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Systematics Section / ASPT

Syring, John V. [2], Cronn, RC [1], Liston, Aaron [2], Willyard, Ann [2].

Choosing genes for resolving pine phylogeny: A screening strategy for low-copy nuclear loci..

Members of the pine genus Pinus are long-lived, wind-pollinated, outcrossing trees that form a highly variable and species-rich monophyletic clade amongst conifers. Molecular studies of this ancient lineage (originating in the early Cretaceous) based on cpDNA and nrDNA have returned conflicting topologies with regard to more ancient divergence events, and largely failed to resolve the numerous (possibly rapid) radiations that unite terminal taxa. Resolution of these apparent conflicts and polytomies demands new sources of characters that yield independent assessments from cpDNA and nrDNA, and diverge at rates appropriate for resolving Pinus-specific divergence events. Genomics efforts directed at Loblolly (P. taeda) and Monterey (P. radiata) Pines have produced a wealth of potentially useful nuclear markers that can be used to resolve phylogenetic relationships among pines, and possibly other coniferous taxa. Preliminary DNA sequence analysis of four mapped conifer anchor loci (4CL, agp6, IFG1934 and IFG8612) from select lineage exemplars highlights three key features that effect the success of applying nuclear genes to addressing phylogenetic questions in Pinus; 1) intron presence and size; 2) range of pairwise sequence divergence within the genus; and 3) taxonomic level being addressed. In this presentation, we discuss the results of this four locus screen relative to results derived from cpDNA and nrDNA, and propose a screening strategy that identifies the most informative gene(s) for a given phylogenetic question by examining key performance characteristics (rate of divergence, degree of coalescence, number of resolved nodes, consistency index). This method represents an alternative to the frequently employed “universal gene” and “pick a gene and run” strategies.

1 - USDA Forest Service, Forest Genetics, Pacific Nothwest Research Station, 3200 SW Jefferson Way, Corvallis, Oregon, 97331-4401, USA
2 - Oregon State University, Department of Botany and Plant Pathology, 2082 Cordley Hall, Corvallis, Oregon, 97331-2902, USA

low-copy nuclear gene
molecular phylogeny
gene screening

Presentation Type: Paper
Session: 49-5
Location: Cottonwood C (Snowbird Center)
Date: Wednesday, August 4th, 2004
Time: 11:45 AM
Abstract ID:358

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