Data from: Population genomic footprints of fine-scale differentiation between habitats in Mediterranean blue tits

Szulkin M, Gagnaire P, Bierne N, Charmantier A

Date Published: November 19, 2015

DOI: http://dx.doi.org/10.5061/dryad.713v1

 

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Content in the Dryad Digital Repository is offered "as is." By downloading files, you agree to the Dryad Terms of Service. To the extent possible under law, the authors have waived all copyright and related or neighboring rights to this data. CC0 (opens a new window) Open Data (opens a new window)

Title Szulkin_Blue_Tit_working_dataset_MAF0.02_callrate0.9
Downloaded 11 times
Description The filtered VCF file containing 12K SNPs from Continental and Corsican populations of Mediterranean blue tit. The 12K SNP VCF file can be filtered further to subsets of individuals where no family ties are present, or that contribute to the symmetrical minimal dataset (more info about these datasets can be found in the Materials & Methods section and in Supplementary Information files).
Download Szulkin_Blue_Tit_working_dataset_MAF0.02_....9.vcf (33.81 Mb)
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Title szulkin_blue_tit_sample_details
Downloaded 13 times
Description An excel spreadsheet providing further details regarding each sequenced bird (GPS coordinates, information on birth year, population of origin, nestbox of first reproduction, nestbox coordinates and nr of reads obtained for each individual). The relationships between the different nested datasets are also provided and can be used to generate 6K and 3K datasets.
Download szulkin_blue_tit_sample_details.xlsx (78.45 Kb)
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Title List_19760_Consensus_RAD_Stacks_1_80
Downloaded 10 times
Description Full list of consensus RAD tag sequences (in fasta format) that were used for blast annotations.
Download List_19760_Consensus_RAD_Stacks_1_80.fa (2.092 Mb)
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Title Szulkin_Blue_Tit_raw_unfiltered_209K_SNPs_from_Stacks_maf1
Downloaded 7 times
Description The raw VCF file generated with Stacks, containing 209K SNPs with a global minor allele frequency of at least 0.01. This dataset was then filtered based on quality and population genetic criteria in vcftools to produce the working dataset conatining 12 SNPs.
Download Szulkin_Blue_Tit_raw_unfiltered_209K_SNPs...f1.vcf (576.4 Mb)
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When using this data, please cite the original publication:

Szulkin M, Gagnaire P, Bierne N, Charmantier A (2015) Population genomic footprints of fine-scale differentiation between habitats in Mediterranean blue tits. Molecular Ecology, 25(2):542-558. http://dx.doi.org/10.1111/mec.13486

Additionally, please cite the Dryad data package:

Szulkin M, Gagnaire P, Bierne N, Charmantier A (2015) Data from: Population genomic footprints of fine-scale differentiation between habitats in Mediterranean blue tits. Dryad Digital Repository. http://dx.doi.org/10.5061/dryad.713v1
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