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Native American admixture in the Quebec founder population - PubMed

  • ️Tue Jan 01 2013

Native American admixture in the Quebec founder population

Claudia Moreau et al. PLoS One. 2013.

Abstract

For years, studies of founder populations and genetic isolates represented the mainstream of genetic mapping in the effort to target genetic defects causing Mendelian disorders. The genetic homogeneity of such populations as well as relatively homogeneous environmental exposures were also seen as primary advantages in studies of genetic susceptibility loci that underlie complex diseases. European colonization of the St-Lawrence Valley by a small number of settlers, mainly from France, resulted in a founder effect reflected by the appearance of a number of population-specific disease-causing mutations in Quebec. The purported genetic homogeneity of this population was recently challenged by genealogical and genetic analyses. We studied one of the contributing factors to genetic heterogeneity, early Native American admixture that was never investigated in this population before. Consistent admixture estimates, in the order of one per cent, were obtained from genome-wide autosomal data using the ADMIXTURE and HAPMIX software, as well as with the fastIBD software evaluating the degree of the identity-by-descent between Quebec individuals and Native American populations. These genomic results correlated well with the genealogical estimates. Correlations are imperfect most likely because of incomplete records of Native founders' origin in genealogical data. Although the overall degree of admixture is modest, it contributed to the enrichment of the population diversity and to its demographic stratification. Because admixture greatly varies among regions of Quebec and among individuals, it could have significantly affected the homogeneity of the population, which is of importance in mapping studies, especially when rare genetic susceptibility variants are in play.

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Conflict of interest statement

Competing Interests: The authors have declared that no competing interests exist.

Figures

Figure 1
Figure 1. Map of Quebec subpopulations.

In colors are the 10 regions/subpopulations included in the analyses.

Figure 2
Figure 2. Barplots of ancestry proportions.

The global ancestry was estimated using the model-based approach implemented in the ADMIXTURE software : in Awith K = 2 to distinguish between Native American (green) and European (red) ancestry and in B with K = 3 in the presence of Siberian populations (cyan).

Figure 3
Figure 3. Scatter plots of correlations.

Scatter plots showing the correlations between different Native American genetic ancestry estimates in the Quebec subpopulations (upper) and between genetic ancestry estimates and genealogical genetic contribution of Native American founders to the Quebec individuals (lower). The Pearson correlation coefficient (r) is shown on each plot.

Figure 4
Figure 4. Plots of LD decay.

LD decay of admixed fragments was assessed using the ALDER software to test for admixture in the Quebec (A) and European (B) sample using the Native North Americans as the reference population.

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This research was supported by Réseau de Médecine Génétique Appliquée of Fonds de Recherche en Santé du Québec (FRSQ) (HV and DL) and by FRSQ grant (MHRG). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.

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