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The likely extinction of hundreds of palm species threatens their contributions to people and ecosystems

Nature Ecology & Evolution volume 6, pages 1710–1722 (2022)Cite this article

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Abstract

Protecting nature’s contributions to people requires accelerating extinction risk assessment and better integrating evolutionary, functional and used diversity with conservation planning. Here, we report machine learning extinction risk predictions for 1,381 palm species (Arecaceae), a plant family of high socio-economic and ecological importance. We integrate these predictions with published assessments for 508 species (covering 75% of all palm species) and we identify top-priority regions for palm conservation on the basis of their proportion of threatened evolutionarily distinct, functionally distinct and used species. Finally, we explore palm use resilience to identify non-threatened species that could potentially serve as substitutes for threatened used species by providing similar products. We estimate that over a thousand palms (56%) are probably threatened, including 185 species with documented uses. Some regions (New Guinea, Vanuatu and Vietnam) emerge as top ten priorities for conservation only after incorporating machine learning extinction risk predictions. Potential substitutes are identified for 91% of the threatened used species and regional use resilience increases with total palm richness. However, 16 threatened used species lack potential substitutes and 30 regions lack substitutes for at least one of their threatened used palm species. Overall, we show that hundreds of species of this keystone family face extinction, some of them probably irreplaceable, at least locally. This highlights the need for urgent actions to avoid major repercussions on palm-associated ecosystem processes and human livelihoods in the coming decades.

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Fig. 1: Percentages of threatened palm species in different diversity and use categories.
Fig. 2: Priority regions for palm conservation and research.
Fig. 3: Availability of potential alternatives for threatened used palm species.

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Data availability

All data necessary to perform the analyses are provided as Supplementary Tables or on Zenodo (https://zenodo.org/)167. Source data are provided with this paper.

Code availability

All scripts necessary to perform the analyses are provided on Zenodo (https://zenodo.org/)167.

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Acknowledgements

We are grateful to Naturalis Biodiversity Center (Leiden, the Netherlands) and Kew Herbarium (United Kingdom) for sharing their geographic coordinates databases, to O. A. Pérez-Escobar for insightful discussion and to T. Couvreur for insightful discussion and critical reading of an earlier version of the manuscript. A.A. is supported by funding from the Swedish Research Council and the Royal Botanic Gardens, Kew. W.D.K. acknowledges funding of palm research from the Netherlands Organisation for Scientific Research (grant no. 824.15.007).

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Author notes

  1. These authors jointly supervised this work: R. Cámara-Leret, S. P. Bachman.

Authors and Affiliations

  1. Royal Botanic Gardens, Kew, Richmond, UK

    S. Bellot, Y. Lu, A. Antonelli, W. J. Baker, J. Dransfield, F. Forest, I. J. Leitch, E. Nic Lughadha, I. Ondo, S. Pironon, B. E. Walker & S. P. Bachman

  2. Department of Biological and Environmental Sciences, Gothenburg Global Biodiversity Centre, Gothenburg, Sweden

    A. Antonelli

  3. Department of Plant Sciences, University of Oxford, Oxford, UK

    A. Antonelli

  4. Institute for Biodiversity and Ecosystem Dynamics (IBED), University of Amsterdam, Amsterdam, the Netherlands

    W. D. Kissling

  5. Department of Evolutionary Biology and Environmental Studies, University of Zurich, Zurich, Switzerland

    R. Cámara-Leret

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Contributions

S.B. and S.P.B. conceived the study, with input from Y.L., R.C.-L. and W.J.B. Y.L. compiled most of the data, did preliminary random forest ML analyses and wrote part of an early draft, with input and training from S.B. and S.P.B. S.B. compiled traits and use data with help from R.C.-L., I.O. and S.P. I.O. and S.P.B. provided and ran scripts to retrieve numbers of ecoregions and TDWG3 regions. J.D. provided a preliminary guess of the extinction risk of ~400 species without occurrence data or extinction risk assessment. Y.L. and S.B. cleaned the data. S.B. did all final random forest analyses, all neural network analyses and all analyses using the predictions, except the SHAP analysis, done by B.E.W., who also wrote the corresponding Supplementary Note and methods sections. R.C.-L., F.F., I.O., S.P.B. and S.P. advised on some analyses. S.B. wrote most of the final manuscript, with extensive input from S.P.B. and R.C.-L. and contributions from all authors. A.A., W.J.B., R.C.-L., J.D., F.F., W.D.K., I.J.L., E.N.L., I.O. and S.P. provided transformative feedback.

Corresponding authors

Correspondence to S. Bellot or R. Cámara-Leret.

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Nature Ecology & Evolution thanks Tinde van Andel, Rafael Molina-Venegas and Danilo Neves for their contribution to the peer review of this work. Peer reviewer reports are available.

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Extended data

Extended Data Fig. 1 Study design.

a. Model training and testing. b. Datasets. NI: not included; N-T: non-threatened; T: threatened. See Methods for further details.

Source data

Extended Data Fig. 2 Threatened palm species in different diversity and use categories.

a. Comparison between global estimates obtained with or without ML predictions in different areas of the world. Triangles: Estimates obtained by combining recent published assessments and ML predictions from the most accurate model (total evidence approach). Circles: Extrapolations based on published assessments only. Grey: all published assessments; Black: Only recent (that is ≤ 10-year-old) published assessments. America spans longitudes ∈ [−180°, −25°[, Africa / West Asia spans longitudes ∈ [−25°, 68°[, and East Asia / Pacific spans longitudes ∈ [68°, 180°]. b. Relationships between regional percentage of threatened species and total species number in the region (top) and between regional percentage of threatened species in different diversity and use categories (bottom). Percentages were obtained following the total evidence approach. Each dot represents a region with at least one palm species with data in the considered categories (n = 225, 93, 132, 224, 218 and 218 from top to bottom and left to right). The associations between the variables were measured using Pearson’s product moment correlation coefficient in two-sided Pearson’s correlation tests. r is Pearson’s correlation coefficient and p is the associated p-value. The grey error band corresponds to the 95% confidence interval of the correlation coefficient.

Source data

Extended Data Fig. 3 Changes in regional percentage of threatened species and associated region rank depending on the diversity category and the extinction risk information used.

‘total evidence’ is the combination of recent published extinction risk assessments and most accurate machine learning predictions. Each line corresponds to a region, and lines are coloured by the total number of palm species in the region. Regions with ≥40% threatened species of interest (that is top priorities) according to the total evidence approach are annotated, and the lines linking estimates from the total evidence approach and estimates based only on published assessments for these regions are thicker and dotted.

Source data

Extended Data Fig. 4 Replaceability of threatened utilized species and potential for substitution of non-threatened species.

The replaceability of a species is defined as the number of potential alternatives identified for that species. The potential for substitution of a species is defined as the number of threatened utilized species that may be substituted by that species. a. Regional replaceability of threatened utilized species across use categories. b. Global replaceability of threatened utilized species across use categories. The ‘violins’ represent the kernel density distributions. In a violin, the bold line represents the median value, the box spans values from the first to the third quartile, and the lines outside the box extend until the smallest and largest values, no further than 1.5 times the distance between the first and third quartiles. c. Functional traits and phylogenetic distribution of species replaceability and potential for substitution, for all uses taken together. The phylogenetic tree displayed was obtained by removing species without data from a maximum clade credibility consensus tree summarizing 750 palm phylogenetic trees estimated by Faurby et al.56 (see Methods and Supplementary Data).

Source data

Extended Data Fig. 5 Regional use resilience for all uses taken together.

a. Correlation between median number of alternatives per threatened utilized species and total palm species richness in the region. Each dot represents a region with at least one threatened utilized palm species (n = 92). The association between the variables was measured using Pearson’s product moment correlation coefficient in a two-sided Pearson’s correlation test. r is Pearson’s correlation coefficient and p is the associated p-value. The grey error band corresponds to the 95% confidence interval of the correlation coefficient. b. Regional percentages of threatened utilized species with alternatives.

Source data

Supplementary information

Supplementary Information

Supplementary Note, Figs. 1–3 and references.

Reporting Summary

Peer Review File

Supplementary Tables

Supplementary Tables 1–10.

Supplementary Data

Phylogenetic tree as a txt file.

Source data

Source Data Fig. 1

Statistical source data.

Source Data Fig. 2

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Source Data Fig. 3

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Source Data Extended Data Fig. 1

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Source Data Extended Data Fig. 2

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Source Data Extended Data Fig. 3

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Bellot, S., Lu, Y., Antonelli, A. et al. The likely extinction of hundreds of palm species threatens their contributions to people and ecosystems. Nat Ecol Evol 6, 1710–1722 (2022). https://doi.org/10.1038/s41559-022-01858-0

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