TY - JOUR

T1 - Population genomics of the critically endangered kākāpō

AU - Dussex, Nicolas

AU - van der Valk, Tom

AU - Morales, Hernán E.

AU - Wheat, Christopher W.

AU - Díez-del-Molino, David

AU - von Seth, Johanna

AU - Foster, Yasmin

AU - Kutschera, Verena E.

AU - Guschanski, Katerina

AU - Rhie, Arang

AU - Phillippy, Adam M.

AU - Korlach, Jonas

AU - Howe, Kerstin

AU - Chow, William

AU - Pelan, Sarah

AU - Mendes Damas, Joanna D.

AU - Lewin, Harris A.

AU - Hastie, Alex R.

AU - Formenti, Giulio

AU - Fedrigo, Olivier

AU - Guhlin, Joseph

AU - Harrop, Thomas W. R.

AU - Le Lec, Marissa F.

AU - Dearden, Peter K.

AU - Haggerty, Leanne

AU - Martin, Fergal J.

AU - Kodali, Vamsi

AU - Thibaud-Nissen, Françoise

AU - Iorns, David

AU - Knapp, Michael

AU - Gemmell, Neil J.

AU - Robertson, Fiona

AU - Moorhouse, Ron

AU - Digby, Andrew

AU - Eason, Daryl

AU - Vercoe, Deidre

AU - Howard, Jason

AU - Jarvis, Erich D.

AU - Robertson, Bruce C.

AU - Dalén, Love

PY - 2021

Y1 - 2021

N2 - 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.

AB - 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.

U2 - 10.1016/j.xgen.2021.100002

DO - 10.1016/j.xgen.2021.100002

M3 - Journal article

VL - 1

JO - Cell Genomics

JF - Cell Genomics

SN - 2666-979x

IS - 1

M1 - 100002

ER -