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Series GSE29851 Query DataSets for GSE29851
Status Public on Jun 09, 2011
Title Genetic analysis of ancestry, admixture, and selection in Bolivian and Totonac populations of the New World
Organism Homo sapiens
Experiment type SNP genotyping by SNP array
Summary The genetic structure of some native Bolivians has been substantially influenced by admixture from Europeans, which we estimate to have occurred approximately 360 – 384 years ago. Consistent with historical accounts of male admixture, Y-chromosome haplogroups typical of Europeans were found in 39% of our Bolivian samples. No evidence of African admixture was found in native Bolivians. The Mesoamerican Totonacs have little evidence of European or African admixture. Our analysis indicates that some admixed Bolivians have Native American mtDNA and Y-chromosomes but harbor up to 30% European autosomal ancestry, demonstrating the need for autosomal markers to assess ancestry in admixed populations.
From a dense genome-wide panel of 815,377 markers, we developed a set of 324 AIMs, specific for Native American ancestry. As few a 40-50 of these markers successfully predict New World ancestry in the ascertainment panel of Bolivians and Totonacs. The markers easily distinguish New World from Old World ancestry, even for populations more closely related to the Americas such as central and eastern Asians, and were effective for New World vs. Old World comparisons in five other geographically and culturally distinct populations of the Americas. SNPs demonstrating very high divergence between the two Native American populations and major Old World populations are found on haplotypes that are shared and occur at similar frequencies in other indigenous low-admixture American populations examined here (i.e. Pima, Maya, Colombian, Karitiana, and Surui). After excluding the possibility of recent relatedness, our results indicate that native Bolivians and Totonacs share ancestry with other American populations through a substantial contribution from a common founding population, population bottlenecks, and possible natural selection on functional variation.
 
Overall design Population structure, admixture, and selection were assessed with a genome-wide panel of 815,377 autosomal markers, Y-chromosome STR and SNPs, and mtDNA sequence data.
 
Contributor(s) Watkins S, Xing J, Huff C, Witherspoon D, Zhang Y, Perego UA, Woodward SR, Jorde LB
Citation(s) 22606979
Submission date Jun 08, 2011
Last update date Nov 27, 2018
Contact name Scott Watkins
E-mail(s) scott.watkins@genetics.utah.edu
Phone 801-585-3385
Fax 801-585-9148
Organization name University of Utah
Department Human Genetics
Street address 15 N 2030 E Rm2100
City Salt Lake City
State/province UT
ZIP/Postal code 84112
Country USA
 
Platforms (1)
GPL6801 [GenomeWideSNP_6] Affymetrix Genome-Wide Human SNP 6.0 Array
Samples (47)
GSM739510 South American Bolivian male F065038
GSM739511 South American Bolivian male F065040
GSM739512 South American Bolivian male F065042
Relations
BioProject PRJNA140899

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE29851_RAW.tar 1.3 Gb (http)(custom) TAR (of CEL)
GSE29851_Ychromosome_and_mtDNA_data.xls.gz 11.9 Kb (ftp)(http) XLS
GSE29851_data_matrix.csv.gz 14.6 Mb (ftp)(http) CSV
Raw data provided as supplementary file
Processed data included within Sample table
Processed data are available on Series record

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