DOI: 10.5061/dryad.f6154
title: Data from: Extraordinarily rapid speciation in a marine fish

description: Divergent selection may initiate ecological speciation extremely rapidly.
 How often and at what pace ecological speciation proceeds to yield strong
 reproductive isolation is more uncertain. Here, we document a case of
 extraordinarily rapid speciation associated with ecological selection in
 the postglacial Baltic Sea. European flounders (Platichthys flesus) in the
 Baltic exhibit two contrasting reproductive behaviors: pelagic and
 demersal spawning. Demersal spawning enables flounders to thrive in the
 low salinity of the Northern Baltic, where eggs cannot achieve neutral
 buoyancy. We show that demersal and pelagic flounders are a species pair
 arising from a recent event of speciation. Despite having a parapatric
 distribution with extensive overlap, the two species are reciprocally
 monophyletic and show strongly bimodal genotypic clustering and no
 evidence of contemporary migration, suggesting strong reproductive
 isolation. Divergence across the genome is weak but shows strong
 signatures of selection, a pattern suggestive of a recent ecological
 speciation event. We propose that spawning behavior in Baltic flounders is
 the trait under ecologically based selection causing reproductive
 isolation, directly implicating a process of ecological speciation. We
 evaluated different possible evolutionary scenarios under the approximate
 Bayesian computation framework and estimate that the speciation process
 started in allopatry ∼2,400 generations ago, following the colonization of
 the Baltic by the demersal lineage. This is faster than most known cases
 of ecological speciation and represents the most rapid event of speciation
 ever reported for any marine vertebrate.
description: pyRAD parameters
 fileThis 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.pyRAD_parameters_file.txtUnfiltered Called SNPs (VCF format)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.FL-RAD-SphI-ALL.vcfUnfiltered Called SNPs (".loci" format)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.FL-RAD-SphI-ALL.lociFiltered SNPsSNP 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.Called_SNPs_Filtered.txtAlignment for phylogenyThis 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.Alignment_for_phylogeny.phySamples and populations listText file with sampling location information for each individual.Samples_and_populations_list.txtDIY-ABC Input fileThis 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.SNPs_DYABC_NO_OUTLIERS_MAF10.txtScenario codes and priors for simulations Torunament#1In 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.Codes_for_simulations_Torunament#1.txtScenario codes and priors for simulations Torunament#2In 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 SeaCodes_for_simulations_Torunament#2.txtScenario codes and priors for simulations Torunament#3In 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.Codes_for_simulations_Torunament#3.txtScenario codes and priors for simulations Final ScenarioIn 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.Codes_for_simulations_FinalScenario.txt