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Smithsonian Agave Research Project

The Verde Valley Archaeology Center and Museum is involved in a comprehensive Smithsonian research project on the paleogenomics of agave with Desert Botanical Garden and the National Autonomous University of Mexico. 


VVAC is a partner of this larger project that aims to learn more about prehistoric agave trade networks, plant domestication and the subsistence strategies of people over time. The center will be supplying agave and yucca for plant testing.


VVAC has a large collection of prehistoric agave and yucca fiber quids that were found at the Dyck Cliff Dwelling site. Quids are fibrous remnants that are left behind after the soft tissue has been chewed. After mature plants were harvested, the leaves were removed and the cabeza, or head, was then pit-baked for several days until the indigestible complex carbohydrates were converted to simple sugars. The crowns of the plant are cut off and roasted underground, then stripped into small parts to be chewed. The cooked plant material is very sweet. 


The Sinagua used agave in a variety of ways, including for weaving, as cordage, traps, sandals and netting. They were very resourceful, even using quids to fill gaps in masonry. 

The project was initiated by Dr. Marcela Sandoval-Velasco, formerly a Postdoctoral Fellow at National Autonomous University of Mexico, Institute of Ecology and a Peter Buck Postdoctoral Fellow in Anthropology at the Smithsonian National Museum of Natural History (NMNH), and now Assistant Professor at the Center for Genomic Sciences at UNAM, along with Logan Kistler at NMNH and Daniel Piñero at UNAM. She proposed the project on agaves of Mexico and soon a collaboration with Andrew Salywon, Herbarium Curator and Research Botanist at Desert Botanical Garden and Wendy Hodgson, Herbarium Curator Emerita and Senior Researcher Botanist at Desert Botanical Garden, and began to expand the study to include agaves of the American Southwest. It’s a broad project that involves institutions from both Mexico and the United States and funding from several institutions. 


The project started a couple of years ago with the study of four sites in Mexico and Central America. Agaves were present to such an extent that Sandoval-Velasco thought that through paleogenomics they could access past information to understand the domestication process of this important group of plants, as it was once hypothesized by the archaeobotanist C.E. Smith that their cultivation may have laid down the ecological and cultural basis for the later domestication of other crops. 


The project focuses on agave in the greater American Southwest, Mexico and Latin America. DBG approached VVAC with an interest in the agaves and yuccas from the Dyck site.

Sandoval-Velasco presented “Paleogenomics of Agave: History of Usage and Domestication” for VVAC staff and volunteers to understand the goals and process of the research project. 


Archaeobotanical remains, such as the prehistoric agave remains found at the Dyck site, have been found in all archaeological sites associated with humans. Sandoval-Velasco said that this offers a window into past diversity. 


Sandoval-Velasco discussed some of the limitations of working with ancient DNA, including its degradation over time. Biological and environmental factors can also chemically modify DNA. She said that it’s very different than working with a fresh sample of DNA and likened ancient DNA studies to reconstructing a book. Pages get lost over time, even paragraphs and individual letters, yet even with fragments these pieces tell a part of the larger story. 


“Although limitations exist, it allows us to study things from a molecular perspective that we were not able to do in the past, or were not able to do only through archaeological or morphological studies,” said Sandoval-Velasco. 


Modern DNA consists of long fragments while ancient DNA has shorter fragments. Sandoval-Velasco said that they find patterns within these shorter fragments. 


Sandoval-Velasco said that they are able to extract all kinds of DNA, but only plant DNA will be used and studied for this project. 


To avoid further contamination of the ancient samples, the research team has been working in specialized ancient DNA laboratories at UNAM and NMNH. 


Sandoval-Velasco said that agave is well preserved, understudied and had a wide range of uses from different parts of the plant. She added that the archaeobotanical remains are a gold mine to study the evolutionary processes of domestication resulting from the relationship between humans and agave. 


The project is taking a multidisciplinary approach to answer the questions of which agave species were used, for what purpose, when, where, the human impact of this usage and whether the species were cultivated or domesticated. The project will focus on these questions on both a geographical and temporal scale to shed light on the human relationship with agave. 

The research team plans to compare the paleogenomic data from agave and yucca remains to a modern genomic reference library constructed from present day plants. They currently have around 90 agave species included in the reference dataset and are looking to include more. 


While extracting DNA is usually a destructive process, the team is trying to make the damages minimal or imperceptible. The research team is seeing a 40% success rate of extracting plant DNA samples, which is typically around 30% in paleogenomics. Sandoval-Velasco said that this is in part due to the environmental conditions of the caves the material was found in which allows organic matter to be well preserved. 


The team then sends the DNA to a genomics facility that sequences the data. They will then map it and compare it to the reference genome of both chloroplast and nuclear DNA. 

Hodgson said that by studying agaves through this project, they will gain a better understanding of trade routes and agriculture through the lens of plant trade, cultivation and selection. She added that the Verde Valley region is often overlooked as a center of domestication. 


Salywon stressed the importance of studying an entire collection and that a whole new world can be opened up through it. 


“It's really a privilege to be asked to be brought into such a prestigious Smithsonian research project and to work with renowned scientists and botanists Wendy Hodgson, Andrew Salywon, and Dr. Marcela Sandoval-Velasco,” said Monica Buckle, VVAC’s Executive Director. She added that the museum also functions as a research facility. “It is fantastic that our lab is further being used as a place of study.” 


The research team will be able to carry out the sampling directly at the lab, not risking damaging the quids by sending them to Mexico City or to the Smithsonian. The sampled fibers will be then taken to the special ancient DNA laboratory facilities at the NMNH where the experiments will be carried out. The project at VVAC will most likely start in Fall of 2024 after all permissions have been granted from all interested and involved parties.


“It's first-rate how these collaborations are possible in modern times,” said Buckle. “We've had several online meetings together despite our geographic locations, so it’s terrific that we're able to connect on a virtual level, and then we can connect in-person, and the research can be carried out here at the museum.”


“It's imperative for our donors and members to know of the impeccable work museum staff and volunteers are conducting,” Buckle continued. “VVAC is a multifaceted organization, we're a museum yet we're also a research facility. There are so many possibilities that can grow from this partnership and collaborations with these organizations. This project is just the beginning and there is more to come.” 


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