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 (>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.
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.zip
Super-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.zip
SNP 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 markers
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.
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.nex
SNAPP 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.nex
Best 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.nwk
Best 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.nwk
Brief log of RADseq data processing, including custom scripts
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.
Log_and_custom_scripts.txt
concatenatenexus_edMSR
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.