### General information
 
Authors: Marlene Jahnke, Per-Olav Moksnes, Alan Le Moan, Gerrit A Martens, Per R Jonsson
Contact e-mail:marlene.jahnke@gu.se
DOI: 10.17044/scilifelab.17836025
Licence: CC BY 4.0
This readme file was last updates: 27-01-2022

Please cite as: Jahnke, Marlene; Moksnes, Per-Olav; Le Moan, Alan; Martens, Gerrit; Jonsson, Per R (2022): Data and scripts for Mol Ecol article by Jahnke et al: Seascape genomics identify adaptive barriers correlated to tidal amplitude in the shore crab Carcinus maenas. SciLifeLab. Dataset. https://doi.org/10.17044/scilifelab.17836025

### Dataset description

This repository includes data files and scripts used in the publication "Seascape genomics 
identify adaptive barriers correlated to tidal amplitude in the shore crab Carcinus maenas" 
published in Molecular Ecology in 2022.

In this publication we assessed 12 sites in the native range of the European shore crab 
Carcinus maenas spanning >2000 km, and examined genetic structure and selection to tidal 
gradient using 24,000 Single Nucleotide Polymorphisms (SNPs) derived from 2b-RAD 
sequencing. Additionally, we performed biophysical modelling, and gene expression analyses 
of candidate clock genes.

Data in this repository includes: 
final filtered vcf files for all, neutral and outlier loci.
Raw sequence data is archived in GenBank's SRA: BioProject ID PRJNA797386 and BioSample 
IDs SAMN25002278 -SAMN25002565. 

New population genomic and biophysical modelling script are provided as well, while 
scripts for the 2b-RAD bioinformatic analysis are available at: 
https://github.com/z0on/2bRAD_denovo, and scripts for demographic inferences are 
available at: https://github.com/alanlm-speciation/moments_optimization.

### Available variables 

File list and usage notes:

'Cmaenas_Jahnkeetal2022_all_loci.vcf': final filtered vcf of all loci

'Cmaenas_Jahnkeetal2022_neutral0.5.vcf': final filtered vcf of neutral loci at relaxed 
threshold

'Cmaenas_Jahnkeetal2022_neutral0.00011.vcf': final filtered vcf of neutral loci at 
stringent threshold

'Cmaenas_Jahnkeetal2022_outliers_full0.00011_2.vcf': final filtered vcf of outlier loci 
at stringent threshold

'ConnectivityMatrixSurface.txt’: Probability (0 to 1) of modelled dispersal of Carcinus 
maenaslarvae drifting in surface water with spawning from 1360 model grid cells along the 
North Sea-Skagerrak-Kattegat coast. The file is in table format with three columns: 
matrix row number, matrix column number, probability of dispersal.
 
‘ConnectivityMatrixDiurnal.txt’: Probability (0 to 1) of modelled dispersal of Carcinus 
maenaslarvae showing vertical migration in rhythm with the day/night cycle, with spawning 
from 1360 model grid cells along the North Sea-Skagerrak-Kattegat coast. The file is in 
table format with three columns: matrix row number, matrix column number, probability of 
dispersal.
 
‘ConnectivityMatrixTide.txt’: Probability (0 to 1) of modelled dispersal of Carcinus 
maenaslarvae showing vertical migration in rhythm with the local tide cycle, with 
spawning from 1360 model grid cells along the North Sea-Skagerrak-Kattegat coast. 
The file is in table format with three columns: matrix row number, matrix column number, 
probability of dispersal.

‘ConnectivityScript.m’: Biophysical analyses script for MatLab 2020b showing code for 
loading the connectivity matrix files, expanding them to filled matrices and performing 
matrix multiplication to estimate multi-generation, stepping-stone connectivity.

‘GridCellGeoCode.txt’: The file consists of three columns: grid cell number (1 to 1360), 
longitude of grid cell centre, latitude of grid cell centre. The grid cell number 
corresponds to the row and column numbers in the connectivity matrix.

'LDna.R': R scripts for LDna analysis to detect linkage disequilibrium.

'Mantel_tests_and_networks_R_script.R': R scripts to perform Mantel tests and network 
analyses

'Sea_dist.txt': the geographic distance without crossing land among all sites as 
calculated with the R package marmap