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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)
DOI PMC
Creative Commons Lizenzvertrag
Open Access Gold as soon as Publ. Version/Full Text is submitted to ZB.
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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Publication type Article: Journal article
Document type Scientific Article
Corresponding Author
Keywords 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
ISSN (print) / ISBN 2050-084X
e-ISSN 2050-084X
Journal eLife
Quellenangaben Volume: 12, Issue: , Pages: , Article Number: RP84553 Supplement: ,
Publisher eLife Sciences Publications
Publishing Place Sheraton House, Castle Park, Cambridge, Cb3 0ax, England
Non-patent literature Publications
Reviewing status Peer reviewed
Institute(s) Helmholtz Artifical Intelligence Cooperation Unit (HAICU)
Helmholtz Pioneer Campus (HPC)
Grants Birds New Zealand
Department of Conservation
University of Otago
Alexander von Humboldt Foundation
Revive Restore