RESEARCH ARTICLE A consensus phylogenomic approach highlights paleopolyploid and rapid radiation in the history of Ericales Drew A. Larson1,4 , Joseph F. Walker2 , Oscar M. Vargas3 , and Stephen A. Smith1 Manuscript received 8 December 2019; revision accepted 12 February PREMISE: Large genomic data sets offer the promise of resolving historically recalcitrant 2020. species relationships. However, different methodologies can yield conflicting results, 1 Department of Ecology & Evolutionary Biology, University of especially when clades have experienced ancient, rapid diversification. Here, we analyzed Michigan, Ann Arbor, MI 48109, USA the ancient radiation of Ericales and explored sources of uncertainty related to species tree 2 Sainsbury Laboratory (SLCU), University of Cambridge, Cambridge, inference, conflicting gene tree signal, and the inferred placement of gene and genome CB2 1LR, UK duplications. 3 Department of Ecology & Evolutionary Biology, University of California, Santa Cruz, CA 95060, USA METHODS: We used a hierarchical clustering approach, with tree-based homology and 4Author for correspondence (e-mail:
[email protected]) orthology detection, to generate six filtered phylogenomic matrices consisting of data Citation: Larson, D. A., J. F. Walker, O. M. Vargas, and S. A. Smith. from 97 transcriptomes and genomes. Support for species relationships was inferred 2020. A consensus phylogenomic approach highlights paleopolyploid from multiple lines of evidence including shared gene duplications, gene tree conflict, and rapid radiation