A Method to Analyze Low-Quality Archaic Human Genomes and its Application to the Teshik-Tash 1 Neandertal

The Teshik-Tash 1 child, discovered in Uzbekistan, marks the farthest southeastern point of the recognized Neandertal range. This discovery creates a significant connection to the more extensively studied Caucasus and Altai Mountain ranges. Despite the proximity, analyzing the genetics of Teshik-Tash 1 has been challenging due to its poor DNA preservation, which has been heavily contaminated with modern human DNA.

In an effort to overcome this obstacle, researchers introduced a novel computational method called admixslug. This tool is specifically designed to model contamination and population relationships, enabling the inference of an individual's genetic relationship to high-quality archaic human genomes when only low-quality nuclear DNA is available.

Upon validating the effectiveness of admixslug, researchers applied it to Teshik-Tash 1's genome. The findings revealed that Teshik-Tash 1 shares a closer genetic relationship with later Neandertals from Western Eurasia compared to older Neandertals from the Altai Mountains. By estimating the divergence time between Teshik-Tash 1 and the Western Eurasian lineage, scientists determined that this occurred between 80,000 and 100,000 years ago.

Interestingly, the study found no evidence of Denisovan ancestry in the Teshik-Tash 1 genome, despite the geographical closeness of his location to the Denisovan range. These results highlight the potential of admixslug in studying archaic human specimens, even when DNA preservation was previously deemed unsuitable for population genetic analyses.