Yakut communities from northeastern Siberia inhabit some of the coldest environments on Earth, preserving an extraordinary archaeological record. Their history was profoundly reshaped by the Russian conquest, which introduced cereals, pathogens and Christianity beginning in 1632 (refs. 1–5). However, the biological impact of these transformations remains unknown. Here we generated extensive ancient DNA data to elucidate contemporary changes in Yakut genomic diversity and oral microbiomes. We found Yakut origins tracing back to local populations that admixed with Trans-Baikal groups migrating as the Great Mongol Empire spread. Despite the Russian conquest, the Yakut gene pool and oral microbiomes appeared largely stable, although smallpox strains distinct from those documented in Europe by approximately 1650 circulated. Marital practices generally maintained low consanguinity, with the exception of one female bearing the latest markers of traditional shamanism, who was the daughter of second-degree relatives.
