Unravelling the hidden ancestry of American admixed populations

Abstract

The movement of people into the Americas has brought different populations into contact, and contemporary American genomes are the product of a range of complex admixture events. Here we apply a haplotype-based ancestry identification approach to a large set of genome-wide SNP data from a variety of American, European and African populations to determine the contributions of different ancestral populations to the Americas. Our results provide a fine-scale characterization of the source populations, identify a series of novel, previously unreported contributions from Africa and Europe and highlight geohistorical structure in the ancestry of American admixed populations.

Figure 1. Approximate geographic sampling location of donor and recipient populations analysed.

Colours refer to the 13 groups as described in Fig. 2 and Supplementary Table 2. Circles and diamond refer, respectively, to donors and recipients.

Figure 2. fineSTRUCTURE clustering of the analysed individuals.

Tree of the analysed individuals pooled in 78 clusters as inferred by fineSTRUCTURE. Colours follow macro-area affiliations as in Fig. 1.

Figure 3. Contribution of the most by informative 23 clusters inferred by fineSTRUCTURE to the analysed recipient populations.

Contribution of the most informative 23 clusters to the American and Caribbean populations estimated using the non-negative least square approach. Standard error based on jack-knife resampling (22 replicates) is reported.

Figure 4. Hierarchical consensus trees of the continental components for American and Caribbean populations.

Consensus tree using Hierarchical clustering for (a) European component; (b) African component. Bar plots at the tips of the trees indicate the relative ancestry composition of the analysed population; colours refer to the 13 groups in Fig. 1. Only branches supported by more than 80% of the 1,000 trees built by bootstrap described in Methods are retained.