M. N. Van Dyke et al. reply | Nature

M. N. Van Dyke et al. reply | Nature

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Access through your institution Buy or subscribe replying to: J. C. D. Terry _Nature_ https://doi.org/10.1038/s41586-023-06859-y (2024) replying to: D. W. Armitage _Nature_


https://doi.org/10.1038/s41586-023-06919-3 (2024) This is a preview of subscription content, access via your institution ACCESS OPTIONS Access through your institution Access Nature and 54


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which are calculated during checkout ADDITIONAL ACCESS OPTIONS: * Log in * Learn about institutional subscriptions * Read our FAQs * Contact customer support DATA AVAILABILITY Data are all


from the original paper1 and are available at Zenodo (https://doi.org/10.5281/zenodo.7083314)25. CODE AVAILABILITY All codes needed for this reply are provided in Supplementary Information 


1–3. All code needed for the original paper1 is available at Zenodo (https://doi.org/10.5281/zenodo.7083314)25. REFERENCES * Van Dyke, M. N., Levine, J. M. & Kraft, N. J. B. Small


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coexistence’. _Zenodo_ https://doi.org/10.5281/zenodo.7083314 (2022). Download references ACKNOWLEDGEMENTS We thank D. W. Armitage and J. C. D. Terry for constructive discussion. AUTHOR


INFORMATION AUTHORS AND AFFILIATIONS * Department of Ecology and Evolutionary Biology, University of California Los Angeles, Los Angeles, CA, USA Mary N. Van Dyke * Forestry and Rangeland


Stewardship Department, Colorado State University, Fort Collins, CO, USA Mary N. Van Dyke & Nathan J. B. Kraft * Department of Ecology and Evolutionary Biology, Princeton University,


Princeton, NJ, USA Jonathan M. Levine Authors * Mary N. Van Dyke View author publications You can also search for this author inPubMed Google Scholar * Jonathan M. Levine View author


publications You can also search for this author inPubMed Google Scholar * Nathan J. B. Kraft View author publications You can also search for this author inPubMed Google Scholar


CONTRIBUTIONS M.N.V.D. led the writing with substantial contributions from J.M.L. and N.J.B.K. M.N.V.D. performed the additional analyses and created the figures. CORRESPONDING AUTHOR


Correspondence to Mary N. Van Dyke. ETHICS DECLARATIONS COMPETING INTERESTS The authors declare no competing interests. ADDITIONAL INFORMATION PUBLISHER’S NOTE Springer Nature remains


neutral with regard to jurisdictional claims in published maps and institutional affiliations. EXTENDED DATA FIGURES AND TABLES EXTENDED DATA FIG. 1 PREDICTIONS OF COMPETITIVE OUTCOMES FOR


THE 15 SPECIES PAIRS. Points represent stabilizing niche and fitness differences calculated from non-parametric bootstrap samples. Points lying inside the grey shaded region indicate


coexistence, and outside indicate competitive exclusion. Median predictions are where the error bars (+/− 1 SD) cross. p(switch) in each panel reports the probability that pair switched


coexistence outcome with treatment. EXTENDED DATA FIG. 2 DENSITY YIELD PLOTS FOR EACH SPECIES MONOCULTURES UNDER BOTH TREATMENTS. The BH model estimates are shown in orange1 and the EBH


model estimates are shown in blue3. The shaded pink area indicates the range of neighbourhood densities which were sown in our experiment for each species. EXTENDED DATA FIG. 3 DISTRIBUTIONS


OF THE PROPORTION OF PAIRS THAT SWITCHED COEXISTENCE OUTCOMES IN THE NULL MODEL DRAWS COMPARED TO THE MEAN FROM THE BOOTSTRAPS OF THE REAL DATA. Panel (a) shows the distribution of the


proportion of pairs found to switch coexistence outcomes in Terry’s simulated ‘no treatment’ data and the mean proportion from the bootstrap samples of the real data (solid black line) when


we include all 15 pairs, and panel (b) shows the proportion when we only include the ten pairs our original paper found switched coexistence outcomes. SUPPLEMENTARY INFORMATION SUPPLEMENTARY


INFORMATION Supplementary Information 1–3. Supplementary Information 1: calculation of the parameters for the exponential Beverton–Holt model and the corresponding yield density plots and


contains code for Fig. 1, Table 1, Extended Data Fig. 2 and Extended Data Table 1. Supplementary Information 2: an explanation and code for the changes in the determination of invasion


growth rates analysis, an explanation and code for the null model analysis, and code for Fig. 2 and Extended Data Fig. 3. Supplementary Information 3: probability of coexistence outcome


changes, and code for Fig. 3. REPORTING SUMMARY RIGHTS AND PERMISSIONS Reprints and permissions ABOUT THIS ARTICLE CITE THIS ARTICLE Van Dyke, M.N., Levine, J.M. & Kraft, N.J.B. M. N.


Van Dyke et al. reply. _Nature_ 632, E21–E29 (2024). https://doi.org/10.1038/s41586-024-07777-3 Download citation * Published: 28 August 2024 * Issue Date: 29 August 2024 * DOI:


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