This track shows per-continent integrated haplotype score (iHS,
Voight et al.), a measure of very recent positive selection.
Scores were calculated using SNPs genotyped in 53 populations worldwide by the
Genome Diversity Project in collaboration with the
du Polymorphisme Humain (HGDP-CEPH).
This track and several others are available from the
HGDP Selection Browser.
Samples collected by the HGDP-CEPH from 1,043 individuals from around the
world were genotyped for 657,000 SNPs at
The 53 populations were divided into seven continental groups: Africa
(Bantu populations only),
Middle East, Europe, South Asia, East Asia, Oceania and the Americas.
Bantu populations in Africa were chosen instead of all African populations
because a more closely related group was desired for comparison with
other continental groups.
iHS was then calculated for each population group using the program ihs
(source code available) and then normalizing the
resulting unstandardized iHS scores in derived allele frequency bins
as described in (Voight et al.).
Per-SNP iHS scores were smoothed in windows of 31 SNPs, centered on
each SNP. The final score is -log10 of the proportion of
smoothed scores higher than each SNP's smoothed score.
Thanks to the HGDP-CEPH and Joe Pickrell in the
lab at the University of Chicago for providing these data.
Voight BF, Kudaravalli S, Wen X, Pritchard JK.
A map of recent positive selection in the human genome.
PLoS Biol. 2006 Mar;4(3):e72.
Pickrell JK, Coop G, Novembre J, Kudaravalli S, Li J, Absher D,
Srinivasan BS, Barsh GS, Myers RM, Feldman MW, Pritchard JK.
Signals of recent positive selection in a worldwide sample of
human populations. Genome Res. 2009 May;19(5):826-37.
Li JZ, Absher DM, Tang H, Southwick AM, Casto AM, Ramachandran S,
Cann HM, Barsh GS, Feldman M, Cavalli-Sforza LL, Myers RM.
Worldwide human relationships inferred from genome-wide
patterns of variation. Science. 2008 Feb 22;319(5866):1100-4.
Cann HM, de Toma C, Cazes L, Legrand MF, Morel V, Piouffre L, Bodmer
J, Bodmer WF, Bonne-Tamir B, Cambon-Thomsen A et al.
A human genome diversity cell line panel.
Science. 2002 Apr 12;296(5566):261-2.