Cape Verde Islands Arabidopsis thaliana

This repository contains scripts for the paper:

Parallel reduction in flowering time enabled evolutionary rescue and establishment in a colonizing Arabidopsis lineage

Authors: Andrea Fulgione1,2,3*, Célia Neto1*, Ahmed F. Elfarargi1, Emmanuel Tergemina1, Mehmet Göktay1, Herculano Dinis4,5, Nina Döring1, Pádraic J. Flood1‡, Sofia Rodriguez-Pacheco1, Nora Walden6§, Markus Koch6, Fabrice Roux7, Joachim Hermisson2, Angela M. Hancock1,2†

Folders:

genotype_calling

Contains the pipelines used for genotype calling in the paper.

data

Contains supporting data for scripts and analyses.

java_programs

Java programs to preprocess the vcf, produce input files for analyses and compute summary statistics on the genomic data.

population_structure

Scripts for the inference of population structure in Cape Verde Islands and worldwide accessions, and for plotting

demographic_inference

Scripts for demographic inference in Cape Verde Islands and worldwide accessions, and for plotting

dNdS_dfe_alpha

Script to test for evidence of adaptive evolution by computing dN/dS (the rate ratio of nonsynonymous to synonymous substitutions), distribution of fitness effects and alpha (the proportion of adaptive substitutions).

qtl_candidate-genes_functional-variants

Testing the percentage of private variation across QTL regions, candidate genes and functional variants

gwas_and_flowering_time_fitness_analyses

Scripts to analyse and compute summary statistics from flowering time and fitness data, including the identification of functional variants involved in flowering time and fitness in Santo Antao and Fogo.

adaptive_variants_history

Scripts to infer the history of adaptive variants in CVI (FRI and FLC) with relate and clues, and to simulate the history of adaptive variants with slim