Data from: Unique evolutionary trajectories in repeated adaptation to hydrogen sulphide-toxic habitats of a neotropical fish (Poecilia mexicana)

Pfenninger M, Patel S, Arias-Rodriguez L, Feldmeyer B, Riesch R, Plath M

Date Published: September 25, 2015

DOI: http://dx.doi.org/10.5061/dryad.ts351

 

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Title SNP FST file
Downloaded 6 times
Description This is the pairwise fst output for individual snps. The non-informative sites have been suppressed, so all the rows are the SNPs that meet the coverage criteria. the columns are: col1: scaffold number col2: SNP position on scaffold col3: number of snps in window (because the window size was set to 1 to get individual SNP estimates, all values should be 1) col4: fraction of the window covered (more relevant for sliding window analyses) col5: mean coverage at SNP over all four populations col6: pairwise Fst for Tac-C:Tac-S col7: pairwise Fst for Tac-C:Puy-C col8: pairwise Fst for Tac-C:Puy-S col9: pairwise Fst for Tac-S:Puy-C col10: pairwise Fst for Tac-S:Puy-S col11: pairwise Fst for Puy-C:Puy-S population codes: 1=Tac-C, 2=Tac-S, 3=Puy-C, 4=Puy-S Note that the Fst values that are 0.000000000 are not polymorphic SNPs for a given pairwise comparison. For example, snp 'NW_006799939.1 19911' has an Fst of 0.00000000 in the Tac-C:Tac-S comparison because it is not polymorphic between Tac-C and Tac-S. From the sync file: NW_006799939.1 19911 A 21:0:0:0:0:0 21:0:0:0:0:0 39:0:0:2:0:0 37:0:0:5:0:0 you can see that Tac-C and Tac-S are fixed for the A allele (21 counts in each). The only reason it is included as a SNP in the .fst file is because it is polymorphic in the Puy-C & Puy-S populations (and polmorhic in the comparison across Tac & Puy).
Download Tac-C_Tac-S_Puy-C_Puy-S.fst (388.7 Mb)
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Title Fisher's exact test data
Downloaded 8 times
Description This is the fisher's exact test output for each SNP, in each pairwise comparison. The same SNP definition ws used as for the .fst output, so these are the FET results for the same snps included in the Fst output. The structure of the file is the same as for Tac-C_Tac-S_Puy-C_Puy-S.fst. Instead of Fst values, the numbers are -log10 P-values.
Download Tac-C_Tac-S_Puy-C_Puy-S.fet (389.3 Mb)
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Title 1kb window FST
Downloaded 6 times
Description This file contains the output of the 1000bp sliding window Fst analysis. Structure of the output file is similar to Tac-C_Tac-S_Puy-C_Puy-S.fst: col1: reference contig (chromosome) col2: mean position of the sliding window col3: number of SNPs found in the window (not considering sites with a deletion) col4: fraction of the window which has a sufficient coverage (min. coverage <= cov <= max. coverage) in every population; col5: average minimum coverage in all populations col6: 1:2 the pairwise Fst for population 1 and 2 col7: 1:3 the pairwise Fst for population 1 and 3 ....
Download Tac-C_Tac-S_Puy-C_Puy-S.1000.fst (54.06 Mb)
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Title Puy-C Tajima's D
Downloaded 4 times
Description Tajima's D output for 1000bp windows for Puy-C. There is no option in the script to suppress the non-informative windows, so there are lots of windows with "na" that fail the coverage criteria so no calculation is made.
Download Puy-C.D (29.85 Mb)
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Title Puy-S Tajima's D
Downloaded 4 times
Description Tajima's D output for 1000bp windows for Puy-S. There is no option in the script to suppress the non-informative windows, so there are lots of windows with "na" that fail the coverage criteria so no calculation is made.
Download Puy-S.D (30.05 Mb)
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Title Tac-C Tajima's D
Downloaded 4 times
Description Tajima's D output for 1000bp windows for Tac-C. There is no option in the script to suppress the non-informative windows, so there are lots of windows with "na" that fail the coverage criteria so no calculation is made.
Download Tac-C.D (30.06 Mb)
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Title Tac-S Tajima's D
Downloaded 5 times
Description Tajima's D output for 1000bp windows for Tac-S. There is no option in the script to suppress the non-informative windows, so there are lots of windows with "na" that fail the coverage criteria so no calculation is made.
Download Tac-S.D (29.68 Mb)
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Title infilePuy68 for Migrate
Downloaded 4 times
Description Data input file for Migrate-N analysis
Download infilePuy68.txt (135.7 Kb)
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Title infileTac67 for Migrate-N
Downloaded 7 times
Description Data input file for Migrate-N
Download infileTac67.txt (134.3 Kb)
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Title parmfile Migrate-N
Downloaded 5 times
Description Parameter file used for both population pairs
Download parmfile.txt (26.96 Kb)
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Title Allele frequency estimates from PoolSeq analysis
Downloaded 4 times
Description Popoolation output file containing the read count data for polymorphic sites. The first column is the scaffold number (chr), the second the position on the scaffold (pos), the third is the base in the reference genome (rc), number of alleles (allele_count), allelic states (allele_states), number of deletions (deletion_sum), whether the snp is variable among populations or against the reference (snp_type), the major alleles in the populations in the order Tac-C, Tac-S, Puy-C, Puy-S (major_alleles(maa)), the same for minor alleles (minor_alleles(mia)), alleles frequency estimates of the major allele expressed as ratio of reads for the respective population (maa_1, maa_2, maa_3, maa_4), and the same for the minor alleles (mia_1, mia_2, mia_3, mia_4)
Download Tac-C_Tac-S_Puy-C_Puy-S_rc (674.0 Mb)
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When using this data, please cite the original publication:

Pfenninger M, Patel S, Arias-Rodriguez L, Feldmeyer B, Riesch R, Plath M (2015) Unique evolutionary trajectories in repeated adaptation to hydrogen sulphide-toxic habitats of a neotropical fish (Poecilia mexicana). Molecular Ecology 24(21): 5446–5459. http://dx.doi.org/10.1111/mec.13397

Additionally, please cite the Dryad data package:

Pfenninger M, Patel S, Arias-Rodriguez L, Feldmeyer B, Riesch R, Plath M (2015) Data from: Unique evolutionary trajectories in repeated adaptation to hydrogen sulphide-toxic habitats of a neotropical fish (Poecilia mexicana). Dryad Digital Repository. http://dx.doi.org/10.5061/dryad.ts351
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