Supporting files for Lopez, Kousathanas et al. 2018 paper in Nature Ecology and Evolution (https://www.nature.com/articles/s41559-018-0496-4).
Files provided:
Input files for fastsimcoal simulation program.
Provided (.par) files can be used to simulate 3 models described in the paper with the maximum likelihood parameter estimates.
Provided (.est) and (.tpl) files were used to obtain the maximum likelihood estimates for the three models.
There are 5 population samples: eAGR, wAGR, eRHG, wRHG, EUR, corresponding to eastern and western agriculturalists (AGR) and rainforest hunter-gatherers (RHG) and Europeans (EUR) from Belgium. The three models were developed to test three branching hypotheses EUR-first, RHG-first and AGR-first, relating to the first branching event of human populations.
SLiM input files used to simulate the mutation load trajectories. File name tags describe which simulations they were used for, i.e., dominance coefficient (h)=0.5 or h=0 or h=0.25, migration turned on and off (NOMIG), using the EUR distribution of fitness effects (DFE) or wAGR DFE (EURDFE, wAGRFE), default files use the RHG-first branching model (see paper Figure 2) and files with tag EURfirst use the EUR-first model.
5pops_AGRHUM_sel_dom=0.5_realisticsynnonsyn2EURDFE_chromindependent_fulltraj_source.slim
5pops_AGRHUM_sel_dom=0.5_realisticsynnonsyn2wAGRDFE_chromindependent_fulltraj_source.slim
5pops_AGRHUM_sel_dom=0.5_realisticsynnonsyn2wAGRDFE_EURfirst_chromindependent_fulltraj_source.slim
5pops_AGRHUM_sel_dom=0_realisticsynnonsyn2EURDFE_chromindependent_fulltraj_source.slim
5pops_AGRHUM_sel_dom=0_realisticsynnonsyn2wAGRDFE_chromindependent_fulltraj_source.slim
5pops_AGRHUM_sel_dom=0_realisticsynnonsyn2wAGRDFE_EURfirst_chromindependent_fulltraj_source.slim
5pops_AGRHUM_sel_dom=0.5_NOMIG_realisticsynnonsyn2EURDFE_chromindependent_fulltraj_source.slim
5pops_AGRHUM_sel_dom=0.5_NOMIG_realisticsynnonsyn2wAGRDFE_chromindependent_fulltraj_source.slim
5pops_AGRHUM_sel_dom=0.5_NOMIG_realisticsynnonsyn2wAGRDFE_EURfirst_chromindependent_fulltraj_source.slim
5pops_AGRHUM_sel_dom=0_NOMIG_realisticsynnonsyn2EURDFE_chromindependent_fulltraj_source.slim
5pops_AGRHUM_sel_dom=0_NOMIG_realisticsynnonsyn2wAGRDFE_chromindependent_fulltraj_source.slim
5pops_AGRHUM_sel_dom=0_NOMIG_realisticsynnonsyn2wAGRDFE_EURfirst_chromindependent_fulltraj_source.slim
5pops_AGRHUM_sel_dom=0.25_realisticsynnonsyn2wAGRDFE_chromindependent_fulltraj_source.slim