Phylogenomics in the Hard Pines (<i>Pinus</i> subsection <i>Ponderosae</i>; Pinaceae) Confirms Paraphyly in <i>Pinus ponderosa,</i> and Places <i>Pinus jeffreyi</i> with the California Big Cone Pines

Abstract— We sampled 130 individuals (2 to 25 per taxon) of Pinus subsections Ponderosae and Sabinianae . Nucleotide sequences were obtained by targeting 703 low copy nuclear genes. From the unenriched portion short reads, we assembled nearly complete plastome nucleotide sequences. used 600 genes create phylogenies species trees that compared evaluate cytonuclear concordance reticulation. found jeffreyi belongs with subsect. based on morphological synapomorphies as well strong molecular phylogenetic support. ponderosa sensu lato is paraphyletic, suggest treatment three species: P. stricto (with var. , benthamiana washoensis ), scopulorum brachyptera The persistence lineages footprints ancient introgression (labeled bpw in clade N4) chloroplast capture P1) should caution identification subsection limited data. hybrid frequency was discordance, an P1 plastid a better explanation than hybridization between for unexpected associations western Sierra Nevada, USA. identified new potential zone admixture Idaho, Some populations arizonica engelmannii USA are more closely related taxa distributions Mexico they each other. To integrate phylogeny taxonomy, future work sample widely USA, score characters (including seedling from known seed parent), same individual data, use methods rather population frequencies.