Jorge A. Pérez de la Rosa

Phylogenetic Relationships and Species Delimitation in Pinus Section Trifoliae Inferrred from Plastid DNA

Recent diversification followed by secondary contact and hybridization may explain complex patterns of intra- and interspecific morphological and genetic variation in the North American hard pines (Pinus section Trifoliae), a group of approximately 49 tree species distributed in North and Central America and the Caribbean islands. We concatenated five plastid DNA markers for an average of 3.9 individuals per putative species and assessed the suitability of the five regions as DNA bar codes for species identification, species delimitation, and phylogenetic reconstruction. The ycf1 gene accounted for the greatest proportion of the alignment (46.9%), the greatest proportion of variable sites (74.9%), and the most unique sequences (75 haplotypes). Phylogenetic analysis recovered clades corresponding to subsections Australes, Contortae, and Ponderosae. Sequences for 23 of the 49 species were monophyletic and sequences for another 9 species were paraphyletic. Morphologically similar species within subsections usually grouped together, but there were exceptions consistent with incomplete lineage sorting or introgression. Bayesian relaxed molecular clock analyses indicated that all three subsections diversified relatively recently during the Miocene. The general mixed Yule-coalescent method gave a mixed model estimate of only 22 or 23 evolutionary entities for the plastid sequences, which corresponds to less than half the 49 species recognized based on morphological species assignments. Including more unique haplotypes per species may result in higher estimates, but low mutation rates, recent diversification, and large effective population sizes may limit the effectiveness of this method to detect evolutionary entities.

Phylogenetic Relationships of Pinus Subsection Ponderosae Inferred from Rapidly Evolving cpDNA Regions

Abstract Pinus subsection Ponderosae includes approximately 17 tree species distributed from western Canada to Nicaragua. We inferred phylogenetic relationships of multiple accessions for all widely recognized species from 3.7 kb of CpDNA sequence (matK, trnD-trnY-trnE spacer, chlN-ycf1 spacer, and ycf1). The sister relationship between subsections Ponderosae and Australes was corroborated with high branch support, and several clades, most with lower branch support, were identified within subsection Ponderosae. Pinus jeffreyi was sister to P. coulteri, P. sabiniana, and P. torreyana. Californian accessions of P. ponderosa and P. washoensis occurred in a clade separate from P. arizonica and P. scopulorum from the southwestern United States. Western Mexican species P. cooperi and P. durangensis had CpDNA sequences identical to one or more accessions of P. arizonica and P. scopulorum, and together these taxa were closely related to clades of P. engelmannii-P. devoniana (Mexico) and P. douglasiana-P. yecorensis-P. maximinoi (western Mexico to Guatemala). A well supported clade of taxa from Mexico and Central America included P. pseudostrobus, P. montezumae, P. hartwegii, P. maximinoi (one of three accessions), P. nubicola, and P. donnell-smithii. Chloroplast DNA sequences were nonmonophyletic for most species, although the degree of support varied.

The leaf oil of Juniperus martinezii Perez de la Rosa and taxonomic status

ABSTRACT The essential leaf oil of juniperus martinezii, from the type locality, is dominated by α-pinene, camphor, sabinene, terpinen-4-ol, β-phellandrene, myrcene, linalool, kaur-16-ene, and bornyl acetate. Both morphologically and chemically, it appears to be more closely related to J. flaccida than to other Mexican junipers, and hence is recognized as a variety, J. flaccida var. martinezii (Perez de la Rosa) J. Silba. A distribution map of the 5 known populations is presented.

Pinus georginae (Pinaceae), a new species from western Jalisco, Mexico

Pinus georginae is described and illustrated as a new endemic species from the valleys in the southern basin of Río Ameca, Jalisco, western Mexico. It is closely related to Pinus praetermissa; however, after studying the cones and anatomy of the leaves in detail, characteristics were revealed that identify P. georginae as a distinct species.ResumenSe describe e ilustra Pinus georginae como una especie nueva, endémica de algunos valles intermontanos al sur del Río Ameca, Jalisco, en el Occidente de México. Los árboles se parecen a Pinus praetermissa; sin embargo, al estudiar con detalle los conos y la anatomía de las acículas lo ubican a Pinus georginae como una entidad biológica con categoría específica independiente.Pinus georginae is described and illustrated as a new endemic species from the valleys in the southern basin of Río Ameca, Jalisco, western Mexico. It is closely related to Pinus praetermissa; however, after studying the cones and anatomy of the leaves in detail, characteristics were revealed that identify P. georginae as a distinct species. Se describe e ilustra Pinus georginae como una especie nueva, endémica de algunos valles intermontanos al sur del Río Ameca, Jalisco, en el Occidente de México. Los árboles se parecen a Pinus praetermissa; sin embargo, al estudiar con detalle los conos y la anatomía de las acículas lo ubican a Pinus georginae como una entidad biológica con categoría específica independiente.

Multi-locus phylogenetics, lineage sorting, and reticulation in Pinus subsection Australes

PREMISE OF THE STUDY Both incomplete lineage sorting and reticulation have been proposed as causes of phylogenetic incongruence. Disentangling these factors may be most difficult in long-lived, wind-pollinated plants with large population sizes and weak reproductive barriers. METHODS We used solution hybridization for targeted enrichment and massive parallel sequencing to characterize low-copy-number nuclear genes and high-copy-number plastomes (Hyb-Seq) in 74 individuals of Pinus subsection Australes, a group of ~30 New World pine species of exceptional ecological and economic importance. We inferred relationships using methods that account for both incomplete lineage sorting and reticulation. KEY RESULTS Concatenation- and coalescent-based trees inferred from nuclear genes mainly agreed with one another, but they contradicted the plastid DNA tree in recovering the Attenuatae (the California closed-cone pines) and Oocarpae (the egg-cone pines of Mexico and Central America) as monophyletic and the Australes sensu stricto (the southern yellow pines) as paraphyletic to the Oocarpae. The plastid tree featured some relationships that were discordant with morphological and geographic evidence and species limits. Incorporating gene flow into the coalescent analyses better fit the data, but evidence supporting the hypothesis that hybridization explains the non-monophyly of the Attenuatae in the plastid tree was equivocal. CONCLUSIONS Our analyses document cytonuclear discordance in Pinus subsection Australes. We attribute this discordance to ancient and recent introgression and present a phylogenetic hypothesis in which mostly hierarchical relationships are overlain by gene flow.

Morphological, Molecular, and Ecological Divergence in Pinus douglasiana and P. maximinoi

Abstract Pinus douglasiana and P. maximinoi (Pinus subsection Ponderosae) are closely-related New World pines with vague taxonomic boundaries where their natural ranges overlap in western Mexico. They are distinguished from each other by the width of their leaves and thickness of their cone scale apophyses. They are also sometimes confused with two other close relatives, Pinus pseudostrobus and P. yecorensis. We integrated morphological, molecular, and ecological data to clarify the taxonomic limits among these four species. Following previous studies, we evaluated 16 quantitative leaf and seed cone characters. Pinus douglasiana, P. maximinoi, and P. pseudostrobus formed non-discrete groups in multivariate space. The absence of leaf hypodermal intrusions, a persistent peduncle, and the shape of the seed cone are useful for differentiating P. pseudostrobus and P. yecorensis from P. douglasiana or P. maximinoi, and the latter two can usually be distinguished by needle width or cone scale apophysis thickness. Most individuals identified as P. douglasiana, and P. maximinoi shared haplotypes for a plastid ycf1 fragment that is relatively variable for the genus, while P. yecorensis has a closely related, exclusive haplotype. A distinct haplogroup included all individuals of P. pseudostrobus and the remaining individuals of P. douglasiana and P. maximinoi. Leaf width and cone scale thickness of P. douglasiana and P. maximinoi are correlated with elevation. According to potential distribution models, P. yecorensis is distributed in drier areas than P. douglasiana or P. maximinoi, while P. pseudostrobus occurs in more temperate areas, commonly at higher elevations. Pinus douglasiana and P. maximinoi can be considered as incipient species undergoing divergent evolution characterized by incomplete morphological, molecular, and ecological divergence.