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author Dussex, Nicolas
van der Valk, Tom
Morales, Hernán E.
Wheat, Christopher W.
Díez-del-Molino, David
von Seth, Johanna
Foster, Yasmin
Kutschera, Verena E.
Guschanski, Katerina
Rhie, Arang
Phillippy, Adam M.
Korlach, Jonas
Howe, Kerstin
Chow, William
Pelan, Sarah
Mendes Damas, Joanna D.
Lewin, Harris A.
Hastie, Alex R.
Formenti, Giulio
Fedrigo, Olivier
Guhlin, Joseph
Harrop, Thomas W.R.
Le Lec, Marissa F.
Dearden, Peter K.
Haggerty, Leanne
Martin, Fergal J.
Kodali, Vamsi
Thibaud-Nissen, Françoise
Iorns, David
Knapp, Michael
Gemmell, Neil J.
Robertson, Fiona
Moorhouse, Ron
Digby, Andrew
Eason, Daryl
Vercoe, Deidre
Howard, Jason
Jarvis, Erich D.
Robertson, Bruce C.
Dalén, Love
author_facet Dussex, Nicolas
van der Valk, Tom
Morales, Hernán E.
Wheat, Christopher W.
Díez-del-Molino, David
von Seth, Johanna
Foster, Yasmin
Kutschera, Verena E.
Guschanski, Katerina
Rhie, Arang
Phillippy, Adam M.
Korlach, Jonas
Howe, Kerstin
Chow, William
Pelan, Sarah
Mendes Damas, Joanna D.
Lewin, Harris A.
Hastie, Alex R.
Formenti, Giulio
Fedrigo, Olivier
Guhlin, Joseph
Harrop, Thomas W.R.
Le Lec, Marissa F.
Dearden, Peter K.
Haggerty, Leanne
Martin, Fergal J.
Kodali, Vamsi
Thibaud-Nissen, Françoise
Iorns, David
Knapp, Michael
Gemmell, Neil J.
Robertson, Fiona
Moorhouse, Ron
Digby, Andrew
Eason, Daryl
Vercoe, Deidre
Howard, Jason
Jarvis, Erich D.
Robertson, Bruce C.
Dalén, Love
author_sort Dussex, Nicolas
collection PubMed
description 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.
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spelling pubmed-99038282023-02-10 Population genomics of the critically endangered kākāpō Dussex, Nicolas van der Valk, Tom Morales, Hernán E. Wheat, Christopher W. Díez-del-Molino, David von Seth, Johanna Foster, Yasmin Kutschera, Verena E. Guschanski, Katerina Rhie, Arang Phillippy, Adam M. Korlach, Jonas Howe, Kerstin Chow, William Pelan, Sarah Mendes Damas, Joanna D. Lewin, Harris A. Hastie, Alex R. Formenti, Giulio Fedrigo, Olivier Guhlin, Joseph Harrop, Thomas W.R. Le Lec, Marissa F. Dearden, Peter K. Haggerty, Leanne Martin, Fergal J. Kodali, Vamsi Thibaud-Nissen, Françoise Iorns, David Knapp, Michael Gemmell, Neil J. Robertson, Fiona Moorhouse, Ron Digby, Andrew Eason, Daryl Vercoe, Deidre Howard, Jason Jarvis, Erich D. Robertson, Bruce C. Dalén, Love Cell Genom Short Article 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. Elsevier 2021-09-08 /pmc/articles/PMC9903828/ /pubmed/36777713 http://dx.doi.org/10.1016/j.xgen.2021.100002 Text en © 2021 The Author(s) https://creativecommons.org/licenses/by/4.0/This is an open access article under the CC BY license (http://creativecommons.org/licenses/by/4.0/).
spellingShingle Short Article
Dussex, Nicolas
van der Valk, Tom
Morales, Hernán E.
Wheat, Christopher W.
Díez-del-Molino, David
von Seth, Johanna
Foster, Yasmin
Kutschera, Verena E.
Guschanski, Katerina
Rhie, Arang
Phillippy, Adam M.
Korlach, Jonas
Howe, Kerstin
Chow, William
Pelan, Sarah
Mendes Damas, Joanna D.
Lewin, Harris A.
Hastie, Alex R.
Formenti, Giulio
Fedrigo, Olivier
Guhlin, Joseph
Harrop, Thomas W.R.
Le Lec, Marissa F.
Dearden, Peter K.
Haggerty, Leanne
Martin, Fergal J.
Kodali, Vamsi
Thibaud-Nissen, Françoise
Iorns, David
Knapp, Michael
Gemmell, Neil J.
Robertson, Fiona
Moorhouse, Ron
Digby, Andrew
Eason, Daryl
Vercoe, Deidre
Howard, Jason
Jarvis, Erich D.
Robertson, Bruce C.
Dalén, Love
Population genomics of the critically endangered kākāpō
title Population genomics of the critically endangered kākāpō
title_full Population genomics of the critically endangered kākāpō
title_fullStr Population genomics of the critically endangered kākāpō
title_full_unstemmed Population genomics of the critically endangered kākāpō
title_short Population genomics of the critically endangered kākāpō
title_sort population genomics of the critically endangered kākāpō
topic Short Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9903828/
https://www.ncbi.nlm.nih.gov/pubmed/36777713
http://dx.doi.org/10.1016/j.xgen.2021.100002
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