This Datta archive contains the following files:


Code:
Alpine_whitefish_WGS-v1.0.0.zip Scripts and codes for all analyses
	(DOI: https://doi.org/10.5281/zenodo.6807278 - archived from https://github.com/RishiDeKayne/Alpine_whitefish_WGS)


Raw Reads:
Raw reads can be found under the following links are under two project IDs on ENA.
  Indivs from this paper - PRJEB47792 (https://www.ebi.ac.uk/ena/browser/view/PRJEB47792)

##Indivs from Frei et al. 2022 - PRJEB43605 (https://www.ebi.ac.uk/ena/browser/view/PRJEB43605)

Main VCF file
99indiv_15mil_SNPs_output.vcf.gz




SourceData.zip Source data for all figures.

Contents of SourceData.zip
README.txt (copy of this file)

--BACKGROUND
	- background_2021_99.csv
	- SupplementaryData1.csv (SRA accessions and phenotypes for each individual used)
	
--MAIN TEXT FIGURES
  --Figure1:
    To produce Genome-wide pca file 
	- all99_filt_noout.eigenval 
	- all99_filt_noout.eigenvec
    To produce Phylogenetic tree 
	- RAxML_bipartitions.99_500kb_903904removed.GTRGAMMA.raxmlout
    To produce Admixture analysis
	- all99_filt_noout.7.Q
	- all99_filt_noout.fam


  --Figure 2:
    To produce css landscape plot  
	- all_CSS_output_100kpermutations_50000basepair50000step.window.pca.full_noheaders.txt  
	- chrom_names.txt
	- wtdbg2ChromosomeLengths.txt
    To produce css pca 
	- All_1659_allsnps_filt.eigenval 
	- All_1659_allsnps_filt.eigenvec 
    To produce standard length vs. css pc1 
	- All_1659_allsnps_filt.eigenval 
	- All_1659_allsnps_filt.eigenvec 
    To produce gill raker count vs. css pc1 
	- All_1659_allsnps_filt.eigenval 
	- All_1659_allsnps_filt.eigenvec 
    To produce allele freq of outliers 
	- *_freq.frq
    To produce gill raker gwas output 
	- emmax_GR_SNP_pvalue_output_not0.05.txt
    To produce sex gwas output 
	- emmax_sex_SNP_pvalue_output_not0.05.txt
	
	
  --Figure 3:
	- collapsed_tree_no_bootstraps_rotated.nwk
	- fbranch_collapsed.txt
	- all_new_zscore_sig.txt
	
	
--SUPPLEMENTARY FIGURES
  --Figure S1 - Phenotype info
	- background_2021_99.csv

  --Figure S2 - Cv error admixture
	- admixture_cv_error_output.txt

  --Figure S3 - Admixture
	- *.Q
	
  --Figure S4 - F4 plots
	- f4_output.txt
	
  --Figure S5 - Go enrichment length differences
	- GO_filt.out
	- gene_names1659.txt
	- allr3.genes_filt_out.txt
	- *_extractedannotation_unique_gene_names.txt
	- scaffoldannotation2.bed
	
  --Figure S6 - Full css pca
	- All_1659_allsnps_filt.eigenval XXX
	- All_1659_allsnps_filt.eigenvec XXX
	
  --Figure S7 - CSS vs. traits leave-some-out
	- All_1659_allsnps_wout_filt.eigenval XXX
	- All_1659_allsnps_wout_filt.eigenvec XXX

  --Figure S8 - Fst landscapes
	- *.fst

  --Figure S9 - Species allele frequencies
	- *.frq.out

  --Figure S10 - F-branch with boxes
	- collapsed_tree_no_bootstraps_rotated.nwk
	- fbranch_collapsed.txt
	- all_new_zscore_sig.txt
