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.
Allele coverage counts top Bayenv2.0 SNPs
We 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 => Population 1, 176 m a.s.l.
2 => Population 2, 297 m a.s.l.
3 => Population 3, 588 m a.s.l.
4 => Population 4, 842 m a.s.l.
5 => Population 5, 1,125 m a.s.l.
6 => 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.sync
Allele coverage counts for differentially fixed SNPs
We 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 => Population 1, 176 m a.s.l.
2 => Population 2, 297 m a.s.l.
3 => Population 3, 588 m a.s.l.
4 => Population 4, 842 m a.s.l.
5 => Population 5, 1,125 m a.s.l.
6 => 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.sync
Aligned DNA sequences for six genetic markers
Aligned DNA sequences in fasta format for six genetic markers (linked to Additional file 3).
Alignments_6_loci.fasta
Annotated features for genic and promoter SNPs
Annotated features for genic and promoter SNPs in the Lasallia pustulata genome.
all_SNPs_features_genic_promoter.txt
GO terms for 5,742 genes of Lasallia pustulata
The complete list of GO terms for 5,742 genes of the lichen-forming fungus Lasallia pustulata.
GOs_5742genes_topGO.txt
Lasallia pustulata genome annotation
Lasallia pustulata genome annotation file in GTF format.
Lpus_genes_Ascomycota_ALLFEATURES.gtf
Input for Migrate-N
Data input file for Migrate-N analysis.
migraten-infile_3pops.txt
π for 10Kbp windows for six L. pustulata populations
π output for 10Kbp windows for six populations of Lasallia pustulata along an elevational cline. "na" indicates windows that fail the coverage criteria.
PI_10Kbp_P123456
Tajima's D for 10Kbp windows for six L. pustulata populations
Tajima'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_P123456
Watterson's θ for 10Kbp windows for six L. pustulata populations
Watterson'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_P123456
Whole gene pairwise FST
This 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 => Population 1, 176 m a.s.l.
2 => Population 2, 297 m a.s.l.
3 => Population 3, 588 m a.s.l.
4 => Population 4, 842 m a.s.l.
5 => Population 5, 1,125 m a.s.l.
6 => Population 6, 1,303 m a.s.l.
subsampled_filtered.p123456_GENE_whole_gene.fst
Pairwise FST for six L. pustulata populations
This 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 => Population 1, 176 m a.s.l.
2 => Population 2, 297 m a.s.l.
3 => Population 3, 588 m a.s.l.
4 => Population 4, 842 m a.s.l.
5 => Population 5, 1,125 m a.s.l.
6 => 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.fst
Pairwise 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 => Population 1, 176 m a.s.l.
2 => Population 2, 297 m a.s.l.
3 => Population 3, 588 m a.s.l.
4 => Population 4, 842 m a.s.l.
5 => Population 5, 1,125 m a.s.l.
6 => Population 6, 1,303 m a.s.l.
top5quantile_subsampled_filtered.p123456_GENE_whole_gene.fst
Allele coverage counts for all L. pustulata SNPs
We 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 => Population 1, 176 m a.s.l.
2 => Population 2, 297 m a.s.l.
3 => Population 3, 588 m a.s.l.
4 => Population 4, 842 m a.s.l.
5 => Population 5, 1,125 m a.s.l.
6 => 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.zip
Pairwise 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 => Population 1, 176 m a.s.l.
2 => Population 2, 297 m a.s.l.
3 => Population 3, 588 m a.s.l.
4 => Population 4, 842 m a.s.l.
5 => Population 5, 1,125 m a.s.l.
6 => 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.fst
Top 1% Bayenv2.0 SNPs allele coverage counts
We provide here the Sync file of allele coverage counts for the top 1% (Z score) Bayenv2.0 SNPs.
Used populations and abbreviations:
1 => Population 1, 176 m a.s.l.
2 => Population 2, 297 m a.s.l.
3 => Population 3, 588 m a.s.l.
4 => Population 4, 842 m a.s.l.
5 => Population 5, 1,125 m a.s.l.
6 => 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