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Metabarcoding of Fecal Samples to Determine Herbivore Diets: A Case Study of the Endangered Pacific Pocket Mouse

Overview of attention for article published in PLOS ONE, November 2016
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About this Attention Score

  • In the top 25% of all research outputs scored by Altmetric
  • High Attention Score compared to outputs of the same age (82nd percentile)
  • High Attention Score compared to outputs of the same age and source (80th percentile)

Mentioned by

blogs
1 blog
twitter
4 tweeters
facebook
1 Facebook page

Citations

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24 Dimensions

Readers on

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101 Mendeley
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Title
Metabarcoding of Fecal Samples to Determine Herbivore Diets: A Case Study of the Endangered Pacific Pocket Mouse
Published in
PLOS ONE, November 2016
DOI 10.1371/journal.pone.0165366
Pubmed ID
Authors

Deborah D. Iwanowicz, Amy G. Vandergast, Robert S. Cornman, Cynthia R. Adams, Joshua R. Kohn, Robert N. Fisher, Cheryl S. Brehme

Abstract

Understanding the diet of an endangered species illuminates the animal's ecology, habitat requirements, and conservation needs. However, direct observation of diet can be difficult, particularly for small, nocturnal animals such as the Pacific pocket mouse (Heteromyidae: Perognathus longimembris pacificus). Very little is known of the dietary habits of this federally endangered rodent, hindering management and restoration efforts. We used a metabarcoding approach to identify source plants in fecal samples (N = 52) from the three remaining populations known. The internal transcribed spacers (ITS) of the nuclear ribosomal loci were sequenced following the Illumina MiSeq amplicon strategy and processed reads were mapped to reference databases. We evaluated a range of threshold mapping criteria and found the best-performing setting generally recovered two distinct mock communities in proportions similar to expectation. We tested our method on captive animals fed a known diet and recovered almost all plant sources, but found substantial heterogeneity among fecal pellets collected from the same individual at the same time. Observed richness did not increase with pooling of pellets from the same individual. In field-collected samples, we identified 4-14 plant genera in individual samples and 74 genera overall, but over 50 percent of reads mapped to just six species in five genera. We simulated the effects of sequencing error, variable read length, and chimera formation to infer taxon-specific rates of misassignment for the local flora, which were generally low with some exceptions. Richness at the species and genus levels did not reach a clear asymptote, suggesting that diet breadth remained underestimated in the current pool of samples. Large numbers of scat samples are therefore needed to make inferences about diet and resource selection in future studies of the Pacific pocket mouse. We conclude that our minimally invasive method is promising for determining herbivore diets given a library of sequences from local plants.

Twitter Demographics

The data shown below were collected from the profiles of 4 tweeters who shared this research output. Click here to find out more about how the information was compiled.

Mendeley readers

The data shown below were compiled from readership statistics for 101 Mendeley readers of this research output. Click here to see the associated Mendeley record.

Geographical breakdown

Country Count As %
Italy 1 <1%
Unknown 100 99%

Demographic breakdown

Readers by professional status Count As %
Researcher 25 25%
Student > Ph. D. Student 21 21%
Student > Master 20 20%
Student > Bachelor 15 15%
Student > Doctoral Student 2 2%
Other 4 4%
Unknown 14 14%
Readers by discipline Count As %
Agricultural and Biological Sciences 43 43%
Environmental Science 16 16%
Biochemistry, Genetics and Molecular Biology 15 15%
Engineering 3 3%
Computer Science 1 <1%
Other 4 4%
Unknown 19 19%

Attention Score in Context

This research output has an Altmetric Attention Score of 10. This is our high-level measure of the quality and quantity of online attention that it has received. This Attention Score, as well as the ranking and number of research outputs shown below, was calculated when the research output was last mentioned on 29 April 2020.
All research outputs
#2,458,157
of 17,585,248 outputs
Outputs from PLOS ONE
#33,464
of 165,740 outputs
Outputs of similar age
#70,624
of 397,864 outputs
Outputs of similar age from PLOS ONE
#1,050
of 5,366 outputs
Altmetric has tracked 17,585,248 research outputs across all sources so far. Compared to these this one has done well and is in the 86th percentile: it's in the top 25% of all research outputs ever tracked by Altmetric.
So far Altmetric has tracked 165,740 research outputs from this source. They typically receive a lot more attention than average, with a mean Attention Score of 13.5. This one has done well, scoring higher than 79% of its peers.
Older research outputs will score higher simply because they've had more time to accumulate mentions. To account for age we can compare this Altmetric Attention Score to the 397,864 tracked outputs that were published within six weeks on either side of this one in any source. This one has done well, scoring higher than 82% of its contemporaries.
We're also able to compare this research output to 5,366 others from the same source and published within six weeks on either side of this one. This one has done well, scoring higher than 80% of its contemporaries.