International Journal of Primatology

, Volume 35, Issue 1, pp 32–54 | Cite as

The Use (and Misuse) of Phylogenetic Trees in Comparative Behavioral Analyses

  • Luca PozziEmail author
  • Christina M. Bergey
  • Andrew S. Burrell


Phylogenetic comparative methods play a critical role in our understanding of the adaptive origin of primate behaviors. To incorporate evolutionary history directly into comparative behavioral research, behavioral ecologists rely on strong, well-resolved phylogenetic trees. Phylogenies provide the framework on which behaviors can be compared and homologies can be distinguished from similarities due to convergent or parallel evolution. Phylogenetic reconstructions are also of critical importance when inferring the ancestral state of behavioral patterns and when suggesting the evolutionary changes that behavior has undergone. Improvements in genome sequencing technologies have increased the amount of data available to researchers. Recently, several primate phylogenetic studies have used multiple loci to produce robust phylogenetic trees that include hundreds of primate species. These trees are now commonly used in comparative analyses and there is a perception that we have a complete picture of the primate tree. But how confident can we be in those phylogenies? And how reliable are comparative analyses based on such trees? Herein, we argue that even recent molecular phylogenies should be treated cautiously because they rely on many assumptions and have many shortcomings. Most phylogenetic studies do not model gene tree diversity and can produce misleading results, such as strong support for an incorrect species tree, especially in the case of rapid and recent radiations. We discuss implications that incorrect phylogenies can have for reconstructing the evolution of primate behaviors and we urge primatologists to be aware of the current limitations of phylogenetic reconstructions when applying phylogenetic comparative methods.


Coalescence Gene tree-species tree Molecular phylogenetics Supermatrix Supertree 



We thank James Higham, Lauren Brent, and Amanda Melin for inviting us to contribute to this special issue of the International Journal of Primatology. We are grateful to Lauren Brent and two anonymous reviewers for helpful comments and suggestions. We also thank Bret Larget for support and advice in running BUCKy.


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Copyright information

© Springer Science+Business Media New York 2013

Authors and Affiliations

  • Luca Pozzi
    • 1
    • 2
    • 3
    Email author
  • Christina M. Bergey
    • 1
    • 2
  • Andrew S. Burrell
    • 1
  1. 1.Department of AnthropologyNew York UniversityNew YorkUSA
  2. 2.New York Consortium in Evolutionary PrimatologyNew YorkUSA
  3. 3.Behavioral Ecology and Sociobiology UnitGerman Primate CenterGöttingenGermany

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