DOI: 10.5061/dryad.hq3vq
title: Data from: Allele phasing greatly improves the phylogenetic utility of ultraconserved elements

description: 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.
description: assembler_testThis zip-archive contains all files related to our testing of different de novo assemblers and their treatment of heterozygous sites. The archive also contains the results of a reference-based assembly of the sequencing reads against reference sequences for all UCE loci.phylogenetic_analysesThis zip-archive contains all input files and results of the Multispecies Coalescent (MSC) analyses from this study. This includes the BEAST analyses of the mitochondrial genome, the STACEY analyses of all sequence data and the SNAPP analyses of all SNP datasets.msc_analyses.zipsummary_coalescent_analysesThis zip-archive contains all files related to the MPEST analyses, which are reported in online Appendix 2. This includes gene trees for all loci inferred by PhyML and the MPEST species tree analyses results.phasing_filesThis zip-archive contains all files related to the reference based assembly of UCE sequencing reads and the subsequent phasing of these reads into allele haplotype sequences.simulationsThis zip-archive contains all files related to the simulation of data generated in this study.alignmentsThis zip-archive contains all sequence and SNP multiple sequence alignment (MSA) files that were analyzed in this study.supplemental_materialZip-archive contains online Appendices 1-5, Supplementary Figs. S1-S11 and Supplementary Tables S1 and S2.tree_processingThis zip-archive contains all steps that were executed post tree inference, including the extraction and plotting of node-height distributions, the generation of similarity matrices and the calculation of the maximum clade credibility trees for all MSC analyses.