Using Only Trace Amounts of Poop in Soil Samples, Researchers Sequenced Entire Genomes of Two Ancient Bear Species

Genetic research involving prehistoric animals usually requires fossilized bone or tooth fragments

A photo of reseachers collecting ancient soil samples from a cave in Northern Mexico
From soil samples, researchers found urine droplets and fecal material that belonged to Upper Paleolithic bears that used the Chiquihuite Cave as their shelter and toilet 16,000 years ago. Devlin A. Gandy

When researchers find fossils, they usually rely on teeth or bones to study ancient DNA. However, while fossils provide crucial information, they only offer a snapshot about an individual's DNA within a species and not about the populations' genetics as a whole, reports Caroline Delbert for Popular Mechanics.

In a "scientific first," a research team has sequenced the entire genomes of two ancient bears using only urine and fecal matter found in soil samples from the Chiquihuite Cave in Northern Mexico. The find shows high-quality DNA and near-complete genomes be reconstructed and studied without fossils. Researchers also used the technique to piece together the history of North American Stone Age bears, reports Elizabeth Pennisi for Science. The study was published this month in Current Biology.

Within Chiquihuite Cave, the study's researchers previously found stone tools and fragments dating between 25,000 and 30,000 years in 2012, Science reports. The tools showed humans inhabited the cave at one point, so the team collected various samples of sediment from the floor to see what else may have occupied the cave long ago. DNA was recovered and sequenced from a total of 48 samples of dirt, Science reports.

From the soil samples, researchers found urine droplets and fecal material that belonged to Upper Paleolithic bears that used the Chiquihuite Cave as their shelter—and toilet—16,000 years ago, reports Michelle Star for Science Alert. Using the excrement, the researchers sequenced entire genomes of two ancient bears. One of the bears was the ancestor of the American black bear that is still around today. The other genome matched a now-extinct species, the giant short-faced bear, that went extinct some 11,000 years ago, reports Science Alert.

"When an animal or a human urinates or defecates, cells from the organism are also excreted. And the DNA fragments from these cells are what we can detect in the soil samples. Using extremely powerful sequencing techniques, we reconstructed genomes – genetic profiles – based on these fragments for the first time," explained Eske Willerslev, a geneticist from the University of Copenhagen in Denmark, in a statement.

To fully sequence the genome of the ancient bears, the researchers used eight modern bears in the Ursidae family, and three extinct bears as a template, reports Popular Mechanics. From the newly reconstructed ancient bear genome, the researchers pieced together how black bears populated and migrated across North America when the Ice Age ended, reports Science. To do so, they compared ancient genome sequences from 83 present-day black bears in North America and three short-faced bears that lived in Canada about 22,000 years ago, Science Alert reports. They found some black bears migrated north as far as Alaska and others went west, where their descendants populated the southwestern United States, Science reports. While researchers don't know when the bears exactly expanded into ice-free zones, they know it occurred 12,000 years ago when the world began to warm up.

Aside from providing new data about the black bears' ancestry, the new research shows how scientists can now use environmental DNA to piece together genomes—without the need for fossils—to further explain how a species evolved, reports Science Alert.

"Analysis of DNA found in soil could have the potential to expand the narrative about everything from the evolution of species to developments in climate change—this is the Moon landing of genomics because fossils will no longer be needed," Willerslev said in a statement.