Smithsonian Scientists Discover That Traditional Agricultural Practices in the Amazon Helped Yield an Enduring Crop Clone

About 10,000 years ago, the ancient inhabitants of the southwestern Amazon took an interest in a leafy shrub with starchy tubers. While the uncooked plant’s roots were toxic, a bit of drying, boiling and cooking transformed them into an edible, energy-packed food source. Local Indigenous communities have been tending to the plants ever since.

Today, this shrub, commonly known as manioc, cassava, or yuca, is among the most important staple crops in the world. Hardy and versatile, the plant can thrive in warm environments across the tropics, even in nutrient-poor and acidic soils. Manioc is also very easy to grow: By simply cutting stems into foot-long sections and burying them, farmers can quickly grow an entire field of genetically identical clones.

This adaptability took manioc from an Amazonian staple to a nutritious crop consumed around the world. But it also impacted the plant’s reproduction and life cycle, said Logan Kistler, the curator of archaeobotany and archaeogenomics at the National Museum of Natural History. While conducting research on the evolution of maize in 2017, he began to also wonder how cultivation practices altered manioc’s genetics.

Eight years later, he finally has an answer. In a new study published earlier this month in Science, Kistler and an international team of collaborators combined a series of interviews with Indigenous Brazilian farmers with a genetic analysis of over 500 manioc plants from around the world. Their results provide the first deep dive into how humans have shaped the crop’s DNA, revealing that traditional agricultural practices have buffered manioc against the dangerous side effects that often plague clonal crops — and created strange genetic patterns in the process.

Many of the world’s most important crops are grown as clones, including sugarcane, potato and avocado. While cloning plants allows land managers to carefully select plants with the most desirable traits, Kistler noted that this mechanism can also leave crops vulnerable to diseases. When every plant in a population is identical, each has the same genetic resistance — and vulnerabilities — to pests and pathogens. “The Great Famine in Ireland and Europe was a diversity issue that began with a clone,” Kistler said.

However, Kistler and his collaborators discovered that manioc’s genes remain surprisingly varied. To understand why, the scientists made several visits to the remote Xingu region of the Brazilian Cerrado, or savannah. Here, Indigenous communities have subsisted on manioc for countless generations. Over this time, they have shaped the plant to best suit their needs. The researchers spoke with several farmers who use traditional methods to cultivate the crop and learned that manioc’s diversity is not a coincidence.

In these communities, farmers carefully cross plants from different lineages and allow them to grow in a specialized area called a kukurro house, closely monitoring their growth to identify candidates that could eventually feed the village. According to Kistler, this controlled breeding helps diversify manioc’s DNA. “It helps grow robust plants and build a catalogue of diversity to withstand challenges,” he said.

According to Kistler’s co-author Fabio de Oliveira Freitas, this finding adds a new dimension to how scientists understand Indigenous people’s relationship with crops. As a biologist for the Brazilian Agricultural Research Corporation, de Oliveira Freitas has worked with communities in the upper Xingu region for nearly 30 years. He noted that while many Indigenous farming methods have spiritual connections and are thus difficult to measure in scientific terms, it is clear that they play a role in shaping crop evolution. “This work proved that it is real — the kukurro house practices show how important Indigenous people are to bringing diversity to the manioc system,” he said.

These Indigenous communities have shaped manioc’s genes in surprising ways. The genetic variation of all other crops is tied to geographic proximity. For example, a staple crop grown in Colombia is more closely related to the same crop grown in Peru than one cultivated in Cambodia. But when Kistler’s team analyzed manioc samples from both living plants and preserved specimens stored in herbaria, they discovered that manioc bucks the trend: the crop shows very little relationship between geography and kinship.

"If we don’t understand the nature of diversity...it’s difficult to imagine the most effective responses to crises."

— Logan Kistler, curator of archaeobotany and archaeogenomics at the National Museum of Natural History

The unlikely finding is an artifact of manioc’s long generation time and its importance in cultural exchanges. The Brazilian farmers revealed that nearby villages often trade manioc with one another, both as a marital custom and through incidental swaps. As communities clone these plants, individual lineages can persist for generations. “There are deliberate decisions made about when to adopt a new variety as a new clone,” Kistler said. “It slows the pace of new variety development to the point that everything is related to something else.” As a result, proximity matters less than who traded what with whom.

All of that trading and cloning has given manioc a tightly-knit family tree. Kistler described how a plant collected in the Amazon in the 1960s was found to have genetic offspring — that is, a plant that inherited 50 percent of its DNA — living in such disparate times and places as the Bahamas in the 1890s and Amazonia in the 1980s. “That’s weird!” he said. “That is unprecedented in a crop.”

Unprecedented — but perhaps not as unique as it seems. Kistler suspects future work may reveal similar phenomena in other clonally propagated crops like tree fruits. However, these studies are rare as agricultural science often focuses more on maximizing future productivity than understanding a crop’s genetic history.

While that type of applied research is critical to help feed the planet, Kistler believes that a complete picture of a plant’s evolution is critical. Especially as humans continue to shuffle Earth’s botanical deck by moving plants across the planet.

“There’s absolutely no reason to suspect that as we continue messing with our environment, the plants will go along the way we predict,” Kistler said. “If we don’t understand the nature of diversity, how it’s maintained and how it adapts, it’s difficult to imagine the most effective responses to crises.”

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Benjamin Hack | READ MORE

Benjamin Hack is Science Writing Intern at the Smithsonian National Museum of Natural History. He covers anything and everything related to the natural world for Smithsonian Voices, the museum’s blog. Ever fascinated by ecology, Ben studied and conducted research in biology as an undergraduate at Cornell before transitioning into science communication. His work, which has appeared in magazines such as Audubon and Living Bird, highlights both the joy of nature and the dire challenges facing the world’s biodiversity. In his spare time, Ben can often be found outside birdwatching.