Palaeogenomics

At the Pleistocene Genomics Lab, we investigate the bones of mammals that are thousands of years old. The data we obtain from them provides an “evolutionary time machine”, enabling us to directly study genetic processes that occurred in the past, even in extinct species and populations.

Cave bears

One group on animals that particularly interests us are cave bears (Ursus spelaeus complex). Cave bears are giant extinct bears that roamed parts of Europe and Asia during the Pleistocene. Although cave bears went extinct at the end of the Pleistocene, around 25,00 years ago, their bones can still be found in the caves they used for winter hibernation. Working with Prof. Michi Hofreiter’s Group, we sequenced the nuclear genomes four different cave bears to learn more about their evolutionary history (see Barlow et al. 2018). This palaeogenomic data allowed us to reconstruct the evolutionary relationships among different types of cave bear with very high confidence, overturning previous ideas based on mitochondrial DNA.

Cave bears went extinct around 25,000 years ago. Huge accumulations of their bones can still be found inside their former hibernation caves (left). From these bones, we sequenced their genomes to investigate the evolutionary relationships among cave bears, and their relatives brown bears and polar bears. See Barlow et al. 2018.

We also found a significant genomic signal of past hybridisation between cave bears and brown bears (Ursus arctos). So although cave bears and brown bears diverged more than a million years ago, they were still able to interbreed and produce fertile offspring. We then developed a novel test of directional admixture to show that cave bear DNA was transferred into the brown bear genepool, where it still survives today.

We found that modern brown bears (top right) carry a proportion of extinct cave bear (bottom right) DNA in their genomes as a result of past admixture. On the left is the estimated proportion of cave bear DNA in the genomes of eight different brown bears. See Barlow et al. 2018

Ancient giant panda

Another palaeogenomic study published this year investigated ancient giant pandas (Ailuropoda melanoleuca) from Jiangdongshan in southwestern China (see Sheng et al. 2019). This project was carried out with Prof. Michi Hofreiter’s Group in Potsdam, in collaboration with Prof. Gui-Lian Sheng in Wuhan, China. We investigated a ~5,000 year old giant panda bone recovered from a sinkhole in Jiangdongshan. This bone had accumulated very high levels of contaminating microbial DNA during the thousands of years it lay in the sinkhole. We had previously shown that, for a different panda bone, this contamination could be reduced by treating the sample bone powder with bleach solution (see Basler et al. 2017). By applying this method, we were able to sequence the genome of the ~5,000 year old giant panda individual.

Skeleton of the 5,000 year old panda we used for genome sequencing (photo from Jablonski et al. 2012. Historical Biology 24: 527-536). This animal fell into a sinkhole in Jiangdongshan, southwestern China. It lived hundreds of kilometres away from the nearest modern panda population (right). The femur at the bottom left of the map is the one we used for genome analysis. See Sheng et al. 2019.

Analysis of the panda palaeogenome showed that it was very distantly related to the genomes of modern pandas. This indicated that the Jingdongshang animals represented a distinct and divergent population that went extinct around the Middle Holocene. This shows that modern pandas have retained a very small fraction of the total genetic diversity present in their recent evolutionary history, due to the extinction of genetically distinct and divergent populations like the one occurring in Jiangdongshang.

PCA of ancient and modern panda genomes showed that the Jiangdongshang population was distinct from any living population of giant pandas See Sheng et al. 2019.
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