Dataset Open Access

The Evolution and Genomic Basis of Beetle Diversity

McKenna, Duane; Shin, Seunggwan; Ahrens, Dirk; Balke, Michael; Beza-Beza, Cristian; Clarke, Dave; Donath, Alexander; Escalona, Hermes; Friedrich, Frank; Letsch, Harald; Liu, Shanlin; Maddison, David; Mayer, Christoph; Misof, Bernhard; Murin, Peyton; Niehuis, Oliver; Peters, Ralph; Podsiadlowski, Lars; Pohl, Hans; Scully, Erin; Yan, Evgeny; Zhou, Xin; Ślipiński, Adam; Beutel, Rolf

Datasets S1-S4. (each is contained in a separate .zip file)

Dataset S1.

Gene trees for plant cell wall degrading enzyme phylogenetic analyses in the directory ‘Pfam Candidate Genes trees and phy’

1. Phylip formatted files for each gene used in ML analyses.

2. ML tree files for each gene studied showing TBE bootstrap support (100 replicates) (corresponding to Figs. S15-S26).

3. ML tree files for each gene studied showing ML bootstrap support (100 replicates) from IQtree (corresponding to Figs. S15-S26).

Dataset S2.

Directory (Blast_10best_hits_Pfam_Candidate_Genes) including: Blast results (10 best hits) for all sequences extracted from the transcriptome and genome assemblies for the plant cell wall degrading enzyme analysis in the directory ‘Pfam_Candidate_Genes_Fas’ (before filtering).

Dataset S3.

Directory (Pfam_Candidate_Genes_Fas) including: Candidate genes/transcripts encoding plant cell wall degrading enzymes extracted from the transcriptome and genome assemblies (before filtering).

Dataset S4.

Directory (Supermatrices_partitions) including:

  • Supermatrix for Fig. 1 (amino acid and nucleotide level, PHYLIP formats) and Supermatrix for Fig. S10 (amino acid level, PHYLIP format).
  • Partition schemes for supermatrix for Fig. 1 (Fig_1_Partition_finder_best_scheme).
  • Partition schemes for supermatrix for Fig. 1 prior to Partitionfinder (AA_partitions).
  • Partition schemes for supermatrix for NT prior to Partitionfinder (NT_partitions).
  • Partition schemes for supermatrix for Fig. S10 (Fig_S10_Partition_finder_best_scheme)

Data Use Statement. Data on genetic material contained in this paper are published for non-commercial use only. Utilization by third parties for purposes other than non-commercial scientific research may infringe the conditions under which the genetic resources were originally accessed, and should not be undertaken without obtaining consent from the corresponding author of the paper and/or obtaining permission from the original provider of the genetic material.

Files (115.2 MB)
Name Size
Dataset_S1_Pfam_Candidate_Genes_trees and phy.zip
md5:0d3a3e7182567375c96bf4eb66b67ed6
802.2 kB Download
Dataset_S2_Blast_10best_hits_Pfam_Candidate_Genes.zip
md5:2ef55bc58514007ddccbf81077486997
1.2 MB Download
Dataset_S3_Pfam_Candidate_Genes_Fas.zip
md5:e896c159447c5d12bae73e91709e5535
1.3 MB Download
Dataset_S4_Supermatrices_partitions.zip
md5:36161b47856f30b44540e829a8ba0338
111.9 MB Download
101
35
views
downloads
All versions This version
Views 101101
Downloads 3535
Data volume 1.3 GB1.3 GB
Unique views 8989
Unique downloads 2020

Share

Cite as