Evolutionary relationships among Pinus (Pinaceae) subsections inferred from multiple low‐copy nuclear loci

Abstract

Sequence data from nrITS and cpDNA have failed to fully resolve phylogenetic relationships among Pinus species. Four low-copy nuclear genes, developed from the screening of 73 mapped conifer anchor loci, were sequenced from 12 species representing all subsections. Individual loci do not uniformly support either the nrITS or cpDNA hypotheses and in some cases produce unique topologies. Combined analysis of low-copy nuclear loci produces a well-supported subsectional topology of two subgenera, each divided into two sections, congruent with prior hypotheses of deep divergence in Pinus. The placements of P. nelsonii, P. krempfii, and P. contorta have been of continued systematic interest. Results strongly support the placement of P. nelsonii as sister to the remaining members of sect. Parrya, suggest a moderately well-supported and consistent position of P. krempfii as sister to the remaining members of sect. Quinquefoliae, and are ambiguous about the placement of P. contorta. A successful phylogenetic strategy in Pinus will require many low-copy nuclear loci that include a high proportion of silent sites and derive from independent linkage groups. The locus screening and evaluation strategy presented here can be broadly applied to facilitate the development of phylogenetic markers from the increasing number of available genomic resources.

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.…”

Pinus nelsonii and a Cladistic Analysis of Pinaceae Ovulate Cone Characters

“…1A ; Gernandt et al 2001 ;Syring et al 2005 ;Parks et al 2009 ). Neither species was available to Miller (1976a) when he proposed diagnostic features that fossil cones must possess to be classified in Pinus rather than Pityostrobus .…”

Mosaic genetic differentiation along environmental and geographic gradients indicate divergent selection in a white pine species complex

“…Seven other genes were tested for amplification but rejected because they could not be consistently amplified (lp3-1, dhn2Pp, rd21A2, dhn2-1, dhn3, a3ip2 and ino3; González-Martínez et al 2006;Pyhäjärvi et al 2007;Eveno et al 2008;Grivet et al 2011). The housekeeping genes amplified was agp6, IFG8612, and cesA1 (Table 1; Syring et al 2005). A fourth gene, WD-40, could not be amplified consistently (Willyard et al 2009).…”