Skip to main content

Thank you for visiting nature.com. You are using a browser version with limited support for CSS. To obtain the best experience, we recommend you use a more up to date browser (or turn off compatibility mode in Internet Explorer). In the meantime, to ensure continued support, we are displaying the site without styles and JavaScript.

  • Matters Arising
  • Published:

To remain modern the coexistence program requires modern statistical rigour

Nature volume 632, pages E15–E20 (2024)Cite this article

Subjects

The Original Article was published on 02 November 2022

arising from: M. N. Van Dyke et al. Nature https://doi.org/10.1038/s41586-022-05391-9 (2022).

A 2022 study by Van Dyke et al.1 paired experimental drought manipulations with demographic models and trait data to project major shifts in coexistence among a number of annual plant taxa. A reanalysis of these data that includes comparisons of alternative competition models reveals that the authors’ original conclusions are strongly sensitive to model choice. Furthermore, propagating error in model parameters into coexistence predictions results in relatively weak support for the majority of coexistence shifts that were predicted by the authors’ original model. These results suggest that there is a need for increased statistical rigour when treating binary predictions of species coexistence as observed experimental outcomes.

This is a preview of subscription content, access via your institution

Access options

Buy this article

  • Purchase on SpringerLink
  • Instant access to full article PDF
Buy now

Prices may be subject to local taxes which are calculated during checkout

Fig. 1: Error-aware predictions of coexistence outcomes for 15 species pairs under the best-fit alternative model.
Fig. 2: Posterior distributions of coexistence predictions for 15 species pairs under the authors’ original model.

Code availability

Code to replicate this analysis is available at https://doi.org/10.5281/zenodo.7460881

References

  1. Van Dyke, M. N., Levine, J. M. & Kraft, N. J. B. Small rainfall changes drive substantial changes in plant coexistence. Nature 611, 501–511 (2022).

    Google Scholar 

  2. Matías, L., Godoy, O., Gómez-Aparicio, L. & Pérez-Ramos, I. M. An experimental extreme drought reduces the likelihood of species to coexist despite increasing intransitivity in competitive networks. J. Ecol. 106, 826–837 (2018).

    Article  Google Scholar 

  3. Díaz, S. & Cabido, M. Vive la différence: plant functional diversity matters to ecosystem processes. Trends Ecol. Evol. 16, 646–655 (2001).

    Article  Google Scholar 

  4. Chesson, P. in Ecological Systems: Selected Entries from the Encyclopedia of Sustainability Science and Technology (ed. Leemans, R.) 223–256 (Springer, 2013).

  5. Law, R. & Watkinson, A. R. Response-surface analysis of two-species competition: an experiment on Phleum arenarium and Vulpia fasciculata. J. Ecol. 75, 871–886 (1987).

    Article  Google Scholar 

  6. Levine, J. M. & HilleRisLambers, J. The importance of niches for the maintenance of species diversity. Nature 461, 254–257 (2009).

    Article  ADS  CAS  PubMed  Google Scholar 

  7. Kraft, N. J. B., Godoy, O. & Levine, J. M. Plant functional traits and the multidimensional nature of species coexistence. Proc. Natl Acad. Sci. USA 112, 797–802 (2015).

    Article  ADS  CAS  PubMed  PubMed Central  Google Scholar 

  8. Hart, S. P., Freckleton, R. P. & Levine, J. M. How to quantify competitive ability. J. Ecol. 106, 1902–1909 (2018).

    Article  Google Scholar 

  9. Watanabe, S. A widely applicable Bayesian information criterion. J. Mach. Learn. Res. 14, 867–897 (2013).

    MathSciNet  Google Scholar 

  10. Bowler, C. H., Weiss-Lehman, C., Towers, I. R., Mayfield, M. M. & Shoemaker, L. G. Accounting for demographic uncertainty increases predictions for species coexistence: a case study with annual plants. Ecol. Lett. 25, 1618–1628 (2022).

    Article  PubMed  PubMed Central  Google Scholar 

  11. Jeffreys, H. Theory of Probability 3rd edn (Oxford Univ. Press, 1961).

  12. Terry, J. C. D., Chen, J. & Lewis, O. T. Natural enemies have inconsistent impacts on the coexistence of competing species. J. Anim. Ecol. 90, 2277–2288 (2021).

    Article  PubMed  Google Scholar 

  13. Godoy, O. & Levine, J. M. Phenology effects on invasion success: insights from coupling field experiments to coexistence theory. Ecology 95, 726–736 (2014).

    Article  PubMed  Google Scholar 

  14. Armitage, D. W. & Jones, S. E. Coexistence barriers confine the poleward range of a globally distributed plant. Ecol. Lett. 23, 1838–1848 (2020).

    Article  PubMed  Google Scholar 

  15. Stouffer, D. B. A critical examination of models of annual-plant population dynamics and density-dependent fecundity. Methods Ecol. Evol. 13, 2516–2530 (2022).

    Article  Google Scholar 

Download references

Acknowledgements

I thank M. Van Dyke, C. Terry and J. Spaak for constructive discussion and debate.

Author information

Authors and Affiliations

  1. Integrative Community Ecology Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Japan

    David W. Armitage

Authors
  1. David W. Armitage
    View author publications

    You can also search for this author in PubMed Google Scholar

Contributions

D.W.A. performed all writing and analyses.

Corresponding author

Correspondence to David W. Armitage.

Ethics declarations

Competing interests

The author declares 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 An alternative competition model removes the predicted effects of trait differences on coexistence mechanisms.

a–e, Using coefficients of model 7 has the effect of removing statistically significant trends in the relative magnitudes of treatment differences in demographic potential and competition coefficients (t = − 1.68, p = 0.10) (a). This also has the consequence of removing the positive associations between functional trait distances and absolute changes in FD between treatments (b), absolute changes in ND between treatments (c), and overall fitness differences (d) and overall niche differences (e). ND results remain unchanged from the original analysis.

Extended Data Table 1 Comparisons of predicted equilibria
Full size table

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Armitage, D.W. To remain modern the coexistence program requires modern statistical rigour. Nature 632, E15–E20 (2024). https://doi.org/10.1038/s41586-023-06919-3

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1038/s41586-023-06919-3

Comments

By submitting a comment you agree to abide by our Terms and Community Guidelines. If you find something abusive or that does not comply with our terms or guidelines please flag it as inappropriate.

Search

Advanced search

Quick links

Nature Briefing

Sign up for the Nature Briefing newsletter — what matters in science, free to your inbox daily.

Get the most important science stories of the day, free in your inbox. Sign up for Nature Briefing