title: Kiwi genome provides insights into evolution of a nocturnal lifestyle.
abstract: BACKGROUND
  Kiwi, comprising five species from the genus Apteryx, are endangered, ground-dwelling bird species endemic to New Zealand. They are the smallest and only nocturnal representatives of the ratites. The timing of kiwi adaptation to a nocturnal niche and the genomic innovations, which shaped sensory systems and morphology to allow this adaptation, are not yet fully understood.
  
  
  RESULTS
  We sequenced and assembled the brown kiwi genome to 150-fold coverage and annotated the genome using kiwi transcript data and non-redundant protein information from multiple bird species. We identified evolutionary sequence changes that underlie adaptation to nocturnality and estimated the onset time of these adaptations. Several opsin genes involved in color vision are inactivated in the kiwi. We date this inactivation to the Oligocene epoch, likely after the arrival of the ancestor of modern kiwi in New Zealand. Genome comparisons between kiwi and representatives of ratites, Galloanserae, and Neoaves, including nocturnal and song birds, show diversification of kiwi's odorant receptors repertoire, which may reflect an increased reliance on olfaction rather than sight during foraging. Further, there is an enrichment of genes influencing mitochondrial function and energy expenditure among genes that are rapidly evolving specifically on the kiwi branch, which may also be linked to its nocturnal lifestyle.
  
  
  CONCLUSIONS
  The genomic changes in kiwi vision and olfaction are consistent with changes that are hypothesized to occur during adaptation to nocturnal lifestyle in mammals. The kiwi genome provides a valuable genomic resource for future genome-wide comparative analyses to other extinct and extant diurnal ratites.
authors.affiliation: Institute of Biochemistry, Medical Faculty, University of Leipzig, Johannisallee 30, Leipzig, 04103, Germany. diana_leduc@eva.mpg.de.|Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, 04103, Germany. diana_leduc@eva.mpg.de.
authors.forename: Diana
authors.initials: D
authors.lastname: Le Duc
authors.affiliation: Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, 04103, Germany. gabriel_renaud@eva.mpg.de.
authors.forename: Gabriel
authors.initials: G
authors.lastname: Renaud
authors.affiliation: Department of Neuroscience, Unit of Functional Pharmacology, Uppsala University, Box 593, Husargatan 3, Uppsala, 751 24, Sweden. arunkumar.krishnan@neuro.uu.se.
authors.forename: Arunkumar
authors.initials: A
authors.lastname: Krishnan
authors.affiliation: Department of Neuroscience, Unit of Functional Pharmacology, Uppsala University, Box 593, Husargatan 3, Uppsala, 751 24, Sweden. markus.sallman-almen@neuro.uu.se.
authors.forename: Markus Sällman
authors.initials: MS
authors.lastname: Almén
authors.affiliation: Griffith School of Environment and School of Biomolecular and Physical Sciences, Griffith University, Nathan, Queensland, 4111, Australia. l.huynen@griffith.edu.au.
authors.forename: Leon
authors.initials: L
authors.lastname: Huynen
authors.affiliation: Department of Computer Science, and Interdisciplinary Center for Bioinformatics, University of Leipzig, Leipzig, 04103, Germany. sonja@bioinf.uni-leipzig.de.
authors.forename: Sonja J
authors.initials: SJ
authors.lastname: Prohaska
authors.affiliation: Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, 04103, Germany. matthias_ongyerth@eva.mpg.de.
authors.forename: Matthias
authors.initials: M
authors.lastname: Ongyerth
authors.affiliation: Department of Genetics and Evolutionary Biology, University of São Paulo, São Paulo, SP, 05508-090, Brazil. barbarabitarello@gmail.com.
authors.forename: Bárbara D
authors.initials: BD
authors.lastname: Bitarello
authors.affiliation: Department of Neuroscience, Unit of Functional Pharmacology, Uppsala University, Box 593, Husargatan 3, Uppsala, 751 24, Sweden. helgi.schioth@neuro.uu.se.
authors.forename: Helgi B
authors.initials: HB
authors.lastname: Schiöth
authors.affiliation: Adaptive Evolutionary Genomics, Institute for Biochemistry and Biology, University Potsdam, Potsdam, 14469, Germany. michi@palaeo.eu.
authors.forename: Michael
authors.initials: M
authors.lastname: Hofreiter
authors.affiliation: Department of Computer Science, and Interdisciplinary Center for Bioinformatics, University of Leipzig, Leipzig, 04103, Germany. studla@bioinf.uni-leipzig.de.
authors.forename: Peter F
authors.initials: PF
authors.lastname: Stadler
authors.affiliation: Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, 04103, Germany. pruefer@eva.mpg.de.
authors.forename: Kay
authors.initials: K
authors.lastname: Prüfer
authors.affiliation: Griffith School of Environment and School of Biomolecular and Physical Sciences, Griffith University, Nathan, Queensland, 4111, Australia. d.lambert@griffith.edu.au.
authors.forename: David
authors.initials: D
authors.lastname: Lambert
authors.affiliation: Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, 04103, Germany. kelso@eva.mpg.de.
authors.forename: Janet
authors.initials: J
authors.lastname: Kelso
authors.affiliation: Institute of Biochemistry, Medical Faculty, University of Leipzig, Johannisallee 30, Leipzig, 04103, Germany. schoberg@medizin.uni-leipzig.de.
authors.forename: Torsten
authors.initials: T
authors.lastname: Schöneberg
mesh_terms: D000220:Adaptation, Biological / Q000235:genetics*; D000818:Animals; D003624:Darkness; D019143:Evolution, Molecular; D016678:Genome; D023281:Genomics; D058977:Molecular Sequence Annotation; D008969:Molecular Sequence Data; D005810:Multigene Family; D046108:Palaeognathae / Q000033:anatomy & histology / Q000235:genetics*; D012641:Selection, Genetic; D012903:Smell / Q000235:genetics; D014785:Vision, Ocular / Q000235:genetics