An analysis of X-linked genetic variation in human populations provides insights into population structure and demographic patterns

Absher, Devin

Casto, Amanda M

Feldman, Marcus W

Li, Jun Z

Myers, Richard

Ramachandran, Sohini

English

PubMed

Amanda M Casto

Jun Z Li

Devin Absher

Richard Myers

Sohini Ramachandran

Marcus W Feldman

Springer - Publisher Connector

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

Crossref

Abstract
              
                Background
                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.
              
              
                Results
                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.
              
              
                Conclusions
                The relationship between male and female demographic histories is likely to be complex as evidence supporting different conclusions can be found in the same dataset. Although demography may have contributed to the excess of SNPs with large allele frequency differences observed on the X chromosome, we believe that selection is at least partially responsible. Finally, our results reveal the geographical complexities of selective sweeps on the X chromosome and argue for the use of diverse populations in studies of selection.http://deepblue.lib.umich.edu/bitstream/2027.42/112705/1/13059_2009_Article_2303.pd

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7-kilobase deletion, and evidence of balancing selection in the human protocadherin alpha cluster.

A fast and flexible statistical model for large-scale genotype data: applications to inferring missing genotypes and haplotypic phase.

Accelerated genetic drift on chromosome X during the human dispersal out of Africa. Nat Genet

Arlequin ver 3.0: An integrated software package for population genetics data analysis. Evol Bioinform Online

CA: Doublecortin is a microtubule-associated protein and is expressed widely by migrating neurons. Neuron

Calpain 6 is involved in microtubule stabilization and cytoskeletal organization. Mol Cell Biol

Crow TJ: Inactivation status of PCDH11X: sexual dimorphisms in gene experession levels in brain. Hum Genet

Distruct: A program for the graphical display of population structure. Mol Ecol Notes

Dixit VM: Two-amino acid molecular switch in an epithelial morphogen that regulates binding to two distinct receptors. Science

DJ: TRPC channel activation by extracellular thioredoxin. Nature

EH: ARHGEF9 distruption in a female patient is associated with X linked mental retardation and sensory hyperarousal.

Estimation of individual admixture: analytical and study design considerations. Genet Epidemiol

Extensive linkage disequilibrium, a common

Feldman MW: Genetic structure of human populations. Science

Feldman MW: Robustness of the inference of human population structure: A comparison of X-chromosomal and autosomal microsatellites. Hum Genomics

Genetic risk factors in male infertility. Arch Androl

Genomic scans for selective sweeps using SNP data. Genome Res

GJ: Hephaestin, a ceruloplasmin homologue implicated in intestinal iron transport, is defective in the sla mouse. Nat Genet

H: A comparative expression analysis of four MRX genes regulation intracellular signaling via small GTPases.

Haussler D: The human genome browser at UCSC. Genome Res

I: PAK3 related mental disability: further characterization of the phenotype.

JD: Sex-biased evolutionary forces shape genomic patterns of human diversity.

JK: A map of recent positive selection in the human genome. PLoS Biol

JK: Signals of recent positive selection in a worldwide sample of human populations. Genome Res

JK: The Role of Geography in Human Adaptation.

Jongeneel CV: Rapid evolution of cancer/testis genes on the X chromosome.

MW: Searching for evidence of positive selection in the human genome using patterns of microsatellite variability. Mol Biol Evol

Neve RL: DNA synthesis and neuronal apoptosis caused by familial Alzheimer disease mutants of the amyloid precursor protein are mediated by the p21 activated kinase PAK3.

NH: The relative rates of evolution of sex chromosomes and autosomes. Am Nat

NL: Extranigral neurodegeneration in Parkinson's disease.

Nothen MM: Genetic variation in the human androgen receptor gene is the major determinant of common early-onset androgenetic alopecia.

PC: PLINK: a toolset for wholegenome association and population-based linkage analysis.

Pirastu M: EDA2R is associated with androgenic alopecia.

Population size changes reshape genomic patterns of diversity. Evolution

Quintana-Murci L: Natural selection has driven population differentiation in modern humans. Nat Genet

Ramachandran S: Evaluating signatures of sex-specific processes in the human genome. Nat Genet

RE: EthnicAffiliation Estimation by Use of Population-Specific DNA Markers.

S: Positive selection in East Asians for an EDAR allele that enhances NFKB activation. PLoS One

Sirotkin : dbSNP: the NCBI database of genetic variation. Nucleic Acids Res

Stefansson K: A highresolution recombination map of the human genome. Nat Genet

Sugano S: Identification of a Novel Protocadherin Gene (PCDH11) on the Human XY Homology Region in Xq21.3. Genomics

The International HapMap Consortium: Genome-wide detection and characterization of positive selection in human populations. Nature

The population genetics of haplo-diploids and X-linked genes. Genetical Res

The UCSC Human Genome Browser [http://genome.ucsc.edu/]

The X chromosome in population genetics.

Venkatasubramanian G: Evidence for positive selection on protocadherin Y gene in Homo sapiens: implications for schizophrenia. Schizophr Res

Vitalis R: SexSpecific Genetic Structure and Social Organization in Central Asia: Insights from a Multi-Locus Study. PLOS Genet

Worldwide human relationships inferred from genome-wide patterns of variation. Science

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

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