Domestication of the Amazonian fruit tree cupuaçu may have stretched over the past 8000 years

Amazonia, one of the largest and most biodiverse ecosystems on Earth, is a significant yet less-known arena for ancient plant domestication. Here, we traced the origins of cupuaçu (Theobroma grandiflorum), an Amazonian tree crop closely related to cacao (T. cacao), cherished for its flavorful seed-pulp, by employing an extensive genomic analysis based on data from four sites in Brazil. Our results indicate that cupuaçu is a domesticated variant of its wild relative, cupuí (T. subincanum), probably originating from the Middle-Upper Rio Negro basin. A first phase of domestication is observed through a genetic bottleneck that we estimated to have occurred 5000–8000 years before the present. Moreover, we found further reductions in genetic diversity that we estimated to have occurred during the modern era. This is consistent with a second phase of domestication that was accompanied by an increase in the geographic distribution of cupuaçu over the last two centuries. Unraveling cupuaçu’s origins adds it to the roster of plants domesticated by Amazonian indigenous people in the early to mid-Holocene. Our results suggest that Amazonia’s current patterns of genetic diversity and distribution of domesticated plants were influenced by both pre-Columbian and modern histories.