Sequence variations in the public human genome data reflect a bottlenecked population history

Gabor Marth, Greg Schuler, Raymond Yeh, Ruth Davenport, Richa Agarwala, Deanna Church, Sarah Wheelan, Jonathan Baker, Ming Ward, Michael Kholodov, Lon Phan, Eva Czabarka, Janos Murvai, David Cutler, Stephen Wooding, Alan Rogers, Aravinda Chakravarti, Henry C. Harpending, Pui Yan Kwok, Stephen T. Sherry

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Abstract

Single-nucleotide polymorphisms (SNPs) constitute the great majority of variations in the human genome, and as heritable variable landmarks they are useful markers for disease mapping and resolving population structure. Redundant coverage in overlaps of large-insert genomic clones, sequenced as part of the Human Genome Project, comprises a quarter of the genome, and it is representative in terms of base compositional and functional sequence features. We mined these regions to produce 500,000 high-confidence SNP candidates as a uniform resource for describing nucleotide diversity and its regional variation within the genome. Distributions of marker density observed at different overlap length scales under a model of recombination and population size change show that the history of the population represented by the public genome sequence is one of collapse followed by a recent phase of mild size recovery. The inferred times of collapse and recovery are Upper Paleolithic, in agreement with archaeological evidence of the initial modern human colonization of Europe.

Original languageEnglish (US)
Pages (from-to)376-381
Number of pages6
JournalProceedings of the National Academy of Sciences of the United States of America
Volume100
Issue number1
DOIs
StatePublished - Jan 7 2003

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Marth, G., Schuler, G., Yeh, R., Davenport, R., Agarwala, R., Church, D., Wheelan, S., Baker, J., Ward, M., Kholodov, M., Phan, L., Czabarka, E., Murvai, J., Cutler, D., Wooding, S., Rogers, A., Chakravarti, A., Harpending, H. C., Kwok, P. Y., & Sherry, S. T. (2003). Sequence variations in the public human genome data reflect a bottlenecked population history. Proceedings of the National Academy of Sciences of the United States of America, 100(1), 376-381. https://doi.org/10.1073/pnas.222673099