Data from: Linkage disequilibrium network analysis (LDna) gives a global view of chromosomal inversions, local adaptation and geographic structure

Kemppainen P, Knight CG, Sarma DK, Hlaing T, Prakash A, Maung Maung YN, Somboon P, Mahanta J, Walton C

Date Published: January 16, 2015

DOI: http://dx.doi.org/10.5061/dryad.2t764

 

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Title RAD_baimaii_RAW_alleles
Downloaded 9 times
Description This 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.
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Title RAD_baimaii_RAW_numbers
Downloaded 12 times
Description This 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.
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Title RAD_baimaii_filtered
Downloaded 6 times
Description Contains 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".
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Title RAD_baimaii_filtered_fullsequence
Downloaded 5 times
Description Same information as file "RAD_baimaii_filtered.tsv" except contains the full sequence (96 bps including restriction site overhang).
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Title RAD_baimaii_Rqtl
Downloaded 5 times
Description RData file that contains all necessary information for the Anopheles baimaii linkage map. See documentation for the R-package 'qtl' for more info.
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Title RAD_baimaii_filtered_SNPs
Downloaded 4 times
Description This file contains all bi-allelic SNPs with a minimum allele frequency>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.
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Title RAD_baimaii_geographic_coordinates
Downloaded 7 times
Description Contains geographic coordinates for the 184 individuals in the A baimaii RAD sequence data set
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Title RAD_LDna_sample_Rcode
Downloaded 41 times
Description Compressed file with all necessary files (data, custom functions and R-code) to reproduce figures 3,4 and 5 in the original paper.
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Title RAD_baimaii_BLAT
Downloaded 8 times
Description BLAT 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.
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Title Stickleback_SNPs_filtered
Downloaded 8 times
Description Filtered Stickleback SNP data
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Title Stickleback_r2
Downloaded 34 times
Description Pairwise r-squared values between all SNPs from file: "Stickleback_SNPs_filtered"
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Title LDna_simulation
Downloaded 33 times
Description Includes .par, .arp, the associated r-squared data sets and R-code to produce figures in Appendix S3 (LDna on simulated data).
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When using this data, please cite the original publication:

Kemppainen P, Knight CG, Sarma DK, Hlaing T, Prakash A, Maung Maung YN, Somboon P, Mahanta J, Walton C (2015) Linkage disequilibrium network analysis (LDna) gives a global view of chromosomal inversions, local adaptation and geographic structure. Molecular Ecology Resources 15(5): 1031-1045. http://dx.doi.org/10.1111/1755-0998.12369

Additionally, please cite the Dryad data package:

Kemppainen P, Knight CG, Sarma DK, Hlaing T, Prakash A, Maung Maung YN, Somboon P, Mahanta J, Walton C (2015) Data from: Linkage disequilibrium network analysis (LDna) gives a global view of chromosomal inversions, local adaptation and geographic structure. Dryad Digital Repository. http://dx.doi.org/10.5061/dryad.2t764
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