Data from: Targeted enrichment of large gene families for phylogenetic inference: phylogeny and molecular evolution of photosynthesis genes in the Portullugo clade (Caryophyllales)

Moore AJ, de Vos JM, Hancock LP, Goolsby E, Edwards EJ

Date Published: September 19, 2017

DOI: https://doi.org/10.5061/dryad.7h3f6

Files in this package

Content in the Dryad Digital Repository is offered "as is." By downloading files, you agree to the Dryad Terms of Service. To the extent possible under law, the authors have waived all copyright and related or neighboring rights to this data. CC0 (opens a new window) Open Data (opens a new window)

Title Supp_Table_1
Downloaded 3 times
Description Supp Table 1. Gene families included in the bait design and sequencing project, showing the full name of each gene family, the shortened version of its name that is used in the paper, and whether the gene was classified as related to C4 or CAM photosynthesis.
Download Supp_Table_1.csv (3.439 Kb)
Details View File Details
Title Supp_Table_2
Downloaded 2 times
Description Supp. Table 2. Voucher table for all individuals included in phylogenetic analyses, including statistics on enrichment success and NCBI SRA accession numbers.
Download Supp_Table_2.csv (11.69 Kb)
Details View File Details
Title Supp_Table_3
Downloaded 1 time
Description Supp. Table 3. Sequencing statistics for g2, g5, g9, i37, and i57 datasets.
Download Supp_Table_3.csv (708 bytes)
Details View File Details
Title Supp_Table_4
Downloaded 2 times
Description Supp. Table 4. Paralogs per individual per gene family (the same data shown in the heatmap in Supp. Fig. 2).
Download Supp_Table_4.csv (13.26 Kb)
Details View File Details
Title locusMAPTreePlots
Downloaded 3 times
Description The results of the MrBayes analyses for all loci with individuals color-coded according to family and posterior probabilities for major groups shown.
Download locusMAPTreePlots.pdf (379.6 Kb)
Details View File Details
Title combined_analyses.tar
Downloaded 2 times
Description An archived folder containing the following files for each of the five datasets (g2, g5, g9, i37, and i57; example file names for the g5 dataset are given): concatenated alignment in fasta format (c2p1pgtc2_g5_combined_72inds_163seqs.fa), the RAxML tree from the concatenated alignment (RAxML_bipartitions.c2p1pgtc2_g5_combined_72inds_163seqs), the astral tree (c2p1pgts2_g5_astral.tre), and the list of included loci for each of the five datasets (c2p1gt2_Locus_List_g5.txt).
Download combined_analyses.tar.gz (14.18 Mb)
Details View File Details
Title individual_loci.tar
Downloaded 2 times
Description An archived folder containing the following files for each of the individual loci (example file names for ppc2 are given): alignment in fasta format (c2p1pgts2_ppc2.fa), the RAxML tree without bootstrap values (RAxML_bestTree.c2p1pgts2_ppc2), and trees from 100 bootstrap replicates conducted in RAxML (RAxML_bootstrap.c2p1pgts2_ppc2). (The latter two files are the input for an Astral analysis.)
Download individual_loci.tar.gz (3.726 Mb)
Details View File Details
Title ppc1E1_alignment.fa
Downloaded 1 time
Description The alignment of the ppc1E1 gene family in fasta format (used in the analysis shown in Fig. 5).
Download ppc1E1.fa (705.4 Kb)
Details View File Details
Title ppc1E1_tree.tre
Downloaded 9 times
Description The gene family tree for the ppc1E1 gene family created in RAxML (used in the analysis shown in Fig. 5).
Download ppc1E1.tre (22.37 Kb)
Details View File Details
Title contigs.tar.gz
Downloaded 3 times
Description An archived folder containing separate folders for each of the nine families in the portullugo (the groups used for the pipeline). Each folder contains two files for each gene family an sc_*.fa file with the contigs for that gene family and an sb3_*.out file that has the results of BLASTing that fasta file against the database of exons. These two files are the input for part II of the pipeline.
Download contigs.tar.gz (30.57 Mb)
Details View File Details
Title Supp_Table_5a.csv
Downloaded 1 time
Description Supp. Table 5a. Results from the validation analyses after the transcript fragments were run through part II of the pipeline only.
Download Supp_Table_5a.csv (1.766 Kb)
Details View File Details
Title Supp_Table_5b.csv
Downloaded 2 times
Description Supp. Table 5b. Results from the validation analyses after the transcript fragments were run through both parts II and III of the pipeline.
Download Supp_Table_5b.csv (1.755 Kb)
Details View File Details
Title Supp_Table_5c.csv
Downloaded 1 time
Description Supp. Table 5c. Summary statistics from the validation analyses.
Download Supp_Table_5c.csv (1.576 Kb)
Details View File Details
Title Supp_Table_6.csv
Downloaded 1 time
Description Supp. Table 6. Node support for all nodes that conflict or have less than 95% bootstrap support in any of the concatenated or Astral trees (the trees shown in Fig. 3).
Download Supp_Table_6.csv (2.726 Kb)
Details View File Details
Title Supp_Table_7.pdf
Downloaded 2 times
Description Supp. Table 7: Concordance factors from BUCKy analysis for all putative clades with at least 10% genome-wide support.
Download Supp_Table_7.pdf (85.09 Kb)
Details View File Details
Title backbone_trees.tar.gz
Downloaded 1 time
Description An archived folder containing two folders: The trees folder contains the original backbone trees and the list of outgroups for running parts II and III of the pipeline. The blastdbs folder contains the fasta files to make the two BLAST databases (te original database for the start of part I of the pipeline, called forblast20150128b.fa and the individual databases for each locus with sequences that have been divided into exons for the end of part I of the pipeline).
Download backbone_trees.tar.gz (1.791 Mb)
Details View File Details
Title suppl_methods_2018_08_19.pdf
Downloaded 3 times
Description Supplementary methods, focused on bait design and an expanded explanation of the pipeline.
Download suppl_methods_2018_08_19.pdf (125.2 Kb)
Details View File Details
Title Supplementary_Figures_new
Downloaded 3 times
Download Supplementary_Figures_new.pdf (6.345 Mb)
Details View File Details

When using this data, please cite the original publication:

Moore AJ, de Vos JM, Hancock LP, Goolsby E, Edwards EJ (2017) Targeted Enrichment of Large Gene Families for Phylogenetic Inference: Phylogeny and Molecular Evolution of Photosynthesis Genes in the Portullugo Clade (Caryophyllales). Systematic Biology, online in advance of print. https://doi.org/10.1093/sysbio/syx078

Additionally, please cite the Dryad data package:

Moore AJ, de Vos JM, Hancock LP, Goolsby E, Edwards EJ (2017) Data from: Targeted enrichment of large gene families for phylogenetic inference: phylogeny and molecular evolution of photosynthesis genes in the Portullugo clade (Caryophyllales). Dryad Digital Repository. https://doi.org/10.5061/dryad.7h3f6
Cite | Share
Download the data package citation in the following formats:
   RIS (compatible with EndNote, Reference Manager, ProCite, RefWorks)
   BibTex (compatible with BibDesk, LaTeX)

Search for data

Be part of Dryad

We encourage organizations to: