Combining methods for non-invasive fecal DNA enables whole genome and metagenomic analyses in wildlife biology
dc.contributor.author | De Flamingh, Alida | |
dc.contributor.author | Ishida, Yasuko | |
dc.contributor.author | Pecnerova, Patrícia | |
dc.contributor.author | Vilchis, Sahara | |
dc.contributor.author | Siegismund, Hans R. | |
dc.contributor.author | Van Aarde, Rudi J. | |
dc.contributor.author | Malhi, Ripan S. | |
dc.contributor.author | Roca, Alfred L. | |
dc.date.accessioned | 2024-06-13T10:30:32Z | |
dc.date.available | 2024-06-13T10:30:32Z | |
dc.date.issued | 2023-01-12 | |
dc.description | DATA 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.abstract | Non-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.department | Zoology and Entomology | en_US |
dc.description.librarian | am2024 | en_US |
dc.description.sdg | SDG-15:Life on land | en_US |
dc.description.sponsorship | The 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.uri | http://www.frontiersin.org/Genetics | en_US |
dc.identifier.citation | De 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.issn | 1664-8021 (online) | |
dc.identifier.other | 10.3389/fgene.2022.1021004 | |
dc.identifier.uri | http://hdl.handle.net/2263/96474 | |
dc.language.iso | en | en_US |
dc.publisher | Frontiers Media | en_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.subject | Endangered species | en_US |
dc.subject | Fecal DNA | en_US |
dc.subject | Metagenomic analysis | en_US |
dc.subject | Molecular pipeline | en_US |
dc.subject | Nuclear genome | en_US |
dc.subject | Deoxyribonucleic acid (DNA) | en_US |
dc.subject | African elephant (Loxodonta africana) | en_US |
dc.subject | SDG-15: Life on land | en_US |
dc.title | Combining methods for non-invasive fecal DNA enables whole genome and metagenomic analyses in wildlife biology | en_US |
dc.type | Article | en_US |
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