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Genetic analysis of ancestry, admixture and selection in Bolivian and Totonac populations of the New World

W Scott Watkins1, Jinchuan Xing2, Chad Huff1, David J Witherspoon1, Yuhua Zhang1, Ugo A Perego34, Scott R Woodward3 and Lynn B Jorde1*

Author affiliations

1 Department of Human Genetics, Eccles Institute of Human Genetics, University of Utah, 15 N 2030 E Rm 2100, Salt Lake City, UT, 84112, USA

2 Department of Genetics and the Human Genetics Institute of New Jersey, Rutgers, The State University of New Jersey, 145 Bevier Rd, Piscataway, NJ, 08854, USA

3 Dipartimento di Genetica e Microbiologia, Università di Pavia, Via Ferrata 1, 27100, Pavia, Italy

4 Sorenson Molecular Genealogy Foundation, 2480 South Main Street, Suite 200, Salt Lake City, UT, 84115, USA

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Citation and License

BMC Genetics 2012, 13:39  doi:10.1186/1471-2156-13-39

Published: 20 May 2012



Populations of the Americas were founded by early migrants from Asia, and some have experienced recent genetic admixture. To better characterize the native and non-native ancestry components in populations from the Americas, we analyzed 815,377 autosomal SNPs, mitochondrial hypervariable segments I and II, and 36 Y-chromosome STRs from 24 Mesoamerican Totonacs and 23 South American Bolivians.

Results and Conclusions

We analyzed common genomic regions from native Bolivian and Totonac populations to identify 324 highly predictive Native American ancestry informative markers (AIMs). As few as 40–50 of these AIMs perform nearly as well as large panels of random genome-wide SNPs for predicting and estimating Native American ancestry and admixture levels. These AIMs have greater New World vs. Old World specificity than previous AIMs sets. We identify highly-divergent New World SNPs that coincide with high-frequency haplotypes found at similar frequencies in all populations examined, including the HGDP Pima, Maya, Colombian, Karitiana, and Surui American populations. Some of these regions are potential candidates for positive selection. European admixture in the Bolivian sample is approximately 12%, though individual estimates range from 0–48%. We estimate that the admixture occurred ~360–384 years ago. Little evidence of European or African admixture was found in Totonac individuals. Bolivians with pre-Columbian mtDNA and Y-chromosome haplogroups had 5–30% autosomal European ancestry, demonstrating the limitations of Y-chromosome and mtDNA haplogroups and the need for autosomal ancestry informative markers for assessing ancestry in admixed populations.

Admixture; Ancestry Informative Markers (AIMs); Native Americans; Bolivian; Totonac; Positive selection