Extended Data Table 3.
Significant correlation of Neanderthal ancestry estimate with specimen age
| Subset of samples | N | P-value for date correlation | Decrease in ancestry per 10,000 years | Estimate of Neanderthal ancestry at different time points | |||
|---|---|---|---|---|---|---|---|
| 0 years ago (present) | 50,000 years ago | 55,000 years ago | 60,000 years ago | ||||
| f4-ratio estimates | |||||||
| Core Set 1 (all ancient samples (except Oase1) + Han + Dai) | 57 | 5 × 10−22 | 0.48–0.73% | 1.1–2.2% | 4.0–5.4% | 4.3–5.7% | 4.5–6.0% |
| Subset of Core Set 1 (<32kya) | 50 | 2 × 10−15 | 0.59–0.98% | 0.9–2.1% | 4.5–6.4% | 4.8–6.9% | 5.1–7.4% |
| Subset of Core Set 1 (>32kya or <25kya) | 44 | 4 × 10−18 | 0.44–0.69% | 1.0–2.2% | 3.7–5.2% | 4.0–5.5% | 4.2–5.8% |
| Subset of Core Set 1 (>25kya or <14kya) | 47 | 5 × 10−21 | 0.48–0.73% | 1.0–2.2% | 3.9–5.3% | 4.2–5.7% | 4.5–6.0% |
| Subset of Core Set 1 (>14kya or present day) | 37 | 2 × 10−18 | 0.47–0.74% | 1.1–2.4% | 4.1–5.5% | 4.3–5.8% | 4.6–6.2% |
| Subset of Core Set 1 (only ancient samples) | 50 | 4 × 10−15 | 0.46–0.76% | 1.0–2.3% | 4.0–5.4% | 4.3–5.8% | 4.5–6.1% |
| Subset of Core Set 1 (individuals with >200,000 SNPs) | 28 | 4 × 10−19 | 0.46–0.71% | 1.1–2.3% | 3.9–5.3% | 4.2–5.7% | 4.4–6.0% |
| Modification of Core Set 1 (replace East Asians with Europeans) | 58 | 2 × 10−23 | 0.49–0.73% | 1.1–2.3% | 4.0–5.4% | 4.3–5.8% | 4.6–6.1% |
| All ancient samples including Oase1 + Han + Dai | 58 | 8 × 10−29 | 0.57–0.81% | 1.0–2.2% | 4.3–5.7% | 4.7–6.1% | 5.0–6.5% |
| All ancient samples | 51 | 1 × 10−20 | 0.57–0.86% | 0.9–2.2% | 4.4–5.8% | 4.7–6.2% | 5.0–6.6% |
| All ancient samples except Oase1 or UstIshim | 49 | 8 × 10−12 | 0.45–0.81% | 1.0–2.3% | 4.0–5.6% | 4.2–6.0% | 4.5–6.4% |
| Ancestry informative SNPs | |||||||
| Core Set 2 (all ancient samples (except Oase1) + Han + Dai + Karitiana) | 29 | 4 × 10−11 | 0.21–0.39% | 1.8–2.3% | 3.1–4.0% | 3.2–4.2% | 3.3–4.3% |
| Subset of Core Set 2 (no Han, Dai, Karitiana, Stuttgart) | 25 | 1 × 10−4 | 0.11–0.36% | 1.8–2.5% | 2.9–3.8% | 3.0–4.0% | 3.0–4.1% |
| Subset of Core Set 2 (no Han, Dai, Karitiana, Stuttgart, UstIshim) | 24 | 2 × 10−4 | 0.11–0.37% | 1.8–2.5% | 2.9–3.8% | 2.9–4.0% | 3.0–4.2% |
Note: The “Core Set 1,” used for the f4-ratio analyses, refers to 50 ancient samples (removing Oase1 as an outlier) along with 7 East Asians (Dai and Han). “Core Set 2,” used for the analyses of Neanderthal ancestry informative SNPs, refers to 26 ancient samples (removing Oase1) along with Han, Dai, and Karitiana