Data from: Disentangling the complex evolutionary history of the Western Palearctic blue tits (Cyanistes spp.) – phylogenomic analyses suggest radiation by multiple colonisation events and subsequent isolation

Stervander M, Illera JC, Kvist L, Barbosa P, Keehnen NP, Pruisscher P, Bensch S, Hansson B

Date Published: March 10, 2015

DOI: http://dx.doi.org/10.5061/dryad.67dn4

 

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Title Alignments of Sanger sequences per locus (nexus format)
Downloaded 9 times
Description Locus-specific alignments of Sanger sequences in nexus format. For information about loci, refer to Supplementary Table 2; for information about individuals/samples, refer to Supplementary Table 1 in the original publication.
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Title Super-matrices of concatenated RADseq loci (phylip format)
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Description Super-matrices STRICT and RELAXED consisting of concatenated RAD sequencing loci, in phylip format. Key for the sample codes are given in separate text files.
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Title SNP matrix from RAD sequences (nexus format)
Downloaded 13 times
Description Matrix of effectively non-linked and non-automorphic Single Nucleotide Polymorphisms (SNP's) of Cyanistes samples, based on RAD sequences, in nexus format. Key for the sample codes are given in a separate text file.
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Title *BEAST species tree 18nc + 2mt DNA Sanger markers (Fig 2a)
Downloaded 17 times
Description Tree file for Figure 2a, 18 nuclear and 2 mitochondrial Sanger sequence markers. The tree is in nexus format. A translation table between taxon names used in the file, and taxon names used in the figure is found in the readme file. For further details, see the manuscript.
Download Sanger_starBEAST_speciestree_Fig2a.nex (43.77 Mb)
Download README.txt (692 bytes)
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Title *BEAST marker-specific trees 18nc + 2mt DNA Sanger markers
Downloaded 3 times
Description The compressed tarball contains 20 marker specific (18 nuclear and 2 mitochondrial) tree files (nexus format) from the *BEAST analysis of Sanger sequence markers. The tree files are in nexus format. Markers are named according to Supplementary Table 2, samples according to Supplementary Table 1.
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Title *BEAST species tree 18 ncDNA Sanger markers (Suppl Fig 2)
Downloaded 5 times
Description Tree file for Supplementary Figure 2, 18 nuclear (but no mitochondrial) Sanger sequence markers. The tree is in nexus format. A translation table between taxon names used in the file, and taxon names used in the figure is found in the readme file. For further details, see the manuscript.
Download Sanger_starBEAST_speciestree_Suppl_Fig2.nex (60.33 Mb)
Download README.txt (713 bytes)
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Title SNAPP species tree, based on RADseq SNP's (nexus format)
Downloaded 30 times
Description Species tree file for Figure 2b, RADseq SNP matrix analysed with SNAPP. The tree is in nexus format. A translation table between taxon names used in the file, and taxon names used in the figure, is found in the readme file. For further details, see the manuscript.
Download RAD_SNAPP_tree_Fig2b.nex (19.74 Mb)
Download README.txt (570 bytes)
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Title Best ML tree for RAD sequence super-matrix RELAXED (Fig 4; newick format)
Downloaded 5 times
Description Best ML tree computed in RAxML for RAD sequence matrix RELAXED, corresponding to Figure 4. The tree is in newick format. A translation table between taxon names used in the file, and taxon names used in the figure, is found in the readme file. For further details, see the manuscript.
Download RAD_concat_tree_RELAXED_Fig4.nwk (2.023 Kb)
Download README.txt (606 bytes)
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Title Best ML tree for RAD sequence super-matrix STRICT (Suppl Fig 5; newick format)
Downloaded 4 times
Description Best ML tree computed in RAxML for RAD sequence matrix STRICT, corresponding to Supplementary Figure 5. The tree is in newick format. A translation table between taxon names used in the file, and taxon names used in the figure, is found in the readme file. For further details, see the manuscript.
Download RAD_concat_tree_STRICT_Suppl_Fig5.nwk (2.023 Kb)
Download README.txt (624 bytes)
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Title Brief log of RADseq data processing, including custom scripts
Downloaded 41 times
Description Brief work log for analyses of RADseq data. I have used little snippets of custom scripts (which you are free to use and modify), but this log also makes use of plenty of neat little scripts made by other people. One script, by Shannon Hedtke, was modified to fit the purposes in this workflow, and that modified script is provided separately.
Download Log_and_custom_scripts.txt (14.24 Kb)
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Title concatenatenexus_edMSR
Downloaded 6 times
Description This program is written by Shannon Hedtke, and takes all nexus files in a directory and concatenates them. I have modified the original script, which splits sequence names on "_" and removes all duplicates of the left hand side - something that is good for cleaning up among GenBank versions of the same sequence, but bad for removing allelles.
Download concatenatenexus_edMSR.pl (9.21 Kb)
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When using this data, please cite the original publication:

Stervander M, Illera JC, Kvist L, Barbosa P, Keehnen NP, Pruisscher P, Bensch S, Hansson B (2015) Disentangling the complex evolutionary history of the Western Palearctic blue tits (Cyanistes spp.) – phylogenomic analyses suggest radiation by multiple colonisation events and subsequent isolation. Molecular Ecology 24(10): 2477-2494. http://dx.doi.org/10.1111/mec.13145

Additionally, please cite the Dryad data package:

Stervander M, Illera JC, Kvist L, Barbosa P, Keehnen NP, Pruisscher P, Bensch S, Hansson B (2015) Data from: Disentangling the complex evolutionary history of the Western Palearctic blue tits (Cyanistes spp.) – phylogenomic analyses suggest radiation by multiple colonisation events and subsequent isolation. Dryad Digital Repository. http://dx.doi.org/10.5061/dryad.67dn4
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