Skip to main page content
Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
, 6 (1), e16513

History Shaped the Geographic Distribution of Genomic Admixture on the Island of Puerto Rico


History Shaped the Geographic Distribution of Genomic Admixture on the Island of Puerto Rico

Marc Via et al. PLoS One.


Contemporary genetic variation among Latin Americans human groups reflects population migrations shaped by complex historical, social and economic factors. Consequently, admixture patterns may vary by geographic regions ranging from countries to neighborhoods. We examined the geographic variation of admixture across the island of Puerto Rico and the degree to which it could be explained by historic and social events. We analyzed a census-based sample of 642 Puerto Rican individuals that were genotyped for 93 ancestry informative markers (AIMs) to estimate African, European and Native American ancestry. Socioeconomic status (SES) data and geographic location were obtained for each individual. There was significant geographic variation of ancestry across the island. In particular, African ancestry demonstrated a decreasing East to West gradient that was partially explained by historical factors linked to the colonial sugar plantation system. SES also demonstrated a parallel decreasing cline from East to West. However, at a local level, SES and African ancestry were negatively correlated. European ancestry was strongly negatively correlated with African ancestry and therefore showed patterns complementary to African ancestry. By contrast, Native American ancestry showed little variation across the island and across individuals and appears to have played little social role historically. The observed geographic distributions of SES and genetic variation relate to historical social events and mating patterns, and have substantial implications for the design of studies in the recently admixed Puerto Rican population. More generally, our results demonstrate the importance of incorporating social and geographic data with genetics when studying contemporary admixed populations.

Conflict of interest statement

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


Figure 1
Figure 1. Distribution of individuals and their ancestry estimates.
(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. (D) Interpolation plots showing the geographical distribution of ancestry.
Figure 2
Figure 2. Goodness of fit of the regression model of historic variables on African ancestry.
Local R2 values were calculated using a geographically weighted regression (GWR) model and interpolation plots showed geographical variation in the accuracy of the regression model.
Figure 3
Figure 3. Distribution of socioeconomic status (SES) across regions.
(A) Boxplots comparing African ancestry between regions by SES category. (B) Mean elevation (in meters) by geographical region and SES category.

Similar articles

See all similar articles

Cited by 47 PubMed Central articles

See all "Cited by" articles


    1. Menozzi P, Piazza A, Cavalli-Sforza L. Synthetic maps of human gene frequencies in Europeans. Science. 1978;201:786–792. - PubMed
    1. Piazza A, Menozzi P, Cavalli-Sforza LL. Synthetic gene frequency maps of man and selective effects of climate. Proc Natl Acad Sci U S A. 1981;78:2638–2642. - PMC - PubMed
    1. King R, Underhill PA. Congruent distribution of Neolithic painted pottery and ceramic figurines with Y-chromosome lineages. Antiquity. 2002;76:707–714.
    1. Henn BM, Gignoux CR, Feldman MW, Mountain JL. Characterizing the time dependency of human mitochondrial DNA mutation rate estimates. Mol Biol Evol. 2009;26:217–230. - PubMed
    1. Cavalli-Sforza LL, Menozzi P, Piazza A. xi, 541, 518. Princeton, N.J.: Princeton University Press; 1994. The history and geography of human genes.

Publication types