Using DNA sequencing on ancient pack rat nests made of plants, insects, bones, fecal matter and urine could give us a look into Earth’s past, according to research published Thursday in the journal Ecology and Evolution. The study could help scientists better understand how plant communities, as well as potentially animals, bacteria and fungi, will react to climate change.
“Rodent middens are powerful tools in paleoecology,” Michael Tessler, a postdoctoral fellow at the American Museum of Natural History, said in a statement. “We wanted to see how we could take this invaluable resource and expand its use to give us a big-picture view of what life in the Americas was like 1,000, 10,000, or even 30,000 years ago, and measure how it has changed in the time since then.”
Pack rats are nocturnal rodents that use plant materials to build nests in dry caves. Their urine helps to hold the nests together. This allows the nests to be preserved for tens of thousands of years, with some dating to before the last ice age.
Because pack rats have a limited foraging range, their middens are made up of contents representative of the local environment at the time the materials were collected. This could give us clues about previous environments and climates, the study says.
“Midden contents are so well preserved that fragments of ancient DNA can be extracted and analyzed across millennia,” Rob Harbert, an assistant professor at Stonehill College, said in the statement. “They have been used to identify an extinct ground sloth preserved in southern Argentina, tell us about the history of bighorn sheep in California, and provided evidence of papillomavirus infection in packrats over the last 27,000 years.”
Fossil middens throughout the Americas could allow us to “genetically profile entire communities through time and space,” Harbert added, but we first need to improve how we analyze data from the deposits — a key goal of the study.
Researchers analyzed DNA from 25 pack rat midden samples ranging from 300 to 48,000 years old, which came from City of Rocks National Reserve in Idaho and Guadalupe Canyon in Northern Baja California, Mexico. Scientists focused on a sequencing technique for comparing DNA, called shotgun, that randomly chooses DNA fragments to sequence. They found that pack rat middens as old as 32,000 years have recoverable DNA consistent with fossils found in the deposits.
Because the shotgun technique sequences random bits of DNA, researchers need to have a solid database to match the sequences to an organism. If there isn’t any data for that organism, they’ll only get either the nearest match or no match. This, in addition to DNA degradation, allowed researchers to definitively match the DNA fragments only to the family level, and not to genus or species groupings.
“As the costs of DNA sequencing continue to decrease and computational power increases, the prospects for using this technique will greatly improve,” Harbert said. “Further investigation into the taxonomic composition of middens could refine our understanding of the timeline of past climate change, species migration, and extinction, and this will better inform the study of the effects of current and future climate change.”