Supplementary Materials

Phylogenomics resolves the timing and pattern of insect evolution

Bernhard Misof, Shanlin Liu, Karen Meusemann, Ralph S. Peters, Alexander Donath, Christoph Mayer, Paul B. Frandsen, Jessica Ware, Tomas Flouri, Rolf G. Beutel, Oliver Niehuis, Malte Petersen, Fernando Izquierdo-Carrasco, Torsten Wappler, Jes Rust, Andre J. Aberer, Ulrike Aspock, Horst Aspock, Daniela Bartel, Alexander Blanke, Simon Berger, Alexander Bohm, Thomas R. Buckley, Brett Calcott, Junqing Chen, Frank Friedrich, Makiko Fukui, Mari Fujita, Carola Greve, Peter Grobe, Shengchang Gu, Ying Huang, Lars S. Jermiin, Akito Y. Kawahara, Lars Krogmann, Martin Kubiak, Robert Lanfear, Harald Letsch, Yiyuan Li, Zhenyu Li, Jiguang Li, Haorong Lu, Ryuichiro Machida, Yuta Mashimo, Pashalia Kapli, Duane D. McKenna, Guanliang Meng, Yasutaka Nakagaki, Jose Luis Navarrete-Heredia, Michael Ott, Yanxiang Ou, Gunther Pass, Lars Podsiadlowski, Hans Pohl, Bjorn M. von Reumont, Kai Schutte, Kaoru Sekiya, Shota Shimizu, Adam Slipinski, Alexandros Stamatakis, Wenhui Song, Xu Su, Nikolaus U. Szucsich, Meihua Tan, Xuemei Tan, Min Tang, Jingbo Tang, Gerald Timelthaler, Shigekazu Tomizuka, Michelle Trautwein, Xiaoli Tong, Toshiki Uchifune, Manfred G. Walzl, Brian M. Wiegmann, Jeanne Wilbrandt, Benjamin Wipfler, Thomas K. F. Wong, Qiong Wu, Gengxiong Wu, Yinlong Xie, Shenzhou Yang, Qing Yang, David K. Yeates, Kazunori Yoshizawa, Qing Zhang, Rui Zhang, Wenwei Zhang, Yunhui Zhang, Jing Zhao, Chengran Zhou, Lili Zhou, Tanja Ziesmann, Shijie Zou, Yingrui Li, Xun Xu, Yong Zhang, Huanming Yang, Jian Wang, Jun Wang, Karl M. Kjer, and Xin Zhou

Materials/Methods, Supplementary Text, Tables, Figures, and/or References

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  • Materials and Methods
  • Supplementary Text
  • Figs. S1 to S27
  • Tables S10, S15 to S17, S20, and S24
  • References
  • Database captions S1 to S14
Table S1
Detailed species list included for de novo transcriptome sequencing in 1KITE.
Table S2
Published transcriptome data included in this study.
Table S3
Gene descriptions for the 1478 ortholog groups (OGs) as present in OrthoDB 5 (32).
Table S4
Overview of official gene sets of twelve reference species used for transcript orthology assessment, including the source, version and number of genes.
Table S5
List of species and NCBI Accession Numbers for BioProject PRJNA183205: "The 1KITE project: evolution of insects."
Table S6
Selected taxonomic groups required to be present in all data blocks to generate supermatrix C.
Table S7
Selected phylogenetic hypotheses and groups (four groups, G1 – G4, for each hypothesis) for the Four-cluster Likelihood Mapping (FcLM) analyses with included species for each group.
Table S8
Fossils used in the analyses for estimating divergence dates and calibration point prior settings.
Table S9
Constraints on taxonomic calibration points (supermatrix C).
Table S11
Sequence statistics after assembly and after contamination screen by NCBI Transcriptome Shotgun Assembly (TSA) database.
Table S12
Transcriptome statistics and transcript assignment to ortholog groups (OGs) of insect species sequenced in the 1KITE project and of published genomes, published insect and outgroup transcriptomes.
Table S13
Statistics describing the results of the orthology assignment to 1478 OGs.
Table S14
TopGO results (Fisher's exact test with TopGO elim algorithm) for the test of each reference species showing the over-representation of GO terms within the 1478 ortholog groups compared to the official genes sets
Table S18
Descriptive statistics of supermatrices A, B, C and D.
Table S19
Descriptive statistics of species-pairwise amino acid site coverage of supermatrices C and D.
Table S21
Summary of different sliding window combinations of the Bowker test on supermatrix C.
Table S22
SRH and non-SRH alignment blocks (sections 'worth including' and 'worth excluding') of supermatrix C based on matched-pairs test of symmetry (Bowker's test) of the selected combination no. 9 for phylogenetic inference.
Table S23
Results comparing partition schemes for 1478 OGs and for 2673 domain data blocks for supermatrix A with 595,033 amino acid sites.
Table S25
Estimated divergence dates based on 37 calibration points.
Table S26
Number of runs and MCMC iterations per run for each of the included meta-partitions.
Correction (19 November 2014): The revised figures are included, in particular, Fig. S2, a flow chart.
The original version is accessible here.
Data Archives S1 to S14 as gzipped archives, provided as data files (available at the Dryad Digital Repository http://dx.doi.org/10.5061/dryad.3c0f1)