Assessing the potential of environmental DNA metabarcoding for monitoring Neotropical mammals: a case study in the Amazon and Atlantic Forest, Brazil
Corresponding Author
Naiara Guimarães Sales
Environment and Ecosystem Research Centre, School of Science, Engineering and Environment, University of Salford, Salford, M5 4WT UK
Correspondence authors
Search for more papers by this authorMariane da Cruz Kaizer
Environment and Ecosystem Research Centre, School of Science, Engineering and Environment, University of Salford, Salford, M5 4WT UK
Search for more papers by this authorIlaria Coscia
Environment and Ecosystem Research Centre, School of Science, Engineering and Environment, University of Salford, Salford, M5 4WT UK
Search for more papers by this authorJoseph C. Perkins
Environment and Ecosystem Research Centre, School of Science, Engineering and Environment, University of Salford, Salford, M5 4WT UK
Search for more papers by this authorAndrew Highlands
Environment and Ecosystem Research Centre, School of Science, Engineering and Environment, University of Salford, Salford, M5 4WT UK
Search for more papers by this authorJean P. Boubli
Environment and Ecosystem Research Centre, School of Science, Engineering and Environment, University of Salford, Salford, M5 4WT UK
Search for more papers by this authorWilliam E. Magnusson
Coordenação de Biodiversidade, Instituto Nacional de Pesquisas da Amazônia, Manaus, Amazonas, Brazil
Search for more papers by this authorMaria Nazareth Ferreira Da Silva
Coleção de Mamíferos, Instituto Nacional de Pesquisas da Amazônia, Manaus, Amazonas, Brazil
Search for more papers by this authorChiara Benvenuto
Environment and Ecosystem Research Centre, School of Science, Engineering and Environment, University of Salford, Salford, M5 4WT UK
Search for more papers by this authorCorresponding Author
Allan D. Mcdevitt
Environment and Ecosystem Research Centre, School of Science, Engineering and Environment, University of Salford, Salford, M5 4WT UK
Correspondence authors
Search for more papers by this authorCorresponding Author
Naiara Guimarães Sales
Environment and Ecosystem Research Centre, School of Science, Engineering and Environment, University of Salford, Salford, M5 4WT UK
Correspondence authors
Search for more papers by this authorMariane da Cruz Kaizer
Environment and Ecosystem Research Centre, School of Science, Engineering and Environment, University of Salford, Salford, M5 4WT UK
Search for more papers by this authorIlaria Coscia
Environment and Ecosystem Research Centre, School of Science, Engineering and Environment, University of Salford, Salford, M5 4WT UK
Search for more papers by this authorJoseph C. Perkins
Environment and Ecosystem Research Centre, School of Science, Engineering and Environment, University of Salford, Salford, M5 4WT UK
Search for more papers by this authorAndrew Highlands
Environment and Ecosystem Research Centre, School of Science, Engineering and Environment, University of Salford, Salford, M5 4WT UK
Search for more papers by this authorJean P. Boubli
Environment and Ecosystem Research Centre, School of Science, Engineering and Environment, University of Salford, Salford, M5 4WT UK
Search for more papers by this authorWilliam E. Magnusson
Coordenação de Biodiversidade, Instituto Nacional de Pesquisas da Amazônia, Manaus, Amazonas, Brazil
Search for more papers by this authorMaria Nazareth Ferreira Da Silva
Coleção de Mamíferos, Instituto Nacional de Pesquisas da Amazônia, Manaus, Amazonas, Brazil
Search for more papers by this authorChiara Benvenuto
Environment and Ecosystem Research Centre, School of Science, Engineering and Environment, University of Salford, Salford, M5 4WT UK
Search for more papers by this authorCorresponding Author
Allan D. Mcdevitt
Environment and Ecosystem Research Centre, School of Science, Engineering and Environment, University of Salford, Salford, M5 4WT UK
Correspondence authors
Search for more papers by this authorAbstract
The application of environmental DNA (eDNA) metabarcoding as a biomonitoring tool has greatly increased, but studies have focused on temperate aquatic macro-organisms. We apply eDNA metabarcoding to detecting the mammalian community in two high-biodiversity regions of Brazil: the Amazon and Atlantic Forests. We identified Critically Endangered and Endangered mammalian species and found overlap with species identified via camera trapping. We highlight the potential for using eDNA monitoring for mammals in biodiverse regions and identify challenges: we need a better understanding of the ecology of eDNA within variable environments and more appropriate reference sequences for species identification in these anthropogenically impacted biomes.
Supporting Information
Raw sequence data are available on figshare (https://doi.org/10.6084/m9.figshare.10045940 and https://doi.org/10.6084/m9.figshare.10045910).
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| mam12183-sup-0001-AppendixS1-3andS5-7.pdfPDF document, 2.3 MB |
Appendix S1. Examples of four sampling areas for environmental DNA (eDNA): A = Santa Marta in the Atlantic Forest (Area E in Fig. 1); B and C = Acará (Area B in Fig. 1); and D = meeting of the waters, Amazon River (Area C in Fig. 1) in the Amazon. Appendix S2. Co-ordinates and dates of eDNA sampling localities in the Atlantic Forest and Amazon. Information is provided on which samples were placed on each of two MiSeq sequencing runs. Appendix S3. Detailed methods and references. Appendix S4. Molecular operational taxonomic units (MOTUs) that were identified and their assignment to family, genus and species. Appendix S5. Bubble graph representing presence–absence and categorical values of the number of reads retained (after bioinformatic filtering) for eDNA (water in blue and sediment in orange) from each family identified at each site (Areas D and E) in Caparaó National Park, Atlantic Forest. Appendix S6. Collage of images representing examples of mammals captured from ground and canopy camera traps in Caparaó National Park, Atlantic Forest. Appendix S7. Species captured by ground (G) and canopy (C) camera traps in Caparaó National Park, Atlantic Forest. |
| mam12183-sup-0002-AppendixS4.xlsxapplication/excel, 14.7 KB |
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Please note: The publisher is not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing content) should be directed to the corresponding author for the article.
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