DOI: 10.5061/dryad.255hj
title: Data from: Adaptive differentiation coincides with local bioclimatic conditions along an elevational cline in populations of a lichen-forming fungus

description: Background: Many fungal species occur across a variety of habitats.
 Particularly lichens, fungi forming symbioses with photosynthetic
 partners, have evolved remarkable tolerances for environmental extremes.
 Despite their ecological importance and ubiquity, little is known about
 the genetic basis of adaption in lichen populations. Here we studied
 patterns of genome-wide differentiation in the lichen-forming fungus
 Lasallia pustulata along an altitudinal gradient in the Mediterranean
 region. We resequenced six populations as pools and identified highly
 differentiated genomic regions. We then detected gene-environment
 correlations while controlling for shared population history and pooled
 sequencing bias, and performed ecophysiological experiments to assess
 fitness differences of individuals from different environments. Results:
 We detected two strongly differentiated genetic clusters linked to
 Mediterranean and temperate-oceanic climate, and an admixture zone, which
 coincided with the transition between the two bioclimates. High altitude
 individuals showed ecophysiological adaptations to wetter and more shaded
 conditions. Highly differentiated genome regions contained a number of
 genes associated with stress response, local environmental adaptation, and
 sexual reproduction. Conclusions: Taken together our results provide
 evidence for a complex interplay between demographic history and spatially
 varying selection acting on a number of key biological processes,
 suggesting a scenario of ecological speciation.
description: Allele coverage counts
 top Bayenv2.0 SNPsWe provide here the Sync
 file of allele coverage counts for 2,978 SNPs for six populations of
 Lasallia pustulata that showed the highest score possible for Z in the
 Bayenv2.0 analysis. Used populations and abbreviations: 1 =&gt; Population
 1, 176 m a.s.l. 2 =&gt; Population 2, 297 m a.s.l. 3 =&gt; Population 3,
 588 m a.s.l. 4 =&gt; Population 4, 842 m a.s.l. 5 =&gt; Population 5,
 1,125 m a.s.l. 6 =&gt; Population 6, 1,303 m a.s.l. Output of the Sync
 file (for format specification see Kofler et al., PoPoolation2:
 identifying differentiation between populations using sequencing of pooled
 DNA samples (Pool-Seq). Bioinformatics 2011;27:3435-3436): col1: scaffold
 number col2: SNP position on scaffold col3: reference character col4:
 allele frequencies of population number 1 col5: allele frequencies of
 population number 2 coln: allele frequencies of population number n The
 allele frequencies are in the format A:T:C:G:N:del, i.e: count of bases
 'A', count of bases 'T', etc. , and deletion count in
 the end.2978snps_z0_5_bayenv.syncAllele coverage counts for differentially fixed SNPsWe provide here the Sync file of allele coverage counts for the 4,170 SNPs for six populations of Lasallia pustulata that were differentially fixed between the low (1 to 4) and high-altitude (6) population clusters. Used populations and abbreviations: 1 =&gt; Population 1, 176 m a.s.l. 2 =&gt; Population 2, 297 m a.s.l. 3 =&gt; Population 3, 588 m a.s.l. 4 =&gt; Population 4, 842 m a.s.l. 5 =&gt; Population 5, 1,125 m a.s.l. 6 =&gt; Population 6, 1,303 m a.s.l. Output of the Sync file (for format specification see Kofler et al., PoPoolation2: identifying differentiation between populations using sequencing of pooled DNA samples (Pool-Seq). Bioinformatics 2011;27:3435-3436): col1: scaffold number col2: SNP position on scaffold col3: reference character col4: allele frequencies of population number 1 col5: allele frequencies of population number 2 coln: allele frequencies of population number n The allele frequencies are in the format A:T:C:G:N:del, i.e: count of bases 'A', count of bases 'T', etc. , and deletion count in the end.4170SNPs_FIXED_05topquantile_1234and6.syncAligned DNA sequences for six genetic markersAligned DNA sequences in fasta format for six genetic markers (linked to Additional file 3).Alignments_6_loci.fastaAnnotated features for genic and promoter SNPsAnnotated features for genic and promoter SNPs in the Lasallia pustulata genome.all_SNPs_features_genic_promoter.txtGO terms for 5,742 genes of Lasallia pustulataThe complete list of GO terms for 5,742 genes of the lichen-forming fungus Lasallia pustulata.GOs_5742genes_topGO.txtLasallia pustulata genome annotationLasallia pustulata genome annotation file in GTF format.Lpus_genes_Ascomycota_ALLFEATURES.gtfInput for Migrate-NData input file for Migrate-N analysis.migraten-infile_3pops.txtπ for 10Kbp windows for six L. pustulata populationsπ output for 10Kbp windows for six populations of Lasallia pustulata along an elevational cline. "na" indicates windows that fail the coverage criteria.PI_10Kbp_P123456Tajima's D for 10Kbp windows for six L. pustulata populationsTajima's D output for 10Kbp windows for six populations of Lasallia pustulata along an elevational cline. "na" indicates windows that fail the coverage criteria.Tajima_D_10Kbp_P123456Watterson's θ for 10Kbp windows for six L. pustulata populationsWatterson's θ (θw) output for 10Kbp windows for six populations of Lasallia pustulata along an elevational cline. "na" indicates windows that fail the coverage criteria.theta_10Kbp_P123456Whole gene pairwise FSTThis is the pairwise fst output for every gene (bases were subsampled to a uniform coverage of 30) for six populations of Lasallia pustulata along an elevational cline. The columns are: col1: gene name col2: mean position of the sliding window col3: number of polymorphic SNPs in the gene col4: fraction of the window covered (not informative because coverage was fixed to 30) col5: mean coverage at SNP over all four populations (subsampled to a uniform coverage of 30) col6: pairwise Fst for Population 1:Population 2 ... col20: pairwise Fst for Population 5:Population 6 Used populations and abbreviations: 1 =&gt; Population 1, 176 m a.s.l. 2 =&gt; Population 2, 297 m a.s.l. 3 =&gt; Population 3, 588 m a.s.l. 4 =&gt; Population 4, 842 m a.s.l. 5 =&gt; Population 5, 1,125 m a.s.l. 6 =&gt; Population 6, 1,303 m a.s.l.subsampled_filtered.p123456_GENE_whole_gene.fstPairwise FST for six L. pustulata populationsThis is the pairwise fst output for all polymorphic individual SNPs (subsampled to a uniform coverage of 30) for six populations of Lasallia pustulata along an elevational cline. The columns are: col1: scaffold name col2: SNP position on scaffold col3: number of SNPs in window (for individual SNP estimates window size was set to 1, therefore all values are 1) col4: fraction of the window covered (all values are 1) col5: mean coverage at SNP over all four populations (subsampled to a uniform coverage of 30) col6: pairwise Fst for Population 1:Population 2 ... col20: pairwise Fst for Population 5:Population 6 Used populations and abbreviations: 1 =&gt; Population 1, 176 m a.s.l. 2 =&gt; Population 2, 297 m a.s.l. 3 =&gt; Population 3, 588 m a.s.l. 4 =&gt; Population 4, 842 m a.s.l. 5 =&gt; Population 5, 1,125 m a.s.l. 6 =&gt; Population 6, 1,303 m a.s.l. Fst values of 0.000000000 indicate not polymorphic SNPs for a given pairwise comparison.subsampled_filtered.p123456.fstPairwise whole-gene FST (upper 5% tail of the FST distribution)This is the pairwise fst output for the 2,413 genes (bases were subsampled to a uniform coverage of 30) falling into the upper 5% tail of the FST distribution for six populations of Lasallia pustulata along an elevational cline. The columns are: col1: gene name col2: mean position of the sliding window col3: number of polymorphic SNPs in the gene col4: fraction of the window covered (not informative because coverage was fixed to 30) col5: mean coverage at SNP over all four populations (subsampled to a uniform coverage of 30) col6: pairwise Fst for Population 1:Population 2 ... col20: pairwise Fst for Population 5:Population 6 Used populations and abbreviations: 1 =&gt; Population 1, 176 m a.s.l. 2 =&gt; Population 2, 297 m a.s.l. 3 =&gt; Population 3, 588 m a.s.l. 4 =&gt; Population 4, 842 m a.s.l. 5 =&gt; Population 5, 1,125 m a.s.l. 6 =&gt; Population 6, 1,303 m a.s.l.top5quantile_subsampled_filtered.p123456_GENE_whole_gene.fstAllele coverage counts for all L. pustulata SNPsWe provide here the Sync file of allele coverage counts for 37,225,382 called SNPs from six populations of Lasallia pustulata along an elevation gradient (for format specification see Kofler et al., PoPoolation2: identifying differentiation between populations using sequencing of pooled DNA samples (Pool-Seq). Bioinformatics 2011;27:3435-3436). Used populations and abbreviations: 1 =&gt; Population 1, 176 m a.s.l. 2 =&gt; Population 2, 297 m a.s.l. 3 =&gt; Population 3, 588 m a.s.l. 4 =&gt; Population 4, 842 m a.s.l. 5 =&gt; Population 5, 1,125 m a.s.l. 6 =&gt; Population 6, 1,303 m a.s.l. Output of the Sync file: col1: scaffold number col2: SNP position on scaffold col3: reference character col4: allele frequencies of population number 1 col5: allele frequencies of population number 2 coln: allele frequencies of population number n The allele frequencies are in the format A:T:C:G:N:del, i.e: count of bases 'A', count of bases 'T', etc., and deletion count in the end.filtered.p123456.sync.zipPairwise individual SNP FST (upper 0.5% tail of the FST distribution)This is the pairwise fst output for the 30,571 individual SNPs (subsampled to a uniform coverage of 30) falling into the upper 0.5% tail of the FST distribution for six populations of Lasallia pustulata along an elevational cline. The columns are: col1: scaffold name col2: SNP position on scaffold col3: number of SNPs in window (for individual SNP estimates window size was set to 1, therefore all values are 1) col4: fraction of the window covered (all values are 1) col5: mean coverage at SNP over all four populations (subsampled to a uniform coverage of 30) col6: pairwise Fst for Population 1:Population 2 ... col20: pairwise Fst for Population 5:Population 6 Used populations and abbreviations: 1 =&gt; Population 1, 176 m a.s.l. 2 =&gt; Population 2, 297 m a.s.l. 3 =&gt; Population 3, 588 m a.s.l. 4 =&gt; Population 4, 842 m a.s.l. 5 =&gt; Population 5, 1,125 m a.s.l. 6 =&gt; Population 6, 1,303 m a.s.l. Fst values of 0.000000000 indicate not polymorphic SNPs for a given pairwise comparison.05topquantile_filtered.p123456.fstTop 1% Bayenv2.0 SNPs allele coverage countsWe provide here the Sync file of allele coverage counts for the top 1% (Z score) Bayenv2.0 SNPs. Used populations and abbreviations: 1 =&gt; Population 1, 176 m a.s.l. 2 =&gt; Population 2, 297 m a.s.l. 3 =&gt; Population 3, 588 m a.s.l. 4 =&gt; Population 4, 842 m a.s.l. 5 =&gt; Population 5, 1,125 m a.s.l. 6 =&gt; Population 6, 1,303 m a.s.l. Output of the Sync file (for format specification see Kofler et al., PoPoolation2: identifying differentiation between populations using sequencing of pooled DNA samples (Pool-Seq). Bioinformatics 2011;27:3435-3436): col1: scaffold number col2: SNP position on scaffold col3: reference character col4: allele frequencies of population number 1 col5: allele frequencies of population number 2 coln: allele frequencies of population number n The allele frequencies are in the format A:T:C:G:N:del, i.e: count of bases 'A', count of bases 'T', etc. , and deletion count in the end.bayenv_top1percent.sync