This repository contains scripts for the paper:
Durvasula*, A., Fulgione*, A., Gutaker, R. M., Alacakaptan, S. I., Flood, P. J., Neto, C., Tsuchimatsu T., Burbano H.A., Picó F.X., Alonso-Blanco, C., Hancock, A. M. (2017). African genomes illuminate the early history and transition to selfing in Arabidopsis thaliana. Proceedings of the National Academy of Sciences of the United States of America, 114(20), 5213–5218. http://doi.org/10.1073/pnas.1616736114
The analyses are based on a VCF file that contains genotype calls through the SHORE pipeline for all 1001 genomes individuals and the new individuals included with this paper.
This folder contains analyses and plotting scripts for figures 1 and 2 of the paper, which elucidate population structure.
This folder contains analyses scripts for figures 3 and 4, which describe the diversity present in African thaliana populations.
This folder contains analyses scripts for figures 5 and 6, which use MSMC v2 for population history reconstruction.