An introgression breakthrough left by an anthropogenic contact between two ascidians

This zenodo archive contains the vcf files and the R scripts used for the statistical analyses of the paper "An introgression breakthrough left by an anthropogenic contact between two ascidians" published in Molecular Ecology in 2021. The fastq files processed by the stacks reference pipeline to produce the vcf files in this archive are available on NCBI under the bioproject "PRJNA759193".

The analyses of the paper available here are divided in three parts:

1. Analyses of the fine-scale population structure of Ciona intestinalis across the English Channel, the Iroise Sea, and the Bay of biscay
   • Genotype file: Ciona_data1_finescale.vcf.gz
   • Genotype file pruned for physical linkage: Ciona_dataset1_fine_scale_maf_thin.vcf
   • R script file for pop. structure : Finescale_structure_dataset1.R
2. Analyses of the large-scale population structure of C. instestinalis, C. robusta and C. roulei across the Atlantic and the Mediteranean sea
   • Genotype file: Ciona_data2_Largescale.vcf.gz
   • Genotype file pruned for physical linkage: Ciona_dataset2_largescale_maf_thin.vcf
   • R script file for pop. structure : Largescale_structure_dataset2.R
   • Linux + R script file for phylogeny: Phylogeny.R
3. Analyse of introgression from C. robusta into C. intestinalis background:
   • Genotype file: Ciona_data2_Largescale.vcf.gz
   • Ancestry informative genotype: Ciona_diagnistic_SNPs_order.vcf
   • R script for admixture across all chromosome: Ancestry_chromosome.R
   • R script for HMM to detect introgression breakthrough from ancestry informative SNPs: HMM_log10FST+1_3norm_introgression_hotspot.R*

*this script is a modified version of the script by Marques et al.  (2016) available here: https://github.com/marqueda/HMM-detection-of-genomic-islands