Combining methods for non-invasive fecal DNA enables whole genome and metagenomic analyses in wildlife biology

dc.contributor.authorDe Flamingh, Alida
dc.contributor.authorIshida, Yasuko
dc.contributor.authorPecnerova, Patrícia
dc.contributor.authorVilchis, Sahara
dc.contributor.authorSiegismund, Hans R.
dc.contributor.authorVan Aarde, Rudi J.
dc.contributor.authorMalhi, Ripan S.
dc.contributor.authorRoca, Alfred L.
dc.date.accessioned2024-06-13T10:30:32Z
dc.date.available2024-06-13T10:30:32Z
dc.date.issued2023-01-12
dc.descriptionDATA AVAILABILITY STATEMENT : The genomic data for the zoo and free-ranging elephants in the study are available on the NCBI Short-Read Archive (SRA) under bioproject number PRJNA910109, metagenomic result files for replicate sampling of zoo elephant dung are available on DRYAD (https://doi.org/10.5061/dryad.80gb5mktv). Bioinformatic code is available from https://github.com/ adeflamingh/de_Flamingh_et_al_2022_FiG.en_US
dc.description.abstractNon-invasive biological samples benefit studies that investigate rare, elusive, endangered, or dangerous species. Integrating genomic techniques that use non-invasive biological sampling with advances in computational approaches can benefit and inform wildlife conservation and management. Here, we used non-invasive fecal DNA samples to generate low- to medium-coverage genomes (e.g., >90% of the complete nuclear genome at six X-fold coverage) and metagenomic sequences, combining widely available and accessible DNA collection cards with commonly used DNA extraction and library building approaches. DNA preservation cards are easy to transport and can be stored non-refrigerated, avoiding cumbersome or costly sample methods. The genomic library construction and shotgun sequencing approach did not require enrichment or targeted DNA amplification. The utility and potential of the data generated was demonstrated through genome scale and metagenomic analyses of zoo and free-ranging African savanna elephants (Loxodonta africana). Fecal samples collected from freeranging individuals contained an average of 12.41% (5.54–21.65%) endogenous elephant DNA. Clustering of these elephants with others from the same geographic region was demonstrated by a principal component analysis of genetic variation using nuclear genome-wide SNPs. Metagenomic analyses identified taxa that included Loxodonta, green plants, fungi, arthropods, bacteria, viruses and archaea, showcasing the utility of this approach for addressing complementary questions based on host-associated DNA, e.g., pathogen and parasite identification. The molecular and bioinformatic analyses presented here contributes towards the expansion and application of genomic techniques to conservation science and practice.en_US
dc.description.departmentZoology and Entomologyen_US
dc.description.librarianam2024en_US
dc.description.sdgSDG-15:Life on landen_US
dc.description.sponsorshipThe International Fund for Animal Welfare; the Conservation Ecology Research Unit (CERU) of the University of Pretoria; the US Fish and Wildlife Service African Elephant Conservation Fund; the University of Illinois at Urbana-Champaign; the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie grant agreement.en_US
dc.description.urihttp://www.frontiersin.org/Geneticsen_US
dc.identifier.citationDe Flamingh, A., Ishida, Y., Pečnerová, P., Vilchis, S., Siegismund, H.R., Van Aarde, R.J., Malhi, R.S. & Roca, A.L. (2023), Combining methods for non-invasive fecal DNA enables whole genome and metagenomic analyses in wildlife biology. Frontiers in Genetics 13:1021004. DOI: 10.3389/fgene.2022.1021004.en_US
dc.identifier.issn1664-8021 (online)
dc.identifier.other10.3389/fgene.2022.1021004
dc.identifier.urihttp://hdl.handle.net/2263/96474
dc.language.isoenen_US
dc.publisherFrontiers Mediaen_US
dc.rights© 2023 de Flamingh, Ishida, Pečnerová, Vilchis, Siegismund, van Aarde, Malhi and Roca. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY).en_US
dc.subjectEndangered speciesen_US
dc.subjectFecal DNAen_US
dc.subjectMetagenomic analysisen_US
dc.subjectMolecular pipelineen_US
dc.subjectNuclear genomeen_US
dc.subjectDeoxyribonucleic acid (DNA)en_US
dc.subjectAfrican elephant (Loxodonta africana)en_US
dc.subjectSDG-15: Life on landen_US
dc.titleCombining methods for non-invasive fecal DNA enables whole genome and metagenomic analyses in wildlife biologyen_US
dc.typeArticleen_US

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