Description

This track shows single nucleotide polymorphisms (SNPs) used in a genome-wide scan for signals of positive selection in the human lineage since divergence from the Neandertal lineage.

SNP labels represent the ancestral (A) or derived (D) status, determined by comparison with the chimpanzee reference genome, of alleles in the human reference assembly, five modern human genomes of diverse ancestry (see the Modern Human Seq track), and Neandertals. The first six characters of an item name show the status of the allele (A, D or _ if not known) in six genomes: human reference, San, Yoruba, Han, Papuan, and French, in that order. These characters are followed by a colon, the number of derived alleles found in Neandertals, a comma and the number of ancestral alleles found in Neandertals. For example, a SNP labeled AAADAA:0D,2A has the ancestral allele in the reference human genome and in all of the modern human genomes except Han. Among Neandertals, two instances of the ancestral allele were found, but no instances of the derived allele.

SNPs are colored red when at least four of the six modern human genomes are derived while all observed Neandertal alleles are ancestral. An overrepresentation of such SNPs in a region would imply that the region had undergone positive selection in the modern human lineage since divergence from Neandertals; the Sel Swp Scan (S) track displays a signal calculated from these SNPs, and the 5% Lowest S track contains the regions in which the signal most strongly indicates selective pressure on the modern human lineage.

Display Conventions and Configuration

Red SNPs are those where at least four of the six modern human genomes are derived while all observed Neandertal alleles are ancestral. All other SNPs are black.

Methods

For the purposes of this analysis, SNPs were defined as single-base sites that are polymorphic among 5 modern human genomes of diverse ancestry (see the Modern Human Seq track) plus the human reference genome. SNPs at CpG sites were excluded because of the higher mutation rate at CpG sites. Ancestral or derived state was determined by comparison with the chimpanzee genome.

Credits

This track was produced at UCSC using data generated by Ed Green.

Reference

Green RE, Krause J, Briggs AW, Maricic T, Stenzel U, Kircher M, Patterson N, Li H, Zhai W, Fritz MH et al. A draft sequence of the Neandertal genome. Science. 2010 May 7;328(5979):710-22. PMID: 20448178