gradient related to geography.

View Article: PubMed Central - PubMed

Affiliation: Department of Statistics, Facultad de Matemáticas, Pontificia Universidad Católica de Chile, Av. Vicuña Mackenna 4860, Macul, Santiago 6904411, Chile.

ABSTRACT
Identifying the ancestral components of genomes of admixed individuals helps uncovering the genetic basis of diseases and understanding the demographic history of populations. We estimate local ancestry on 313 Chileans and assess the contribution from three continental populations. The distribution of ancestry block-length suggests an average admixing time around 10 generations ago. Sex-chromosome analyses confirm imbalanced contribution of European men and Native-American women. Previously known genes under selection contain SNPs showing large difference in allele frequencies. Furthermore, we show that assessing ancestry is harder at SNPs with higher recombination rates and easier at SNPs with large difference in allele frequencies at the ancestral populations. Two observations, that African ancestry proportions systematically decrease from North to South, and that European ancestry proportions are highest in central regions, show that the genetic structure of Chileans is under the influence of a diffusion process leading to an ancestry gradient related to geography.

Show MeSH