Mitochondrial ancestry from complete mitogenomes highlights a lack of characterization of indigenous haplogroups in Brazilian Amazon population.

Mitochondrial genome is an essential resource to investigate the dispersion and diversification of human populations. However, the lack of genomic data from non-European ancestry hinders demographic, anthropologic and genetic studies. Indigenous people from the Brazilian Amazon are especially underrepresented among large genetic datasets, despite their significative contribution to the Brazilian genetic pool. We investigated 157 mitochondrial genomes from the Brazilian Amazon using bioinformatics tools for ancestry inference and phylogenetics. Results were compared with 2578 global mitogenomes to assess haplogroup frequencies and genetic distances. Thirteen macrohaplogroups were identified from investigated samples, including Indigenous, European and African ancestries. Despite being prominent in our sample, Indigenous haplogroup assignment confidence by prediction tools was lower and many samples lacked key-defining variants, suggesting misassignment due to low representation in reference datasets. We also identified potential new groups sharing specific variants. Thus, underrepresentation of Indigenous haplogroups contributes to phylogenetic inconsistencies and needs future investigations.