Journal article
Species-wide genomics of kakapo provides tools to accelerate recovery
Nature ecology & evolution, Vol.7, pp.1693-1705
10/2023
PMID: 37640765
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Source: InCites
Abstract
The kakapo 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 kakapo, 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.
Details
- Title
- Species-wide genomics of kakapo provides tools to accelerate recovery
- Creators
- Joseph Guhlin - University of OtagoMarissa F. Le Lec - University of OtagoJana Wold - University of CanterburyEmily Koot - The New Zealand Institute for Plant and Food Research Ltd (Palmerston North, Aotearoa New Zealand)David Winter - Massey UniversityPatrick.J. Biggs - Massey UniversityStephanie J. Galla - University of CanterburyLara Urban - University of OtagoYasmin Foster - University of OtagoMurray P. Cox - Massey UniversityAndrew Digby - Kākāpō Recovery Programme, Department of Conservation (Invercargill, Aotearoa New Zealand)Lydia R. Uddstrom - Kākāpō Recovery Programme, Department of Conservation (Invercargill, Aotearoa New Zealand)Daryl Eason - Kākāpō Recovery Programme, Department of Conservation (Invercargill, Aotearoa New Zealand)Deidre Vercoe - Kākāpō Recovery Programme, Department of Conservation (Invercargill, Aotearoa New Zealand)Tane Davis - Rakiura Titi Islands Administering Body, Invercargill, New ZealandKaren Andrew - Kākāpō Recovery Team, Department of Conservation (Invercargill, Aotearoa New Zealand)Lisa Argilla - Kākāpō Recovery Team, Department of Conservation (Invercargill, Aotearoa New Zealand)Karen Arnold - Kākāpō Recovery Team, Department of Conservation (Invercargill, Aotearoa New Zealand)James Bohan - Kākāpō Recovery Team, Department of Conservation (Invercargill, Aotearoa New Zealand)Liam Bolitho - Kākāpō Recovery Team, Department of Conservation (Invercargill, Aotearoa New Zealand)Nichy Brown - Kākāpō Recovery Team, Department of Conservation (Invercargill, Aotearoa New Zealand)Jo Carpenter - Kākāpō Recovery Team, Department of Conservation (Invercargill, Aotearoa New Zealand)Jodie Crane - Kākāpō Recovery Team, Department of Conservation (Invercargill, Aotearoa New Zealand)Margie Grant - Kākāpō Recovery Team, Department of Conservation (Invercargill, Aotearoa New Zealand)Glen Greaves - Kākāpō Recovery Team, Department of Conservation (Invercargill, Aotearoa New Zealand)Brett Halkett - Kākāpō Recovery Team, Department of Conservation (Invercargill, Aotearoa New Zealand)Rory Hannan - Kākāpō Recovery Team, Department of Conservation (Invercargill, Aotearoa New Zealand)Sam Haultain - Kākāpō Recovery Team, Department of Conservation (Invercargill, Aotearoa New Zealand)Bryony Hitchcock - Kākāpō Recovery Team, Department of Conservation (Invercargill, Aotearoa New Zealand)Leigh Joyce - Kākāpō Recovery Team, Department of Conservation (Invercargill, Aotearoa New Zealand)Sara Larcombe - Kākāpō Recovery Team, Department of Conservation (Invercargill, Aotearoa New Zealand)Jo Ledington - Kākāpō Recovery Team, Department of Conservation (Invercargill, Aotearoa New Zealand)Jinty MacTavish - Kākāpō Recovery Team, Department of Conservation (Invercargill, Aotearoa New Zealand)Phil Marsh - Kākāpō Recovery Team, Department of Conservation (Invercargill, Aotearoa New Zealand)Gilbert Mingam - Kākāpō Recovery Team, Department of Conservation (Invercargill, Aotearoa New Zealand)Freya Moore - Kākāpō Recovery Team, Department of Conservation (Invercargill, Aotearoa New Zealand)Lyndsay Murray - Kākāpō Recovery Team, Department of Conservation (Invercargill, Aotearoa New Zealand)Jake Osborne - Kākāpō Recovery Team, Department of Conservation (Invercargill, Aotearoa New Zealand)Lou Parker - Kākāpō Recovery Team, Department of Conservation (Invercargill, Aotearoa New Zealand)Tim Raemaekers - Kākāpō Recovery Team, Department of Conservation (Invercargill, Aotearoa New Zealand)Brodie Philp - Kākāpō Recovery Team, Department of Conservation (Invercargill, Aotearoa New Zealand)Roy Phillips - Kākāpō Recovery Team, Department of Conservation (Invercargill, Aotearoa New Zealand)Chris Phillips - Kākāpō Recovery Team, Department of Conservation (Invercargill, Aotearoa New Zealand)Rachel Rouse - Kākāpō Recovery Team, Department of Conservation (Invercargill, Aotearoa New Zealand)Jason Van de Wetering - Kākāpō Recovery Team, Department of Conservation (Invercargill, Aotearoa New Zealand)Alisha Sherriff - Kākāpō Recovery Team, Department of Conservation (Invercargill, Aotearoa New Zealand)Theo Thompson - Kākāpō Recovery Team, Department of Conservation (Invercargill, Aotearoa New Zealand)Jenny Rickett - Kākāpō Recovery Team, Department of Conservation (Invercargill, Aotearoa New Zealand)Jim Watts - Kākāpō Recovery Team, Department of Conservation (Invercargill, Aotearoa New Zealand)Nicki van Zyl - Kākāpō Recovery Team, Department of Conservation (Invercargill, Aotearoa New Zealand)Errol Nye - Kākāpō Recovery Team, Department of Conservation (Invercargill, Aotearoa New Zealand)Jen Waite - Kākāpō Recovery Team, Department of Conservation (Invercargill, Aotearoa New Zealand)Jason T. Howard - Rockefeller UniversityErich D. Jarvis - Rockefeller UniversityFiona E. Robertson - University of OtagoBruce C. Robertson - University of OtagoNeil J. Gemmell - University of OtagoTammy E. Steeves - University of CanterburyAnna W. Santure - University of AucklandPeter K. Dearden - University of Otago
- Publication Details
- Nature ecology & evolution, Vol.7, pp.1693-1705
- Publisher
- NATURE PORTFOLIO
- Identifiers
- 991013154612902368
- Academic Unit
- Faculty of Science and Engineering; Science
- Language
- English
- Resource Type
- Journal article