Evolution at two time-frames: ancient and common origin of two structural variants involved in local adaptation of the European plaice (Pleuronectes platessa)

This repository contains the following file:

The "Plaice_ddRAD_fasta_file.tar.gz" containing the Individual fasta files of the paper

•  253 European plaices (Pleuronectes platessa), the focal species of the paper
•  9 European flounder (Platichthys flesus), used as outgroup
•  9 Common dab (Limanda limanda), used as outgroup

Samples name code is written: SPECIES_POPULATION_ID-NUMBER. The species code "Pla" stand for the plaice samples, "Flo" for flounder and "Dab" for dab. The population code with a number as label correspond to the fisheries management unit shown on the map provided in the repository, otherwise, "isl" stand for the icelandic samples, "Nor" for Norway and "Bar" for the Barents sea. 

The filtrated vcf file analysed in the manuscript

• the overall vcf file unpruned for LD
• the overall vcf file pruned for LD
• the overall vcf without the chromosome carrying Structural Variants (SV)
• the overall vcf with chromosome 19 only (carrying 1 SV)
• the overall vcf with chromosome 21 only (carrying 1 SV)
• the vcf file containing only the Northern population (Iceland, Barents Sea, Norway) unpruned for LD
• the vcf file containing only the Northern population (North Sea, kattegat, Belt Sea, Baltic Sea) unpruned for LD
• the vcf file used to create the data for demographic inferences (including Norway and Icelance) pruned for LD

The R script file used to draw the figure of the manuscript

The bash and R script used to extract the sequences of the RAD-tag within the inversion and infer the phylogeny.