10.5061/DRYAD.67DN4
Stervander, Martin
Lund University
Illera, Juan Carlos
Lund University
Kvist, Laura
University of Oulu
Barbosa, Pedro
Lund University
Keehnen, Naomi P.
Lund University
Pruisscher, Peter
Lund University
Bensch, Staffan
Lund University
Hansson, Bengt
Lund University
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
dataset
2015
Cyanistes teneriffae
Cyanistes cyanus
Colonisation
Isolation
Cyanistes caeruleus
Miocene
Coalescence
Holocene
2015-03-10T16:58:10Z
2015-03-10T16:58:10Z
en
https://doi.org/10.1111/mec.13145
799885283 bytes
1
CC0 1.0 Universal (CC0 1.0) Public Domain Dedication
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.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.
Canary Islands
Europe
North Africa