Reduced fitness associated with introgression within the Western Mediterranean admixed population of European seabass
Data files
Apr 01, 2025 version files 660.90 MB
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Admixture_AquaE_Hotsex_q2.txt
166.17 KB
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Admixture_Values_EST_ATL_sans25
114.31 KB
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Admixture_Values_sans25.txt
82.96 KB
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AdmixtureVsWeight.R
1.71 KB
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genotype_blup.txt
92.49 MB
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genotypes_imp.txt
94.06 MB
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HotSex_Donnee_indiv_all.txt
92.81 KB
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hotsex_filtered_0.05.recode.vcf
377.85 MB
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HotSex_Fimpute.geno
94.07 MB
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HotSex_genotype_FImpute_param.ctr
356 B
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HotSex_pedigree_Fimpute.txt
91.59 KB
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HotSex_SNP_Fimpute.txt
1.53 MB
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HotSex3trait_genomic_blup_3T.par
799 B
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Merge_Excel_HotSex_sans25.2.Q
62.03 KB
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pedigree_blup.txt
95.34 KB
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pheno_blup_3T.txt
64.95 KB
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phenotype_1850F1.txt
40.72 KB
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popcode25.txt
77.17 KB
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README.md
3.64 KB
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vcf2Fimpute_HotSex.R
2.68 KB
Abstract
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.
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Data associated to the brief communication :
Reduced fitness associated with introgression within the Western Mediterranean admixed population of European seabass
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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
Fish are originating from the Western Mediterranean (WEM) European Sea Bass (Dicentrarchus labrax) 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.