Table 1.

Examples of introductory reviews for further information on each of the groups of methods covered in each section of the current review, and of useful R packages for each group of methods. Sections are given an abbreviated title and their number for clarity. Numbers in the ‘introductory review(s)’ column refer to the numbers in the reference section. References for R packages are given only on their first mention, and packages mention under ‘general comparative biology’ are useful for most of the other sections but are not repeated for each for brevity.

Section	Introductory Reviews	R Packages
General comparative biology	[10,13,15,16,17,18,19,20]	ape [21]; phytools [22]
Accounting for phylogeny (2)	[23,24]	caper [25]; MCMCglmm [26]; phylolm [27]
Estimating ancestral states (3)	[28,29]	corHMM [30]; diversitree [31]
Trait evolution models (4)	[17,19,20]	corHMM; diversitree; geiger [32]
Evolutionary pathways (5)	[33,34,35]	corHMM
Convergent evolution (6)	[36,37,38]	convevol [39]; surface [40]; windex [41]
Diversification dynamics (7)	[31,42,43,44]	BAMMtools [45]; diversitree; geiger