################################################################################################################################

Data associated to the brief communication :

Reduced fitness associated with introgression within the Western Mediterranean admixed population of European seabass

##############################################################################
#############################

Main DATA:

VCF file with genotypes : hotsex_filtered_0.05.recode.vcf

phenotype data: HotSex_Donnee_indiv_all.txt

Description of the phenotype data column name : TAG=individual ID; baczoneD = tank; bac_L1= Tank during larval stage; Temperature= Temperature in °C; Poids_taggage= individual weigth in grams; Long_taggage= individual length in millimeters; sexe=1 for males and 2 for females

subset of phenotype data: phenotype_1850F1.txt : TAG=individual ID, temp= Temperature in °C; sexe=1 for males and 2 for females

DATA imputation with Fimpute:

Transformation of vcf data file to Fimpute format: R script vcf2Fimpute_HotSex.R

FImpute files: SNPs info file : HotSex_SNP_Fimpute.txt

Pedigree File : HotSex_pedigree_Fimpute.txt

parameters file: HotSex_genotype_FImpute_param.ctr

Individuals reared at 25°C were removed due to differential mortalities

BlupF90

BlupF90 code: 

 renumf90 HotSex_genomic_blup_3T.par 

` airemlf90 renf90.par`

Admixture

Admixture code: \
 for K in 1 2 3 4 5 ;\
 do admixture --cv Merge_Excel_HotSex_sans25.bed $K | tee log$K.out;\
` done`

Temperature, sex, weight and Atlantic ancesty

Script for the relationship between Atlantic ancestry, temperature and sex : Rscript AdmixtureVsSex.R

Script for the relationship between Atlantic ancestry, temperature and weigth : Rscript AdmixtureVsWeigth.R

Files description of all files: 

All files can be opened and viewed with text editors. 

• vcf2Fimpute_HotSex.R : R script to transform data in vcf format to Fimpute format
• hotsex_filtered_0.05.recode.vcf : genotype data for all individuals described in the publication
• HotSex_Fimpute.geno: genotype data in Fimpute format
• phenotype_1850F1.txt : phenotype data : TAG=individual ID; Temperature= Temperature in °C; sexe=1 for males and 2 for females
• genotype_blup.txt : genotype data in BlupF90 format
• genotypes_imp.txt : genotype data after Fimpute imputation
• HotSex_Donnee_indiv_all.txt : phenotype data of all individuals: TAG=individual ID; baczoneD = tank; bac_L1= Tank during larval stage; Temperature= Temperature in °C; Poids_taggage= individual weigth in grams; Long_taggage= individual length in milimeters; sexe=1 for males and 2 for females
• HotSex_SNP_Fimpute.txt : SNP information from Fimpute
• HotSex_pedigree_Fimpute.txt : Pedigree in Fimpute format
• Admixture_AquaE_Hotsex_q2.txt : results from Admixture
• AdmixtureVsWeight.R: Rscript to perform GLM from admixture results and phenotype data
• Admixture_Values_sans25.txt: Admixture results without LG25
• HotSex_genotype_FImpute_param.ctr : Parameter file for Fimute
• pheno_blup_3T.txt : Phenotype data for BlupF90
• pedigree_blup.txt : pedigree in BlupF90 format
• HotSex3trait_genomic_blup_3T.par: Parameter file for BlupF90
• popcode25.txt: Individual ID (without individuals present in the 25°C temperature treatment tank) and population Name ID (ATL=Atlantic, WEM: West Mediterranean, and EST= East Mediterranean) 
• Merge_Excel_HotSex_sans25.2.Q: Merge data used for admixture without the 25°C temperature treatment
• Admixture_Values_EST_ATL_sans25: : Admixture results without the 25°C temperature treatment