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.
pyRAD parameters file
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.
pyRAD_parameters_file.txt
Unfiltered 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.vcf
Unfiltered 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.loci
Filtered SNPs
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.
Called_SNPs_Filtered.txt
Alignment for phylogeny
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.
Alignment_for_phylogeny.phy
Samples and populations list
Text file with sampling location information for each individual.
Samples_and_populations_list.txt
DIY-ABC Input file
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.
SNPs_DYABC_NO_OUTLIERS_MAF10.txt
Scenario codes and priors for simulations Torunament#1
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.
Codes_for_simulations_Torunament#1.txt
Scenario codes and priors for simulations Torunament#2
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
Codes_for_simulations_Torunament#2.txt
Scenario codes and priors for simulations Torunament#3
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.
Codes_for_simulations_Torunament#3.txt
Scenario codes and priors for simulations Final Scenario
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.
Codes_for_simulations_FinalScenario.txt