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Population genomics of the critically endangered kākāpō
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 o...
Autores principales: | , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Elsevier
2021
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Materias: | |
Acceso en línea: | 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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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. |
format | Online Article Text |
id | pubmed-9903828 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2021 |
publisher | Elsevier |
record_format | MEDLINE/PubMed |
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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