Supporting data: Phylogenomic analyses re-examine the evolution of reinforcement and hypothesized hybrid speciation in Phlox wildflowers

Sequence data in support of manuscript titled "Phylogenomic analyses re-examine the evolution of reinforcement and hypothesized hybrid speciation in Phlox wildflowers." This data was generated following a ddRAD sequencing protocol and used in phylogenomic studies to examine the evolutionary history of the eastern standing Phlox and evaluate hypotheses about if and how hybridization and gene flow played a role in their diversification. Our results provide novel resolution of the phylogenetic relationships in this group, including paraphyly across some taxa. We identify gene flow during one case of reinforcement and find genomic support for a hybrid lineage underlying one of the five hypothesized homoploid hybrid speciation events. Additionally, we estimate the ancestries of four allotetraploid hybrid species. Our results are consistent with hybridization contributing to diverse evolutionary outcomes within this group; although, not as extensively as previously hypothesized. 

Methods
We extracted genomic DNA from bud tissue, processed this DNA into double-digest restriction-site-associated digestion (ddRAD) sequencing libraries, and paired-end sequenced the libraries as described in Goulet-Scott et al., 2021. Resulting sequence data was demultiplexed by individual following Goulet-Scott et al., 2021.

Goulet-Scott, Benjamin E., Austin G. Garner, and Robin Hopkins. "Genomic analyses overturn two long-standing homoploid hybrid speciation hypotheses." Evolution 75.7 (2021): 1699-1710.