DOI: 10.5061/dryad.vj32s
title: Data from: Anchored phylogenomics improves the resolution of evolutionary relationships in the rapid radiation of Protea L.

description: PREMISE OF THE STUDY: Estimating phylogenetic relationships in relatively
 recent evolutionary radiations is challenging, especially if short
 branches associated with recent divergence result in multiple gene tree
 histories. We combine anchored enrichment next-generation sequencing with
 species tree analyses to produce a robust estimate of phylogenetic
 relationships in the genus Protea (Proteaceae), an iconic radiation in
 South Africa. METHODS: We sampled multiple individuals within 59 out of
 112 species of Protea and 6 outgroup species for a total of 163
 individuals, and obtained sequences for 498 low-copy, orthologous nuclear
 loci using anchored phylogenomics. We compare several approaches for
 building species trees, and explore gene tree–species tree discrepancies
 to determine whether poor phylogenetic resolution reflects a lack of
 informative sites, incomplete lineage sorting, or hybridization. KEY
 RESULTS: Phylogenetic estimates from species tree approaches are similar
 to one another and recover previously well-supported clades within Protea,
 in addition to providing well-supported phylogenetic hypotheses for
 previously poorly resolved intrageneric relationships. Individual gene
 trees are markedly different from one another and from species trees.
 Nonetheless, analyses indicate that differences among gene trees occur
 primarily concerning clades supported by short branches. CONCLUSIONS:
 Species tree methods using hundreds of nuclear loci provided strong
 support for many previously unresolved relationships in the radiation of
 the genus Protea. In cases where support for particular relationships
 remains low, these appear to arise from few informative sites and lack of
 information rather than strongly supported disagreement among gene trees.
description: READMEDescription of files
 contained within this repositoryComplete_Sequence_Files-contains .phy files for all 498 loci and 326 sequences (two alleles per individual) -concatenated.phy contains sequences for all 498 loci together -species-consensus.phy contains concatenated sequence for the species-level consensusesOnePer_Sequence_Files-contains .phylip files for all 498 loci and 65 taxa (one sequence per taxon) -T74_Concat_OnePer.phy contains sequences for all 498 loci togetherConsensus_Sequence_Files-contains .phy files for all 498 loci and 65 taxa based on species-leel consensus -consensus.phy contains sequences for all 498 loci togetherReduced_Sequence_Files-contains .phy files for subset of 354 loci and 60 taxaTree_Files-Astral_Bootstrap.tre newick formatted 100 bootstrap replicates from the COMPLETE ASTRAL-II species analysis -Gene_Trees_Full.tre newick formatted 498 "best" gene trees from RAxML (in ascending order) -Gene_Trees_Reduced.tre newick formatted reduced 354 "best" gene trees form RAxML (in ascending order) -Individual_Trees.tre newick formatted trees based on 326 sequences to check for monophyly -RAxML_Bootstrap.tre -neewick formatted bootstrap replicates from the RAxML species analysis -Species_Trees_Complete.tre newick formatted species trees (ASTRAL-II and SVDquartets) with support values for all 65 taxa, 498 loci (COMPLETE dataset) -Species_Trees_Consensus.tre newick formatted species trees generated using the CONSENSUS dataset -Species_Trees_OnePer.tre newick formatted species trees generated using the ONEPER dataset -Species_Trees_Reduced.tre newick formatted species trees with support values for REDUCED set of 60 taxa, 354 loci -Species_Trees_Schnitzler.tre newick formatted species trees with species and data from Schnitzler et al. included (AUGMENTED dataset) -SVD_bootstrap.tre newick formatted 100 bootstrap replicates from the SVDquartets species analysisDistancescontains pairwise distances among gene trees, among species trees, and between gene trees (observed, randomly generated, and simulated using COAL)Internode_Certaintyfor all four species trees, contains internode certainty and internode certainty all values from RAxML, along with branch lengthsLocus_Infomatches Table 2 in manuscript, contains information on all loci, including length, parsimony informative sites, and distance to species trees.