########Meta Data######## #####B. vosnesenskii ########vos_lfmm.R##### R script for running lfmm and recalibrating P-values, and converting to q-values for false discovery correction. #######vos_maf05.eff.vcf##### VCF file with minor allele frequency of 0.05 and filtered as described in methods. Used for producing .geno, .lfmm, and bayenv2 input files. ########vos_maf05.geno######## file created using the LEA R package to run sNMF. #######vos_maf05_imputed.lfmm##### LFMM input file generated by imputation with LEA from from vos_maf05.eff.vcf general command to generate imputed data in LEA using snmf clustering results is: #snmf run (* = replace with specific vcf file name for particular species) output=vcf2geno("*.vcf") *snmf<-snmf("*.geno", K = 1:5, project = "new", repetitions = 5, CPU = 8, entropy = T) #adjust replication, CPU as needed ###imputation### output=vcf2lfmm("*.vcf") ce = cross.entropy(*snmf, K = 2) # replace K value with best value for particular sp. best = which.min(ce) impute(*snmf, "*.lfmm", method = "mode", K = 2, run = best) ########vos_bayenv2.txt##### Preliminary input file for bayenv2. Counts for each SNP are on two rows and each population is one column. The file should have as many columns as populations and as many rows as N SNPs X 2. This file must be split so that each SNP is in its own file for bayenv2 to run, as per the manual ######vos_maf05_thint.vcf###### VCF file with minor allele frequency of 0.05 and filtered as described in methods and containing only intergenic sites as designated by SNPeff. Used to generate bayenv2 input file for estimating the neutral correlation matrix: vosthintmatrix.txt ######vosthintmatrix.txt##### Neutral correlation matrix for Bayenv2 run estimated from thinned intergenic sites only. ######vosbayenv2.sh####### Shell script used to run bayenv2 on the file generated from splitting vos_bayenv2.txt using the neutral correlation matrix: vosthintmatrix.txt and environment file: vosvars.txt ######vosindivs.txt####### Specimen names present in the VCF file. Created by and used in conjunction with the bayenv2inputgeneration.sh script and various additional tasks ######allvosenvironmentalvariables.txt###### Tab delimited file with specimen name and rank order in vcf file, site, spatial data and 19 bioclim variables for each specimen ######vosallvariables.env###### Scaled environmental variables (across individuals) for each individual used as one of the LFMM inputs (converted from allvosenvironmentalvariables.txt). Contains all variables tested before final determination of thermal variables to consider. Each row is an an individual specimen in the order presented in vosindivs.txt. Each column is a spatial/environmental variable (label in # header). ######vosvars.txt##### Scaled thermal environmental variables (across populations) for each population used for testing associations in Bayenv2. Each row is an environmental variable in the order of biflfmmvars.env