DOI: 10.5061/dryad.1h48b38
title: Data from: Balancing selection and introgression of newt immune-response genes

description: The importance of interspecific introgression as a source of adaptive
 variation is increasingly recognized. Theory predicts that beneficial
 genetic variants cross species boundaries easily even when interspecific
 hybridization is rare and gene flow is strongly constrained throughout the
 genome. However, it remains unclear whether certain classes of genes are
 particularly prone to adaptive introgression. Genes affected by balancing
 selection (BS) may constitute such a class, because forms of BS that favor
 novel, initially rare alleles, should facilitate introgression. We tested
 this hypothesis in hybridizing newts by comparing 13 genes with signatures
 of BS, in particular an excess of common nonsynonymous polymorphisms, to
 the genomic background (154 genes). Parapatric hybridizing taxa were less
 differentiated in BS candidate genes than more closely related allopatric
 lineages, while the opposite was observed in the control genes. Coalescent
 and forward simulations that explored neutral and BS scenarios under
 isolation and migration, showed that processes other than differential
 gene flow are unlikely to account for this pattern. We conclude that BS,
 probably involving a form of novel allele advantage, promotes
 introgression. This mechanism may be a source of adaptively relevant
 variation in hybridizing species over prolonged periods.
description: Reference BS11 gene
 sequencesFasta sequences of 11
 candidate genes under balancing selection selected from Lissotriton
 transcriptome (NewtBase)balancing11.fastaReference control (CR) gene sequencesFasta sequences of control genes randomly selected from Lissotriton transcriptome (NewtBase)random178.fastaSNP variants in BS11 genesSNP variants called with GATK in six Lissotriton lineages and 2 outgroup speciesBS11_SNPs_gatk.vcf.gzSNP variants in CR genesSNP variants called with GATK in six Lissotriton lineages and 2 outgroup speciesCR_SNPs_gatk.vcf.gzGenotypes for BS11 genes in Lissotriton vulgaris ampelensisGenotypes called with GATK in Lissotriton vulgaris ampelensisBS11_GENO_gatk_ampelensis.vcfGenotypes for BS11 genes in Lissotriton graecusGenotypes called with GATK in Lissotriton graecusBS11_GENO_gatk_graecus.vcfGenotypes for BS11 genes in Lissotriton helveticusGenotypes called with GATK in Lissotriton helveticusBS11_GENO_gatk_helveticus.vcfGenotypes for BS11 genes in Lissotriton italicusGenotypes called with GATK in Lissotriton italicusBS11_GENO_gatk_italicus.vcfGenotypes for BS11 genes in Lissotriton kosswigiGenotypes called with GATK in Lissotriton kosswigiBS11_GENO_gatk_kosswigi.vcfGenotypes for BS11 genes in Lissotriton montandoniGenotypes called with GATK in Lissotriton montandoniBS11_GENO_gatk_montandoni.vcfGenotypes for BS11 genes in Lissotriton schmidtleriGenotypes called with GATK in Lissotriton schmidtleriBS11_GENO_gatk_schmidtleri.vcfGenotypes for BS11 genes in Lissotriton vulgaris vulgarisGenotypes called with GATK in Lissotriton vulgaris vulgarisBS11_GENO_gatk_vulgaris.vcfGenotypes for CR genes in Lissotriton vulgaris ampelensisGenotypes for CR genes called with GATK in Lissotriton vulgaris ampelensisCR_GENO_gatk_ampelensis.vcfGenotypes for CR genes in Lissotriton graecusGenotypes for CR genes called with GATK in Lissotriton graecusCR_GENO_gatk_graecus.vcfGenotypes for CR genes in Lissotriton helveticusGenotypes for CR genes called with GATK in Lissotriton helveticusCR_GENO_gatk_helveticus.vcfGenotypes for CR genes in Lissotriton italicusGenotypes for CR genes called with GATK in Lissotriton italicusCR_GENO_gatk_italicus.vcfGenotypes for CR genes in Lissotriton kosswigiGenotypes for CR genes called with GATK in Lissotriton kosswigiCR_GENO_gatk_kosswigi.vcfGenotypes for CR genes in Lissotriton montandoniGenotypes for CR genes called with GATK in Lissotriton montandoniCR_GENO_gatk_montandoni.vcfGenotypes for CR genes in Lissotriton schmidtleriGenotypes for CR genes called with GATK in Lissotriton schmidtleriCR_GENO_gatk_schmidtleri.vcfGenotypes for CR genes in Lissotriton vulgaris vulgarisGenotypes for CR genes called with GATK in Lissotriton vulgaris vulgarisCR_GENO_gatk_vulgaris.vcfGenotypes for TAP1 gene in LissotritonFasta sequences containing concatenated exon sequences of TAP1 gene genotyped in six Lissotriton lineages and an outgroupGenotypes_TAP1.fastaMHCI allelesMHC class I gene alleles in Lissotriton lineagesAlleles_MHC_I_Mon_North_South.fasMHC class I gene genotypes in LissotritonMHC class I gene genotypes in Lissotriton lineagesMHC_I_genotypes_Mon_North_South.xlsxForward simulation script NEUTRALITY M0Forward simulation script for the scenario: Neutrality, migration = 0. Script run in SLiM v2.5. Example command to run the script: "./slim -d simnum=00000 -d u=1.17e-7 -d locus=0 example_simulation_6_pops_00000_0.txt". example_simulation_6_pops_00000_0.txt - name of the SLiM script with one simulation specification; simnum - simulation number; u - locus mutation rate; locus - locus number.slim_simulations_NEUTRALITY_m0.txtSLiM simulation script NEUTRALITY M1Forward simulation script for the scenario: Neutrality, migration M1 = 5.0E-07. Script run in SLiM v2.5. Example command to run the script: "./slim -d simnum=00000 -d u=1.17e-7 -d locus=0 example_simulation_6_pops_00000_0.txt". example_simulation_6_pops_00000_0.txt - name of the SLiM script with one simulation specification; simnum - simulation number; u - locus mutation rate; locus - locus number.slim_simulations_NEUTRALITY_m1.txtSLiM simulation script NEUTRALITY M2Forward simulation script for the scenario: Neutrality, migration M2 = 1.8E-06. Script run in SLiM v2.5. Example command to run the script: "./slim -d simnum=00000 -d u=1.17e-7 -d locus=0 example_simulation_6_pops_00000_0.txt". example_simulation_6_pops_00000_0.txt - name of the SLiM script with one simulation specification; simnum - simulation number; u - locus mutation rate; locus - locus number.slim_simulations_NEUTRALITY_m2.txtSLiM simulation script NEUTRALITY M3Forward simulation script for the scenario: Neutrality, migration M3 = 2.36E-06. Script run in SLiM v2.5. Example command to run the script: "./slim -d simnum=00000 -d u=1.17e-7 -d locus=0 example_simulation_6_pops_00000_0.txt". example_simulation_6_pops_00000_0.txt - name of the SLiM script with one simulation specification; simnum - simulation number; u - locus mutation rate; locus - locus number.slim_simulations_NEUTRALITY_m3.txtSLiM simulation script moderate NFD M0Forward simulation script for the scenario: moderate negative frequency-dependent selection, migration M0 = 0. Script run in SLiM v2.5. Example command to run the script: "./slim -d simnum=00000 -d u=1.17e-7 -d locus=0 example_simulation_6_pops_00000_0.txt". example_simulation_6_pops_00000_0.txt - name of the SLiM script with one simulation specification; simnum - simulation number; u - locus mutation rate; locus - locus number.slim_simulations_NFD_medium_m0.txtSLiM simulation script moderate NFD M1Forward simulation script for the scenario: moderate negative frequency-dependent selection, selection strength s = 0.05, migration M1 = 5.0E-07. Script run in SLiM v2.5. Example command to run the script: "./slim -d simnum=00000 -d u=1.17e-7 -d locus=0 example_simulation_6_pops_00000_0.txt". example_simulation_6_pops_00000_0.txt - name of the SLiM script with one simulation specification; simnum - simulation number; u - locus mutation rate; locus - locus number.slim_simulations_NFD_medium_m1.txtSLiM simulation script moderate NFD M3Forward simulation script for the scenario: moderate negative frequency-dependent selection, selection strength s = 0.05, migration M3 = 2.36E-06. Script run in SLiM v2.5. Example command to run the script: "./slim -d simnum=00000 -d u=1.17e-7 -d locus=0 example_simulation_6_pops_00000_0.txt". example_simulation_6_pops_00000_0.txt - name of the SLiM script with one simulation specification; simnum - simulation number; u - locus mutation rate; locus - locus number.slim_simulations_NFD_medium_m3.txtSLiM simulation script strong NFD M0Forward simulation script for the scenario: strong negative frequency-dependent selection, selection strength s = 0.5, migration M0 = 0. Script run in SLiM v2.5. Example command to run the script: "./slim -d simnum=00000 -d u=1.17e-7 -d locus=0 example_simulation_6_pops_00000_0.txt". example_simulation_6_pops_00000_0.txt - name of the SLiM script with one simulation specification; simnum - simulation number; u - locus mutation rate; locus - locus number.slim_simulations_NFD_strong_m0.txtSLiM simulation script strong NFD M1Forward simulation script for the scenario: strong negative frequency-dependent selection, selection strength s = 0.5, migration M1 = 5.0E-07. Script run in SLiM v2.5. Example command to run the script: "./slim -d simnum=00000 -d u=1.17e-7 -d locus=0 example_simulation_6_pops_00000_0.txt". example_simulation_6_pops_00000_0.txt - name of the SLiM script with one simulation specification; simnum - simulation number; u - locus mutation rate; locus - locus number.slim_simulations_NFD_strong_m1.txtSLiM simulation script strong NFD M3Forward simulation script for the scenario: strong negative frequency-dependent selection, selection strength s = 0.5, migration M3 = 2.36E-06. Script run in SLiM v2.5. Example command to run the script: "./slim -d simnum=00000 -d u=1.17e-7 -d locus=0 example_simulation_6_pops_00000_0.txt". example_simulation_6_pops_00000_0.txt - name of the SLiM script with one simulation specification; simnum - simulation number; u - locus mutation rate; locus - locus number.slim_simulations_NFD_strong_m3.txtSLiM simulation script weak NFD M0Forward simulation script for the scenario: weak negative frequency-dependent selection, selection strength s = 0.02, migration M0 = 0. Script run in SLiM v2.5. Example command to run the script: "./slim -d simnum=00000 -d u=1.17e-7 -d locus=0 example_simulation_6_pops_00000_0.txt". example_simulation_6_pops_00000_0.txt - name of the SLiM script with one simulation specification; simnum - simulation number; u - locus mutation rate; locus - locus number.slim_simulations_NFD_weak_m0.txtSLiM simulation script weak NFD M1Forward simulation script for the scenario: weak negative frequency-dependent selection, selection strength s = 0.02, migration M1 = 5.0E-07. Script run in SLiM v2.5. Example command to run the script: "./slim -d simnum=00000 -d u=1.17e-7 -d locus=0 example_simulation_6_pops_00000_0.txt". example_simulation_6_pops_00000_0.txt - name of the SLiM script with one simulation specification; simnum - simulation number; u - locus mutation rate; locus - locus number.slim_simulations_NFD_weak_m1.txtSLiM simulation script weak NFD M3Forward simulation script for the scenario: weak negative frequency-dependent selection, selection strength s = 0.02, migration M3 = 2.36E-06. Script run in SLiM v2.5. Example command to run the script: "./slim -d simnum=00000 -d u=1.17e-7 -d locus=0 example_simulation_6_pops_00000_0.txt". example_simulation_6_pops_00000_0.txt - name of the SLiM script with one simulation specification; simnum - simulation number; u - locus mutation rate; locus - locus number.slim_simulations_NFD_weak_m3.txtSLiM simulation script weak SOD M0Forward simulation script for the scenario: weak symmetrical overdominance, selection strength s = 0.02, migration M0 = 0. Script run in SLiM v2.5. Example command to run the script: "./slim -d simnum=00000 -d u=1.17e-7 -d locus=0 example_simulation_6_pops_00000_0.txt". example_simulation_6_pops_00000_0.txt - name of the SLiM script with one simulation specification; simnum - simulation number; u - locus mutation rate; locus - locus number.slim_simulations_SOD_02_m0.txtSLiM simulation script weak SOD M1Forward simulation script for the scenario: weak symmetrical overdominance, selection strength s = 0.02, migration M1 = 5.0E-07. Script run in SLiM v2.5. Example command to run the script: "./slim -d simnum=00000 -d u=1.17e-7 -d locus=0 example_simulation_6_pops_00000_0.txt". example_simulation_6_pops_00000_0.txt - name of the SLiM script with one simulation specification; simnum - simulation number; u - locus mutation rate; locus - locus number.slim_simulations_SOD_02_m1.txtSLiM simulation script weak SOD M3Forward simulation script for the scenario: weak symmetrical overdominance, selection strength s = 0.02, migration M3 = 2.36E-06. Script run in SLiM v2.5. Example command to run the script: "./slim -d simnum=00000 -d u=1.17e-7 -d locus=0 example_simulation_6_pops_00000_0.txt". example_simulation_6_pops_00000_0.txt - name of the SLiM script with one simulation specification; simnum - simulation number; u - locus mutation rate; locus - locus number.slim_simulations_SOD_02_m3.txtSLiM simulation script moderate SOD M0Forward simulation script for the scenario: moderate symmetrical overdominance, selection strength s = 0.05, migration M0 = 0. Script run in SLiM v2.5. Example command to run the script: "./slim -d simnum=00000 -d u=1.17e-7 -d locus=0 example_simulation_6_pops_00000_0.txt". example_simulation_6_pops_00000_0.txt - name of the SLiM script with one simulation specification; simnum - simulation number; u - locus mutation rate; locus - locus number.slim_simulations_SOD_05_m0.txtSLiM simulation script moderate SOD M1Forward simulation script for the scenario: moderate symmetrical overdominance, selection strength s = 0.05, migration M1 = 5.0E-07. Script run in SLiM v2.5. Example command to run the script: "./slim -d simnum=00000 -d u=1.17e-7 -d locus=0 example_simulation_6_pops_00000_0.txt". example_simulation_6_pops_00000_0.txt - name of the SLiM script with one simulation specification; simnum - simulation number; u - locus mutation rate; locus - locus number.slim_simulations_SOD_05_m1.txtSLiM simulation script moderate SOD M3Forward simulation script for the scenario: moderate symmetrical overdominance, selection strength s = 0.05, migration M3 = 2.36E-06. Script run in SLiM v2.5. Example command to run the script: "./slim -d simnum=00000 -d u=1.17e-7 -d locus=0 example_simulation_6_pops_00000_0.txt". example_simulation_6_pops_00000_0.txt - name of the SLiM script with one simulation specification; simnum - simulation number; u - locus mutation rate; locus - locus number.slim_simulations_SOD_05_m3.txt