International Journal of Primatology

, Volume 35, Issue 1, pp 32-54

First online:

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

  • Luca PozziAffiliated withDepartment of Anthropology, New York UniversityNew York Consortium in Evolutionary PrimatologyBehavioral Ecology and Sociobiology Unit, German Primate Center Email author 
  • , Christina M. BergeyAffiliated withDepartment of Anthropology, New York UniversityNew York Consortium in Evolutionary Primatology
  • , Andrew S. BurrellAffiliated withDepartment of Anthropology, New York University

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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