[MARMAM] How to use scat DNA sequence data in diet studies: Opinion in Molecular Ecology
austen.thomas at gmail.com
Mon Jun 18 13:05:27 PDT 2018
Counting with DNA in metabarcoding studies: How should we convert sequence
reads to dietary data?
Bruce E. Deagle, Austen C. Thomas, Julie C. McInnes, Laurence J. Clarke,
Eero J. Vesterinen, Elizabeth L. Clare, Tyler R. Kartzinel, J. Paige Eveson
Molecular Ecology. 2018;00:1–16.
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.
Article available upon request: austen.thomas at gmail.com
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