Supplement 1. Annotated computer code in Matlab and SAS for performing the simulations and analyses in examples 1–4.

File List <b><i>Text file</i></b> fullV.txt <b><i>Matlab executable files</i></b> IZ_GLSeg.m IZ_SPACEeg.m Space_MLfunct.m IZ_TIMEeg.m Time_MLfunct.m IZ_MIXEDeg.m IZ_MIXEDegRep.m <b><i>SAS executable files</i></b> SASMIXEDeg.sas SASMIXEDegREG.sas <b><i>File descriptions</i></b> IZ_GLSeg.m – Matlab code simulating and analyzing phylogenetic data as in example #1 fullV.txt – Text file containing covariance matrix needed for IZ_GLSeg.m IZ_SPACEeg.m – Matlab code simulating and analyzing spatial data as in example #2 Space_MLfunct.m – Matlab function giving the likelihood function called by IZ_SPACEeg.m IZ_TIMEeg.m – Matlab code simulating and analyzing time-series data as in example #3 Time_MLfunct.m – Matlab function giving the likelihood function called by IZ_TIMEeg.m IZ_MIXEDeg.m – Matlab code simulating a single data set with spatial and temporal corelations as in example #4 IZ_MIXEDegRep.m – Matlab code simulating multiple data sets with spatial and temporal corelations as in example #4 SASMIXEDeg.sas – SAS code using REML to analyze a single data set produced by IZ_MIXEDeg.m SASMIXEDegREG.sas – SAS code using REML to analyze multiple data sets produced by IZ_MIXEDegRep.m Description Matlab ".m" files are text files that should run under Matlab version 5.0 and 6.5 (MathWorks 1996). The two programs used for example #4, IZ_MIXEDeg.m and IZ_MIXEDegRep.m, generate text files called 'mixedeg.txt'and 'mixedegrep.txt', respecitvely. These text files are then analyzed by the two SAS programs, SASMIXEDeg.sas and SASMIXEDegREG.sas, respectively, which are written in SAS version 6.12 (SAS 1996). To run the SAS programs, the infile line will have to be changed to set the path to the files mixedeg.txt and mixedegrep.txt. The current infile line in SASMIXEDeg.sas is infile 'Macintosh HD:mixedeg.txt'; which finds the file mixedeg.txt on the hard drive 'Macintosh HD'. All files should run under Macintosh, Windows, and Unix operating systems.