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Urban, L. ; Miller, A.K.* ; Eason, D.* ; Vercoe, D.* ; Shaffer, M.* ; Wilkinson, S.P.* ; Jeunen, G.J.* ; Gemmell, N.J.* ; Digby, A.*

Non-invasive real-time genomic monitoring of the critically endangered kākāpō.

eLife 12:RP84553 (2023)
Verlagsversion DOI PMC
Open Access Gold
Creative Commons Lizenzvertrag
We used non-invasive real-time genomic approaches to monitor one of the last surviving populations of the critically endangered kākāpō (Strigops habroptilus). We first established an environmental DNA metabarcoding protocol to identify the distribution of kākāpō and other vertebrate species in a highly localized manner using soil samples. Harnessing real-time nanopore sequencing and the high-quality kākāpō reference genome, we then extracted species-specific DNA from soil. We combined long read-based haplotype phasing with known individual genomic variation in the kākāpō population to identify the presence of individuals, and confirmed these genomically informed predictions through detailed metadata on kākāpō distributions. This study shows that individual identification is feasible through nanopore sequencing of environmental DNA, with important implications for future efforts in the application of genomics to the conservation of rare species, potentially expanding the application of real-time environmental DNA research from monitoring species distribution to inferring fitness parameters such as genomic diversity and inbreeding.
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Publikationstyp Artikel: Journalartikel
Dokumenttyp Wissenschaftlicher Artikel
Schlagwörter Biodiversity Monitoring ; Edna ; Ecology ; Genetics ; Genomics ; Kakapo ; Long-read Genomics ; Non-invasive ; Real-time Genomics; Kakapo Strigops-habroptilus; Environmental Dna; Inbreeding Depression; Soil Dna; Conservation; Degradation; Edna
Sprache englisch
Veröffentlichungsjahr 2023
HGF-Berichtsjahr 2023
ISSN (print) / ISBN 2050-084X
e-ISSN 2050-084X
Zeitschrift eLife
Quellenangaben Band: 12, Heft: , Seiten: , Artikelnummer: RP84553 Supplement: ,
Verlag eLife Sciences Publications
Verlagsort Sheraton House, Castle Park, Cambridge, Cb3 0ax, England
Begutachtungsstatus Peer reviewed
Institut(e) Helmholtz Artifical Intelligence Cooperation Unit (HAICU)
Helmholtz Pioneer Campus (HPC)
POF Topic(s) 30205 - Bioengineering and Digital Health
Forschungsfeld(er) Enabling and Novel Technologies
Pioneer Campus
PSP-Element(e) G-530013-001
G-510011-001
Förderungen Birds New Zealand
Department of Conservation
University of Otago
Alexander von Humboldt Foundation
Revive Restore
DOI 10.7554/eLife.84553
WOS ID 001134180900001
Scopus ID 85181165202
PubMed ID 38153986
Erfassungsdatum 2024-01-07
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