Next generation DNA sequencing helps researchers understand ancient species

University researchers studying 40,000-year-old woodrat DNA to see reaction to climate change


12/29/2015 | By: Whip Villarreal  |

A project to study North American woodrats, otherwise known as packrats, is underway in the College of Agriculture, Biotechnology and Natural Resources to help researchers further understand how the animal's ancestors adapted to climate change 30,000 years ago.

The Death Valley Neotoma project aims to determine the effects of climate changes in the woodrat species in this region. The project is led by Angela Hornsby, doctoral graduate student in the Evolution, Ecology and Conservation Biology program for CABNR, and involves analyzing the homes of the rodents, called middens, usually found in cracks and small crevices of caves or on mountainsides.

The specific middens being analyzed from Death Valley are said to be 40,000 years old, quite a bit older than the Last Glacial Maximum in North American roughly 21,000 years ago, when the continent was covered by a massive ice sheet.

"We're still analyzing the data collected from the middens," Hornsby said. "The type of data sequencing that we are doing is called next generation sequencing. Instead of sequencing one little chunk of data at a time, you end up sequencing millions of chunks of data from the middens."

The woodrat's middens were found in the mountains surrounding Death Valley, where they dried out and were protected from the elements and remained preserved because of the desert climate. The rats' homes also contained DNA from plants, parasites, fungi and bacteria, along with other vertebrates and invertebrates from the environment.

The team is already processing more than 100 paleomidden samples utilizing scientific techniques such as radiocarbon dating and DNA sequencing. The results will allow the team to:

• Definitively identify species.
• Test and confirm the preliminary morphological identifications.
• Determine whether the broad phylogeographic structure of these species has changed relative to the Death Valley region.
• Reconstruct the demographic histories of these species using both contemporary and ancient samples.

The collaborative research team includes Hornsby; Marjorie Matocq, professor of natural resources and environmental science at the University; Professor Felisa Smith at the University of New Mexico; and Professors Hendrik Poinar and Melanie Kuch of McMaster University in Canada. The project has received funding through multiple grants from the National Science Foundation, the Moore Foundation at the University of California, Berkeley and the University of Nevada, Reno.

Hornsby's love for the mountainous landscape of the western United States and her desire to work closely with her advisor, Associate Professor Matocq, led her to the University of Nevada, Reno. She is a full-time graduate student who is also working as a curatorial assistant at the University's Museum of Natural History. Graduating in the spring of 2016, Hornsby plans to continue her work on ancient DNA and has already applied for a post-doctoral position with the National Science Foundation.

"Angela is particularly self-motivated," Matocq said. "For someone at this stage of her career, she is just an incredible scholar, and her expertise is impressive. She doesn't do anything partially. She has really developed her skills and does everything very thoroughly."

During the past year, Hornsby has been rewarded for her hard work and dedication by receiving the 2014 Ecology, Evolution and Conservation Biology Director's Award for Outstanding Contributions to Research and Education and the Outstanding Graduate Student award from the University's Graduate Student Association in spring 2014. She also won first place in the STEM section of the University's "Three Minute Thesis" competition.

"I think it's that people should know that these kinds of resources are local and how beneficial that can be when studying in this field," Hornsby said. "The Great Basin is full of these resources, so if people are interested in asking questions about the last 40,000 years or so, we have the resources closer to where we live than most other places in the world."

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