Drivers of linkage disequilibrium across a species' geographic range

Data from "Drivers of linkage disequilibrium across a species’ geographic range" by Lucek &amp; Willi The files contain all LD estimates used for the analysis in the respective study estimated for genic and intergenic regions of the Arabidopsis lyrata genome. 3 files contain the LD estimates from Pool-Seq data (Genbank project PRJEB19338) using the software Ldx https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0048588 : genic_ld.txt contains the following columns: GeneID =&gt; ID of the respective gene based on the V2 annotation of A. lyrata<br> Scaffold =&gt; Scaffold ID (1-8)<br> Population =&gt; Population ID (see Table S1 in the study)<br> UncorrectedLD =&gt; LD estimates from Ldx<br> Distance_between_LD_pairs =&gt; Distance in bps between SNPs used to calculate LD<br> Fis =&gt; Inbreeding coefficient (Fis) based on microsattelite estimates<br> Expansion_distance =&gt; Range expansion distance (in km) taken from Willi et al. 2018 Mol Biol Evol<br> Genetic_cluster =&gt; Phylogenetic cluster (1= East; 2= West)<br> LD =&gt; Distance corrected LD used for all analyses<br> Average_distance_to_nearest_gene =&gt; average distance to the nearest gene as an estimate for gene density. LD_genic_with_SIFT_annotations.txt<br> A subset of genic_ld.txt for which SNPs were annotated by SIFT4G https://www.nature.com/articles/nprot.2015.123<br> The file contains one additional column:<br> SIFT_comparison =&gt; 3 types of comparisons, T_T (between Tolerated and Tolerated SNPs), T_D (between Tolerated and Deleterious SNPs), D_D (between Deleterious and Deleterious SNPs) intergenic_ld.txt contains the following columns: Scaffold =&gt; Scaffold ID (1-8)<br> Population =&gt; Population ID (see Table S1 in the study)<br> UncorrectedLD =&gt; LD estimates from Ldx<br> Distance_between_LD_pairs =&gt; Distance in bps between SNPs used to calculate LD<br> Fis =&gt; Inbreeding coefficient (Fis) based on microsattelite estimates<br> Expansion_distance =&gt; Range expansion distance (in km) taken from Willi et al. 2018 Mol Biol Evol<br> Genetic_cluster =&gt; Phylogenetic cluster (1= East; 2= West)<br> LD =&gt; Distance corrected LD used for all analyses<br> Size_of_intergenic_region_in_bps =&gt; size in bps of each intergenic region 2 files contain the LD estimates from individually re-sequenced genomes (Genbank project PRJEB30473 ) using the software mlrho https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0048588 : https://onlinelibrary.wiley.com/doi/full/10.1111/j.1365-294X.2009.04482.x Each file contains the correlation of zygosity estimated for each individual for each bp distance as distinct columns, either for all genic (genic_mlrho.txt) or intergenic (intergenic_mlrho.txt) regions. All values were scaled by genome-wide theta.