Open Access Highly Accessed Open Badges Research

Ancestry-related assortative mating in Latino populations

Neil Risch123*, Shweta Choudhry4, Marc Via14, Analabha Basu1, Ronnie Sebro1, Celeste Eng4, Kenneth Beckman5, Shannon Thyne1, Rocio Chapela6, Jose R Rodriguez-Santana7, William Rodriguez-Cintron8, Pedro C Avila9, Elad Ziv14 and Esteban Gonzalez Burchard14

Author affiliations

1 Institute for Human Genetics, University of California, San Francisco, 513 Parnassus Ave, San Francisco, CA 94143, USA

2 Division of Research, Kaiser Permanente, 2000 Broadway, Oakland, CA 94612, USA

3 Department of Epidemiology and Biostatistics, University of California, San Francisco, 185 Berry Street, San Francisco, CA 94107, USA

4 Department of Medicine, University of California, San Francisco, 1550 4th St, San Francisco, CA 94143, USA

5 Biomedical Genomics Center, University of Minnesota, 426 Church St, Minneapolis, MN 55455, USA

6 Instituto Nacional de Enfermedades Respiratorias, Calzada de Tlalpan 4502, Col. Seccion XVI, CP 14080, Tlalpan, Distrito Federal, Mexico

7 Centro de Neumologia Pediatrica, CSP, 735 Ave Ponce de Leon, San Juan, 00917 Puerto Rico

8 Veterans Caribbean Health Care System, 10 Casia St, San Juan, 00921 Puerto Rico

9 Division of Allergy-Immunology, Feinberg School of Medicine, Northwestern University, 676 N St Clair St, Chicago, IL 60611, USA

For all author emails, please log on.

Citation and License

Genome Biology 2009, 10:R132  doi:10.1186/gb-2009-10-11-r132

Published: 20 November 2009



While spouse correlations have been documented for numerous traits, no prior studies have assessed assortative mating for genetic ancestry in admixed populations.


Using 104 ancestry informative markers, we examined spouse correlations in genetic ancestry for Mexican spouse pairs recruited from Mexico City and the San Francisco Bay Area, and Puerto Rican spouse pairs recruited from Puerto Rico and New York City. In the Mexican pairs, we found strong spouse correlations for European and Native American ancestry, but no correlation in African ancestry. In the Puerto Rican pairs, we found significant spouse correlations for African ancestry and European ancestry but not Native American ancestry. Correlations were not attributable to variation in socioeconomic status or geographic heterogeneity. Past evidence of spouse correlation was also seen in the strong evidence of linkage disequilibrium between unlinked markers, which was accounted for in regression analysis by ancestral allele frequency difference at the pair of markers (European versus Native American for Mexicans, European versus African for Puerto Ricans). We also observed an excess of homozygosity at individual markers within the spouses, but this provided weaker evidence, as expected, of spouse correlation. Ancestry variance is predicted to decline in each generation, but less so under assortative mating. We used the current observed variances of ancestry to infer even stronger patterns of spouse ancestry correlation in previous generations.


Assortative mating related to genetic ancestry persists in Latino populations to the current day, and has impacted on the genomic structure in these populations.