Indirect genetic effects are shaped by demographic history and ecology in Arabidopsis thaliana

This folder contains data & code used for the study "Indirect genetic effects are shaped by demographic history and ecology in Arabidopsis thaliana"

All data analyzed in the study are stored in the folder "data":

• "pheno_file.csv": the main phenotypic file corresponding to the experiment with paired plants used to estimate Indirect Genetic Effects.
• "pheno_file_single_plants.csv": phenotypic file with measurements of plant biomasses in the absence of competition (single plants)
• "call_method_75_TAIR9.csv": genomic data (SNPs) for each accession from the RegMap panel (ref [1])
• "Data_geo_RegMap_accessions.csv": geographic localization of each accession from the RegMap panel (ref [2])
• "igeGWAS_scores.csv": Genome-Wide Association Study (GWAS) results reporting for each SNP from the RegMap panel the p-value and estimated effect sizes of their direct and indirect genetic effects
• "1001_accessions_info.csv": geographic localization and admixture group for each accession from the 1001 genomes project (ref [3])
• "snp_data_all_samples.txt": allelic value of each accession from the 1001 genomes project at the eleven top SNPs associated with IGE
• "sample_names.txt": names of  accessions listed in the file "snp_data_all_samples.txt"
• "climatic_data.csv": climatic data for each accessions from the 1001 genomes project (ref [4])
• "candidate_genes_all.csv":  list of all genes (and associated GO terms) with a non-synonymous, nonsense, or frameshift mutation in close proximity (distance < half LD decay distance) and high linkage (r2>0.5) with a SNP significantly associated with IGE
• "genes.coord.bed": list of all genes in a +- 500 kb around top IGE SNPs and their coordinates
• "AllGenes_fst.GeneID.txt": pairwise Fst computed between each pair of admixture groups, for all genes annotated in the genome of A. thaliana

"ABBA_BABA" subfolder contains ABBA_BABA statistics computed for each individual chromosome (Chr1-Chr5) using genomic windows of 20 kb with at least 250 SNPs per windows. ABBA-BABA statistics were computed using custom python scripts from https://github.com/simonhmartin/genomics_general

"GEA" subfolder contains Genome-Environment Association results, with one file per chromosome x climatic variable. Climatique variable are indexed, following the order listed in the file "Climatic_variables.txt" within the subfolder "GEA". GEA analysis were run with the gemma program: https://github.com/genetics-statistics/GEMMA.

"LD_IGE_SNPs" subfolders contains the list of SNPs located at +- 2Mb of a significant IGE SNP (one file per IGE SNP, named "SNPalias_LDSimplified.csv") and their linkage (r2) with the IGE SNP. It also contains the file "LD_windows_sizes.csv" with the half LD decay distances for all significant IGE SNP.

All analysis performed to produce the tables and figures presented in the study (main manuscript & supplementary information) were done with the R script "Arabidopsis_IGE_analysis.R", which uses "manhattan_custom.R" as a source function to produce custom manhattan plots.

REFERENCES:

[1] Horton MW, Hancock AM, Huang YS, Toomajian C, Atwell S, Auton A, Muliyati NW, Platt A, Sperone FG, Vilhjálmsson BJ, et al. 2012. Genome-wide patterns of genetic variation in worldwide Arabidopsis thaliana accessions from the RegMap panel. Nature Genetics 44: 212–216.

[2] Anastasio AE, Platt A, Horton M, Grotewold E, Scholl R, Borevitz JO, Nordborg M, Bergelson J. 2011. Source verification of mis-identified Arabidopsis thaliana accessions. The Plant Journal 67: 554–566.

[3] 1001 Genomes Consortium. 2016. 1,135 genomes reveal the global pattern of polymorphism in Arabidopsis thaliana. Cell 166: 481–491.

[4] Ferrero-Serrano Á, Assmann SM. 2019. Phenotypic and genome-wide association with the local environment of Arabidopsis. Nature Ecology & Evolution 3: 274–285.