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A consensus phylogenomic approach highlights the ancient rapid radiation of Ericales

Premise of study Large genomic datasets offer the promise of resolving historically recalcitrant phylogenetic problems. However, different methodologies can yield conflicting results, especially when diversification occurs rapidly. Here, we used an array of dataset filtering strategies and species tree methods to infer a consensus topology of Ericales and explored sources of uncertainty associated with an ancient radiation. Methods We used a hierarchical clustering approach, along with tree-based homology and orthology detection, to generate multiple phylogenomic datasets. Support for species relationships was inferred from multiple lines of evidence including shared gene duplications, gene tree conflict, gene-wise edge-based analyses, concatenation, and coalescent-based species tree methods and summarize these results in a consensus framework. Key Results Our consensus approach supported a topology largely concordant with the current theorized relationships, but suggests that the data are not capable of resolving several early relationships due to lack of informative characters, sensitivity to methodology, and extensive gene tree conflict. We find evidence of one or more paleopolyploidy events before the radiation of ericalean families that likely contributes to the high levels of gene tree conflict observed. Conclusions Our approach provides a novel hypothesis regarding the history of Ericales and confidently resolves several nodes. However, we also demonstrate that some ancient divergences are unresolvable with our current data. Whether this is because of rapid and unresolvable ancient speciation or lack of data needs to be addressed with additional data collection efforts. The role that paleopolyploidy plays in generating gene tree conflict warrants further investigation.