An international team of researchers has extracted and sequenced DNA from a 360,000-year-old petrous bone of the extinct cave bear Ursus kudarensis found in a cave in the Caucasus Mountains — the oldest genome sequence from a non-permafrost environment. Using this and other cave bear genomes, they’ve determined nuclear and mitochondrial substitution rates and revised the evolutionary history of cave bears.
Reconstruction of the cave bear Ursus spelaeus. Image credit: Sergio de la Larosa / CC BY-SA 3.0.
The fossil analyzed by the team belongs to a Middle Pleistocene cave bear subspecies called Ursus kudarensis praekudarensis, which is thought to be ancestral to the Late Pleistocene Caucasian cave bear Ursus kudarensis kudarensis.
The specimen was found in Kudaro 1 cave located in the Southern Caucasus in South Ossetia, Georgia.
“Our analysis of the whole genome data has revealed a new evolutionary history for cave bears,” said Dr. Axel Barlow, a researcher at Nottingham Trent University and the University of Potsdam.
He and his colleagues produced billions of individual short DNA sequences which represented a mixture of DNA from the cave bear and contaminants the bone had picked up over hundreds of thousands of years.
“Our study shows that this amazing molecule can survive even longer than previously thought, opening up new opportunities for genetic investigation over previously unimaginable timescales,” Dr. Barlow said.
“We analyzed a petrous bone that was around seven times older than any we had previously studied, showing that genome data can be recovered from temperate zone samples spanning more than 300,000 years.”
“To put this in context, this cave bear probably lived before our own species, Homo sapiens, even came into existence.”
The scientists then used computational analysis to sort the target sequences from the contamination, which is done my matching the short sequences to a reference genome of a related organism, in this case the polar bear.
“From a total of 2.6 billion sequenced molecules, we were able to map 2.1 Gb of sequence with high confidence to the reference genome assembly of the polar bear,” they explained.
Cave bear skulls (A-D) from Kudaro Caves in the Caucasus Mountains, including (D) from the Middle Pleistocene. Image credit: Gennady Baryshnikov.
In order to learn more about the evolution of cave bears, once they had the genome data for Ursus kudarensis praekudarensis, they were able to compare with others from between 35,000 and 70,000 years ago to provide broad sampling of all the major cave bear lineages.
Because the time difference between the cave bear samples was so great, they were able to count how many DNA mutations had occurred during this period.
From here they could calculate the rate of DNA mutation in the cave bear genome, as well as the time that the different lineages diverged.
Using the newly calculated mutation rate, they found that cave bears and their living relatives – the brown bear and polar bear — diverged from a common ancestor about 1.5 million years ago.
And while they had previously shown that cave bears interbred with brown bears, with the mutation rate they are now able to date these events.
Calibrated nuclear and mitochondrial phylogenies of cave bears: branches terminate at the sample ages and nodes are centered on the mean of their respective pair-wise estimates; the complete mitochondrial evolutionary history of the European and Uralian cave bears is uncertain; the three recent mitochondrial transfer events that can be inferred from pair-wise estimates are indicated by vertical arrows; shaded trapezoids connecting lineages indicate the two major episodes of nuclear gene flow identified by D-statistic analysis. Image credit: Barlow et al., doi: 10.1016/j.cub.2021.01.073.
The authors found that cave bears exchanged mitochondrial DNA frequently during their evolution, which until now had obscured their true evolutionary relationships.
They also found that many significant events in bear evolution may have been driven by major global climate change about one million years ago, when cold phases became longer and more intense and warm phases much shorter.
“We have been able to determine the mutation rate of the cave bear genome for the first time,” Dr. Barlow said.
“Using this information, we have discovered that major climatic changes may have been a factor driving major evolutionary events in these giant bears.”
A paper on the findings was published in the journal Current Biology.
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Axel Barlow et al. 2021. Middle Pleistocene genome calibrates a revised evolutionary history of extinct cave bears. Current Biology 31: 1-9; doi: 10.1016/j.cub.2021.01.073
Source link: https://www.sci.news/paleontology/ursus-kudarensis-genome-09392.html
