Phylogenetic History and Geography As Joint Predictors of Oak Chloroplast Phylogeny

Due to high rates of introgressive hybridization, the chloroplast is poorly-suited to fine-scale DNA barcoding and phylogenetic studies of the oak genus (Quercus, Fagaceae) and many other tree genera. At the 'tips' of the oak chloroplast genome evolutionary history, recent gene migration and reticulation cause topology to reflect geographic structure, while deeper branches reflect population and lineage divergence history. In this study, we quantify the simple and partial effects of geographic proximity and nucleome-inferred phylogenetic history on oak plastome phylogeny at different evolutionary scales. Our study compares pairwise phylogenetic distances based on complete plastome sequences, pairwise phylogenetic distances from nuclear restriction site-associated DNA sequences (RAD-Seq), and pairwise geographic distances from provenance data for 34 white oaks representing 24 North American and Eurasian species. Within the North American white oaks alone, phylogenetic history has essentially no effect on plastome variation, while geography explains 11–21% of plastome phylogenetic variance. However, across multiple continents and clades, phylogeny predicts 30–41% of plastome variation and geography explains 3–41% of plastome variation. In practical terms, tipwise attenuation of phylogenetic informativeness in the plastome means that this organelle has little use in solving phylogenetic questions. Despite this limitation, chloroplast genomes can still be useful barcoding/phylogenetic markers for resolving questions among major clades, especially when used in tandem with nuclear data.