title: Sequence variations in the public human genome data reflect a bottlenecked population history.
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.
authors.affiliation: National Center for Biotechnology Information, National Institutes of Health, Bethesda, MD 20894, USA. marth@ncbi.nlm.nih.gov
authors.forename: Gabor
authors.initials: G
authors.lastname: Marth
authors.forename: Greg
authors.initials: G
authors.lastname: Schuler
authors.forename: Raymond
authors.initials: R
authors.lastname: Yeh
authors.forename: Ruth
authors.initials: R
authors.lastname: Davenport
authors.forename: Richa
authors.initials: R
authors.lastname: Agarwala
authors.forename: Deanna
authors.initials: D
authors.lastname: Church
authors.forename: Sarah
authors.initials: S
authors.lastname: Wheelan
authors.forename: Jonathan
authors.initials: J
authors.lastname: Baker
authors.forename: Ming
authors.initials: M
authors.lastname: Ward
authors.forename: Michael
authors.initials: M
authors.lastname: Kholodov
authors.forename: Lon
authors.initials: L
authors.lastname: Phan
authors.forename: Eva
authors.initials: E
authors.lastname: Czabarka
authors.forename: Janos
authors.initials: J
authors.lastname: Murvai
authors.forename: David
authors.initials: D
authors.lastname: Cutler
authors.forename: Stephen
authors.initials: S
authors.lastname: Wooding
authors.forename: Alan
authors.initials: A
authors.lastname: Rogers
authors.forename: Aravinda
authors.initials: A
authors.lastname: Chakravarti
authors.forename: Henry C
authors.initials: HC
authors.lastname: Harpending
authors.forename: Pui-Yan
authors.initials: PY
authors.lastname: Kwok
authors.forename: Stephen T
authors.initials: ST
authors.lastname: Sherry
mesh_terms: D030561:Databases, Nucleic Acid; D005787:Gene Frequency; D005819:Genetic Markers; D014644:Genetic Variation; D005828:Genetics, Population; D015894:Genome, Human; D006801:Humans; D008957:Models, Genetic; D011995:Recombination, Genetic; D015203:Reproducibility of Results; D017422:Sequence Analysis, DNA; D013997:Time Factors
chemical_list: D005819:Genetic Markers