DOI: 10.5061/dryad.xwdbrv1n0
title: Reduced fitness associated with introgression within the Western Mediterranean admixed population of European seabass

description: Unraveling hybridization consequences on fitness is of main concern in
 ecology and evolution. Many studies report how evolutionary mechanisms
 modulate the mosaic of introgression within genomes but few assessed the
 associated effect of admixture on fitness traits. The Western
 Mediterranean population of the European seabass (Dicentrarchus labrax)
 results from hybridization between the Atlantic and the Mediterranean
 lineage in the Alboran Sea. By genotyping 1850 admixed fish, we assessed
 the relationship between individual admixture levels and fitness traits in
 different thermal regimes (19°C, 21°C and 23°C). Admixed individuals with
 more Atlantic ancestry displayed a biased sex ratio toward males, and were
 more sensitive to temperature variation. Additionally, they also had a
 lower body weight (which is correlated to fecundity in fish), compared to
 fish with less Atlantic ancestry. Atlantic ancestry is disadvantageous in
 the Mediterranean basin which is consistent with the previously observed
 purging of Atlantic ancestry tracts following hybridization.
description: Fish are originating from the Western Mediterranean (WEM)
 European Sea Bass (<em>Dicentrarchus labrax</em>) population. 
 Fish were reared in common garden at 16°C until 85 days post hatching
 (dph) in six replicate tanks before being divided into four different
 thermal treatments: 19°C, 21°C and 23°C with 4 replicates each, until the
 fish reached about 8 cm in length. Fish were individually tagged,
 fin-clipped for genotyping, weighed, and sexed through gonad
 observation. Fish were genotyped using the Axiom Sea
 Bass 57k SNP DlabChip array. 
description: \################################################################################################################################ ## 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