Sequence variations in the public human genome data reflect a bottlenecked population history.
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.
Marth
Gabor
G
National Center for Biotechnology Information, National Institutes of Health, Bethesda, MD 20894, USA. marth@ncbi.nlm.nih.gov
Schuler
Greg
G
Yeh
Raymond
R
Davenport
Ruth
R
Agarwala
Richa
R
Church
Deanna
D
Wheelan
Sarah
S
Baker
Jonathan
J
Ward
Ming
M
Kholodov
Michael
M
Phan
Lon
L
Czabarka
Eva
E
Murvai
Janos
J
Cutler
David
D
Wooding
Stephen
S
Rogers
Alan
A
Chakravarti
Aravinda
A
Harpending
Henry C
HC
Kwok
Pui-Yan
PY
Sherry
Stephen T
ST
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
D005819:Genetic Markers