Data from: Targeted resequencing reveals geographical patterns of differentiation for loci implicated in parallel evolution

Westram AM, Panova M, Galindo J, Butlin RK

Date Published: May 20, 2016

DOI: http://dx.doi.org/10.5061/dryad.gd4dc

 

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Title Raw capture sequencing reads; Location: ANG; Ecotype: C
Downloaded 3 times
Description Raw capture sequencing reads for Littorina saxatilis from the original Swedish location (ANG), "crab" ecotype. Each fastq file represents reads from one individual.
Download ANG_C_reads.tar.gz (1.278 Gb)
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Title Raw capture sequencing reads; Location: S; Ecotype: C
Downloaded 2 times
Description Raw capture sequencing reads for Littorina saxatilis from the original Spanish location (S), "crab" ecotype. Each fastq file represents reads from one individual.
Download S_C_reads.tar.gz (1.160 Gb)
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Title Raw capture sequencing reads; Location: S; Ecotype: W
Downloaded 2 times
Description Raw capture sequencing reads for Littorina saxatilis from the original Spanish location (S), "wave" ecotype. Each fastq file represents reads from one individual.
Download S_W_reads.tar.gz (1.303 Gb)
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Title Raw capture sequencing reads; Location: ANG; Ecotype: W
Downloaded 2 times
Description Raw capture sequencing reads for Littorina saxatilis from the original Swedish location (ANG), "wave" ecotype. Each fastq file represents reads from one individual.
Download ANG_W_reads.tar.gz (2.143 Gb)
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Title Raw capture sequencing reads; Location: B; Ecotype: C
Downloaded 2 times
Description Raw capture sequencing reads for Littorina saxatilis from the new Spanish location (B), "crab" ecotype. Each fastq file represents reads from one individual.
Download B_C_reads.tar.gz (1.876 Gb)
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Title Raw capture sequencing reads; Location: B; Ecotype: W
Downloaded 2 times
Description Raw capture sequencing reads for Littorina saxatilis from the new Spanish location (B), "wave" ecotype. Each fastq file represents reads from one individual.
Download B_W_reads.tar.gz (1.484 Gb)
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Title Raw capture sequencing reads; Location: OCK; Ecotype: C
Downloaded 2 times
Description Raw capture sequencing reads for Littorina saxatilis from the new Swedish location (OCK), "crab" ecotype. Each fastq file represents reads from one individual.
Download OCK_C_reads.tar.gz (1.528 Gb)
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Title Raw capture sequencing reads; Location: OCK; Ecotype: W
Downloaded 2 times
Description Raw capture sequencing reads for Littorina saxatilis from the new Swedish location (OCK), "wave" ecotype. Each fastq file represents reads from one individual.
Download OCK_W_reads.tar.gz (4.243 Gb)
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Title Raw capture sequencing reads; Location: T; Ecotype: C
Downloaded 1 time
Description Raw capture sequencing reads for Littorina saxatilis from the original United Kingdom location (T), "crab" ecotype. Each fastq file represents reads from one individual.
Download T_C_reads.tar.gz (2.276 Gb)
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Title Raw capture sequencing reads; Location: T; Ecotype: W
Downloaded 4 times
Description Raw capture sequencing reads for Littorina saxatilis from the original United Kingdom location (T), "wave" ecotype. Each fastq file represents reads from one individual.
Download T_W_reads.tar.gz (2.102 Gb)
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Title Raw capture sequencing reads; Location: W; Ecotype: C
Downloaded 2 times
Description Raw capture sequencing reads for Littorina saxatilis from the new United Kingdom location (W), "crab" ecotype. Each fastq file represents reads from one individual.
Download W_C_reads.tar.gz (1.423 Gb)
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Title Raw capture sequencing reads; Location: W; Ecotype: W
Downloaded 2 times
Description Raw capture sequencing reads for Littorina saxatilis from the new United Kingdom location (W), "wave" ecotype. Each fastq file represents reads from one individual.
Download W_W_reads.tar.gz (2.090 Gb)
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Title per-locus alignments
Downloaded 2 times
Description Alignments for 253 loci targeted by capture sequencing. Each file represents one locus, and can consist of alignments for a single or for multiple concatenated reference genome contigs (see manuscript). The files are named by these reference genome contigs. More details about each locus (ID in the original study; type of original study; outlier status) can be found in probes.csv. Each individual in the alignment has two pseudo-haplotypes (H1 and H2). Naming of individuals is in accordance with read files and Figure 1 in the manuscript.
Download alignments.tar.gz (2.674 Mb)
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Title list of capture sequencing probes
Downloaded 3 times
Description Table of 120bp probes used for capture sequencing. ref_contig = ID of targeted contig in L. saxatilis reference genome. start, end: start and end of probe sequence in the reference contig. study: study in which the targeted locus was first identified (EXP = gene expression study; RNA = RNAseq study; RAD = RADseq study; LSD = Littorina sequence database; for references please see main text, e.g. Table 1). type: outlier vs. control locus; SP, SW, UK: locus was outlier (1) or non-outlier (0) in earlier work Spain / Sweden / UK, respectively; probe: probe ID; original_locus: ID of targeted locus in the original work.
Download probes.csv (213.8 Kb)
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Title calculate_dxy
Downloaded 25 times
Description Python script using the EggLib library to calculate dxy between ecotypes for multiple loci and locations. Needs one fasta file per locus (containing aligned sequences from both ecotypes from multiple locations) and a text file with the names of the loci of interest.
Download calculate_dxy.py (3.982 Kb)
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Title calculate_pi
Downloaded 6 times
Description Python script using the EggLib library to calculate Pi for multiple loci and populations (one population = one ecotype within a location). Needs one fasta file per locus (containing aligned sequences from both ecotypes from multiple locations) and a text file with the names of the loci of interest.
Download calculate_pi.py (3.755 Kb)
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Title calculate_Fst
Downloaded 6 times
Description R script to calculate Fst per locus and location from the output of calculate_pi.py and calculate_dxy.py.
Download calculate_Fst.R (836 bytes)
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Title likelihood_analysis
Downloaded 3 times
Description R script to calculate probabilities that outliers fall above the 80% quantile of the control Fst distribution in different locations, and to obtain log likelihoods and AICs for different models. Needs "quantile_table.txt" (a table of all loci indicating for each location whether they fall above the 80% quantile or not) as input.
Download likelihood_analysis.R (7.744 Kb)
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Title quantile_table
Downloaded 2 times
Description Table indicating whether targeted loci showed an Fst estimate above the 80% quantile of the control distribution in the current study. locus = ID of outlier / control locus in original study. contig = location in the current L. saxatilis reference genome. SP / SW / UK = indication whether the locus was an outlier in Spain / Sweden / UK in the original work (0 = non-outlier; 1 = outlier). type = control vs. outlier locus in the original study. S / B / ANG / OCK / T / W = indication whether the locus fell above the 80% quantile of the control Fst distribution in the current work in the six studied locations (TRUE = above, FALSE = below).
Download quantile_table.txt (17.59 Kb)
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When using this data, please cite the original publication:

Westram AM, Panova M, Galindo J, Butlin RK (2016) Targeted resequencing reveals geographical patterns of differentiation for loci implicated in parallel evolution. Molecular Ecology 25(13): 3169-3186. http://dx.doi.org/10.1111/mec.13640

Additionally, please cite the Dryad data package:

Westram AM, Panova M, Galindo J, Butlin RK (2016) Data from: Targeted resequencing reveals geographical patterns of differentiation for loci implicated in parallel evolution. Dryad Digital Repository. http://dx.doi.org/10.5061/dryad.gd4dc
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