Species-wide genomics of kākāpō provides tools to accelerate recovery.

Autor: Guhlin J; Genomics Aotearoa, Biochemistry Department, School of Biomedical Sciences, University of Otago, Dunedin, Aotearoa New Zealand., Le Lec MF; Genomics Aotearoa, Biochemistry Department, School of Biomedical Sciences, University of Otago, Dunedin, Aotearoa New Zealand., Wold J; School of Biological Sciences, University of Canterbury, Christchurch, Aotearoa New Zealand., Koot E; The New Zealand Institute for Plant and Food Research Ltd, Palmerston North, Aotearoa New Zealand., Winter D; School of Natural Sciences, Massey University, Palmerston North, Aotearoa New Zealand., Biggs PJ; School of Natural Sciences, Massey University, Palmerston North, Aotearoa New Zealand.; School of Veterinary Science, Massey University, Palmerston North, Aotearoa New Zealand., Galla SJ; School of Biological Sciences, University of Canterbury, Christchurch, Aotearoa New Zealand.; Department of Biological Sciences, Boise State University, Boise, ID, USA., Urban L; Department of Anatomy, School of Biomedical Sciences, University of Otago, Dunedin, Aotearoa New Zealand.; Helmholtz Pioneer Campus, Helmholtz Zentrum Muenchen, Neuherberg, Germany.; Helmholtz AI, Helmholtz Zentrum Muenchen, Neuherberg, Germany.; School of Life Sciences, Technical University of Munich, Freising, Germany., Foster Y; Department of Zoology, University of Otago, Dunedin, Aotearoa New Zealand., Cox MP; School of Natural Sciences, Massey University, Palmerston North, Aotearoa New Zealand.; Department of Statistics, University of Auckland, Auckland, Aotearoa New Zealand., Digby A; Kākāpō Recovery Programme, Department of Conservation, Invercargill, Aotearoa New Zealand., Uddstrom LR; Kākāpō Recovery Programme, Department of Conservation, Invercargill, Aotearoa New Zealand., Eason D; Kākāpō Recovery Programme, Department of Conservation, Invercargill, Aotearoa New Zealand., Vercoe D; Kākāpō Recovery Programme, Department of Conservation, Invercargill, Aotearoa New Zealand., Davis T; Rakiura Tītī Islands Administering Body, Invercargill, Aotearoa New Zealand., Howard JT; Neurogenetics of Language Lab, The Rockefeller University, New York, NY, USA.; Mirxes, Cambridge, MA, USA., Jarvis ED; The Rockefeller University, New York, NY, USA.; Howard Hughes Medical Institute, Chevy Chase, MD, USA., Robertson FE; Department of Zoology, University of Otago, Dunedin, Aotearoa New Zealand., Robertson BC; Department of Zoology, University of Otago, Dunedin, Aotearoa New Zealand., Gemmell NJ; Department of Anatomy, School of Biomedical Sciences, University of Otago, Dunedin, Aotearoa New Zealand., Steeves TE; School of Biological Sciences, University of Canterbury, Christchurch, Aotearoa New Zealand., Santure AW; School of Biological Sciences, University of Auckland, Auckland, Aotearoa New Zealand., Dearden PK; Genomics Aotearoa, Biochemistry Department, School of Biomedical Sciences, University of Otago, Dunedin, Aotearoa New Zealand. peter.dearden@otago.ac.nz.
Jazyk: angličtina
Zdroj: Nature ecology & evolution [Nat Ecol Evol] 2023 Oct; Vol. 7 (10), pp. 1693-1705. Date of Electronic Publication: 2023 Aug 28.
DOI: 10.1038/s41559-023-02165-y
Abstrakt: 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.
(© 2023. The Author(s), under exclusive licence to Springer Nature Limited.)
Databáze: MEDLINE
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