10.5061/DRYAD.1H48B38
Fijarczyk, Anna
Jagiellonian University
Dudek, Katarzyna
Jagiellonian University
Niedzicka, Marta
Jagiellonian University
Babik, Wieslaw
Jagiellonian University
Data from: Balancing selection and introgression of newt immune-response genes
Dryad
dataset
2018
Balancing selection
Holocene
Lissotriton
2018-07-18T16:42:56Z
2018-07-18T16:42:56Z
en
https://doi.org/10.1098/rspb.2018.0819
1525245234 bytes
1
CC0 1.0 Universal (CC0 1.0) Public Domain Dedication
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.
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
Europe