Supplement 1. Matlab code for phylogenetic linear mixed models (PLMMs).

File List bipartitePLMM.m (MD5: 1faa3ddc7f0b798584516c24a25f0910) LMM_ML_funct.m (MD5: b349b7e49bad43c44c712d6f95b25223) LMM_REML_funct.m (MD5: 50543ce9f7389cfaf48de292576add19) Example_bipartitePLMM_11Apr13.m (MD5: efb0763a133c4320794b326724d16f94) anneal.m (MD5: 70672ad1d98fcf004cea433bbcbc214d) insectVforMatlab_7Apr11.txt (MD5: 79c98da8147d38241d9405d17605b8da) plantVforMatlab_14Apr11.txt (MD5: 70aad149b8a565dc21753a5d23ef97fb) Description bipartitePLMM.m – This function is the general workhorse for bipartite PLMMs. It can be configured to perform the analyses of both equations 2 and 3 in the main text. LMM_ML_funct.m – This is a dependency program for bipartitePLMM.m that computes the likelihood function. LMM_REML_funct.m – This is a dependency program for bipartitePLMM.m that computes the restricted likelihood function. Example_bipartitePLMM_11Apr13.m – This function runs bipartitePLMM.m for the simulations used to produce figures 2 and 3 in the main text. anneal.m – This is a dependency program for bipartitePLMM.m that performs simulated annealing. It was written by Joachim Vandekerckhove and is publicly available at http://www.mathworks.com/matlabcentral/fileexchange/authors/23107. insectVforMatlab_7Apr11.txt – File giving the phylogenetic covariance matrix for insects used in the analyses. plantVforMatlab_14Apr11.txt – File giving the phylogenetic covariance matrix for plants used in the analyses.