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

Abstract

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.

Chromosome banding in the genus <i>Pinus</i> V. Fluorescent banding patterns in 16 diploxylon pines

“…The grouping seems to match with a taxonomic treatment of Farjon (2005) and some molecular phylogeny (Liston et al 1999;López et al 2002;Zhang and Li 2004;Eckert and Hall 2006;Gernandt et al 2009;Hernández-León et al 2013;Wang and Wang 2014). In this observation fluorescent band patterns of chromosomes are performed in moderate number of Pinus species.…”

“…subsection Pinus by unknown structural change of chromosomes and then this karyotype may be advance and divorced recently in pine species. This speculation should be considered with taxonomic treatments (Mirov 1967;Little and Critchfield 1969;Farjon and Styles 1977;Farjon 2005) and molecular phylogeny (Price et al 1998;Liston et al 1999;López et al 2002;Zhang and Li 2004;Eckert and Hall 2006;Gernandt et al 2009;Hernández-León et al 2013;Wang and Wang 2014).…”

High‐throughput multiplex cpDNA resequencing clarifies the genetic diversity and genetic relationships among Brassica napus, Brassica rapa and Brassica oleracea

“…Its six predicted transmembrane segments and two moderately hydrophobic stretches are conserved and are likely the functional domains, and the remaining portions are highly divergent. A protein alignment showed that all of the B. napus ycf1 variants are located in the highly divergent portions, suggesting their nonmutational functionality, which would partially explain why ycf1 has a rapid evolutionary rate (Hernández‐León et al ., ).…”

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

“…Further plastid DNA studies have verified the paraphyly of Pinus subsects. Attenuatae and Australes (Parks et al 2012;Hernández León et al 2013), but nuclear DNA studies are also under way to corroborate the plastid results and to more conclusively establish whether the Oocarpa group is monophyletic. At present, the Oocarpa group, or the Oocarpae, is an appealing descriptive name for the serotinous egg-cone pines (including the Leiophyllae) naturally distributed in the southwestern United States, Mexico, and Central America.…”