A Tale of Two Haplotypes: The EDA2R/AR Intergenic Region is the most Divergent Genomic Segment between Africans and East Asians in the Human Genome

Authors

Amanda M. Casto, Department of Genetics, Stanford University, Mail Stop 5120, Stanford, California, 94305, USAFollow
Brenna M. Henn, Department of Genetics, Stanford University, Mail Stop 5120, Stanford, California, 94305, USA
Jeffery M. Kidd, Department of Human Genetics, University of Michigan, 3726A Med Sci II, Ann Arbor, Michigan, 48109, USA
Carlos D. Bustamante, Department of Genetics, Stanford University, Mail Stop 5120, Stanford, California, 94305, USA
Marcus W. Feldman, Department of Biological Sciences, Stanford University, Gilbert Hall 108, Stanford, California, 94305, USA

Document Type

Open Access Preprint

Anticipated Volume

84

Anticipated Issue

6

Final Published Version

http://digitalcommons.wayne.edu/humbiol/vol84/iss6/2/

Abstract

Single nucleotide polymorphisms (SNPs) with large allele frequency differences between human populations are relatively rare. The longest run of SNPs with an allele frequency difference of one between the Yoruba of Nigeria and the Han Chinese is found on the long arm of the X chromosome in the intergenic region separating the EDA2R and AR genes. It has been proposed that the unusual allele frequency distributions of these SNPs are the result of a selective sweep affecting African populations that occurred after the Out-of-Africa migration. To investigate the evolutionary history of the EDA2R/AR intergenic region, we characterized the haplotype structure of 52 of its highly-differentiated SNPs. Using a publicly-available dataset of 3,000 X chromosomes from 65 human populations, we found that nearly all human X chromosomes carry one of two modal haplotypes for these 52 SNPs. The predominance of two highly divergent haplotypes at this locus was confirmed using a subset of individuals sequenced to high coverage. The first of these haplotypes, the α haplotype, is at high frequencies in most of the African populations surveyed and likely arose prior to the separation of African populations into distinct genetic entities. The second, the β haplotype, is frequent or fixed in all non-African populations and likely arose in East Africa prior to the Out-of-Africa migration. We also observed a small group of rare haplotypes with no clear relationship to the α and β haplotypes. These haplotypes occur at relatively high frequencies in African hunter-gatherer populations, like the San and Mbuti Pygmies. Our analysis indicates that these haplotypes are part of a pool of diverse, ancestral haplotypes that have now been almost entirely replaced by the α and β haplotypes. We suggest that the rise of the α and β haplotypes was the result of the demographic forces that human populations experienced during the formation of modern African populations and the Out-of-Africa migration. However, we also present evidence that this region is the target of selection in the form of positive selection on the α and β haplotypes and of purifying selection against α/β recombinants.

Recommended Citation

Open access pre-print, subsequently published as Casto, A. M., Henn, B. M., Kidd, J. M., Bustamante, C. D., and Feldman, M. W. (2012). "A Tale of Two Haplotypes: The EDA2R/AR Intergenic Region Is the Most Divergent Genomic Segment between Africans and East Asians in the Human Genome," Human Biology 84(6). http://digitalcommons.wayne.edu/humbiol/vol84/iss6/2