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

This folder contains data &amp; 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. This data was produced in a previous study by Wuest et al., 2022 (ref [1]).<br> "pheno_file_single_plants.csv": phenotypic file with measurements of plant biomasses in the absence of competition (single plants)<br> "call_method_75_TAIR9.csv": genomic data (SNPs) for each accession from the RegMap panel (ref [2])<br> "Data_geo_RegMap_accessions.csv": geographic localization of each accession from the RegMap panel (ref [3])<br> "1001_accessions_info.csv": geographic localization and admixture group for each accession from the 1001 genomes project (ref [4])<br> "snp_data_all_samples.txt": allelic value of each accession from the 1001 genomes project at the five top SNPs associated with IGE<br> "sample_names.txt": names of accessions listed in the file "snp_data_all_samples.txt"<br> "climatic_data.csv": climatic data for each accessions from the 1001 genomes project (ref [5])<br> "candidate_genes_all.csv": list of all genes (and associated GO terms) with a non-synonymous mutation in linkage (r2&gt;0.5) with a SNP significantly associated with IGE<br> "candidate_genes_light_response.csv": list of all candidate genes with a GO term related to light response<br> "AllGenes_fst.GeneID.txt": pairwise Fst computed between each pair of admixture groups, for all individual genes 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<br> "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. <br> All analysis performed to produce the tables and figures presented in the study (main manuscript &amp; 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. [1] Wuest SE, Pires ND, Luo S, Vasseur F, Messier J, Grossniklaus U, Niklaus PA. 2022. Increasing plant group productivity through latent genetic variation for cooperation. PLOS Biology 20: e3001842. [2] 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. [3] 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. [4] 1001 Genomes Consortium. 2016. 1,135 genomes reveal the global pattern of polymorphism in Arabidopsis thaliana. Cell 166: 481–491. [5] Ferrero-Serrano Á, Assmann SM. 2019. Phenotypic and genome-wide association with the local environment of Arabidopsis. Nature Ecology &amp; Evolution 3: 274–285.