Description

This track shows 13 regions of the human genome in which there is considerably more haplotype diversity among non-African genomes than within African genomes. A prediction of Neandertal-to-modern human gene flow is that these deeply divergent haplotypes which exist only in non-African populations entered the human gene pool from Neandertals. Of the 12 candidate gene flow regions with tag SNP data, there are 10 regions in which Neandertals match the deep haplotype clade unique to non-Africans (out of Africa, OOA) instead of the cosmopolitan haplotype clade shared by Africans and non-Africans (cosmopolitan, COS).

The table below was copied from Table 5, "Non-African haplotypes match Neandertal at an unexpected rate", from Green et al.:

Region	Genomic Size	ST	Average Frequency in OOA	AM	DM	AN	DN	Qualitative Assessment
chr1:168,110,001-168,220,000	110,000	2.9	6.3%	5	10	1	0	OOA
chr1:223,760,001-223,910,000	150,000	2.8	6.3%	1	4	0	0	OOA
chr4:171,180,001-171,280,000	100,000	1.9	5.2%	1	2	0	0	OOA
chr5:28,950,001-29,070,000	120,000	3.8	3.1%	16	16	6	0	OOA
chr6:66,160,001-66,260,000	100,000	5.7	28.1%	6	6	0	0	OOA
chr9:32,940,001-33,040,000	100,000	2.8	4.2%	7	14	0	0	OOA
chr10:4,820,001-4,920,000	100,000	2.6	9.4%	9	5	0	0	OOA
chr10:38,000,001-38,160,000	160,000	3.5	8.3%	5	9	2	0	OOA
chr10:69,630,001-69,740,000	110,000	4.2	19.8%	2	2	0	1	OOA
chr15:45,250,001-45,350,000	100,000	2.5	1.1%	5	6	1	0	OOA
chr17:35,500,001-35,600,000	100,000	2.9	(no tags)	n/a	n/a	n/a	n/a	n/a
chr20:20,030,001-20,140,000	110,000	5.1	64.6%	0	0	10	5	COS
chr22:30,690,001-30,820,000	130,000	3.5	4.2%	0	2	5	2	COS

S_T = estimated ratio of OOA/African gene tree depth.
Average Frequency in OOA = average (across tag SNPs in the region) of the population frequency in the 48 OOA individuals of the OOA-only allele for each tag SNP.
AM = Neandertal has ancestral allele and matches OOA-specific clade.
DM = Neandertal has derived allele and matches OOA-specific clade.
AN = Neandertal has ancestral allele and does not match OOA-specific clade.
DN = Neandertal has derived allele and does not match OOA-specific clade.

Display Conventions and Configuration

A region is colored green if its qualitative assessment is OOA, blue if COS, and gray if unknown (no tag SNPs in region).

Methods

Green et al. used 1,263,750 Perlegen Class A SNPs, identified in 71 individuals of diverse ancestry (see Hinds et al.), to identify 13 candidate gene flow regions (Supplemental Online Materials Text 17). 24 individuals of European ancestry and 24 individuals of Han Chinese ancestry were used to represent the non-African population, and the remaining 23 individuals, of African American ancestry, were used to represent the African population.

From the 1,263,750 Perlegen Class A SNPs, they identified 166 tag SNPs that separate (see below) 12 of the haplotype clades in non-Africans (OOA) from the cosmopolitan haplotype clades shared between Africans and non-Africans (COS) and for which they had data from the Neandertals. Of the 13 regions, one had no tag SNPs so could not be assessed, two were COS, and 10 were OOA (see final column Table 1).

Overall, the Neandertals match the deep clade unique to non-Africans (OOA) at 133 of the 166 tag SNPs. They assessed the rate at which Neandertal matches each of these clades by further subdividing the 133 tag SNPs based on their ancestral or derived status in Neandertal and whether they matched the OOA-specific clade or not. Candidate regions were qualitatively assessed to be OOA matches for Neandertal when the proportion of tag SNPs matching the OOA-specific clade is much more than 50%.

Credits

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

References

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

Hinds DA, Stuve LL, Nilsen GB, Halperin E, Eskin E, Ballinger DG, Frazer KA, Cox DR. Whole-genome patterns of common DNA variation in three human populations. Science. 2005 Feb 18;307(5712):1072-9. PMID: 15718463