Cell Genomics (Oct 2021)
Population genomics of the critically endangered kākāpō
- Nicolas Dussex,
- Tom van der Valk,
- Hernán E. Morales,
- Christopher W. Wheat,
- David Díez-del-Molino,
- Johanna von Seth,
- Yasmin Foster,
- Verena E. Kutschera,
- Katerina Guschanski,
- Arang Rhie,
- Adam M. Phillippy,
- Jonas Korlach,
- Kerstin Howe,
- William Chow,
- Sarah Pelan,
- Joanna D. Mendes Damas,
- Harris A. Lewin,
- Alex R. Hastie,
- Giulio Formenti,
- Olivier Fedrigo,
- Joseph Guhlin,
- Thomas W.R. Harrop,
- Marissa F. Le Lec,
- Peter K. Dearden,
- Leanne Haggerty,
- Fergal J. Martin,
- Vamsi Kodali,
- Françoise Thibaud-Nissen,
- David Iorns,
- Michael Knapp,
- Neil J. Gemmell,
- Fiona Robertson,
- Ron Moorhouse,
- Andrew Digby,
- Daryl Eason,
- Deidre Vercoe,
- Jason Howard,
- Erich D. Jarvis,
- Bruce C. Robertson,
- Love Dalén
Affiliations
- Nicolas Dussex
- Centre for Palaeogenetics, Svante Arrhenius väg 20C, 10691 Stockholm, Sweden; Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Box 50007, 10405 Stockholm, Sweden; Department of Zoology, Stockholm University, 10691 Stockholm, Sweden; Department of Anatomy, University of Otago, PO Box 913, Dunedin 9016, New Zealand; Corresponding author
- Tom van der Valk
- Centre for Palaeogenetics, Svante Arrhenius väg 20C, 10691 Stockholm, Sweden; Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Box 50007, 10405 Stockholm, Sweden
- Hernán E. Morales
- Section for Evolutionary Genomics, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
- Christopher W. Wheat
- Department of Zoology, Stockholm University, 10691 Stockholm, Sweden
- David Díez-del-Molino
- Centre for Palaeogenetics, Svante Arrhenius väg 20C, 10691 Stockholm, Sweden; Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Box 50007, 10405 Stockholm, Sweden
- Johanna von Seth
- Centre for Palaeogenetics, Svante Arrhenius väg 20C, 10691 Stockholm, Sweden; Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Box 50007, 10405 Stockholm, Sweden; Department of Zoology, Stockholm University, 10691 Stockholm, Sweden
- Yasmin Foster
- Department of Zoology, University of Otago, PO Box 56, Dunedin 9054, New Zealand
- Verena E. Kutschera
- Department of Biochemistry and Biophysics, National Bioinformatics Infrastructure Sweden, Science for Life Laboratory, Stockholm University, Box 1031, 17121 Solna, Sweden
- Katerina Guschanski
- Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, UK; Department of Ecology and Genetics, Animal Ecology, Uppsala University, 75236 Uppsala, Sweden
- Arang Rhie
- Genome Informatics Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
- Adam M. Phillippy
- Genome Informatics Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
- Jonas Korlach
- Pacific Biosciences, 1305 O’Brien Drive, Menlo Park, CA 94025, USA
- Kerstin Howe
- Wellcome Sanger Institute, Wellcome Trust Genome Campus, Hinxton CB10 1SA, UK
- William Chow
- Wellcome Sanger Institute, Wellcome Trust Genome Campus, Hinxton CB10 1SA, UK
- Sarah Pelan
- Wellcome Sanger Institute, Wellcome Trust Genome Campus, Hinxton CB10 1SA, UK
- Joanna D. Mendes Damas
- Department of Evolution and Ecology and the UC Davis Genome Center, 4321 Genome and Biomedical Sciences Facility, University of California Davis, Davis, CA 95616, USA
- Harris A. Lewin
- Department of Evolution and Ecology and the UC Davis Genome Center, 4321 Genome and Biomedical Sciences Facility, University of California Davis, Davis, CA 95616, USA
- Alex R. Hastie
- Bionano Genomics, 9540 Towne Centre Drive, San Diego, CA 92121, USA
- Giulio Formenti
- Vertebrate Genome Laboratory, The Rockefeller University, New York, NY 10065, USA; Laboratory of Neurogenetics of Language, Box 54, The Rockefeller University, New York, NY 10065, USA; Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA
- Olivier Fedrigo
- Vertebrate Genome Laboratory, The Rockefeller University, New York, NY 10065, USA
- Joseph Guhlin
- Genomics Aotearoa and Laboratory for Evolution and Development, Department of Biochemistry, University of Otago, PO Box 56, Dunedin 9016, New Zealand
- Thomas W.R. Harrop
- Genomics Aotearoa and Laboratory for Evolution and Development, Department of Biochemistry, University of Otago, PO Box 56, Dunedin 9016, New Zealand
- Marissa F. Le Lec
- Genomics Aotearoa and Laboratory for Evolution and Development, Department of Biochemistry, University of Otago, PO Box 56, Dunedin 9016, New Zealand
- Peter K. Dearden
- Genomics Aotearoa and Laboratory for Evolution and Development, Department of Biochemistry, University of Otago, PO Box 56, Dunedin 9016, New Zealand
- Leanne Haggerty
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
- Fergal J. Martin
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
- Vamsi Kodali
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
- Françoise Thibaud-Nissen
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
- David Iorns
- The Genetic Rescue Foundation, Wellington, New Zealand
- Michael Knapp
- Department of Anatomy, University of Otago, PO Box 913, Dunedin 9016, New Zealand
- Neil J. Gemmell
- Department of Anatomy, University of Otago, PO Box 913, Dunedin 9016, New Zealand
- Fiona Robertson
- Department of Zoology, University of Otago, PO Box 56, Dunedin 9054, New Zealand
- Ron Moorhouse
- Kākāpō Recovery, Department of Conservation, PO Box 743, Invercargill 9840, New Zealand
- Andrew Digby
- Kākāpō Recovery, Department of Conservation, PO Box 743, Invercargill 9840, New Zealand
- Daryl Eason
- Kākāpō Recovery, Department of Conservation, PO Box 743, Invercargill 9840, New Zealand
- Deidre Vercoe
- Kākāpō Recovery, Department of Conservation, PO Box 743, Invercargill 9840, New Zealand
- Jason Howard
- Vertebrate Genome Laboratory, The Rockefeller University, New York, NY 10065, USA; BioSkryb Genomics, 701 W Main Street, Suite 200, Durham, NC 27701, USA
- Erich D. Jarvis
- Vertebrate Genome Laboratory, The Rockefeller University, New York, NY 10065, USA; Laboratory of Neurogenetics of Language, Box 54, The Rockefeller University, New York, NY 10065, USA; Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA; Corresponding author
- Bruce C. Robertson
- Department of Zoology, University of Otago, PO Box 56, Dunedin 9054, New Zealand; Corresponding author
- Love Dalén
- Centre for Palaeogenetics, Svante Arrhenius väg 20C, 10691 Stockholm, Sweden; Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Box 50007, 10405 Stockholm, Sweden; Department of Zoology, Stockholm University, 10691 Stockholm, Sweden; Corresponding author
- Journal volume & issue
-
Vol. 1,
no. 1
p. 100002
Abstract
Summary: The kākāpō is a flightless parrot endemic to New Zealand. Once common in the archipelago, only 201 individuals remain today, most of them descending from an isolated island population. We report the first genome-wide analyses of the species, including a high-quality genome assembly for kākāpō, one of the first chromosome-level reference genomes sequenced by the Vertebrate Genomes Project (VGP). We also sequenced and analyzed 35 modern genomes from the sole surviving island population and 14 genomes from the extinct mainland population. While theory suggests that such a small population is likely to have accumulated deleterious mutations through genetic drift, our analyses on the impact of the long-term small population size in kākāpō indicate that present-day island kākāpō have a reduced number of harmful mutations compared to mainland individuals. We hypothesize that this reduced mutational load is due to the island population having been subjected to a combination of genetic drift and purging of deleterious mutations, through increased inbreeding and purifying selection, since its isolation from the mainland ∼10,000 years ago. Our results provide evidence that small populations can survive even when isolated for hundreds of generations. This work provides key insights into kākāpō breeding and recovery and more generally into the application of genetic tools in conservation efforts for endangered species.
