Scripts and data from Griffiths, J.S. et al. (in review) Evolutionary change in the Eastern oyster, Crassostrea virginica, following low salinity exposure.
Crosses were re-named for publication. The following table contains the cross name used in the manuscript and its associated naming scheme for sequencing and coding.
| Cross | Coding_Name |
|---|---|
| LA 1 | VB2 |
| LA 2 | VB3 |
| LA 3 | VB3_R2 |
| LA 4 | SL1 |
| LA 5 | SL2 |
| LA 6 | SL3 |
| LA 6 NS | SLNS3 |
| TX 1 | AR2 |
| TX 2 | AR3 |
| TX 3 | AR4 |
| TX 4 | AR5 |
Script: q_trimgalore1_SE, q_bowtie_oysterbait, q_mpileup, q_popoo_make_synfile, q_stat_tests, SNP_filtering.sh
Input files: Raw reads found on NCBI (accession no.: PRJNA699020), CROSS-SE_exact_rc (e.g. AR20SE_exact_rc), CROSS-SE.fet (e.g. AR2-SE.fet), Supplemental_TableS1, Oyster-input-seq.fas
Description: Folder contains scripts for trimming raw sequences (q_trimgalore1_SE), aligning to Oyster-input-seq.fas, formatting files into mpileup format and syncfiles, andd finally running popoolation2 analyses (q_stat_tests), such as Fisher's exact test (example output file: CROSS-SE.fet) and the exact allele frequency estimates (example output file AR20SE_exact_rc). SNP_filtering.sh contains code for filtering SNPs from Fisher's exact test using starting frequency and increases in frequency post-selection.
Script: PCoA_oysters.R
Input files: all_pop_exact_cov20_200_new_rc_edit2, treatments_all.txt, treatments_larvae.txt, PCoA_larval_distances.txt
Description: Script contains code for running a Principal Coordinate Analysis for all samples (parents and larvae) and larvae samples only. The script also contains adonis functions for testing significance of groups. The treatments file contains treatment info for all samples. The distance file contains Manhattan distances for larval samples pre- and post-low salinity selection from the PCoA plot.
Script: Manhattan_plot.R
Input files: CROSS-SE_sig_edit5.fet (e.g. AR2-SE_sig_edit5.fet), cvirginica_exome_genome.txt
Description: After filtering output from Fisher's exact test (see SNP_filtering.sh script), this code will apply FDR correction on pvalues. It will then filter for significant genes where there are at least three significant SNPs per gene. Finally, data formatting is performed for plotting Manhattan plots for crosses that had genes under selection and crosses that did not. The file "cvirginica_exome_genome.txt" contains general genome/chromosome size info for the Manhattan plot.
Script: Annotation.R
Input files: CROSS-SE_sig_edit5.fet (e.g. AR2-SE_sig_edit5.fet), Supplemental_TableS1
Description: Script contains code for determining if genes under seleciton for each cross were enriched in a particular functional or source category (information contained in the file "Supplemental_TableS1".
Script: SNP_position_enrichment_analysis.R
Input files: Annotated Probe Report for CROSS_start.txt (e.g. Annotated Probe Report for AR2_start.txt), Annotated Probe Report for CROSS_sig_SNPs.txt (e.g. Annotated Probe Report for AR2_sig_SNPs.txt), Supplemental_TableS1
Description: Script contains code for determining if genes under selection for each cross were more likely to be found upstream, downstream, or within the gene body. Input files contain SNP positions before selection (start files) and after selection for significant SNPs (sig files).