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.
| Chromo- some |
Start 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 clade |
Neandertal (M)atches OOA-specific clade AM DM |
Neandertal does (N)ot match OOA-specific clade AN DN |
Qualitative assessment* |
||
|---|---|---|---|---|---|---|---|---|---|---|
| 1 | 168,110,000 | 168,220,000 | 110,000 | 2.9 | 6.3% | 5 | 10 | 1 | 0 | OOA |
| 1 | 223,760,000 | 223,910,000 | 150,000 | 2.8 | 6.3% | 1 | 4 | 0 | 0 | OOA |
| 4 | 171,180,000 | 171,280,000 | 100,000 | 1.9 | 5.2% | 1 | 2 | 0 | 0 | OOA |
| 5 | 28,950,000 | 29,070,000 | 120,000 | 3.8 | 3.1% | 16 | 16 | 6 | 0 | OOA |
| 6 | 66,160,000 | 66,260,000 | 100,000 | 5.7 | 28.1% | 6 | 6 | 0 | 0 | OOA |
| 9 | 32,940,000 | 33,040,000 | 100,000 | 2.8 | 4.2% | 7 | 14 | 0 | 0 | OOA |
| 10 | 4,820,000 | 4,920,000 | 100,000 | 2.6 | 9.4% | 9 | 5 | 0 | 0 | OOA |
| 10 | 38,000,000 | 38,160,000 | 160,000 | 3.5 | 8.3% | 5 | 9 | 2 | 0 | OOA |
| 10 | 69,630,000 | 69,740,000 | 110,000 | 4.2 | 19.8% | 2 | 2 | 0 | 1 | OOA |
| 15 | 45,250,000 | 45,350,000 | 100,000 | 2.5 | 1.1% | 5 | 6 | 1 | 0 | OOA |
| 17 | 35,500,000 | 35,600,000 | 100,000 | 2.9 | (no tags) | – | – | – | – | – |
| 20 | 20,030,000 | 20,140,000 | 110,000 | 5.1 | 64.6% | 0 | 0 | 10 | 5 | COS |
| 22 | 30,690,000 | 30,820,000 | 130,000 | 3.5 | 4.2% | 0 | 2 | 5 | 2 | COS |
| Relative tag SNP frequencies in actual data | 34% | 46% | 15% | 5% | ||||||
| Relative tag SNP simulated under a demographic model without introgression | 34% | 5% | 33% | 27% | ||||||
| Relative tag SNP simulated under a demographic model with introgression | 23% | 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.