13 Further readings

To undertand well a new research field, it is always advisable to read a lot on it. Here are some references that you might find useful. The different sources also sometimes explain the theory in different ways or use different examples, which might help you understand better.

  • Felsenstein, J. (1985) Phylogenies and the comparative method. The American Naturalist 125, 1-15. The classic initial paper that launched the field of comparative analyses. The phylogenetic independent contrasts are introduced here
  • Felsenstein, J. (2004) Inferring phylogenies. Sinauer Associates, Inc. Sunderland, MA. A thorough reference on phylogenies, from reconstruction to phylogenetic methods
  • Hadfield, J. D., S. Nakagawa. 2010. General quantitative genetic methods for comparative biology: phylogenies, taxonomies and multi-trait models for continuous and categorical characters. Journal of Evolutionary Biology 23:494–508. This paper describes the phylogenetic mixed model and its implementation in MCMCglmm. It is a very important paper
  • Housworth, E.A., E.P. Martins, M. Lynch. 2004. The phylogenetic mixed model. The American Naturalist 163:84–96. Excellent paper on the Phylogenetic Mixed Model
  • Paradis, E. (2012). Analysis of phylogenetics and evolution with R. New York, USA: Springer. This is the book that explains the analyses available in the R package APE. It is also a great reference on many phylogenetic analyses, including the comparative method. This is a classic and a must for users of phylogenies in R.
  • Revell, L J. (2010). Phylogenetic signal and linear regression on species data. Methods in Ecology and Evolution 1: 319-329. A great paper on PGLS. It uses simulations to show when it is important to use PGLS.
  • Villemereuil, P., S. Nakagawa. 2014. General quantitative genetic methods for comparative biology. Pp. 287–303 in L. Z. Garamszegi, ed. Modern phylogenetic comparative methods and their application in evolutionary biology. Springer-Verlag, Berlin, Heidelberg. Nice book chapter explaining the phylogenetic mixed model
  • Zuur, A.F., E.N. Ieno, N. Walker, A. A. Saveliev, G.M. Smith. (2009). Mixed effects models and extensions in ecology with R. New York, NY: Springer New York. This is not a book on phylogenetic methods, but it is a great book on the analysis of ecological data with examples in R. Its chapter 6 and 7 discuss correlation structures and although they are not about phylogenies, they are very instructive on how to deal with them and how to compare models and analyse complex data. It also has tons of information on how to deal with more complex data, along with correlation structure. A very good read!