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Guhlin, J.* ; Le Lec, M.F.* ; Wold, J.* ; Koot, E.* ; Winter, D.* ; Biggs, P.J.* ; Galla, S.J.* ; Urban, L. ; Foster, Y.* ; Cox, M.P.* ; Digby, A.* ; Uddstrom, L.R.* ; Eason, D.* ; Vercoe, D.* ; Davis, T.* ; Howard, J.T.* ; Jarvis, E.D.* ; Robertson, F.E.* ; Robertson, B.C.* ; Gemmell, N.J.* ; Steeves, T.E.* ; Santure, A.W.* ; Dearden, P.K.*

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

Nat. Ecol. Evol. 7, 1693-1705 (2023)
DOI PMC
Open Access Green möglich sobald Postprint bei der ZB eingereicht worden ist.
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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Publikationstyp Artikel: Journalartikel
Dokumenttyp Wissenschaftlicher Artikel
Korrespondenzautor
Schlagwörter Strigops-habroptilus; Inbreeding Depression; Genetic-variation; Relatedness; Parrot; Parentage; Traits
ISSN (print) / ISBN 2397-334X
e-ISSN 2397-334X
Zeitschrift Nature ecology & evolution
Quellenangaben Band: 7, Heft: 10, Seiten: 1693-1705 Artikelnummer: , Supplement: ,
Verlag Nature Publishing Group
Verlagsort London
Nichtpatentliteratur Publikationen
Institut(e) Helmholtz Pioneer Campus (HPC)
Helmholtz Artifical Intelligence Cooperation Unit (HAICU)
Förderungen Department of Zoology, University of Otago
Genomics Aotearoa