Data from: Adaptive differentiation coincides with local bioclimatic conditions along an elevational cline in populations of a lichen-forming fungus

Dal Grande F, Sharma R, Meiser A, Rolshausen G, Buedel B, Mishra B, Thines M, Otte J, Pfenninger M, Schmitt I

Date Published: March 3, 2017

DOI: http://dx.doi.org/10.5061/dryad.255hj

 

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Title Allele coverage counts top Bayenv2.0 SNPs
Downloaded 9 times
Description 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.
Download 2978snps_z0_5_bayenv.sync (335.0 Kb)
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Title Allele coverage counts for differentially fixed SNPs
Downloaded 2 times
Description 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.
Download 4170SNPs_FIXED_05topquantile_1234and6.sync (454.9 Kb)
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Title Aligned DNA sequences for six genetic markers
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Description Aligned DNA sequences in fasta format for six genetic markers (linked to Additional file 3).
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Title Annotated features for genic and promoter SNPs
Downloaded 6 times
Description Annotated features for genic and promoter SNPs in the Lasallia pustulata genome.
Download all_SNPs_features_genic_promoter.txt (21.34 Mb)
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Title GO terms for 5,742 genes of Lasallia pustulata
Downloaded 5 times
Description The complete list of GO terms for 5,742 genes of the lichen-forming fungus Lasallia pustulata.
Download GOs_5742genes_topGO.txt (327.8 Kb)
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Title Lasallia pustulata genome annotation
Downloaded 3 times
Description Lasallia pustulata genome annotation file in GTF format.
Download Lpus_genes_Ascomycota_ALLFEATURES.gtf (5.078 Mb)
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Title Input for Migrate-N
Downloaded 7 times
Description Data input file for Migrate-N analysis.
Download migraten-infile_3pops.txt (217.6 Kb)
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Title π for 10Kbp windows for six L. pustulata populations
Downloaded 4 times
Description π output for 10Kbp windows for six populations of Lasallia pustulata along an elevational cline. "na" indicates windows that fail the coverage criteria.
Download PI_10Kbp_P123456 (358.3 Kb)
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Title Tajima's D for 10Kbp windows for six L. pustulata populations
Downloaded 4 times
Description 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.
Download Tajima_D_10Kbp_P123456 (367.5 Kb)
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Title Watterson's θ for 10Kbp windows for six L. pustulata populations
Downloaded 5 times
Description 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.
Download theta_10Kbp_P123456 (358.3 Kb)
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Title Whole gene pairwise FST
Downloaded 5 times
Description 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.
Download subsampled_filtered.p123456_GENE_whole_gene.fst (1.877 Mb)
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Title Pairwise FST for six L. pustulata populations
Downloaded 15 times
Description 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.
Download subsampled_filtered.p123456.fst (192.3 Mb)
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Title Pairwise whole-gene FST (upper 5% tail of the FST distribution)
Downloaded 5 times
Description 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.
Download top5quantile_subsampled_filtered.p123456_...ne.fst (619.6 Kb)
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Title Allele coverage counts for all L. pustulata SNPs
Downloaded 4 times
Description 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.
Download filtered.p123456.sync.zip (520.1 Mb)
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Title Pairwise individual SNP FST (upper 0.5% tail of the FST distribution)
Downloaded 4 times
Description 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.
Download 05topquantile_filtered.p123456.fst (8.146 Mb)
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Title Top 1% Bayenv2.0 SNPs allele coverage counts
Downloaded 8 times
Description 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.
Download bayenv_top1percent.sync (638.6 Kb)
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When using this data, please cite the original publication:

Dal Grande F, Sharma R, Meiser A, Rolshausen G, Büdel B, Mishra B, Thines M, Otte J, Pfenninger M, Schmitt I (2017) Adaptive differentiation coincides with local bioclimatic conditions along an elevational cline in populations of a lichen-forming fungus. BMC Evolutionary Biology 17(1): null. http://dx.doi.org/10.1186/s12862-017-0929-8

Additionally, please cite the Dryad data package:

Dal Grande F, Sharma R, Meiser A, Rolshausen G, Buedel B, Mishra B, Thines M, Otte J, Pfenninger M, Schmitt I (2017) Data from: Adaptive differentiation coincides with local bioclimatic conditions along an elevational cline in populations of a lichen-forming fungus. Dryad Digital Repository. http://dx.doi.org/10.5061/dryad.255hj
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