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Open Access Highly Accessed Research article

Molecular phylogenetic analyses support the monophyly of Hexapoda and suggest the paraphyly of Entognatha

Go Sasaki14, Keisuke Ishiwata125, Ryuichiro Machida3, Takashi Miyata1 and Zhi-Hui Su12*

Author Affiliations

1 JT Biohistory Research Hall, 1-1 Murasaki-cho, Takatsuki, Osaka 569–1125, Japan

2 Department of Biological Sciences, Graduate School of Science, Osaka University, Osaka 560-0043, Japan

3 Sugadaira Montane Research Center, University of Tsukuba, Sugadaira Kogen, Ueda, Nagano 386-2204, Japan

4 Present address: School of Medicine, Kumamoto University, Kumamoto 860-8556, Japan

5 Present address: Division of Functional Genomics, Advanced Science Research Center, Kanazawa University, Kanazawa 920-0934, Japan

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BMC Evolutionary Biology 2013, 13:236  doi:10.1186/1471-2148-13-236

Published: 31 October 2013

Additional files

Additional file 1:

A list of the taxa used for the phylogenetic analyses in this study.

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Additional file 2:

The coding sequence (CDS) region of the catalytic subunit of DNA polymerase delta (DPD1) sequenced in this study. The lengths of the gene CDS are shown in accordance with those of Drosophila melanogaster. The locations of the primers used for amplifying and sequencing DPD1 are indicated on the gene CDS of D. melanogaster. The number above or below the primer name indicates the primer’s position in the nucleotide sequence following the initiation codon. The primer names correspond to those shown in Additional file 12.

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Additional file 3:

The CDS region of the largest subunit of RNA polymerase II (RPB1) sequenced in this study. For details, refer to Additional file 2.

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Additional file 4:

The CDS region of the second largest subunit of RNA polymerase II (RPB2) sequenced in this study. For details, refer to Additional file 2.

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Additional file 5:

The ML trees inferred from the individual genes of 64 samples (complete sample set). Bootstrap values from the RAxML analysis (LG model) are shown at the nodes. A, DPD1 tree; B, RPB1 tree; C, RPB2 tree.

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Additional file 6:

The ML trees inferred from the individual genes of 61 samples (55 hexapods and 6 crustaceans). Bootstrap values from the RAxML analysis (LG model) are shown at the nodes. A, DPD1 tree; B, RPB1 tree; C, RPB2 tree.

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Additional file 7:

The ML tree inferred from DPD1, RPB1, and RPB2. The eight taxa that showed long-branches in Figure 2 were excluded in this analysis. The bootstrap values from the RAxML analysis and posterior probabilities from the MrBayes are shown at nodes.

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Additional file 8:

RAxML tree with 61 samples (55 hexapods and 6 crustaceans).

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Additional file 9:

Bayesian inference (MrBayes) with 61 samples (55 hexapods and 6 crustaceans).

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Additional file 10:

RAxML tree with 58 samples, consisting of 52 hexapods (excluding collembolans) and 6 crustaceans.

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Additional file 11:

Bayesian inference (MrBayes) with 58 samples, consisting of 52 hexapods (excluding collembolans) and 6 crustaceans.

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Additional file 12:

The list of primers used for PCR and sequencing in this study.

Format: XLS Size: 22KB Download file

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Open Data