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Nature Ecology & Evolution (2023)Cite this article 22 Altmetric Metrics details The kākāpō is a critically endangered, intensively managed, long-lived nocturnal parrot endemic to Aotearoa New Zealand.

Nature Ecology & Evolution (2023)Cite this article

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The kākāpō is a critically endangered, intensively managed, long-lived nocturnal parrot endemic to Aotearoa New Zealand. We generated and analysed whole-genome sequence data for nearly all individuals living in early 2018 (169 individuals) to generate a high-quality species-wide genetic variant callset. We leverage extensive long-term metadata to quantify genome-wide diversity of the species over time and present new approaches using probabilistic programming, combined with a phenotype dataset spanning five decades, to disentangle phenotypic variance into environmental and genetic effects while quantifying uncertainty in small populations. We find associations for growth, disease susceptibility, clutch size and egg fertility within genic regions previously shown to influence these traits in other species. Finally, we generate breeding values to predict phenotype and illustrate that active management over the past 45 years has maintained both genome-wide diversity and diversity in breeding values and, hence, evolutionary potential. We provide new pathways for informing future conservation management decisions for kākāpō, including prioritizing individuals for translocation and monitoring individuals with poor growth or high disease risk. Overall, by explicitly addressing the challenge of the small sample size, we provide a template for the inclusion of genomic data that will be transformational for species recovery efforts around the globe.

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Genomic reads, variant data and phenotypic data are taonga of Ngāi Tahu and sensitive for the Department of Conservation. Raw and processed data, such as variant files, are available via application to the Aotearoa Genomic Data Repository https://data.agdr.org.nz/.

Scripts, workflows, Jupyter notebooks and other methodology resources are available at the GitHub repo for this paper: https://github.com/GenomicsAotearoa/Kakapo or at Zenodo103.

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We are grateful to the Kākāpō125+ Project led by the New Zealand Department of Conservation (DOC) in partnership with Te Rūnanga o Ngāi Tahu (TRONT). We acknowledge the incredible long-term support and vision from Ngāi Tahu, DOC staff, including office-based support staff, and the many volunteers, veterinarians and others who have contributed to the conservation of this taonga species. Our thanks to the Genetic Rescue Foundation, University of Otago, New Zealand Genomics Limited, Rockefeller Institute, Duke University, Science Exchange and Experiment.com for the generation and availability of the short-read data used in this study. B.C.R. acknowledges support from the Department of Zoology, University of Otago, for funding sample preparation. We extend many thanks to Genomics Aotearoa for financial support of the project including for J.G., J.W., E.K., N.J.G., T.E.S., A.W.S. and P.K.D. We are very grateful to New Zealand eScience Infrastructure for computational resources and support, especially for assistance with data management, transfer and storage, and development and hosting of the AGDR (https://data.agdr.org.nz/), with particular thanks to Dinindu Senanayake.

These authors jointly supervised this work: Tammy E. Steeves, Anna W. Santure, Peter K. Dearden.

Genomics Aotearoa, Biochemistry Department, School of Biomedical Sciences, University of Otago, Dunedin, Aotearoa New Zealand

Joseph Guhlin, Marissa F. Le Lec & Peter K. Dearden

School of Biological Sciences, University of Canterbury, Christchurch, Aotearoa New Zealand

Jana Wold, Stephanie J. Galla & Tammy E. Steeves

The New Zealand Institute for Plant and Food Research Ltd, Palmerston North, Aotearoa New Zealand

Emily Koot

School of Natural Sciences, Massey University, Palmerston North, Aotearoa New Zealand

David Winter, Patrick J. Biggs & Murray P. Cox

School of Veterinary Science, Massey University, Palmerston North, Aotearoa New Zealand

Patrick J. Biggs

Department of Biological Sciences, Boise State University, Boise, ID, USA

Stephanie J. Galla

Department of Anatomy, School of Biomedical Sciences, University of Otago, Dunedin, Aotearoa New Zealand

Lara Urban & Neil J. Gemmell

Helmholtz Pioneer Campus, Helmholtz Zentrum Muenchen, Neuherberg, Germany

Lara Urban

Helmholtz AI, Helmholtz Zentrum Muenchen, Neuherberg, Germany

Lara Urban

School of Life Sciences, Technical University of Munich, Freising, Germany

Lara Urban

Department of Zoology, University of Otago, Dunedin, Aotearoa New Zealand

Yasmin Foster, Fiona E. Robertson & Bruce C. Robertson

Department of Statistics, University of Auckland, Auckland, Aotearoa New Zealand

Murray P. Cox

Kākāpō Recovery Programme, Department of Conservation, Invercargill, Aotearoa New Zealand

Andrew Digby, Lydia R. Uddstrom, Daryl Eason, Deidre Vercoe, Karen Andrew, Lisa Argilla, Karen Arnold, James Bohan, Liam Bolitho, Nichy Brown, Jo Carpenter, Jodie Crane, Margie Grant, Glen Greaves, Brett Halkett, Rory Hannan, Sam Haultain, Bryony Hitchcock, Leigh Joyce, Sara Larcombe, Jo Ledington, Jinty MacTavish, Phil Marsh, Gilbert Mingam, Freya Moore, Lyndsay Murray, Errol Nye, Jake Osborne, Lou Parker, Chris Phillips, Roy Phillips, Brodie Philp, Tim Raemaekers, Jenny Rickett, Rachel Rouse, Rachael Sagar, Alisha Sherriff, Theo Thompson, Jason Van de Wetering, Nicki van Zyl, Jen Waite & Jim Watts

Rakiura Tītī Islands Administering Body, Invercargill, Aotearoa New Zealand

Tāne Davis

Neurogenetics of Language Lab, The Rockefeller University, New York, NY, USA

Jason T. Howard

Mirxes, Cambridge, MA, USA

Jason T. Howard

The Rockefeller University, New York, NY, USA

Erich D. Jarvis

Howard Hughes Medical Institute, Chevy Chase, MD, USA

Erich D. Jarvis

School of Biological Sciences, University of Auckland, Auckland, Aotearoa New Zealand

Anna W. Santure

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Conceptualization: all authors; methodology: J.G., M.F.L.L., E.K., D.W., P.J.B., S.J.G., A.W.S. and J.W.; software and formal analysis: J.G., M.F.L.L., E.K., D.W., P.J.B., S.J.G. and M.P.C.; validation: L.U., Y.F., D.W., P.J.B. and M.P.C.; investigation, resources and data curation: A.D., L.R.U., D.E., D.V., Kākāpō Recovery Team, L.U., B.C.R., F.E.R., D.W., P.J.B., M.P.C. and T.D.; writing—original draft: J.G.; writing—review and editing: J.G., P.K.D., M.F.L.L., A.W.S., L.U., E.D.J., Y.F., T.E.S., E.K., S.J.G., A.D., L.R.U., J.W. and N.J.G; visualization: J.G., E.K., M.F.L.L. and S.J.G.; supervision: T.E.S., A.W.S. and P.K.D.; project administration: J.G. and P.K.D.; funding acquisition: P.K.D., A.W.S., T.E.S., B.C.R., J.T.H. and E.D.J.

Correspondence to Peter K. Dearden.

The authors declare no competing interests.

Nature Ecology & Evolution thanks Rebecca Taylor, Cock van Oosterhout and the other, anonymous, reviewer(s) for their contribution to the peer review of this work. Peer reviewer reports are available.

Publisher’s note Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

Violin plot of all calculated Breeding Values for each trait, with individual breeding values represented as points on the left of the distributions. Green points and distributions represent all birds exclusive of Richard Henry and his lineage, while tan represents Richard Henry and lineage scores (n = 8). Aspergillosis Risk is a risk score derived from case-control (see Supplemental Materials: Aspergillosis Susceptibility for details).

Supplementary text including Supplementary Figs. 1–74.

Supplementary Tables 1–25.

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Guhlin, J., Le Lec, M.F., Wold, J. et al. Species-wide genomics of kākāpō provides tools to accelerate recovery. Nat Ecol Evol (2023). https://doi.org/10.1038/s41559-023-02165-y

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Received: 26 November 2022

Accepted: 11 July 2023

Published: 28 August 2023

DOI: https://doi.org/10.1038/s41559-023-02165-y

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