Use the phylopath package for an easy to use framework to perform phylogenetic path analysis (PPA).

PPA can be used to compare support for competing causal models of trait evolution, while taking shared ancestry into account. All you need is:

  1. A clear set of models to test. 2. A data set of species with trait values. 3. A phylogeny of your species.

For a complete worked example, click “Get Started” above, or see the PeerJ paper.

This method was developed by Von Hardenberg and Gonzalez-Voyer. See citation() for info on correct citations.

The following published papers use phylopath (not up-to-date):


  • Scholer, M. N., Arcese, P., Puterman, M. L., Londoño, G. A. & Jankowski, J. E. Survival is negatively related to basal metabolic rate in tropical Andean birds. Functional Ecology (2019) 00:1–10 doi:10.1111/1365-2435.13375

  • Iglesias-Carrasco, M., Jennions M. D., Ho S. Y. W. & Duchêne, D. A. Sexual selection, body mass and molecular evolution interact to predict diversification in birds. Proceedings B (2019), 286: 20190172. doi:10.1098/rspb.2019.0172

  • Guo W.‐Y., van Kleunen M., Pierce S., et al. Domestic gardens play a dominant role in selecting alien species with adaptive strategies that facilitate naturalization. Global Ecol Biogeogr (2019), 00:1–12. doi:10.1111/geb.12882


  • Santini, L., González‐Suáre, M., Russo, D., Gonzalez-Voyer, A., Von Hardenberg, A. & Ancilotto, L. One strategy does not fit all: determinants of urban adaptation in mammals. Ecol Lett (2018). doi:10.1111/ele.13199.

  • Kennedy, J. D., Borregaard, M. K., Marki, P. Z., Machac, A., Fjeldså, J., and Rahbek, C. Expansion in geographical and morphological space drives continued lineage diversification in a global passerine radiation. Proceedings B (2018): 285. doi:10.1098/rspb.2018.2181.

  • Liedtke, H. C., Gower, D. J., Wilkinson, M. & Gomez-Mestre, I. Macroevolutionary shift in the size of amphibian genomes and the role of life history and climate. Nature Eco Evo. (2018). doi:10.1038/s41559-018-0674-4.

  • Murali, G., Merilaita, S. & Kodandaramaiah, U. Grab my tail: Evolution of dazzle stripes and colourful tails in lizards. J Evol Biol (2018). doi:10.1111/jeb.13364.

  • Mellor, E., McDonald Kinkaid, H. & Mason, G. Phylogenetic comparative methods: Harnessing the power of species diversity to investigate welfare issues in captive wild animals. Zoo biology (2018). doi:10.1002/zoo.21427.

  • Braga, M. P., Araujo, S. B. L., Agosta, S., Brooks, D., Hoberg, E., Nylin, S., Janz, N. & Boeger, W. A. Host use dynamics in a heterogeneous fitness landscape generates oscillations in host range and diversification. Evolution (2018). doi:10.1111/evo.13557.

  • Basset, Y., Dahl, C., Ctvrtecka, R., et al. A cross‐continental comparison of assemblages of seed‐ and fruit‐feeding insects in tropical rain forests: Faunal composition and rates of attack. J Biogeogr. (2018) 00:1–13. doi:10.1111/jbi.13211

  • Liao, W. B., Huang, Y., Zeng, Y., Zhong, M. J., Luo, Y. and Lüpold, S. Ejaculate evolution in external fertilizers: Influenced by sperm competition or sperm limitation? Evolution (2018), 72: 4–17. doi:10.1111/evo.13372

  • Lin Zhang, Kun Guo, Guang-Zheng Zhang, Long-Hui Lin and Xiang Ji. Evolutionary transitions in body plan and reproductive mode alter maintenance metabolism in squamates. BMC Evo Biol (2018), 18:45. doi:10.1186/s12862-018-1166-5

  • Xin Yu, Mao Jun Zhong, Da Yong Li, Long Jin, Wen Bo Liao and Alexander Kotrschal. Large‐brained frogs mature later and live longer. Evolution. (2018). doi:10.1111/evo.13478.

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