Data from: Why do phylogenomic data sets yield conflicting trees? Data type influences the avian tree of life more than taxon sampling

Reddy S, Kimball RT, Pandey A, Hosner PA, Braun MJ, Hackett SJ, Han K, Harshman J, Huddleston CJ, Kingston S, Marks BD, Miglia KJ, Moore WS, Sheldon FH, Witt CC, Yuri T, Braun EL

Date Published: March 23, 2017

DOI: http://dx.doi.org/10.5061/dryad.6536v

 

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Title Reddy_sup_fileS3
Downloaded 20 times
Description List of taxa with voucher information and taxonomic details.An xlsx file with three sheets ("README", "EB2 species list", and "Full taxonomy"). The "Full taxonomy" sheet compares the clades proposed in Jarvis et al. 2014 and those proposed in Prum et al. 2015.
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Title Reddy_sup_fileS4
Downloaded 18 times
Description List of EB2 loci along with information about the partitions within loci. An xlsx file with two sheets ("README" and "EB2 locus information").
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Title Reddy_sup_fileS6_raxml_trees_ALLtaxset.tar
Downloaded 14 times
Description tar.gz file with 56 newick format trees generated by RAxML analyses of the "ALL" taxon set (defined in the manuscript). Folder also contains a README with additional information.
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Title Reddy_sup_fileS8_ASTRAL_nextrees
Downloaded 13 times
Description Nexus treefile with the results of ASTRAL-RAxML and ASTRAL-IQ-TREE analyses for each taxon set. Additional information about the trees can be found as comments in the nexus treefile.
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Title Reddy_sup_figS1_fileS1_indicator_clades
Downloaded 59 times
Description Description of the "magnificent seven" superordinal clades and the "indicator clades" that we used to determine whether an estimate of avian phylogeny has a "Jarvis-like" or "Prum-like" topology. Contains an illustration (Fig. S1) of the relevant clades and text describing the probability of recovering the indicator clades by chance.
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Title Reddy_sup_figS2_Metaves
Downloaded 23 times
Description This figure shows the circumscription of "Metaves" in four previous studies and the topology of the EB2noJAR tree (the tree based on the Early Bird II data excluding overlaps with Jarvis et al. 2014).
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Title Reddy_sup_figS3_Prum_noJAR
Downloaded 21 times
Description This figure shows the topology of the Prum_noJAR tree (the partitioned RAxML tree for the Prum et al. 2015 dataset after excluding the data that overlap with Jarvis et al. 2014).
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Title Reddy_sup_figS4_genetic_code
Downloaded 32 times
Description Structure of the genetic code showing the potential for the physicochemical characteristics of amino acids to lead to site-specific biases in nucleotide frequencies,
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Title Reddy_sup_figS5_GCboxplot
Downloaded 25 times
Description Boxplot showing GC-content variation for each locus in the EB2, Prum, and Jarvis datasets. Only the parsimony informative sites were analyzed, as in Fig. 6 of the manuscript. However, this figure shows the variation when all taxa for each dataset are included in the analysis.
Download Reddy_sup_figS5_GCboxplot.pdf (142.9 Kb)
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Title Reddy_sup_fileS2_PrumLoci
Downloaded 17 times
Description Information about the loci used by Prum et al. 2015. An xlsx file with two sheets ("README" and "Prum locus information").
Download Reddy_sup_fileS2_PrumLoci.xlsx (73.62 Kb)
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Title Reddy_sup_fileS5_alignments.tar
Downloaded 23 times
Description tar.gz file with four nexus format alignments. Folder also contains a README with additional information about the sequence alignments.
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Title Reddy_sup_fileS7_ML_treefiles.tar
Downloaded 12 times
Description tar.gz file of four nexus format treefiles. Each contains the RAxML, IQ-TREE, MrBayes, or Exabayes trees along with additional information about the trees (this information is stored as comments in each of the nexus treefiles).
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Title Reddy_sup_fileS9_EB2noJAR_nextrees
Downloaded 9 times
Description Nexus treefile with the results of RAxML and IQ-TREE analyses of the EB2noJAR and EB2noJARnoFGB datasets using the EB2 taxon set. The data matrices used to generate these trees correspond to the EB2 data after excluding the sites overlapping with the Jarvis et al. (2014) data. The data matrix used to generate the noJARnoFGB trees also excludes the gene encoding beta-fibrinogen (FGB). Additional information about the trees can be found as comments in the nexus treefile.
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Title Reddy_sup_fileS10_Prum_noJAR.tar
Downloaded 7 times
Description tar.gz file with three files: 1) a relaxed phylip format alignment of the Prum_noJAR data (concatenated alignments of the Prum et al. 2015 loci after excluding the loci that overlap with Jarvis et al. 2014); 2) a RAxML format partitioning file for the Prum_noJAR data; and 3) a Nexus format treefile with the estimates of phylogeny for Prum_noJAR generated by RAxML and IQ-TREE analyses. Folder also contains a README with additional information about the files.
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Title Reddy_sup_fileS11_backbone_trees
Downloaded 12 times
Description Nexus file containing: 1) the "backbone trees" (trees reduced to ordinal lineages) used for the tree clustering analysis; and 2) symmetric distances among the trees. The file contains embedded comments. If the file is executed in PAUP* it will echo this information to the screen, print the backbone trees, and conduct the tree clustering analysis.
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Title Reddy_sup_fileS12_squangles_treefiles.tar
Downloaded 7 times
Description tar.gz file of two nexus format treefiles. Each contains squangles trees generated using different quartet amalgamation methods. One treefile is the squangles trees for all loci (concatenated) and the other is the same analyses for the BDNF locus. The BDNF locus also includes the ML tree for that locus. Additional information about the trees can be found as comments in the nexus treefiles.
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Title Reddy_sup_tableS1_evolutionary_rates
Downloaded 24 times
Description Table showing relative rates of sequence evolution for coding regions, introns, UCEs, and a mixed alignment that includes multiple types of genomic data. The data were obtained from the trees described by Jarvis et al. (2014).
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When using this data, please cite the original publication:

Reddy S, Kimball RT, Pandey A, Hosner PA, Braun MJ, Hackett SJ, Han K, Harshman J, Huddleston CJ, Kingston S, Marks BD, Miglia KJ, Moore WS, Sheldon FH, Witt CC, Yuri T, Braun EL (2017) Why do phylogenomic data sets yield conflicting trees? Data type influences the avian tree of life more than taxon sampling. Systematic Biology, online in advance of print. http://dx.doi.org/10.1093/sysbio/syx041

Additionally, please cite the Dryad data package:

Reddy S, Kimball RT, Pandey A, Hosner PA, Braun MJ, Hackett SJ, Han K, Harshman J, Huddleston CJ, Kingston S, Marks BD, Miglia KJ, Moore WS, Sheldon FH, Witt CC, Yuri T, Braun EL (2017) Data from: Why do phylogenomic data sets yield conflicting trees? Data type influences the avian tree of life more than taxon sampling. Dryad Digital Repository. http://dx.doi.org/10.5061/dryad.6536v
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