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Genome Resequencing Study Reveals Giant Panda Population History

NEW YORK (GenomeWeb News) – A giant panda genome re-sequencing study published online yesterday in Nature Genetics is offering new information on both the history and current state of panda populations, revealing three geographically-related genetic clusters within existing wild panda populations in China.

By doing low-coverage genome sequencing on 34 giant pandas from different sites in central China, researchers from the Chinese Academy of Sciences, BGI-Shenzhen and other centers in China and Denmark got a peek at historical giant panda population expansions, bottlenecks, and population divergence events.

Within present-day panda populations, meanwhile, their analysis points to genetic clustering amongst giant pandas from each of the three regions where pandas were sampled — representing more recent divergence events that appear to have been fueled, in part, by human activity such as deforestation.

"[I]ntegration of genomic and population genomics approaches provided a continuous outline of the history of the panda population," senior author Fuwen Wei, an animal ecology and conservation biology researcher with the Chinese Academy of Sciences, and colleagues wrote, "and demonstrated that recent anthropogenic disturbances are likely a major reason for the panda's current endangered status."

The giant panda is the last existing species in a panda lineage that stretches back millions of years, the study's authors explained. And fewer than 2,000 of the animals are estimated to comprise the remaining wild giant panda population, found in a handful of mountain ranges in China.

For the current study, researchers sampled 34 giant pandas from six sites in the central China region. These included Qinling, or QIN, pandas from of the Qinling Mountains in the northeastern part of central China; Minshan, or MIN, pandas sampled in the Minshan Mountains to the west; and, finally, pandas from Qionglai-Daxiangling-Xiaoxiangling-Liangshan, or QXL, populations living in an area to the southwest that encompasses the Qionglai, Daxiangling, Xiaoxiangling, and Liangshan Mountains.

Using Illumina's HiSeq 2000, the team sequenced each of the giant panda genomes to a depth of 4.7-fold apiece across 91.5 percent of the 2.25 billion base panda genome, on average.

When they compared these sequences to a giant panda reference genome — first reported in an online Nature paper by a BGI-led team in 2009 — the investigators identified more than 13 million SNPs, either directly or through imputation.

In the past, study authors noted, genetic clustering has been described for giant pandas from the Qinling region.

Indeed, the new analysis supports the presence of genetic clustering in the QIN pandas, which appear to have diverged from non-QIN pandas some 300,000 years ago. But the investigators saw distinct genetic clusters for the MIN and QXL pandas as well: those groups appear to have diverged from one another far more recently, around 2,800 years ago.

Within pandas from the QXL group, the analysis indicated that there are also two sub-populations: one representing giant pandas from the Xiaoxiangling area and a parts of the Qionglai group and another representing the Daxiangling and Liangshan pandas, along with some from Qionglai.

Humans may have contributed to some of the more recent divergence events, researchers noted. For instance, they explained, the timing of the MIN-QXL panda split seems to coincide with a time when ancient human Shu populations settled along a river that separates the panda populations, building a road that may have widened this divide and cutting down some of the animals' forest habitat.

Likewise, deforestation coupled with the exploitation of panda populations for entertainment, sacrifice, and other purposes may have contributed to recent declines in panda populations, the team speculated, particularly within the QIN region.

The new data also provided an opportunity for researchers to look back further at population expansions and bottlenecks — as well as genetic divergence and adaptation events — stretching back millions of years in the panda lineage.

For instance, they noticed a spurt in panda population growth roughly a million years ago, after pygmy pandas adapted the ability to digest bamboo around three million years back.

Other jumps and dips in panda population sizes seemed to coincide with climate-related events, the team noted, including multiple glaciation periods in China over the past 500,000 to 800,000 years.

Finally, while the genetic diversity within the three existing panda populations appears to be quite high, the team noted that results of the study suggest it will likely be important from a conservation standpoint to consider panda's genetic adaptations to specific habitats.

"For such small populations, translocations of wild-caught individuals or release of captive-bred individuals might be a useful means for genetic rescue by re-establishing gene flow," Wei and co-authors wrote.

"However, our data indicate that it will be important to monitor the evidence for selection and local adaptation in these fragmented panda populations," they added, "as reintroduction candidates ill-suited to a particular environment will be unlikely to promote the development of a robust population."

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