Reddy_sup_fileS2_PrumLoci

Information about the loci used by Prum et al. 2015. An xlsx file with two sheets ("README" and "Prum locus information")

Reddy_sup_fileS8_ASTRAL_nextrees

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

Reddy_sup_figS5_GCboxplot

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

Reddy_sup_tableS1_evolutionary_rates

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)

Reddy_sup_fileS6_raxml_trees_ALLtaxset.tar

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

Reddy_sup_fileS4

List of EB2 loci along with information about the partitions within loci. An xlsx file with two sheets ("README" and "EB2 locus information")

Reddy_sup_figS2_Metaves

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)

Reddy_sup_fileS7_ML_treefiles.tar

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)

Reddy_sup_figS3_Prum_noJAR

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)

Reddy_sup_figS4_genetic_code

Structure of the genetic code showing the potential for the physicochemical characteristics of amino acids to lead to site-specific biases in nucleotide frequencies