https://doi.org/10.5061/dryad.0k6djhb6t

Code and data associated with analysis and figures.

Sharing/Access information

The full list of NCBI Sequence Read Archive accessions can be found at https://dx.doi.org/10.6084/m9.figshare.c.4440284

Code/Software

Figures were generated with R, scripts split up by figure/analysis type.

Details by file

Data

• BayPass_manual.pdf Baypass Software Manual (Version 2.1). Includes complete description of output files and the variables therein starting on page 21.

• Z.csv

  • Key relating sequence library names to treatments. Columns are sample prefix and dummy variables to indicate which treatment each sample was from (founder, core, edge, shuffled).

• baypass_r0.98_d3_L3_M30_q0.99_a35.txt, tribolium.covariates, tribolium.poolsize

  • Input files required to run Baypass and generate outlier loci. See BayPass_manual.pdf for more details about file formats.

• aux_model_summary_yij_pij.out, aux_model_summary_betai.out, core_model_mat_omega.out

  • Unmodified output files generated by Baypass required or downstream analyses. See BayPass_manual.pdf for more details about file formats.

• suppmat_outlier_df.csv

  • Merged information for all outlier loci including genome position and Bayes factors. The first columns (COVARIABLE,MRK,M_Beta,SD_Beta,M_Delta,BF.dB) are generated by Baypass (see page 23 of the BayPass_manual.pdf for description of the (outprefix_)summary_pij.out file format). The subsequent columns are:

    • treatment - which treatment (founder, core, edge, shuffled) the outlier locus the outlier was found in.
    • chrom - The chromosome name for the outlier locus
    • pos - The zero-indexed position of the outlier locus
    • pos2 - The one-indexed position of the outlier locus
    • ref_alt - The reference and alternate nucleotide found at the locus
    • freq - The reference allele frequency at the locus

    • chrom_num - Simplified chromosome name for the outlier locus used for plotting

      The following columns following the VCF format, some of which are redundant with the previous columns but were kept as a sanity check after merging several data frames.

    • CHROM - Identical to chrom

    • POS - Identical to pos

    • ID - Unique identifier used for filtering consisting of values from chrom, pos, and ref_alt

    • REF - The reference nucleotide found at the locus

    • ALT - The alternate nucleotide found at the locus

    • QUAL - Unused column mandatory for VCF format and kept as "." following conventions for the format.

    • FILTER - Unused column mandatory for VCF format and kept as "." following conventions for the format.

    • INFO - Additional information about the locus. In this case output from the Variant Effect Predictor (VEP) software indicting what functional part of the genome the locus fell into (if any).

• core_freq_PCA.csv

  • Principal components of allele frequencies

• GO_summary.txt

  • Final GO output containing p values averaged across genes and treatments that were discovered in.

• go_shuffled.txt, go_founder.txt, go_edge.txt, go_core.txt

  • Genes identified with outliers used as input for GO analyses

• go_shuffled_out.txt, go_founder_out.txt, go_edge_out.txt, go_core_out.txt

  • Output files for GO analyses

software

• fais_baypass.py
  • Script for making input for Baypass from bam files
• make_files.sh
  • Steps for running Baypass
• helper_functions.R
  • functions and file loading used in other scripts
• go.R
  • Steps for selecting genes for GO analysis
• TABLE2_allsites_catogries.R
  • Steps for identifying where loci of interest fall with respect to genome content.
• get_conserved_pij.py
  • Helper script to filter for conserved loci.
• FIGURE1_pca_viz.R
  • Steps to create PCA figure.
• FIGURE2_baypass_BFmc.R
  • Steps to create outlier figure.
• cons_pipeline.sh
  • Steps to indentify conserved loci.
• run_mummer.sh
  • Script to run mummer
• FIGURE5_conserved_sites.R
  • Steps to create distribution of allele frequencies at conserved loci.