Characterization of X-linked SNP genotypic variation in globally distributed human populations.

Genome Biology
Amanda M CastoM W Feldman

Abstract

The transmission pattern of the human X chromosome reduces its population size relative to the autosomes, subjects it to disproportionate influence by female demography, and leaves X-linked mutations exposed to selection in males. As a result, the analysis of X-linked genomic variation can provide insights into the influence of demography and selection on the human genome. Here we characterize the genomic variation represented by 16,297 X-linked SNPs genotyped in the CEPH human genome diversity project samples. We found that X chromosomes tend to be more differentiated between human populations than autosomes, with several notable exceptions. Comparisons between genetically distant populations also showed an excess of X-linked SNPs with large allele frequency differences. Combining information about these SNPs with results from tests designed to detect selective sweeps, we identified two regions that were clear outliers from the rest of the X chromosome for haplotype structure and allele frequency distribution. We were also able to more precisely define the geographical extent of some previously described X-linked selective sweeps. The relationship between male and female demographic histories is likely to be complex as evidenc...Continue Reading

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Methods Mentioned

BETA
chip
genotyping

Software Mentioned

plink
Arlequin
AMOVA
Distruct
fastPHASE
Frappe

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