Data from: Analysis of a rapid evolutionary radiation using ultraconserved elements (UCEs): Evidence for a bias in some multi-species coalescent methods

Supplementary Figure S1FIGURE S1. Example of a UCE alignment showing a short mismatch at one end. This portion of the alignment shows no variation with the exception of a stretch of 13 nucleotides with nine mismatches. Similar stretches are evident in 69 UCE alignments. The terminal gaps in three other taxa simply reflect the failure of those assemblies to extend all of the way to the end of the alignment.Figure S1 Meiklejohn et al.pdfSupplementary Figure S2FIGURE S2. Number of variable (left) and parsimony informative (right) sites present in each UCE locusFigure S2 Meiklejohn et al.pdfSupplementary Figure S3FIGURE S3. Performance of the maximum parsimony (MP) criterion for phylogenetic estimation with UCE data. The topology of the single most parsimonious tree of 50929 steps recovered when UCE data were analyzed (A) was identical to the ML tree for those data. Minimum branch lengths for UCEs (i.e., the number of unambiguous synapomorphies) are shown above branches and bootstrap support is presented below branches. An MP analysis of combined UCEs+introns+mitochondrial data also yielded a single tree (of 59964 steps) with an identical topology. Bootstrap support for both analyses is reported as a percentage of 500 replicates. Full (100%) support is indicated using an asterisk (*). MP and ML branch lengths for the UCE data were strongly correlated (B), suggesting that the MP criterion is likely to have reconstructed character state transformations accurately. The graph was limited to internal branches.Figure S3 Meiklejohn et al.pdfSupplementary Figure S4FIGURE S4. Estimates of gene trees for individual UCEs are poorly resolved. Box plot showing the number of resolved branches when those branches with <50% support in ML bootstrap analyses (using the indicated programs) or posterior probabilities <0.5 (using MrBayes). Similar data are shown for the optimal tree identified using GARLI with very short branches collapsed to form a polytomy (‘GARLI-opt’). Numbers of parsimony informative sites per UCE are used to define the sets of UCEs considered (‘all’ indicates that all UCEs with at least one parsimony informative site were included).Figure S4 Meiklejohn et al.pdfSupplementary File S1Microsoft excel file including the unedited UCE locus lengthsSupplementary File S2Microsoft excel file including the model fit information for individual UCE loci (after editing)Supplementary File S3Microsoft excel file including model fit information for traditional markers (introns and mitochondrial gene regions)Supplementary File S4pdf with the MRE (‘greedy’) consensus trees of UCE gene tree estimates. UCE gene trees used to generate the MRE consensus have polytomies. The polytomies reflect branches with <50% bootstrap support (RAxML, GARLI, and PhyML), posterior probability <0.5 (MrBayes), or short branches (GARLI optimal trees).Supplementary File S5pdf with MP-EST bootstrap trees for UCEsSupplementary File S6pdf with ASTRAL bootstrap trees for UCEsSupplementary File S7pdf with Triplec (rooted triple consensus) trees for UCEs. UCE gene trees used to generate the Triplec trees have polytomies. The trees are the same as those used to generate the MRE consensus trees in file S4.Supplementary File S8pdf with SMRT-ML trees for the UCE dataSupplementary File S9pdf with the sources of images used in Figure 6 of Meiklejohn et al. "Analysis of a rapid evolutionary radiation using ultraconserved elements (UCEs): Evidence for a bias in some multi-species coalescent methods"Meiklejohn et al. UCE alignments, uneditedgzipped tar file containing 1479 individual nexus files, each with a UCE alignmentMeiklejohn-et-al-UCE-data-unedited.tar.gzMeiklejohn combined evidence data filegzipped nexus file with all data (after the editing described in the text). All of the individual UCEs, nuclear introns, and mitochondrial gene regions are indicated using CHARSETS. Partitioning schemes identified using PartitionFinder are also included.Meiklejohn-et-al-combined-evidence.nex.gzSMRT-raxMRP perl scriptperl script for the SMRT-ML analysisSMRT-raxMRP.pl