Widespread Genealogical Nonmonophyly in Species of Pinus Subgenus Strobus

Abstract

Phylogenetic relationships among Pinus species from subgenus Strobus remain unresolved despite combined efforts based on nrITS and cpDNA. To provide greater resolution among these taxa, a 900-bp intron from a late embryogenesis abundant (LEA)-like gene (IFG8612)was sequenced from 39 pine species, with two or more alleles representing 33 species. Nineteen of 33 species exhibited allelic nonmonphyly in the strict consensus tree, and 10 deviated significantly from allelic monophyly based on topology incongruence tests. Intraspecific nucleotide diversity ranged from 0.0 to 0.0211, and analysis of variance shows that nucleotide diversity was strongly associated (P < 0.0001)with the degree of species monophyly. Although species nonmonophyly complicates phylogenetic interpretations, this nuclear locus offers greater topological support than previously observed for cpDNA or nrITS. Lacking evidence for hybridization, recombination, or imperfect taxonomy, we feel that incomplete lineage sorting remains the best explanation for the polymorphisms shared among species. Depending on the species, coalescent expectations indicate that reciprocal monophyly will be more likely than paraphyly in 1.71 to 24.0 x 10(6) years, and that complete genome-wide coalescence in these species may require up to 76.3 x 10(6) years. The absence of allelic coalescence is a severe constraint in the application of phylogenetic methods in Pinus, and taxa sharing similar life history traits with Pinus are likely to show species nonmonophyly using nuclear markers.

Autumn Snowfall Controls the Annual Radial Growth of Centenarian Whitebark Pine (Pinus albicaulis) in the Southern Coast Mountains, British Columbia, Canada

“…However, recent phylogenetic, DNA-based studies (Liston et al 1999Gernandt et al 2005;Eckert and Hall 2006;Syring et al 2005Syring et al , 2007 show no evidence for monophyly in subsections Cembrae and Strobi and thus, merge the two into a new subsection Strobus. Whitebark Pine forms a clade with the 12 Eurasian species in Strobus plus Sugar Pine (P. lambertiana), another North American species.…”

The Evolutionary Genetics of the Genes Underlying Phenotypic Associations for Loblolly Pine (Pinus taeda, Pinaceae)

“…This effect, moreover, is likely related to standing levels of population structure, our conservative sequence analysis pipeline, and inclusion of small coverage classes (i.e., n = 2-5). We have also used a recently diverged outgroup, and only a single sequence from this outgroup for analysis, that may in fact not be reciprocally monophyletic (Syring et al 2007). As such, estimates of divergence may be biased and thus by extension so would estimates of long-term positive selection.…”

Chromosome banding in the genus <i>Pinus</i> IV. Fluorescent banding patterns of chromosomes in eight taxa of haploxylone pines

“…On the basis of pioneer works of Shaw (1914), Mirov (1967) and, Little and Critchfield (1969) their taxonomic treatments are used widely and, subgenera Pinus and Strobus are accepted. Several revisions have made adjustments to the species status and modified the taxonomic treatment at the ranks of subgenera, sections and/or subsections (Farjon 1984;Farjon and Styles 1997;Gernandt et al 2003Gernandt et al , 2005Price et al 1998;Liston et al 1999;Syring et al 2007;Hernández-León et al 2013). In recent years molecular phylogenetic analyses using various DNA sequences of cytoplasmic and nuclear genomes were applied frequently to phylogenetic and taxonomic studies on Pinus species, and revealed reliable phylogenetic relationships among species.…”