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

The Amazon rainforest, renowned for its exceptional biodiversity, harbors a wealth of plant species, many of which have been utilized and domesticated by indigenous communities over millennia. While significant progress has been made in understanding the domestication of certain Amazonian crops like cacao and cassava, many species remain understudied. This research focuses on cupuaçu (*Theobroma grandiflorum*), a commercially important fruit tree closely related to cacao, whose domestication history is largely unknown. Cupuaçu's seed pulp is highly valued for its flavor and used in various food products, making it economically significant in the region. While traditionally considered “incipiently domesticated,” suggesting only limited human influence, recent studies have hinted at lower genetic diversity than expected for a wild species. This study aims to clarify cupuaçu’s domestication history using advanced genomic techniques, providing crucial insights into the long-term interactions between humans and Amazonian flora and contributing to our understanding of the region's agrobiodiversity.

Previous research has documented the long history of plant domestication in Amazonia, with evidence suggesting that indigenous populations cultivated and managed numerous plant species for thousands of years. Studies on cacao (*Theobroma cacao*) have revealed a complex domestication history involving selection for desirable traits and geographical spread. Similar investigations have been conducted on other Amazonian crops such as cassava (*Manihot esculenta*) and pineapple (*Ananas comosus*), shedding light on the diverse strategies employed by indigenous communities. However, the domestication history of cupuaçu remained unclear, with existing studies primarily focusing on its genetic diversity and commercial potential. This study builds upon previous research by utilizing more comprehensive genomic data to gain deeper insight into cupuaçu's origins and development.

This study employed population RAD-seq (Restriction-site Associated DNA sequencing) to analyze genomic data from cupuaçu and cupuí samples collected from four locations in the Brazilian Amazon: Xapuri-Acre (ACRE), Balbina-Amazonas (BALB), Tapajós-Pará (PARA), and São Gabriel da Cachoeira-Amazonas (SGCA). Multiple approaches were used to determine genomic relationships and compare genetic diversity. These included an UPGMA (Unweighted Pair Group Method with Arithmetic Mean) tree, a haplotype network, principal component analysis (PCA), and STRUCTURE analysis to infer population structure and admixture. To investigate the “cost-of-domestication” hypothesis—the idea that domestication leads to an accumulation of deleterious mutations—the researchers calculated dN/dS ratios (ratios of non-synonymous to synonymous mutations) and examined selection signals using linkage disequilibrium-based scores. Finally, a stairway plot was used to estimate the demographic history of cupuaçu, including past population sizes and bottleneck events.

The study's key findings strongly support the hypothesis that cupuaçu is a domesticated form derived from cupuí. The genomic analysis revealed a significant reduction in genetic diversity in cupuaçu compared to its wild relative, consistent with a domestication bottleneck. This bottleneck was estimated to have occurred between 5347 and 7943 years before present (yBP), suggesting an initial domestication phase in the mid-Holocene. Furthermore, a second, more recent bottleneck was detected, likely representing a second phase of domestication associated with the expansion of cupuaçu cultivation in the last two centuries. The geographical analysis points towards the Middle-Upper Rio Negro basin in Northwestern Amazonia as the most likely center of origin for domesticated cupuaçu. The analysis of selection signals supported the "cost of domestication" hypothesis, with cupuaçu showing an excess of non-synonymous mutations compared to cupuí. This suggests that during domestication, selection for desirable traits may have come at the cost of accumulating slightly deleterious mutations. The study suggests that cupuaçu's initial domestication occurred long before European contact, aligning with archeological evidence of early human settlements and plant cultivation in the Amazon.

The findings provide compelling evidence for the domestication of cupuaçu by Amazonian indigenous populations thousands of years ago. The two-phase domestication model suggests an initial period of localized domestication followed by a later expansion driven by increased economic importance and cultivation. This contrasts with the long-held view of cupuaçu as merely incipiently domesticated. The results underscore the significance of pre-Columbian agriculture in shaping the genetic landscape of Amazonian plants and highlight the complex interplay between human activities and biodiversity. The study’s findings contribute significantly to our understanding of the long history of human interaction with Amazonian ecosystems, demonstrating the sophistication of indigenous agricultural practices.

This study provides strong evidence for the domestication of cupuaçu, a significant Amazonian fruit tree, over two distinct phases. The initial phase occurred in the mid-Holocene in the Middle-Upper Rio Negro Basin, followed by a second phase associated with modern cultivation and expansion. The findings highlight the long history of human agricultural practices in Amazonia and support the hypothesis that the region served as an important center for plant domestication. Further research could focus on expanding geographical sampling to refine the origin of cupuaçu and on identifying specific genes selected during domestication.

The study's geographical sampling, while extensive within Brazil, could be expanded to include samples from other Amazonian regions, such as Colombia and Peru, to gain a more comprehensive understanding of cupuaçu's distribution and genetic diversity. Additionally, while the study utilizes advanced genomic methods, further research utilizing archaeobotanical data could provide additional corroboration of the timeline of cupuaçu domestication.