Data from: Resolving rapid radiations within angiosperm families using anchored phylogenomics

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.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.Funding provided by: National Science FoundationCrossref Funder Registry ID: http://dx.doi.org/10.13039/100000001Award Number: IIP-131355