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This software contains the computer code of "Evo-devo dynamics of hominin brain size" by Mauricio González-Forero. Below I describe and explain the files needed to run the brain model and make the figures in the main text and supplementary information. These files were prepared to run in Julia 1.7.2 using the editor Visual Studio Code 1.81.1. Julia and Visual Studio Code can be installed as indicated in https://www.julia-vscode.org/docs/dev/gettingstarted/. The files are divided in five sets. To run these files, run the afarensis scenario first as explained in Set 2 below since its solution is used for the other scenarios. The second line of each file changes directory to the working directory. Enter there the path of your working directory in each file. Set 1 RunBrain.jl: Main file. Run this file to run the brain model. BrainParameters.jl: This file specifies the parameter values. BrainFunctions.jl: This file defines the functions used to run the brain model, except for the functions used in the socio-devo dynamics phase. BrainFunctionsSDS.jl: This file defines the functions used in the socio-devo dynamics phase. Set 2 SixHomoPlot.jl: This file makes the plot of Fig. 1 of the main text. This file loads the solutions of the seven scenarios, so they must be run before running this file. To run each scenario, set the corresponding parameter values in BrainParameters.jl and then run RunBrain.jl. Run the afarensis scenario first as its solution is used for the other scenarios. Parameter values to be set in BrainParameters.jl: afarensis: yinit = 6, competence = 1, cooperation 3, P1 = 0.0, P2 = 0.9, P3 = 0.0, P4 = 0.1. sapiens: yinit = 7, competence = 2, cooperation 3, P1 = 0.6, P2 = 0.3, P3 = 0.0, P4 = 0.1. neanderthal: yinit = 7, competence = 2, cooperation 3, P1 = 0.8, P2 = 0.2, P3 = 0.0, P4 = 0.0. heidelbergensis: yinit = 7, competence = 2, cooperation 3, P1 = 0.4, P2 = 0.6, P3 = 0.0, P4 = 0.0. erectus: yinit = 7, competence = 1, cooperation 1, P1 = 0.8, P2 = 0.2, P3 = 0.0, P4 = 0.0. ergaster: yinit = 7, competence = 1, cooperation 1, P1 = 0.5, P2 = 0.5, P3 = 0.0, P4 = 0.0. habilis: yinit = 7, competence = 1, cooperation 1, P1 = 0.1, P2 = 0.6, P3 = 0.1, P4 = 0.2. Set 3 allometry-plot.jl: This file makes the plot of Fig. 2b. Run this file after having run the afarensis and sapiens scenarios. Set 4 MakeBrainPlots.jl: This file makes the plots for Figs. 3, 4, and 6 of the main text, Extended Data Figs. 1-3 and Figs. S1-S7 and S9-S11 of the Supplementary Materials. As described in each of these figures, they have different parameter values or ancestral conditions, which must be entered in BrainParameters.jl. This file contains code to make many different kinds of plots but it does not need to be run all at once. Run only the first 72 lines and then run only the part of the file with the plot you want to make. BrainPlotFunctions.jl: This file defines the functions used to make these plots. Set 5 PlotBrainAllometry-Randomy.jl: This file makes the plots for Fig. 2a of the main text and Fig. S8 of the Supplementary Information. To make these figures, in BrainParameters.jl, set the parameter \tauend to 1000000 (this specifies the sample size) and yinit to 1 (this is so that no file with ancestral conditions is loaded). xFunction.jl: This file defines the phenotype x as a function of the genotype y, which is used to compute the phenotype with random genotypes in PlotBrainAllometry-Randomy.jl.
Evolution, Evo-devo, Brain, Model, Dynamics
Evolution, Evo-devo, Brain, Model, Dynamics
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