Data from: Extraordinarily rapid speciation in a marine fish

Momigliano P, Jokinen H, Fraimout A, Florin A, Norkko A, Merilä J

Date Published: May 24, 2017

DOI: http://dx.doi.org/10.5061/dryad.f6154

 

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Title pyRAD parameters file
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Description This is the parameter file containing all parameters used for de novo SNP calling using the pyRAD pipeline. Running pyRAD using these parameters on the deposited raw data (accessible in GenBank BioProject PRJNA382467) will produce the "FL-RAD-SphI-ALL.vcf" and "FL-RAD-SphI-ALL.loci" files deposited in this repositiory.
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Title Unfiltered Called SNPs (VCF format)
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Description This file is the output of the pyRAD pipeline (VCF format) ran on the raw sequence reads (accessible via GenBank, BioProject PRJNA382467) using the parameters which are given in the the pyRAD parameter file despoted in this repository ("pyRAD_parameters_file.txt"). It contains several technical replicates (which are denoted by the suffix "_R"), which are used in the study to determine the consistency of SNP calls.
Download FL-RAD-SphI-ALL.vcf (21.88 Mb)
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Title Unfiltered Called SNPs (".loci" format)
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Description This file is the output of the pyRAD pipeline (pyRAD ".loci" format) ran on the raw sequence reads (accessible via GenBank, BioProject PRJNA382467) using the parameters which are given in the the pyRAD parameter file despoted in this repository ("pyRAD_parameters_file.txt"). It contains several technical replicates (which are denoted by the suffix "_R"), which are used in the study to determine the consistency of SNP calls.
Download FL-RAD-SphI-ALL.loci (175.9 Mb)
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Title Filtered SNPs
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Description SNP genotypes for each individual, filtered according to the parameters explained in the manuscripts (and in the comments to the file). This is the main data-set used for population genetic analyses.
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Title Alignment for phylogeny
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Description This is a multiple sequence alignment file (in PHYLIP format) obtained by concatenating the sequences of the 2051 loci for a subset of 57 individuals. This file is the input file used for phylogenetic analyses.
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Title Samples and populations list
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Description Text file with sampling location information for each individual.
Download Samples_and_populations_list.txt (4.809 Kb)
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Title DIY-ABC Input file
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Description This is the input data for all ABC analyses. It includes genotypes of individuals from the North Sea (coded as NS), The Baltic Pelagic (PEL) and the Baltic demersal (DEM) lineages. Outlier loci and individuals from the transition zone were removed from this dataset.
Download SNPs_DYABC_NO_OUTLIERS_MAF10.txt (1.071 Mb)
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Title Scenario codes and priors for simulations Torunament#1
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Description In this file we report the scenario codes to reproduce, using the software DIY-ABC, the reference table which can then be analyzed by the R package "abcrf" to produce the results from the first random forest tournament we carried out. This reproduces the results which are reported in the Table S6 in the supplementary materials, i.e. the tournament aimed at identifying the main divergence scenario.
Download Codes_for_simulations_Torunament#1.txt (12.72 Kb)
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Title Scenario codes and priors for simulations Torunament#2
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Description In this file we report the scenario codes to reproduce, using the software DIY-ABC, the reference table which can then be analyzed by the R package "abcrf" to produce the results from the second random forest tournament we carried out. This reproduces the results which are reported in the Table S7 in the supplementary materials, i.e. the tournament aimed to determine whether or not the two Baltic lineages underwent a bottleneck followed by a demographic expansion during and after the invasion of the Baltic Sea
Download Codes_for_simulations_Torunament#2.txt (7.072 Kb)
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Title Scenario codes and priors for simulations Torunament#3
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Description In this file we report the scenario codes to reproduce, using the software DIY-ABC, the reference table which can then be analyzed by the R package "abcrf" to produce the results from the third random forest tournament we carried out. This reproduces the results which are reported in the Table S8 in the supplementary materials, i.e. the tournament aimed to determine whether or not there was secondary introgression among the two Baltic lineages and whether or not there had been an expansion in the ancestral population.
Download Codes_for_simulations_Torunament#3.txt (4.106 Kb)
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Title Scenario codes and priors for simulations Final Scenario
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Description In this file we report the scenario codes and priors to reproduce, using the software DIY-ABC, the reference table (500 0000 simulations) used to estimate the final parameters and to check the final model.
Download Codes_for_simulations_FinalScenario.txt (1.196 Kb)
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When using this data, please cite the original publication:

Momigliano P, Jokinen H, Fraimout A, Florin A, Norkko A, Merilä J (2017) Extraordinarily rapid speciation in a marine fish. Proceedings of the National Academy of Sciences of the United States of America 114(23): 6074-6079. http://dx.doi.org/10.1073/pnas.1615109114

Additionally, please cite the Dryad data package:

Momigliano P, Jokinen H, Fraimout A, Florin A, Norkko A, Merilä J (2017) Data from: Extraordinarily rapid speciation in a marine fish. Dryad Digital Repository. http://dx.doi.org/10.5061/dryad.f6154
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