DOI: 10.5061/dryad.67dn4
title: 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

description: Isolated islands and their often unique biota continue to play key roles
 for understanding the importance of drift, genetic variation and
 adaptation in the process of population differentiation and speciation.
 One island system that has inspired and intrigued evolutionary biologists
 is the blue tit complex (Cyanistes spp.) in Europe and Africa, in
 particular the complex evolutionary history of the multiple genetically
 distinct taxa of the Canary Islands. Understanding Afrocanarian
 colonization events is of particular importance because of recent
 unconventional suggestions that these island populations acted as source
 of the widespread population in mainland Africa. We investigated the
 relationship between mainland and island blue tits using a combination of
 Sanger sequencing at a population level (20 loci; 12 500 nucleotides) and
 next-generation sequencing of single population representatives (&gt;3
 200 000 nucleotides), analysed in coalescence and phylogenetic frameworks.
 We found (i) that Afrocanarian blue tits are monophyletic and represent
 four major clades, (ii) that the blue tit complex has a continental origin
 and that the Canary Islands were colonized three times, (iii) that all
 island populations have low genetic variation, indicating low long-term
 effective population sizes and (iv) that populations on La Palma and in
 Libya represent relicts of an ancestral North African population. Further,
 demographic reconstructions revealed (v) that the Canary Islands,
 conforming to traditional views, hold sink populations, which have not
 served as source for back colonization of the African mainland. Our study
 demonstrates the importance of complete taxon sampling and an extensive
 multimarker study design to obtain robust phylogeographical inferences.
description: Alignments of Sanger
 sequences per locus (nexus format)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.Sanger_alignments_nexus.zipSuper-matrices of concatenated RADseq loci (phylip format)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.RAD_super-matrices_phylip.zipSNP matrix from RAD sequences (nexus format)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.RAD_SNP_matrix_nexus.zip*BEAST species tree 18nc + 2mt DNA Sanger markers (Fig 2a)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.Sanger_starBEAST_speciestree_Fig2a.nex*BEAST marker-specific trees 18nc + 2mt DNA Sanger markersThe 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.Sanger_starBEAST_marker_trees.tar.gz*BEAST species tree 18 ncDNA Sanger markers (Suppl Fig 2)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.Sanger_starBEAST_speciestree_Suppl_Fig2.nexSNAPP species tree, based on RADseq SNP's (nexus format)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.RAD_SNAPP_tree_Fig2b.nexBest ML tree for RAD sequence super-matrix RELAXED (Fig 4; newick format)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.RAD_concat_tree_RELAXED_Fig4.nwkBest ML tree for RAD sequence super-matrix STRICT (Suppl Fig 5; newick format)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.RAD_concat_tree_STRICT_Suppl_Fig5.nwkBrief log of RADseq data processing, including custom scriptsBrief 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.Log_and_custom_scripts.txtconcatenatenexus_edMSRThis 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.