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Supplemental Information

Clustering/heatmap analysis depicting degree of shared data between each species pair; missing data reduction (matrix 3, Table 2)

Degree of positive data overlap indicated by a color-coded heatmap (yellow = low, red = high); species order from right to left in the same order as listed from top to bottom on right side of figure. Lack of phylogenetic clustering indicates bias from shared data does not explain relationships seen in phylogenomic analyses.

DOI: 10.7287/peerj.preprints.1482v1/supp-1

Clustering/heatmap analysis depicting degree of shared data between each species pair; missing data reduction (matrix 2, Table 2)

Degree of positive data overlap indicated by a color-coded heatmap (yellow = low, red = high); species order from right to left in the same order as listed from top to bottom on right side of figure. Lack of phylogenetic clustering indicates bias from shared data does not explain relationships seen in phylogenomic analyses.

DOI: 10.7287/peerj.preprints.1482v1/supp-2

Clustering/heatmap analysis depicting degree of shared data between each species pair; BaCoCa reduced matrix (matrix 4, Table 2)

Degree of positive data overlap indicated by a color-coded heatmap (yellow = low, red = high); species order from right to left in the same order as listed from top to bottom on right side of figure. Lack of phylogenetic clustering indicates bias from shared data does not explain relationships seen in phylogenomic analyses. 40

DOI: 10.7287/peerj.preprints.1482v1/supp-3

Clustering/heatmap analysis depicting degree of shared data between each species pair; arthropod core ortholog matrix (matrix 5, Table 2)

Degree of positive data overlap indicated by a color-coded heatmap (yellow = low, red = high); species order from right to left in the same order as listed from top to bottom on right side of figure. Lack of phylogenetic clustering indicates bias from shared data does not explain relationships seen in phylogenomic analyses.

DOI: 10.7287/peerj.preprints.1482v1/supp-4

Clustering/heatmap analysis depicting degree of shared data between each species pair; full spider ortholog matrix (matrix 1, Table 2)

Degree of positive data overlap indicated by a color-coded heatmap (yellow = low, red = high); species order from right to left in the same order as listed from top to bottom on right side of figure. Lack of phylogenetic clustering indicates bias from shared data does not explain relationships seen in phylogenomic analyses. 42

DOI: 10.7287/peerj.preprints.1482v1/supp-5

Clustering/heatmap analysis depicting degree of shared data between each species pair; MARE matrix (matrix 7, Table 2)

Degree of positive data overlap indicated by a color-coded heatmap (yellow = low, red = high); species order from right to left in the same order as listed from top to bottom on right side of figure. Lack of phylogenetic clustering indicates bias from shared data does not explain relationships seen in phylogenomic analyses.

DOI: 10.7287/peerj.preprints.1482v1/supp-6

Gene occupancy of matrix 1 (see Table 2)

Colored squares represent partitions present in matrix for each OTU (x-axis, in descending order of OTU representation from left to right) and each partition or gene (y-axis, in ascending order of partition representation).

DOI: 10.7287/peerj.preprints.1482v1/supp-7

Gene occupancy of matrix 2 (see Table 2)

Colored squares represent partitions present in matrix for each OTU (x-axis, in descending order of OTU representation from left to right) and each partition or gene (y-axis, in ascending order of partition representation).

DOI: 10.7287/peerj.preprints.1482v1/supp-8

Gene occupancy of matrix 3 (see Table 2)

Colored squares represent partitions present in matrix for each OTU (y-axis, in descending order of OTU representation from bottom to top) and each partition or gene (x-axis, in descending order of partition representation from left to right).

DOI: 10.7287/peerj.preprints.1482v1/supp-9

Gene occupancy of matrix 4 (see Table 2)

Colored squares represent partitions present in matrix for each OTU (y-axis, in descending order of OTU representation from bottom to top) and each partition or gene (x-axis, in descending order of partition representation from left to right). Figure

DOI: 10.7287/peerj.preprints.1482v1/supp-10

Gene occupancy of matrix 7 (see Table 2)

Colored squares represent partitions present in matrix for each OTU (y-axis, in descending order of OTU representation from bottom to top) and each partition or gene (x-axis, in descending order of partition representation from left to right).

DOI: 10.7287/peerj.preprints.1482v1/supp-11

Gene occupancy of matrix 5 (see Table 2)

Colored squares represent partitions present in matrix for each OTU (y-axis, in descending order of OTU representation from bottom to top) and each partition or gene (x-axis, in descending order of partition representation from left to right).

DOI: 10.7287/peerj.preprints.1482v1/supp-12

Gene Ontology molecular functions, levels 2 for OGs shared by Arthropod and Spider Core sets

Figures generated by Blast2GO analysis.

DOI: 10.7287/peerj.preprints.1482v1/supp-13

Gene Ontology molecular functions, level 3 for OGs shared by Arthropod and Spider Core sets

Figures generated by Blast2GO analysis.

DOI: 10.7287/peerj.preprints.1482v1/supp-14

Partition file for data matrix 1

DOI: 10.7287/peerj.preprints.1482v1/supp-15

Additional Information

Competing Interests

The authors declare that they have no competing interests.

Author Contributions

Nicole L Garrison conceived and designed the experiments, performed the experiments, analyzed the data, wrote the paper, prepared figures and/or tables, reviewed drafts of the paper.

Juanita Rodriguez conceived and designed the experiments, performed the experiments, analyzed the data, wrote the paper, reviewed drafts of the paper.

Ingi Agnarsson reviewed drafts of the paper.

Jonathan A Coddington wrote the paper, reviewed drafts of the paper.

Charles E Griswold contributed reagents/materials/analysis tools, wrote the paper, reviewed drafts of the paper.

Christopher A Hamilton analyzed the data, reviewed drafts of the paper.

Marshal Hedin contributed reagents/materials/analysis tools, wrote the paper, reviewed drafts of the paper.

Kevin M Kocot conceived and designed the experiments, performed the experiments, analyzed the data, wrote the paper, reviewed drafts of the paper.

Joel M Ledford contributed reagents/materials/analysis tools, reviewed drafts of the paper.

Jason E Bond conceived and designed the experiments, performed the experiments, analyzed the data, contributed reagents/materials/analysis tools, wrote the paper, prepared figures and/or tables, reviewed drafts of the paper.

DNA Deposition

The following information was supplied regarding the deposition of DNA sequences:

Illumina transcriptome sequence data are available from NCBI database archive under accession numbers SAMNXXXXX-SAMNXXXXX. Phylogenomics data matrices were deposited on XX November 2015 in the Dryad Digital Repository at http://dx.doi.org/xx.xxxx/drayd.xxxxx.

Data Deposition

The following information was supplied regarding data availability:

Data sets to uploaded are the complete phylogenetic supermatrix and accompanying partition file.

Funding

This work was partially funded by Auburn University and National Science Foundation grant DEB 1256139. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.


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