Contrasting patterns of nucleotide diversity for four conifers of Alpine European forests
Article first published online: 27 MAR 2012
© 2012 The Authors. Evolutionary Applications published by Blackwell Publishing Ltd.
This is an open access article under the terms of the Creative Commons Attribution-NonCommercial License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited and is not used for commercial purposes.
Volume 5, Issue 7, pages 762–775, November 2012
How to Cite
Mosca, E., Eckert, A. J., Liechty, J. D., Wegrzyn, J. L., La Porta, N., Vendramin, G. G. and Neale, D. B. (2012), Contrasting patterns of nucleotide diversity for four conifers of Alpine European forests. Evolutionary Applications, 5: 762–775. doi: 10.1111/j.1752-4571.2012.00256.x
- Issue published online: 30 OCT 2012
- Article first published online: 27 MAR 2012
- Received: 3 February 2012 Accepted: 11 February 2012
- candidate gene;
- neutrality tests;
- nucleotide diversity;
- single nucleotide polymorphisms
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.