Data for paper: The making of a genetic cline: introgression of oceanic genes into coastal cod populations in the North East Atlantic

Files included in this data package includes data, scripts and a simulation program to replicate

simulations of genetic divergence patterns and comparision with observations, as described in the paper.

Filename: content

coastalcoddata.csv: genotypes and metadata, described in detail below

IBD.dat: data, pairwise observed Fst among cod samples

report_pairwise_Fst_Vikingbank.R: R-script to extract relevant data from IBD.dat

connectivity_matrix.txt: output from oceanographic modelling, for simulations

popfile.dat: population data, for simulations

simmat: compiled simulation program (linux 64 bit, dynamically linked)

simmat.c: C source code for simmat simulation program

simloop.R: R-script for running simulations

(R.scripts uses the R computing environment: https://www.r-project.org/)

The coastalcoddata.csv file contains SNP genotypes and metadata for individual cod (one line per individual),

coastal cod as well as reference samples:

Column name: Explanation

RefSamp: 0 = coastal cod sample, 1 = North Sea reference sample, 2 = NEAC reference sample

Region: County (prior to 2020 county revision)

Locality: Name of sample locality

Year: Year of sampling

Lat: Latitude of sample locality

Long: Longitude of sample locality

SampleID: Internal ID og sample locality and year

IndividualID: Individual number

Otype: Otolith type of individual (1 = certain CC/NS, 2 = uncertain CC/NS, 4 = uncertain NEAC, 5 = certain NEAC, where NS=North Sea cod, CC=coastalcod, NEAC=North East Arctic cod)

Missing: Number of missing genotypes for individual

cgpGmoS1026 (and so on): SNP genotype in Genepop 3-digit format (missing genotype =000000)

Methods
SNP genotyping, ocenographic modelling, computer simulations