1 Genome Research and Molecular Bio Medicine, Department of Biology, Faculty of Science, Københavns Universitet2 Chinese Academy of Sciences3 BGI-Shenzhen4 China Wildlife Conservation Society5 China Conservation and Research Center for the Giant Panda6 Chengdu Research Base of Giant Panda Breeding7 Shaanxi Wild Animal Rescue and Research Center8 Beijing Zoo9 Department of Biology, Faculty of Science, Københavns Universitet10 Department of Biology, Faculty of Science, Københavns Universitet
The panda lineage dates back to the late Miocene and ultimately leads to only one extant species, the giant panda (Ailuropoda melanoleuca). Although global climate change and anthropogenic disturbances are recognized to shape animal population demography their contribution to panda population dynamics remains largely unknown. We sequenced the whole genomes of 34 pandas at an average 4.7-fold coverage and used this data set together with the previously deep-sequenced panda genome to reconstruct a continuous demographic history of pandas from their origin to the present. We identify two population expansions, two bottlenecks and two divergences. Evidence indicated that, whereas global changes in climate were the primary drivers of population fluctuation for millions of years, human activities likely underlie recent population divergence and serious decline. We identified three distinct panda populations that show genetic adaptation to their environments. However, in all three populations, anthropogenic activities have negatively affected pandas for 3,000 years.