The Archaeogenomics Equation

What do you get when you mix archaeology, ecology, wildlife management, and conservation genomics? No, this isn’t a tagline similar to a duck-in-a-bar joke. What you have is an emerging field of studying called conservation archaeogenomics.

At the forefront of this work are Robert Fleischer and Jesús Maldonado, both of the Center for Conservation Genomics (CCG) at the Smithsonian Conservation Biology Institute and National Zoo. The purpose of archaeogenomics is to use genomic methods to learn how humans impacted the environment over time, and Fleischer and Maldonado use this information to make recommendations for conservation.

Fleischer said researchers do more than just look at archaeological samples’ genetic data in their work. There’s a comparison process. Archaeological information is compared to data from paleontological specimens, that can be more than 500 years old, as well as to genomic information from modern or museum specimens.

However, when it comes to extracting ancient DNA found in archaeological, paleontological and even museum samples, Fleischer said they can run into problems. Ancient DNA (aDNA) is often degraded, averaging only a couple hundred base pairs, rather than the tens of thousands of base pairs that you would find in a modern sample. And although museum specimens are far younger than archaeological or even paleontological samples, without proper preservation DNA degradation happens quickly. In both modern and older specimens, scientists also routinely find “extraneous DNA” from the surrounding environment contaminating their samples. However, that issue becomes more of a problem when aDNA is already far degraded.

“(Working with) modern DNA helps us develop the tools and the markers we’re going to use to screen for the ancient samples,” Maldonado said.

And while modern samples may have the best DNA, Maldonado describes the collections at the Smithsonian as a “gold mine,” saying it’s nearly impossible to replicate some of those specimens in this day and age.

“The collections have such importance in terms of materials we can obtain for our research,” he said.

“In many cases the species don’t exist anymore,” Fleischer added.

This is why it is important to integrate their work across collections, utilizing the specimens’ DNA.

“To be able to do DNA analyses of old material … that gives us a window to the past that we never had,” Fleischer said. “... So (DNA is) very useful from the standpoint of looking at changes in variability, changes in population size over time. But it’s also useful for looking at situations where you don’t know what species existed at a site in the past.”

aDNA work isn’t the only thing done in Fleischer and Maldonado’s lab at the CCG. They also work in non-invasive DNA techniques, disease diagnosis, genetic management of wild and captive populations and more.

“If you team up with the experts that have compelling questions in their field, we can help with applying the tools that we know can answer some of those questions,” Maldonado said. “... We’re promoting more collaborative work so it can be applied to conservation.”


References
Courtney A. Hofman, Torben C. Rick, Robert C. Fleischer, Jesús E. Maldonado (2015, September). Conservation archaeogenomics: ancient DNA and biodiversity in the Anthropocene. Trends in Ecology and Evolution, Volume 30, Issue 9, p540–549. DOI: http://dx.doi.org/10.1016/j.tree.2015.06.008

Glossary

Ancient DNA (aDNA)
DNA extracted from nonliving sources, including teeth, bones, toepads, desiccated tissue, seeds, plant remains, and paleofeces.
Archaeogenomics
Using material from archaeological sites to get genomic information.