title: Contrasting patterns of nucleotide diversity for four conifers of Alpine European forests.
abstract: A candidate gene approach was used to identify levels of nucleotide diversity and to identify genes departing from neutral expectations in coniferous species of the Alpine European forest. Twelve samples were collected from four species that dominate montane and subalpine forests throughout Europe: Abies alba Mill, Larix decidua Mill, Pinus cembra L., and Pinus mugo Turra. A total of 800 genes, originally resequenced in Pinus taeda L., were resequenced across 12 independent trees for each of the four species. Genes were assigned to two categories, candidate and control, defined through homology-based searches to Arabidopsis. Estimates of nucleotide diversity per site varied greatly between polymorphic candidate genes (range: 0.0004-0.1295) and among species (range: 0.0024-0.0082), but were within the previously established ranges for conifers. Tests of neutrality using stringent significance thresholds, performed under the standard neutral model, revealed one to seven outlier loci for each species. Some of these outliers encode proteins that are involved with plant stress responses and form the basis for further evolutionary enquiries.
authors.affiliation: Department of Plant Sciences, University of California at Davis Davis, CA, USA ; IASMA Research and Innovation Centre, Fondazione Edmund Mach, S. Michele all'Adige Italy.
authors.forename: Elena
authors.initials: E
authors.lastname: Mosca
authors.forename: Andrew J
authors.initials: AJ
authors.lastname: Eckert
authors.forename: John D
authors.initials: JD
authors.lastname: Liechty
authors.forename: Jill L
authors.initials: JL
authors.lastname: Wegrzyn
authors.forename: Nicola
authors.initials: N
authors.lastname: La Porta
authors.forename: Giovanni G
authors.initials: GG
authors.lastname: Vendramin
authors.forename: David B
authors.initials: DB
authors.lastname: Neale
keywords: candidate gene; neutrality tests; nucleotide diversity; single nucleotide polymorphisms