Phylogenomic patterns of divergence and gene flow detail the evolution of reinforcement and hybrid speciation in Phlox wildflowers

SO_SCPLOWUMMARYC_SCPLOWO_LIThe tree of life is riddled with reticulate evolutionary histories, and some clades, such as the eastern standing Phlox, appear to be hotspots of hybridization. In this group there are two cases of reinforcement and nine hypothesized hybrid species. Given the historical importance of this group for our understanding of plant speciation, the relationships of these taxa and the role of hybridization and gene flow in their diversification require genomic validation. C_LIO_LIUsing phylogenomic analyses, we resolve the evolutionary relationships of the eastern standing Phlox and test hypotheses about if and how hybridization and gene flow were creative forces in their diversification. C_LIO_LIOur results provide novel resolution of the phylogenetic relationships in this group, including well-supported paraphyly across some species. We identify gene flow during one of two cases of reinforcement and find support for one of the five hypothesized homoploid hybrid speciation events. Additionally, we infer the ancestries of four allotetraploid hybrid species. C_LIO_LIHybridization has contributed to diverse evolutionary outcomes within this Phlox group; although, not as extensively as previously hypothesized. This study demonstrates the importance of phylogenomics in confirming hypothesized histories of non-model systems and adds to the growing evidence of interspecific genetic exchange in the generation of biodiversity. C_LI