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Modelling extinction risk in multispecies data sets: phylogenetically independent contrasts versus decision trees

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Abstract

Many recent studies of extinction risk have attempted to determine what differences exist between threatened and non-threatened species. One potential problem in such studies is that species-level data may contain phylogenetic non-independence. However, the use of phylogenetic comparative methods (PCM) to account for non-independence remains controversial, and some recent studies of extinction have recommended other methods that do not account for phylogenetic non-independence, notably decision trees (DTs). Here we perform a systematic comparison of techniques, comparing the performance of PCM regression models with corresponding non-phylogenetic regressions and DTs over different clades and response variables. We found that predictions were broadly consistent among techniques, but that predictive precision varied across techniques with PCM regression and DTs performing best. Additionally, despite their inability to account for phylogenetic non-independence, DTs were useful in highlighting interaction terms for inclusion in the PCM regression models. We discuss the implications of these findings for future comparative studies of extinction risk.

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Abbreviations

DTs:

Decision trees

PCM:

Phylogenetic comparative methods

TIPS:

Comparative analyses using species (the ‘tips’ of phylogenetic tree branches) as independent data-points

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Acknowledgments

The authors would like to thank Andrew King, Amber Teacher and two anonymous reviewers for useful comments on the manuscript. This work was conducted thanks to NERC studentship NER/S/A/2004/12987.

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Authors and Affiliations

  1. Institute of Zoology, The Zoological Society of London, Regent’s Park, London, NW1 4RY, UK

    J. Bielby

  2. Department of Biological Sciences, Imperial College London, Silwood Park Campus, Ascot, SL5 7PY, UK

    J. Bielby, N. Cooper & A. Purvis

  3. Centre for Macroevolution and Macroecology, Research School of Biology, Australian National University, Canberra, ACT, 0200, Australia

    M. Cardillo

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  1. J. Bielby
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  2. M. Cardillo
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  3. N. Cooper
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  4. A. Purvis
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Correspondence to J. Bielby.

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Bielby, J., Cardillo, M., Cooper, N. et al. Modelling extinction risk in multispecies data sets: phylogenetically independent contrasts versus decision trees. Biodivers Conserv 19, 113–127 (2010). https://doi.org/10.1007/s10531-009-9709-0

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