DOI: 10.5061/dryad.p1m52
title: Data from: Analysis of a rapid evolutionary radiation using ultraconserved elements (UCEs): Evidence for a bias in some multi-species coalescent methods

description: Rapid evolutionary radiations are expected to require large amounts of
 sequence data to resolve. To resolve these types of relationships many
 systematists believe that it will be necessary to collect data by
 next-generation sequencing (NGS) and use multispecies coalescent (“species
 tree”) methods. Ultraconserved element (UCE) sequence capture is becoming
 a popular method to leverage the high throughput of NGS to address
 problems in vertebrate phylogenetics. Here we examine the performance of
 UCE data for gallopheasants (true pheasants and allies), a clade that
 underwent a rapid radiation 10–15 Ma. Relationships among gallopheasant
 genera have been difficult to establish. We used this rapid radiation to
 assess the performance of species tree methods, using ∼600 kilobases of
 DNA sequence data from ∼1500 UCEs. We also integrated information from
 traditional markers (nuclear intron data from 15 loci and three
 mitochondrial gene regions). Species tree methods exhibited troubling
 behavior. Two methods [Maximum Pseudolikelihood for Estimating Species
 Trees (MP-EST) and Accurate Species TRee ALgorithm (ASTRAL)] appeared to
 perform optimally when the set of input gene trees was limited to the most
 variable UCEs, though ASTRAL appeared to be more robust than MP-EST to
 input trees generated using less variable UCEs. In contrast, the rooted
 triplet consensus method implemented in Triplec performed better when the
 largest set of input gene trees was used. We also found that all three
 species tree methods exhibited a surprising degree of dependence on the
 program used to estimate input gene trees, suggesting that the details of
 likelihood calculations (e.g., numerical optimization) are important for
 loci with limited phylogenetic information. As an alternative to summary
 species tree methods we explored the performance of SuperMatrix Rooted
 Triple - Maximum Likelihood (SMRT-ML), a concatenation method that is
 consistent even when gene trees exhibit topological differences due to the
 multispecies coalescent. We found that SMRT-ML performed well for UCE
 data. Our results suggest that UCE data have excellent prospects for the
 resolution of difficult evolutionary radiations, though specific attention
 may need to be given to the details of the methods used to estimate
 species trees.
description: 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 &lt;50% support in ML
 bootstrap analyses (using the indicated programs) or posterior
 probabilities &lt;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 &lt;50% bootstrap support (RAxML, GARLI,
 and PhyML), posterior probability &lt;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