Combining stable isotope analysis with DNA metabarcoding improves inferences of trophic ecology

PLoS One. 2019 Jul 22;14(7):e0219070. doi: 10.1371/journal.pone.0219070. eCollection 2019.

Abstract

Knowing what animals eat is fundamental to our ability to understand and manage biodiversity and ecosystems, but researchers often must rely on indirect methods to infer trophic position and food intake. Using an approach that combines evidence from stable isotope analysis and DNA metabarcoding, we assessed the diet and trophic position of Anthene usamba butterflies, for which there are no known direct observations of larval feeding. An earlier study that analyzed adults rather than caterpillars of A. usamba inferred that this butterfly was aphytophagous, but we found that the larval guts of A. usamba and two known herbivorous lycaenid species contain chloroplast 16S sequences. Moreover, chloroplast barcoding revealed high sequence similarity between chloroplasts found in A. usamba guts and the chloroplasts of the Vachellia drepanolobium trees on which the caterpillars live. Stable isotope analysis provided further evidence that A. usamba caterpillars feed on V. drepanolobium, and the possibilities of strict herbivory versus limited omnivory in this species are discussed. These results highlight the importance of combining multiple approaches and considering ontogeny when using stable isotopes to infer trophic ecology where direct observations are difficult or impossible.

Publication types

  • Research Support, Non-U.S. Gov't
  • Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

  • Animals
  • Ants / physiology
  • Butterflies / physiology*
  • Carbon Isotopes
  • DNA Barcoding, Taxonomic
  • DNA, Chloroplast / genetics
  • DNA, Chloroplast / isolation & purification
  • Diet*
  • Ecosystem*
  • Fabaceae / chemistry
  • Fabaceae / genetics
  • Gastrointestinal Microbiome / genetics
  • Herbivory / genetics
  • Larva / physiology
  • Nitrogen Isotopes
  • Symbiosis

Substances

  • Carbon Isotopes
  • DNA, Chloroplast
  • Nitrogen Isotopes

Grants and funding

MRLW was supported by a National Science Foundation Postdoctoral Research Fellowship in Biology (1309425); CCMB and MRLW received funding from the Putnam Expeditionary Fund of the Museum of Comparative Zoology at Harvard University; SMS was supported by a NSF Graduate Research Fellowship; the research was funded by grants to MRLW from the British Ecological Society (6007210), the Wildlife Reserves Singapore Conservation Fund, and the Explorer’s Club; and an FQEB grant no. RFP-12-06 from the National Philanthropic Trust and NSF SES 0750480 to NEP. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.