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

Mark D Shriver,Jing Huang,Vibhor Sonpar,Joshua M Akey,Keith W Jones,Esteban J Parra,Giulia C Kennedy,Heather A Lawson

doi:10.1186/1479-7364-1-4-274

Mark D Shriver, Jing Huang + Show 6 more

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https://doi.org/10.1186/1479-7364-1-4-274

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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.

Highlights

The completion of the primary human genome sequence was announced in 2003 and millions of single nucleotide polymorphisms (SNPs) are already available in public databases [eg The SNP Consortium (TSC), dbSNP, HGVbase]
We are on the brink of an unprecedented understanding of human variation and the evolution of our species
The average level of FST for autosomal SNPs, 0.132, is very similar to FST values previously described for major continental groups,[9] confirming the well-known fact that most variability in human populations is observed within populations and that a minor fraction of genetic variation (5 – 15 per cent) is due to differences between major continental groups

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Introduction

The completion of the primary human genome sequence was announced in 2003 and millions of single nucleotide polymorphisms (SNPs) are already available in public databases [eg The SNP Consortium (TSC), dbSNP, HGVbase]. Paralleling these advances in our knowledge of the human genome have been remarkable breakthroughs in genotyping technologies, providing .1,000-fold increases in genotyping capacity. We are on the brink of an unprecedented understanding of human variation and the evolution of our species. A detailed understanding of the extent, pattern and meaning of human variation is fundamental to the effective application of genomics to studies of human biology. Patterns of structure within and between human populations can be important in terms of epidemiological risks and the evaluation of drug response.[3]

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