TY - JOUR
T1 - Ethiopian genetic diversity reveals linguistic stratification and complex influences on the Ethiopian gene pool
AU - Pagani, Luca
AU - Kivisild, Toomas
AU - Tarekegn, Ayele
AU - Ekong, Rosemary
AU - Plaster, Chris
AU - Gallego Romero, Irene
AU - Ayub, Qasim
AU - Mehdi, S. Qasim
AU - Thomas, Mark G.
AU - Luiselli, Donata
AU - Bekele, Endashaw
AU - Bradman, Neil
AU - Balding, David J.
AU - Tyler-Smith, Chris
N1 - Funding Information:
The authors would like to acknowledge all the Ethiopian donors and collaborators, as well as Sarah Edkins, Emma Gray, Sarah Hunt, Avazeh Tashakkori Ghanbarian, and the staff at the Sanger Institute who performed the genotyping. Great help has also been provided by Priya Moorjani, David Reich, and Nick Patterson for a better understanding of the mathematics underlying the ROLLOFF approach. This work was supported by grant number 098051 from the Wellcome Trust. L.P. would like to thank the providers of a Domestic Research Scholarship, the Cambridge European Trust, and Emmanuel College, Cambridge, UK for sponsoring his research. N.B. is the settlor and senior trustee of Melford Charitable Trust and owner of Cordell Homes Ltd., which have in part funded this research. Neither N.B., the charitable trust, nor the company have any intellectual property or other rights with respect to the results of the study.
PY - 2012/7/13
Y1 - 2012/7/13
N2 - Humans and their ancestors have traversed the Ethiopian landscape for millions of years, and present-day Ethiopians show great cultural, linguistic, and historical diversity, which makes them essential for understanding African variability and human origins. We genotyped 235 individuals from ten Ethiopian and two neighboring (South Sudanese and Somali) populations on an Illumina Omni 1M chip. Genotypes were compared with published data from several African and non-African populations. Principal-component and STRUCTURE-like analyses confirmed substantial genetic diversity both within and between populations, and revealed a match between genetic data and linguistic affiliation. Using comparisons with African and non-African reference samples in 40-SNP genomic windows, we identified "African" and "non-African" haplotypic components for each Ethiopian individual. The non-African component, which includes the SLC24A5 allele associated with light skin pigmentation in Europeans, may represent gene flow into Africa, which we estimate to have occurred ∼3 thousand years ago (kya). The non-African component was found to be more similar to populations inhabiting the Levant rather than the Arabian Peninsula, but the principal route for the expansion out of Africa ∼60 kya remains unresolved. Linkage-disequilibrium decay with genomic distance was less rapid in both the whole genome and the African component than in southern African samples, suggesting a less ancient history for Ethiopian populations.
AB - Humans and their ancestors have traversed the Ethiopian landscape for millions of years, and present-day Ethiopians show great cultural, linguistic, and historical diversity, which makes them essential for understanding African variability and human origins. We genotyped 235 individuals from ten Ethiopian and two neighboring (South Sudanese and Somali) populations on an Illumina Omni 1M chip. Genotypes were compared with published data from several African and non-African populations. Principal-component and STRUCTURE-like analyses confirmed substantial genetic diversity both within and between populations, and revealed a match between genetic data and linguistic affiliation. Using comparisons with African and non-African reference samples in 40-SNP genomic windows, we identified "African" and "non-African" haplotypic components for each Ethiopian individual. The non-African component, which includes the SLC24A5 allele associated with light skin pigmentation in Europeans, may represent gene flow into Africa, which we estimate to have occurred ∼3 thousand years ago (kya). The non-African component was found to be more similar to populations inhabiting the Levant rather than the Arabian Peninsula, but the principal route for the expansion out of Africa ∼60 kya remains unresolved. Linkage-disequilibrium decay with genomic distance was less rapid in both the whole genome and the African component than in southern African samples, suggesting a less ancient history for Ethiopian populations.
UR - http://www.scopus.com/inward/record.url?scp=84863986908&partnerID=8YFLogxK
U2 - 10.1016/j.ajhg.2012.05.015
DO - 10.1016/j.ajhg.2012.05.015
M3 - Article
C2 - 22726845
AN - SCOPUS:84863986908
SN - 0002-9297
VL - 91
SP - 83
EP - 96
JO - American Journal of Human Genetics
JF - American Journal of Human Genetics
IS - 1
ER -