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

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Abstract

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.

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Acknowledgments

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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  1. Luca Pozzi

    Present address: Behavioral Ecology and Sociobiology Unit, German Primate Center, Kellnerweg 4, 37077, Göttingen, Germany

Authors and Affiliations

  1. Department of Anthropology, New York University, New York, New York, 10003, USA

    Luca Pozzi, Christina M. Bergey & Andrew S. Burrell

  2. New York Consortium in Evolutionary Primatology, New York, USA

    Luca Pozzi & Christina M. Bergey

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  1. Luca Pozzi
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  2. Christina M. Bergey
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Correspondence to Luca Pozzi.

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Pozzi, L., Bergey, C.M. & Burrell, A.S. The Use (and Misuse) of Phylogenetic Trees in Comparative Behavioral Analyses. Int J Primatol 35, 32–54 (2014). https://doi.org/10.1007/s10764-013-9701-0

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  • DOI: https://doi.org/10.1007/s10764-013-9701-0

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