Data from: Distinguishing noise from signal in patterns of genomic divergence in a highly polymorphic avian radiation

Campagna L, Gronau I, Silveira LF, Siepel A, Lovette IJ

Date Published: July 22, 2015

DOI: http://dx.doi.org/10.5061/dryad.6mp65

 

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Title Input file for the GPhoCS analysis.
Downloaded 39 times
Description Sequence data for 60 individuals of 6 capuchino species in GPhoCS format.
Download Campagna_Sporophila.gphocs.txt (14.24 Mb)
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Title Genotypes in Arlequin format
Downloaded 7 times
Description Genotypes for all SNPs in Arlequin format (as in Figure 1c)
Download Genotypes_ALL_SNPs_Arlequin.arp (5.450 Mb)
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Title Genotypes in Arlequin format for the randomized dataset
Downloaded 3 times
Download Randomized_ALL_SNPs_Arlequin.arp (7.678 Mb)
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Title Genotypes_Structure_Figure1
Downloaded 6 times
Description Genotypes in Structure format. One SNP per RAD locus as in Figure 1b.
Download Genotypes_Structure_Figure1.txt (656.8 Kb)
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Title Genotypes_Structure_Figure4
Downloaded 5 times
Description Gentoypes in Structure format. One SNP per RAD locus as in Figure 4c.
Download Genotypes_Structure_Figure4.txt (333.5 Kb)
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Title Restriction Site Associated DNA data
Downloaded 12 times
Description Compressed file containing quality-filtered and demultiplexed reads for each individual in the study. Files are identified by species name followed by sample number as shown in Table S1.
Download demultiplexed_ddRAD_data.tar.gz (18.24 Gb)
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Title Fst estimates for each locus - RANDOMIZED dataset
Downloaded 2 times
Description Species are coded as follows: 1-S. bouvreuil; 2-S. pileata; 3-S. hypoxantha; 4-S. melanogaster; 5-S. palustris; 6-S. ruficollis.
Download FST_randomized_data.zip (4.652 Mb)
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Title Fst estimates for each locus
Downloaded 2 times
Description Species are coded as follows: 1-S. bouvreuil; 2-S. pileata; 3-S. hypoxantha; 4-S. melanogaster; 5-S. palustris; 6-S. ruficollis.
Download FST_species_data.zip (3.093 Mb)
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Title Output from Stacks assembly
Downloaded 15 times
Description This folder contains the Stacks output from the RAD assembly (M=n=5). There are four files per sample (72 samples in total) plus three catalog files (291 files in total). Samples are identified by species name followed by collection number as indicated in Table S1.
Download RAD_assembly.tar.gz (1.935 Gb)
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Title Inter-species average PhiST matrix
Downloaded 2 times
Description Inter-species average PhiST matrix displayed in a Neighbor-joining tree built in PHYLIP (Figure 1a)
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Title Stacks output with identified variants in VCF format
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Description Variants identified by Stacks. Assembly parameters M=n=5.
Download Stacks_variants.vcf (20.51 Mb)
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When using this data, please cite the original publication:

Campagna L, Gronau I, Silveira LF, Siepel A, Lovette IJ (2015) Distinguishing noise from signal in patterns of genomic divergence in a highly polymorphic avian radiation. Molecular Ecology 24(16): 4238–4251. http://dx.doi.org/10.1111/mec.13314

Additionally, please cite the Dryad data package:

Campagna L, Gronau I, Silveira LF, Siepel A, Lovette IJ (2015) Data from: Distinguishing noise from signal in patterns of genomic divergence in a highly polymorphic avian radiation. Dryad Digital Repository. http://dx.doi.org/10.5061/dryad.6mp65
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