Biodiversity and Conservation

, Volume 19, Issue 1, pp 113–127

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

Original paper


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.


Comparative analyses Conservation Decision trees Extinction risk Non-independent data Phylogenetic comparative methods 



Decision trees


Phylogenetic comparative methods


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

Supplementary material

10531_2009_9709_MOESM1_ESM.doc (70 kb)
(DOC 70 kb)
10531_2009_9709_MOESM2_ESM.txt (72 kb)
(TXT 71 kb)
10531_2009_9709_MOESM3_ESM.docx (17 kb)
(DOCX 17 kb)

Copyright information

© Springer Science+Business Media B.V. 2009

Authors and Affiliations

  1. 1.Institute of ZoologyThe Zoological Society of LondonLondonUK
  2. 2.Department of Biological SciencesImperial College LondonAscotUK
  3. 3.Centre for Macroevolution and Macroecology, Research School of BiologyAustralian National UniversityCanberraAustralia

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