/African_A.thaliana

Durvasula and Fulgione et al 2017. "African genomes illuminate the early history and transition to selfing in Arabidopsis thaliana" PNAS 2017, 114(20):5213-5218. URL: http://www.pnas.org/content/114/20/5213.long

Primary LanguageJava

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.

pop_structure

This folder contains analyses and plotting scripts for figures 1 and 2 of the paper, which elucidate population structure.

diversity

This folder contains analyses scripts for figures 3 and 4, which describe the diversity present in African thaliana populations.

msmc

This folder contains analyses scripts for figures 5 and 6, which use MSMC v2 for population history reconstruction.