10.5061/DRYAD.05QFTTF1Q
Willyard, Ann
0000-0002-0289-7355
Hendrix College
Gernandt, David S.
National Autonomous University of Mexico
Cooper, Blake
Hendrix College
Douglas, Connor
Hendrix College
Finch, Kristen
Hendrix College
Karemera, Hassan
Hendrix College
Lindberg, Erik
Texas Tech University
Langer, Stephen K.
,
Lefler, Julia
Hendrix College
Marquardt, Paula
Agricultural Research Service
Pouncey, Dakota
Hendrix College
Telewski, Frank
Michigan State University
Phylogenomics in the hard pines (Pinus subsection Ponderosae; Pinaceae)
confirms paraphyly in Pinus ponderosa, and places Pinus jeffreyi with the
California big cone pines
Dryad
dataset
2020
cytonuclear discordance
low copy nuclear genes
Jeffrey pine
ponderosa pine
FOS: Natural sciences
2022-02-05T00:00:00Z
2022-02-05T00:00:00Z
en
122176798 bytes
5
CC0 1.0 Universal (CC0 1.0) Public Domain Dedication
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 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 between P. 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.
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.