Ancient Corn Domestication

The domestication of corn (Zea mays ssp. mays), a global food staple with great economic and cultural importance, began in southwestern Mexico 9,000 years ago and humans dispersed this important grain to South America by at least 7,000 years ago as a partial domesticate. South America served as a secondary improvement center where the domestication syndrome became fixed and improved varieties emerged in parallel with similar processes in Mesoamerica. Now, researchers from the United Kingdom and the United States have extracted and sequenced DNA from 2,000-year-old corn cobs found in El Gigante rock shelter, Honduras, and found that hybrids of some of South American varieties were likely reintroduced back to Central America.

Three roughly 2,000-year-old corn cobs from the El Gigante rock shelter site in Honduras. Image credit: Thomas Harper.

“We show that humans were carrying corn from South America back towards the domestication center in Mexico,” said co-lead author Dr. Logan Kistler, curator of archaeogenomics and archaeobotany at the Smithsonian’s National Museum of Natural History.

“This would have provided an infusion of genetic diversity that may have added resilience or increased productivity.”

“It also underscores that the process of domestication and crop improvement doesn’t just travel in a straight line.”

Humans first started selectively breeding corn’s wild ancestor teosinte around 9,000 years ago in Mexico, but partially domesticated varieties of the crop did not reach the rest of Central and South America for another 1,500 and 2,000 years, respectively.

For many years, conventional thinking among scholars had been that corn was first fully domesticated in Mexico and then spread elsewhere.

However, after 5,000-year-old cobs found in Mexico turned out to only be partially domesticated, scholars began to reconsider whether this thinking captured the full story of corn’s domestication.

In 2018, Dr. Kistler and colleagues used ancient DNA to show that while teosinte’s first steps toward domestication occurred in Mexico, the process had not yet been completed when people first began carrying it south to Central and South America.

In each of these three regions, the process of domestication and crop improvement moved in parallel but at different speeds.

In an earlier effort to hone in on the details of this richer and more complex domestication story, the researchers found that 4,300-year-old corn remnants from the Central American El Gigante rock shelter site had come from a fully domesticated and highly productive variety.

Surprised to find fully domesticated corn at El Gigante coexisting in a region not far from where partially domesticated corn had been discovered in Mexico, they aimed to genetically determine where the El Gigante corn originated.

“El Gigante rock shelter is remarkable because it contains well-preserved plant remains spanning the last 11,000 years,” Dr. Kennett said.

Over two years, the authors attempted to sequence 30 samples from the El Gigante rock shelter, but only three were of suitable quality to sequence a full genome.

The three viable samples all came from the more recent layer of the rock shelter’s occupation — carbon dated between 2,300 and 1,900 years ago.

With the newly-sequenced three genomes, the team analyzed them against a panel of 121 published genomes of various corn varieties, including 12 derived from ancient corn cobs and seeds.

The comparison revealed snippets of genetic overlap between the El Gigante samples and corn varieties from South America.

“The genetic link to South America was subtle but consistent,” Dr. Kistler said.

“We repeated the analysis many times using different methods and sample compositions but kept getting the same result.”

The researchers hypothesize that the reintroduction of these South American varieties to Central America may have jump-started the development of more productive hybrid varieties in the region.

They also think that it was the introduction of the South American varieties of corn and their genes, likely at least 4,300 years ago, which may have increased the productivity of the region’s corn and the prevalence of corn in the diet of the people who lived in the broader region.

“We are starting to see a confluence of data from multiple studies in Central America indicating that corn was becoming a more productive staple crop of increasing dietary importance between 4,700 and 4,000 years ago,” Dr. Kennett said.

The study was published this week in the Proceedings of the National Academy of Science.

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Logan Kistler et al. Archaeological Central American maize genomes suggest ancient gene flow from South America. PNAS, published online December 14, 2020; doi: 10.1073/pnas.2015560117