Advances in high-throughput sequencing techniques now allow relatively easy and 
affordable sequencing of large portions of the genome, even for nonmodel 
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 model. Our empirical 
analyses of ultraconserved element 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 3 myr. 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.