Four published genomes from Tiwanaku contexts in La Paz provide a cautious molecular window into the population. Three males carried Y-chromosome haplogroup Q, a lineage widespread among Indigenous peoples of the Americas; the maternal lineages are dominated by mtDNA B2 (three individuals) with one instance of C1c. These markers are consistent with predominant Native American ancestry typical of Andean populations.
Archaeogenetic patterns align with an Andean highland profile, but several caveats apply. With only four samples, statistical power is limited: population substructure, sex-biased migration, and temporal changes across the 650–1200 CE span cannot be robustly resolved. The prevalence of haplogroup Q among males here mirrors broader continental distributions, yet subclade resolution and autosomal affinities that might reveal finer-scale connections to modern Aymara, Quechua, or neighboring groups remain uncertain unless further samples are analyzed.
Where autosomal data exist from regional studies, they often indicate long-term genetic continuity in the highlands with signals of local gene flow rather than large-scale replacement during the Middle Horizon. For Tiwanaku specifically, these four genomes tentatively support continuity with Andean lineages, but more extensive sampling from multiple burial contexts and time slices is required to test hypotheses about migration, elite mobility, or demographic shifts.