Phylogenomics in the hard pines (Pinus subsection Ponderosae; Pinaceae) confirms paraphyly in Pinus ponderosa, and places Pinus jeffreyi with the California big cone pines

We sampled 130 individuals (2 to 25 per taxon) of subsections Ponderosae and Sabinianae. Nucleotide sequences were obtained by targeting 703 low copy nuclear genes. From the unenriched portion of the short reads, we assembled nearly complete plastome nucleotide sequences. We used 600 nuclear genes and the plastome sequences to create phylogenies and species trees that we compared to evaluate cytonuclear concordance and reticulation. We found that Pinus jeffreyi belongs with subsect. Sabinianae based on morphological synapomorphies as well as strong molecular phylogenetic support. Pinus ponderosa sensu lato is paraphyletic, and we suggest treatment as threes species: P. ponderosa sensu stricto (with var. ponderosa, var. benthamiana, and var. washoensis), P. scopulorum, and P. brachyptera. The persistence of lineages with the footprints of ancient nuclear introgression (labeled bpw in clade N4) and chloroplast capture (labeled bpw in clade P1) should caution species identification in the ...