Genome-wide evidence for the local ancestry of the Agotes from Navarra, Spain

The Agotes are among the most enigmatic minority social groups in the Iberian Peninsula, historically subjected to long-standing social marginalization by their non-Agote neighbors. Nowadays, all Agotes live in the small town of Bozate (Baztan valley, Navarra, Spain), but their origins remain disputed, with different hypotheses. In this study, we analyze genome-wide genotype data from 125 newly sampled individuals from Bozate, the Baztan valley, and Navarra. Our findings indicate that the Agotes have a local genetic origin and exhibit high levels of homozygosity. Their isolation is likely due to socio-cultural reasons. Additionally, we find fine-scale genetic substructure within the broader Basque-like landscape, detecting the Agote and Baztan components as part of these microstructures, due to social or geographic isolation, respectively. Overall, our findings challenge the long-standing historical perception of the Agotes as a foreign group and suggest a shared genetic ancestry with the local populations.