Data and scripts for "Genomic underpinnings of head and body shape in Arctic charr ecomorph pairs" by Sam Fenton, Arne Jacobs, Colin W. Bean, Colin E. Adams, & Kathryn R. Elmer
published in Molecular Ecology

Folder contains the landmark and filtered SNPs dataset used for all analyses

Files included:
-R scripts are provided for major phenotypic and genetic analyses
-Filtered.snps.vcf is the VCF file for the filtered SNP data (N=13,071 SNPs and 200 individuals)
-Headshape and Bodyshape landmark TPS files contain all landmark data (N=341 and N=335 individuals respectively)
-Charr_IDS files are provided to be used with the phenotypic data to conduct PCA analysis 
-PC1-5 scores for head shape and body shape are provided and are sued as input (alongside vcf) as input for Gemma model
-AC_linkagemap and AC_LM files are the recombination rate data used to conduct the recombination rate analysis using the MareMap R package
-Marey_map_cubic_spline contains the output from MareyMap with the cubic spline values assigned for each chromosome 
-Sample List provides a list of all individuals across the different datasets and the corresponding datatypes they have (genetics, phenotpyic or genetics+phenotypic)

All individuals are named with a unique code followed by lake of origin and then ecotype (bn= benthivore, pl=planktivore) as such Individualcode_lake_ecotype
Codes provided in the sample list file are consistent with names in the TPS and VCF files where relevant

Information on the QTL database can be found in the QTL database folder