Origin and health status of first-generation Africans from early Colonial Mexico City.

The diverse ethnic roots of the modern-day Mexican population are largely shaped by genetic admixture among Africans, Europeans, Native Americans and Asians that occurred during the New Spain period. The presence of African ancestry in historical periods in Mexico has so far been documented mostly through exhaustive archival evidence. Here we employ a thorough bioarchaeological approach to gain further insights into the origins and life history of three 16th century Africans from a mass burial at the San José de los Naturales Royal Hospital in Mexico City (Hospital Real de San José de los Naturales), by bringing together ancient genomic data, osteological analysis, strontium isotope data from tooth enamel, d13C and d15N isotope data from dentine, and ethnohistorical information. Anthropological analysis of skeletal features, uniparental markers, genome-wide analyses and HLA haplotypes are consistent with a sub-Saharan African origin for all three individuals. Complete genomes of Treponema pallidum sub. pertenue (causative agent of yaws) and Hepatitis B Virus (HBV) were recovered from those individuals. Phylogenetic analysis of the reconstructed Treponema genome reveals it to be closely related to a strain identified in more recent individuals from colonial Mexico, as well as strains found in humans in Africa. The HBV strain type is mainly found in modern Western Africans, further supporting that the individual who carried the virus originated in this region. These findings highlight the prominent role of the transatlantic slave trade in the introduction and dissemination of pathogens into the New World. Overall, our results provide insights into the origin, health status and life history of these three individuals, who were among the first Africans to reach the New World in the 16th century through forced migration.