A multivariate phylogenetic comparative method incorporating a flexible function between discrete and continuous traits

Abstract

One major challenge of using the phylogenetic comparative method (PCM) is the analysis of the evolution of interrelated continuous and discrete traits in a single multivariate statistical framework. In addition, more intricate parameters such as branch-specific directional selection have rarely been integrated into such multivariate PCM frameworks. Here, originally motivated to analyze the complex evolutionary trajectories of group size (continuous variable) and social systems (discrete variable) in African subterranean rodents, we develop a flexible approach using approximate Bayesian computation (ABC). Specifically, our multivariate ABC-PCM method allows the user to flexibly model an underlying latent evolutionary function between continuous and discrete traits. The ABC-PCM also simultaneously incorporates complex evolutionary parameters such as branch-specific selection. This study highlights the flexibility of ABC-PCMs in analyzing the evolution of phenotypic traits interrelated in a complex manner.

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Acknowledgements

We would like to thank Dustin R. Rubenstein, Rafael Maia, and Margaret E. O’Brien at Columbia University and Jessica Zung at Princeton University for useful comments and advice. Masahito Tsuboi at University of Oslo also provided useful insights on the earlier version of manuscript. Two reviewers gave detailed and helpful comments on the manuscript. This study was financially supported by MEXT (No. 25711025) to K. N.

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YH and KN conceived, designed, and performed the analysis. Both discussed the result and wrote the final manuscript.

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Correspondence to Yuki Haba.

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Haba, Y., Kutsukake, N. A multivariate phylogenetic comparative method incorporating a flexible function between discrete and continuous traits. Evol Ecol 33, 751–768 (2019). https://doi.org/10.1007/s10682-019-10011-6

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Keywords

  • Phylogenetic comparative method (PCM)
  • Approximate Bayesian computation (ABC)
  • Multivariate analysis
  • Social evolution
  • African mole rats