DOI: 10.5061/dryad.j5n06
title: Data from: Comparison of target-capture and restriction-site associated DNA sequencing for phylogenomics: a test in cardinalid tanagers (Aves, genus: Piranga)

description: Restriction-site associated DNA sequencing (RAD-seq) and target capture of
 specific genomic regions, such as ultraconserved elements (UCEs), are
 emerging as two of the most popular methods for phylogenomics using
 reduced-representation genomic datasets. These two methods were designed
 to target different evolutionary timescales: RAD-seq was designed for
 population-genomic level questions and UCEs for deeper phylogenetics. The
 utility of both datasets to infer phylogenies across a variety of
 taxonomic levels has not been adequately compared within the same
 taxonomic system. Additionally, the effects of uninformative gene trees on
 species tree analyses (for target capture data) have not been explored.
 Here, we utilize RAD-seq and UCE data to infer a phylogeny of the bird
 genus Piranga. The group has a range of divergence dates (0.5 my – 6 my),
 contains eleven recognized species, and lacks a resolved phylogeny. We
 compared two species tree methods for the RAD-seq data and six species
 tree methods for the UCE data. Additionally, in the UCE data, we analyzed
 a complete matrix as well as datasets with only highly informative loci. A
 complete matrix of 189 UCE loci with ten or more parsimony informative
 (PI) sites, and an ~80% complete matrix of 1128 PI SNPs (from RAD-seq)
 yield the same fully resolved phylogeny of Piranga. We inferred
 non-monophyletic relationships of P. lutea individuals, with all other a
 priori species identified as monophyletic. Finally, we found that species
 tree analyses that included predominantly uninformative gene trees
 provided strong support for different topologies, with consistent
 phylogenetic results when limiting species tree analyses to highly
 informative loci or only using less informative loci with concatenation or
 methods meant for SNPs alone.
description: piranga_snps.structureSNPs from restriction-site associated DNA sequencing in STRUCTURE format.uce_nexusNexus files of all target capture UCE sequences used in this study.uce_beastOutput of one replicate of *BEAST species tree analyses for the UCE dataset. Three .trees files for the three UCE datasets: complete, only including 10 or more parsimony informative sites, and only including 20 or more parsimony informative sites.uce_phymlResults of species tree analyses (both bootstraps and summarized tree) using PhyML gene trees as input. Output is shown for three UCE datasets, including all 734 loci, only loci with 10 or more parsimony informative sites, and only loci with 20 or more parsimony informative sites.uce_raxmlResults of species tree analyses (both bootstraps and summarized tree) using RAxML gene trees as input. Output is shown for three UCE datasets, including all 734 loci, only loci with 10 or more parsimony informative sites, and only loci with 20 or more parsimony informative sites.uce_beast_inputInput files for *BEAST with each of the three UCE datasets, including all loci, only those with 10 or more parsimony informative sites (PI), and only loci with 20 or more PI sites.rad_snapp_treesOutput of two runs of SNAPP using the RAD-seq SNP data.rad_snapp.ziprad_species_inputInput nexus files from the RAD-seq dataset for SNAPP and SVDquartets.Piranga TreesPictures of species trees for all RAD-seq and UCE analyses used in this study. Descriptions in the PDF.Piranga_Supp_Info.pdfmultilocus_bootstrapsMultilocus bootstraps for each dataset (734 loci, 10 PI dataset, and 20PI dataset) using either PhyML or RAxML.piranga_supp_tableSummary information and statistics for each sample, including barcodes used for RAD sequencing, number of RAD tags, coverage of RAD loci, adapters used in UCE library prep, UCE sequencing coverage, number of recovered UCEs, and length of UCEs.piranga_uce_snappFiles associated with SNAPP analysis of UCE SNPs. Input nexus file, and output of two SNAPP runs. Output includes posterior sampling of all trees (.trees files), tree summaries (.tre) and pictures of the output trees (.pdf).