Analysis

Analysis

This directory contains several markdown files in .md format, each of which describes the order of necessary scripts to reproduce figures and tables in the main text and supplement.

Main Text Figures

• Figure 1: Data and schematic of putative demographic models.
• Figure 2: Demographic inference of common commensal gut microbes.
• Figure 3. Phylogenetically sorted distributions of fitness effects.
• Figure 4: Comparison of evolutionary summary statistics inferred from the full SFS (X-axis) versus after low-recombination and selective sweeps are removed (filtered SFS) (Y-axis).
• Figure 5: Differences in selective effects between core and accessory genes.

Supplemental Figures

• Figure S1: Effects of control and downsampling on the site-frequency spectra
• Figure S2: Akaike information criterion for one-epoch, two-epoch, and three-epoch demographic models inferred in this paper
• Figure S3: SFSs and likelihood surfaces for demographic and DFE inference with core genes
• Figure S4: Confidence intervals for nu and tau for demographic inference from core genes
• Figure S5: Neu+gamma-distributed DFE inferred from core genes
• Figure S6: Statistics for comparing within-genera and between-genera DFEs
• Figure S7: Likelihood ratio test comparing pairs of DFEs in 39 species
• Figure S8: SFSs and likelihood surfaces for demographic inference from accessory genes
• Figure S9: Empirical SFS of core and accessory genes
• Figure S10: Summary statistics inferred from the core vs. accessory genome
• Figure S11: Phylogenetically ordered analysis of core and accessory gene DFE
• Figure S12: Distribution of N_Curr for core genes

Supplemental Tables

• Table S1: Fecal sample metadata
• Table S2: Demographic inference for core genes
• Table S3: Lower and upper bounds of 95% confidence intervals of ν and time for two-epoch demographic models
• Table S4: Upper and lower bounds of 95% confidence intervals for and under two-epoch demographic model
• Table S5: Demographic inference for accessory genes
• Table S6: DFE inference for accessory genes
• Table S7: LRT statistics for core vs. accessory genes
• Table S8: Demographic inference for filtered SFS
• Table S9: DFE inference for filtered SFS