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Unreliable prediction of B-vitamin source species

Nature Plants volume 9, pages 31–33 (2023)Cite this article

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Matters Arising to this article was published on 21 December 2022

The Original Article was published on 24 February 2022

arising from: A. Cantwell-Jones et al. Nature Plants https://doi.org/10.1038/s41477-022-01100-6 (2022)

Cantwell-Jones et al.1 proposed a list of 1,044 species as promising key sources of B vitamins primarily on the basis of phylogenetic predictions. The authors used 232 to 280 nutritionally known species (observed B-vitamins data) to predict B-vitamin profiles for 6,460 to 6,508 edible but nutritionally unknown species, and the latter were defined as sources of a B vitamin if the predicted vitamin content was ≥ 15% towards recommended dietary allowances. Unfortunately, very weak to moderate phylogenetic signal in the observed data and the fact that the dataset contains an extremely high percentage of missing values cast doubt on the predictions conducted in the study.

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Fig. 1: Conceptual model.

Data availability

All the datasets generated for this study are available from the Figshare digital repository at https://doi.org/10.6084/m9.figshare.19682880.v1.

Code availability

The R scripts for conducting all the analyses of the study are available as Supplementary Software 1–5.

References

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Author information

Authors and Affiliations

  1. Department of Ecology, Faculty of Sciences, Universidad Autónoma de Madrid, Madrid, Spain

    Rafael Molina-Venegas

  2. Department of Life Sciences, Global Change Ecology and Evolution Group, Universidad de Alcalá, Alcalá de Henares, Spain

    Rafael Molina-Venegas, Ignacio Morales-Castilla & Miguel Á. Rodríguez

Authors
  1. Rafael Molina-Venegas
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  2. Ignacio Morales-Castilla
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  3. Miguel Á. Rodríguez
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Contributions

R.M.-V. conceived and discussed the idea with M.A.R. and I.M.-C., performed the calculations and led the writing. I.M.-C. drew the figure. All the authors contributed to the writing.

Corresponding author

Correspondence to Rafael Molina-Venegas.

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Competing interests

The authors declare no competing interests.

Peer review

Peer review information

Nature Plants thanks Christine Foyer and the other, anonymous, reviewer(s) for their contribution to the peer review of this work.

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Supplementary information

Supplementary Information

Supplementary Methods and Discussion.

Reporting Summary

Supplementary Table 1

Predicted values with 95% CIs estimated for n = 500 randomized sets that resulted from reshuffling the observed values of the B vitamin thiamine across the species with known value of the vitamin. The predictions were conducted following the approach of Cantwell-Jones et al.1.

Supplementary Table 2

Predicted values with 95% CIs estimated for n = 500 randomized sets that resulted from reshuffling the observed values of the B vitamin riboflavin across the species with known value of the vitamin. The predictions were conducted following the approach of Cantwell-Jones et al.1.

Supplementary Table 3

Predicted values with 95% CIs estimated for n = 500 randomized sets that resulted from reshuffling the observed values of the B vitamin niacin across the species with known value of the vitamin. The predictions were conducted following the approach of Cantwell-Jones et al.1.

Supplementary Table 4

Predicted values with 95% CIs estimated for n = 500 randomized sets that resulted from reshuffling the observed values of the B vitamin pantothenic acid across the species with known value of the vitamin. The predictions were conducted following the approach of Cantwell-Jones et al.1.

Supplementary Table 5

Predicted values with 95% CIs estimated for n = 500 randomized sets that resulted from reshuffling the observed values of the B vitamin folate across the species with known value of the vitamin. The predictions were conducted following the approach of Cantwell-Jones et al.1.

Supplementary Table 6

Exact and adjusted P values (Bonferroni correction) of two-sample Wilcoxon tests between P2sim and P2sim-null scores (one test for each B vitamin and candidate species, totalling 1,616 tests).

Supplementary Table 7

P2sim and P2sim-null scores obtained for each B vitamin and candidate species.

Supplementary Software 1

R script for reshuffling the observed values of the B vitamins analysed in the study.

Supplementary Software 2

R script for conducting predictions with 95% CIs for the randomized sets following the approach of Cantwell-Jones et al.1.

Supplementary Software 3

R script for applying the method described in Molina-Venegas et al.4 to evaluate the expected accuracy of the predictions that informed the list of candidate species proposed in Cantwell-Jones et al.1.

Supplementary Software 4

R script for applying the method described in Molina-Venegas et al.4 to evaluate the expected accuracy of predictions conducted under a white-noise model of evolution.

Supplementary Software 5

R script for comparing the performance of the approach of Cantwell-Jones et al.1 and Rphylopars10.

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Molina-Venegas, R., Morales-Castilla, I. & Rodríguez, M.Á. Unreliable prediction of B-vitamin source species. Nat. Plants 9, 31–33 (2023). https://doi.org/10.1038/s41477-022-01299-4

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