Data from: Allele phasing greatly improves the phylogenetic utility of ultraconserved elements

Advances in high-throughput sequencing techniques now allow relatively
easy and affordable sequencing of large portions of the genome, even for
non-model organisms. Many phylogenetic studies reduce costs by focusing
their sequencing efforts on a selected set of targeted loci, commonly
enriched using sequence capture. The advantage of this approach is that it
recovers a consistent set of loci, each with high sequencing depth, which
leads to more confidence in the assembly of target sequences. High
sequencing depth can also be used to identify phylogenetically informative
allelic variation within sequenced individuals, but allele sequences are
infrequently assembled in phylogenetic studies. Instead, many scientists
perform their phylogenetic analyses using contig sequences which result
from the de novo assembly of sequencing reads into contigs containing only
canonical nucleobases, and this may reduce both statistical power and
phylogenetic accuracy. Here, we develop an easy-to-use pipeline to recover
allele sequences from sequence capture data, and we use simulated and
empirical data to demonstrate the utility of integrating these allele
sequences to analyses performed under the Multispecies Coalescent (MSC)
model. Our empirical analyses of Ultraconserved Element (UCE) locus data
collected from the South American hummingbird genus Topaza demonstrate
that phased allele sequences carry sufficient phylogenetic information to
infer the genetic structure, lineage divergence, and biogeographic history
of a genus that diversified during the last three million years. The
phylogenetic results support the recognition of two species, and suggest a
high rate of gene flow across large distances of rainforest habitats but
rare admixture across the Amazon River. Our simulations provide evidence
that analyzing allele sequences leads to more accurate estimates of tree
topology and divergence times than the more common approach of using
contig sequences.