Preprint: New computational method recovers nuclear DNA from the heavily contaminated Teshik-Tash 1 Neandertal

A bioRxiv preprint introduces admixslug, a new computational framework designed to extract population-genetic signal from archaic human genome data that is heavily contaminated with present-day human DNA — a common obstacle when working with ancient specimens from regions where good DNA preservation is rare.

The method is applied to nuclear DNA extracted from Teshik-Tash 1, the remains of a Neandertal child recovered from a cave in Uzbekistan. The site represents the south-easternmost known extent of the Neandertal range, placing it at a geographic crossroads between the better-studied Neandertals of Europe and the Caucasus and those associated with Altai Mountain specimens. Previous attempts to characterise the nuclear genetics of Teshik-Tash 1 have been limited by poor DNA preservation and high contamination levels.

Admixslug jointly models contamination and population relationships, enabling the authors to place Teshik-Tash 1 within the broader Neandertal phylogenetic picture despite the challenging data quality. The preprint will be of interest to researchers in palaeogenomics, computational population genetics, and archaeogenomics, and to educators teaching ancient DNA methodology. The paper also connects to ongoing interest in the geographic and population structure of Neandertals across Eurasia. This is a preprint and has not yet undergone peer review.