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Table S7

Supplemental Table 7 details the likelihood ratio test statistic comparing the DFE of core and accessory genes for the 18 species we performed this analysis over.

To recreate this table, you must:

Perform demographic inference using Dadi

An example .bash script which performs demographic inference using Dadi for all of the species analyzed in this paper can be found at ../Scripts/fit_demographic_model.bash. Uncomment appropriate lines to do so for core genes and for accessory genes.

Fit the Distribution of Fitness Effects (DFE) using FitDadi

An example .bash script which fits the DFE using FitDadi for all of the species analyzed in this paper can be found at ../Scripts/fit_dfe.bash. Uncomment appropriate lines to do so for core genes and for accessory genes.

Compare the DFE between core and accessory genes

This was performed using two different null expectations: one in which the selection coefficient s is assumed constant between two sets of genes, and one in which we assume that the population-scaled selection coefficient 2N_Anc*s is assumed constant between two sets of genes. Uncomment appropriate lines to do so for core genes and for accessory genes.

  • To compare DFEs using a null expectation of s, an example .bash script which does so for all of the species analyzed in this paper can be found at ../Scripts/constant_s_dfe.bash.
  • To compare DFEs using a null expectation of 2N_Anc*s, an example .bash script which does so for all of the species analyzed in this paper can be found at ../Scripts/cross_species_dfe_inference.bash.

generate_tables.R

This .R script generates all novel supplemental tables and saves them automatically in Supplement.