The aim of this study is to assess dental non-metric trait frequencies of Middle Holocene hunter–gatherer populations from the western Lake Baikal region of Siberia, the Russian Federation, for evidence of population discontinuity. Mortuary practices, cranial morphology, and mitochondrial DNA data have led to the hypothesis of a discontinuity event between the Early Neolithic (EN; ∼7500–7025 cal BP) and Late Neolithic–Early Bronze Age (LN–EBA; ∼5500–3700 cal BP) populations. Dental non-metric traits are highly heritable and can be used to infer biological affinity between populations. Mean measure of divergence results find that dental non-metric trait frequencies vary between archaeological periods in statistical terms, but the extent of difference is minor. In the LN–EBA sample, several, but not all, trait frequencies shift towards the range characteristic of populations with Western European genetic admixture. Gene flow from a population to the south of the Baikal region is the most likely explanation for this shift, although the role of genetic drift and the impact of small sample sizes cannot be discounted. Two cemeteries along the Angara River on either side of the discontinuity event have the most similar dental non-metric trait patterns. The similarity of traits between the EN site of Lokomotiv and the LN component of the site of Ust'-Ida I could suggest population continuity or genetic admixture between groups in this area. Dental non-metric trait data are shown to be an informative avenue for assessing past population events, revealing trends not detected by other data types, and directing research into our reconstruction of the history of these groups away from the shores of Lake Baikal to along the Angara River.
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