Premise of the Study: Chestnuts and chinquapins are some of the best known and most widely loved of any plants in North America. Despite the fame of this clade, relatively little genomic sequencing has been done, and much is still unknown about their evolution. 

Methods: Here we use ddRAD data to infer the species-level phylogeny for Castanea and assess the phylogeography of the North American species using samples collected from populations that span the full extent of the species’ ranges. We also construct species distribution models using digitized herbarium specimens and observational data from field surveys. 

Key Results: We identified strong population structure within Castanea dentata (American Chestnut) that reflects a stepwise northern migration since the last glacial maximum. Our species distribution models further confirm this scenario and match closely with the Castanea fossil pollen record. We also found significant structure within the Castanea pumila lineage, most notably a genetic cluster that corresponds to the frequently recognized “Castanea pumila var. ozarkensis.”

Conclusions: The two North American Castanea species have contrasting patterns of population structure, but each is typical of plant phylogeography in North America. Within the C. pumila complex we find novel genetic structure that provides new insights to C. pumila taxonomy. Our results also identify a series of distinctive populations that will be valuable in on going efforts to conserve and restore the Chestnuts and Chinquapins in North America.

This sumbission contains the RADseq data matrices and geographical data associated with this study. Sequence data was processed in Stacks (Catchen et al. 2013) and ipyrad (Eaton 2014) using the Castanea mollissima genome from Staton et al. 2015 as a reference. Only loci shared across at least 50% of loci were retained. For full methodology see the Methods section of the paper. Raw sequence data has been submitted to the NCBI SRA (https://www.ncbi.nlm.nih.gov/sra).