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

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.