TY - JOUR T1 - Anchored Phylogenomics of Angiosperms I: Assessing the Robustness of Phylogenetic Estimates JF - bioRxiv DO - 10.1101/086298 SP - 086298 AU - Chris Buddenhagen AU - Alan R. Lemmon AU - Emily Moriarty Lemmon AU - Jeremy Bruhl AU - Jennifer Cappa AU - Wendy L. Clement AU - Michael J. Donoghue AU - Erika J. Edwards AU - Andrew L. Hipp AU - Michelle Kortyna AU - Nora Mitchell AU - Abigail Moore AU - Christina J. Prychid AU - Maria C. Segovia-Salcedo AU - Mark P. Simmons AU - Pamela S. Soltis AU - Stefan Wanke AU - Austin Mast Y1 - 2016/01/01 UR - http://biorxiv.org/content/early/2016/11/08/086298.abstract N2 - We leverage genomic resources from 43 angiosperm species to develop enrichment probes useful for collecting ~500 loci from non-model taxa across the diversity of angiosperms. By taking an anchored phylogenomics approach, in which probes are designed to represent sequence diversity across the group, we are able to efficiently target loci with sufficient phylogenetic signal to resolve deep, intermediate, and shallow angiosperm relationships. After demonstrating the utility of this resource, we present a method that generates a heat map for each node on a phylogeny that reveals the sensitivity of support for the node across analysis conditions, as well as different locus, site and taxon schemes. Focusing on the effect of locus and site sampling, we use this approach to statistically evaluate relative support for the alternative relationships among eudicots, monocots, and magnoliids. Although the results from supermatrix and coalescent analyses are largely consistent across the tree, we find support for this deep relationship to be more sensitive to the particular choice of sites and loci when a supermatrix approach as employed. Averaged across analysis approaches and data subsampling schemes, our data support a eudicot-monocot sister relationship, which is supported by a number of recent angiosperm studies. ER -