Ancient genomics study reveals low HLA diversity in eastern hunter-gatherers

Abstract

Background: Eastern hunter-gatherers (EHG) contributed varying proportions of genetic ancestry to many modern Europeans. However, how this contribution shaped the human leukocyte antigen (HLA) gene diversity remains unexplored. Sakhtysh in western Russia comprises one of the largest EHG-affiliated burial complexes. The site's continuous use offers a rare opportunity to investigate the genetic history, immune-gene diversity, and pathogen exposure within a hunter-gatherer population. Results: Genome-wide data from 36 individuals (spanning Lyalovo-Volosovo traditions, 6800-4800 cal BP) place the Sakhtysh population within the EHG cluster, with high genetic affinity to contemporaneous groups across northwestern Russia and the eastern Baltic. This genetic composition remained stable for over two millennia and there is no evidence of admixture with neighboring western hunter-gatherer or farmer groups. We report HLA genotypes for 27 Sakhtysh individuals, representing the first true HLA calls from ancient hunter-gatherers. HLA diversity is low in the Sakhtysh population, likely due to their small population size. Specific alleles like B*27:05 are observed at high frequencies (~50%), despite being relatively rare in modern populations, suggesting shifts in selective pressures. Pathogen screening identified a restricted spectrum of causal agents including possible zoonoses with Erysipelothrix rhusiopathiae and chronic infections with hepatitis B virus and parvovirus B19. Conclusions: The Sakhtysh community shows genetic continuity across cultural transitions. This population exhibits limited HLA diversity and unexpectedly high frequency of certain alleles. These patterns were likely influenced by low pathogen diversity and possible adaptation to specific environmental factors.