English: Distribution of individuals and their ancestry estimates in Puerto Rico. (A) Distribution of samples across the island. Symbols are proportional to the number of samples included for each census block. Location of sugar mills and ports is also included. (B) Ancestry estimates for each individual are shown as a thin vertical line partitioned into different colored components representing inferred membership in the ancestral groups. (C) Comparisons of African ancestry between municipalities, grouped by region.

We applied the Bayesian clustering algorithm STRUCTUR using an ancestral reference set of Native Americans, Africans and Europeans to estimate admixture proportions in our census-based the Puerto Rican sample (Figure A). Average ancestry values for the Puerto Rican population were 15.2% (±7.2), 21.2% (±14.4), and 63.7% (±15.2) for the Native American, African, and European contributions, respectively (Table 1). As previously shown for other Latin American populations, extensive variation among individuals was observed (Figure B) especially in the European and African components. Overall, these ancestral components showed greater variances than the Native American component.