Table 5

Non-African haplotypes match Neandertal at an unexpected rate. We identified 13 candidate gene flow regions by using 48 CEU+ASN to represent the OOA population, and 23 African Americans to represent the AFR population. We identified tag SNPs for each region that separate an out-of-Africa specific clade (OOA) from a cosmopolitan clade (COS) and then assessed the rate at which Neandertal matches each of these clades by further subdividing tag SNPs based on their ancestral and derived status in Neandertal and whether they match the OOA-specific clade or not. Thus, the categories are AN (Ancestral Nonmatch), DN (Derived Nonmatch), DM (Derived Match), and AM (Ancestral Match). We do not list the sites where matching is ambiguous.

ChromosomeStart of candidate
region in Build 36
End of candidate
region in Build 36
Span (bp)ST
(estimated ratio of OOA/AFR gene tree depth)
Average frequency of tag in OOA cladeNeandertal (M)atches OOA-specific clade
AM DM
Neandertal does (N)ot match OOA-specific clade
AN DN
Qualitative assessment*
1168,110,000168,220,000110,0002.96.3%51010OOA
1223,760,000223,910,000150,0002.86.3%1400OOA
4171,180,000171,280,000100,0001.95.2%1200OOA
528,950,00029,070,000120,0003.83.1%161660OOA
666,160,00066,260,000100,0005.728.1%6600OOA
932,940,00033,040,000100,0002.84.2%71400OOA
104,820,0004,920,000100,0002.69.4%9500OOA
1038,000,00038,160,000160,0003.58.3%5920OOA
1069,630,00069,740,000110,0004.219.8%2201OOA
1545,250,00045,350,000100,0002.51.1%5610OOA
1735,500,00035,600,000100,0002.9(no tags)
2020,030,00020,140,000110,0005.164.6%00105COS
2230,690,00030,820,000130,0003.54.2%0252COS
Relative tag SNP frequencies in actual data34%46%15%5%
Relative tag SNP simulated under a demographic model without introgression34%5%33%27%
Relative tag SNP simulated under a demographic model with introgression23%31%37%9%

*To qualitatively assess the regions in terms of which clade the Neandertal matches, we asked whether the proportion matching the OOA-specific clade (AM and DM) is much more than 50%. If so, we classify it as an OOA region, and otherwise a COS region. One region is unclassified because no tag SNPs were found. We also compared to simulations with and without gene flow (SOM Text 17), which show that the rate of DM and DN tag SNPs where Neandertal is derived are most informative for distinguishing gene flow from no gene flow.