title: Whole-genome sequencing of giant pandas provides insights into demographic history and local adaptation.
abstract: 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.
authors.affiliation: Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China.
authors.forename: Shancen
authors.initials: S
authors.lastname: Zhao
authors.forename: Pingping
authors.initials: P
authors.lastname: Zheng
authors.forename: Shanshan
authors.initials: S
authors.lastname: Dong
authors.forename: Xiangjiang
authors.initials: X
authors.lastname: Zhan
authors.forename: Qi
authors.initials: Q
authors.lastname: Wu
authors.forename: Xiaosen
authors.initials: X
authors.lastname: Guo
authors.forename: Yibo
authors.initials: Y
authors.lastname: Hu
authors.forename: Weiming
authors.initials: W
authors.lastname: He
authors.forename: Shanning
authors.initials: S
authors.lastname: Zhang
authors.forename: Wei
authors.initials: W
authors.lastname: Fan
authors.forename: Lifeng
authors.initials: L
authors.lastname: Zhu
authors.forename: Dong
authors.initials: D
authors.lastname: Li
authors.forename: Xuemei
authors.initials: X
authors.lastname: Zhang
authors.forename: Quan
authors.initials: Q
authors.lastname: Chen
authors.forename: Hemin
authors.initials: H
authors.lastname: Zhang
authors.forename: Zhihe
authors.initials: Z
authors.lastname: Zhang
authors.forename: Xuelin
authors.initials: X
authors.lastname: Jin
authors.forename: Jinguo
authors.initials: J
authors.lastname: Zhang
authors.forename: Huanming
authors.initials: H
authors.lastname: Yang
authors.forename: Jian
authors.initials: J
authors.lastname: Wang
authors.forename: Jun
authors.initials: J
authors.lastname: Wang
authors.forename: Fuwen
authors.initials: F
authors.lastname: Wei
mesh_terms: D000220:Adaptation, Biological / Q000235:genetics*; D000818:Animals; D005075:Biological Evolution; D005828:Genetics, Population; D016678:Genome; D055106:Genome-Wide Association Study; D005843:Geography; D008957:Models, Genetic; D058977:Molecular Sequence Annotation; D020641:Polymorphism, Single Nucleotide; D001503:Ursidae / Q000235:genetics*