Skip to main content
SpringerLink
Log in

Phylogenetic Analysis Within Comparative Psychology

  • Reference work entry
  • First Online:
Encyclopedia of Evolutionary Psychological Science

Synonyms

Independent contrasts; Model comparison; Phylogenetic comparative methods; Phylogenetic generalized least squares regression; Phylogenetic meta-analysis; Phylogenetic path analysis; Phylogenetic signal

Definition

A class of statistical methods that incorporate information about phylogeny in order to test evolutionary hypotheses.

Introduction

Phylogenetic comparative methods are an array of statistical procedures developed to analyze evolutionary models including the reconstruction of ancestral traits; the coevolution of morphological, physiological, behavioral, and cognitive features; the effects of socioecological factors upon these characteristics; and the degree of evolutionary diversification and extinction, among others (Nunn 2011). The pertinence of their use is due to the fact that closely related species are expected to resemble more to each other than more distant taxa. This poses serious pseudo-replication issues at the time of conducting statistical analyses....

This is a preview of subscription content, log in via an institution to check access.

Access this chapter

Log in via an institution

Institutional subscriptions

References

  • Abouheif, E. (1999). A method for testing the assumption of phylogenetic independence in comparative data. Evolutionary Ecology Research, 1(8), 895–909.

    Google Scholar 

  • Adams, D. C. (2008). Phylogenetic meta-analysis. Evolution, 62(3), 567–572.

    Article  PubMed  Google Scholar 

  • Blomberg, S. P., Garland, T., Jr., & Ives, A. R. (2003). Testing for phylogenetic signal in comparative data: Behavioral traits are more labile. Evolution, 57(4), 717–745.

    Article  PubMed  Google Scholar 

  • Blomberg, S. P., Lefevre, J. G., Wells, J. A., & Waterhouse, M. (2012). Independent contrasts and PGLS regression estimators are equivalent. Systematic Biology, 61(3), 382–391.

    Article  PubMed  Google Scholar 

  • Butler, M. A., & King, A. A. (2004). Phylogenetic comparative analysis: A modeling approach for adaptive evolution. The American Naturalist, 164(6), 683–695.

    Article  PubMed  Google Scholar 

  • Chamberlain, S. A., Hovick, S. M., Dibble, C. J., Rasmussen, N. L., Van Allen, B. G., Maitner, B. S., ... & Carrillo, J. (2012). Does phylogeny matter? Assessing the impact of phylogenetic information in ecological meta-analysis. Ecology Letters, 15(6), 627–636.

    Google Scholar 

  • Felsenstein, J. (1985). Phylogenies and the comparative method. The American Naturalist, 125(1), 1–15.

    Article  Google Scholar 

  • FitzJohn, R. G. (2010). Quantitative traits and diversification. Systematic Biology, 59(6), 619–633.

    Article  PubMed  Google Scholar 

  • Freckleton, R. P., Harvey, P. H., & Pagel, M. (2002). Phylogenetic analysis and comparative data: A test and review of evidence. The American Naturalist, 160(6), 712–726.

    Article  PubMed  Google Scholar 

  • Gonzalez-Voyer, A., & Von Hardenberg, A. (2014). An introduction to phylogenetic path analysis. In L. Z. Garamszegi (Ed.), Modern phylogenetic comparative methods and their application in evolutionary biology (pp. 201–229). Berlin: Springer.

    Chapter  Google Scholar 

  • Grafen, A. (1989). The phylogenetic regression. Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences, 326(1233), 119–157.

    PubMed  Google Scholar 

  • Hansen, T. F. (1997). Stabilizing selection and the comparative analysis of adaptation. Evolution, 51(5), 1341–1351.

    Article  PubMed  Google Scholar 

  • Hardenberg, A. V., & Gonzalez-Voyer, A. (2013). Disentangling evolutionary cause-effect relationships with phylogenetic confirmatory path analysis. Evolution, 67(2), 378–387.

    Article  Google Scholar 

  • Harmon, L. J., Losos, J. B., Jonathan Davies, T., Gillespie, R. G., Gittleman, J. L., Bryan Jennings, W., ... & Purvis, A. (2010). Early bursts of body size and shape evolution are rare in comparative data. Evolution, 64(8), 2385–2396.

    Google Scholar 

  • Higgins, J. P., Thompson, S. G., Deeks, J. J., & Altman, D. G. (2003). Measuring inconsistency in meta-analyses. British Medical Journal, 327(7414), 557–560.

    Article  PubMed  PubMed Central  Google Scholar 

  • Ingram, T., Harmon, L. J., & Shurin, J. B. (2012). When should we expect early bursts of trait evolution in comparative data? Predictions from an evolutionary food web model. Journal of Evolutionary Biology, 25(9), 1902–1910.

    Article  PubMed  Google Scholar 

  • Ives, A. R., & Garland, T. (2010). Phylogenetic logistic regression for binary dependent variables. Systematic Biology, 59(1), 9–2.

    Article  PubMed  Google Scholar 

  • Ives, A. R., & Garland, T., Jr. (2014). Phylogenetic regression for binary dependent variables. In L. Z. Garamszegi (Ed.), Modern phylogenetic comparative methods and their application in evolutionary biology (pp. 231–261). Berlin: Springer.

    Chapter  Google Scholar 

  • Lajeunesse, M. J. (2009). Meta-analysis and the comparative phylogenetic method. The American Naturalist, 174(3), 369–381.

    Article  PubMed  Google Scholar 

  • Lajeunesse, M. J., Rosenberg, M. S., & Jennions, M. D. (2013). Phylogenetic nonindependence and meta-analysis. In J. Koricheva, J. Gurevitch, & K. Mengersen (Eds.), Handbook of meta-analysis in ecology and evolution (pp. 284–299). New York: Princeton University Press.

    Google Scholar 

  • Maclean, E. L., & Nunn, C. L. (2017). Phylogenetic approaches for research in comparative cognition. In J. Call (Ed.), APA handbook of comparative psychology: vol 1. Basic concepts, methods, neural substrate, and behavior. Washington, DC: American Psychological Association.

    Google Scholar 

  • Maddison, W. P., & Slatkin, M. (1991). Null models for the number of evolutionary steps in a character on a phylogenetic tree. Evolution, 45(5), 1184–1197.

    Article  PubMed  Google Scholar 

  • Moran, P. A. (1950). Notes on continuous stochastic phenomena. Biometrika, 37(1/2), 17–23.

    Article  PubMed  Google Scholar 

  • Navarro, D. (2013). Learning statistics with R. Adelaide: University of Adelaide.

    Google Scholar 

  • Nunn, C. L. (2011). The comparative approach in evolutionary anthropology and biology. Chicago: University of Chicago Press.

    Book  Google Scholar 

  • Pagel, M. (1994). Detecting correlated evolution on phylogenies: A general method for the comparative analysis of discrete characters. Proceedings of the Royal Society of London B, 255(1342), 37–45.

    Article  Google Scholar 

  • Pagel, M. (1999). Inferring the historical patterns of biological evolution. Nature, 401(6756), 877–884.

    Article  PubMed  Google Scholar 

  • Pagel, M. D. (2002). Modelling the evolution of continuously varying characters on phylogenetic trees. In N. MacLeod & P. L. Foley (Eds.), Morphology, shape and phylogeny (pp. 269–286). London: Taylor and Francis.

    Chapter  Google Scholar 

  • Paradis, E. (2006). Analysis of phylogenetics and evolution with R. New York: Springer Science & Business Media.

    Book  Google Scholar 

  • Rosenberg, M. S. (2005). The file-drawer problem revisited: A general weighted method for calculating fail-safe numbers in meta-analysis. Evolution, 59(2), 464–468.

    Article  PubMed  Google Scholar 

  • Rosenthal, R. (1979). The file drawer problem and tolerance for null results. Psychological Bulletin, 86(3), 638–641.

    Article  Google Scholar 

  • Shipley, B. (2000). A new inferential test for path models based on directed acyclic graphs. Structural Equation Modeling, 7(2), 206–218.

    Article  Google Scholar 

  • Shipley, B. (2013). The AIC model selection method applied to path analytic models compared using ad-separation test. Ecology, 94(3), 560–564.

    Article  PubMed  Google Scholar 

  • Shipley, B. (2016). Cause and correlation in biology: A user’s guide to path analysis, structural equations and causal inference with R. Cambridge, MA: Cambridge University Press.

    Book  Google Scholar 

  • Simpson, G. G. (1953). The major features of evolution. New York: Columbia University Press.

    Book  Google Scholar 

  • Swenson, N. G. (2014). Functional and phylogenetic ecology in R. New York: Springer.

    Book  Google Scholar 

  • Symonds, M. R., & Blomberg, S. P. (2014). A primer on phylogenetic generalised least squares. In L. Z. Garamszegi (Ed.), Modern phylogenetic comparative methods and their application in evolutionary biology (pp. 105–130). Berlin: Springer.

    Chapter  Google Scholar 

  • Von Neumann, J., Kent, R. H., Bellinson, H. R., & Hart, B. T. (1941). The mean square successive difference. The Annals of Mathematical Statistics, 12(2), 153–162.

    Article  Google Scholar 

Download references

Author information

Authors and Affiliations

  1. Department of Psychology, University of Arizona, Tucson, AZ, USA

    Mateo Peñaherrera Aguirre & Heitor BarcellosFerreira Fernandes

  2. Department of Psychology, University of New Brunswick, Fredericton, NB, Canada

    Mateo Peñaherrera Aguirre

  3. Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil

    Heitor BarcellosFerreira Fernandes

Authors
  1. Mateo Peñaherrera Aguirre
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Heitor BarcellosFerreira Fernandes
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Mateo Peñaherrera Aguirre .

Editor information

Editors and Affiliations

  1. Department of Psychology, Oakland University, Rochester, MI, USA

    Todd K Shackelford

  2. Department of Psychology, Oakland University, Rochester, MI, USA

    Viviana A Weekes-Shackelford

Section Editor information

  1. University of Redlands, Redlands, CA, USA

    Catherine Salmon

Rights and permissions

Reprints and permissions

Copyright information

© 2021 Springer Nature Switzerland AG

About this entry

Check for updates. Verify currency and authenticity via CrossMark

Cite this entry

Peñaherrera Aguirre, M., Fernandes, H.B. (2021). Phylogenetic Analysis Within Comparative Psychology. In: Shackelford, T.K., Weekes-Shackelford, V.A. (eds) Encyclopedia of Evolutionary Psychological Science. Springer, Cham. https://doi.org/10.1007/978-3-319-19650-3_3605

Download citation

Publish with us

Policies and ethics

Search

Navigation