Ancient Americans Sparked Genetic Diversity Of Avocados

Researchers used leaf samples and insights from local farmers to reveal significant avocado diversity in Central America that could boost sustainable agriculture and commercial varieties by increasing genetic diversity and safeguarding production of the savoury fruit.

Archaeobotanist Kevin Wann, who conducted the research as a fellow of the Smithsonian’s National Museum of Natural History in Washington, D.C., and his colleagues examined DNA from avocado leaves collected in Nicaragua, Honduras, and southern Mexico. They also spoke with the farmers and gardeners to learn how they cultivate these local avocados.

“There is a much wider breadth of avocado diversity that science had not yet documented,” said Wann, who is now pursuing his doctorate in the Department of Anthropology in the College of Arts and Sciences at Texas A&M and had never eaten an avocado before this project. “We could potentially tap into this genetic diversity to conserve commercial avocado plants that are vulnerable to disease.”

Scientists from the Smithsonian Institution and Texas A&M University uncovered genetic traces of ancient migration in DNA from avocados growing in Nicaragua. There is evidence that, around 5,000 years ago, people migrating north from South America carried the oversized seeds of one of their favorite fruits—avocados. As these seeds were dispersed throughout the humid lowlands of Central America, they hybridized with native varieties, producing a diversity of avocados that bear the large, smooth-skinned fruits now enjoyed throughout Central America. Despite resembling avocados from humid regions like Florida and the Caribbean, these local varieties are genetically distinct from the commercially grown fruits used in guacamole.

The research was published in the journal Plants, People, Planet.

A Crop of Clones

The natural range of avocado trees (Persea americana) extends from Mexico to Peru. For more than 10,000 years, humans in this area have coveted the plant’s fruit, whose yellowish-green flesh is packed with nutrients and fats. These superfoods are now cultivated around the world. In 2024, growers produced more than 11 million metric tons of avocados worldwide.

More than 80% of these avocados were a single variety known as the Hass avocado, which was developed in the United States decades ago. These large, long-lasting avocados are produced through clonal grafting, where a branch is taken off one Hass avocado tree and attached to another tree to bear the same fruit. As a result, most avocados in grocery stores are genetically indistinguishable. This makes all Hass avocados vulnerable to the same threats. A single disease or change in temperature or precipitation can wipe out an entire population of Hass avocados. 

Increasing the genetic diversity of avocados is crucial to protecting this multi-billion-dollar industry. According to Wann, the muggy lowlands of countries like Nicaragua and Honduras are rich in avocado diversity. Here, traditional agricultural practices have honed the region’s native avocado varieties, also known as landraces, for thousands of years. 

A Hotbed of Avocado Diversity 

To document the diversity of avocado landraces in Central America, Wann and his colleagues collected leaf samples from dozens of varieties in southern Mexico, Nicaragua, and coastal Honduras.  The researchers also interviewed local gardeners and rural farmers in Nicaragua and Honduras to learn more about native avocado varieties. This agricultural perspective was crucial, according to Logan Kistler, the Smithsonian museum’s curator of archaeobotany and archaeogenomics who advised Wann during his fellowship and was the senior author of the new paper.

“You can't think about biodiversity without considering agriculture, because it's one of the most impactful ecological activities we do,” Kistler said. “Traditional agricultural practices have shaped these plants for thousands of years.”

During a tour of one grove in Nicaragua, a farmer offered Wann an avocado, unaware that the scientist had never tasted the fruit he studied. “I wanted to see how far I could go into my dissertation studying avocados without ever eating one,” he said. “I made it four years, but when one of the native farmers offered me one, I couldn’t turn him down. And it was delicious,” adds Wann, who now routinely enjoys guacamole.

The locals shared valuable insights with the researchers. They confirmed that these lowland avocado landraces had not experienced root rot, the most common disease affecting commercial avocados. Some Nicaraguan farmers even graft commercial avocado branches onto native avocado trees, which are better adapted to the local environment.

Ancient Genetic Clues

In the lab, the team extracted and analyzed DNA from the harvested leaf samples. In total, the team collected DNA from 47 native avocado landraces (32 of which came from Nicaragua). The scientists compared the DNA from the various landraces with previously published genetic data from more than 200 other avocado lineages.

The team discovered that the avocado samples collected in southern Mexico were closely related to ancestral highland populations found in other parts of Mexico as well as commercial varieties. In contrast, the landraces sampled in the lowlands of Nicaragua were genetically tied to avocados found further south, including populations along the coast of Colombia.

This revealed that many local landraces in this part of Central America are planted from fruits originally grown in South America. The team posits that human populations brought their local avocado varieties with them as they migrated through the Americas. Based on the genetics, this avocado relocation likely occurred around 5,000 years ago, which is roughly when other South American crops, like chocolate and certain varieties of maize, appear in the Central American archaeological record. Kistler thinks varieties of this fleshy fruit continued to move back and forth as ancient communities migrated over thousands of years.  “It was a very connected landscape throughout Central and South America,” Kistler said. “It's not one big episode of people moving avocados and other food species around, it's a constant interchange.”

Avocados collected at roadside stands in Mexico revealed genetics proving that native and commercial avocado varieties had recently hybridized. Avocados grown for export thrive in the higher elevations of southern Mexico where hybridization was expected. However, avocados grown in the Central American lowlands were different. They are not like commercial varieties but were more similar to avocados from South America. Avocados tested in lowland Nicaragua and Honduras descend from those brought by ancient Americans to Central America thousands of years ago. Wann said that the presence of these avocados matches “a pattern we see in many other plants, like South American corn and even the chocolate tree,” Wann says. The plants came with the people.

More genetic diversity may be waiting to discover, and may surprise future scientists. Avocado trees hybridize between native and commercial varieties. The Benik avocado, which is grown in Nicaragua for export, was thought to have been agriculturally created in Guatemala. Howeve,r it is actually native to Nicaragua but hybridized with a commercial variety from Guatemala. Such hybridization may be a key to ensuring the future of fruit. 
 

The Fruit’s Future 

Wann thinks the trove of avocado diversity preserved in Central America’s lowlands could help protect commercial avocados from the fate of other clonal crops like bananas, which have been devastated by fungal pathogens in the past. The region’s local landraces are also adapted to warmer and wetter climates.

However, some of these local avocado varieties are at risk. Wann and his colleagues heard that several Nicaraguan farmers have cut down some of their local avocado trees to make more space for commercial varieties. Decreasing this ancient avocado diversity could threaten the fruit’s future. “These locally grown fruit trees are vital to the longevity of avocados as a species,” Wann said. “Their high levels of genetic diversity make them more prepared to face potential shifts in climate or diseases compared to the ones you’d buy at a supermarket,” he added.

Increasing the genetic diversity of avocados is crucial to protecting the multi-billion-dollar industry surrounding the fruit. Wann thinks the trove of avocado diversity preserved in Central America’s lowlands could help protect commercial avocados from the fate of other clonal crops like bananas, which have been devastated by fungal pathogens in the past. The region’s local varieties are also adapted to warmer and wetter climates.