Scientists have successfully sequenced the genome of an extinct cave bear using its 360,000-year-old bone. This is the oldest genome of any organism from a place where there is no permafrost.
This research revealed a new evolutionary history for the giant cave bear, which became extinct about 25,000 years ago. Scientists have found that cave bears and their living relatives – brown and polar bears – split from a common ancestor about 1.5 million years ago.
Cave bears, which were larger than brown bears and weighed up to a ton, were widespread in Eurasia during the Pleistocene. They coexisted with and interbred with brown bears, and modern brown bears still bear the traces of extinct cave bears.
Unlike the brown bear, cave bears were vegetarians. Their name comes from the fact that they slept in caves in winter, and many died because they could not fatten enough.
The reason for their disappearance is unknown. It is believed that climate change may have been a factor, along with the arrival of modern humans from Africa, which coincided with its decline. The bones of a cave bear were found with human spearheads carved into them, and the ancients also painted images of cave bears on the walls of their caves.
The researchers also found that many important events in the evolution of bears could have been caused by global climate change about a million years ago, when the cold phases (ice ages) became longer and more intense, and the warm phases were much shorter.
The researchers analyzed a sample of a cave bear that lived in the South Caucasus, on the territory of modern Georgia, in about the Middle Pleistocene. The oldest genome sequences previously came from an area where there is permafrost, and, accordingly, the DNA is much better preserved there.
For this study, the scientists wanted to push the timeline for sequencing the Paleogenome much further into warmer and more temperate zones, where many more species lived.
The work involved extracting ancient DNA from a tiny piece of stony bone (0.05 g) of the part of the skull where the parts of the inner ear are located, and which is known to be resistant to infection from external DNA sources.
The DNA was then prepared for sequencing, resulting in billions of individual, short sequences that were a mixture of the cave bear genome and pollutants that the bone had captured over hundreds of thousands of years.
Computational analysis was used to sort DNA from contamination by matching short sequences to a reference genome of a related organism, in this case a polar bear.
To learn more about the evolution of the cave bear, once the team obtained the genome data for the 360,000-year-old bear, they were able to compare it to other bears dating from 35,000 to 70,000 years ago to obtain a broad sample of all the major lineages of these animals.
Because the time difference between the cave bear samples was so great, the team was able to calculate how many DNA mutations occurred during this period. And then we found out the rate of DNA mutation in the cave bear genome, as well as the time during which the different lines diverged.
Using a recently calculated mutation rate, the researchers found that cave bears and their living relatives, brown and polar bears, were different from their common ancestor. Cave bears interbred with brown bears, now, given the rate of mutation, they can date these events.
For the first time, scientists were able to determine the frequency of mutations in the cave bear genome. Using this information, they found that severe climatic changes could be a contributing factor to important evolutionary events in these giant bears.
DNA can be used to decipher the genetic code of extinct animals long after they disappeared, but after thousands of years, the DNA present in ancient specimens is slowly disappearing, creating a time frame for how far back in time you can usually go back. The study showed that this amazing molecule could last even longer than previously thought, opening up new possibilities for genetic research on previously unimaginable time scales.
This is because they analyzed a stone bone that was about seven times older than any of the previously studied, and showed that genome data can be extracted from samples of the temperate zone, covering more than 300 thousand years.