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Disclaimer: Supplementary materials have been peer-reviewed but not copyedited.

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evo12280-sup-0001-Figure1.eps6862K

Avian DNA sequences used to build character matrices are available from NCBI Genbank (accession HQ719474–HQ720138). Character matrices and tree files for analyses are available from TreeBase (http://purl.org/phylo/treebase/phylows/study/TB2:S13400?x-access-code=cedcb32d3f14a97d24682621836fae1f&format=html).

Figure S1. Map of ingroup (Poecile) species ranges in North America and sampling localities.

evo12280-sup-0002-Figure2.eps4566KFigure S2. Diagrams showing the workflow used in this study to sample, partition, and analyze loci.
evo12280-sup-0003-Figure3.eps514KFigure S3. Principal component analysis conducted in R using the number of parsimony informative sites, variable sites, and nodes resolved.
evo12280-sup-0004-Figure4.pdf133KFigure S4. Individual nuclear RAxML gene trees with circles at nodes indicating bootstrap values: black > 95%, gray > 75%, and white < 75%.
evo12280-sup-0005-Figure5.eps610KFigure S5. The gene tree given by the concatenated mitochondrial DNA with branch lengths and posterior probabilities from the MrBayes analysis.
evo12280-sup-0006-Figure6.eps2728KFigure S6. The top most likely species networks conducted in PhyloNet accounting for both incomplete lineage sorting and gene flow.
evo12280-sup-0007-Figure7.eps1185KFigure S7. The bootstrap version of the STEM analysis using 40 nuclear loci.
evo12280-sup-0008-SuppMat.docx111K

Table S1. Sample identification numbers, museums, and collecting locations of samples.

Table S2. Nuclear loci GenBank IDs, primer sequences, and annealing temperatures.

Table S3. List of molecular markers and descriptions.

Table S4. Composition of randomly sampled loci for each data set.

Table S5. Composition of loci for data sets based on ranked attributes.

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