DOI: 10.5061/dryad.2t764
title: Data from: Linkage disequilibrium network analysis (LDna) gives a global view of chromosomal inversions, local adaptation and geographic structure

description: Recent advances in sequencing allow population-genomic data to be
 generated for virtually any species. However, approaches to analyse such
 data lag behind the ability to generate it, particularly in nonmodel
 species. Linkage disequilibrium (LD, the nonrandom association of alleles
 from different loci) is a highly sensitive indicator of many evolutionary
 phenomena including chromosomal inversions, local adaptation and
 geographical structure. Here, we present linkage disequilibrium network
 analysis (LDna), which accesses information on LD shared between multiple
 loci genomewide. In LD networks, vertices represent loci, and connections
 between vertices represent the LD between them. We analysed such networks
 in two test cases: a new restriction-site-associated DNA sequence
 (RAD-seq) data set for Anopheles baimaii, a Southeast Asian malaria
 vector; and a well-characterized single nucleotide polymorphism (SNP) data
 set from 21 three-spined stickleback individuals. In each case, we readily
 identified five distinct LD network clusters (single-outlier clusters,
 SOCs), each comprising many loci connected by high LD. In A. baimaii,
 further population-genetic analyses supported the inference that each SOC
 corresponds to a large inversion, consistent with previous cytological
 studies. For sticklebacks, we inferred that each SOC was associated with a
 distinct evolutionary phenomenon: two chromosomal inversions, local
 adaptation, population-demographic history and geographic structure. LDna
 is thus a useful exploratory tool, able to give a global overview of LD
 associated with diverse evolutionary phenomena and identify loci
 potentially involved. LDna does not require a linkage map or reference
 genome, so it is applicable to any population-genomic data set, making it
 especially valuable for nonmodel species.
description: RAD_baimaii_RAW_allelesThis file contains RAW data from the software STACKS containing the RAD genotypes. The file "RAD_baimaii_RAW_numbers" contains the corresponding stack depths for each allele and these provided the raw data for quality filtering of the RAD sequence data set as described in the original paper. See also STACKs documentation for more details.RAD_baimaii_RAW_numbersThis file contains RAW data from the software STACKS containing stack depths for the RAD genotypes for Anopheles baimaii. The file "RAD_baimaii_RAW_alleles" contains the corresponding alleles. These two files provided the raw data for quality filtering of the RAD sequence data set as described in the original paper. See also STACKs documentation for more details.RAD_baimaii_filteredContains the filtered Anopheles baimaii RAD sequence data set. (184 individuals and 3008 RAD loci). The rad sequence here contains only sites that were polymorphic in the RAW data (e.g. file "RAD_baimaii_RAW_alleles.tsv"). Monomorphic loci have alleles called "consensus".RAD_baimaii_filtered_fullsequenceSame information as file "RAD_baimaii_filtered.tsv" except contains the full sequence (96 bps including restriction site overhang).RAD_baimaii_RqtlRData file that contains all necessary information for the Anopheles baimaii linkage map. See documentation for the R-package 'qtl' for more info.RAD_baimaii_filtered_SNPsThis file contains all bi-allelic SNPs with a minimum allele frequency&gt;0.1 from the RAD sequence data set: RAD_baimaii_filtered_fullsequence.tsv. The first part of the locus name give the RAD locus and the second part (after ".") gives the position of the SNP (starting from 1) along the 96 bp sequence. 3828 loci and 184 individuals.RAD_baimaii_geographic_coordinatesContains geographic coordinates for the 184 individuals in the A baimaii RAD sequence data setRAD_LDna_sample_RcodeCompressed file with all necessary files (data, custom functions and R-code) to reproduce figures 3,4 and 5 in the original paper.RAD_baimaii_BLATBLAT results against the A. dirus draft genom (https://olive.broadinstitute.org/genomes/anop_diru_wrair2.1). Contains results from both RAD landscape genomics loci and the linkage map. Loci denoted with a "u" means the loci are unique to the linkage map.Stickleback_SNPs_filteredFiltered Stickleback SNP dataStickleback_r2Pairwise r-squared values between all SNPs from file: "Stickleback_SNPs_filtered"LDna_simulationIncludes .par, .arp, the associated r-squared data sets and R-code to produce figures in Appendix S3 (LDna on simulated data).