We compared the presence of non-indigenous lineages in populations from southern Brazil and in Amazonian populations. Our study shows that there is a greater presence of non-indigenous lineages in the populations of southern Brazil than in the populations of the Amazon region, probably due to greater admixture with non-indigenous in the populations of the South than in the Amazon region.

          The presence of mitochondrial DNA of non-indigenous origin was rare, in contrast to the Y-chromosome data. This is a reflection of the uneven admixture, common during the first centuries of the arrival of Europeans on the American continent. This admixture involved mainly European men and indigenous and African women.

The main genetic consequence of this historical contact was the formation of current Latin American populations, characterized by having the majority of Y chromosomes of European origin and mitochondrial DNA of indigenous or African origin. In other words, they are populations with a greater predominance of European paternal heritage and indigenous and/or African maternal heritage.

          According to our study, it is notable that most of the Native American mitochondrial DNA variability is intrapopulational. This means that individuals that are part of the same population have more genetic diversity among themselves than compared to individuals from other populations. This genetic diversity was influenced by the geography and language of each population. But some additional factors may also have influenced this diversity: distinct patterns of male and female migration, as well as cultural characteristics and other factors that continue to be studied.

          Our study highlights that the genetic variability of Amazonian human populations is altered by different factors and that it is even influenced differently in their maternal and paternal lineages.