Phylogenomics in the Hard Pines (Pinus subsection Ponderosae; Pinaceae) Confirms Paraphyly in Pinus ponderosa, and Places Pinus jeffreyi 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 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 Pinus subsect. Sabinianae based on morphological synapomorphiesas well as strong molecular phylogenetic support. Pinus ponderosa sensu lato is paraphyletic, and we suggest treatment as three species: P. ponderosa sensu stricto (with P. ponderosa var. ponderosa, P. ponderosa var. benthamiana, and P. ponderosa 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 (labeledbpw in clade P1) should caution species identification in Pinus subsection Ponderosae based on limited molecular data. The hybrid frequency was low based on cytonuclear discordance, and the persistence of an ancient P1 plastid clade is a better explanation than hybridization betweenP. ponderosa and P. jeffreyi for unexpected plastid associations in the western Sierra Nevada, USA. We identified a new potential zone of ancient admixture between P. ponderosa and P. scopulorum in Idaho, USA. Some populations of P. arizonica, P. brachyptera, P. engelmannii, and P. scopulorum in the USA are more closely related to taxa with distributions limited to Mexico than they are to each other. To integrate phylogeny and taxonomy, future work should sample widely in Mexico and the USA, score morphological characters (including seedling characters from the known seed parent), on the same individual as used for molecular data, and use methods that are based on individuals rather than population frequencies.

Coalescent‐based species delimitation in North American pinyon pines using low‐copy nuclear genes and plastomes

“…Pinus L. classification and species delimitation initially used a small number of morphological characters. Over time additional evidence was incorporated from anatomy, reproductive biology, biochemistry, and molecular markers (Price et al, 1998;Gernandt et al, 2001Gernandt et al, , 2003Gernandt et al, , 2005Syring et al, 2005;Parks et al, 2012;Willyard et al, 2021). Nevertheless, each source of evidence used undergoes processes that can introduce error, such as plasticity of certain morphological characters in response to the environment (e.g., number of needles per fascicle and needle length and width), transfer of genetic information among genomic compartments, low interspecific variability (e.g., plastid DNA markers), and uniparental inheritance of plastid DNA, which is susceptible to "plastid capture" (Mirov, 1967;Rieseberg and Soltis, 1991;Liston et al, 1999;Gernandt et al, 2003;Kan et al, 2007;Mort et al, 2007;Poulos and Berlyn, 2007;Cole et al, 2008;Tsutsui et al, 2009;Turna and Güney, 2009;Nobis et al, 2012;Cole et al, 2013).…”

Morpho‐palynological investigation of gymnospermal flora from subalpine and alpine zones of northern Pakistan using LM and SEM

“…pindrow is 45 × 48 (77 × 106) 110 × 140 μm. Exine of central body 2.5 μm thick and exine of cap 3–5 μm thick (Willyard et al, 2021). Wodehouse (1935) has given the size range 58–111 μm mostly over 90 μm for the genus Abies which is close to present finding.…”