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      DNA metabarcoding analysis of the bare‐nosed wombat ( Vombatus ursinus) diet

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          Abstract

          Wombats are native herbivorous grazers that have adapted to Australia's low‐quality forage. Studies on diet selection by bare‐nosed wombats ( Vombatus ursinus) are limited and are either observational or based on microhistological studies. The current study determined the diet of wombats through DNA metabarcoding across five study sites in New South Wales over a one‐year period. Metabarcoding was chosen as it is non‐invasive, less time consuming and more specific than traditional techniques. The list of 209 plant species identified as eaten by wombats in this study is much higher than previously reported, with grasses being the most common plant group identified in all samples. Most dietary items identified were introduced plant species. Seasonal differences in plants eaten occurred at four of the five study sites and may reflect dietary abundance and floristic composition at different times of year. Further studies are required to determine if the dietary items differ markedly across the entire range of wombats, and if nutrition influences dietary preferences.

          Abstract

          Using metabarcoding we found bare‐nosed wombats ( Vombatus ursinus) eat mostly grasses, but dietary preferences are significant across season and are habitat specific. Future studies should be investigated across the broader wombat distribution.

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          Most cited references52

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          QIIME allows analysis of high-throughput community sequencing data.

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            UPARSE: highly accurate OTU sequences from microbial amplicon reads.

            Amplified marker-gene sequences can be used to understand microbial community structure, but they suffer from a high level of sequencing and amplification artifacts. The UPARSE pipeline reports operational taxonomic unit (OTU) sequences with ≤1% incorrect bases in artificial microbial community tests, compared with >3% incorrect bases commonly reported by other methods. The improved accuracy results in far fewer OTUs, consistently closer to the expected number of species in a community.
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              Counting with DNA in metabarcoding studies: How should we convert sequence reads to dietary data?

              Abstract Advances in DNA sequencing technology have revolutionized the field of molecular analysis of trophic interactions, and it is now possible to recover counts of food DNA sequences from a wide range of dietary samples. But what do these counts mean? To obtain an accurate estimate of a consumer's diet should we work strictly with data sets summarizing frequency of occurrence of different food taxa, or is it possible to use relative number of sequences? Both approaches are applied to obtain semi‐quantitative diet summaries, but occurrence data are often promoted as a more conservative and reliable option due to taxa‐specific biases in recovery of sequences. We explore representative dietary metabarcoding data sets and point out that diet summaries based on occurrence data often overestimate the importance of food consumed in small quantities (potentially including low‐level contaminants) and are sensitive to the count threshold used to define an occurrence. Our simulations indicate that using relative read abundance (RRA) information often provides a more accurate view of population‐level diet even with moderate recovery biases incorporated; however, RRA summaries are sensitive to recovery biases impacting common diet taxa. Both approaches are more accurate when the mean number of food taxa in samples is small. The ideas presented here highlight the need to consider all sources of bias and to justify the methods used to interpret count data in dietary metabarcoding studies. We encourage researchers to continue addressing methodological challenges and acknowledge unanswered questions to help spur future investigations in this rapidly developing area of research.
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                Author and article information

                Contributors
                j.old@westernsydney.edu.au
                Journal
                Ecol Evol
                Ecol Evol
                10.1002/(ISSN)2045-7758
                ECE3
                Ecology and Evolution
                John Wiley and Sons Inc. (Hoboken )
                2045-7758
                20 May 2024
                May 2024
                : 14
                : 5 ( doiID: 10.1002/ece3.v14.5 )
                : e11432
                Affiliations
                [ 1 ] School of Science, Hawkesbury Western Sydney University Penrith New South Wales Australia
                [ 2 ] School of Agricultural, Environmental and Veterinary Sciences Wagga Wagga, Charles Sturt University Wagga Wagga New South Wales Australia
                Author notes
                [*] [* ] Correspondence

                Julie M. Old, School of Science, Hawkesbury, Western Sydney University, Locked bag 1797, Penrith, NSW 2751, Australia.

                Email: j.old@ 123456westernsydney.edu.au

                Author information
                https://orcid.org/0000-0002-2754-7757
                https://orcid.org/0000-0002-6657-5435
                Article
                ECE311432 ECE-2023-11-02082.R1
                10.1002/ece3.11432
                11103767
                38770127
                6f1b66b1-8f0d-46d4-8fba-fef906008d0e
                © 2024 The Authors. Ecology and Evolution published by John Wiley & Sons Ltd.

                This is an open access article under the terms of the http://creativecommons.org/licenses/by/4.0/ License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited.

                History
                : 29 April 2024
                : 24 November 2023
                : 02 May 2024
                Page count
                Figures: 4, Tables: 3, Pages: 13, Words: 8600
                Funding
                Funded by: Charles Perkins Centre
                Funded by: Wildlife Disease Association Challenge Grant
                Categories
                Zoology
                Research Article
                Research Articles
                Custom metadata
                2.0
                May 2024
                Converter:WILEY_ML3GV2_TO_JATSPMC version:6.4.3 mode:remove_FC converted:20.05.2024

                Evolutionary Biology
                herbivore,itsf2,marsupial diet,next‐generation sequencing
                Evolutionary Biology
                herbivore, itsf2, marsupial diet, next‐generation sequencing

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