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Genotypic variability enhances the reproducibility of an ecological study

Abstract

Many scientific disciplines are currently experiencing a 'reproducibility crisis' because numerous scientific findings cannot be repeated consistently. A novel but controversial hypothesis postulates that stringent levels of environmental and biotic standardization in experimental studies reduce reproducibility by amplifying the impacts of laboratory-specific environmental factors not accounted for in study designs. A corollary to this hypothesis is that a deliberate introduction of controlled systematic variability (CSV) in experimental designs may lead to increased reproducibility. To test this hypothesis, we had 14 European laboratories run a simple microcosm experiment using grass (Brachypodium distachyon L.) monocultures and grass and legume (Medicago truncatula Gaertn.) mixtures. Each laboratory introduced environmental and genotypic CSV within and among replicated microcosms established in either growth chambers (with stringent control of environmental conditions) or glasshouses (with more variable environmental conditions). The introduction of genotypic CSV led to 18% lower among-laboratory variability in growth chambers, indicating increased reproducibility, but had no significant effect in glasshouses where reproducibility was generally lower. Environmental CSV had little effect on reproducibility. Although there are multiple causes for the 'reproducibility crisis', deliberately including genetic variability may be a simple solution for increasing the reproducibility of ecological studies performed under stringently controlled environmental conditions.

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Fig. 1: Experimental design of one block.
Fig. 2: Net legume effect for the 12 response variables in 14 laboratories as affected by laboratory and setup (growth chamber versus glasshouse) treatments.
Fig. 3: Among- and within-laboratory s.d. of the net legume effect as affected by experimental treatments.
Fig. 4: Relationship between within-laboratory s.d. and among-laboratory s.d. of the net legume effect as affected by experimental treatments.

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Acknowledgements

This study benefited from the Centre Nationnal de la Recherche Scientifique human and technical resources allocated to the Ecotrons research infrastructures, the state allocation ‘Investissement d’Avenir’ ANR-11-INBS-0001 and financial support from the ExpeER (grant 262060) consortium funded under the EU-FP7 research programme (FP2007–2013). Brachypodium seeds were provided by R. Sibout (Observatoire du Végétal, Institut Jean-Pierre Bourgin) and Medicago seeds were supplied by J.-M. Prosperi (Institut National de la Recherche Agronomique Biological Resource Centre). We further thank J. Varale, G. Hoffmann, P. Werthenbach, O. Ravel, C. Piel, D. Landais, D. Degueldre, T. Mathieu, P. Aury, N. Barthès, B. Buatois and R. Leclerc for assistance during the study. For additional acknowledgements, see the Supplementary Information.

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Authors

Contributions

A.M. and J.R. designed the study with input from M. Blouin, S.B., M. Bonkowski and J.-C.L. Substantial methodological contributions were provided by S.S., T.G., L.R. and M.S.-L. Conceptual feedback on an early version was provided by G.T.F., N.E., J.R. and A.M.E. Data were analysed by A.M. with input from A.M.E. A.M. wrote the manuscript with input from all authors. All authors were involved in carrying out the experiments and/or analyses.

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Correspondence to Alexandru Milcu.

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Supplementary information

Supplementary Tables 1–3; Supplementary Figures 1–5; Model outputs; Supplementary Acknowledgements.

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Milcu, A., Puga-Freitas, R., Ellison, A.M. et al. Genotypic variability enhances the reproducibility of an ecological study. Nat Ecol Evol 2, 279–287 (2018). https://doi.org/10.1038/s41559-017-0434-x

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