THE INFLUENCE OF SAMPLING DESIGN ON SPECIES TREE INFERENCE: A NEW RELATIONSHIP FOR THE NEW WORLD CHICKADEES (AVES: POECILE)
Article first published online: 24 OCT 2013
© 2013 The Author(s). Evolution © 2013 The Society for the Study of Evolution.
Volume 68, Issue 2, pages 501–513, February 2014
How to Cite
Harris, R. B., Carling, M. D. and Lovette, I. J. (2014), THE INFLUENCE OF SAMPLING DESIGN ON SPECIES TREE INFERENCE: A NEW RELATIONSHIP FOR THE NEW WORLD CHICKADEES (AVES: POECILE). Evolution, 68: 501–513. doi: 10.1111/evo.12280
- Issue published online: 28 JAN 2014
- Article first published online: 24 OCT 2013
- Accepted manuscript online: 2 OCT 2013 09:49AM EST
- Manuscript Accepted: 19 SEP 2013
- Manuscript Received: 11 APR 2013
Disclaimer: Supplementary materials have been peer-reviewed but not copyedited.
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.eps||4566K||Figure S2. Diagrams showing the workflow used in this study to sample, partition, and analyze loci.|
|evo12280-sup-0003-Figure3.eps||514K||Figure S3. Principal component analysis conducted in R using the number of parsimony informative sites, variable sites, and nodes resolved.|
|evo12280-sup-0004-Figure4.pdf||133K||Figure S4. Individual nuclear RAxML gene trees with circles at nodes indicating bootstrap values: black > 95%, gray > 75%, and white < 75%.|
|evo12280-sup-0005-Figure5.eps||610K||Figure S5. The gene tree given by the concatenated mitochondrial DNA with branch lengths and posterior probabilities from the MrBayes analysis.|
|evo12280-sup-0006-Figure6.eps||2728K||Figure S6. The top most likely species networks conducted in PhyloNet accounting for both incomplete lineage sorting and gene flow.|
|evo12280-sup-0007-Figure7.eps||1185K||Figure S7. The bootstrap version of the STEM analysis using 40 nuclear loci.|
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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