DOI: 10.5061/dryad.55h30
title: Data from: Resolving rapid radiations within angiosperm families using anchored phylogenomics

description: Despite the promise that molecular data would provide a seemingly
 unlimited source of independent characters, many plant phylogenetic
 studies are still based on only two regions, the plastid genome and
 nuclear ribosomal DNA (nrDNA). Their popularity can be explained by high
 copy numbers and universal PCR primers that make their sequences easily
 amplified and converted into parallel datasets. Unfortunately, their
 utility is limited by linked loci and limited characters resulting in low
 confidence in the accuracy of phylogenetic estimates, especially when
 rapid radiations occur. In another contribution on anchored phylogenomics
 in angiosperms, we presented flowering plant-specific anchored enrichment
 probes for hundreds of conserved nuclear genes and demonstrated their use
 at the level of all angiosperms. In this contribution, we focus on a
 common problem in phylogenetic reconstructions below the family level:
 weak or unresolved backbone due to rapid radiations (≤10 million years)
 followed by long divergence, using the Cariceae-Dulichieae-Scirpeae clade
 (CDS, Cyperaceae) as a test case. By comparing our nuclear matrix of 461
 genes to a typical Sanger-sequence dataset consisting of a few plastid
 genes (matK, ndhF) and an nrDNA marker (ETS), we demonstrate that our
 nuclear data is fully compatible with the Sanger dataset and resolves
 short backbone internodes with high support in both concatenated and
 coalescence-based analyses. In addition, we show that nuclear gene tree
 incongruence is inversely proportional to phylogenetic information
 content, indicating that incongruence is mostly due to gene tree
 estimation error. This suggests that large numbers of conserved nuclear
 loci could produce more accurate trees than sampling rapidly evolving
 regions prone to saturation and long-branch attraction. The robust
 phylogenetic estimates obtained here, and high congruence with previous
 morphological and molecular analyses, are strong evidence for a complete
 tribal revision of CDS. The anchored hybrid enrichment probes used in this
 study should be similarly effective in other flowering plant groups.
description: onlineAppendix1--locus_characteristicsOnline Appendix 1. Characteristics of loci used in anchored phylogenomics analyses after masking and trimming of alignments. AVE: average value for all loci, MIN: minimum value for all loci, MAX: maximum value for all loci, Locus#: locus identification number, New#: new number assigned to locus for this analysis (necessary because of paralogs), cov: average coverage across all species, ntax: number of taxa possessing the locus, flank%: percentage of total locus length estimated to be in the "flanking region", aveC: average number of copies of locus across species, before orthology filtering, maxC: maximum number of distinct copies of locus, before orthology filtering, len: alignment length, var: number of variable characters, pi: number of parsimony informative characters, GC%: percentage of GC across all non-gapped bases, amb%: percentage of ambiguous bases, miss%: percentage of missing data.onlineAppendix2--saturationPlotOnline Appendix 2. Saturation plot as calculated in DAMBE, showing GTR distance estimated for the ⅓ fastest-evolving sites in relation to the number of transitions and transversions at these sites. Regression lines (forced through the origin) and slope coefficients are shown. Dashed line indicates slope of 1.onlineAppendix3--MPtreeOnline Appendix 3. Single shortest tree found in PAUP* maximum parsimony searches. Support as MP jackknife, and ACCTRAN branch lengths.onlineAppendix4--MLtreeOnline Appendix 4. Maximum likelihood tree in RAxML searches. Support as ML bootstrap.P0082_Final_NGS_matrix.nexConcatenated sequence matrix.