title: Two Antarctic penguin genomes reveal insights into their evolutionary history and molecular changes related to the Antarctic environment.
abstract: BACKGROUND
  Penguins are flightless aquatic birds widely distributed in the Southern Hemisphere. The distinctive morphological and physiological features of penguins allow them to live an aquatic life, and some of them have successfully adapted to the hostile environments in Antarctica. To study the phylogenetic and population history of penguins and the molecular basis of their adaptations to Antarctica, we sequenced the genomes of the two Antarctic dwelling penguin species, the Adélie penguin [Pygoscelis adeliae] and emperor penguin [Aptenodytes forsteri].
  
  
  RESULTS
  Phylogenetic dating suggests that early penguins arose ~60 million years ago, coinciding with a period of global warming. Analysis of effective population sizes reveals that the two penguin species experienced population expansions from ~1 million years ago to ~100 thousand years ago, but responded differently to the climatic cooling of the last glacial period. Comparative genomic analyses with other available avian genomes identified molecular changes in genes related to epidermal structure, phototransduction, lipid metabolism, and forelimb morphology.
  
  
  CONCLUSIONS
  Our sequencing and initial analyses of the first two penguin genomes provide insights into the timing of penguin origin, fluctuations in effective population sizes of the two penguin species over the past 10 million years, and the potential associations between these biological patterns and global climate change. The molecular changes compared with other avian genomes reflect both shared and diverse adaptations of the two penguin species to the Antarctic environment.
authors: China National GeneBank, BGI-Shenzhen, Shenzhen, 518083 China ; Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen, Denmark.
authors: Cai
authors: C
authors: Li
authors: China National GeneBank, BGI-Shenzhen, Shenzhen, 518083 China.
authors: Yong
authors: Y
authors: Zhang
authors: China National GeneBank, BGI-Shenzhen, Shenzhen, 518083 China.
authors: Jianwen
authors: J
authors: Li
authors: MRC Functional Genomics Unit, Department of Physiology, Anatomy and Genetics, University of Oxford, South Parks Road, Oxford, OX1 3QX UK.
authors: Lesheng
authors: L
authors: Kong
authors: China National GeneBank, BGI-Shenzhen, Shenzhen, 518083 China.
authors: Haofu
authors: H
authors: Hu
authors: China National GeneBank, BGI-Shenzhen, Shenzhen, 518083 China.
authors: Hailin
authors: H
authors: Pan
authors: China National GeneBank, BGI-Shenzhen, Shenzhen, 518083 China.
authors: Luohao
authors: L
authors: Xu
authors: China National GeneBank, BGI-Shenzhen, Shenzhen, 518083 China.
authors: Yuan
authors: Y
authors: Deng
authors: China National GeneBank, BGI-Shenzhen, Shenzhen, 518083 China ; Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen, Denmark.
authors: Qiye
authors: Q
authors: Li
authors: China National GeneBank, BGI-Shenzhen, Shenzhen, 518083 China.
authors: Lijun
authors: L
authors: Jin
authors: China National GeneBank, BGI-Shenzhen, Shenzhen, 518083 China.
authors: Hao
authors: H
authors: Yu
authors: China National GeneBank, BGI-Shenzhen, Shenzhen, 518083 China.
authors: Yan
authors: Y
authors: Chen
authors: China National GeneBank, BGI-Shenzhen, Shenzhen, 518083 China.
authors: Binghang
authors: B
authors: Liu
authors: China National GeneBank, BGI-Shenzhen, Shenzhen, 518083 China.
authors: Linfeng
authors: L
authors: Yang
authors: China National GeneBank, BGI-Shenzhen, Shenzhen, 518083 China.
authors: Shiping
authors: S
authors: Liu
authors: China National GeneBank, BGI-Shenzhen, Shenzhen, 518083 China.
authors: Yan
authors: Y
authors: Zhang
authors: China National GeneBank, BGI-Shenzhen, Shenzhen, 518083 China.
authors: Yongshan
authors: Y
authors: Lang
authors: China National GeneBank, BGI-Shenzhen, Shenzhen, 518083 China.
authors: Jinquan
authors: J
authors: Xia
authors: China National GeneBank, BGI-Shenzhen, Shenzhen, 518083 China.
authors: Weiming
authors: W
authors: He
authors: China National GeneBank, BGI-Shenzhen, Shenzhen, 518083 China.
authors: Qiong
authors: Q
authors: Shi
authors: Environmental Futures Centre, Griffith University, Nathan, QLD 4111 Australia.
authors: Sankar
authors: S
authors: Subramanian
authors: Allan Wilson Centre for Molecular Ecology and Evolution, School of Biological Sciences, University of Auckland, Private Bag 92019, Auckland, New Zealand.
authors: Craig D
authors: CD
authors: Millar
authors: MRC Functional Genomics Unit, Department of Physiology, Anatomy and Genetics, University of Oxford, South Parks Road, Oxford, OX1 3QX UK.
authors: Stephen
authors: S
authors: Meader
authors: MRC Functional Genomics Unit, Department of Physiology, Anatomy and Genetics, University of Oxford, South Parks Road, Oxford, OX1 3QX UK.
authors: Chris M
authors: CM
authors: Rands
authors: MRC Functional Genomics Unit, Department of Physiology, Anatomy and Genetics, University of Oxford, South Parks Road, Oxford, OX1 3QX UK ; Department of Biology, University of Texas at Arlington, Arlington, TX 76019 USA.
authors: Matthew K
authors: MK
authors: Fujita
authors: Department of Biological Sciences, University of South Carolina, Columbia, SC USA.
authors: Matthew J
authors: MJ
authors: Greenwold
authors: Department of Biochemistry and Molecular Genetics, School of Medicine, University of Colorado, Aurora, CO 80045 USA ; Biology Department, University of Texas Arlington, Arlington, TX 76016 USA.
authors: Todd A
authors: TA
authors: Castoe
authors: Department of Biochemistry and Molecular Genetics, School of Medicine, University of Colorado, Aurora, CO 80045 USA.
authors: David D
authors: DD
authors: Pollock
authors: Research Centre of Learning Sciences, Southeast University, Nanjing, 210096 China.
authors: Wanjun
authors: W
authors: Gu
authors: Department of Evolutionary Biology, Uppsala University, Norbyvagen 18D, SE-752 36 Uppsala, Sweden ; Bioinformatics Research Centre (BiRC), Aarhus University, C.F.Møllers Allé 8, 8000 Aarhus C, Denmark.
authors: Kiwoong
authors: K
authors: Nam
authors: Department of Evolutionary Biology, Uppsala University, Norbyvagen 18D, SE-752 36 Uppsala, Sweden.
authors: Hans
authors: H
authors: Ellegren
authors: School of Biological Sciences, University of Sydney, Sydney, NSW 2006 Australia.
authors: Simon Yw
authors: SY
authors: Ho
authors: Department of Genomics and Genetics, The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush Campus Midlothian, Edinburgh, EH25 9RG UK.
authors: David W
authors: DW
authors: Burt
authors: MRC Functional Genomics Unit, Department of Physiology, Anatomy and Genetics, University of Oxford, South Parks Road, Oxford, OX1 3QX UK.
authors: Chris P
authors: CP
authors: Ponting
authors: Department of Neurobiology, Howard Hughes Medical Institute, Duke University Medical Center, Durham, NC27710 USA.
authors: Erich D
authors: ED
authors: Jarvis
authors: Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen, Denmark ; Trace and Environmental DNA Laboratory, Department of Environment and Agriculture, Curtin University, Perth, WA 6102 Australia.
authors: M Thomas P
authors: MT
authors: Gilbert
authors: China National GeneBank, BGI-Shenzhen, Shenzhen, 518083 China ; Princess Al Jawhara Center of Excellence in the Research of Hereditary Disorders, King Abdulaziz University, Jeddah, 21589 Saudi Arabia.
authors: Huanming
authors: H
authors: Yang
authors: China National GeneBank, BGI-Shenzhen, Shenzhen, 518083 China.
authors: Jian
authors: J
authors: Wang
authors: Environmental Futures Centre, Griffith University, Nathan, QLD 4111 Australia.
authors: David M
authors: DM
authors: Lambert
authors: China National GeneBank, BGI-Shenzhen, Shenzhen, 518083 China ; Princess Al Jawhara Center of Excellence in the Research of Hereditary Disorders, King Abdulaziz University, Jeddah, 21589 Saudi Arabia ; Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, 2200 Copenhagen, Denmark ; Macau University of Science and Technology, Avenida Wai long, Taipa, Macau, 999078 China ; Department of Medicine, University of Hong Kong, Hong Kong, Hong Kong.
authors: Jun
authors: J
authors: Wang
authors: China National GeneBank, BGI-Shenzhen, Shenzhen, 518083 China ; Centre for Social Evolution, Department of Biology, University of Copenhagen, Universitetsparken 15, Copenhagen, DK-2100 Denmark.
authors: Guojie
authors: G
authors: Zhang
keywords: Adaptation; Antarctica; Avian genomics; Evolution; Penguins