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Recent studies have expanded and refined the founding haplogroups of the Americas using wholemitochondrial (mtDNA) genome analysis. In addition to pan-American lineages, specific variants havebeen identified in a number of studies that show higher frequencies in restricted geographical areas. Tofurther characterize Native American maternal lineages and specifically examine local patterns withinSouth America, we analyzed 12 maternally unrelated Yekuana whole mtDNA genomes from one village(Sharamaña) that include the four major Native American haplogroups A2, B2, C1, and D1. Based on ourresults, we propose a reconfiguration of one subhaplogroup A2 (A2aa) that is specific to South Americaand identify other singleton branches across the four haplogroups. Furthermore, we show nucleotidediversity values that increase from north to south for haplogroups C1 and D1. The results from our workadd to the growing mitogenomic data that highlight local phylogenies and support the rapid geneticdiffferentiation of South American populations, which has been correlated with the linguistic diversityin the region by previous studies.