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The genomic distribution of population substructure in four populations using 8,525 autosomal SNPs.

ABSTRACT: Understanding the nature of evolutionary relationships among persons and populations is important for the efficient application of genome science to biomedical research. We have analysed 8,525 autosomal single nucleotide polymorphisms (SNPs) in 84 individuals from four populations: African-American, European-American, Chinese and Japanese. Individual relationships were reconstructed using the allele sharing distance and the neighbour-joining tree making method. Trees show clear clustering according to population, with the root branching from the African-American clade. The African-American cluster is much less star-like than European-American and East Asian clusters, primarily because of admixture. Furthermore, on the East Asian branch, all ten Chinese individuals cluster together and all ten Japanese individuals cluster together. Using positional information, we demonstrate strong correlations between inter-marker distance and both locus-specific FST (the proportion of total variation due to differentiation) levels and branch lengths. Chromosomal maps of the distribution of locus-specific branch lengths were constructed by combining these data with other published SNP markers (total of 33,704 SNPs). These maps clearly illustrate a non-uniform distribution of human genetic substructure, an instructional and useful paradigm for education and research.

SUBMITTER: Shriver MD

PROVIDER: S-EPMC3525267 | biostudies-literature | 2004 May

REPOSITORIES: biostudies-literature

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The genomic distribution of population substructure in four populations using 8,525 autosomal SNPs.

Shriver Mark D MD Kennedy Giulia C GC Parra Esteban J EJ Lawson Heather A HA Sonpar Vibhor V Huang Jing J Akey Joshua M JM Jones Keith W KW

Human genomics 20040501 4

Understanding the nature of evolutionary relationships among persons and populations is important for the efficient application of genome science to biomedical research. We have analysed 8,525 autosomal single nucleotide polymorphisms (SNPs) in 84 individuals from four populations: African-American, European-American, Chinese and Japanese. Individual relationships were reconstructed using the allele sharing distance and the neighbour-joining tree making method. Trees show clear clustering accord ...[more]

PMID: 15588487

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Dataset Information

The genomic distribution of population substructure in four populations using 8,525 autosomal SNPs.

Publications

The genomic distribution of population substructure in four populations using 8,525 autosomal SNPs.

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