A1 Journal article (refereed)
isotracer: An R package for the analysis of tracer addition experiments (2022)

Bruneaux, M., & López‐Sepulcre, A. (2022). isotracer: An R package for the analysis of tracer addition experiments. Methods in Ecology and Evolution, 13(5), 1119-1134. https://doi.org/10.1111/2041-210x.13822

JYU authors or editors

Bruneaux, Matthieu
Lopez-Sepulcre, Andres

Publication details

All authors or editors: Bruneaux, Matthieu; López‐Sepulcre, Andrés

Journal or series: Methods in Ecology and Evolution

eISSN: 2041-210X

Publication year: 2022

Publication date: 13/02/2022

Volume: 13

Issue number: 5

Pages range: 1119-1134

Publisher: Wiley

Publication country: United States

Publication language: English

DOI: https://doi.org/10.1111/2041-210x.13822

Research data link: https://cran.r-project.org/package=isotracer

Publication open access: Openly available

Publication channel open access: Partially open access channel

Publication is parallel published (JYX): https://jyx.jyu.fi/handle/123456789/79778

Additional information: The isotracer package is available from CRAN at https://cran.r-project.org/package=isotracer. The CRAN package contains the datasets used in the case studies presented in this manuscript.

Abstract

Tracer addition experiments, particularly using isotopic tracers, are becoming increasingly important in a variety of studies aiming at characterizing the flows of molecules or nutrients at different levels of biological organization, from the cellular and tissue levels, to the organismal and ecosystem levels. However, performing rigorous statistical analyses to gain reliable quantitative insights from these experiments often remains challenging.

We present an approach based on Hidden Markov Models (HMM) to estimate nutrient flow parameters across a network, and its implementation in the R package isotracer. The isotracer package is capable of handling a variety of tracer study designs, including continuous tracer drips, pulse experiments, and pulse-chase experiments. It can also take into account tracer decay when radioactive isotopes are used.

To illustrate its use, we present three case studies based on published data and spanning different levels of biological organization: a molecular-level study of protein synthesis and degradation in Arabidopsis thaliana, an organismal-level study of phosphorus incorporation in the eelgrass Zostera marina, and an ecosystem-level study of nitrogen dynamics in Trinidadian montane streams. With these case studies, we illustrate how isotracer can be used to estimate uptake rates, turnover rates, and total flows, as well as their uncertainty. We also show how to perform model selection to compare alternative hypotheses.

The isotracer package allows researchers from a broad range of disciplines to fully take advantage of their datasets through rigorous statistical analyses. We conclude by discussing isotracer's further applications, limitations, and possible future improvements and expansions.

Keywords: tracers (indicators); molecules; cells; tissues (parts of the body); nutrients (plants); isotopes; measuring methods