Long-term human influence on the demography and genetic diversity of the hyperdominant Bertholletia excelsa in the Amazon Basin.

The Amazon rainforest is characterized by a limited number of hyperdominant trees that play an oversized role in its ecosystems, nutrient cycle, and rainfall production. Some of these, such as the Brazil nut, appear to have been intensively exploited and dispersed by Indigenous populations since their earliest arrival in this part of South America around 13,000 years ago. However, the genetic diversity-and geographic structure-of these species remains poorly understood, as does their exact relationship with past human land use. We use a new genome assembly for Brazil nut to analyze 270 individuals sampled at areas with varying intensities of archaeological evidence. We demonstrate that overall low genetic diversity, with a notable decrease since the Late Pleistocene, is accompanied by significant geographic structure, where evidence for improved gene flow and regeneration by long-term traditional human management is linked to increased genetic diversity. We argue that historical perspectives on the genetic diversity of key tree species, such as the Brazil nut, can support the development of more active management strategies today.