Mitochondrial DNA of 22,000-Year-Old Giant Panda Reveals Long-Lost Lineage

A research team led by scientists at the Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences, has analyzed mitochondrial DNA isolated from a 22,000-year-old panda specimen found in southern China and found that the ancient bear separated from present-day giant pandas (Ailuropoda melanoleuca) around 183,000 years ago, suggesting that it belonged to a distinct group not found today.

Giant pandas are found in the mountains of central China in dense bamboo and coniferous forests at altitudes of 5,000 to 10,000 feet (1,500-3,000 m). Image credit: Chester Ho.

The skull of an ancient giant panda (radiocarbon dated to 21,910-21,495 years before present) was found in Cizhutuo Cave in Leye county, China’s Guangxi province.

Its age and location in Guangxi province, where no wild giant pandas live today, as well as the difficulty of DNA preservation in a hot and humid region, placed it as a unique specimen to learn about ancient giant pandas from the last Ice Age.

“Using a single complete mitochondrial DNA (mtDNA) sequence, we find a distinct mitochondrial lineage, suggesting that the Cizhutuo panda, while genetically more closely related to present-day pandas than other bears, has a deep, separate history from the common ancestor of present-day pandas,” explained lead author Dr. Qiaomei Fu, a researcher in the Key Laboratory of Vertebrate Evolution and Human Origins at the Institute of Vertebrate Paleontology and Paleoanthropology.

“This really highlights that we need to sequence more DNA from ancient pandas to really capture how their genetic diversity has changed through time and how that relates to their current, much more restricted and fragmented habitat.”

In the study, Dr. Fu and co-authors used sophisticated methods to extract mtDNA from the ancient cave specimen.

That’s a particular challenge because the specimen comes from a subtropical environment, which makes preservation and recovery of DNA difficult.

To recover the Cizhutuo panda’s complete mitochondrial genome, the researchers sequenced 148,326 DNA fragments and aligned them to the giant panda mitochondrial genome reference sequence.

They then used the new genome along with mitochondrial genomes from 138 present-day bears and 32 ancient bears to construct a family tree.

Their analysis shows that the split between the Cizhutuo panda and the ancestor of present-day pandas goes back about 183,000 years.

The Cizhutuo panda also possesses 18 mutations that would alter the structure of proteins across six mitochondrial genes.

Those amino acid changes may be related to the ancient panda’s distinct habitat in Guangxi province or perhaps climate differences during the last Ice Age.

“The Cizhutuo individual lived in a subtropical environment during the last Ice Age, while present-day pandas live in a temperate environment,” the scientists said.

“That, along with a colder climate across East Asia around 200,000 years ago when their populations likely diverged, might have played a role in the diverging histories observed in their mtDNA lineages.”

“Comparing the Cizhutuo panda’s nuclear DNA to present-day genome-wide data would allow a more thorough analysis of the evolutionary history of the Cizhutuo specimen, as well as its shared history with present-day pandas,” Dr. Fu added.

The study was published in the June 18 edition of the journal Current Biology.

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Albert Min-Shan Ko et al. 2018. Mitochondrial genome of a 22,000-year-old giant panda from southern China reveals a new panda lineage. Current Biology 28 (12): R693-R694; doi: 10.1016/j.cub.2018.05.008