A genuine genetic and anthropological mystery. From Ars Technica:
The authors focused on a tribe that originally lived in the south-east of Brazil called the Botocudo. This group was violent and independent, and didn't come under the control of the Portuguese colonial power. In 1808, the authorities essentially declared war against any group that fit this description. By the end of that century, the Botocudo had essentially ceased to exist as a distinctive ethnic group.The study's authors reportedly have discounted the possibility of a common Asian ancestor, or that a Polynesian group directly colonized part of Brazil. Although a seeming long shot, they believe that the explanation is that Polynesians were imported as slaves (probably from Madagascar), escaped, and that a group happened to pass along the Polynesian variances.
The remains of several Botocudo individuals, however, were preserved in museums, and the authors obtained DNA from over a dozen of them. That DNA was used to study parts of the mitochondrial genome, which is inherited exclusively through female lineages. Because it's relatively easy to obtain and sequence, mitochondrial DNA has been used for a variety of studies of human evolution, and there's a wealth of data available on the variations associated with different populations.
A dozen of these samples produced the sorts of sequences you'd typically see in Native American populations. But two others have a set of distinctive changes that, to date, have only been found in populations associated with Polynesian cultures.