Neanderthal and Denisovan ancestry

When the ancestors of modern non-African populations left Africa starting about 60,000 years ago, they encountered other archaic human groups already living across Eurasia. The Neanderthals were spread from western Europe to central Asia, and the Denisovans occupied at least parts of Siberia and Southeast Asia. Genetic and fossil evidence shows that interbreeding occurred on multiple occasions, and the introgressed segments still circulate in the genomes of their descendants today.

Population-level baselines

The fraction of archaic DNA in a person's genome depends primarily on their population background.

• Europeans: about 1.9% Neanderthal, near-zero Denisovan.
• East Asians: about 2.35% Neanderthal, around 0.15% Denisovan.
• South Asians: about 2.1% Neanderthal, around 0.01% Denisovan.
• Africans: roughly 0.3% Neanderthal, near-zero Denisovan, mostly attributable to back-migration from Eurasia.
• Oceanians (Melanesians and Papuans in particular): roughly 1.9% Neanderthal and up to 4.3% Denisovan, the highest known.

How Haeckel measures it

The platform combines several converging methods because no single one is bulletproof.

• A curated panel of 53 marker SNPs (35 Neanderthal-associated, 18 Denisovan-associated) with literature-validated allele frequencies in modern and archaic genomes.
• The S-star statistic, which detects long haplotypes that survive in modern genomes despite being too divergent to plausibly come from a recent common ancestor.
• D-statistics, also known as the ABBA-BABA test, which compares allele patterns across four populations to test whether one of them shares a disproportionate fraction of derived alleles with an archaic reference genome.
• A four-state Viterbi hidden Markov model that segments your genome into modern, Neanderthal, Denisovan, and unknown-archaic tracts, and dates each tract using a coalescent model.

Your reported Neanderthal and Denisovan percentages are weighted averages across these methods, calibrated against the published baselines for your inferred ancestry. The headline number is comparable across users, although the individual tract calls vary in confidence and the Methods page reports the per-tract uncertainty.

Notable archaic variants

• rs3827760 (EDAR): Neanderthal-derived variant linked to thicker hair shafts and more sweat glands. Common in East Asians.
• rs1426654 (SLC24A5): contributes to lighter skin pigmentation in West Eurasians.
• rs4988235 (LCT): drives lactase persistence into adulthood.
• rs3211938 (OAS1): Neanderthal-derived antiviral variant associated with reduced COVID-19 severity.
• rs1048990 (EPAS1): Denisovan-derived high-altitude adaptation found at high frequency in Tibetan populations.